1
|
Manthey JD, Spellman GM. Recombination rate variation shapes genomic variability of phylogeographic structure in a widespread North American songbird (Aves: Certhia americana). Mol Phylogenet Evol 2024; 196:108088. [PMID: 38697377 DOI: 10.1016/j.ympev.2024.108088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/11/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024]
Abstract
The nonrandom distribution of chromosomal characteristics and functional elements-genomic architecture-impacts the relative strengths and impacts of population genetic processes across the genome. Due to this relationship, genomic architecture has the potential to shape variation in population genetic structure across the genome. Population genetic structure has been shown to vary across the genome in a variety of taxa, but this body of work has largely focused on pairwise population genomic comparisons between closely related taxa. Here, we used whole genome sequencing of seven phylogeographically structured populations of a North American songbird, the Brown Creeper (Certhia americana), to determine the impacts of genomic architecture on phylogeographic structure variation across the genome. Using multiple methods to infer phylogeographic structure-ordination, clustering, and phylogenetic methods-we found that recombination rate variation explained a large proportion of phylogeographic structure variation. Genomic regions with low recombination showed phylogeographic structure consistent with the genome-wide pattern. In regions with high recombination, we found strong phylogeographic structure, but with discordant patterns relative to the genome-wide pattern. In regions with high recombination rate, we found that populations with small effective population sizes evolve relatively more rapidly than larger populations, leading to discordant signatures of phylogeographic structure. These results suggest that the interplay between recombination rate variation and effective population sizes shape the relative impacts of selection and genetic drift in different parts of the genome. Overall, the combined interactions of population genetic processes, genomic architecture, and effective population sizes shape patterns of variability in phylogeographic structure across the genome of the Brown Creeper.
Collapse
Affiliation(s)
- Joseph D Manthey
- Department of Biological Sciences, Texas Tech University. Lubbock, TX, USA.
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO, USA
| |
Collapse
|
2
|
Scutari R, Costabile V, Galli L, Bellocchi MC, Carioti L, Barbaliscia S, Poli A, Galli A, Perno CF, Santoro MM, Castagna A, Ceccherini-Silberstein F, Alteri C, Spagnuolo V. Impact of Analytical Treatment Interruption on Burden and Diversification of HIV Peripheral Reservoir: A Pilot Study. Viruses 2021; 13:v13071403. [PMID: 34372609 PMCID: PMC8310290 DOI: 10.3390/v13071403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/03/2021] [Accepted: 07/13/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND If analytical antiretroviral-treatment (ART) interruption (ATI) might significantly impact quantitative or qualitative peripheral-total HIV-DNA is still debated. METHODS Six chronically HIV-1 infected patients enrolled in APACHE-study were analysed for peripheral-total HIV-DNA and residual viremia, major-resistance-mutations (MRMs) and C2-V3-C3 evolution at pre-ATI (T1), during ATI (T2) and at achievement of virological success after ART-resumption (post-ATI, T3). These data were obtained at three comparable time-points in five chronically HIV-1 infected patients on suppressive ART for ≥1 year, enrolled in MODAt-study. RESULTS At T1, APACHE and MODAt individuals had similar peripheral-total HIV-DNA and residual viremia (p = 0.792 and 0.662, respectively), and no significant changes for these parameters were observed between T1 and T3 in both groups. At T1, 4/6 APACHE and 2/5 MODAt carried HIV-DNA MRMs. MRMs disappeared at T3 in 3/4 APACHE. All disappearing MRMs were characterized by T1 intra-patient prevalence <80%, and mainly occurred in APOBEC3-related sites. All MRMs persisted over-time in the 2 MODAt. C2-V3-C3 genetic-distance significantly changed from T1 to T3 in APACHE individuals (+0.36[0.11-0.41], p = 0.04), while no significant changes were found in MODAt. Accordingly, maximum likelihood trees (bootstrap > 70%) and genealogical sorting indices (GSI > 0.50 with p-value < 0.05) showed that T1 C2-V3-C3 DNA sequences were distinct from T2 and T3 viruses in 4/6 APACHE. Virus populations at all three time-points were highly interspersed in MODAt. CONCLUSIONS This pilot study indicates that short ATI does not alter peripheral-total HIV-DNA burden and residual viremia, but in some cases could cause a genetic diversification of peripheral viral reservoir in term of both MRMs rearrangement and viral evolution.
Collapse
Affiliation(s)
- Rossana Scutari
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (M.C.B.); (L.C.); (S.B.); (M.M.S.); (F.C.-S.)
| | - Valentino Costabile
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy;
| | - Laura Galli
- Infectious Diseases, San Raffaele Scientific Institute, 20132 Milan, Italy; (L.G.); (A.P.); (A.G.); (A.C.); (V.S.)
| | - Maria Concetta Bellocchi
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (M.C.B.); (L.C.); (S.B.); (M.M.S.); (F.C.-S.)
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (M.C.B.); (L.C.); (S.B.); (M.M.S.); (F.C.-S.)
| | - Silvia Barbaliscia
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (M.C.B.); (L.C.); (S.B.); (M.M.S.); (F.C.-S.)
| | - Andrea Poli
- Infectious Diseases, San Raffaele Scientific Institute, 20132 Milan, Italy; (L.G.); (A.P.); (A.G.); (A.C.); (V.S.)
| | - Andrea Galli
- Infectious Diseases, San Raffaele Scientific Institute, 20132 Milan, Italy; (L.G.); (A.P.); (A.G.); (A.C.); (V.S.)
| | - Carlo Federico Perno
- Unit of Diagnostic Microbiology and Immunology, Department of Laboratories, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
| | - Maria Mercedes Santoro
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (M.C.B.); (L.C.); (S.B.); (M.M.S.); (F.C.-S.)
| | - Antonella Castagna
- Infectious Diseases, San Raffaele Scientific Institute, 20132 Milan, Italy; (L.G.); (A.P.); (A.G.); (A.C.); (V.S.)
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Francesca Ceccherini-Silberstein
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (M.C.B.); (L.C.); (S.B.); (M.M.S.); (F.C.-S.)
| | - Claudia Alteri
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy;
- Multimodal Medicine Research Area, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
- Correspondence: ; Tel.: +39-(0)6-6859-7096
| | - Vincenzo Spagnuolo
- Infectious Diseases, San Raffaele Scientific Institute, 20132 Milan, Italy; (L.G.); (A.P.); (A.G.); (A.C.); (V.S.)
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, 20132 Milan, Italy
| |
Collapse
|
3
|
Sukumaran J, Holder MT, Knowles LL. Incorporating the speciation process into species delimitation. PLoS Comput Biol 2021; 17:e1008924. [PMID: 33983918 PMCID: PMC8118268 DOI: 10.1371/journal.pcbi.1008924] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/29/2021] [Indexed: 11/22/2022] Open
Abstract
The "multispecies" coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus that of populations within species. Consequently, as both the genomic and spatial resolution of data increases, a proliferation of artifactual species results as within-species population lineages, detected due to restrictions in gene flow, are identified as distinct species. The toll of this extends beyond systematic studies, getting magnified across the many disciplines that rely upon an accurate framework of identified species. Here we present the first of a new class of approaches that addresses this issue by incorporating an extended speciation process for species delimitation. We model the formation of population lineages and their subsequent development into independent species as separate processes and provide for a way to incorporate current understanding of the species boundaries in the system through specification of species identities of a subset of population lineages. As a result, species boundaries and within-species lineages boundaries can be discriminated across the entire system, and species identities can be assigned to the remaining lineages of unknown affinities with quantified probabilities. In addition to the identification of species units in nature, the primary goal of species delimitation, the incorporation of a speciation model also allows us insights into the links between population and species-level processes. By explicitly accounting for restrictions in gene flow not only between, but also within, species, we also address the limits of genetic data for delimiting species. Specifically, while genetic data alone is not sufficient for accurate delimitation, when considered in conjunction with other information we are able to not only learn about species boundaries, but also about the tempo of the speciation process itself.
Collapse
Affiliation(s)
- Jeet Sukumaran
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Mark T. Holder
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| |
Collapse
|
4
|
Coalescence-based species delimitation using genome-wide data reveals hidden diversity in a cosmopolitan group of lichens. ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-019-00424-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
5
|
Arnold B, Sohail M, Wadsworth C, Corander J, Hanage WP, Sunyaev S, Grad YH. Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen. Mol Biol Evol 2020; 37:417-428. [PMID: 31589312 PMCID: PMC6993868 DOI: 10.1093/molbev/msz225] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Identifying genetic variation in bacteria that has been shaped by ecological differences remains an important challenge. For recombining bacteria, the sign and strength of linkage provide a unique lens into ongoing selection. We show that derived alleles <300 bp apart in Neisseria gonorrhoeae exhibit more coupling linkage than repulsion linkage, a pattern that cannot be explained by limited recombination or neutrality as these couplings are significantly stronger for nonsynonymous alleles than synonymous alleles. This general pattern is driven by a small fraction of highly diverse genes, many of which exhibit evidence of interspecies horizontal gene transfer and an excess of intermediate frequency alleles. Extensive simulations show that two distinct forms of positive selection can create these patterns of genetic variation: directional selection on horizontally transferred alleles or balancing selection that maintains distinct haplotypes in the presence of recombination. Our results establish a framework for identifying patterns of selection in fine-scale haplotype structure that indicate specific ecological processes in species that recombine with distantly related lineages or possess coexisting adaptive haplotypes.
Collapse
Affiliation(s)
- Brian Arnold
- Division of Informatics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Mashaal Sohail
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Crista Wadsworth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, Finland
| | - William P Hanage
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Shamil Sunyaev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| |
Collapse
|
6
|
Optimal markers for the identification of Colletotrichum species. Mol Phylogenet Evol 2019; 143:106694. [PMID: 31786239 DOI: 10.1016/j.ympev.2019.106694] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/15/2019] [Accepted: 11/25/2019] [Indexed: 01/19/2023]
Abstract
Colletotrichum is among the most important genera of fungal plant pathogens. Molecular phylogenetic studies over the last decade have resulted in a much better understanding of the evolutionary relationships and species boundaries within the genus. There are now approximately 200 species accepted, most of which are distributed among 13 species complexes. Given their prominence on agricultural crops around the world, rapid identification of a large collection of Colletotrichum isolates is routinely needed by plant pathologists, regulatory officials, and fungal biologists. However, there is no agreement on the best molecular markers to discriminate species in each species complex. Here we calculate the barcode gap distance and intra/inter-specific distance overlap to evaluate each of the most commonly applied molecular markers for their utility as a barcode for species identification. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone-3 (HIS3), DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locus MAT1-2-1 (APN2/MAT-IGS), and intergenic spacer between GAPDH and a hypothetical protein (GAP2-IGS) have the properties of good barcodes, whereas sequences of actin (ACT), chitin synthase (CHS-1) and nuclear rDNA internal transcribed spacers (nrITS) are not able to distinguish most species. Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA). Although GAPDH, HIS3 and β-tubulin (TUB2) were frequently among the best markers, there was not a single set of markers that were best for all species complexes. Eliminating markers with low phylogenetic signal tends to decrease uncertainty in the topology, regardless of species complex, and leads to a larger proportion of markers that support each lineage in the Bayesian concordance analyses. Finally, we reconstruct the phylogeny of each species complex using a minimal set of phylogenetic markers with the strongest phylogenetic signal and find the majority of species are strongly supported as monophyletic.
Collapse
|
7
|
Hu GL, Gao K, Wang JS, Hebert PDN, Hua BZ. Molecular phylogeny and species delimitation of the genus Dicerapanorpa (Mecoptera: Panorpidae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Given that species is the fundamental unit in systematic biology, rigorous species delimitation is crucial for taxonomic studies, yet routine species delimitation remains an ongoing challenge in the taxonomic practice of insects. The two-horned scorpionfly Dicerapanorpa is a small genus in Panorpidae (Mecoptera) endemic to the Qinling-Bashan and Hengduan mountains, a biodiversity hotspot. However, species of Dicerapanorpa are difficult to delineate owing to marked intraspecific variation and interspecific similarity. Here, we investigate the diversity and species boundaries of Dicerapanorpa using an integrative approach based on DNA barcoding, morphological, geometric morphometric and molecular phylogenetic analyses. This integrative analyses confirmed the 13 described species of Dicerapanorpa and revealed three new species: Dicerapanorpa lativalva sp. nov., Dicerapanorpa hualongshana sp. nov. and Dicerapanorpa minshana sp. nov. Most molecular operational taxonomic units are in congruence with morphological clusters. Possible reasons for several discordances in Dicerapanorpa are tentatively discussed.
Collapse
Affiliation(s)
- Gui-Lin Hu
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Kai Gao
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Ji-Shen Wang
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Bao-Zhen Hua
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| |
Collapse
|
8
|
de Santana CD, Crampton WGR, Dillman CB, Frederico RG, Sabaj MH, Covain R, Ready J, Zuanon J, de Oliveira RR, Mendes-Júnior RN, Bastos DA, Teixeira TF, Mol J, Ohara W, Castro NCE, Peixoto LA, Nagamachi C, Sousa L, Montag LFA, Ribeiro F, Waddell JC, Piorsky NM, Vari RP, Wosiacki WB. Unexpected species diversity in electric eels with a description of the strongest living bioelectricity generator. Nat Commun 2019; 10:4000. [PMID: 31506444 PMCID: PMC6736962 DOI: 10.1038/s41467-019-11690-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/25/2019] [Indexed: 11/09/2022] Open
Abstract
Is there only one electric eel species? For two and a half centuries since its description by Linnaeus, Electrophorus electricus has captivated humankind by its capacity to generate strong electric discharges. Despite the importance of Electrophorus in multiple fields of science, the possibility of additional species-level diversity in the genus, which could also reveal a hidden variety of substances and bioelectrogenic functions, has hitherto not been explored. Here, based on overwhelming patterns of genetic, morphological, and ecological data, we reject the hypothesis of a single species broadly distributed throughout Greater Amazonia. Our analyses readily identify three major lineages that diverged during the Miocene and Pliocene-two of which warrant recognition as new species. For one of the new species, we recorded a discharge of 860 V, well above 650 V previously cited for Electrophorus, making it the strongest living bioelectricity generator.
Collapse
Affiliation(s)
- C David de Santana
- Division of Fishes, Department of Vertebrate Zoology, MCR 159, National Museum of Natural History, PO Box 37012, Smithsonian Institution, Washington, DC, WA, 20013-7012, USA.
| | | | - Casey B Dillman
- Division of Fishes, Department of Vertebrate Zoology, MCR 159, National Museum of Natural History, PO Box 37012, Smithsonian Institution, Washington, DC, WA, 20013-7012, USA.,Cornell University Museum of Vertebrates, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Renata G Frederico
- Laboratório de Ecologia e Conservação, Universidade Federal do Pará, Instituto de Ciências Biológicas, Belém, Pará, Brazil.,Laboratório de ecologia de peixes, Universidade Federal de Minas Gerias, Institudo de Ciências Biológicas, Belo Horizonte, Minas Gerais, Brazil
| | - Mark H Sabaj
- Department of Ichthyology, The Academy of Natural Sciences of Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA, 19103, USA
| | - Raphaël Covain
- Muséum d'histoire naturelle, Département d'herpétologie et d'ichtyologie, route de Malagnou 1, case postale 6434, CH-1211, Genève 6, Switzerland
| | - Jonathan Ready
- Laboratório de Lepidopterologia e Ictiologia Integrada, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Jansen Zuanon
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Renildo R de Oliveira
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Raimundo N Mendes-Júnior
- RESEX do Rio Cajari, Instituto Chico Mendes da Conservação da Biodiversidade, Macapá, Amapá, Brazil
| | - Douglas A Bastos
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Tulio F Teixeira
- Museu de Zoologia da Universidade de São Paulo, Laboratório de Ictiologia, São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação em Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Jan Mol
- Anton de Kom University of Suriname, Paramaribo, Suriname
| | - Willian Ohara
- Museu de Zoologia da Universidade de São Paulo, Laboratório de Ictiologia, São Paulo, São Paulo, Brazil.,Laboratório de Ciências Ambientais, Universidade Federal de Rondônia, Presidente Médice, Rondônia, Brazil
| | | | - Luiz A Peixoto
- Museu de Zoologia da Universidade de São Paulo, Laboratório de Ictiologia, São Paulo, São Paulo, Brazil
| | - Cleusa Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Leandro Sousa
- Laboratório de Ictiologia, Faculdade de Ciências Biológicas, Universidade Federal do Pará, Altamira, Pará, Brazil
| | - Luciano F A Montag
- Laboratório de Ecologia e Conservação, Universidade Federal do Pará, Instituto de Ciências Biológicas, Belém, Pará, Brazil
| | - Frank Ribeiro
- Instituto de Ciências e Tecnologia das Águas, Universidade Federal do Oeste do Pará, Campus Amazônia, Santarém, Pará, Brazil
| | - Joseph C Waddell
- Department of Biology, University of Central Florida, Orlando, FL, 32816, USA
| | - Nivaldo M Piorsky
- Universidade Federal do Maranhão, Departamento de Biologia, Laboratório de Ecologia e Sistemática de Peixes, São Luis, Maranhão, Brazil
| | - Richard P Vari
- Division of Fishes, Department of Vertebrate Zoology, MCR 159, National Museum of Natural History, PO Box 37012, Smithsonian Institution, Washington, DC, WA, 20013-7012, USA
| | - Wolmar B Wosiacki
- Museu Paraense Emílio Goeldi, Caixa Postal 399, 66040-170, Belém, Pará, Brazil
| |
Collapse
|
9
|
Feng C, Tang Y, Liu S, Tian F, Zhang C, Zhao K. Multiple convergent events created a nominal widespread species: Triplophysa stoliczkae (Steindachner, 1866) (Cobitoidea: Nemacheilidae). BMC Evol Biol 2019; 19:177. [PMID: 31484504 PMCID: PMC6724303 DOI: 10.1186/s12862-019-1503-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 08/26/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Triplophysa stoliczkae is the most widespread species in the genus Triplophysa and may have originated from morphological convergence. To understand the evolutionary history of T. stoliczkae, we employed a multilocus approach to investigate the phylogenetics and the morphological evolution of T. stoliczkae on the Qinghai-Tibetan Plateau. RESULTS All phylogenetic analyses (two mitochondrial and five nuclear loci), a genealogical sorting index and species tree inferences suggested that T. stoliczkae consists of distinct lineages that were not closest relatives. The time estimation indicated that the divergence events between "T. stoliczkae" and other Triplophysa species occurred from approximately 0.10 to 4.51 Ma. The ancestral state analyses supported the independent evolution of T. stoliczkae morphology in distinct lineages. The morphometric analysis and convergence estimates demonstrated significant phenotypic convergence among "T. stoliczkae" lineages. CONCLUSIONS Triplophysa stoliczkae includes 4 different lineages with similar morphologies. The increasingly harsh environments that have occurred since the Pliocene have driven the occurrences of scrape-feeding fish in the genus Triplophysa. Morphological adaptations associated with scrape-feeding behavior resulted in convergences and the artificial lumping of four different species in the nominal taxon T. stoliczkae. A taxonomic revision for T. stoliczkae is needed.
Collapse
Affiliation(s)
- Chenguang Feng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, Qinghai, China.,Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongtao Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, Qinghai, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sijia Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, Qinghai, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, Qinghai, China
| | - Cunfang Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, Qinghai, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, Qinghai, China.
| |
Collapse
|
10
|
Wagner F, Ott T, Zimmer C, Reichhart V, Vogt R, Oberprieler C. 'At the crossroads towards polyploidy': genomic divergence and extent of homoploid hybridization are drivers for the formation of the ox-eye daisy polyploid complex (Leucanthemum, Compositae-Anthemideae). THE NEW PHYTOLOGIST 2019; 223:2039-2053. [PMID: 30851196 DOI: 10.1111/nph.15784] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/06/2019] [Indexed: 05/23/2023]
Abstract
Polyploidy plays a paramount role in phytodiversity, but the causes of this evolutionary pathway require further study. Here, we use phylogenetic methods to examine possible polyploidy-promoting factors by comparing diploid representatives of the comprehensive European polyploid complex Leucanthemum with members of its strictly diploid North African counterpart Rhodanthemum. We investigate genetic divergence and gene flow among all diploid lineages of both genera to evaluate the role of genomic differentiation and hybridization for polyploid speciation. To test whether hybridization in Leucanthemum has been triggered by the geological conditions during its diversification, we additionally generate a time-calibrated phylogeny of 46 species of the subtribe Leucantheminae. Leucanthemum shows a significantly higher genetic divergence and hybridization signal among diploid lineages compared with Rhodanthemum, in spite of a similar crown age and diversification pattern during the Quaternary. Our study demonstrates the importance of genetic differentiation among diploid progenitors and their concurrent affinity for natural hybridization for the formation of a polyploid complex. Furthermore, the role of climate-induced range overlaps on hybridization and polyploid speciation during the Quaternary is discussed.
Collapse
Affiliation(s)
- Florian Wagner
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Tankred Ott
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Claudia Zimmer
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Verena Reichhart
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Robert Vogt
- Botanic Garden & Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, D-14191, Berlin, Germany
| | - Christoph Oberprieler
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| |
Collapse
|
11
|
Nicola MV, Johnson LA, Pozner R. Unraveling patterns and processes of diversification in the South Andean-Patagonian Nassauvia subgenus Strongyloma (Asteraceae, Nassauvieae). Mol Phylogenet Evol 2019; 136:164-182. [PMID: 30858079 DOI: 10.1016/j.ympev.2019.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 02/11/2019] [Accepted: 03/07/2019] [Indexed: 12/26/2022]
Abstract
Congruence among different sources of data is highly desirable in phylogenetic analyses. However, plastid and nuclear DNA may record different evolutionary processes such that incongruence among results from these sources can help unravel complex evolutionary histories. That is the case of Nassauvia subgenus Strongyloma (Asteraceae), a taxon with five putative species distributed in the southern Andes and Patagonian steppe. Morphometric and phylogeographic information cast doubt on the integrity of its species, and previous molecular data even questioned the monophyly of the subgenus. We tested those questions using plastid and nuclear DNA sequences by the application of different methods such as phylogenetic trees, networks, a test of genealogical sorting, an analysis of population structure, calibration of the trees, and hybridization test, assembling non-synchronous incongruent results at subgenus and species levels in a single reconstruction. The integration of our molecular analyses and previous taxonomic, morphological, and molecular studies support subgenus Strongyloma as a monophyletic group. However, the topology of the nuclear trees and the evidence of polyploids within subgenus Nassauvia, suggest a hypothetical origin and initial radiation of Nassauvia related to an ancient hybridization event that occurred around 17-6.3 Myr ago near the Andes in west-central Patagonia. Plastid data suggest a recent diversification within subgenus Strongyloma, at most 9.8 Myr ago, towards the Patagonian steppe east of the Andes. These processes cause phylogenies to deviate from the species tree since each putative species lack exclusive ancestry. The non-monophyly of its species using both plastid and nuclear data is caused mainly by incomplete lineage sorting occurred since the Miocene. The final uplift of the Andes and Pliocene-Pleistocene glacial-interglacial and its consequences on the landscape and climate structured the genetic composition of this group of plants in the Patagonian steppe. The molecular data presented here agree with previous morphological studies, in that the five putative species typically accepted in this subgenus are not independent taxa. This study emphasizes that adding more than one sequence per species, not combining data with dissimilar inheritance patterns without first performed incongruence tests, exploring data through different methodologies, considering the timing of events, and searching for the causes of poorly resolved and/or incongruent phylogenies help to reveal complex biological underlying processes, which might otherwise remain hidden.
Collapse
Affiliation(s)
- Marcela V Nicola
- Instituto de Botánica Darwinion (CONICET-ANCEFN), Labardén 200, C.C. 22, B1642HYD, San Isidro, Provincia de Buenos Aires, Argentina.
| | - Leigh A Johnson
- Department of Biology and Bean Life Science Museum, 4102 LSB, Brigham Young University, Provo, UT 84602, USA
| | - Raúl Pozner
- Instituto de Botánica Darwinion (CONICET-ANCEFN), Labardén 200, C.C. 22, B1642HYD, San Isidro, Provincia de Buenos Aires, Argentina
| |
Collapse
|
12
|
Multilocus phylogeography of the brown-spotted pitviper Protobothrops mucrosquamatus (Reptilia: Serpentes: Viperidae) sheds a new light on the diversification pattern in Asia. Mol Phylogenet Evol 2018; 133:82-91. [PMID: 30594733 DOI: 10.1016/j.ympev.2018.12.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 12/13/2018] [Accepted: 12/21/2018] [Indexed: 11/21/2022]
Abstract
Understanding the influence of geographical events and climate changes on genetic diversity is essential in explaining current patterns of genetic structure and geographic distribution of organisms. We inferred phylogenetic relationships, investigated historical demography, explored the evolutionary history, and clarified intraspecific taxonomy of Protobothrops mucrosquamatus, which is one of the commonest and most wide-ranging Asian pitvipers. A total of 184 samples from 54 localities were sequenced and analyzed for two mitochondrial gene fragments and two nuclear genes. Phylogenetic reconstruction based on mtDNA sequences revealed the existence of a minimum of five geographically structured and well-supported lineages within P. mucrosquamatus. Based on the mtDNA gene tree, and the geographic relationship between populations allied by matrilineal lineages, a complex longitudinal and latitudinal diversification pattern was uncovered in P. mucrosquamatus. The estimated date of the origin of the species (about 5.3 Ma) and divergence of the intraspecific lineages match the rapid uplifting of Qinghai-Xizang Plateau, and is also consistent with those of some other co-distributed Asian pitvipers. Formation of the two island lineages (Taiwan and Hainan) was generally congruent with the first isolation of the islands, but the two lineages showed different relationships with the continental Asian populations in comparison with some other pitvipers. Population historical demographic analyses, based on three methods, showed that all lineages have experienced slight population expansion in and around the Dali Glacial. Tests of intraspecific taxonomy indicated that no cryptic taxon is present within this widely distributed snake.
Collapse
|
13
|
Mark K, Randlane T, Thor G, Hur JS, Obermayer W, Saag A. Lichen chemistry is concordant with multilocus gene genealogy in the genus Cetrelia (Parmeliaceae, Ascomycota). Fungal Biol 2018; 123:125-139. [PMID: 30709518 DOI: 10.1016/j.funbio.2018.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 11/02/2018] [Accepted: 11/22/2018] [Indexed: 12/18/2022]
Abstract
The lichen genus Cetrelia represents a taxonomically interesting case where morphologically almost uniform populations differ considerably from each other chemically. Similar variation is not uncommon among lichenized fungi, but it is disputable whether such populations should be considered entities at the species level. Species boundaries in Cetrelia are traditionally delimited either as solely based on morphology or as combinations of morpho- and chemotypes. A dataset of four nuclear markers (ITS, IGS, Mcm7, RPB1) from 62 specimens, representing ten Cetrelia species, was analysed within Bayesian and maximum likelihood frameworks. Analyses recovered a well-resolved phylogeny where the traditional species generally were monophyletic, with the exception of Cetrelia chicitae and Cetrelia pseudolivetorum. Species delimitation analyses supported the distinction of 15 groups within the studied Cetrelia taxa, dividing three traditionally identified species into some species candidates. Chemotypes, distinguished according to the major medullary substance, clearly correlated with clades recovered within Cetrelia, while samples with the same reproductive mode were dispersed throughout the phylogenetic tree. Consequently, delimiting Cetrelia species based only on reproductive morphology is not supported phylogenetically. Character analyses suggest that chemical characters have been more consistent compared to reproductive mode and indicate that metabolite evolution in Cetrelia towards more complex substances is probable.
Collapse
Affiliation(s)
- Kristiina Mark
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu 51005, Estonia; Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51014, Estonia
| | - Tiina Randlane
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu 51005, Estonia.
| | - Göran Thor
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, 255 Jungang-Ro, South Korea
| | | | - Andres Saag
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu 51005, Estonia
| |
Collapse
|
14
|
Azithromycin Resistance through Interspecific Acquisition of an Epistasis-Dependent Efflux Pump Component and Transcriptional Regulator in Neisseria gonorrhoeae. mBio 2018; 9:mBio.01419-18. [PMID: 30087172 PMCID: PMC6083905 DOI: 10.1128/mbio.01419-18] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Mosaic interspecifically acquired alleles of the multiple transferable resistance (mtr) efflux pump operon correlate with increased resistance to azithromycin in Neisseria gonorrhoeae in epidemiological studies. However, whether and how these alleles cause resistance is unclear. Here, we use population genomics, transformations, and transcriptional analyses to dissect the relationship between variant mtr alleles and azithromycin resistance. We find that the locus encompassing the mtrR transcriptional repressor and the mtrCDE pump is a hot spot of interspecific recombination introducing alleles from Neisseria meningitidis and Neisseria lactamica into N. gonorrhoeae, with multiple rare haplotypes in linkage disequilibrium at mtrD and the mtr promoter region. Transformations demonstrate that resistance to azithromycin, as well as to other antimicrobial compounds such as polymyxin B and crystal violet, is mediated through epistasis between these two loci and that the full-length mosaic mtrD allele is required. Gene expression profiling reveals the mechanism of resistance in mosaics couples novel mtrD alleles with promoter mutations that increase expression of the pump. Overall, our results demonstrate that epistatic interactions at mtr gained from multiple neisserial species has contributed to increased gonococcal resistance to diverse antimicrobial agents.IMPORTANCENeisseria gonorrhoeae is the sexually transmitted bacterial pathogen responsible for more than 100 million cases of gonorrhea worldwide each year. The incidence of resistance to the macrolide azithromycin has increased in the past decade; however, a large proportion of the genetic basis of resistance remains unexplained. This study is the first to conclusively demonstrate the acquisition of macrolide resistance through mtr alleles from other Neisseria species, demonstrating that commensal Neisseria bacteria are a reservoir for antibiotic resistance to macrolides, extending the role of interspecies mosaicism in resistance beyond what has been previously described for cephalosporins. Ultimately, our results emphasize that future fine-mapping of genome-wide interspecies mosaicism may be valuable in understanding the pathways to antimicrobial resistance. Our results also have implications for diagnostics and public health surveillance and control, as they can be used to inform the development of sequence-based tools to monitor and control the spread of antibiotic-resistant gonorrhea.
Collapse
|
15
|
Cornejo C, Chabanenko S, Scheidegger C. Are species-pairs diverging lineages? A nine-locus analysis uncovers speciation among species-pairs of the Lobaria meridionalis-group (Ascomycota). Mol Phylogenet Evol 2018; 129:48-59. [PMID: 30036698 DOI: 10.1016/j.ympev.2018.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 03/13/2018] [Accepted: 07/14/2018] [Indexed: 01/17/2023]
Abstract
In spite of considerable effort to verify the theory of species-pairs, uncertainty still exists about the relationship between sexually or vegetatively reproducing populations of morphologically indistinguishable, sympatric lichen species. The current paper studies putative species-pairs within the Asian Lobaria meridionalis-group, using a nine-locus and time calibrated species-tree approach. Analyses demonstrate that pairs of sexually or vegetatively reproducing lineages split into highly supported monophyletic clades-confirming molecularly the species-pair concept for the L. meridionalis-group. In the broader context of evolution and speciation dynamics in lichenized fungi, this paper attempts to synthesize molecular findings from the last two decades to promote a more modern perception of the species-pair concept. Taxonomically, eight species were found to currently conform to the L. meridionalis-group, which differentiated during the Pliocene and Pleistocene. The coincidence of paleoclimatic events with estimated dates of divergence support a bioclimatic hypothesis for the evolution of species in the L. meridionalis-group, which also explains their current eco-geographic distribution patterns. Greater recognition for species with a long and independent evolutionary history, which merit high conservation priority, will be especially critical for preserving geographically restricted endemics from Southeast Asia, where habitat loss is driving rapid declines.
Collapse
Affiliation(s)
- Carolina Cornejo
- Swiss Federal Research Institute WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland.
| | - Svetlana Chabanenko
- Sakhalin Branch of the Botanical Garden-Institute FEB RAS, Gorky-street 25, 693023 Yuzhno-Sakhalinsk, Russia.
| | - Christoph Scheidegger
- Swiss Federal Research Institute WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland.
| |
Collapse
|
16
|
Salantes DB, Zheng Y, Mampe F, Srivastava T, Beg S, Lai J, Li JZ, Tressler RL, Koup RA, Hoxie J, Abdel-Mohsen M, Sherrill-Mix S, McCormick K, Overton ET, Bushman FD, Learn GH, Siliciano RF, Siliciano JM, Tebas P, Bar KJ. HIV-1 latent reservoir size and diversity are stable following brief treatment interruption. J Clin Invest 2018; 128:3102-3115. [PMID: 29911997 PMCID: PMC6026010 DOI: 10.1172/jci120194] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/24/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The effect of a brief analytical treatment interruption (ATI) on the HIV-1 latent reservoir of individuals who initiate antiretroviral therapy (ART) during chronic infection is unknown. METHODS We evaluated the impact of transient viremia on the latent reservoir in participants who underwent an ATI and at least 6 months of subsequent viral suppression in a clinical trial testing the effect of passive infusion of the broadly neutralizing Ab VRC01 during ATI. RESULTS Measures of total HIV-1 DNA, cell-associated RNA, and infectious units per million cells (IUPM) (measured by quantitative viral outgrowth assay [QVOA]) were not statistically different before or after ATI. Phylogenetic analyses of HIV-1 env sequences from QVOA and proviral DNA demonstrated little change in the composition of the virus populations comprising the pre- and post-ATI reservoir. Expanded clones were common in both QVOA and proviral DNA sequences. The frequency of clonal populations differed significantly between QVOA viruses, proviral DNA sequences, and the viruses that reactivated in vivo. CONCLUSIONS The results indicate that transient viremia from ATI does not substantially alter measures of the latent reservoir, that clonal expansion is prevalent within the latent reservoir, and that characterization of latent viruses that can reactivate in vivo remains challenging. TRIAL REGISTRATION ClinicalTrials.gov NCT02463227FUNDING. Funding was provided by the NIH.
Collapse
Affiliation(s)
| | - Yu Zheng
- Harvard University, Cambridge, Massachusetts, USA
| | - Felicity Mampe
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Subul Beg
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jun Lai
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Randall L. Tressler
- Division of AIDS (DAIDS), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | | | - James Hoxie
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | | | | | | | - Robert F. Siliciano
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Pablo Tebas
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | |
Collapse
|
17
|
Gates DJ, Pilson D, Smith SD. Filtering of target sequence capture individuals facilitates species tree construction in the plant subtribe Iochrominae (Solanaceae). Mol Phylogenet Evol 2018; 123:26-34. [DOI: 10.1016/j.ympev.2018.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 10/18/2022]
|
18
|
Collins RA, Bifi AG, de Oliveira RR, Ribeiro ED, Lujan NK, Rapp Py-Daniel LH, Hrbek T. Biogeography and species delimitation of the rheophilic suckermouth catfish genus Pseudolithoxus (Siluriformes: Loricariidae), with the description of a new species from the Brazilian Amazon. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1468362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Rupert A. Collins
- Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas, Manaus, AM, Brazil
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Alessandro G. Bifi
- Coordenação em Biodiversidade, Coleção de Peixes, Programa de Coleções Científicas Biológicas-PCCB, Instituto Nacional de Pesquisas da Amazônia-INPA, Av. Andre Araújo 2936, Petrópolis, CEP 69067-375 Manaus, AM, Brazil
| | - Renildo R. de Oliveira
- Coordenação em Biodiversidade, Coleção de Peixes, Programa de Coleções Científicas Biológicas-PCCB, Instituto Nacional de Pesquisas da Amazônia-INPA, Av. Andre Araújo 2936, Petrópolis, CEP 69067-375 Manaus, AM, Brazil
| | - Emanuell D. Ribeiro
- Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas, Manaus, AM, Brazil
- Department of Biology, University of Puerto Rico – Río Piedras, PO Box 23360, San Juan, Puerto Rico
| | - Nathan K. Lujan
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Lúcia H. Rapp Py-Daniel
- Coordenação em Biodiversidade, Coleção de Peixes, Programa de Coleções Científicas Biológicas-PCCB, Instituto Nacional de Pesquisas da Amazônia-INPA, Av. Andre Araújo 2936, Petrópolis, CEP 69067-375 Manaus, AM, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas, Manaus, AM, Brazil
| |
Collapse
|
19
|
E G, Zhao Y, Chen L, Ma Y, Chu M, Li X, Hong Q, Li L, Guo J, Zhu L, Han Y, Gao H, Zhang J, Jiang H, Jiang C, Wang G, Ren H, Jin M, Sun Y, Zhou P, Huang Y. Genetic diversity of the Chinese goat in the littoral zone of the Yangtze River as assessed by microsatellite and mtDNA. Ecol Evol 2018; 8:5111-5123. [PMID: 29876086 PMCID: PMC5980450 DOI: 10.1002/ece3.4100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 03/21/2018] [Accepted: 03/27/2018] [Indexed: 11/10/2022] Open
Abstract
The objective of this study was to assess the genetic diversity and population structure of goats in the Yangtze River region using microsatellite and mtDNA to better understand the current status of those goat genetic diversity and the effects of natural landscape in fashion of domestic animal genetic diversity. The genetic variability of 16 goat populations in the littoral zone of the Yangtze River was estimated using 21 autosomal microsatellites, which revealed high diversity and genetic population clustering with a dispersed geographical distribution. A phylogenetic analysis of the mitochondrial D-loop region (482 bp) was conducted in 494 goats from the Yangtze River region. In total, 117 SNPs were reconstructed, and 173 haplotypes were identified, 94.5% of which belonged to lineages A and B. Lineages C, D, and G had lower frequencies (5.2%), and lineage F haplotypes were undetected. Several high-frequency haplotypes were shared by different ecogeographically distributed populations, and the close phylogenetic relationships among certain low-frequency haplotypes indicated the historical exchange of genetic material among these populations. In particular, the lineage G haplotype suggests that some west Asian goat genetic material may have been transferred to China via Muslim migration.
Collapse
Affiliation(s)
- Guang‐Xin E
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Yong‐Ju Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Li‐Peng Chen
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Yue‐Hui Ma
- Institute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Ming‐Xing Chu
- Institute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xiang‐Long Li
- College of Animal Science and TechnologyHebei Normal University of Science & TechnologyQinghuangdaoChina
| | - Qiong‐Hua Hong
- Yunnan Animal Scinence and Veterinary InstituteKunmingChina
| | - Lan‐Hui Li
- College of Animal Science and TechnologyAgricultural University of HebeiBaoding, HebeiChina
| | - Ji‐Jun Guo
- Animal Husbandry Station of Qinghai ProvinceXining, QinghaiChina
| | - Lan Zhu
- Yunnan Animal Scinence and Veterinary InstituteKunmingChina
| | - Yan‐Guo Han
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Hui‐Jiang Gao
- Institute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Jia‐Hua Zhang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Huai‐Zhi Jiang
- Animal Science and Technology CollegeJilin Agriculture UniversityChangchun, JilinChina
| | - Cao‐De Jiang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Gao‐Fu Wang
- Chongqing Academy of Animal SciencesChongqingChina
| | | | - Mei‐Lan Jin
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Yuan‐Zhi Sun
- Wuhan Tianyi Huiyuan Bioscience & Technology IncWuhanChina
| | - Peng Zhou
- Chongqing Academy of Animal SciencesChongqingChina
| | - Yong‐Fu Huang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| |
Collapse
|
20
|
Ravinet M, Yoshida K, Shigenobu S, Toyoda A, Fujiyama A, Kitano J. The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression. PLoS Genet 2018; 14:e1007358. [PMID: 29791436 PMCID: PMC5988309 DOI: 10.1371/journal.pgen.1007358] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 06/05/2018] [Accepted: 04/11/2018] [Indexed: 12/17/2022] Open
Abstract
Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus) and the Japan Sea stickleback (G. nipponicus), which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.
Collapse
Affiliation(s)
- Mark Ravinet
- Division of Ecological Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Kohta Yoshida
- Division of Ecological Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
- Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Jun Kitano
- Division of Ecological Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| |
Collapse
|
21
|
Pérez-Moreno JL, Balázs G, Wilkins B, Herczeg G, Bracken-Grissom HD. The role of isolation on contrasting phylogeographic patterns in two cave crustaceans. BMC Evol Biol 2017; 17:247. [PMID: 29216829 PMCID: PMC5721366 DOI: 10.1186/s12862-017-1094-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/24/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The underlying mechanisms and processes that prompt the colonisation of extreme environments, such as caves, constitute major research themes of evolutionary biology and biospeleology. The special adaptations required to survive in subterranean environments (low food availability, hypoxic waters, permanent darkness), and the geographical isolation of caves, nominate cave biodiversity as ideal subjects to answer long-standing questions concerning the interplay amongst adaptation, biogeography, and evolution. The present project aims to examine the phylogeographic patterns exhibited by two sympatric species of surface and cave-dwelling peracarid crustaceans (Asellus aquaticus and Niphargus hrabei), and in doing so elucidate the possible roles of isolation and exaptation in the colonisation and successful adaptation to the cave environment. RESULTS Specimens of both species were sampled from freshwater hypogean (cave) and epigean (surface) habitats in Hungary, and additional data from neighbouring countries were sourced from Genbank. Sequencing of mitochondrial and nuclear loci revealed, through haplotype network reconstruction (TCS) and phylogenetic inference, the genetic structure, phylogeographic patterns, and divergence-time estimates of A. aquaticus and N. hrabei surface and cave populations. Contrasting phylogeographic patterns were found between species, with A. aquaticus showing strong genetic differentiation between cave and surface populations and N. hrabei lacking any evidence of genetic structure mediated by the cave environment. Furthermore, N. hrabei populations show very low levels of genetic differentiation throughout their range, which suggests the possibility of recent expansion events over the last few thousand years. CONCLUSIONS Isolation by cave environment, rather than distance, is likely to drive the genetic structuring observed between immediately adjacent cave and surface populations of A. aquaticus, a predominantly surface species with only moderate exaptations to subterranean life. For N. hrabei, in which populations exhibit a fully 'cave-adapted' (troglomorphic) phenotype, the lack of genetic structure suggests that subterranean environments do not pose a dispersal barrier for this surface-cave species.
Collapse
Affiliation(s)
- Jorge L. Pérez-Moreno
- Department of Biological Sciences, Florida International University - Biscayne Bay Campus, 3000 NE 151 St., North Miami, FL 33181 USA
| | - Gergely Balázs
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, H-1117 Hungary
| | - Blake Wilkins
- Department of Biological Sciences, Florida International University - Biscayne Bay Campus, 3000 NE 151 St., North Miami, FL 33181 USA
| | - Gábor Herczeg
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, H-1117 Hungary
| | - Heather D. Bracken-Grissom
- Department of Biological Sciences, Florida International University - Biscayne Bay Campus, 3000 NE 151 St., North Miami, FL 33181 USA
| |
Collapse
|
22
|
Berner D, Roesti M. Genomics of adaptive divergence with chromosome-scale heterogeneity in crossover rate. Mol Ecol 2017; 26:6351-6369. [PMID: 28994152 DOI: 10.1111/mec.14373] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 09/15/2017] [Accepted: 09/18/2017] [Indexed: 12/17/2022]
Abstract
Genetic differentiation between divergent populations is often greater in chromosome centres than peripheries. Commonly overlooked, this broadscale differentiation pattern is sometimes ascribed to heterogeneity in crossover rate and hence linked selection within chromosomes, but the underlying mechanisms remain incompletely understood. A literature survey across 46 organisms reveals that most eukaryotes indeed exhibit a reduced crossover rate in chromosome centres relative to the peripheries. Using simulations of populations diverging into ecologically different habitats through sorting of standing genetic variation, we demonstrate that such chromosome-scale heterogeneity in crossover rate, combined with polygenic divergent selection, causes stronger hitchhiking and especially barriers to gene flow across chromosome centres. Without requiring selection on new mutations, this rapidly leads to elevated population differentiation in the low-crossover centres relative to the high-crossover peripheries of chromosomes ("Chromosome Centre-Biased Differentiation", CCBD). Using simulated and empirical data, we then show that strong CCBD between populations can provide evidence of polygenic adaptive divergence with a phase of gene flow. We further demonstrate that chromosome-scale heterogeneity in crossover rate impacts analyses beyond that of population differentiation, including the inference of phylogenies and parallel adaptive evolution among populations, the detection of genetic loci under selection, and the interpretation of the strength of selection on genomic regions. Overall, our results call for a greater appreciation of chromosome-scale heterogeneity in crossover rate in evolutionary genomics.
Collapse
Affiliation(s)
- Daniel Berner
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Marius Roesti
- Zoological Institute, University of Basel, Basel, Switzerland.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
23
|
Abstract
Aspergillus section Restricti together with sister section Aspergillus (formerly Eurotium) comprises xerophilic species, that are able to grow on substrates with low water activity and in extreme environments. We adressed the monophyly of both sections within subgenus Aspergillus and applied a multidisciplinary approach for definition of species boundaries in sect. Restricti. The monophyly of sections Aspergillus and Restricti was tested on a set of 102 isolates comprising all currently accepted species and was strongly supported by Maximum likelihood (ML) and Bayesian inferrence (BI) analysis based on β-tubulin (benA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) loci. More than 300 strains belonging to sect. Restricti from various isolation sources and four continents were characterized by DNA sequencing, and 193 isolates were selected for phylogenetic analyses and phenotypic studies. Species delimitation methods based on multispecies coalescent model were employed on DNA sequences from four loci, i.e., ID region of rDNA (ITS + 28S), CaM, benA and RPB2, and supported recognition of 21 species, including 14 new. All these species were also strongly supported in ML and BI analyses. All recognised species can be reliably identified by all four examined genetic loci. Phenotype analysis was performed to support the delimitation of new species and includes colony characteristics on seven cultivation media incubated at several temperatures, growth on an osmotic gradient (six media with NaCl concentration from 0 to 25 %) and analysis of morphology including scanning electron microscopy. The micromorphology of conidial heads, vesicle dimensions, temperature profiles and growth parameters in osmotic gradient were useful criteria for species identification. The vast majority of species in sect. Restricti produce asperglaucide, asperphenamate or both in contrast to species in sect. Aspergillus. Mycophenolic acid was detected for the first time in at least six members of the section. The ascomata of A. halophilicus do not contain auroglaucin, epiheveadride or flavoglaucin which are common in sect. Aspergillus, but shares the echinulins with sect. Aspergillus.
Collapse
Key Words
- Aspergillus canadensis Visagie, Yilmaz, F. Sklenar & Seifert
- Aspergillus clavatophorus F. Sklenar, S.W. Peterson & Hubka
- Aspergillus destruens Zalar, F. Sklenar, S.W. Peterson & Hubka
- Aspergillus domesticus F. Sklenar, Houbraken, Zalar & Hubka
- Aspergillus glabripes F. Sklenar, Ž. Jurjević & Hubka
- Aspergillus hordei F. Sklenar, S.W. Peterson & Hubka
- Aspergillus infrequens F. Sklenar, S.W. Peterson & Hubka
- Aspergillus magnivesiculatus F. Sklenar, Zalar, Ž. Jurjević & Hubka
- Aspergillus pachycaulis F. Sklenar, S.W. Peterson, Ž. Jurjević & Hubka
- Aspergillus penicillioides
- Aspergillus pseudogracilis F. Sklenar, Ž. Jurjević & Hubka
- Aspergillus restrictus
- Aspergillus reticulatus F. Sklenar, Ž. Jurjević, S.W. Peterson & Hubka
- Aspergillus salinicola Zalar, F. Sklenar, Visagie & Hubka
- Aspergillus tardicrescens F. Sklenar, Houbraken, Zalar, & Hubka
- Aspergillus villosus F. Sklenar, S.W. Peterson & Hubka
- Eurotium
- food spoilage
- indoor fungi
- linear discriminant analysis
- multigene phylogeny
- multispecies coalescent model
- sick building syndrome
- xerophilic fungi
Collapse
|
24
|
Agnarsson I, van Patten C, Sargeant L, Chomitz B, Dziki A, Binford GJ. A radiation of the ornate Caribbean ‘smiley-faced spiders’, with descriptions of 15 new species (Araneae: Theridiidae, Spintharus). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Ingi Agnarsson
- Department of Biology, University of Vermont, Burlington, VT, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution NWWashington, DC, USA
| | - Chloe van Patten
- Department of Biology, University of Vermont, Burlington, VT, USA
| | - Lily Sargeant
- Department of Biology, University of Vermont, Burlington, VT, USA
| | - Ben Chomitz
- Department of Biology, University of Vermont, Burlington, VT, USA
| | - Austin Dziki
- Department of Biology, University of Vermont, Burlington, VT, USA
| | - Greta J Binford
- Department of Biology, Lewis and Clark College, Portland, OR, USA
| |
Collapse
|
25
|
Zimmers J, Thomas M, Yang L, Bombarely A, Mancuso M, Wojciechowski M, Smith J. Species boundaries in the Astragalus cusickii complex delimited using molecular phylogenetic techniques. Mol Phylogenet Evol 2017; 114:93-110. [DOI: 10.1016/j.ympev.2017.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 05/01/2017] [Accepted: 06/07/2017] [Indexed: 10/19/2022]
|
26
|
Pabijan M, Zieliński P, Dudek K, Stuglik M, Babik W. Isolation and gene flow in a speciation continuum in newts. Mol Phylogenet Evol 2017; 116:1-12. [PMID: 28797693 DOI: 10.1016/j.ympev.2017.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/04/2017] [Accepted: 08/06/2017] [Indexed: 02/06/2023]
Abstract
Because reproductive isolation often evolves gradually, differentiating lineages may retain the potential for genetic exchange for prolonged periods, providing an opportunity to quantify and to understand the fundamental role of gene flow during speciation. Here we delimit evolutionary lineages, reconstruct the phylogeny and infer gene flow in newts of the Lissotriton vulgaris species complex based on 74 nuclear markers sampled from 127 localities. We demonstrate that distinct lineages along the speciation continuum in newts exchange nontrivial amounts of genes, affecting their evolutionary trajectories. By integrating a wide array of methods, we delimit nine evolutionary lineages and show that two principal factors have driven their genetic differentiation: time since the last common ancestor determining levels of shared ancestral polymorphism, and shifts in geographic distributions determining the extent of secondary contact. Post-divergence gene flow, indicative of evolutionary non-independence, has been most extensive in Central Europe, while four southern European lineages have acquired the population-genetic hallmarks of independent species (L. graecus, L. kosswigi, L. lantzi, L. schmidtleri). We obtained strong statistical support for widespread mtDNA introgression following secondary contact, previously suggested by discordance between mtDNA phylogeny and morphology. Our study reveals long-term evolutionary persistence of evolutionary lineages that may periodically exchange genes with one another: although some of these lineages may become extinct or fuse, others will acquire complete reproductive isolation and will carry signatures of this complex history in their genomes.
Collapse
Affiliation(s)
- Maciej Pabijan
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland.
| | - Piotr Zieliński
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland.
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland.
| | - Michał Stuglik
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland; Scotland's Rural College, Integrative Animal Sciences, Easter Bush Campus, Midlothian EH25 9RG, Scotland, UK.
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland.
| |
Collapse
|
27
|
Abstract
BACKGROUND Bacillus cereus sensu lato (s. l.) is an ecologically diverse bacterial group of medical and agricultural significance. In this study, I use publicly available genomes and novel bioinformatic workflows to characterize the B. cereus s. l. pan-genome and perform the largest phylogenetic and population genetic analyses of this group to date in terms of the number of genes and taxa included. With these fundamental data in hand, I identify genes associated with particular phenotypic traits (i.e., "pan-GWAS" analysis), and quantify the degree to which taxa sharing common attributes are phylogenetically clustered. METHODS A rapid k-mer based approach (Mash) was used to create reduced representations of selected Bacillus genomes, and a fast distance-based phylogenetic analysis of this data (FastME) was performed to determine which species should be included in B. cereus s. l. The complete genomes of eight B. cereus s. l. species were annotated de novo with Prokka, and these annotations were used by Roary to produce the B. cereus s. l. pan-genome. Scoary was used to associate gene presence and absence patterns with various phenotypes. The orthologous protein sequence clusters produced by Roary were filtered and used to build HaMStR databases of gene models that were used in turn to construct phylogenetic data matrices. Phylogenetic analyses used RAxML, DendroPy, ClonalFrameML, PAUP*, and SplitsTree. Bayesian model-based population genetic analysis assigned taxa to clusters using hierBAPS. The genealogical sorting index was used to quantify the phylogenetic clustering of taxa sharing common attributes. RESULTS The B. cereus s. l. pan-genome currently consists of ≈60,000 genes, ≈600 of which are "core" (common to at least 99% of taxa sampled). Pan-GWAS analysis revealed genes associated with phenotypes such as isolation source, oxygen requirement, and ability to cause diseases such as anthrax or food poisoning. Extensive phylogenetic analyses using an unprecedented amount of data produced phylogenies that were largely concordant with each other and with previous studies. Phylogenetic support as measured by bootstrap probabilities increased markedly when all suitable pan-genome data was included in phylogenetic analyses, as opposed to when only core genes were used. Bayesian population genetic analysis recommended subdividing the three major clades of B. cereus s. l. into nine clusters. Taxa sharing common traits and species designations exhibited varying degrees of phylogenetic clustering. CONCLUSIONS All phylogenetic analyses recapitulated two previously used classification systems, and taxa were consistently assigned to the same major clade and group. By including accessory genes from the pan-genome in the phylogenetic analyses, I produced an exceptionally well-supported phylogeny of 114 complete B. cereus s. l. genomes. The best-performing methods were used to produce a phylogeny of all 498 publicly available B. cereus s. l. genomes, which was in turn used to compare three different classification systems and to test the monophyly status of various B. cereus s. l. species. The majority of the methodology used in this study is generic and could be leveraged to produce pan-genome estimates and similarly robust phylogenetic hypotheses for other bacterial groups.
Collapse
Affiliation(s)
- Adam L Bazinet
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, 21702, MD, USA.
| |
Collapse
|
28
|
Yusseff-Vanegas SZ, Agnarsson I. DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region. PeerJ 2017; 5:e3516. [PMID: 28761780 PMCID: PMC5531032 DOI: 10.7717/peerj.3516] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/07/2017] [Indexed: 11/20/2022] Open
Abstract
Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identifying immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study, recovering substantial geographic variation for Lucilia eximia, Lucilia retroversa, Lucilia rica and Chloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance of employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids, and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.
Collapse
Affiliation(s)
| | - Ingi Agnarsson
- Department of Biology, University of Vermont, Burlington, VT, United States of America
| |
Collapse
|
29
|
Wang J, Ai B, Kong H, Kang M. Speciation history of a species complex of Primulina eburnea (Gesneriaceae) from limestone karsts of southern China, a biodiversity hot spot. Evol Appl 2017; 10:919-934. [PMID: 29151883 PMCID: PMC5680421 DOI: 10.1111/eva.12495] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/22/2017] [Indexed: 11/30/2022] Open
Abstract
Limestone karsts in southern China are characterized by high edaphic and topographic heterogeneity and host high levels of species richness and endemism. However, the evolutionary mechanisms for generating such biodiversity remain poorly understood. Here, we performed species delimitation, population genetic analyses, simulations of gene flow and analyses of floral morphological traits to infer the geographic history of speciation in a species complex of Primulina eburnea from limestone karsts of southern China. Using Bayesian species delimitation, we determined that there are seven distinct species that correspond well to the putative morphological species. Species tree reconstruction, Structure and Neighbor‐Net analyses all recovered four lineages in agreement with currently species geographic boundaries. High levels of genetic differentiation were observed both within and among species. Isolation–migration coalescent analysis provides evidence for significant but low gene flow among species. Approximate Bayesian computation (ABC) analysis supports a scenario of historical gene flow rather than recent contemporary gene flow for most species divergences. Finally, we found no evidence of divergent selection contributing to population differentiation of a suite of flower traits. These results support the prevalence of allopatric speciation and highlight the role of geographic isolation in the diversification process. At small geographic scales, limited hybridization occurred in the past between proximate populations but did not eliminate species boundaries. We conclude that limited gene flow might have been the predominant evolutionary force in promoting population differentiation and speciation.
Collapse
Affiliation(s)
- Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Bin Ai
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China.,Southeast Asia Biodiversity Research Institute Chinese Academy of Sciences Nay Pyi Taw Myanmar
| |
Collapse
|
30
|
Graham MR, Wood DA, Henault JA, Valois ZJ, Cushing PE. Ancient lakes, Pleistocene climates and river avulsions structure the phylogeography of a large but little-known rock scorpion from the Mojave and Sonoran deserts. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
|
31
|
Koç I, Caetano-Anollés G. The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data. PLoS One 2017; 12:e0176129. [PMID: 28467492 PMCID: PMC5414959 DOI: 10.1371/journal.pone.0176129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 04/05/2017] [Indexed: 11/18/2022] Open
Abstract
The origin and natural history of molecular functions hold the key to the emergence of cellular organization and modern biochemistry. Here we use a genomic census of Gene Ontology (GO) terms to reconstruct phylogenies at the three highest (1, 2 and 3) and the lowest (terminal) levels of the hierarchy of molecular functions, which reflect the broadest and the most specific GO definitions, respectively. These phylogenies define evolutionary timelines of functional innovation. We analyzed 249 free-living organisms comprising the three superkingdoms of life, Archaea, Bacteria, and Eukarya. Phylogenies indicate catalytic, binding and transport functions were the oldest, suggesting a 'metabolism-first' origin scenario for biochemistry. Metabolism made use of increasingly complicated organic chemistry. Primordial features of ancient molecular functions and functional recruitments were further distilled by studying the oldest child terms of the oldest level 1 GO definitions. Network analyses showed the existence of an hourglass pattern of enzyme recruitment in the molecular functions of the directed acyclic graph of molecular functions. Older high-level molecular functions were thoroughly recruited at younger lower levels, while very young high-level functions were used throughout the timeline. This pattern repeated in every one of the three mappings, which gave a criss-cross pattern. The timelines and their mappings were remarkable. They revealed the progressive evolutionary development of functional toolkits, starting with the early rise of metabolic activities, followed chronologically by the rise of macromolecular biosynthesis, the establishment of controlled interactions with the environment and self, adaptation to oxygen, and enzyme coordinated regulation, and ending with the rise of structural and cellular complexity. This historical account holds important clues for dissection of the emergence of biomcomplexity and life.
Collapse
Affiliation(s)
- Ibrahim Koç
- Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| |
Collapse
|
32
|
Riesch R, Muschick M, Lindtke D, Villoutreix R, Comeault AA, Farkas TE, Lucek K, Hellen E, Soria-Carrasco V, Dennis SR, de Carvalho CF, Safran RJ, Sandoval CP, Feder J, Gries R, Crespi BJ, Gries G, Gompert Z, Nosil P. Transitions between phases of genomic differentiation during stick-insect speciation. Nat Ecol Evol 2017; 1:82. [PMID: 28812654 DOI: 10.1038/s41559-017-0082] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 01/12/2017] [Indexed: 01/17/2023]
Abstract
Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow. Transitions to genome-wide differentiation are also observed with gene flow, in association with differentiation in polygenic chemical traits affecting mate choice. Thus, intermediate phases of speciation are associated with genome-wide differentiation and mate choice, but not growth of a few genomic islands. We also find a gap in genomic differentiation between sympatric taxa that still exchange genes and those that do not, highlighting the association between differentiation and complete reproductive isolation. Our results suggest that substantial progress towards speciation may involve the alignment of multi-faceted aspects of differentiation.
Collapse
Affiliation(s)
- Rüdiger Riesch
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Moritz Muschick
- Aquatic Ecology &Evolution, Institute of Ecology and Evolution, University of Bern, CH-3012, Bern, Switzerland
| | - Dorothea Lindtke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Romain Villoutreix
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Aaron A Comeault
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Timothy E Farkas
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06369, USA
| | - Kay Lucek
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Elizabeth Hellen
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Víctor Soria-Carrasco
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Stuart R Dennis
- Department of Aquatic Ecology, Eawag Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Zurich, Switzerland
| | - Clarissa F de Carvalho
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Rebecca J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Cristina P Sandoval
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, USA
| | - Jeff Feder
- Department of Biology, Notre Dame University, South Bend, Indiana 11111, USA
| | - Regine Gries
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Bernard J Crespi
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Gerhard Gries
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Zach Gompert
- Department of Biology, Utah State University, Logan, Utah 84322, USA
| | - Patrik Nosil
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| |
Collapse
|
33
|
Liu S, Jin W, Liu Y, Murphy RW, Lv B, Hao H, Liao R, Sun Z, Tang M, Chen W, Fu J. Taxonomic position of Chinese voles of the tribe Arvicolini and the description of 2 new species from Xizang, China. J Mammal 2017; 98:166-182. [PMID: 29674783 PMCID: PMC5901085 DOI: 10.1093/jmammal/gyw170] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 09/10/2016] [Indexed: 11/22/2022] Open
Abstract
China has 26 species in the tribe Arvicolini. The taxonomic status of these voles remains controversial despite much effort. Herein, we evaluate the taxonomic position of 22 species plus 2 unidentified taxa using mitochondrial DNA gene sequences (cytb + CO1). We also evaluate 18 species and 2 unidentified taxa using morphological data. Phylogenetic analyses of cytb resolve monophyly for the genera Alexandromys, Lasiopodomys, Microtus, Neodon, Proedromys, and Volemys with strong support. Stenocranius clusters with Chionomys but with very weak support. Analyses of concatenated cytb + CO1 resolve the same genera with strong support, but the topology of the tree differs from that of cytb in that Chionomys roots at the base of the tree independent of Stenocranius, which forms the sister-group of Lasiopodomys in a more terminal position. The matrilineal genealogy excludes the type species Arvicola amphibius from the rest of the Arvicolini. This species forms the sister-group of Ondatra with high support. Neodon includes N. irene, N. linzhiensis, N. fuscus, N. leucurus, N. sikimensis, Microtus clarkei, and 2 unidentified specimens. Alexandromys includes the former species Microtus oeconomus, M. kikuchii, M. limnophilus, M. fortis, and M. maximowiczii. Finally, Microtus has the subgenera Blanfordimys, Microtus, Mynomes, Pedomys, Pitymys, and Terricola, which includes the Chinese species M. agrestis, M. arvalis, and Blanfordimys juldaschi. General mixed Yule-coalescent species delimitation modeling demarcates 6 currently recognized species and 2 new species of Neodon. A principal component analysis of the morphological data among 7 matrilines shows that all variables have positive loadings of high magnitude on the 1st component. Canonical discriminant analysis for Neodon (including M. clarkei and 2 unidentified species) correctly classifies 93.0% of specimens. Overall, our analyses support the recognition of Alexandromys, Lasiopodomys, Microtus, Neodon, Proedromys, and Volemys as genera. Stenocranius includes Microtus gregalis, and the genealogical position of Stenocranius remains uncertain. The status of Arvicola requires further study. We assign M. clarkei to Neodon and describe 2 new species of Neodon.
Collapse
Affiliation(s)
- Shaoying Liu
- Sichuan Academy of Forestry, No. 18, Xinghui Xilu Road, Chengdu 610081, Sichuan, China (SL, WJ, YL, RL, ZS, MT, JF)
| | - Wei Jin
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario M5S 2C6, Canada (RWM)
| | - Yang Liu
- Chengdu Biology Institute of Chinese Academy of Science, Chengdu 610041, Sichuan, China (LB)
| | - Robert W Murphy
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (HH)
| | - Bin Lv
- Guangxi Natural History Museum, Nanning, Guangxi 530012, China (WC)
| | - Haibang Hao
- Sichuan Academy of Forestry, No. 18, Xinghui Xilu Road, Chengdu 610081, Sichuan, China (SL, WJ, YL, RL, ZS, MT, JF)
| | - Rui Liao
- Sichuan Academy of Forestry, No. 18, Xinghui Xilu Road, Chengdu 610081, Sichuan, China (SL, WJ, YL, RL, ZS, MT, JF)
| | - Zhiyu Sun
- Sichuan Academy of Forestry, No. 18, Xinghui Xilu Road, Chengdu 610081, Sichuan, China (SL, WJ, YL, RL, ZS, MT, JF)
| | - Mingkun Tang
- Sichuan Academy of Forestry, No. 18, Xinghui Xilu Road, Chengdu 610081, Sichuan, China (SL, WJ, YL, RL, ZS, MT, JF)
| | - Weicai Chen
- Sichuan Academy of Forestry, No. 18, Xinghui Xilu Road, Chengdu 610081, Sichuan, China (SL, WJ, YL, RL, ZS, MT, JF)
| | - Jianrong Fu
- Sichuan Academy of Forestry, No. 18, Xinghui Xilu Road, Chengdu 610081, Sichuan, China (SL, WJ, YL, RL, ZS, MT, JF)
| |
Collapse
|
34
|
Potts AJ. Catchments catch all in South African coastal lowlands: topography and palaeoclimate restricted gene flow in Nymania capensis (Meliaceae)-a multilocus phylogeographic and distribution modelling approach. PeerJ 2017; 5:e2965. [PMID: 28168122 PMCID: PMC5289106 DOI: 10.7717/peerj.2965] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/06/2017] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND This study investigates orbitally-forced range dynamics at a regional scale by exploring the evolutionary history of Nymania capensis (Meliaceae) across the deeply incised landscapes of the subescarpment coastal lowlands of South Africa; a region that is home to three biodiversity hotspots (Succulent Karoo, Fynbos, and Maputaland-Pondoland-Albany hotspots). METHODS A range of methods are used including: multilocus phylogeography (chloroplast and high- and low-copy nuclear DNA), molecular dating and species distribution modelling (SDM). RESULTS The results support an 'evolutionarily distinct catchment' hypothesis where: (1) different catchments contain genetically distinct lineages, (2) limited genetic structuring was detected within basins whilst high structuring was detected between basins, and (3) within primary catchment populations display a high degree of genealogical lineage sorting. In addition, the results support a glacial refugia hypothesis as: (a) the timing of chloroplast lineage diversification is restricted to the Pleistocene in a landscape that has been relatively unchanged since the late Pliocene, and (b) the projected LGM distribution of suitable climate for N. capensis suggest fragmentation into refugia that correspond to the current phylogeographic populations. DISCUSSION This study highlights the interaction of topography and subtle Pleistocene climate variations as drivers limiting both seed and pollen flow along these lowlands. This lends support to the region's large-scale conservation planning efforts, which used catchments as foundational units for conservation as these are likely to be evolutionarily significant units.
Collapse
Affiliation(s)
- Alastair J Potts
- Department of Botany, Nelson Mandela Metropolitan University, Port Elizabeth, South Africa; Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
35
|
Iyer SS, Bibollet-Ruche F, Sherrill-Mix S, Learn GH, Plenderleith L, Smith AG, Barbian HJ, Russell RM, Gondim MVP, Bahari CY, Shaw CM, Li Y, Decker T, Haynes BF, Shaw GM, Sharp PM, Borrow P, Hahn BH. Resistance to type 1 interferons is a major determinant of HIV-1 transmission fitness. Proc Natl Acad Sci U S A 2017; 114:E590-E599. [PMID: 28069935 PMCID: PMC5278458 DOI: 10.1073/pnas.1620144114] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Sexual transmission of HIV-1 is an inefficient process, with only one or few variants of the donor quasispecies establishing the new infection. A critical, and as yet unresolved, question is whether the mucosal bottleneck selects for viruses with increased transmission fitness. Here, we characterized 300 limiting dilution-derived virus isolates from the plasma, and in some instances genital secretions, of eight HIV-1 donor and recipient pairs. Although there were no differences in the amount of virion-associated envelope glycoprotein, recipient isolates were on average threefold more infectious (P = 0.0001), replicated to 1.4-fold higher titers (P = 0.004), were released from infected cells 4.2-fold more efficiently (P < 0.00001), and were significantly more resistant to type I IFNs than the corresponding donor isolates. Remarkably, transmitted viruses exhibited 7.8-fold higher IFNα2 (P < 0.00001) and 39-fold higher IFNβ (P < 0.00001) half-maximal inhibitory concentrations (IC50) than did donor isolates, and their odds of replicating in CD4+ T cells at the highest IFNα2 and IFNβ doses were 35-fold (P < 0.00001) and 250-fold (P < 0.00001) greater, respectively. Interestingly, pretreatment of CD4+ T cells with IFNβ, but not IFNα2, selected donor plasma isolates that exhibited a transmitted virus-like phenotype, and such viruses were also detected in the donor genital tract. These data indicate that transmitted viruses are phenotypically distinct, and that increased IFN resistance represents their most distinguishing property. Thus, the mucosal bottleneck selects for viruses that are able to replicate and spread efficiently in the face of a potent innate immune response.
Collapse
Affiliation(s)
- Shilpa S Iyer
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Frederic Bibollet-Ruche
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Lindsey Plenderleith
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Andrew G Smith
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Hannah J Barbian
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ronnie M Russell
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Marcos V P Gondim
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Catherine Y Bahari
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Christiana M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Timothy Decker
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Barton F Haynes
- Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710
- Department of Medicine, Duke University Medical Center, Durham, NC 27710
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
| | - George M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Paul M Sharp
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| |
Collapse
|
36
|
Smith JF, Clark JL, Amaya-Márquez M, Marín-Gómez OH. Resolving incongruence: Species of hybrid origin in Columnea (Gesneriaceae). Mol Phylogenet Evol 2017; 106:228-240. [DOI: 10.1016/j.ympev.2016.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 01/19/2023]
|
37
|
Ramdial H, Latchoo RK, Hosein FN, Rampersad SN. Phylogeny and Haplotype Analysis of Fungi Within the Fusarium incarnatum-equiseti Species Complex. PHYTOPATHOLOGY 2017; 107:109-120. [PMID: 27901448 DOI: 10.1094/phyto-05-16-0209-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Fusarium spp. are ranked among the top 10 most economically and scientifically important plant-pathogenic fungi in the world and are associated with plant diseases that include fruit decay of a number of crops. Fusarium isolates infecting bell pepper in Trinidad were identified based on sequence comparisons of the translation elongation factor gene (EF-1a) with sequences of Fusarium incarnatum-equiseti species complex (FIESC) verified in the FUSARIUM-ID database. Eighty-two isolates were identified as belonging to one of four phylogenetic species within the subclades FIESC-1, FIESC-15, FIESC-16, and FIESC-26, with the majority of isolates belonging to FIESC-15. A comparison of the level of DNA polymorphism and phylogenetic inference for sequences of the internal transcribed spacer region (ITS1-5.8S-ITS2) and EF-1a sequences for Trinidad and FUSARIUM-ID type species was carried out. The ITS sequences were less informative, had lower haplotype diversity and restricted haplotype distribution, and resulted in poor resolution and taxa placement in the consensus maximum-likelihood tree. EF-1a sequences enabled strongly supported phylogenetic inference with highly resolved branching patterns of the 30 phylogenetic species within the FIESC and placement of representative Trinidad isolates. Therefore, global phylogeny was inferred from EF-1a sequences representing 11 countries, and separation into distinct Incarnatum and Equiseti clades was again evident. In total, 42 haplotypes were identified: 12 were shared and the remaining were unique haplotypes. The most diverse haplotype was represented by sequences from China, Indonesia, Malaysia, and Trinidad and consisted exclusively of F. incarnatum isolates. Spain had the highest haplotype diversity, perhaps because both F. equiseti and F. incarnatum sequences were represented; followed by the United States, which contributed both F. equiseti and F. incarnatum sequences to the data set; then by countries representing Southeast Asia (China, Indonesia, Malaysia, Thailand, and Philippines) and Trinidad; both of these regions were represented by only F. incarnatum sequences. Trinidad shared two haplotypes with China and one haplotype with the United States for only F. incarnatum isolates. The findings of this study are important for devising disease management strategies and for understanding the phylogenetic relationships among members of the FIESC.
Collapse
Affiliation(s)
- H Ramdial
- The University of the West Indies, Department of Life Sciences, Faculty of Science and Technology, St. Augustine, Trinidad and Tobago, West Indies
| | - R K Latchoo
- The University of the West Indies, Department of Life Sciences, Faculty of Science and Technology, St. Augustine, Trinidad and Tobago, West Indies
| | - F N Hosein
- The University of the West Indies, Department of Life Sciences, Faculty of Science and Technology, St. Augustine, Trinidad and Tobago, West Indies
| | - S N Rampersad
- The University of the West Indies, Department of Life Sciences, Faculty of Science and Technology, St. Augustine, Trinidad and Tobago, West Indies
| |
Collapse
|
38
|
Ecological divergence in the yellow-bellied kingsnake (Lampropeltis calligaster) at two North American biodiversity hotspots. Mol Phylogenet Evol 2017; 106:61-72. [DOI: 10.1016/j.ympev.2016.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 08/25/2016] [Accepted: 09/12/2016] [Indexed: 11/22/2022]
|
39
|
A new species of Ophiognomonia from Northern China inhabiting the lesions of chestnut leaves infected with Diaporthe eres. Mycol Prog 2016. [DOI: 10.1007/s11557-016-1255-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
40
|
Pino-Bodas R, Pérez-Vargas I, Stenroos S, Ahti T, Burgaz A. Sharpening the species boundaries in the Cladonia mediterranea complex ( Cladoniaceae, Ascomycota). PERSOONIA 2016; 37:1-12. [PMID: 28232757 PMCID: PMC5315283 DOI: 10.3767/003158516x688081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 03/24/2015] [Indexed: 11/25/2022]
Abstract
The complex Cladonia mediterranea belongs to the section Impexae and is formed by C. azorica, C. macaronesica and C.mediterranea. These species are basically distributed in the Mediterranean and Macaronesian Regions. In the present work the limits between the species of this complex are re-examined. To this end, the morphological characters were studied along with the secondary metabolites and the DNA sequences from three loci (ITS rDNA, IGS rDNA and rpb2). The morphological data were studied by principal component analysis (PCA), while the DNA sequences were analyzed using several approaches available to delimit species: genealogical concordance phylogenetic species recognition, species tree (BEAST* and spedeSTEM) and cohesion species recognition. In addition, the genealogical sorting index was used in order to assess the monophyly of the species. The different procedures used in our study turned out to be highly congruent with respect to the limits they establish, but these limits are not the ones separating the prior species. Either the morphological analysis or the different approaches to species delimitation indicate that C. mediterranea is a different species from C. macaronesica, while C. azorica and C. macaronesica, which are reduced to synonyms of C. portentosa, constitute a separate lineage.
Collapse
Affiliation(s)
- R. Pino-Bodas
- Botanical Museum, Finnish Museum of Natural History, P.O. Box 7, FI-00014 University of Helsinki, Finland
| | - I. Pérez-Vargas
- Departamento de Botánica, Ecología y Fisiología Vegetal, Facultad de Farmacia, Universidad de La Laguna, Tenerife 38071, Canary Islands, Spain
| | - S. Stenroos
- Botanical Museum, Finnish Museum of Natural History, P.O. Box 7, FI-00014 University of Helsinki, Finland
| | - T. Ahti
- Botanical Museum, Finnish Museum of Natural History, P.O. Box 7, FI-00014 University of Helsinki, Finland
| | - A.R. Burgaz
- Departamento de Biología Vegetal 1, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Spain
| |
Collapse
|
41
|
Paired quantitative and qualitative assessment of the replication-competent HIV-1 reservoir and comparison with integrated proviral DNA. Proc Natl Acad Sci U S A 2016; 113:E7908-E7916. [PMID: 27872306 DOI: 10.1073/pnas.1617789113] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
HIV-1-infected individuals harbor a latent reservoir of infected CD4+ T cells that is not eradicated by antiretroviral therapy (ART). This reservoir presents the greatest barrier to an HIV-1 cure and has remained difficult to characterize, in part, because the vast majority of integrated sequences are defective and incapable of reactivation. To characterize the replication-competent reservoir, we have combined two techniques, quantitative viral outgrowth and qualitative sequence analysis of clonal outgrowth viruses. Leukapheresis samples from four fully ART-suppressed, chronically infected individuals were assayed at two time points separated by a 4- to 6-mo interval. Overall, 54% of the viruses emerging from the latent reservoir showed gp160 env sequences that were identical to at least one other virus. Moreover, 43% of the env sequences from viruses emerging from the reservoir were part of identical groups at the two time points. Groups of identical expanded sequences made up 54% of proviral DNA, and, as might be expected, the sequences of replication-competent viruses in the active reservoir showed limited overlap with integrated proviral DNA, most of which is known to represent defective viruses. Finally, there was an inverse correlation between proviral DNA clone size and the probability of reactivation, suggesting that replication-competent viruses are less likely to be found among highly expanded provirus-containing cell clones.
Collapse
|
42
|
Manthey JD, Tollis M, Lemmon AR, Moriarty Lemmon E, Boissinot S. Diversification in wild populations of the model organism Anolis carolinensis: A genome-wide phylogeographic investigation. Ecol Evol 2016; 6:8115-8125. [PMID: 27891220 PMCID: PMC5108263 DOI: 10.1002/ece3.2547] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/14/2016] [Accepted: 09/19/2016] [Indexed: 01/14/2023] Open
Abstract
The green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary history in association with morphological, physiological, or reproductive biology studies among sampling localities and necessitate increased effort to resolve evolutionary relationships among natural populations. Here, we used anchored hybrid enrichment of hundreds of genetic markers across the genome of A. carolinensis and identified five strongly supported phylogeographic groups. Using multiple analyses, we produced a fully resolved species tree, investigated relative support for each lineage across all gene trees, and identified mito‐nuclear discordance when comparing our results to previous studies. We found fixed differences in only one clade—southern Florida restricted to the Everglades region—while most polymorphisms were shared between lineages. The southern Florida group likely diverged from other populations during the Pliocene, with all other diversification during the Pleistocene. Multiple lines of support, including phylogenetic relationships, a latitudinal gradient in genetic diversity, and relatively more stable long‐term population sizes in southern phylogeographic groups, indicate that diversification in A. carolinensis occurred northward from southern Florida.
Collapse
Affiliation(s)
| | - Marc Tollis
- Biodesign Institute Arizona State University Tempe AZ USA
| | - Alan R Lemmon
- Department of Scientific Computing Florida State University Tallahassee FL USA
| | | | | |
Collapse
|
43
|
Haley BJ, Kim SW, Pettengill J, Luo Y, Karns JS, Van Kessel JAS. Genomic and Evolutionary Analysis of Two Salmonella enterica Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America. PLoS One 2016; 11:e0161225. [PMID: 27695032 PMCID: PMC5047448 DOI: 10.1371/journal.pone.0161225] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 08/02/2016] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Kentucky is frequently isolated from healthy poultry and dairy cows and is occasionally isolated from people with clinical disease. A genomic analysis of 119 isolates collected in the United States from dairy cows, ground beef, poultry and poultry products, and human clinical cases was conducted. Results of the analysis demonstrated that the majority of poultry and bovine-associated S. Kentucky were sequence type (ST) 152. Several bovine-associated (n = 3) and food product isolates (n = 3) collected from the United States and the majority of human clinical isolates were ST198, a sequence type that is frequently isolated from poultry and occasionally from human clinical cases in Northern Africa, Europe and Southeast Asia. A phylogenetic analysis indicated that both STs are more closely related to other Salmonella serovars than they are to each other. Additionally, there was strong evidence of an evolutionary divergence between the poultry-associated and bovine-associated ST152 isolates that was due to polymorphisms in four core genome genes. The ST198 isolates recovered from dairy farms in the United States were phylogenetically distinct from those collected from human clinical cases with 66 core genome SNPs differentiating the two groups, but more isolates are needed to determine the significance of this distinction. Identification of S. Kentucky ST198 from dairy animals in the United States suggests that the presence of this pathogen should be monitored in food-producing animals.
Collapse
Affiliation(s)
- Bradd J. Haley
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Seon Woo Kim
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America
| | - James Pettengill
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States of America
| | - Yan Luo
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States of America
| | - Jeffrey S. Karns
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Jo Ann S. Van Kessel
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America
- * E-mail:
| |
Collapse
|
44
|
Malaquias MAE, Ohnheiser LT, Oskars TR, Willassen E. Diversity and systematics of philinid snails (Gastropoda: Cephalaspidea) in West Africa with remarks on the biogeography of the region. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manuel António E. Malaquias
- Phylogenetic Systematics and Evolution Research Group; Section of Taxonomy and Evolution; Department of Natural History; University Museum of Bergen; University of Bergen; PB 7800 5020 Bergen Norway
| | - Lena T. Ohnheiser
- Phylogenetic Systematics and Evolution Research Group; Section of Taxonomy and Evolution; Department of Natural History; University Museum of Bergen; University of Bergen; PB 7800 5020 Bergen Norway
| | - Trond R. Oskars
- Phylogenetic Systematics and Evolution Research Group; Section of Taxonomy and Evolution; Department of Natural History; University Museum of Bergen; University of Bergen; PB 7800 5020 Bergen Norway
| | - Endre Willassen
- Phylogenetic Systematics and Evolution Research Group; Section of Taxonomy and Evolution; Department of Natural History; University Museum of Bergen; University of Bergen; PB 7800 5020 Bergen Norway
| |
Collapse
|
45
|
Piwczyński M, Pabijan M, Grzywacz A, Glinkowski W, Bereś PK, Buszko J. High regional genetic diversity and lack of host-specificity in Ostrinia nubilalis (Lepidoptera: Crambidae) as revealed by mtDNA variation. BULLETIN OF ENTOMOLOGICAL RESEARCH 2016; 106:512-521. [PMID: 27019346 DOI: 10.1017/s0007485316000195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The European corn borer (Ostrinia nubilalis) infests a wide array of host plants and is considered one of the most serious pests of maize in Europe. Recent studies suggest that individuals feeding on maize in Europe should be referred to O. nubilalis (sensu nov.), while those infesting dicots as Ostrinia scapulalis (sensu nov.). We test if the clear genetic distinctiveness among individuals of O. nubilalis living on maize vs. dicots is tracked by mitochondrial DNA (mtDNA). We used fragments of COI and COII genes of 32 individuals traditionally recognized as O. nubilalis collected on three host plants, maize, mugwort and hop, growing in different parts of Poland. In addition, we reconstructed the mtDNA phylogeny of Ostrinia species based on our data and sequences retrieved from GenBank to assess host and/or biogeographic patterns. We also compared haplotype variation found in Poland (east-central Europe) with other regions (Anatolia, Eastern Europe, Balkans, Far East, North America). Our study showed high mtDNA diversity of O. nubilalis in Poland in comparison with other regions and revealed rare haplotypes likely of Asian origin. We did not find distinct mtDNA haplotypes in larvae feeding on maize vs. dicotyledonous plants. Phylogenetic analyses showed an apparent lack of mtDNA divergence among putatively distinct lineages belonging to the O. nubilalis group as identical haplotypes are shared by Asian and European individuals. We argue that human-mediated dispersal, hybridization and sporadic host jumps are likely responsible for the lack of a geographic pattern in mtDNA variation.
Collapse
Affiliation(s)
- M Piwczyński
- Chair of Ecology and Biogeography,Nicolaus Copernicus University in Toruń,Lwowska 1,PL-87-100 Toruń,Poland
| | - M Pabijan
- Department of Comparative Anatomy,Institute of Zoology,Jagiellonian University,Gronostajowa 9,30-387 Kraków,Poland
| | - A Grzywacz
- Chair of Ecology and Biogeography,Nicolaus Copernicus University in Toruń,Lwowska 1,PL-87-100 Toruń,Poland
| | - W Glinkowski
- Chair of Ecology and Biogeography,Nicolaus Copernicus University in Toruń,Lwowska 1,PL-87-100 Toruń,Poland
| | - P K Bereś
- Institute of Plant Protection - National Research Institute,Regional Experimental Station,Langiewicza 28,35-101 Rzeszów,Poland
| | - J Buszko
- Chair of Ecology and Biogeography,Nicolaus Copernicus University in Toruń,Lwowska 1,PL-87-100 Toruń,Poland
| |
Collapse
|
46
|
Origin of a cryptic lineage in a threatened reptile through isolation and historical hybridization. Heredity (Edinb) 2016; 117:358-366. [PMID: 27460499 DOI: 10.1038/hdy.2016.56] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 12/26/2022] Open
Abstract
Identifying phylogenetically distinct lineages and understanding the evolutionary processes by which they have arisen are important goals of phylogeography. This information can also help define conservation units in endangered species. Such analyses are being transformed by the availability of genomic-scale data sets and novel analytical approaches for statistically comparing different historical scenarios as causes of phylogeographic patterns. Here, we use genomic-scale restriction-site-associated DNA sequencing (RADseq) data to test for distinct lineages in the endangered Eastern Massasauga Rattlesnake (Sistrurus catenatus). We then use coalescent-based modeling techniques to identify the evolutionary mechanisms responsible for the origin of the lineages in this species. We find equivocal evidence for distinct phylogenetic lineages within S. catenatus east of the Mississippi River, but strong support for a previously unrecognized lineage on the western edge of the range of this snake, represented by populations from Iowa, USA. Snakes from these populations show patterns of genetic admixture with a nearby non-threatened sister species (Sistrurus tergeminus). Tests of historical demographic models support the hypothesis that the genetic distinctiveness of Iowa snakes is due to a combination of isolation and historical introgression between S. catenatus and S. tergeminus. Our work provides an example of how model-based analysis of genomic-scale data can help identify conservation units in rare species.
Collapse
|
47
|
Guo P, Liu Q, Zhu F, Zhong GH, Chen X, Myers EA, Che J, Zhang L, Ziegler T, Nguyen TQ, Burbrink FT. Complex longitudinal diversification across South China and Vietnam in Stejneger's pit viper,Viridovipera stejnegeri(Schmidt, 1925) (Reptilia: Serpentes: Viperidae). Mol Ecol 2016; 25:2920-36. [DOI: 10.1111/mec.13658] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 03/16/2016] [Accepted: 03/29/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Peng Guo
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Qin Liu
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Fei Zhu
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Guang H. Zhong
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Xin Chen
- Department of Biological Sciences; Dartmouth College; Hanover NH 03755 USA
| | - Edward A. Myers
- Department of Biology; The Graduate School and University Center; The City University of New York; 365 5th Avenue New York NY 10016 USA
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
- Southeast Asia Biodiversity Research Institute; Chinese Academy of Sciences; Menglun Mengla Yunnan 666303 China
| | - Liang Zhang
- South China Institute of Endangered Animals; Guangzhou 510260 China
| | - Thomas Ziegler
- AG Zoologischer Garten Köln; Riehler Strasse 173 D-50735 Cologne Germany
| | - Truong Q. Nguyen
- Institute of Ecology and Biological Resources; Vietnam Academy of Science and Technology; 18 Hoang Quoc Viet Street Hanoi Vietnam
| | - Frank T. Burbrink
- Department of Herpetology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024-5192 USA
| |
Collapse
|
48
|
Meeus S, Janssens S, Helsen K, Jacquemyn H. Evolutionary trends in the distylous genus Pulmonaria (Boraginaceae): Evidence of ancient hybridization and current interspecific gene flow. Mol Phylogenet Evol 2016; 98:63-73. [DOI: 10.1016/j.ympev.2015.11.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 11/28/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
|
49
|
Fiorentino V, Manganelli G, Giusti F, Ketmaier V. Recent expansion and relic survival: Phylogeography of the land snail genus Helix (Mollusca, Gastropoda) from south to north Europe. Mol Phylogenet Evol 2016; 98:358-72. [DOI: 10.1016/j.ympev.2016.02.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 02/18/2016] [Accepted: 02/20/2016] [Indexed: 11/27/2022]
|
50
|
Breure ASH. Caribbean Bulimulus revisited: physical moves and molecular traces (Mollusca, Gastropoda, Bulimulidae). PeerJ 2016; 4:e1836. [PMID: 27069787 PMCID: PMC4824910 DOI: 10.7717/peerj.1836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 03/02/2016] [Indexed: 12/05/2022] Open
Abstract
Twenty-five samples of Bulimulus species are studied, partly from localities within their known distribution range, partly based on interceptions where the material originates from localities where the species seem to be recently introduced and non-native. Molecular study of cytochrome oxidase 1 (CO1) reveals the origin of some of these introductions, but is less conclusive for others. Four different methods for species delimitation were applied, which did not result in unambiguous species hypotheses. For a rapid identification of morphologically indistinct species, a more comprehensive database of sequences is needed.
Collapse
|