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Kato S, Arakaki S, Nagano AJ, Kikuchi K, Hirase S. Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes. Mol Ecol 2023. [PMID: 38047388 DOI: 10.1111/mec.17216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/23/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023]
Abstract
Extinct lineages can leave legacies in the genomes of extant lineages through ancient introgressive hybridization. The patterns of genomic survival of these extinct lineages provide insight into the role of extinct lineages in current biodiversity. However, our understanding on the genomic landscape of introgression from extinct lineages remains limited due to challenges associated with locating the traces of unsampled 'ghost' extinct lineages without ancient genomes. Herein, we conducted population genomic analyses on the East China Sea (ECS) lineage of Chaenogobius annularis, which was suspected to have originated from ghost introgression, with the aim of elucidating its genomic origins and characterizing its landscape of introgression. By combining phylogeographic analysis and demographic modelling, we demonstrated that the ECS lineage originated from ancient hybridization with an extinct ghost lineage. Forward simulations based on the estimated demography indicated that the statistic γ of the HyDe analysis can be used to distinguish the differences in local introgression rates in our data. Consistent with introgression between extant organisms, we found reduced introgression from extinct lineage in regions with low recombination rates and with functional importance, thereby suggesting a role of linked selection that has eliminated the extinct lineage in shaping the hybrid genome. Moreover, we identified enrichment of repetitive elements in regions associated with ghost introgression, which was hitherto little known but was also observed in the re-analysis of published data on introgression between extant organisms. Overall, our findings underscore the unexpected similarities in the characteristics of introgression landscapes across different taxa, even in cases of ghost introgression.
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Affiliation(s)
- Shuya Kato
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Seiji Arakaki
- Amakusa Marine Biological Laboratory, Kyushu University, Amakusa, Kumamoto, Japan
| | - Atsushi J Nagano
- Department of Life Sciences, Faculty of Agriculture, Ryukoku University, Ōtsu, Shiga, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
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Dusadeepong R, Maquart PO, Hide M, Boyer S. Phylogeny and spatial distribution of Japanese encephalitis virus vector species in Cambodia. Med Vet Entomol 2023; 37:737-744. [PMID: 37404158 DOI: 10.1111/mve.12678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 06/08/2023] [Indexed: 07/06/2023]
Abstract
In Southeast Asia, despite the use of Japanese encephalitis vaccines and vaccination coverage, Japanese encephalitis (JE) transmission is still a major public health issue. The main vectors of this virus are mosquitoes from the genus Culex, which diversity and density are important in Southeast Asia. The main vector species of Japanese encephalitis virus (JEV) in Cambodia belong to the Vishnui subgroup. However, their morphological identification solely based on the adult stage remains challenging, making their segregation and detection difficult. In order to identify and describe the distribution of the three main JEV vector species in Cambodia, namely Culex vishnui, Cx. pseudovishnui and Cx. tritaeniorhynchus, mosquito samplings were carried out throughout the country in different environments. Phylogenetic analysis of the cytochrome c oxidase subunit I (coI) gene using maximum-likelihood tree with ultrafast bootstrap and phylogeographic analysis were performed. The three main Culex species are phylogenetically separated, and represent two distinct clades, one with Cx. tritaeniorhynchus and the second with Cx. vishnui and Cx. pseudovishnui, the latter appearing as a subgroup of Cx. vishnui. The phylogeographic analysis shows a distribution of the Vishnui subgroup on the entire Cambodian territory with an overlapped distribution areas leading to a sympatric distribution of these species. The three JEV vector species are geographically well-defined with a strong presence of Cx. pseudovishnui in the forest. Combined with the presence of Cx. tritaeniorhynchus and Cx. vishnui in rural, peri-urban, and urban areas, the presence of JEV-competent vectors is widespread in Cambodia.
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Affiliation(s)
- Rutaiwan Dusadeepong
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Pierre-Olivier Maquart
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Mallorie Hide
- Medical Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
- MIVEGEC, Université de Montpellier, IRD (Institut de Recherche pour le Développement), CNRS, Montpellier, France
- LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sebastien Boyer
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
- Ecology and Emergence of Arthropod-borne diseases, Institut Pasteur, Paris, France
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53
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Ong HG, Kim Y, Lee J, Kim B, Kang D, Jung E, Shin J, Kim Y. Approximate Bayesian computation and ecological niche models elucidate the demographic history and current fragmented population distribution of a Korean endemic shrub. Ecol Evol 2023; 13:e10792. [PMID: 38077507 PMCID: PMC10700048 DOI: 10.1002/ece3.10792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/15/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Climatic fluctuations and geological events since the LGM are believed to have significantly impacted the population size, distribution, and mobility of many species that we observe today. In this paper, we determined the processes driving the phylogeographic structure of the Korean endemic white forsythia by combining the use of genome-wide SNPs and predicting paleoclimatic habitats during the LGM (21 kya), Early Holocene (10 kya), Mid-Holocene (6 kya), and Late Holocene (3 kya). Using a maximum of 1897 SNPs retrieved from 124 samples across nine wild populations, five environmental predictors, and the species' natural occurrence records, we aimed to infer the species' demographic history and reconstruct its possible paleodistributions with the use of approximate Bayesian computation and ecological niche models, respectively. Under this integrated framework, we found strong evidence for patterns of range shift and expansion, and population divergence events from the onset of the Holocene, resulting in the formation of its five distinct genetic units. The most highly supported model inferred that after the split of an ancestral population into the southern group and a larger central metapopulation lineage, the latter gave rise to the eastern and northern clusters, before finally dividing into two sub-central groups. While the use of molecular data allowed us to identify and refine the (phylo)genetic relationships of the species' lineages and populations, the use of ecological data helped us infer a past LGM refugium and the directions of post-glacial range dynamics. The time frames of these demographic events were shown to be congruent with climatic and geological events that affected the central Korean Peninsula during these periods. These findings gave us a better understanding of the consequences of past spatiotemporal factors that may have resulted in the current fragmented population distribution of this endangered plant.
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Affiliation(s)
| | - Yong‐In Kim
- On Biological Resource Research Institute (OBRRI)ChuncheonSouth Korea
| | - Jung‐Hoon Lee
- On Biological Resource Research Institute (OBRRI)ChuncheonSouth Korea
| | - Bo‐Yun Kim
- National Institute of Biological Resources (NIBR)IncheonSouth Korea
| | - Dae‐Hyun Kang
- Korea National Park Research InstituteWonjuSouth Korea
| | - Eui‐Kwon Jung
- Department of Life ScienceHallym UniversityChuncheonSouth Korea
| | - Jae‐Seo Shin
- Department of Life ScienceHallym UniversityChuncheonSouth Korea
| | - Young‐Dong Kim
- Multidisciplinary Genome InstituteHallym UniversityChuncheonSouth Korea
- Department of Life ScienceHallym UniversityChuncheonSouth Korea
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Sánchez-Acevedo V, González-Rodríguez A, Torres-Miranda CA, Rodríguez-Correa H, Valencia-Á S, De-la-Cruz IM, Oyama K. Nuclear and chloroplast DNA phylogeography reveals high genetic diversity and postglacial range expansion in Quercus mexicana. American J of Botany 2023; 110:e16251. [PMID: 37843974 DOI: 10.1002/ajb2.16251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/18/2023]
Abstract
PREMISE Phylogeographical studies are fundamental for understanding factors that influence the spatial distribution of genetic lineages within species. Population expansions and contractions, distribution shifts, and climate changes are among the most important factors shaping the genetic compositions of populations. METHODS We investigated the phylogeography of an endemic oak, Quercus mexicana (Fagaceae), which has a restricted distribution in northeastern Mexico along the Sierra Madre Oriental and adjacent areas. Nuclear and chloroplast DNA microsatellite markers were used to describe the genetic diversity and structure of 39 populations of Q. mexicana along its entire distribution area. We tested whether population expansion or contraction events influenced the genetic diversity and structure of the species. We also modeled the historical distributional range of Q. mexicana (for the Mid Holocene, the Last Glacial Maximum, and the Last Interglacial) to estimate the extent to which climate fluctuations have impacted the distribution of this oak species. RESULTS Our results revealed high genetic diversity and low genetic structure in Q. mexicana populations. Ecological niche models suggested historical fluctuations in the distributional range of Q. mexicana. Historical range changes, gene flow, and physical barriers seem to have played an important role in shaping the phylogeographic structure of Q. mexicana. CONCLUSIONS Our study indicates that the genetic structure of Q. mexicana may have been the result of responses of oak trees not only to heterogeneous environments present in the Sierra Madre Oriental and adjacent areas, but also to elevational and latitudinal shifts in response to climate changes in the past.
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Affiliation(s)
- Vanessa Sánchez-Acevedo
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM). Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José del Cerrito, Morelia, Michoacán, México
- Posgrado en Ciencias Biológicas, UNAM. Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, C.P. 04510, CDMX, México
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, UNAM. Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José del Cerrito, Morelia, Michoacán, México
| | - César Andrés Torres-Miranda
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM). Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José del Cerrito, Morelia, Michoacán, México
| | - Hernando Rodríguez-Correa
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM). Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José del Cerrito, Morelia, Michoacán, México
| | - Susana Valencia-Á
- Facultad de Ciencias, UNAM. Av. Universidad 3000. Coyoacán, Ciudad de México, 04510, México
| | - Ivan M De-la-Cruz
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM). Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José del Cerrito, Morelia, Michoacán, México
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM). Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José del Cerrito, Morelia, Michoacán, México
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55
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Molnár ÁP, Demeter L, Biró M, Chytrý M, Bartha S, Gantuya B, Molnár Z. Is there a massive glacial-Holocene flora continuity in Central Europe? Biol Rev Camb Philos Soc 2023; 98:2307-2319. [PMID: 37646107 DOI: 10.1111/brv.13007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
The prevailing paradigm about the Quaternary ecological and evolutionary history of Central European ecosystems is that they were repeatedly impoverished by regional extinctions of most species during the glacial periods, followed by massive recolonizations from southern and eastern refugia during interglacial periods. Recent literature partially contradicts this view and provides evidence to re-evaluate this Postglacial Recolonization Hypothesis and develop an alternative one. We examined the long-term history of the flora of the Carpathian (Pannonian) Basin by synthesising recent advances in ecological, phylogeographical, palaeoecological and palaeoclimatological research, and analysing the cold tolerance of the native flora of a test area (Hungary, the central part of the Carpathian Basin). We found that (1) many species have likely occurred there continuously since before the Last Glacial Maximum (LGM); (2) most of the present-day native flora (1404 species, about 80%) can occur in climates as cold as or colder than the LGM (mean annual temperature ≤+3.5°C); and (3) grasslands and forests can be species-rich under an LGM-like cold climate. These arguments support an alternative hypothesis, which we call the Flora Continuity Hypothesis. It states that long-term continuity of much of the flora in the Carpathian Basin is more plausible than regional extinctions during the LGM followed by massive postglacial recolonizations. The long-term continuity of the region's flora may have fundamental implications not only for understanding local biogeography and ecology (e.g. the temporal scale of processes), but also for conservation strategies focusing on protecting ancient species-rich ecosystems and local gene pools.
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Affiliation(s)
- Ábel Péter Molnár
- Hungarian University of Agriculture and Life Sciences, Institute for Wildlife Management and Nature Conservation, Páter Károly u. 1., Gödöllő, 2100, Hungary
- Doctoral School of Biological Sciences, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1., Gödöllő, 2100, Hungary
| | - László Demeter
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
| | - Marianna Biró
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
| | - Milan Chytrý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Sándor Bartha
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
| | - Batdelger Gantuya
- Botanic Garden and Research Institute, Mongolian Academy of Sciences, 13th Street, Peace Avenue 54a, Bayanzurkh district, Ulaanbaatar, 13330, Mongolia
- Doctoral School of Biology, Eötvös Lorand University, Budapest, Pázmány P. stny. 1/C., Budapest, 1117, Hungary
| | - Zsolt Molnár
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
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56
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Pereira AC, Reis AC, Cunha MV. Genomic epidemiology sheds light on the emergence and spread of Mycobacterium bovis Eu2 Clonal Complex in Portugal. Emerg Microbes Infect 2023; 12:2253340. [PMID: 37640285 PMCID: PMC10484045 DOI: 10.1080/22221751.2023.2253340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 08/31/2023]
Abstract
ABSTRACTAnimal tuberculosis (TB) remains a serious concern for animal and human health. Mycobacterium bovis circulates in multi-host systems, dominated by the European 2 clonal complex (Eu2) in Iberia. In this work, we use genomic epidemiology to infer the emergence, spread, and spatiotemporal patterns of Eu2 in the official epidemiological risk area of animal TB in Portugal. Phylogenetic analysis of 144 M. bovis whole-genome sequences from cattle, wild boar, and red deer, representing the 2002-2021 period, distinguished three Eu2 clades that evolved independently. The major Eu2 clade underwent phylodynamic inferences to estimate the time and location of outbreaks, host transitions, and spatial diffusion as well. The origin of this Eu2 clade was attributed to the red deer population in the Castelo Branco district, near the border with Spain. Most host transitions were intraspecific (80%), while interspecific transmissions between wildlife species (wild boar-red deer), and between wild boar and cattle, were highly supported. Phylogeographic reconstruction evidenced that most transitions (82%) occur within municipalities, highlighting local transmission corridors.Our study indicates that M. bovis continues to spread at the cattle-wildlife interface within the animal TB hotspot area, possibly driven by the foraging behaviour of wild boar near agricultural lands. Red deer seems to be an important driver of TB within wildlife hosts, while the wild boar links the multi-host wildlife community and livestock. This work highlights the value of combining genomic epidemiology with phylodynamic inference to resolve host jumps and spatial patterns of M. bovis, providing real-time clues about points of intervention.
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Affiliation(s)
- André C. Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE – Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana C. Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE – Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE – Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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Sephton-Clark P, Temfack E, Tenor JL, Toffaletti DL, Loyse A, Molloy SF, Perfect JR, Bicanic T, Harrison TS, Lortholary O, Kouanfack C, Cuomo CA. Genetic diversity and microevolution in clinical Cryptococcus isolates from Cameroon. Med Mycol 2023; 61:myad116. [PMID: 37952096 PMCID: PMC10709296 DOI: 10.1093/mmy/myad116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
Cryptococcal meningitis is the second most common cause of death in people living with HIV/AIDS, yet we have a limited understanding of how cryptococcal isolates change over the course of infection. Cryptococcal infections are environmentally acquired, and the genetic diversity of these infecting isolates can also be geographically linked. Here, we employ whole genome sequences for 372 clinical Cryptococcus isolates from 341 patients with HIV-associated cryptococcal meningitis obtained via a large clinical trial, across both Malawi and Cameroon, to enable population genetic comparisons of isolates between countries. We see that isolates from Cameroon are highly clonal, when compared to those from Malawi, with differential rates of disruptive variants in genes with roles in DNA binding and energy use. For a subset of patients (22) from Cameroon, we leverage longitudinal sampling, with samples taken at days 7 and 14 post-enrollment, to interrogate the genetic changes that arise over the course of infection, and the genetic diversity of isolates within patients. We see disruptive variants arising over the course of infection in several genes, including the phagocytosis-regulating transcription factor GAT204. In addition, in 13% of patients sampled longitudinally, we see evidence for mixed infections. This approach identifies geographically linked genetic variation, signatures of microevolution, and evidence for mixed infections across a clinical cohort of patients affected by cryptococcal meningitis in Central Africa.
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Affiliation(s)
- Poppy Sephton-Clark
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Elvis Temfack
- Internal Medicine Unit, Douala General Hospital, Douala, Cameroon
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR 2000, Paris, France
| | - Jennifer L Tenor
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Dena L Toffaletti
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Angela Loyse
- Institute of Infection and Immunity, St George's University of London, London, UK
- Clinical Academic Group in Infection, St George's University Hospital, London, UK
| | - Síle F Molloy
- Institute of Infection and Immunity, St George's University of London, London, UK
| | - John R Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Tihana Bicanic
- Institute of Infection and Immunity, St George's University of London, London, UK
- Clinical Academic Group in Infection, St George's University Hospital, London, UK
| | - Thomas S Harrison
- Institute of Infection and Immunity, St George's University of London, London, UK
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Olivier Lortholary
- Department of Infectious Diseases and Tropical Medicine, Paris Cité University, Necker-Enfants Malades Hospital, AP-HP, IHU Imagine, Paris, France
- Mycology Department and National Reference Center for Invasive Mycoses and Antifungals, Institut Pasteur, Paris, France
| | - Charles Kouanfack
- Department of Public Health, Faculty of Medicine and Pharmaceutical Sciences, University of Dschang, Dschang, Cameroon
- Day Hospital, Hospital Central Yaoundé, Yaoundé, Cameroon
- Research Center for Emerging and Re-emerging Diseases, Cameroon Baptist Convention Health Services (CBCHS), Yaoundé, Cameroon
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Van Borm S, Dellicour S, Martin DP, Lemey P, Agianniotaki EI, Chondrokouki ED, Vidanovic D, Vaskovic N, Petroviċ T, Laziċ S, Koleci X, Vodica A, Djadjovski I, Krstevski K, Vandenbussche F, Haegeman A, De Clercq K, Mathijs E. Complete genome reconstruction of the global and European regional dispersal history of the lumpy skin disease virus. J Virol 2023; 97:e0139423. [PMID: 37905838 PMCID: PMC10688313 DOI: 10.1128/jvi.01394-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE Lumpy skin disease virus (LSDV) has a complex epidemiology involving multiple strains, recombination, and vaccination. Its DNA genome provides limited genetic variation to trace outbreaks in space and time. Sequencing of LSDV whole genomes has also been patchy at global and regional scales. Here, we provide the first fine-grained whole genome sequence sampling of a constrained LSDV outbreak (southeastern Europe, 2015-2017), which we analyze along with global publicly available genomes. We formally evaluate the past occurrence of recombination events as well as the temporal signal that is required for calibrating molecular clock models and subsequently conduct a time-calibrated spatially explicit phylogeographic reconstruction. Our study further illustrates the importance of accounting for recombination events before reconstructing global and regional dynamics of DNA viruses. More LSDV whole genomes from endemic areas are needed to obtain a comprehensive understanding of global LSDV dispersal dynamics.
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Affiliation(s)
- Steven Van Borm
- Scientific Directorate Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Philippe Lemey
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Eirini I. Agianniotaki
- National Reference Laboratory for Capripoxviruses, Department of Molecular Diagnostics, FMD, Virological, Rickettsial and Exotic Diseases, Directorate of Athens Veterinary Center, Ministry of Rural Development and Food, Athens, Greece
| | - Eleni D. Chondrokouki
- National Reference Laboratory for Capripoxviruses, Department of Molecular Diagnostics, FMD, Virological, Rickettsial and Exotic Diseases, Directorate of Athens Veterinary Center, Ministry of Rural Development and Food, Athens, Greece
| | - Dejan Vidanovic
- Department for laboratory diagnostics, Veterinary Specialized Institute, Kraljevo, Serbia
| | - Nikola Vaskovic
- Department for laboratory diagnostics, Veterinary Specialized Institute, Kraljevo, Serbia
| | - Tamaš Petroviċ
- Department for Virology, Scientific Veterinary Institute, Novi Sad, Serbia
| | - Sava Laziċ
- Department for Virology, Scientific Veterinary Institute, Novi Sad, Serbia
| | - Xhelil Koleci
- Faculty of Veterinary Medicine, The Agricultural University of Tirana, Tirana, Albania
| | - Ani Vodica
- Animal Health Department, Food Safety and Veterinary Institute, Tirana, Albania
| | - Igor Djadjovski
- Faculty of Veterinary Medicine, Ss. Cyril and Methodius University in Skopje, Skopje, Macedonia
| | - Kiril Krstevski
- Faculty of Veterinary Medicine, Ss. Cyril and Methodius University in Skopje, Skopje, Macedonia
| | - Frank Vandenbussche
- Scientific Directorate Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Andy Haegeman
- Scientific Directorate Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Kris De Clercq
- Scientific Directorate Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Elisabeth Mathijs
- Scientific Directorate Animal Infectious Diseases, Sciensano, Brussels, Belgium
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59
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Ramirez JL, Machado CB, de Mello Affonso PRA, Galetti PM. Speciation in Coastal Basins Driven by Staggered Headwater Captures: Dispersal of a Species Complex, Leporinus bahiensis, as Revealed by Genome-wide SNP Data. Syst Biol 2023; 72:973-983. [PMID: 37260367 PMCID: PMC10627554 DOI: 10.1093/sysbio/syad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
Past sea level changes and geological instability along watershed boundaries have largely influenced fish distribution across coastal basins, either by dispersal via palaeodrainages now submerged or by headwater captures, respectively. Accordingly, the South American Atlantic coast encompasses several small and isolated drainages that share a similar species composition, representing a suitable model to infer historical processes. Leporinus bahiensis is a freshwater fish species widespread along adjacent coastal basins over narrow continental shelf with no evidence of palaeodrainage connections at low sea level periods. Therefore, this study aimed to reconstruct its evolutionary history to infer the role of headwater captures in the dispersal process. To accomplish this, we employed molecular-level phylogenetic and population structure analyses based on Sanger sequences (5 genes) and genome-wide SNP data. Phylogenetic trees based on Sanger data were inconclusive, but SNPs data did support the monophyletic status of L. bahiensis. Both COI and SNP data revealed structured populations according to each hydrographic basin. Species delimitation analyses revealed from 3 (COI) to 5 (multilocus approach) MOTUs, corresponding to the sampled basins. An intricate biogeographic scenario was inferred and supported by Approximate Bayesian Computation (ABC) analysis. Specifically, a staggered pattern was revealed and characterized by sequential headwater captures from basins adjacent to upland drainages into small coastal basins at different periods. These headwater captures resulted in dispersal throughout contiguous coastal basins, followed by deep genetic divergence among lineages. To decipher such recent divergences, as herein represented by L. bahiensis populations, we used genome-wide SNPs data. Indeed, the combined use of genome-wide SNPs data and ABC method allowed us to reconstruct the evolutionary history and speciation of L. bahiensis. This framework might be useful in disentangling the diversification process in other neotropical fishes subject to a reticulate geological history.
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Affiliation(s)
- Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
- Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Carolina B Machado
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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60
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Garrick RC. Genetic signatures of lineage fusion closely resemble population decline. Ecol Evol 2023; 13:e10725. [PMID: 37964788 PMCID: PMC10641302 DOI: 10.1002/ece3.10725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
Accurate interpretation of the genetic signatures of past demographic events is crucial for reconstructing evolutionary history. Lineage fusion (complete merging, resulting in a single panmictic population) is a special case of secondary contact that is seldom considered. Here, the circumstances under which lineage fusion can be distinguished from population size constancy, growth, bottleneck, and decline were investigated. Multi-locus haplotype data were simulated under models of lineage fusion with different divergence versus sampling lag times (D:L ratios). These pseudo-observed datasets also differed in their allocation of a fixed amount of sequencing resources (number of sampled alleles, haplotype length, number of loci). Distinguishability of lineage fusion versus each of 10 untrue non-fusion scenarios was quantified based on six summary statistics (neutrality tests). Some datasets were also analyzed using extended Bayesian skyline plots. Results showed that signatures of lineage fusion very closely resemble those of decline-high distinguishability was generally limited to the most favorable scenario (D:L = 9), using the most sensitive summary statistics (F S and Z nS), coupled with the optimal sequencing resource allocation (maximizing number of loci). Also, extended Bayesian skyline plots often erroneously inferred population decline. Awareness of the potential for lineage fusion to carry the hallmarks of population decline is critical.
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Affiliation(s)
- Ryan C. Garrick
- Department of BiologyUniversity of MississippiOxfordMississippiUSA
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61
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Weber JN, Kojima W, Boisseau RP, Niimi T, Morita S, Shigenobu S, Gotoh H, Araya K, Lin CP, Thomas-Bulle C, Allen CE, Tong W, Lavine LC, Swanson BO, Emlen DJ. Evolution of horn length and lifting strength in the Japanese rhinoceros beetle Trypoxylus dichotomus. Curr Biol 2023; 33:4285-4297.e5. [PMID: 37734374 DOI: 10.1016/j.cub.2023.08.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/28/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
What limits the size of nature's most extreme structures? For weapons like beetle horns, one possibility is a tradeoff associated with mechanical levers: as the output arm of the lever system-the beetle horn-gets longer, it also gets weaker. This "paradox of the weakening combatant" could offset reproductive advantages of additional increases in weapon size. However, in contemporary populations of most heavily weaponed species, males with the longest weapons also tend to be the strongest, presumably because selection drove the evolution of compensatory changes to these lever systems that ameliorated the force reductions of increased weapon size. Therefore, we test for biomechanical limits by reconstructing the stages of weapon evolution, exploring whether initial increases in weapon length first led to reductions in weapon force generation that were later ameliorated through the evolution of mechanisms of mechanical compensation. We describe phylogeographic relationships among populations of a rhinoceros beetle and show that the "pitchfork" shaped head horn likely increased in length independently in the northern and southern radiations of beetles. Both increases in horn length were associated with dramatic reductions to horn lifting strength-compelling evidence for the paradox of the weakening combatant-and these initial reductions to horn strength were later ameliorated in some populations through reductions to horn length or through increases in head height (the input arm for the horn lever system). Our results reveal an exciting geographic mosaic of weapon size, weapon force, and mechanical compensation, shedding light on larger questions pertaining to the evolution of extreme structures.
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Affiliation(s)
- Jesse N Weber
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Wataru Kojima
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan
| | - Romain P Boisseau
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Teruyuki Niimi
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki 444-8585, Japan
| | - Shinichi Morita
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki 444-8585, Japan
| | - Shuji Shigenobu
- Trans-Scale Biology Center, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki 444-8585, Japan
| | - Hiroki Gotoh
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oya, Suruga Ward, Shizuoka, Japan
| | - Kunio Araya
- Faculty of Social and Cultural Studies, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka-city Fukuoka 819-0395, Japan
| | - Chung-Ping Lin
- Department of Life Science, National Taiwan Normal University, No.88 Sec. 4, Tingzhou Rd, Taipei 11677, Taiwan
| | - Camille Thomas-Bulle
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA; Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
| | - Cerisse E Allen
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Wenfei Tong
- Cornell Laboratory of Ornithology, Ithaca, NY 14850, USA
| | - Laura Corley Lavine
- Department of Entomology, Washington State University, Pullman, WA 99164, USA
| | - Brook O Swanson
- Department of Biology, Gonzaga University, 502 East Boone Avenue, Spokane, WA 99258-0102, USA
| | - Douglas J Emlen
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA.
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Louge Uriarte EL, Badaracco A, Spetter MJ, Miño S, Armendano JI, Zeller M, Heylen E, Späth E, Leunda MR, Moreira AR, Matthijnssens J, Parreño V, Odeón AC. Molecular Epidemiology of Rotavirus A in Calves: Evolutionary Analysis of a Bovine G8P[11] Strain and Spatio-Temporal Dynamics of G6 Lineages in the Americas. Viruses 2023; 15:2115. [PMID: 37896894 PMCID: PMC10611311 DOI: 10.3390/v15102115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Rotavirus A (RVA) causes diarrhea in calves and frequently possesses the G6 and P[5]/P[11] genotypes, whereas G8 is less common. We aimed to compare RVA infections and G/P genotypes in beef and dairy calves from major livestock regions of Argentina, elucidate the evolutionary origin of a G8 strain and analyze the G8 lineages, infer the phylogenetic relationship of RVA field strains, and investigate the evolution and spatio-temporal dynamics of the main G6 lineages in American countries. Fecal samples (n = 422) from diarrheic (beef, 104; dairy, 137) and non-diarrheic (beef, 78; dairy, 103) calves were analyzed by ELISA and semi-nested multiplex RT-PCR. Sequencing, phylogenetic, phylodynamic, and phylogeographic analyses were performed. RVA infections were more frequent in beef (22.0%) than in dairy (14.2%) calves. Prevalent genotypes and G6 lineages were G6(IV)P[5] in beef (90.9%) and G6(III)P[11] (41.2%) or mixed genotypes (23.5%) in dairy calves. The only G8 strain was phylogenetically related to bovine and artiodactyl bovine-like strains. Re-analyses inside the G8 genotype identified G8(I) to G8(VIII) lineages. Of all G6 strains characterized, the G6(IV)P[5](I) strains from "Cuenca del Salado" (Argentina) and Uruguay clustered together. According to farm location, a clustering pattern for G6(IV)P[5] strains of beef farms was observed. Both G6 lineage strains together revealed an evolutionary rate of 1.24 × 10-3 substitutions/site/year, and the time to the most recent common ancestor was dated in 1853. The most probable ancestral locations were Argentina in 1981 for G6(III) strains and the USA in 1940 for G6(IV) strains. The highest migration rates for both G6 lineages together were from Argentina to Brazil and Uruguay. Altogether, the epidemiology, genetic diversity, and phylogeny of RVA in calves can differ according to the production system and farm location. We provide novel knowledge about the evolutionary origin of a bovine G8P[11] strain. Finally, bovine G6 strains from American countries would have originated in the USA nearly a century before its first description.
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Affiliation(s)
- Enrique L. Louge Uriarte
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (M.R.L.); (A.R.M.)
| | - Alejandra Badaracco
- Instituto Nacional de Tecnología Agropecuaria, EEA Montecarlo, Av. El Libertador Nº 2472, Montecarlo CP3384, Misiones, Argentina;
| | - Maximiliano J. Spetter
- Facultad de Ciencias Veterinarias, Departamento de Fisiopatología, Centro de Investigación Veterinaria de Tandil (CIVETAN), Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco s/n, Tandil CP7000, Buenos Aires, Argentina; (M.J.S.); (J.I.A.)
| | - Samuel Miño
- Instituto Nacional de Tecnología Agropecuaria, EEA Cerro Azul, Ruta 14, km 836, Cerro Azul CP3313, Misiones, Argentina;
| | - Joaquín I. Armendano
- Facultad de Ciencias Veterinarias, Departamento de Fisiopatología, Centro de Investigación Veterinaria de Tandil (CIVETAN), Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco s/n, Tandil CP7000, Buenos Aires, Argentina; (M.J.S.); (J.I.A.)
| | - Mark Zeller
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; (M.Z.); (E.H.)
| | - Elisabeth Heylen
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; (M.Z.); (E.H.)
| | - Ernesto Späth
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (E.S.); (A.C.O.)
| | - María Rosa Leunda
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (M.R.L.); (A.R.M.)
| | - Ana Rita Moreira
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (M.R.L.); (A.R.M.)
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; (M.Z.); (E.H.)
| | - Viviana Parreño
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Virología e Innovaciones Tecnológicas, Nicolas Repetto y de los Reseros s/n, Hurlingham CP1686, Buenos Aires, Argentina
| | - Anselmo C. Odeón
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (E.S.); (A.C.O.)
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Musher LJ, Del-Rio G, Marcondes RS, Brumfield RT, Bravo GA, Thom G. Geogenomic predictors of genetree heterogeneity explain phylogeographic and introgression history: a case study in an Amazonian bird (Thamnophilus aethiops). Syst Biol 2023:syad061. [PMID: 37804132 DOI: 10.1093/sysbio/syad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Indexed: 10/08/2023] Open
Abstract
Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of four populations of an Amazonian antbird, Thamnophilus aethiops, whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 Ka, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered two primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence and was recovered for the Z chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length and found that smaller chromosomes experienced higher gene flow. Given that (1) gene-trees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future phylogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification.
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Affiliation(s)
- Lukas J Musher
- The Academy of Natural Sciences of Drexel University, Department of Ornithology, Philadelphia, PA, USA
- American Museum of Natural History, Department of Ornithology, New York, NY, USA
| | - Glaucia Del-Rio
- Cornell Laboratory of Ornithology and Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL
| | - Rafael S Marcondes
- Department of Biology and Museum of Natural Science, Louisiana State University; Department of BioSciences, Rice University, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Gustavo A Bravo
- Sección de Ornitología, Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá, Colombia
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Gregory Thom
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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Samarskaya VO, Ryabov EV, Gryzunov N, Spechenkova N, Kuznetsova M, Ilina I, Suprunova T, Taliansky ME, Ivanov PA, Kalinina NO. The Temporal and Geographical Dynamics of Potato Virus Y Diversity in Russia. Int J Mol Sci 2023; 24:14833. [PMID: 37834280 PMCID: PMC10573581 DOI: 10.3390/ijms241914833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Potato virus Y, an important viral pathogen of potato, has several genetic variants and geographic distributions which could be affected by environmental factors, aphid vectors, and reservoir plants. PVY is transmitted to virus-free potato plants by aphids and passed on to the next vegetative generations through tubers, but the effects of tuber transmission in PVY is largely unknown. By using high-throughput sequencing, we investigated PVY populations transmitted to potato plants by aphids in different climate zones of Russia, namely the Moscow and Astrakhan regions. We analyzed sprouts from the tubers produced by field-infected plants to investigate the impact of tuber transmission on PVY genetics. We found a significantly higher diversity of PVY isolates in the Astrakhan region, where winters are shorter and milder and summers are warmer compared to the Moscow region. While five PVY types, NTNa, NTNb, N:O, N-Wi, and SYR-I, were present in both regions, SYRI-II, SYRI-III, and 261-4 were only found in the Astrakhan region. All these recombinants were composed of the genome sections derived from PVY types O and N, but no full-length sequences of such types were present. The composition of the PVY variants in the tuber sprouts was not always the same as in their parental plants, suggesting that tuber transmission impacts PVY genetics.
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Affiliation(s)
- Viktoriya O. Samarskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.O.S.); (N.G.); (N.S.); (M.K.); (I.I.); (M.E.T.)
| | - Eugene V. Ryabov
- Department of Entomology, University of Maryland, College Park, MD 20742, USA;
| | - Nikita Gryzunov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.O.S.); (N.G.); (N.S.); (M.K.); (I.I.); (M.E.T.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Nadezhda Spechenkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.O.S.); (N.G.); (N.S.); (M.K.); (I.I.); (M.E.T.)
| | - Maria Kuznetsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.O.S.); (N.G.); (N.S.); (M.K.); (I.I.); (M.E.T.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Irina Ilina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.O.S.); (N.G.); (N.S.); (M.K.); (I.I.); (M.E.T.)
| | | | - Michael E. Taliansky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.O.S.); (N.G.); (N.S.); (M.K.); (I.I.); (M.E.T.)
| | - Peter A. Ivanov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Natalia O. Kalinina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.O.S.); (N.G.); (N.S.); (M.K.); (I.I.); (M.E.T.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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65
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Carnegie L, Raghwani J, Fournié G, Hill SC. Phylodynamic approaches to studying avian influenza virus. Avian Pathol 2023; 52:289-308. [PMID: 37565466 DOI: 10.1080/03079457.2023.2236568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.
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Affiliation(s)
- L Carnegie
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - J Raghwani
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - G Fournié
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint Genes Champanelle, France
| | - S C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
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66
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Pfau RS, Kozora AN, Gatica‐Colima AB, Sudman PS. Population genetic structure of a Chihuahuan Desert endemic mammal, the desert pocket gopher, Geomys arenarius. Ecol Evol 2023; 13:e10576. [PMID: 37780089 PMCID: PMC10539045 DOI: 10.1002/ece3.10576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 08/30/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023] Open
Abstract
The biogeographic history of the Chihuahuan Desert is complex, driven by numerous physiographic events and climatic changes. This dynamic history would have influenced the flora and fauna of the region including the desert pocket gopher, Geomys arenarius, a subterranean rodent endemic to the northern Chihuahuan Desert. G. arenarius is restricted to sandy soils and are considered to have a disjunct distribution. Two subspecies are recognized: G. a. arenarius and G. a. brevirostris. We used multilocus nuclear (amplified fragment length polymorphisms) and mitochondrial DNA (ND2) sequence data to uncover patterns of genetic diversity within and among populations of G. arenarius. We evaluated correspondence of genetic patterns to traditionally accepted subspecies boundaries, mapped the distribution of potentially suitable soils to identify barriers or corridors to dispersal and to guide future survey efforts, provided evidence that could be used to recognize distinct population segments, and quantified genetic diversity within populations. Both datasets were largely concordant and demonstrated hierarchical patterns of genetic divergence. The greatest divergence was consistent with the two recognized subspecies. Mapping of potentially habitable soils revealed likely barriers to dispersal contributing to the allopatric pattern of geographic distribution and areas, which may be occupied by G. arenarius but not yet documented. Because G. arenarius is restricted to soils with high sand content, and these habitable soils are disjunct within the region occupied by this species, historical factors that impacted soil deposition and deflation likely contributed to the observed patterns of genetic divergence. Genetic diversity was higher within populations of the southern subspecies (G. a. arenarius) compared to G. a. brevirostris. This may be due to a greater availability of continuous suitable soils within the range of G. a. arenarius or higher density due to greater food availability (currently or historically)-both of which could allow for a higher effective population size.
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Affiliation(s)
- Russell S. Pfau
- Department of Biological SciencesTarleton State UniversityStephenvilleTexasUSA
| | | | - Ana B. Gatica‐Colima
- Departamento de Ciencias Químico‐BiológicasInstituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad JuárezCiudad JuarezMexico
| | - Philip S. Sudman
- Department of Biological SciencesTarleton State UniversityStephenvilleTexasUSA
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Sromek L, Ylinen E, Kunnasranta M, Maduna SN, Sinisalo T, Michell CT, Kovacs KM, Lydersen C, Ieshko E, Andrievskaya E, Alexeev V, Leidenberger S, Hagen SB, Nyman T. Loss of species and genetic diversity during colonization: Insights from acanthocephalan parasites in northern European seals. Ecol Evol 2023; 13:e10608. [PMID: 37869427 PMCID: PMC10585441 DOI: 10.1002/ece3.10608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023] Open
Abstract
Studies on host-parasite systems that have experienced distributional shifts, range fragmentation, and population declines in the past can provide information regarding how parasite community richness and genetic diversity will change as a result of anthropogenic environmental changes in the future. Here, we studied how sequential postglacial colonization, shifts in habitat, and reduced host population sizes have influenced species richness and genetic diversity of Corynosoma (Acanthocephala: Polymorphidae) parasites in northern European marine, brackish, and freshwater seal populations. We collected Corynosoma population samples from Arctic, Baltic, Ladoga, and Saimaa ringed seal subspecies and Baltic gray seals, and then applied COI barcoding and triple-enzyme restriction-site associated DNA (3RAD) sequencing to delimit species, clarify their distributions and community structures, and elucidate patterns of intraspecific gene flow and genetic diversity. Our results showed that Corynosoma species diversity reflected host colonization histories and population sizes, with four species being present in the Arctic, three in the Baltic Sea, two in Lake Ladoga, and only one in Lake Saimaa. We found statistically significant population-genetic differentiation within all three Corynosoma species that occur in more than one seal (sub)species. Genetic diversity tended to be high in Corynosoma populations originating from Arctic ringed seals and low in the landlocked populations. Our results indicate that acanthocephalan communities in landlocked seal populations are impoverished with respect to both species and intraspecific genetic diversity. Interestingly, the loss of genetic diversity within Corynosoma species seems to have been less drastic than in their seal hosts, possibly due to their large local effective population sizes resulting from high infection intensities and effective intra-host population mixing. Our study highlights the utility of genomic methods in investigations of community composition and genetic diversity of understudied parasites.
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Affiliation(s)
- Ludmila Sromek
- Department of Marine Ecosystems Functioning, Institute of OceanographyUniversity of GdanskGdyniaPoland
| | - Eeva Ylinen
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
| | - Mervi Kunnasranta
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
- Natural Resources Institute FinlandJoensuuFinland
| | - Simo N. Maduna
- Department of Ecosystem in the Barents RegionNorwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Tuula Sinisalo
- Department of Biological and Environmental SciencesUniversity of JyväskyläJyväskyläFinland
| | - Craig T. Michell
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
- Red Sea Research CenterKing Abdullah University of Science and TechnologyJeddahSaudi Arabia
| | | | | | - Evgeny Ieshko
- Institute of Biology, Karelian Research CentreRussian Academy of SciencesPetrozavodskRussia
| | | | | | - Sonja Leidenberger
- Department of Biology and Bioinformatics, School of BioscienceUniversity of SkövdeSkövdeSweden
| | - Snorre B. Hagen
- Department of Ecosystem in the Barents RegionNorwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Tommi Nyman
- Department of Ecosystem in the Barents RegionNorwegian Institute of Bioeconomy ResearchSvanvikNorway
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Artamonova VS, Bizin MS, Efeykin BD, Makarova OL. Two Lineages of Oribatid Mites Morphologically Correspond to the Circumpolar Species Ameronothrus nigrofemoratus (Acari, Oribatida) but Differ Genetically as Distinct Species Are Revealed on the Kolguev Island. Dokl Biol Sci 2023; 512:321-325. [PMID: 38087021 DOI: 10.1134/s0012496623700631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 12/18/2023]
Abstract
Data reported from Northern Canada were until recently the only available data on the genetic characteristics of the oribatid mite Ameronothrus nigrofemoratus, which has a circumpolar distribution on the coasts of Arctic seas. A partial cytochrome oxidase I gene (COI) mtDNA sequence was examined in mites morphologically assigned to this species from the Kolguev Island. Two highly divergent phylogenetic lineages of A. nigrofemoratus (7% divergence) were revealed, neither of which was found on the Canadian coast. Four COI amino acid substitutions distinguished one of the lineages from North American A. nigrofemoratus, corresponding to the degree of difference between A. nigrofemoratus and its sister species A. lineatus.
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Affiliation(s)
- V S Artamonova
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - M S Bizin
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia.
| | - B D Efeykin
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - O L Makarova
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
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Kirschner P, Záveská E, Hülber K, Wessely J, Willner W, Schönswetter P, Frajman B. Evolutionary dynamics of Euphorbia carniolica suggest a complex Plio-Pleistocene history of understorey species of deciduous forest in southeastern Europe. Mol Ecol 2023; 32:5350-5368. [PMID: 37632417 PMCID: PMC10946815 DOI: 10.1111/mec.17102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/22/2023] [Accepted: 07/19/2023] [Indexed: 08/28/2023]
Abstract
Deciduous forests form the dominant natural vegetation of Europe today, but were restricted to small refugia during Pleistocene cold stages, implying an evolutionary past shaped by recurrent range contractions and expansions. Cold-stage forest refugia were probably widespread in southern and central Europe, with the northwestern Balkan Peninsula being of particular importance. However, the actual number and location of deciduous forest refugia, as well as the connections between them, remain disputed. Here, we address the evolutionary dynamics of the deciduous forest understorey species Euphorbia carniolica as a proxy for past forest dynamics. To do so, we obtained genomic and morphometric data from populations representing the species' entire range, investigated phylogenetic position and intraspecific genetic variation, tested explicit demographic scenarios and applied species distribution models. Our data support two disjoint groups linked to separate refugia on the northwestern and central Balkan Peninsula. We find that genetic differentiation between groups started in the early Pleistocene via vicariance, suggesting a larger distribution in the past. Both refugia acted as sources for founder events to the southeastern Alps and the Carpathians; the latter were likely colonised before the last cold stage. In line with traditional views on the pre-Pleistocene origin of many southeastern European deciduous forest species, the origin of E. carniolica was dated to the late Pliocene. The fact that E. carniolica evolved at a time when a period of continuous forestation was ending in much of Eurasia provides an interesting biogeographical perspective on the past links between Eurasian deciduous forests and their biota.
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Affiliation(s)
- Philipp Kirschner
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
- Faculty of Agricultural, Environmental and Food SciencesFree University of Bozen‐BolzanoBolzanoItaly
| | - Eliška Záveská
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
- Institute of Botany of the Czech Academy of SciencesPrůhoniceCzechia
| | - Karl Hülber
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Johannes Wessely
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Wolfgang Willner
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | | | - Božo Frajman
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
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Gräf T, Ferreira CDN, de Lima GB, de Lima RE, Machado LC, Campos TDL, Schemberger MO, Faoro H, Paiva MHS, Bezerra MF, Nascimento V, Souza V, Nascimento F, Mejía M, Silva D, de Oliveira YS, Gonçalves L, Ramos TCA, de Castro DB, Arcanjo AR, Dantas HAP, Presibella MM, Fernandes SB, Gregianini TS, Paz E Silva KM, Sacchi CT, Cruz ACR, Duarte dos Santos CN, Bispo de Filippis AM, Bello G, Wallau GL, Salvato RS, Naveca F. Multiple introductions and country-wide spread of DENV-2 genotype II (Cosmopolitan) in Brazil. Virus Evol 2023; 9:vead059. [PMID: 38288387 PMCID: PMC10824474 DOI: 10.1093/ve/vead059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/28/2023] [Accepted: 09/20/2023] [Indexed: 01/31/2024] Open
Abstract
Dengue virus serotype 2, genotype Cosmopolitan (DENV-2-GII), is one of the most widespread DENV strains globally. In the USA, DENV-2 epidemics have been dominated by DENV-2 genotype Asian-American (DENV-2-GIII), and the first cases of DENV-2-GII were only described in 2019, in Peru, and in 2021 in Brazil. To gain new information about the circulation of DENV-2-GII in Brazil, we sequenced 237 DENV-2 confirmed cases sampled between March 2021 and March 2023 and revealed that DENV-2-GII is already present in all geographic regions of Brazil. The phylogeographic analysis inferred that DENV-2-GII was introduced at least four times in Brazil, between May 2020 and August 2022, generating multiple clades that spread throughout the country with different success. Despite multiple introductions of DENV-2-GII, analysis of the country-wide laboratory surveillance data showed that the Brazilian dengue epidemic in 2022 was dominated by DENV-1 in most states. We hypothesize that massive circulation of DENV-2-GIII in previous years in Brazil might have created a population immune barrier against symptomatic homotypic reinfections by DENV-2-GII, leading to sustained cryptic circulation in asymptomatic cases and localized outbreaks of this new genotype. In summary, our study stresses the importance of arboviral genomic surveillance to close monitoring and better understanding the potential impact of DENV-2-GII in the coming years.
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Affiliation(s)
- Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba 81350-010, Brazil
| | | | - Gustavo Barbosa de Lima
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco 50740-465, Brazil
| | - Raul Emídio de Lima
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco 50740-465, Brazil
| | - Lais Ceschini Machado
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco 50740-465, Brazil
| | - Tulio de Lima Campos
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco 50740-465, Brazil
| | - Michelle Orane Schemberger
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba 81350-010, Brazil
| | - Helisson Faoro
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba 81350-010, Brazil
| | - Marcelo Henrique Santos Paiva
- Núcleo de Ciências da Vida, Universidade Federal de Pernambuco (UFPE), Centro Acadêmico do Agreste-Rodovia BR-104, km 59-Nova Caruaru, Caruaru 55002-970, Brazil
| | - Matheus Filgueira Bezerra
- Departamento de Microbiologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco 50740-465, Brazil
| | - Valdinete Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus 69057-070, Brazil
| | - Victor Souza
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus 69057-070, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus 69057-070, Brazil
| | - Matilde Mejía
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus 69057-070, Brazil
| | - Dejanane Silva
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus 69057-070, Brazil
| | - Yasmin Silva de Oliveira
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus 69057-070, Brazil
| | - Luciana Gonçalves
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus 69057-070, Brazil
- Fundação de Vigilância em Saúde do Amazonas—Dra Rosemary Costa Pinto, Manaus, Amazonas 69093-018, Brazil
| | - Tatyana Costa Amorim Ramos
- Fundação de Vigilância em Saúde do Amazonas—Dra Rosemary Costa Pinto, Manaus, Amazonas 69093-018, Brazil
| | - Daniel Barros de Castro
- Fundação de Vigilância em Saúde do Amazonas—Dra Rosemary Costa Pinto, Manaus, Amazonas 69093-018, Brazil
| | - Ana Ruth Arcanjo
- Laboratório Central de Saúde Pública do Amazonas (LACEN-AM), Manaus, Amazonas 69020-040, Brazil
| | | | - Mayra Marinho Presibella
- Laboratório Central de Saúde Pública do Estado do Paraná (LACEN-PR), São José dos Pinhais, Paraná 83060-500, Brazil
| | - Sandra Bianchini Fernandes
- Laboratório Central de Saúde Pública do Estado de Santa Catarina (LACEN-SC), Florianópolis, Santa Catarina 88010-001, Brazil
| | - Tatiana Schaffer Gregianini
- Laboratório Central de Saúde Pública do Rio Grande do Sul (LACEN-RS), Porto Alegre, Rio Grande do Sul 90610-000, Brazil
| | - Keilla Maria Paz E Silva
- Laboratório Central de Saúde Pública de Pernambuco (LACEN-PE), Recife, Pernambuco 50050-210, Brazil
| | | | - Ana Cecília Ribeiro Cruz
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua, Para 670030-000, Brazil
- Institute of Biological Sciences, Federal University of Pará, Belém, Para 66075-110, Brazil
| | | | - Ana Maria Bispo de Filippis
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil
| | - Gonzalo Bello
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco 50740-465, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Bernhard-Nocht-Straße 74, Hamburg 20359, Germany
| | - Richard Steiner Salvato
- Laboratório Central de Saúde Pública do Rio Grande do Sul (LACEN-RS), Porto Alegre, Rio Grande do Sul 90610-000, Brazil
| | - Felipe Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus 69057-070, Brazil
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil
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Mokrousov I, Vinogradova T, Dogonadze M, Zabolotnykh N, Vyazovaya A, Vitovskaya M, Solovieva N, Ariel B. A multifaceted interplay between virulence, drug resistance, and the phylogeographic landscape of Mycobacterium tuberculosis. Microbiol Spectr 2023; 11:e0139223. [PMID: 37768091 PMCID: PMC10581221 DOI: 10.1128/spectrum.01392-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/06/2023] [Indexed: 09/29/2023] Open
Abstract
Latin-American Mediterranean (LAM) family is one of the most significant and global genotypes of Mycobacterium tuberculosis. Here, we used the murine model to study the virulence and lethality of the genetically and epidemiologically distinct LAM strains. The pathobiological characteristics of the four LAM strains (three drug resistant and one drug susceptible) and the susceptible reference strain H37Rv were studied in the C57BL/6 mouse model. The whole-genome sequencing was performed using the HiSeq Illumina platform, followed by bioinformatics and phylogenetic analysis. The susceptible strain H37Rv showed the highest virulence. Drug-susceptible LAM strain (spoligotype SIT264) was more virulent than three multidrug-resistant (MDR) strains (SIT252, SIT254, and SIT266). All three MDR isolates were low lethal, while the susceptible isolate and H37Rv were moderately/highly lethal. Putting the genomic, phenotypic, and virulence features of the LAM strains/spoligotypes in the context of their dynamic phylogeography over 20 years reveals three types of relationships between virulence, resistance, and transmission. First, the most virulent and more lethal drug-susceptible SIT264 increased its circulation in parts of Russia. Second, moderately virulent and pre-XDR SIT266 was prevalent in Belarus and continues to be visible in North-West Russia. Third, the low virulent and MDR strain SIT252 previously considered as emerging has disappeared from the population. These findings suggest that strain virulence impacts the transmission, irrespective of drug resistance properties. The increasing circulation of susceptible but more virulent and lethal strains implies that personalized TB treatment should consider not only resistance but also the virulence of the infecting M. tuberculosis strains. IMPORTANCE The study is multidisciplinary and investigates the epidemically/clinically important and global lineage of Mycobacterium tuberculosis, named Latin-American-Mediterranean (LAM), yet insufficiently studied with regard to its pathobiology. We studied different LAM strains (epidemic vs endemic and resistant vs susceptible) in the murine model and using whole-genome analysis. We also collected long-term, 20-year data on their prevalence in Eurasia. The findings are both expected and unexpected. (i) We observe that a drug-susceptible but highly virulent strain increased its prevalence. (ii) By contrast, the multidrug-resistant (MDR) but low-virulent, low-lethal strain (that we considered as emerging 15 years ago) has almost disappeared. (iii) Finally, an intermediate case is the MDR strain with moderate virulence that continues to circulate. We conclude that (i) the former and latter strains are the most hazardous and require close epidemiological monitoring, and (ii) personalized TB treatment should consider not only drug resistance but also the virulence of the infecting strains and development of anti-virulence drugs is warranted.
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Affiliation(s)
- Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Tatiana Vinogradova
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Marine Dogonadze
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Natalia Zabolotnykh
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Anna Vyazovaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Maria Vitovskaya
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Boris Ariel
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
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Blinova EA, Makenov MT, Morozkin ES, Kholodilov IS, Fedorova MV, Zhurenkova OB, Roev GV, Khafizov KF, Karan LS. Genetic features of the Puumala virus (Hantaviridae: Orthohantavirus) identified in the Moscow region. Vopr Virusol 2023; 68:283-290. [PMID: 38156585 DOI: 10.36233/0507-4088-177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Indexed: 12/30/2023]
Abstract
INTRODUCTION Puumala virus (family Hantaviridae, genus Orthohantavirus) is distributed in most regions of the European part of Russia. However, information about its genetic variants circulating on the territory of the Central Federal District is extremely scarce. MATERIALS AND METHODS Rodents' tissue samples were tested after reverse transcription by PCR for the presence of hantaviral RNA. The amplified fragments of the L segment were sequenced by the Sanger method. For two samples, sequences of all three segments were obtained using the NGS method. Phylogenetic trees were built in the MEGA-X software. RESULTS Puumala virus was found in six samples. Based on the phylogenetic analysis of sequences of three segments, the obtained genetic variants belong to the sublineage previously designated as W-RUS. CONCLUSION A genetic variant of the Puumala virus, belonging to the subline W-RUS, circulates on the territory of the Volokolamsk district of Moscow region.
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Affiliation(s)
- E A Blinova
- Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
- Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of poliomyelitis)
| | - M T Makenov
- Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
| | - E S Morozkin
- Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
| | - I S Kholodilov
- Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of poliomyelitis)
| | - M V Fedorova
- Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
| | - O B Zhurenkova
- Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
| | - G V Roev
- Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
- Moscow Institute of Physics and Technology (National Research University)
| | - K F Khafizov
- Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
| | - L S Karan
- Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
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73
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Li J, Zhang C, Mipam TD, Zhou Q, Chen S. Effects of Climatic Change on Phylogeography and Ecological Niche of the Endemic Herb Elymus breviaristatus on the Qinghai-Tibet Plateau. Plants (Basel) 2023; 12:3326. [PMID: 37765492 PMCID: PMC10535585 DOI: 10.3390/plants12183326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023]
Abstract
Past climatic and topographic variations have created strong biogeographic barriers for alpine species and are key drivers of the distribution of genetic variation and population dynamics of species on the Qinghai-Tibet Plateau (QTP). Therefore, to better conserve and use germplasm resources, it is crucial to understand the distribution and differentiation of genetic variation within species. Elymus breviaristatus, an ecologically important rare grass species with strong resistance, is restricted to a limited area of the QTP. In this study, we investigated the phylogeography of E. breviaristatus using five chloroplast genes and spacer regions in natural populations distributed along the eastern QTP. We identified a total of 25 haplotypes among 216 individuals from 18 E. breviaristatus populations, which were further classified into four haplogroups based on geographical distribution and haplotype network analysis. Notably, we did not observe any signs of population expansion. High genetic diversity was exhibited at both species and population levels, with precipitation being the main limiting factor for population genetic diversity levels. Higher genetic diversity was exhibited by populations located near the Mekong-Salween Divide genetic barrier, suggesting that they may have served as a glacial refuge. The significant pattern of genetic differentiation by environmental isolation highlights the influence of heterogeneous environments on the genetic structure of E. breviaristatus populations. Additionally, the results of ecological niche models indicated that the geographic distribution of E. breviaristatus populations has decreased rapidly since the Last Glacial Maximum but is not threatened by future global warming.
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Affiliation(s)
- Jin Li
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu 610041, China
| | | | - Tserang Donko Mipam
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu 610041, China
| | - Qingping Zhou
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu 610041, China
| | - Shiyong Chen
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu 610041, China
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
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74
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Urbaniak J, Kwiatkowski P. The Role of the Hercynian Mountains of Central Europe in Shaping Plant Migration Patterns in the Pleistocene-A Review. Plants (Basel) 2023; 12:3317. [PMID: 37765481 PMCID: PMC10537488 DOI: 10.3390/plants12183317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 08/31/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
The climatic changes that took place in Europe during the Quaternary period influenced plant habitats as well as their species and vegetation composition. In this article, biogeographical studies on Hercynian mountain plants that include data for the Alps, Carpathians, and European lowlands are reviewed in order to discuss the phylogeographical structure and divergence of the Hercynian populations from those in other European mountain ranges, Scandinavia, and lowlands. The analyzed studies show specific phylogeographical relations between the Hercynian mountains, Alps, Scandinavia, Carpathians, and European lowlands. The results also indicate that the genetic patterns of plant populations in the Hercynian Mountains may differ significantly in terms of origin. The main migration routes of species to the Hercynian ranges began in the Alps or Carpathians. Some species, such as Rubus chamaemorus L., Salix lapponum L., and Salix herbacea L., are glacial relics that may have arrived and settled in the Hercynian Mountains during the Ice Age and that survived in isolated habitats. The Hercynian Mountains are composed of various smaller mountain ranges and are a crossroads of migration routes from different parts of Europe; thus, intensive hybridization has occurred between the plant populations therein, which is indicated by the presence of several divergent genetic lines.
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Affiliation(s)
- Jacek Urbaniak
- Department of Botany and Plant Ecology, Wrocław University of Environmental and Life Sciences, 50-363 Wrocław, Poland
| | - Paweł Kwiatkowski
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland;
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75
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Layan M, Dacheux L, Lemey P, Brunker K, Ma L, Troupin C, Dussart P, Chevalier V, Wood JLN, Ly S, Duong V, Bourhy H, Dellicour S. Uncovering the endemic circulation of rabies in Cambodia. Mol Ecol 2023; 32:5140-5155. [PMID: 37540190 DOI: 10.1111/mec.17087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/18/2023] [Indexed: 08/05/2023]
Abstract
In epidemiology, endemicity characterizes sustained pathogen circulation in a geographical area, which involves a circulation that is not being maintained by external introductions. Because it could potentially shape the design of public health interventions, there is an interest in fully uncovering the endemic pattern of a disease. Here, we use a phylogeographic approach to investigate the endemic signature of rabies virus (RABV) circulation in Cambodia. Cambodia is located in one of the most affected regions by rabies in the world, but RABV circulation between and within Southeast Asian countries remains understudied. Our analyses are based on a new comprehensive data set of 199 RABV genomes collected between 2014 and 2017 as well as previously published Southeast Asian RABV sequences. We show that most Cambodian sequences belong to a distinct clade that has been circulating almost exclusively in Cambodia. Our results thus point towards rabies circulation in Cambodia that does not rely on external introductions. We further characterize within-Cambodia RABV circulation by estimating lineage dispersal metrics that appear to be similar to other settings, and by performing landscape phylogeographic analyses to investigate environmental factors impacting the dispersal dynamic of viral lineages. The latter analyses do not lead to the identification of environmental variables that would be associated with the heterogeneity of viral lineage dispersal velocities, which calls for a better understanding of local dog ecology and further investigations of the potential drivers of RABV spread in the region. Overall, our study illustrates how phylogeographic investigations can be performed to assess and characterize viral endemicity in a context of relatively limited data.
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Affiliation(s)
- Maylis Layan
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, UMR2000, CNRS, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Laurent Dacheux
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Université Paris Cité, Paris, France
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Laurence Ma
- Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Université Paris Cité, Paris, France
| | - Cécile Troupin
- Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Véronique Chevalier
- CIRAD, UMR ASTRE, Montpellier, France
- ASTRE, Univ. Montpellier CIRAD, INRAE, Montpellier, France
- Epidemiology and Clinical Research, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - James L N Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sowath Ly
- Epidemiology and Public Health, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Université Paris Cité, Paris, France
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
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Herczeg D, Palomar G, Zieliński P, van Riemsdijk I, Babik W, Dankovics R, Halpern B, Cvijanović M, Vörös J. Genomic analysis reveals complex population structure within the smooth newt, Lissotriton vulgaris, in Central Europe. Ecol Evol 2023; 13:e10478. [PMID: 37664508 PMCID: PMC10469019 DOI: 10.1002/ece3.10478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
Species with wide-range distributions usually display high genetic variation. This variation can be partly explained by historical lineages that were temporally isolated from each other and are back into secondary reproductive contact, and partly by local adaptations. The smooth newt (Lissotriton vulgaris) is one of the most widely distributed amphibians species across Eurasia and forms a species complex with a partially overlapping distribution and morphology. In the present study, we explored the population genomic structure of smooth newt lineages in the Carpathian Basin (CB) relying on single-nucleotide polymorphisms. Our dataset included new and previously published data to study the secondary contact zone between lineages in the CB and also tested for the barrier effect of rivers to gene flow between these lineages. We confirmed the presence of the South L. v. vulgaris Lineage distributed in Transdanubia and we provided new distribution records of L. v. ampelensis inhabiting the eastern territories of the CB. High genetic diversity of smooth newts was observed, especially in the North Hungarian Mountains and at the interfluves of the main rivers in the South with four distinct lineages of L. v. vulgaris and one lineage of L. v. ampelensis showing a low level of admixture with the spatially closest L. v. vulgaris lineage. Moreover, admixture detected at the interfluve of the main rivers (i.e. Danube and Tisza) suggested a secondary contact zone in the area. Finally, we found that the river Danube has a very weak effect on population divergence, while the river Tisza is a geographical barrier limiting gene flow between smooth newt lineages. As the range boundaries of L. v. vulgaris and L. v. ampelensis in the CB coincide with the river Tisza, our study underpins the influence of rivers in lineage diversification.
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Affiliation(s)
- Dávid Herczeg
- ELKH‐ELTE‐MTM Integrative Ecology Research GroupBudapestHungary
- Department of Systematic Zoology and Ecology, Institute of BiologyELTE Eötvös Loránd UniversityBudapestHungary
| | - Gemma Palomar
- Department of Genetics, Physiology, and Microbiology, Faculty of Biological SciencesComplutense University of MadridMadridSpain
- Institute of Environmental SciencesFaculty of Biology, Jagiellonian UniversityKrakówPoland
| | - Piotr Zieliński
- Institute of Environmental SciencesFaculty of Biology, Jagiellonian UniversityKrakówPoland
| | | | - Wiesław Babik
- Institute of Environmental SciencesFaculty of Biology, Jagiellonian UniversityKrakówPoland
| | | | - Bálint Halpern
- ELKH‐ELTE‐MTM Integrative Ecology Research GroupBudapestHungary
- Department of Systematic Zoology and Ecology, Institute of BiologyELTE Eötvös Loránd UniversityBudapestHungary
- MME Birdlife HungaryBudapestHungary
| | - Milena Cvijanović
- Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of SerbiaUniversity of BelgradeBelgradeSerbia
| | - Judit Vörös
- Department of ZoologyHungarian Natural History MuseumBudapestHungary
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Holmes IA, Monagan IV, Westphal MF, Johnson PJ, Rabosky ARD. Parsing variance by marker type: Testing biogeographic hypotheses and differential contribution of historical processes to population structure in a desert lizard. Mol Ecol 2023; 32:4880-4897. [PMID: 37466017 PMCID: PMC10530499 DOI: 10.1111/mec.17076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 07/20/2023]
Abstract
A fundamental goal of population genetic studies is to identify historical biogeographic patterns and understand the processes that generate them. However, localized demographic events can skew population genetic inference. Assessing populations with multiple types of genetic markers, each with unique mutation rates and responses to changes in population size, can help to identify potentially confounding population-specific demographic processes. Here, we compared population structure and connectivity inferred from microsatellites and restriction site-associated DNA loci among 17 populations of an arid-specialist lizard, the desert night lizard, Xantusia vigilis, in central California to test among historical processes structuring population genetic diversity. We found that both marker types yielded generally concordant insights into population genetic structure including a major phylogenetic break maintained between two populations separated by less than 10 km, suggesting that either marker type could be used to understand generalized demographic patterns across the region for management purposes. However, we also found that the effects of demography on marker discordance could be used to elucidate population histories and distinguish among competing biogeographic hypotheses. Our results suggest that comparisons of within-population diversity across marker types provide powerful opportunities for leveraging marker discordance, particularly for understanding the creation and maintenance of contact zones among clades.
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Affiliation(s)
- Iris A. Holmes
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI USA
- Cornell Institute of Host Microbe Interactions and Disease and Department of Microbiology, Cornell University, Ithaca, NY 14853 USA
| | - Ivan V. Monagan
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI USA
- Department of Ecology, Evolution, and Environmental Biology, Columbia University and American Museum of Natural History, NY, USA
| | | | | | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI USA
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA USA
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Shen-Gunther J, Gunther RS, Cai H, Wang Y. A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping. Int J Mol Sci 2023; 24:13505. [PMID: 37686313 PMCID: PMC10488239 DOI: 10.3390/ijms241713505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
The field of mitochondrial genomics has advanced rapidly and has revolutionized disciplines such as molecular anthropology, population genetics, and medical genetics/oncogenetics. However, mtDNA next-generation sequencing (NGS) analysis for matrilineal haplotyping and phylogeographic inference remains hindered by the lack of a consolidated mitogenome database and an efficient bioinformatics pipeline. To address this, we developed a customized human mitogenome database (hMITO DB) embedded in a CLC Genomics workflow for read mapping, variant analysis, haplotyping, and geo-mapping. The database was constructed from 4286 mitogenomes. The macro-haplogroup (A to Z) distribution and representative phylogenetic tree were found to be consistent with published literature. The hMITO DB automated workflow was tested using mtDNA-NGS sequences derived from Pap smears and cervical cancer cell lines. The auto-generated read mapping, variants track, and table of haplotypes and geo-origins were completed in 15 min for 47 samples. The mtDNA workflow proved to be a rapid, efficient, and accurate means of sequence analysis for translational mitogenomics.
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Affiliation(s)
- Jane Shen-Gunther
- Gynecologic Oncology & Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, San Antonio, TX 78234, USA
| | - Rutger S. Gunther
- Nuclear Medicine & Molecular Imaging, Department of Radiology, Brooke Army Medical Center, Fort Sam Houston, San Antonio, TX 78234, USA;
| | - Hong Cai
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA;
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Yufeng Wang
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA;
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
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79
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Pérez T, Romero-Bascones A, Pirhadi N, Coya R, Fernández-Rueda MDP, Márquez I, García-Flórez L, Borrell YJ. Insights on the Evolutionary History and Genetic Patterns of Octopus vulgaris Cuvier, 1797 in the Northeastern Atlantic Using Mitochondrial DNA. Animals (Basel) 2023; 13:2708. [PMID: 37684972 PMCID: PMC10486628 DOI: 10.3390/ani13172708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/20/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Octopus vulgaris is one of the most harvested octopus species in the world. In the Iberian Peninsula, there are several small-scale fisheries that have a long-term tradition of harvesting octopus. The Asturias fleet (in Northern Spain) has an internationally recognized MSC label for its exploitation. Of concern, genetic assessments of exploited stocks are currently scarce, which could prevent the implementation of adequate managing strategies. We use two mitochondrial regions (cytochrome oxidase subunit 1 and control region) to analyze the genetic status and evolutionary events that conditioned octopus populations' characteristics in the Northeastern Atlantic. A total of 90 individuals were sampled from three different localities in the Iberian Peninsula as well as a location in Macaronesia. Temporal genetic analyses on Asturias and Algarve populations were also performed. Results indicated the absence of fine spatial genetic structuring but showed the Canary Islands (in Macaronesia) as the most distinct population. Our analyses detected two distinct clades, already described in the literature, but, for the first time, we confirmed the presence of the α-southern haplogroup in the Northern Iberian Peninsula. This result indicates a more continuous cline for the distribution of these two haplogroups than previously reported. Temporal changes in the distribution of both haplogroups in contact zones were also detected.
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Affiliation(s)
- Trinidad Pérez
- Department of Functional Biology, Genetics, University of Oviedo, 33006 Oviedo, Spain; (A.R.-B.); (N.P.); (R.C.); (Y.J.B.)
| | - Andrea Romero-Bascones
- Department of Functional Biology, Genetics, University of Oviedo, 33006 Oviedo, Spain; (A.R.-B.); (N.P.); (R.C.); (Y.J.B.)
| | - Negin Pirhadi
- Department of Functional Biology, Genetics, University of Oviedo, 33006 Oviedo, Spain; (A.R.-B.); (N.P.); (R.C.); (Y.J.B.)
| | - Ruth Coya
- Department of Functional Biology, Genetics, University of Oviedo, 33006 Oviedo, Spain; (A.R.-B.); (N.P.); (R.C.); (Y.J.B.)
| | - María del Pino Fernández-Rueda
- CEP Fisheries Experimentation Centre, Directorate General of Maritime Fisheries (DGPM), Regional Ministry of Rural Development and Natural Resources from the Principality of Asturias, 33212 Gijón, Spain; (M.d.P.F.-R.); (L.G.-F.)
| | | | - Lucía García-Flórez
- CEP Fisheries Experimentation Centre, Directorate General of Maritime Fisheries (DGPM), Regional Ministry of Rural Development and Natural Resources from the Principality of Asturias, 33212 Gijón, Spain; (M.d.P.F.-R.); (L.G.-F.)
| | - Yaisel J. Borrell
- Department of Functional Biology, Genetics, University of Oviedo, 33006 Oviedo, Spain; (A.R.-B.); (N.P.); (R.C.); (Y.J.B.)
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80
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Nnamani EI, Spruill-Harrell B, Williams EP, Taylor MK, Owen RD, Jonsson CB. Deep Sequencing to Reveal Phylo-Geographic Relationships of Juquitiba Virus in Paraguay. Viruses 2023; 15:1798. [PMID: 37766205 PMCID: PMC10537311 DOI: 10.3390/v15091798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Several hantaviruses result in zoonotic infections of significant public health concern, causing hemorrhagic fever with renal syndrome (HFRS) or hantavirus cardiopulmonary syndrome (HCPS) in the Old and New World, respectively. Given a 35% case fatality rate, disease-causing New World hantaviruses require a greater understanding of their biology, genetic diversity, and geographical distribution. Juquitiba hantaviruses have been identified in Oligoryzomys nigripes in Brazil, Paraguay, and Uruguay. Brazil has reported the most HCPS cases associated with this virus. We used a multiplexed, amplicon-based PCR strategy to screen and deep-sequence the virus harbored within lung tissues collected from Oligoryzomys species during rodent field collections in southern (Itapúa) and western (Boquerón) Paraguay. No Juquitiba-like hantaviruses were identified in Boquerón. Herein, we report the full-length S and M segments of the Juquitiba hantaviruses identified in Paraguay from O. nigripes. We also report the phylogenetic relationships of the Juquitiba hantaviruses in rodents collected from Itapúa with those previously collected in Canindeyú. We showed, using the TN93 nucleotide substitution model, the coalescent (constant-size) population tree model, and Bayesian inference implemented in the Bayesian evolutionary analysis by sampling trees (BEAST) framework, that the Juquitiba virus lineage in Itapúa is distinct from that in Canindeyú. Our spatiotemporal analysis showed significantly different time to the most recent ancestor (TMRA) estimates between the M and S segments, but a common geographic origin. Our estimates suggest the additional geographic diversity of the Juquitiba virus within the Interior Atlantic Forest and highlight the need for more extensive sampling across this biome.
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Affiliation(s)
- Evans Ifebuche Nnamani
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (E.I.N.); (B.S.-H.); (E.P.W.); (M.K.T.)
| | - Briana Spruill-Harrell
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (E.I.N.); (B.S.-H.); (E.P.W.); (M.K.T.)
| | - Evan Peter Williams
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (E.I.N.); (B.S.-H.); (E.P.W.); (M.K.T.)
| | - Mariah K. Taylor
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (E.I.N.); (B.S.-H.); (E.P.W.); (M.K.T.)
| | - Robert D. Owen
- Centro Para El Desarrollo de Investigación Científica, Asunción C.P. 1255, Paraguay;
| | - Colleen B. Jonsson
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (E.I.N.); (B.S.-H.); (E.P.W.); (M.K.T.)
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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81
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De-la-Mora M, Pinero D. Helmet Shape and Phylogeography of the Treehopper Membracis mexicana. Insects 2023; 14:704. [PMID: 37623414 PMCID: PMC10455800 DOI: 10.3390/insects14080704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
Membracis mexicana (Hemiptera: Membracidae) is distributed in four biogeographic provinces of Mexico. Field observations indicate that there are different forms of this species, but the distribution of the phenotype and the genetic variation of this species have not been clarified. The aim of this study was to quantify the phenotypic and genetic variation of M. mexicana and determine whether the configuration of biogeographic provinces impacts the distribution of this variation. To achieve this, we analyzed 307 photographs using 19 landmarks and geometric morphometrics to quantify the phenotypic variation in helmets. We sequenced five molecular markers for 205 individuals to describe the phylogeographic pattern. As a result, we identified three morphological configurations of the helmet of M. mexicana and two genetic lineages. The morphotypes are (1) a large and wide helmet with small dorsal spots, (2) a small and narrow helmet with large dorsal spots, and (3) a small and narrow helmet with small spots. Genetic lineages are distributed in southeast and western Mexico. The western lineage corresponds to two helmet morphotypes (1 and 2) and the southeast lineage to morphotype 3. We found that the larger helmets correspond to the western lineage and are distributed in Trans-Mexican Volcanic Belt and Pacific lowlands provinces, whereas the smallest helmets correspond to the southeast lineage and are present in the Veracruzan and Yucatan Peninsula provinces.
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Affiliation(s)
- Marisol De-la-Mora
- Escuela Nacional de Estudios Superiores Campus Juriquilla, Universidad Nacional Autónoma de México, Boulevard Villas del Mesón 3001, Querétaro 76230, Mexico
| | - Daniel Pinero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510, Mexico;
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82
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Hope AG, Headlee KM, Olson ZH, Wiens BJ. Systematics, biogeography and phylogenomics of northern bog lemmings (Cricetidae), cold-temperate rodents of conservation concern under global change. SYST BIODIVERS 2023; 21:2237050. [PMID: 38523662 PMCID: PMC10959253 DOI: 10.1080/14772000.2023.2237050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Northern bog lemmings, Mictomys (Synaptomys) borealis, are currently being assessed for protections under the U.S. Endangered Species Act. A major impediment to comprehensive evaluation is a deficiency of data towards understanding the biology of these rodents. Inherent rarity and scarce specimen sampling, despite a continent-wide distribution, has precluded our ability to implement modern methods for resolving taxonomy, evolutionary history, and investigating multiple other species traits. Here we use a maternally inherited locus (mitochondrial cytochrome b) and between 5,939 and 11,513 nuclear loci from reduced representation sequencing (ddRADseq) to investigate the evolutionary history of northern bog lemmings. We 1) qualify evidence based on morphological and early molecular studies for the genus assignment of Mictomys, 2) test the validity of multiple sub-species designations, 3) provide spatial and temporal historical biogeographic perspectives, and 4) discuss how incomplete sampling might influence conservation efforts. Both mitochondrial and nuclear datasets exhibit deep divergence and paraphyly between two recognized species, the northern (Mictomys borealis) and southern (Synaptomys cooperi) bog lemmings. Based on mtDNA, the geographically isolated subspecies (M. b. sphagnicola) was found to be divergent from all other specimens. The remainder of the species exhibited shallow intra-specific differentiation in mtDNA, however nuclear data supports genetic distinction consistent with four geographic subspecies. Recent coalescence of all northern bog lemmings (except for M. b. sphagnicola) reflects divergence in multiple refugia through the last glacial cycle, including a well-known coastal center of endemism and multiple regions south of continental ice-sheets. Regional lineages across North America suggest strong latitudinal displacement with global climate change, coupled with isolation-reconnection dynamics. This taxon suffers from a lack of modern samples through most of its distribution, severely limiting interpretation of ongoing evolutionary processes, particularly in southern portions of the species' range. Limited voucher specimen sampling of vulnerable populations could aid in rigorous conservation decision-making.
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Affiliation(s)
- Andrew G Hope
- Division of Biology, Kansas State University, Manhattan, Kansas 66506, USA
| | - Kaitlyn M Headlee
- Division of Biology, Kansas State University, Manhattan, Kansas 66506, USA
| | - Zachary H Olson
- School of Social and Behavioral Science, University of New England, Biddeford, Maine 04005, USA
| | - Ben J Wiens
- Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA
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83
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Finch KN, Leaché AD. Population dynamics in newts of the Carpathian Mountains. Mol Ecol 2023; 32:4464-4466. [PMID: 37454275 DOI: 10.1111/mec.17077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/05/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
Rarity, range restriction, and narrow endemism tend to carry dire and urgent conservation implications for imperilled species. What is also clear is that human-associated extinction risk factors such as urbanization and deforestation pose overwhelming threats to range-restricted species. In this issue of Molecular Ecology, Antunes et al. (2022) demonstrate that these threats can also impact widespread species. By comparing newts in the genus Lissotriton that co-occur in the same geographical region, they expose the distinctness of risks facing species with different habitat preferences. Their study emphasizes the importance of local-scale landscape genetics to reveal the nuances of population connectivity that might otherwise be missed by studying a broader spatial scale.
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Affiliation(s)
- Kristen N Finch
- Department of Biology, University of Washington, Seattle, Washington, USA
- Center for Environmental Forensic Science, University of Washington, Seattle, Washington, USA
| | - Adam D Leaché
- Department of Biology, University of Washington, Seattle, Washington, USA
- Burke Museum of Natural History & Culture, University of Washington, Seattle, Washington, USA
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84
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Cid-Alda FP, Montecinos AE, Guillemin ML. A temporal and spatial study of genetic structure in four species of bladed Bangiales (Rhodophyta) from the southeastern Pacific coast of Chile. J Phycol 2023; 59:712-724. [PMID: 37166446 DOI: 10.1111/jpy.13343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/12/2023]
Abstract
The coastline is a heterogeneous and highly dynamic environment influenced by abiotic and biotic variables affecting the temporal stability of genetic diversity and structure of marine organisms. The aim of this study was to determine how much the genetic structure of four species of marine Bangiales vary in time and space. Partial sequences of the cytochrome oxidase I (COI) gene obtained from two Pyropia (Py. sp. CHJ and Py. orbicularis) and two Porphyra (P. mumfordii and P. sp. FIH) species were used to compare the effect of the 40° S/41° S biogeographic break (spatial-regional scale) and the one of the Valdivia River discharges (spatial-local scale) and determine their temporal stability. Four seasonal samplings were taken during 1 year at five sites, one site located in Melinka (Magallanes province) and four sites along the coast of Valdivia (Intermediate area), on both sides of the river mouth. Results showed a strong genetic spatial structure at regional scale (ΦST > 0.4) in Py. sp. CHJ, Py. orbicularis, and P. mumfordii, congruent with the 41° S/42° S biogeographic break. A potential barrier to gene flow, related to the Valdivia River discharge, was detected only in P. mumfordii. In P. sp. FIH, spatial genetic structure was not detected at any scale. The genetic structure of all four species is stable throughout the year. The potential effect of main currents and river discharge in limiting the transport of Bangiales spores are discussed. We propose that both a restricted propagule dispersal and the formation potential for persistent banks of microscopic stages could lead to a temporally stable spatial partitioning of genetic variation in bladed Bangiales.
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Affiliation(s)
- Fernanda P Cid-Alda
- Post-doctoral researcher in Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Alejandro E Montecinos
- Núcleo Milenio MASH, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Marie Laure Guillemin
- Núcleo Milenio MASH, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, Roscoff, France
- Centro FONDAP de Investigación de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
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85
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Sitam FT, Salgado‐Lynn M, Denel A, Panjang E, McEwing R, Lightson A, Ogden R, Maruji NA, Yahya NK, Ngau C, Mohd Kulaimi NA, Ithnin H, Rovie‐Ryan J, Abu Bakar MS, Ewart KM. Phylogeography of the Sunda pangolin, Manis javanica: Implications for taxonomy, conservation management and wildlife forensics. Ecol Evol 2023; 13:e10373. [PMID: 37593756 PMCID: PMC10427774 DOI: 10.1002/ece3.10373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 08/19/2023] Open
Abstract
The Sunda pangolin (Manis javanica) is the most widely distributed Asian pangolin species, occurring across much of Southeast Asia and in southern China. It is classified as Critically Endangered and is one of the most trafficked mammals in the world, which not only negatively impacts wild Sunda pangolin populations but also poses a potential disease risk to other species, including humans and livestock. Here, we aimed to investigate the species' phylogeography across its distribution to improve our understanding of the species' evolutionary history, elucidate any taxonomic uncertainties and enhance the species' conservation genetic management and potential wildlife forensics applications. We sequenced mtDNA genomes from 23 wild Sunda pangolins of known provenance originating from Malaysia to fill sampling gaps in previous studies, particularly in Borneo. To conduct phylogenetic and population genetic analyses of Sunda pangolins across their range, we integrated these newly generated mitochondrial genomes with previously generated mtDNA and nuclear DNA data sets (RAD-seq SNP data). We identified an evolutionarily distinct mtDNA lineage in north Borneo, estimated to be ~1.6 million years divergent from lineages in west/south Borneo and the mainland, comparable to the divergence time from the Palawan pangolin. There appeared to be mitonuclear discordance, with no apparent genetic structure across Borneo based on analysis of nuclear SNPs. These findings are consistent with the 'out of Borneo hypothesis', whereby Sunda pangolins diversified in Borneo before subsequently migrating throughout Sundaland, and/or a secondary contact scenario between mainland and Borneo. We have elucidated possible taxonomic issues in the Sunda/Palawan pangolin complex and highlight the critical need for additional georeferenced samples to accurately apportion its range-wide genetic variation into appropriate taxonomic and conservation units. Additionally, these data have improved forensic identification testing involving these species and permit the implementation of geographic provenance testing in some scenarios.
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Affiliation(s)
- Frankie T. Sitam
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | - Milena Salgado‐Lynn
- Danau Girang Field Centre (DGFC)Kota KinabaluMalaysia
- Wildlife Health, Genetic and Forensic Laboratory (WHGFL)Kota KinabaluMalaysia
- Organisms and Environment Division, Cardiff School of BiosciencesCardiff UniversityCardiffUK
| | - Azroie Denel
- Sarawak Forestry Corporation (SFC)KuchingMalaysia
| | - Elisa Panjang
- Danau Girang Field Centre (DGFC)Kota KinabaluMalaysia
- Organisms and Environment Division, Cardiff School of BiosciencesCardiff UniversityCardiffUK
| | | | | | - Rob Ogden
- TRACE Wildlife Forensics NetworkEdinburghUK
- Royal (Dick) School of Veterinary Studies and the Roslin InstituteUniversity of EdinburghEdinburghUK
| | - Nur Alwanie Maruji
- Wildlife Health, Genetic and Forensic Laboratory (WHGFL)Kota KinabaluMalaysia
- Sabah Wildlife Department (SWD)Kota KinabaluMalaysia
| | - Nurhartini Kamalia Yahya
- Danau Girang Field Centre (DGFC)Kota KinabaluMalaysia
- Wildlife Health, Genetic and Forensic Laboratory (WHGFL)Kota KinabaluMalaysia
| | - Cosmas Ngau
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | - Noor Azleen Mohd Kulaimi
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | - Hartini Ithnin
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | | | | | - Kyle M. Ewart
- TRACE Wildlife Forensics NetworkEdinburghUK
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
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86
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Duvernell DD, Remex NS, Miller JT, Schaefer JF. Variable rates of hybridization among contact zones between a pair of topminnow species, Fundulus notatus and F. olivaceus. Ecol Evol 2023; 13:e10399. [PMID: 37560181 PMCID: PMC10408002 DOI: 10.1002/ece3.10399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023] Open
Abstract
Pairs of species that exhibit broadly overlapping distributions, and multiple geographically isolated contact zones, provide opportunities to investigate the mechanisms of reproductive isolation. Such naturally replicated systems have demonstrated that hybridization rates can vary substantially among populations, raising important questions about the genetic basis of reproductive isolation. The topminnows, Fundulus notatus and F. olivaceus, are reciprocally monophyletic, and co-occur in drainages throughout much of the central and southern United States. Hybridization rates vary substantially among populations in isolated drainage systems. We employed genome-wide sampling to investigate geographic variation in hybridization, and to assess the possible importance of chromosome fusions to reproductive isolation among nine separate contact zones. The species differ by chromosomal rearrangements resulting from Robertsonian (Rb) fusions, so we hypothesized that Rb fusion chromosomes would serve as reproductive barriers, exhibiting steeper genomic clines than the rest of the genome. We observed variation in hybridization dynamics among drainages that ranged from nearly random mating to complete absence of hybridization. Contrary to predictions, our use of genomic cline analyses on mapped species-diagnostic SNP markers did not indicate consistent patterns of variable introgression across linkage groups, or an association between Rb fusions and genomic clines that would be indicative of reproductive isolation. We did observe a relationship between hybridization rates and population phylogeography, with the lowest rates of hybridization tending to be found in populations inferred to have had the longest histories of drainage sympatry. Our results, combined with previous studies of contact zones between the species, support population history as an important factor in explaining variation in hybridization rates.
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Affiliation(s)
- David D. Duvernell
- Department of Biological SciencesMissouri University of Science and TechnologyRollaMissouriUSA
| | - Naznin S. Remex
- Department of Biological SciencesMissouri University of Science and TechnologyRollaMissouriUSA
- Present address:
Department of Molecular and Cellular PhysiologyLouisiana State University Health Sciences CenterShreveportLouisianaUSA
| | - Jeffrey T. Miller
- Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
| | - Jacob F. Schaefer
- Department of Biological SciencesUniversity of Southern MississippiHattiesburgMississippiUSA
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87
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McCormack JE, Hill MM, DeRaad DA, Kirsch EJ, Reckling KR, Mutchler MJ, Ramirez BR, Campbell RML, Salter JF, Pizarro AK, Tsai WLE, Bonaccorso E. An elevational shift facilitated the Mesoamerican diversification of Azure-hooded Jays ( Cyanolyca cucullata) during the Great American Biotic Interchange. Ecol Evol 2023; 13:e10411. [PMID: 37589041 PMCID: PMC10425738 DOI: 10.1002/ece3.10411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/18/2023] [Accepted: 07/23/2023] [Indexed: 08/18/2023] Open
Abstract
The Great American Biotic Interchange (GABI) was a key biogeographic event in the history of the Americas. The rising of the Panamanian land bridge ended the isolation of South America and ushered in a period of dispersal, mass extinction, and new community assemblages, which sparked competition, adaptation, and speciation. Diversification across many bird groups, and the elevational zonation of others, ties back to events triggered by the GABI. But the exact timing of these events is still being revealed, with recent studies suggesting a much earlier time window for faunal exchange, perhaps as early as 20 million years ago (Mya). Using a time-calibrated phylogenetic tree, we show that the jay genus Cyanolyca is emblematic of bird dispersal trends, with an early, pre-land bridge dispersal from Mesoamerica to South America 6.3-7.3 Mya, followed by a back-colonization of C. cucullata to Mesoamerica 2.3-4.8 Mya, likely after the land bridge was complete. As Cyanolyca species came into contact in Mesoamerica, they avoided competition due to a prior shift to lower elevation in the ancestor of C. cucullata. This shift allowed C. cucullata to integrate itself into the Mesoamerican highland avifauna, which our time-calibrated phylogeny suggests was already populated by higher-elevation, congeneric dwarf-jays (C. argentigula, C. pumilo, C. mirabilis, and C. nanus). The outcome of these events and fortuitous elevational zonation was that C. cucullata could continue colonizing new highland areas farther north during the Pleistocene. Resultingly, four C. cucullata lineages became isolated in allopatric, highland regions from Panama to Mexico, diverging in genetics, morphology, plumage, and vocalizations. At least two of these lineages are best described as species (C. mitrata and C. cucullata). Continued study will further document the influence of the GABI and help clarify how dispersal and vicariance shaped modern-day species assemblages in the Americas.
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Affiliation(s)
- John E. McCormack
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | - Molly M. Hill
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | - Devon A. DeRaad
- Biodiversity Institute and Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKansasUSA
| | - Eliza J. Kirsch
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | | | | | - Brenda R. Ramirez
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | | | - Jessie F. Salter
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
- Ornithology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCaliforniaUSA
| | - Alana K. Pizarro
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | | | - Elisa Bonaccorso
- Laboratorio de Biología Evolutiva, Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de QuitoQuitoEcuador
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88
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Fu J, Wen L. Impacts of Quaternary glaciation, geological history and geography on animal species history in continental East Asia: A phylogeographic review. Mol Ecol 2023; 32:4497-4514. [PMID: 37332105 DOI: 10.1111/mec.17053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/20/2023]
Abstract
Continental East Asia has a mild Pleistocene climate and a complex recent geological history. Phylogeographic studies of animals over the last 30 years have produced several distinctive patterns. Glaciation refugia are numerous and are not restricted to any particular regions. Most of them are localized and species-specific, although several large refugia, for example the mountains of SW China, are shared by multiple species and have refugia-within-refugia. Furthermore, postglaciation range expansion events vary greatly in time, scale and direction. Large-scale south-to-north post-LGM expansions are few and mostly occurred in the northern regions. Additionally, several unique geographic features, including the three-step terrain of China and the northern arid belt, have significant impacts on many species histories. Overall, the impacts of Pleistocene glaciations, particularly the LGM, on species history vary drastically from nondetectable to significant. The impacts are the least for species from the southwestern region and are most dominant for species from the north. Geological events play a more significant role in shaping species history than Pleistocene climatic changes. Phylogeographic patterns among animals species are highly consistent with those of plants. Future phylogeographic endeavour in East Asia should be hypothesis-driven and seek processes that underlie common patterns. The wide use of genomic data allow accurate estimates of historical population processes and exploration of older history beyond the Pleistocene.
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Affiliation(s)
- Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Longying Wen
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Key Laboratory of Sichuan Institute for Protecting Endangered Birds in the Southwest Mountains, College of Life Sciences, Leshan Normal University, Leshan, China
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89
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Hernández CL. Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era. Genes (Basel) 2023; 14:1534. [PMID: 37628587 PMCID: PMC10453943 DOI: 10.3390/genes14081534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is a small fraction of our hereditary material. However, this molecule has had an overwhelming presence in scientific research for decades until the arrival of high-throughput studies. Several appealing properties justify the application of mtDNA to understand how human populations are-from a genetic perspective-and how individuals exhibit phenotypes of biomedical importance. Here, I review the basics of mitochondrial studies with a focus on the dawn of the field, analysis methods and the connection between two sides of mitochondrial genetics: anthropological and biomedical. The particularities of mtDNA, with respect to inheritance pattern, evolutionary rate and dependence on the nuclear genome, explain the challenges of associating mtDNA composition and diseases. Finally, I consider the relevance of this single locus in the context of omics research. The present work may serve as a tribute to a tool that has provided important insights into the past and present of humankind.
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Affiliation(s)
- Candela L Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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90
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Tegally H, Wilkinson E, Tsui JLH, Moir M, Martin D, Brito AF, Giovanetti M, Khan K, Huber C, Bogoch II, San JE, Poongavanan J, Xavier JS, Candido DDS, Romero F, Baxter C, Pybus OG, Lessells RJ, Faria NR, Kraemer MUG, de Oliveira T. Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern. Cell 2023; 186:3277-3290.e16. [PMID: 37413988 PMCID: PMC10247138 DOI: 10.1016/j.cell.2023.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 07/08/2023]
Abstract
The Alpha, Beta, and Gamma SARS-CoV-2 variants of concern (VOCs) co-circulated globally during 2020 and 2021, fueling waves of infections. They were displaced by Delta during a third wave worldwide in 2021, which, in turn, was displaced by Omicron in late 2021. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of VOCs worldwide. We find that source-sink dynamics varied substantially by VOC and identify countries that acted as global and regional hubs of dissemination. We demonstrate the declining role of presumed origin countries of VOCs in their global dispersal, estimating that India contributed <15% of Delta exports and South Africa <1%-2% of Omicron dispersal. We estimate that >80 countries had received introductions of Omicron within 100 days of its emergence, associated with accelerated passenger air travel and higher transmissibility. Our study highlights the rapid dispersal of highly transmissible variants, with implications for genomic surveillance along the hierarchical airline network.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | | | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Darren Martin
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil; Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
| | - Kamran Khan
- BlueDot, Toronto, ON, Canada; Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada
| | | | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jenicca Poongavanan
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Joicymara S Xavier
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
| | - Darlan da S Candido
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Filipe Romero
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK; Pandemic Sciences Institute, University of Oxford, Oxford, UK; Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno R Faria
- Department of Biology, University of Oxford, Oxford, UK; MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK; Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Moritz U G Kraemer
- Department of Biology, University of Oxford, Oxford, UK; Pandemic Sciences Institute, University of Oxford, Oxford, UK.
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Department of Global Health, University of Washington, Seattle, WA, USA.
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91
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Kusuma J, Couderc M, Scarcelli N, Duminil J. Complete chloroplast genome of two nutmeg species, Myristica argentea Warb. 1891 and Myristica fatua Houtt. 1774 (Myristicaceae). Mitochondrial DNA B Resour 2023; 8:751-755. [PMID: 37485420 PMCID: PMC10361002 DOI: 10.1080/23802359.2023.2233154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/29/2023] [Indexed: 07/25/2023] Open
Abstract
Myristica argentea Warb. 1891 and M. fatua Houtt. 1774 are two South-East Asian food tree species. They are harvested from the wild or cultivated for local uses as a condiment (nutmeg and mace), medicine, and source of wood. In this study, we reconstructed the complete chloroplast (cp) genomes of these two species from whole genome sequencing data using the Illumina NovaSeq platform. The genome sizes of M. argentea and M. fatua were respectively 155,871 base pairs (bp) and 155,898 bp, including 126 genes and an overall GC content of 39.20% in both species. Our study provides useful resources for future evolutionary research and diversity analysis of Myristica species.
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Affiliation(s)
- Jakty Kusuma
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
- Politeknik Negeri Lampung, Lampung, Indonesia
| | - Marie Couderc
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Nora Scarcelli
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Jérôme Duminil
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
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92
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Nejat F, Benovics M, Řehulková E, Vukić J, Šanda R, Kaya C, Tarkan AS, Abdoli A, Aksu S, Šimková A. Diversity, phylogeny and intraspecific variability of Paradiplozoon species (Monogenea: Diplozoidae) parasitizing endemic cyprinoids in the Middle East. Parasitology 2023; 150:705-722. [PMID: 37157105 PMCID: PMC10410381 DOI: 10.1017/s0031182023000446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
Diplozoidae are common monogenean ectoparasites of cyprinoid fish, with the genus Paradiplozoon being the most diversified. Despite recent studies on Diplozoidae from Europe, Africa and Asia, the diversity, distribution and phylogeny of this parasite group appears to be still underestimated in the Middle East. The objective of this study was to investigate the diversity, endemism and host specificity of diplozoids parasitizing cyprinoid fish from the Middle East, considering this region as an important historical interchange of fish fauna, and to elucidate the phylogenetic position of Middle Eastern Paradiplozoon species within Diplozoidae. Four Paradiplozoon species were collected from 48 out of 94 investigated cyprinoid species. Three known species, Paradiplozoon homoion, Paradiplozoon bliccae and Paradiplozoon bingolensis, were recorded on new cyprinoid host species, and a new species, Paradiplozoon koubkovae n. sp., was recorded on Luciobarbus capito and Capoeta capoeta from the Caspian Sea basin in Iran and Turkey. Paradiplozoon bliccae, exhibiting a wide host range in the Middle East, expressed both morphological and genetic intraspecific variabilities. The four Paradiplozoon species collected in the Middle East were placed in divergent clades, showing the rich evolutionary history of diplozoid parasites in the Middle East. Our study also revealed that two lineages of African diplozoids have a Middle Eastern origin. We stress the importance of applying an integrative approach combining morphological, ecological and molecular methods to reveal the real diversity of diplozoids.
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Affiliation(s)
- Farshad Nejat
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Michal Benovics
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Eva Řehulková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2 128 44, Czech Republic
| | - Radek Šanda
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2 128 44, Czech Republic
- Department of Zoology, National Museum, Václavské náměstí 68, Prague 1 110 00, Czech Republic
| | - Cüneyt Kaya
- Faculty of Fisheries, Recep Tayyip Erdogan University, 53100 Rize, Turkey
| | - Ali Serhan Tarkan
- Department of Basic Sciences, Faculty of Fisheries, Muğla Sıtkı Koçman University, 48000 Menteşe, Muğla, Turkey
| | - Asghar Abdoli
- Department of Biodiversity and Ecosystem Management, Environmental Science Research Institute, Shahid Beheshti University, Shahid Shahriari Sq. Velenjak, 1983969411 Tehran, Iran
| | - Sadi Aksu
- Vocational School of Health Services, Eskişehir Osmangazi University, Büyükdere Meşelik Yerleşkesi, 26040 Eskişehir, Turkey
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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93
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Hu X, Wang X, He Y, Hu M, Jin L, Zhang H, Jin Y, Wang B, Yue J, Liang S, Zhang C, Li K, Peng Z, Tian S, Qiu S, Song H, Ren H. Genetic characteristics of classical astroviruses in Shenzhen, China, 2016-2019. J Med Virol 2023; 95:e28902. [PMID: 37394758 DOI: 10.1002/jmv.28902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/24/2023] [Accepted: 06/12/2023] [Indexed: 07/04/2023]
Abstract
Human astrovirus (HAstV) is a single-stranded, positive-sense RNA virus and is the leading cause of viral gastroenteritis. However, despite its prevalence, astroviruses still remain one of the least studied enteroviruses. In this study, we sequenced 11 classical astrovirus strains from clinical samples collected in Shenzhen, China from 2016 to 2019, analyzed their genetic characteristics, and deposited them into GenBank. We conducted phylogenetic analysis using IQ-TREE software, with references to astrovirus sequences worldwide. The phylogeographic analysis was performed using the Bayesian Evolutionary Analysis Sampling Trees program, through Bayesian Markov Chain Monte Carlo sampling. We also conducted recombination analysis with the Recombination Detection Program. The newly sequenced strains were categorized as HAstV genotype 1, which is the predominant genotype in Shenzhen. Phylogeographic reconstruction indicated that HAstV-1 may have migrated from the United States to China, followed by frequent transmission between China and Japan. The recombination analysis revealed recombination events within and across genotypes, and identified a recombination-prone region that produced relatively uniform recombination breakpoints and fragment lengths. The genetic analysis of HAstV strains in Shenzhen addresses the current lack of astrovirus data in the region of Shenzhen and provides key insights to the evolution and transmission of astroviruses worldwide. These findings highlight the importance of improving surveillance of astroviruses.
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Affiliation(s)
- Xiaofeng Hu
- Health Supervision and Surveillance, Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xin Wang
- Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yaqing He
- Institute of Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Mingda Hu
- Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Lianqun Jin
- Health Supervision and Surveillance, Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hailong Zhang
- Institute of Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yuan Jin
- Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Boqian Wang
- Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Junjie Yue
- Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Shengnan Liang
- Health Supervision and Surveillance, Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Chuanfu Zhang
- Health Supervision and Surveillance, Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kexin Li
- Health Supervision and Surveillance, Chinese PLA Center for Disease Control and Prevention, Beijing, China
- The School of Public Health, China Medical University, Shenyang, China
| | - Zhixi Peng
- Health Supervision and Surveillance, Chinese PLA Center for Disease Control and Prevention, Beijing, China
- The School of Public Health, China Medical University, Shenyang, China
| | - Sai Tian
- Health Supervision and Surveillance, Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Shaofu Qiu
- Health Supervision and Surveillance, Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbin Song
- Health Supervision and Surveillance, Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongguang Ren
- Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China
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94
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Vitales D, Guerrero C, Garnatje T, Romeiras MM, Santos A, Fernandes F, Vallès J. Parallel anagenetic patterns in endemic Artemisia species from three Macaronesian archipelagos. AoB Plants 2023; 15:plad057. [PMID: 37649982 PMCID: PMC10465267 DOI: 10.1093/aobpla/plad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023]
Abstract
Anagenetic speciation is an important mode of evolution in oceanic islands, yet relatively understudied compared to adaptive radiation. In the Macaronesian region, three closely related species of Artemisia (i.e. A. argentea, A. thuscula and A. gorgonum) are each endemic from a single archipelago (i.e. Madeira, Canary Islands and Cape Verde, respectively), representing a perfect opportunity to study three similar but independent anagenetic speciation processes. By analysing plastid and nuclear DNA sequences, as well as nuclear DNA amount data, generated from a comprehensive sampling in all the islands and archipelagos where these species are currently distributed, we intend to find common evolutionary patterns that help us explain the limited taxonomic diversification experienced by endemic Macaronesian Artemisia. Our time-calibrated phylogenetic reconstruction suggested that divergence among the three lineages occurred in a coincidental short period of time during the Pleistocene. Haplotype and genetic differentiation analyses showed similar diversity values among A. argentea, A. thuscula and A. gorgonum. Clear phylogeographic patterns-showing comparable genetic structuring among groups of islands-were also found within the three archipelagos. Even from the cytogenetic point of view, the three species presented similarly lower genome size values compared to the mainland closely related species A. arborescens. We hypothesize that the limited speciation experienced by the endemic Artemisia in Madeira, Canary Islands and Cape Verde archipelagos could be related to their recent parallel evolutionary histories as independent lineages, combined with certain shared characteristics of seed dispersal, pollen transport and type of habitat.
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Affiliation(s)
- Daniel Vitales
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona, Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica (UB), Unitat Associada al CSIC, Facultat de Farmàcia i Ciències de l’Alimentació-Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Carmen Guerrero
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona, Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona, Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
| | - Maria M Romeiras
- LEAF—Linking Landscape, Environment, Agriculture and Food Research Center & Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1340-017 Lisboa, Portugal
| | - Arnoldo Santos
- Calle Guaidil 16, 38280 Tegueste, Tenerife, Islas Canarias, Spain
| | - Francisco Fernandes
- Jardim Botânico da Madeira Eng. Rui Vieira, Caminho do Meio Bom Sucesso, Madeira, Portugal
| | - Joan Vallès
- Laboratori de Botànica (UB), Unitat Associada al CSIC, Facultat de Farmàcia i Ciències de l’Alimentació-Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
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95
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van Elst T, Schüßler D, Rakotondravony R, Rovanirina VST, Veillet A, Hohenlohe PA, Ratsimbazafy JH, Rasoloarison RM, Rasoloharijaona S, Randrianambinina B, Ramilison ML, Yoder AD, Louis EE, Radespiel U. Diversification processes in Gerp's mouse lemur demonstrate the importance of rivers and altitude as biogeographic barriers in Madagascar's humid rainforests. Ecol Evol 2023; 13:e10254. [PMID: 37408627 PMCID: PMC10318617 DOI: 10.1002/ece3.10254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/23/2023] [Accepted: 06/21/2023] [Indexed: 07/07/2023] Open
Abstract
Madagascar exhibits exceptionally high levels of biodiversity and endemism. Models to explain the diversification and distribution of species in Madagascar stress the importance of historical variability in climate conditions which may have led to the formation of geographic barriers by changing water and habitat availability. The relative importance of these models for the diversification of the various forest-adapted taxa of Madagascar has yet to be understood. Here, we reconstructed the phylogeographic history of Gerp's mouse lemur (Microcebus gerpi) to identify relevant mechanisms and drivers of diversification in Madagascar's humid rainforests. We used restriction site associated DNA (RAD) markers and applied population genomic and coalescent-based techniques to estimate genetic diversity, population structure, gene flow and divergence times among M. gerpi populations and its two sister species M. jollyae and M. marohita. Genomic results were complemented with ecological niche models to better understand the relative barrier function of rivers and altitude. We show that M. gerpi diversified during the late Pleistocene. The inferred ecological niche, patterns of gene flow and genetic differentiation in M. gerpi suggest that the potential for rivers to act as biogeographic barriers depended on both size and elevation of headwaters. Populations on opposite sides of the largest river in the area with headwaters that extend far into the highlands show particularly high genetic differentiation, whereas rivers with lower elevation headwaters have weaker barrier functions, indicated by higher migration rates and admixture. We conclude that M. gerpi likely diversified through repeated cycles of dispersal punctuated by isolation to refugia as a result of paleoclimatic fluctuations during the Pleistocene. We argue that this diversification scenario serves as a model of diversification for other rainforest taxa that are similarly limited by geographic factors. In addition, we highlight conservation implications for this critically endangered species, which faces extreme habitat loss and fragmentation.
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Affiliation(s)
- Tobias van Elst
- Institute of ZoologyUniversity of Veterinary Medicine Hannover, FoundationHannoverGermany
| | - Dominik Schüßler
- Research Group Vegetation Ecology and Nature Conservation, Institute of Biology and ChemistryUniversity of HildesheimHildesheimGermany
| | - Romule Rakotondravony
- Ecole Doctorale Ecosystèmes Naturels (EDEN)University of MahajangaMahajangaMadagascar
- Faculté des Sciences, de Technologies et de l'EnvironnementUniversity of MahajangaMahajangaMadagascar
| | - Valisoa S. T. Rovanirina
- Faculté des Sciences, de Technologies et de l'EnvironnementUniversity of MahajangaMahajangaMadagascar
| | - Anne Veillet
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdahoUSA
| | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdahoUSA
| | | | | | - Solofonirina Rasoloharijaona
- Ecole Doctorale Ecosystèmes Naturels (EDEN)University of MahajangaMahajangaMadagascar
- Faculté des Sciences, de Technologies et de l'EnvironnementUniversity of MahajangaMahajangaMadagascar
| | - Blanchard Randrianambinina
- Ecole Doctorale Ecosystèmes Naturels (EDEN)University of MahajangaMahajangaMadagascar
- Faculté des Sciences, de Technologies et de l'EnvironnementUniversity of MahajangaMahajangaMadagascar
| | - Miarisoa L. Ramilison
- Faculté des Sciences, de Technologies et de l'EnvironnementUniversity of MahajangaMahajangaMadagascar
- Department of Primate Behavior and EcologyCentral Washington UniversityEllensburgWashingtonUSA
| | - Anne D. Yoder
- Department of BiologyDuke UniversityDurhamNorth CarolinaUSA
| | - Edward E. Louis
- Grewcock Center for Conservation and ResearchOmaha's Henry Doorly Zoo and AquariumOmahaNebraskaUSA
| | - Ute Radespiel
- Institute of ZoologyUniversity of Veterinary Medicine Hannover, FoundationHannoverGermany
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96
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Li YQ, Ghafari M, Holbrook AJ, Boonen I, Amor N, Catalano S, Webster JP, Li YY, Li HT, Vergote V, Maes P, Chong YL, Laudisoit A, Baelo P, Ngoy S, Mbalitini SG, Gembu GC, Musaba AP, Goüy de Bellocq J, Leirs H, Verheyen E, Pybus OG, Katzourakis A, Alagaili AN, Gryseels S, Li YC, Suchard MA, Bletsa M, Lemey P. The evolutionary history of hepaciviruses. bioRxiv 2023:2023.06.30.547218. [PMID: 37425679 PMCID: PMC10327235 DOI: 10.1101/2023.06.30.547218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
In the search for natural reservoirs of hepatitis C virus (HCV), a broad diversity of non-human viruses within the Hepacivirus genus has been uncovered. However, the evolutionary dynamics that shaped the diversity and timescale of hepaciviruses evolution remain elusive. To gain further insights into the origins and evolution of this genus, we screened a large dataset of wild mammal samples (n = 1,672) from Africa and Asia, and generated 34 full-length hepacivirus genomes. Phylogenetic analysis of these data together with publicly available genomes emphasizes the importance of rodents as hepacivirus hosts and we identify 13 rodent species and 3 rodent genera (in Cricetidae and Muridae families) as novel hosts of hepaciviruses. Through co-phylogenetic analyses, we demonstrate that hepacivirus diversity has been affected by cross-species transmission events against the backdrop of detectable signal of virus-host co-divergence in the deep evolutionary history. Using a Bayesian phylogenetic multidimensional scaling approach, we explore the extent to which host relatedness and geographic distances have structured present-day hepacivirus diversity. Our results provide evidence for a substantial structuring of mammalian hepacivirus diversity by host as well as geography, with a somewhat more irregular diffusion process in geographic space. Finally, using a mechanistic model that accounts for substitution saturation, we provide the first formal estimates of the timescale of hepacivirus evolution and estimate the origin of the genus to be about 22 million years ago. Our results offer a comprehensive overview of the micro- and macroevolutionary processes that have shaped hepacivirus diversity and enhance our understanding of the long-term evolution of the Hepacivirus genus.
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Affiliation(s)
- YQ Li
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - M Ghafari
- Department of Biology, University of Oxford, Oxford, OX1, UK
| | - AJ Holbrook
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - I Boonen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - N Amor
- Laboratory of Biodiversity, Parasitology, and Ecology of Aquatic Ecosystems, Department of Biology - Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - S Catalano
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - JP Webster
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - YY Li
- College of Life Sciences, Linyi University, Linyi, 276000, China
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - HT Li
- College of Life Sciences, Liaocheng University, Liaocheng, 252000, China
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - V Vergote
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - P Maes
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - YL Chong
- Animal Resource Science and Management Group, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak (UNIMAS), 94300, Malaysia
- Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong, 999077, China
| | - A Laudisoit
- EcoHealth Alliance, New York, NY 10018, USA
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - P Baelo
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - S Ngoy
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - SG Mbalitini
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - GC Gembu
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Akawa P Musaba
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - J Goüy de Bellocq
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
| | - H Leirs
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - E Verheyen
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - OG Pybus
- Department of Biology, University of Oxford, Oxford, OX1, UK
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - A Katzourakis
- Department of Biology, University of Oxford, Oxford, OX1, UK
| | - AN Alagaili
- Laboratory of Biodiversity, Parasitology, and Ecology of Aquatic Ecosystems, Department of Biology - Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - S Gryseels
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - YC Li
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - MA Suchard
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - M Bletsa
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, 11527, Greece
| | - P Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
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97
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Berman GH, Johnson SB, Seid CA, Vrijenhoek RC, Rouse GW. Range extensions of Pacific bone-eating worms (Annelida, Siboglinidae, Osedax). Biodivers Data J 2023; 11:e102803. [PMID: 38327359 PMCID: PMC10848615 DOI: 10.3897/bdj.11.e102803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/16/2023] [Indexed: 02/09/2024] Open
Abstract
First described in 2004 off California, Osedax worms are now known from many of the world's oceans, ranging from 10 to over 4000 m in depth. Currently, little is known about species ranges, since most descriptions are from single localities. In this study, we used new sampling in the north-eastern Pacific and available GenBank data from off Japan and Brazil to report expanded ranges for five species: Osedaxfrankpressi, O.knutei, O.packardorum, O.roseus and O.talkovici. We also provided additional DNA sequences from previously reported localities for two species: Osedaxpriapus and O.randyi. To assess the distribution of each species, we used cytochrome c oxidase subunit I (COI) sequences to generate haplotype networks and assess connectivity amongst localities where sampling permitted. Osedaxfrankpressi, O.packardorum, O.priapus, O.roseus and O.talkovici all had one or more dominant COI haplotypes shared by individuals at multiple localities, suggesting high connectivity throughout some or all of their ranges. Low ΦST values amongst populations for O.packardorum, O.roseus and O.talkovici confirmed high levels of gene flow throughout their known ranges. High ΦST values for O.frankpressi between the eastern Pacific and the Brazilian Atlantic showed little gene flow, reflected by the haplotype network, which had distinct Pacific and Atlantic haplotype clusters. This study greatly expands the ranges and provides insights into the phylogeography for these nine species.
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Affiliation(s)
- Gabriella H. Berman
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of AmericaScripps Institution of Oceanography, University of California San DiegoLa Jolla, CAUnited States of America
| | - Shannon B. Johnson
- Monterey Bay Aquarium Research Institute, Moss Landing, United States of AmericaMonterey Bay Aquarium Research InstituteMoss LandingUnited States of America
| | - Charlotte A. Seid
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of AmericaScripps Institution of Oceanography, University of California San DiegoLa Jolla, CAUnited States of America
| | - Robert C. Vrijenhoek
- Monterey Bay Aquarium Research Institute, Moss Landing, United States of AmericaMonterey Bay Aquarium Research InstituteMoss LandingUnited States of America
| | - Greg W. Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of AmericaScripps Institution of Oceanography, University of California San DiegoLa Jolla, CAUnited States of America
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98
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Hasegawa N, Techer MA, Adjlane N, Al-Hissnawi MS, Antúnez K, Beaurepaire A, Christmon K, Delatte H, Dukku UH, Eliash N, El-Niweiri MAA, Esnault O, Evans JD, Haddad NJ, Locke B, Muñoz I, Noël G, Panziera D, Roberts JMK, De la Rúa P, Shebl MA, Stanimirovic Z, Rasmussen DA, Mikheyev AS. Evolutionarily diverse origins of deformed wing viruses in western honey bees. Proc Natl Acad Sci U S A 2023; 120:e2301258120. [PMID: 37339224 DOI: 10.1073/pnas.2301258120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 05/05/2023] [Indexed: 06/22/2023] Open
Abstract
Novel transmission routes can allow infectious diseases to spread, often with devastating consequences. Ectoparasitic varroa mites vector a diversity of RNA viruses, having switched hosts from the eastern to western honey bees (Apis cerana to Apis mellifera). They provide an opportunity to explore how novel transmission routes shape disease epidemiology. As the principal driver of the spread of deformed wing viruses (mainly DWV-A and DWV-B), varroa infestation has also driven global honey bee health declines. The more virulent DWV-B strain has been replacing the original DWV-A strain in many regions over the past two decades. Yet, how these viruses originated and spread remains poorly understood. Here, we use a phylogeographic analysis based on whole-genome data to reconstruct the origins and demography of DWV spread. We found that, rather than reemerging in western honey bees after varroa switched hosts, as suggested by previous work, DWV-A most likely originated in East Asia and spread in the mid-20th century. It also showed a massive population size expansion following the varroa host switch. By contrast, DWV-B was most likely acquired more recently from a source outside East Asia and appears absent from the original varroa host. These results highlight the dynamic nature of viral adaptation, whereby a vector's host switch can give rise to competing and increasingly virulent disease pandemics. The evolutionary novelty and rapid global spread of these host-virus interactions, together with observed spillover into other species, illustrate how increasing globalization poses urgent threats to biodiversity and food security.
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Affiliation(s)
- Nonno Hasegawa
- Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan
| | - Maeva A Techer
- Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan
- Department of Entomology, Texas A&M University, College Station, TX 77483
- Behavioral Plasticity Research Institute, NSF-BII, College Station, TX 77483
| | - Noureddine Adjlane
- Department of Agronomy, Faculty of Science, University M'hamed Bougara, Boumerdes 35000, Algeria
| | | | - Karina Antúnez
- Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, 11600 Montevideo, Uruguay
| | - Alexis Beaurepaire
- Swiss Bee Research Center, Agroscope, 3003 Bern, Switzerland
- Institute of Bee Health, University of Bern, 3003 Bern, Switzerland
| | - Krisztina Christmon
- United States Department of Agriculture, Agricultural Research Service, Bee Research Lab, Beltsville, MD 20705
| | - Helene Delatte
- Centre de coopération internationale en recherche agronomique pour le développement, UMR Unité Mixte de Recherche Peuplements Végétaux et Bioagresseurs en Milieu Tropical, F-97410 Saint-Pierre, La Réunion, France
| | - Usman H Dukku
- Department of Biological Sciences, Abubakar Tafawa Balewa University, Bauchi 740211, Nigeria
| | - Nurit Eliash
- Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan
- Shamir Research Institute, Haifa University, Haifa 3498838, Israel
| | - Mogbel A A El-Niweiri
- Department of Bee Research, Environment, Natural Resources and Desertification Research Institute, National Centre for Research, Khartoum, Sudan
| | - Olivier Esnault
- Groupement de Défense Sanitaire, Réunion, La plaine des Cafres 97418, La Réunion, France
| | - Jay D Evans
- United States Department of Agriculture, Agricultural Research Service, Bee Research Lab, Beltsville, MD 20705
| | - Nizar J Haddad
- Bee Research Department, National Agricultural Research Center, 19381 Baqa', Jordan
| | - Barbara Locke
- Department of Ecology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Irene Muñoz
- Department of Zoology and Physical Anthropology, Faculty of Veterinary, University of Murcia, 30100 Murcia, Spain
| | - Grégoire Noël
- Functional and Evolutionary Entomology, TERRA, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Delphine Panziera
- Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - John M K Roberts
- Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Pilar De la Rúa
- Department of Zoology and Physical Anthropology, Faculty of Veterinary, University of Murcia, 30100 Murcia, Spain
| | - Mohamed A Shebl
- Department of Plant Protection, Faculty of Agriculture, Suez Canal University, 41522 Ismailia, Egypt
| | - Zoran Stanimirovic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695
| | - Alexander S Mikheyev
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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99
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Maduranga S, Valencia BM, Sigera C, Adikari T, Weeratunga P, Fernando D, Rajapakse S, Lloyd AR, Bull RA, Rodrigo C. Genomic Surveillance of Recent Dengue Outbreaks in Colombo, Sri Lanka. Viruses 2023; 15:1408. [PMID: 37515097 PMCID: PMC10384240 DOI: 10.3390/v15071408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
All four serotypes of the dengue virus (DENV1-4) cause a phenotypically similar illness, but serial infections from different serotypes increase the risk of severe disease. Thus, genomic surveillance of circulating viruses is important to detect serotype switches that precede community outbreaks of disproportionate magnitude. A phylogenetic analysis was conducted on near full length DENV genomes sequenced from serum collected from a prospective cohort study from the Colombo district, Sri Lanka during a 28-month period using Oxford nanopore technology, and the consensus sequences were analyzed using maximum likelihood and Bayesian evolutionary analysis. From 523 patients, 328 DENV sequences were successfully generated (DENV1: 43, DENV2: 219, DENV3:66). Most circulating sequences originated from a common ancestor that was estimated to have existed from around 2010 for DENV2 and around 2015/2016 for DENV1 and DENV3. Four distinct outbreaks coinciding with monsoon rain seasons were identified during the observation period mostly driven by DENV2 cosmopolitan genotype, except for a large outbreak in 2019 contributed by DENV3 genotype I. This serotype switch did not result in a more clinically severe illness. Phylogeographic analyses showed that all outbreaks started within Colombo city and then spread to the rest of the district. In 2019, DENV3 genotype I, previously, rarely reported in Sri Lanka, is likely to have contributed to a disease outbreak. However, this did not result in more severe disease in those infected, probably due to pre-existing DENV3 immunity in the community. Targeted vector control within Colombo city before anticipated seasonal outbreaks may help to limit the geographic spread of outbreaks.
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Affiliation(s)
- Sachith Maduranga
- School of Biomedical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
- Kirby Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | | | - Chathurani Sigera
- Faculty of Medicine, University of Colombo, Colombo 00800, Sri Lanka
| | - Thiruni Adikari
- School of Biomedical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | | | - Deepika Fernando
- Faculty of Medicine, University of Colombo, Colombo 00800, Sri Lanka
| | - Senaka Rajapakse
- Faculty of Medicine, University of Colombo, Colombo 00800, Sri Lanka
| | - Andrew R Lloyd
- Kirby Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Rowena A Bull
- School of Biomedical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
- Kirby Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Chaturaka Rodrigo
- School of Biomedical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
- Kirby Institute, UNSW Sydney, Sydney, NSW 2052, Australia
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Orf GS, Pérez LJ, Ciuoderis K, Cardona A, Villegas S, Hernández-Ortiz JP, Baele G, Mohaimani A, Osorio JE, Berg MG, Cloherty GA. The Principles of SARS-CoV-2 Intervariant Competition Are Exemplified in the Pre-Omicron Era of the Colombian Epidemic. Microbiol Spectr 2023; 11:e0534622. [PMID: 37191534 PMCID: PMC10269686 DOI: 10.1128/spectrum.05346-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/25/2023] [Indexed: 05/17/2023] Open
Abstract
The first 18 months of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in Colombia were characterized by three epidemic waves. During the third wave, from March through August 2021, intervariant competition resulted in Mu replacing Alpha and Gamma. We employed Bayesian phylodynamic inference and epidemiological modeling to characterize the variants in the country during this period of competition. Phylogeographic analysis indicated that Mu did not emerge in Colombia but acquired increased fitness there through local transmission and diversification, contributing to its export to North America and Europe. Despite not having the highest transmissibility, Mu's genetic composition and ability to evade preexisting immunity facilitated its domination of the Colombian epidemic landscape. Our results support previous modeling studies demonstrating that both intrinsic factors (transmissibility and genetic diversity) and extrinsic factors (time of introduction and acquired immunity) influence the outcome of intervariant competition. This analysis will help set practical expectations about the inevitable emergences of new variants and their trajectories. IMPORTANCE Before the appearance of the Omicron variant in late 2021, numerous SARS-CoV-2 variants emerged, were established, and declined, often with different outcomes in different geographic areas. In this study, we considered the trajectory of the Mu variant, which only successfully dominated the epidemic landscape of a single country: Colombia. We demonstrate that Mu competed successfully there due to its early and opportune introduction time in late 2020, combined with its ability to evade immunity granted by prior infection or the first generation of vaccines. Mu likely did not effectively spread outside of Colombia because other immune-evading variants, such as Delta, had arrived in those locales and established themselves first. On the other hand, Mu's early spread within Colombia may have prevented the successful establishment of Delta there. Our analysis highlights the geographic heterogeneity of early SARS-CoV-2 variant spread and helps to reframe the expectations for the competition behaviors of future variants.
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Affiliation(s)
- Gregory S. Orf
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
| | - Lester J. Pérez
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
| | - Karl Ciuoderis
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
- UW-GHI One Health Colombia, Universidad Nacional de Colombia Sede en Medellín, Medellín, Colombia
| | - Andrés Cardona
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
- UW-GHI One Health Colombia, Universidad Nacional de Colombia Sede en Medellín, Medellín, Colombia
| | - Simón Villegas
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
- UW-GHI One Health Colombia, Universidad Nacional de Colombia Sede en Medellín, Medellín, Colombia
| | - Juan P. Hernández-Ortiz
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
- UW-GHI One Health Colombia, Universidad Nacional de Colombia Sede en Medellín, Medellín, Colombia
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Evolutionary Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Aurash Mohaimani
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
| | - Jorge E. Osorio
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
- UW-GHI One Health Colombia, Universidad Nacional de Colombia Sede en Medellín, Medellín, Colombia
- UW-GHI One Health Colombia, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Michael G. Berg
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
| | - Gavin A. Cloherty
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
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