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Pérez-Escobar OA, Bogarín D, Przelomska NAS, Ackerman JD, Balbuena JA, Bellot S, Bühlmann RP, Cabrera B, Cano JA, Charitonidou M, Chomicki G, Clements MA, Cribb P, Fernández M, Flanagan NS, Gravendeel B, Hágsater E, Halley JM, Hu AQ, Jaramillo C, Mauad AV, Maurin O, Müntz R, Leitch IJ, Li L, Negrão R, Oses L, Phillips C, Rincon M, Salazar GA, Simpson L, Smidt E, Solano-Gomez R, Parra-Sánchez E, Tremblay RL, van den Berg C, Tamayo BSV, Zuluaga A, Zuntini AR, Chase MW, Fay MF, Condamine FL, Forest F, Nargar K, Renner SS, Baker WJ, Antonelli A. The origin and speciation of orchids. THE NEW PHYTOLOGIST 2024; 242:700-716. [PMID: 38382573 DOI: 10.1111/nph.19580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/04/2023] [Indexed: 02/23/2024]
Abstract
Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.
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Affiliation(s)
| | - Diego Bogarín
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
- Naturalis Biodiversity Centre, Leiden, CR 2333, the Netherlands
| | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - James D Ackerman
- University of Puerto Rico - Rio Piedras, San Juan, PR, 00925-2537, USA
| | | | | | | | - Betsaida Cabrera
- Jardín Botánico Rafael Maria Moscoso, Santo Domingo, 21-9, Dominican Republic
| | | | | | | | - Mark A Clements
- Centre for Australian National Biodiversity Research (joint venture between Parks Australia and CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | - Melania Fernández
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
| | - Nicola S Flanagan
- Universidad Pontificia Javeriana, Seccional Cali, Cali, 760031, Colombia
| | | | | | | | - Ai-Qun Hu
- Singapore Botanic Gardens, 1 Cluny Road, Singapore, 257494, Singapore
| | - Carlos Jaramillo
- Smithsonian Tropical Research Institute, Apartado, Panama City, 0843-03092, Panama
| | | | | | - Robert Müntz
- Reserva Biológica Guaitil, Eisenstadt, 7000, Austria
| | | | - Lan Li
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | - Lizbeth Oses
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
| | - Charlotte Phillips
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Milton Rincon
- Jardín Botánico Jose Celestino Mutis, Bogota, 111071, Colombia
| | | | - Lalita Simpson
- Australian Tropical Herbarium, James Cook University, GPO Box 6811, Cairns, Qld, 4878, Australia
| | - Eric Smidt
- Universidade Federal do Paraná, Curitiba, 19031, Brazil
| | | | | | | | - Cassio van den Berg
- Universidade Estadual de Feira de Santana, Feira de Santana, 44036-900, Brazil
| | | | | | | | - Mark W Chase
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- Department of Environment and Agriculture, Curtin University, Perth, WA, 6102, Australia
| | | | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier|CNRS|IRD|EPHE), Place Eugène Bataillon, Montpellier, 34000, France
| | | | - Katharina Nargar
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
- Australian Tropical Herbarium, James Cook University, GPO Box 6811, Cairns, Qld, 4878, Australia
- Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | | | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Gothenburg, 417 56, Sweden
- University of Gothenburg, Gothenburg, 417 56, Sweden
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
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152
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Dobbs JT, Caballero JRI, Ata JP, Babiker E, Copes WE, Stewart JE. Genomic and Transcriptomic Comparisons of the Twig Blight Pathogen, Passalora sequoiae, with Mycosphaerellaceae Foliar and Conifer Pathogens. PHYTOPATHOLOGY 2024; 114:732-742. [PMID: 37942864 DOI: 10.1094/phyto-08-23-0271-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Passalora sequoiae is a foliar pathogen to conifer tree species. In this study, we conducted whole-genome and transcriptome analyses on isolates of P. sequoiae collected from symptomatic Leyland cypress leaves from a Christmas tree farm in Mississippi. The objectives for this research were to elucidate the pathogenicity mechanisms of P. sequoiae by characterizing the genome and transcriptome and possibly identify unique and shared predicted genes in comparison with non-conifer/canker and foliar pathogens in the family Mycosphaerellaceae. P. sequoiae was found to be similar to other foliar Mycosphaerellaceae pathogens and likely represents a hemibiotrophic lifestyle based on comparisons across pathogens. The genome and in planta transcriptome highlighted some unique features of P. sequoiae: the significant presence of chitin synthases and fructose-degrading carbohydrate-degrading enzymes, trans-AT PKS genes, and antibiotic gene clusters that were unique to P. sequoiae compared with the other Mycosphaerellaceae species genomes. Several transcripts that were highly expressed in planta were identified as effectors, yet the functions were not characterized. These targets provide ample resources to continue to characterize pathogen-conifer host interactions in conifer foliar pathogens. Furthermore, this research helps build genomic resources for an important plant pathogen on Leyland cypress that will further our ability to develop novel management practices that could begin with breeding for resistance.
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Affiliation(s)
- John T Dobbs
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, U.S.A
| | | | - Jessa P Ata
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, U.S.A
- Department of Forest Biological Sciences, University of the Philippines Los Baños, Los Baños, Philippines
| | - Ebrahiem Babiker
- Thad Cochran Southern Horticultural Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, U.S.A
| | - Warren E Copes
- Thad Cochran Southern Horticultural Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, U.S.A
| | - Jane E Stewart
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, U.S.A
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153
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Bossert S, Pauly A, Danforth BN, Orr MC, Murray EA. Lessons from assembling UCEs: A comparison of common methods and the case of Clavinomia (Halictidae). Mol Ecol Resour 2024; 24:e13925. [PMID: 38183389 DOI: 10.1111/1755-0998.13925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024]
Abstract
Sequence data assembly is a foundational step in high-throughput sequencing, with untold consequences for downstream analyses. Despite this, few studies have interrogated the many methods for assembling phylogenomic UCE data for their comparative efficacy, or for how outputs may be impacted. We study this by comparing the most commonly used assembly methods for UCEs in the under-studied bee lineage Nomiinae and a representative sampling of relatives. Data for 63 UCE-only and 75 mixed taxa were assembled with five methods, including ABySS, HybPiper, SPAdes, Trinity and Velvet, and then benchmarked for their relative performance in terms of locus capture parameters and phylogenetic reconstruction. Unexpectedly, Trinity and Velvet trailed the other methods in terms of locus capture and DNA matrix density, whereas SPAdes performed favourably in most assessed metrics. In comparison with SPAdes, the guided-assembly approach HybPiper generally recovered the highest quality loci but in lower numbers. Based on our results, we formally move Clavinomia to Dieunomiini and render Epinomia once more a subgenus of Dieunomia. We strongly advise that future studies more closely examine the influence of assembly approach on their results, or, minimally, use better-performing assembly methods such as SPAdes or HybPiper. In this way, we can move forward with phylogenomic studies in a more standardized, comparable manner.
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Affiliation(s)
- Silas Bossert
- Department of Entomology, Washington State University, Pullman, Washington, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Alain Pauly
- Royal Belgian Institute of Natural Sciences, O.D. Taxonomy and Phylogeny, Brussels, Belgium
| | - Bryan N Danforth
- Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Michael C Orr
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Elizabeth A Murray
- Department of Entomology, Washington State University, Pullman, Washington, USA
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154
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Payne M, Williamson S, Wang Q, Zhang X, Sintchenko V, Pavic A, Lan R. Emergence of Poultry-Associated Human Salmonella enterica Serovar Abortusovis Infections, New South Wales, Australia. Emerg Infect Dis 2024; 30:691-700. [PMID: 38526124 PMCID: PMC10977856 DOI: 10.3201/eid3004.230958] [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] [Indexed: 03/26/2024] Open
Abstract
Salmonella enterica serovar Abortusovis is a ovine-adapted pathogen that causes spontaneous abortion. Salmonella Abortusovis was reported in poultry in 2009 and has since been reported in human infections in New South Wales, Australia. Phylogenomic analysis revealed a clade of 51 closely related isolates from Australia originating in 2004. That clade was genetically distinct from ovine-associated isolates. The clade was widespread in New South Wales poultry production facilities but was only responsible for sporadic human infections. Some known virulence factors associated with human infections were only found in the poultry-associated clade, some of which were acquired through prophages and plasmids. Furthermore, the ovine-associated clade showed signs of genome decay, but the poultry-associated clade did not. Those genomic changes most likely led to differences in host range and disease type. Surveillance using the newly identified genetic markers will be vital for tracking Salmonella Abortusovis transmission in animals and to humans and preventing future outbreaks.
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155
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Gonzalez G, Carr M, Kelleher TM, O'Byrne E, Banka W, Keogan B, Bennett C, Franzoni G, Keane P, Kenna C, Meredith LW, Fletcher N, Urtasun-Elizari JM, Dean J, Browne C, Lyons F, Crowley B, Igoe D, Robinson E, Martin G, Connell J, De Gascun CF, Hare D. Multiple introductions of monkeypox virus to Ireland during the international mpox outbreak, May 2022 to October 2023. Euro Surveill 2024; 29:2300505. [PMID: 38639093 PMCID: PMC11027473 DOI: 10.2807/1560-7917.es.2024.29.16.2300505] [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: 09/18/2023] [Accepted: 02/05/2024] [Indexed: 04/20/2024] Open
Abstract
BackgroundMpox, caused by monkeypox virus (MPXV), was considered a rare zoonotic disease before May 2022, when a global epidemic of cases in non-endemic countries led to the declaration of a Public Health Emergency of International Concern. Cases of mpox in Ireland, a country without previous mpox reports, could reflect extended local transmission or multiple epidemiological introductions.AimTo elucidate the origins and molecular characteristics of MPXV circulating in Ireland between May 2022 and October 2023.MethodsWhole genome sequencing of MPXV from 75% of all Irish mpox cases (182/242) was performed and compared to sequences retrieved from public databases (n = 3,362). Bayesian approaches were used to infer divergence time between sequences from different subclades and evaluate putative importation events from other countries.ResultsOf 242 detected mpox cases, 99% were males (median age: 35 years; range: 15-60). All 182 analysed genomes were assigned to Clade IIb and, presence of 12 distinguishable subclades suggests multiple introductions into Ireland. Estimation of time to divergence of subclades further supports the hypothesis for multiple importation events from numerous countries, indicative of extended and sustained international spread of mpox. Further analysis of sequences revealed that 92% of nucleotide mutations were from cytosine to thymine (or from guanine to adenine), leading to a high number of non-synonymous mutations across subclades; mutations associated with tecovirimat resistance were not observed.ConclusionWe provide insights into the international transmission dynamics supporting multiple introductions of MPXV into Ireland. Such information supported the implementation of evidence-informed public health control measures.
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Affiliation(s)
- Gabriel Gonzalez
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Japan Initiative for World-leading Vaccine Research and Development Centers, Hokkaido University, Institute for Vaccine Research and Development, Sapporo, Japan
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Michael Carr
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Tomás M Kelleher
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Emer O'Byrne
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Weronika Banka
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Brian Keogan
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Charlene Bennett
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Geraldine Franzoni
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Patrice Keane
- Department of Virology, St. James's Hospital, Dublin, Ireland
| | - Cliona Kenna
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Luke W Meredith
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Nicola Fletcher
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
- Veterinary Sciences Centre, University College Dublin, Dublin, Ireland
| | | | - Jonathan Dean
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Ciaran Browne
- National MPOX Crisis Management Lead, Acute Operations, Health Service Executive, Dublin, Ireland
| | - Fiona Lyons
- Sexual Health and Crisis Pregnancy Programme, Health and Wellbeing, Strategy and Research, Healthcare Strategy, Health Service Executive, Dublin, Ireland
| | - Brendan Crowley
- Department of Virology, St. James's Hospital, Dublin, Ireland
| | - Derval Igoe
- Health Service Executive Public Health: National Health Protection, Ireland
| | - Eve Robinson
- Health Protection Surveillance Centre, Dublin, Ireland
| | - Greg Martin
- Health Protection Surveillance Centre, Dublin, Ireland
| | - Jeff Connell
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Cillian F De Gascun
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Daniel Hare
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
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156
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Wilinski M, Castro L, Keithley J, Manore C, Campos J, Romero-Severson E, Domman D, Lokhov AY. Congruity of genomic and epidemiological data in modelling of local cholera outbreaks. Proc Biol Sci 2024; 291:20232805. [PMID: 38503333 PMCID: PMC10950457 DOI: 10.1098/rspb.2023.2805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
Cholera continues to be a global health threat. Understanding how cholera spreads between locations is fundamental to the rational, evidence-based design of intervention and control efforts. Traditionally, cholera transmission models have used cholera case-count data. More recently, whole-genome sequence data have qualitatively described cholera transmission. Integrating these data streams may provide much more accurate models of cholera spread; however, no systematic analyses have been performed so far to compare traditional case-count models to the phylodynamic models from genomic data for cholera transmission. Here, we use high-fidelity case-count and whole-genome sequencing data from the 1991 to 1998 cholera epidemic in Argentina to directly compare the epidemiological model parameters estimated from these two data sources. We find that phylodynamic methods applied to cholera genomics data provide comparable estimates that are in line with established methods. Our methodology represents a critical step in building a framework for integrating case-count and genomic data sources for cholera epidemiology and other bacterial pathogens.
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Affiliation(s)
- Mateusz Wilinski
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Lauren Castro
- Analytics, Intelligence and Technology Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Jeffrey Keithley
- Analytics, Intelligence and Technology Division, Los Alamos National Laboratory, Los Alamos, NM, USA
- Department of Computer Science, University of Iowa, Iowa City, IA, USA
| | - Carrie Manore
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Josefina Campos
- UO Centro Nacional de Genómica y Bioinformtica, ANLIS ‘Dr. Carlos G. Malbrán, Buenos Aires, Argentina
| | | | - Daryl Domman
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Andrey Y. Lokhov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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157
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Ngoepe CE, Shumba W, Sabeta C. Evidence for a host switching in the maintenance of canid rabies variant in two wild carnivore species in the Northern Cape Province, South Africa. J S Afr Vet Assoc 2024; 95:16-25. [PMID: 38533811 DOI: 10.36303/jsava.527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
Rabies is a zoonotic infectious disease that causes at least 59 000 human deaths worldwide annually, with 95% of the cases occurring in the developing countries of Asia and Africa. There are two Lyssavirus rabies (RABV) variants circulating in South Africa, notably the canid and mongoose RABV biotypes. The canid RABV biotype is maintained in the domestic dog and two wild carnivore species, the black-backed jackal (Canis mesomelas) and the bat-eared fox (Otocyon megalotis). The yellow mongoose, a member of the Herpestidae family, is a reservoir and vector species for the mongoose RABV biotype. Rabies trends showed an increase in rabiespositive cases in aardwolves between 2011 and 2016 surpassing the bat-eared fox as the most rabies-affected wild carnivore in the Northern Cape Province of South Africa. The aim of the study was to establish the genetic relationships amongst rabies viruses recovered from both the aardwolves and bat-eared foxes. A partial region of the glycoprotein gene and the variable G-L intergenic region of the viral genome were analysed using nucleotide sequences generated from PCR amplicons. The rabies viruses recovered from the aardwolves between the year 2015 and 2017 were 100% nucleotide sequence identical, suggesting a single or common source and possible evidence for a host shift. Furthermore, the phylogenetic reconstruction demonstrated that the rabies viruses obtained from the two wild carnivore species from the Northern Cape Province clustered independently of each o ther with 96% nucleotide sequence identity, suggesting that the aardwolf may be able to maintain the canid RABV variant in this geographical area.
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Affiliation(s)
- C E Ngoepe
- WOAH Rabies Reference Laboratory, Agricultural Research Council, Onderstepoort Veterinary Research, South Africa
| | - W Shumba
- Epidemiology and Laboratory Services, Northern Cape Department of Agriculture, Environmental Affairs, Rural Development and Land Reform, South Africa
| | - C Sabeta
- WOAH Rabies Reference Laboratory, Agricultural Research Council, Onderstepoort Veterinary Research, South Africa
- Department of Veterinary Tropical Diseases, University of Pretoria, South Africa
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158
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Białkowski J, Rossa R, Ziemiakowicz A, Gohli J, Dymek J, Goczał J. Evolution, types, and distribution of flight control devices on wings and elytra in bark beetles. Sci Rep 2024; 14:6999. [PMID: 38523182 PMCID: PMC10961309 DOI: 10.1038/s41598-024-57658-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/20/2024] [Indexed: 03/26/2024] Open
Abstract
Gaining the ability to fly actively was a ground-breaking moment in insect evolution, providing an unprecedented advantage over other arthropods. Nevertheless, active flight was a costly innovation, requiring the development of wings and flight muscles, the provision of sufficient energetic resources, and a complex flight control system. Although wings, flight muscles, and the energetic budget of insects have been intensively studied in the last decades, almost nothing is known regarding the flight-control devices of many crucial insect groups, especially beetles (Coleoptera). Here, we conducted a phylogenetic-informed analysis of flight-related mechanosensors in 28 species of bark beetles (Curculionidae: Scolytinae, Platypodinae), an economically and ecologically important group of insects characterized by striking differences in dispersal abilities. The results indicated that beetle flight apparatus is equipped with different functional types of mechanosensors, including strain- and flow-encoding sensilla. We found a strong effect of allometry on the number of mechanosensors, while no effect of relative wing size (a proxy of flight investment) was identified. Our study constitutes the first step to understanding the drivers and constraints of the evolution of flight-control devices in Coleoptera, including bark beetles. More research, including a quantitative neuroanatomical analysis of beetle wings, should be conducted in the future.
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Affiliation(s)
- Jakub Białkowski
- Department of Forest Ecosystems Protection, University of Agriculture in Krakow, 29 Listopada 54, 31-425, Kraków, Poland
| | - Robert Rossa
- Department of Forest Ecosystems Protection, University of Agriculture in Krakow, 29 Listopada 54, 31-425, Kraków, Poland
| | - Anna Ziemiakowicz
- Department of Forest Ecosystems Protection, University of Agriculture in Krakow, 29 Listopada 54, 31-425, Kraków, Poland
| | - Jostein Gohli
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Jakub Dymek
- Department of Biology and Cell Imaging, Faculty of Biology, Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland
| | - Jakub Goczał
- Department of Forest Ecosystems Protection, University of Agriculture in Krakow, 29 Listopada 54, 31-425, Kraków, Poland.
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159
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Nong Y, Steinig E, Pollock GL, Taiaroa G, Carter GP, Monk IR, Pang S, Daley DA, Coombs GW, Forde BM, Harris PNA, Sherry NL, Howden BP, Pasricha S, Baines SL, Williamson DA. Emergence and clonal expansion of a qacA-harbouring sequence type 45 lineage of methicillin-resistant Staphylococcus aureus. Commun Biol 2024; 7:349. [PMID: 38514781 PMCID: PMC10957945 DOI: 10.1038/s42003-024-06012-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
The past decade has seen an increase in the prevalence of sequence type (ST) 45 methicillin-resistant Staphylococcus aureus (MRSA), yet the underlying drivers for its emergence and spread remain unclear. To better understand the worldwide dissemination of ST45 S. aureus, we performed phylogenetic analyses of Australian isolates, supplemented with a global population of ST45 S. aureus genomes. Our analyses revealed a distinct lineage of multidrug-resistant ST45 MRSA harbouring qacA, predominantly found in Australia and Singapore. Bayesian inference predicted that the acquisition of qacA occurred in the late 1990s. qacA was integrated into a structurally variable region of the chromosome containing Tn552 (carrying blaZ) and Tn4001 (carrying aac(6')-aph(2")) transposable elements. Using mutagenesis and in vitro assays, we provide phenotypic evidence that qacA confers tolerance to chlorhexidine. These findings collectively suggest both antimicrobial resistance and the carriage of qacA may play a role in the successful establishment of ST45 MRSA.
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Affiliation(s)
- Yi Nong
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Eike Steinig
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Georgina L Pollock
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - George Taiaroa
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Glen P Carter
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Doherty Applied Microbial Genomics, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Ian R Monk
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Stanley Pang
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Denise A Daley
- Australian Group on Antimicrobial Resistance, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Brian M Forde
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
| | - Patrick N A Harris
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Norelle L Sherry
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Shivani Pasricha
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
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160
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Zhao W, Gao J, Hall D, Andersson BA, Bruxaux J, Tomlinson KW, Drouzas AD, Suyama Y, Wang XR. Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow. THE NEW PHYTOLOGIST 2024. [PMID: 38515228 DOI: 10.1111/nph.19694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers withc . $$ c. $$ 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.
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Affiliation(s)
- Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - David Hall
- Forestry Research Institute of Sweden (Skogforsk), Sävar, SE-91833, Sweden
| | - Bea Angelica Andersson
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Jade Bruxaux
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Kyle W Tomlinson
- Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephant, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Andreas D Drouzas
- Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, Miyagi, 989-6711, Japan
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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161
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Paredes MI, Ahmed N, Figgins M, Colizza V, Lemey P, McCrone JT, Müller N, Tran-Kiem C, Bedford T. Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic. Cell 2024; 187:1374-1386.e13. [PMID: 38428425 PMCID: PMC10962340 DOI: 10.1016/j.cell.2024.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/15/2023] [Accepted: 02/02/2024] [Indexed: 03/03/2024]
Abstract
The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and phylodynamic models to analyze MPXV genomes from five global regions together with air traffic and epidemiological data. Our models reveal community transmission prior to detection, changes in case reporting throughout the epidemic, and a large degree of transmission heterogeneity. We find that viral introductions played a limited role in prolonging spread after initial dissemination, suggesting that travel bans would have had only a minor impact. We find that mpox transmission in North America began declining before more than 10% of high-risk individuals in the USA had vaccine-induced immunity. Our findings highlight the importance of broader routine specimen screening surveillance for emerging infectious diseases and of joint integration of genomic and epidemiological information for early outbreak control.
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Affiliation(s)
- Miguel I Paredes
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Nashwa Ahmed
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Marlin Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, Paris, France
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - John T McCrone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Nicola Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Cécile Tran-Kiem
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Trevor Bedford
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA
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162
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Müller NF, Bouckaert RR, Wu CH, Bedford T. MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583734. [PMID: 38496513 PMCID: PMC10942421 DOI: 10.1101/2024.03.06.583734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The spread of infectious diseases is shaped by spatial and temporal aspects, such as host population structure or changes in the transmission rate or number of infected individuals over time. These spatiotemporal dynamics are imprinted in the genome of pathogens and can be recovered from those genomes using phylodynamics methods. However, phylodynamic methods typically quantify either the temporal or spatial transmission dynamics, which leads to unclear biases, as one can potentially not be inferred without the other. Here, we address this challenge by introducing a structured coalescent skyline approach, MASCOT-Skyline that allows us to jointly infer spatial and temporal transmission dynamics of infectious diseases using Markov chain Monte Carlo inference. To do so, we model the effective population size dynamics in different locations using a non-parametric function, allowing us to approximate a range of population size dynamics. We show, using a range of different viral outbreak datasets, potential issues with phylogeographic methods. We then use these viral datasets to motivate simulations of outbreaks that illuminate the nature of biases present in the different phylogeographic methods. We show that spatial and temporal dynamics should be modeled jointly even if one seeks to recover just one of the two. Further, we showcase conditions under which we can expect phylogeographic analyses to be biased, particularly different subsampling approaches, as well as provide recommendations of when we can expect them to perform well. We implemented MASCOT-Skyline as part of the open-source software package MASCOT for the Bayesian phylodynamics platform BEAST2.
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Affiliation(s)
- Nicola F. Müller
- Division of HIV, ID and Global Medicine, University of California San Francisco, San Francisco, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Remco R. Bouckaert
- Centre for Computational Evolution, The University of Auckland, New Zealand
| | - Chieh-Hsi Wu
- School of Mathematical Sciences, University of Southampton, UK
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
- Howard Hughes Medical Institute, Seattle, USA
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163
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Guitart X, Porubsky D, Yoo D, Dougherty ML, Dishuck PC, Munson KM, Lewis AP, Hoekzema K, Knuth J, Chang S, Pastinen T, Eichler EE. Independent expansion, selection and hypervariability of the TBC1D3 gene family in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584650. [PMID: 38654825 PMCID: PMC11037872 DOI: 10.1101/2024.03.12.584650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
TBC1D3 is a primate-specific gene family that has expanded in the human lineage and has been implicated in neuronal progenitor proliferation and expansion of the frontal cortex. The gene family and its expression have been challenging to investigate because it is embedded in high-identity and highly variable segmental duplications. We sequenced and assembled the gene family using long-read sequencing data from 34 humans and 11 nonhuman primate species. Our analysis shows that this particular gene family has independently duplicated in at least five primate lineages, and the duplicated loci are enriched at sites of large-scale chromosomal rearrangements on chromosome 17. We find that most humans vary along two TBC1D3 clusters where human haplotypes are highly variable in copy number, differing by as many as 20 copies, and structure (structural heterozygosity 90%). We also show evidence of positive selection, as well as a significant change in the predicted human TBC1D3 protein sequence. Lastly, we find that, despite multiple duplications, human TBC1D3 expression is limited to a subset of copies and, most notably, from a single paralog group: TBC1D3-CDKL. These observations may help explain why a gene potentially important in cortical development can be so variable in the human population.
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Affiliation(s)
- Xavi Guitart
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Max L. Dougherty
- Tisch Cancer Institute, Division of Hematology and Medical Oncology, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Philip C. Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M. Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P. Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jordan Knuth
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Stephen Chang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
| | - Tomi Pastinen
- Department of Pediatrics, Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO, USA
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical institute, University of Washington, Seattle, WA, USA
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164
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Huanel OR, Montecinos AE, Sepúlveda-Espinoza F, Guillemin ML. Impact of persistent barrier to gene flow and catastrophic events on red algae evolutionary history along the Chilean coast. Front Genet 2024; 15:1336427. [PMID: 38525243 PMCID: PMC10957783 DOI: 10.3389/fgene.2024.1336427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/23/2024] [Indexed: 03/26/2024] Open
Abstract
Historical vicariance events, linked to the existence of stable physical barriers to gene flow, generate concordant genetic breaks in co-distributed species while stochastic processes (e.g., costal uplift) could cause species-specific genetic breaks as a result of local strong demographic bottlenecks or extinction. In Chile, previous studies show that the area of the 30°S-33°S could correspond to a stable barrier to gene flow that have affected the genetic structure of various algae and marine invertebrates. Here we sequenced two organellar genes (COI and rbcL) in four taxonomically accepted co-distributed red seaweeds species characterized by a low dispersal potential: Mazzaella laminarioides, M. membranacea, Asterfilopsis disciplinalis, and Ahnfeltiopsis vermicularis. Our results revealed the existence of ten strongly differentiated linages in the taxa studied. Strong genetic breaks, concordant in both space and time (divergence estimated to have occurred some 2.9-12.4 million years ago), were observed between taxa distributed across the 33°S. Conversely, in the Central/South part of the Chilean coast, the localization of the genetic breaks/sub-structure observed varied widely (36°S, 38°S, 39°S, and 40°S). These results suggest that a major historical vicariance event has modeled the genetic structure of several Chilean marine organisms in the north of the Chilean coast during the mid-Miocene, while more recent stochastic events and genetic drift could be the driving forces of genetic divergence/structuration in the central-southern part of the coast.
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Affiliation(s)
- Oscar R. Huanel
- Núcleo Milenio MASH, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- IRL 3614 Evolutionary Biology and Ecology of Algae, Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique, Roscoff, France
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Santiago, Chile
| | - Alejandro E. Montecinos
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Francisco Sepúlveda-Espinoza
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Marie-Laure Guillemin
- IRL 3614 Evolutionary Biology and Ecology of Algae, Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique, Roscoff, France
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Núcleo Milenio MASH, Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Centro FONDAP de Investigación de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
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165
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Zhang C, Liu H, Huang X, Yuan Z, Zhang S, Xu S, Liu J, Wang Y, Wang D, Hu J. Comparative Analysis of the Systematics and Evolution of the Pampus Genus of Fish (Perciformes: Stromateidae) Based on Osteology, Population Genetics and Complete Mitogenomes. Animals (Basel) 2024; 14:814. [PMID: 38473197 DOI: 10.3390/ani14050814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/20/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Pampus is a widespread species of fish in the western Pacific and Indian Oceans that has significant commercial worth. Its evolutionary history and phylogenetics are still poorly understood, and details on its intraspecific taxonomy are debatable, despite some morphological and molecular research. Here, we analyzed this species using skeletal structure data as well as nuclear (S7 gene) and mitochondrial genetic information (COI, D-loop and mitogenomes). We found that the genetic distance between P. argenteus and P. echinogaster was much smaller than that between other Pampus species, and both maximum likelihood and Bayesian phylogenetic trees yielded almost identical tree topologies. An additional and adjacent M repeat was found in the downstream region of the IQM gene cluster of P. argenteus and P. echinogaster, and the trnL2 gene of P. minor was translocated. The genus Pampus experienced early rapid radiation during the Palaeocene with major lineages diversifying within a relatively narrow timescale. Additionally, three different methods were conducted to distinguish the genus Pampus species, proving that P. argenteus and P. echinogaster are the same species, and P. liuorum is speculated to be a valid species. Overall, our study provides new insights not only into the evolutionary history of Pampus but its intraspecific taxonomy as well.
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Affiliation(s)
- Cheng Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Hanjing Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiang Huang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Zi Yuan
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Shun Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Shanliang Xu
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Jing Liu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, and The Key Laboratory of Experimental Marine Biology, Centre for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yajun Wang
- School of Marine Science, Ningbo University, Ningbo 315211, China
- Key Laboratory of Applied Marine Biotechnology (Ningbo University), Ministry of Education, Ningbo 315211, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo 315211, China
| | - Danli Wang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Jiabao Hu
- School of Marine Science, Ningbo University, Ningbo 315211, China
- Key Laboratory of Applied Marine Biotechnology (Ningbo University), Ministry of Education, Ningbo 315211, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo 315211, China
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166
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Karimi N, Krieg CP, Spalink D, Lemmon AR, Lemmon EM, Eifler E, Hernández AI, Chan PW, Rodríguez A, Landis JB, Strickler SR, Specht CD, Givnish TJ. Chromosomal evolution, environmental heterogeneity, and migration drive spatial patterns of species richness in Calochortus (Liliaceae). Proc Natl Acad Sci U S A 2024; 121:e2305228121. [PMID: 38394215 DOI: 10.1073/pnas.2305228121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 12/20/2023] [Indexed: 02/25/2024] Open
Abstract
We used nuclear genomic data and statistical models to evaluate the ecological and evolutionary processes shaping spatial variation in species richness in Calochortus (Liliaceae, 74 spp.). Calochortus occupies diverse habitats in the western United States and Mexico and has a center of diversity in the California Floristic Province, marked by multiple orogenies, winter rainfall, and highly divergent climates and substrates (including serpentine). We used sequences of 294 low-copy nuclear loci to produce a time-calibrated phylogeny, estimate historical biogeography, and test hypotheses regarding drivers of present-day spatial patterns in species number. Speciation and species coexistence require reproductive isolation and ecological divergence, so we examined the roles of chromosome number, environmental heterogeneity, and migration in shaping local species richness. Six major clades-inhabiting different geographic/climatic areas, and often marked by different base chromosome numbers (n = 6 to 10)-began diverging from each other ~10.3 Mya. As predicted, local species number increased significantly with local heterogeneity in chromosome number, elevation, soil characteristics, and serpentine presence. Species richness is greatest in the Transverse/Peninsular Ranges where clades with different chromosome numbers overlap, topographic complexity provides diverse conditions over short distances, and several physiographic provinces meet allowing immigration by several clades. Recently diverged sister-species pairs generally have peri-patric distributions, and maximum geographic overlap between species increases over the first million years since divergence, suggesting that chromosomal evolution, genetic divergence leading to gametic isolation or hybrid inviability/sterility, and/or ecological divergence over small spatial scales may permit species co-occurrence.
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Affiliation(s)
- Nisa Karimi
- Science and Conservation Division, Missouri Botanical Garden, St. Louis, MO 63110
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706
| | | | - Daniel Spalink
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX 77845
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306
| | | | - Evan Eifler
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706
| | - Adriana I Hernández
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- L. H. Bailey Hortorium, Cornell University, Ithaca, NY 14853
| | - Patricia W Chan
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706
| | - Aarón Rodríguez
- Departamento de Botánica y Zoología, Universidad de la Guadalajara, Zapopan, Jalisco 45200, Mexico
| | - Jacob B Landis
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- Departamento de Botánica y Zoología, Universidad de la Guadalajara, Zapopan, Jalisco 45200, Mexico
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853
| | | | - Chelsea D Specht
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- L. H. Bailey Hortorium, Cornell University, Ithaca, NY 14853
| | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706
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167
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Sciandra C, Amoriello S, Degli EI, Nicotera V, Barbieri F, Mazza G, Torrini G, Roversi PF, Strangi A. First report of Rhabditis ( Rhabditella) axei with the invasive palm borer Paysandisia archon. J Nematol 2024; 56:20240005. [PMID: 38495930 PMCID: PMC10940275 DOI: 10.2478/jofnem-2024-0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Indexed: 03/19/2024] Open
Abstract
Rhabditis (Rhabditella) axei is a free-living, pseudoparasitic, necromenic, and parasitic nematode, depending on the host. This species feeds mainly on bacteria present in decaying organic matter, soil, and other substrates; however, in its parasitic form, it can colonize some species of snails. Moreover, the presence of R. axei has also been detected in birds and mammals, including humans. In 2021-2023, during monitoring of the palm borer Paysandisia archon in Central Italy, R. axei emerged from dead larvae of this alien invasive moth and was extracted from palm fibres of Trachycarpus fortunei in three independent sites. The nematode was identified by morphological and morphometric analyses. Molecular analyses using SSU and LSU gene fragments were used to confirm the identification and to perform Bayesian reconstruction of the phylogeny. Each sampling site showed a unique haplotype. Concerning the pathogenicity of this nematode against insects, the test performed on Galleria mellonella larvae did not show any entomopathogenic effect. This is the first time that R. axei was found associated with P. archon, and this recurrent association was discussed.
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Affiliation(s)
- Chiara Sciandra
- Consiglio per la Ricerca in agricoltura e l'analisi dell'economia agraria – Centro di Ricerca Difesa e Certificazione, Firenze, Italy
- Università degli Studi di Siena, Dipartimento di Scienze della Vita, Siena, Italy
| | - Sara Amoriello
- Consiglio per la Ricerca in agricoltura e l'analisi dell'economia agraria – Centro di Ricerca Difesa e Certificazione, Firenze, Italy
| | - Emilia Innocenti Degli
- Consiglio per la Ricerca in agricoltura e l'analisi dell'economia agraria – Centro di Ricerca Difesa e Certificazione, Firenze, Italy
| | - Valentina Nicotera
- Consiglio per la Ricerca in agricoltura e l'analisi dell'economia agraria – Centro di Ricerca Difesa e Certificazione, Firenze, Italy
| | - Francesco Barbieri
- Consiglio per la Ricerca in agricoltura e l'analisi dell'economia agraria – Centro di Ricerca Difesa e Certificazione, Firenze, Italy
| | - Giuseppe Mazza
- Consiglio per la Ricerca in agricoltura e l'analisi dell'economia agraria – Centro di Ricerca Difesa e Certificazione, Firenze, Italy
- National Biodiversity Future Center, Palermo90133, Italy
| | - Giulia Torrini
- Consiglio per la Ricerca in agricoltura e l'analisi dell'economia agraria – Centro di Ricerca Difesa e Certificazione, Firenze, Italy
| | - Pio Federico Roversi
- Consiglio per la Ricerca in agricoltura e l'analisi dell'economia agraria – Centro di Ricerca Difesa e Certificazione, Firenze, Italy
| | - Agostino Strangi
- Consiglio per la Ricerca in agricoltura e l'analisi dell'economia agraria – Centro di Ricerca Difesa e Certificazione, Firenze, Italy
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168
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Dufresnes C, Monod-Broca B, Bellati A, Canestrelli D, Ambu J, Wielstra B, Dubey S, Crochet PA, Denoël M, Jablonski D. Piecing the barcoding puzzle of Palearctic water frogs (Pelophylax) sheds light on amphibian biogeography and global invasions. GLOBAL CHANGE BIOLOGY 2024; 30:e17180. [PMID: 38465701 DOI: 10.1111/gcb.17180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 03/12/2024]
Abstract
Palearctic water frogs (genus Pelophylax) are an outstanding model in ecology and evolution, being widespread, speciose, either threatened or threatening to other species through biological invasions, and capable of siring hybrid offspring that escape the rules of sexual reproduction. Despite half a century of genetic research and hundreds of publications, the diversity, systematics and biogeography of Pelophylax still remain highly confusing, in no small part due to a lack of correspondence between studies. To provide a comprehensive overview, we gathered >13,000 sequences of barcoding genes from >1700 native and introduced localities and built multigene mitochondrial (~17 kb) and nuclear (~10 kb) phylogenies. We mapped all currently recognized taxa and their phylogeographic lineages (>40) to get a grasp on taxonomic issues, cyto-nuclear discordances, the genetic makeup of hybridogenetic hybrids, and the origins of introduced populations. Competing hypotheses for the molecular calibration were evaluated through plausibility tests, implementing a new approach relying on predictions from the anuran speciation continuum. Based on our timetree, we propose a new biogeographic paradigm for the Palearctic since the Paleogene, notably by attributing a prominent role to the dynamics of the Paratethys, a vast paleo-sea that extended over most of Europe. Furthermore, our results show that distinct marsh frog lineages from Eastern Europe, the Balkans, the Near East, and Central Asia (P. ridibundus ssp.) are naturally capable of inducing hybridogenesis with pool frogs (P. lessonae). We identified 14 alien lineages (mostly of P. ridibundus) over ~20 areas of invasions, especially in Western Europe, with genetic signatures disproportionally pointing to the Balkans and Anatolia as the regions of origins, in line with exporting records of the frog leg industry and the stocks of pet sellers. Pelophylax thus emerges as one of the most invasive amphibians worldwide, and deserves much higher conservation concern than currently given by the authorities fighting biological invasions.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory of Amphibian Systematics and Evolutionary Research (LASER), College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Benjamin Monod-Broca
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Adriana Bellati
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Daniele Canestrelli
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Johanna Ambu
- Laboratory of Amphibian Systematics and Evolutionary Research (LASER), College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Ben Wielstra
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Sylvain Dubey
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Mathieu Denoël
- Laboratory of Ecology and Conservation of Amphibians (LECA), FOCUS, University of Liège, Liège, Belgium
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
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169
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Majander K, Pla-Díaz M, du Plessis L, Arora N, Filippini J, Pezo-Lanfranco L, Eggers S, González-Candelas F, Schuenemann VJ. Redefining the treponemal history through pre-Columbian genomes from Brazil. Nature 2024; 627:182-188. [PMID: 38267579 PMCID: PMC10917687 DOI: 10.1038/s41586-023-06965-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024]
Abstract
The origins of treponemal diseases have long remained unknown, especially considering the sudden onset of the first syphilis epidemic in the late 15th century in Europe and its hypothesized arrival from the Americas with Columbus' expeditions1,2. Recently, ancient DNA evidence has revealed various treponemal infections circulating in early modern Europe and colonial-era Mexico3-6. However, there has been to our knowledge no genomic evidence of treponematosis recovered from either the Americas or the Old World that can be reliably dated to the time before the first trans-Atlantic contacts. Here, we present treponemal genomes from nearly 2,000-year-old human remains from Brazil. We reconstruct four ancient genomes of a prehistoric treponemal pathogen, most closely related to the bejel-causing agent Treponema pallidum endemicum. Contradicting the modern day geographical niche of bejel in the arid regions of the world, the results call into question the previous palaeopathological characterization of treponeme subspecies and showcase their adaptive potential. A high-coverage genome is used to improve molecular clock date estimations, placing the divergence of modern T. pallidum subspecies firmly in pre-Columbian times. Overall, our study demonstrates the opportunities within archaeogenetics to uncover key events in pathogen evolution and emergence, paving the way to new hypotheses on the origin and spread of treponematoses.
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Affiliation(s)
- Kerttu Majander
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| | - Marta Pla-Díaz
- Unidad Mixta Infección y Salud Pública, FISABIO/Universidad de Valencia-I2SysBio, Valencia, Spain
- CIBER in Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, Spain
| | - Louis du Plessis
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, Switzerland
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Jose Filippini
- Department of Genetic and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Luis Pezo-Lanfranco
- Department of Genetic and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
- Institute of Environmental Science and Technology (ICTA) and Prehistory Department, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sabine Eggers
- Department of Genetic and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública, FISABIO/Universidad de Valencia-I2SysBio, Valencia, Spain.
- CIBER in Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, Spain.
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
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170
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Pianezza R, Scarpa A, Narayanan P, Signor S, Kofler R. Spoink, a LTR retrotransposon, invaded D. melanogaster populations in the 1990s. PLoS Genet 2024; 20:e1011201. [PMID: 38530818 DOI: 10.1371/journal.pgen.1011201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/27/2024] [Indexed: 03/28/2024] Open
Abstract
During the last few centuries D. melanogaster populations were invaded by several transposable elements, the most recent of which was thought to be the P-element between 1950 and 1980. Here we describe a novel TE, which we named Spoink, that has invaded D. melanogaster. It is a 5216nt LTR retrotransposon of the Ty3/gypsy superfamily. Relying on strains sampled at different times during the last century we show that Spoink invaded worldwide D. melanogaster populations after the P-element between 1983 and 1993. This invasion was likely triggered by a horizontal transfer from the D. willistoni group, much as the P-element. Spoink is probably silenced by the piRNA pathway in natural populations and about 1/3 of the examined strains have an insertion into a canonical piRNA cluster such as 42AB. Given the degree of genetic investigation of D. melanogaster it is perhaps surprising that Spoink was able to invade unnoticed.
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Affiliation(s)
- Riccardo Pianezza
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Almorò Scarpa
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Prakash Narayanan
- Biological Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Sarah Signor
- Biological Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
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171
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Chauhan PK, Upadhyay SK. Mixed Consortium of Salt-Tolerant Phosphate Solubilizing Bacteria Improves Maize (Zea mays) Plant Growth and Soil Health Under Saline Conditions. Mol Biotechnol 2024; 66:489-499. [PMID: 37243838 DOI: 10.1007/s12033-023-00771-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/10/2023] [Indexed: 05/29/2023]
Abstract
The rhizobacterial isolate SP-167 exhibited considerable phosphate solubilization, IAA production, exo-polysaccharides, proline, APX, and CAT at a concentration of 6% NaCl (w/v). 16S rDNA sequencing and BLAST analysis showed that isolate SP-167 was Klebsiella sp. In this study, T2 and T8 consortium was developed on the basis of the compatibility of isolate SP-167 with Kluyvera sp. and Enterobacter sp. At 6% NaCl (w/v) concentration, T2 and T8 showed increased PGP properties such as phosphate solubilization, IAA, Proline activity, CAT, POD, and EPS than isolate SP-167. The maximum increase in shoot length was recorded in T2-treated maize plants as compared to the control after 60 days in 1% NaCl stress. The N, P, and K content of leaves were significantly increased in maize plants with the inoculation of both the T2 and T8 consortium. The electrical conductivity of soil was decreased significantly in the T2 inoculated 1% NaCl (w/v) treated pot after 30, 60, and 90 days. In this study, soil enzymes DHA and PPO were significantly increased in both T2 and T8 treated combinations. The Na concentration in root and shoot were significantly decreased in T8 inoculated plant than in T2, as confirmed by the translocation factor study.
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Affiliation(s)
- Prabhat K Chauhan
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, 222003, India
| | - Sudhir K Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, 222003, India.
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172
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Sin SYW, Ke F, Chen G, Huang PY, Enbody ED, Karubian J, Webster MS, Edwards SV. Genetic Basis and Evolution of Structural Color Polymorphism in an Australian Songbird. Mol Biol Evol 2024; 41:msae046. [PMID: 38415852 PMCID: PMC10962638 DOI: 10.1093/molbev/msae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/02/2024] [Accepted: 02/22/2024] [Indexed: 02/29/2024] Open
Abstract
Island organisms often evolve phenotypes divergent from their mainland counterparts, providing a useful system for studying adaptation under differential selection. In the white-winged fairywren (Malurus leucopterus), subspecies on two islands have a black nuptial plumage whereas the subspecies on the Australian mainland has a blue nuptial plumage. The black subspecies have a feather nanostructure that could in principle produce a blue structural color, suggesting a blue ancestor. An earlier study proposed independent evolution of melanism on the islands based on the history of subspecies divergence. However, the genetic basis of melanism and the origin of color differentiation in this group are still unknown. Here, we used whole-genome resequencing to investigate the genetic basis of melanism by comparing the blue and black M. leucopterus subspecies to identify highly divergent genomic regions. We identified a well-known pigmentation gene ASIP and four candidate genes that may contribute to feather nanostructure development. Contrary to the prediction of convergent evolution of island melanism, we detected signatures of a selective sweep in genomic regions containing ASIP and SCUBE2 not in the black subspecies but in the blue subspecies, which possesses many derived SNPs in these regions, suggesting that the mainland subspecies has re-evolved a blue plumage from a black ancestor. This proposed re-evolution was likely driven by a preexisting female preference. Our findings provide new insight into the evolution of plumage coloration in island versus continental populations, and, importantly, we identify candidate genes that likely play roles in the development and evolution of feather structural coloration.
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Affiliation(s)
- Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Fushi Ke
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Guoling Chen
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Pei-Yu Huang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Erik D Enbody
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Jordan Karubian
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Michael S Webster
- Cornell Lab of Ornithology and Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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173
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Jackson I, Woodman P, Dowd M, Fibiger L, Cassidy LM. Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts. Mol Biol Evol 2024; 41:msae017. [PMID: 38533900 DOI: 10.1093/molbev/msae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 03/28/2024] Open
Abstract
Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old teeth from an Irish limestone cave. These contained bacteria implicated in periodontitis, as well as Streptococcus mutans, the major cause of caries and rare in the ancient genomic record. Despite deriving from the same individual, these teeth produced divergent Tannerella forsythia genomes, indicating higher levels of strain diversity in prehistoric populations. We find evidence of microbiome dysbiosis, with a disproportionate quantity of S. mutans sequences relative to other oral streptococci. This high abundance allowed for metagenomic assembly, resulting in its first reported ancient genome. Phylogenetic analysis indicates major postmedieval population expansions for both species, highlighting the inordinate impact of recent dietary changes. In T. forsythia, this expansion is associated with the replacement of older lineages, possibly reflecting a genome-wide selective sweep. Accordingly, we see dramatic changes in T. forsythia's virulence repertoire across this period. S. mutans shows a contrasting pattern, with deeply divergent lineages persisting in modern populations. This may be due to its highly recombining nature, allowing for maintenance of diversity through selective episodes. Nonetheless, an explosion in recent coalescences and significantly shorter branch lengths separating bacteriocin-carrying strains indicate major changes in S. mutans demography and function coinciding with sugar popularization during the industrial period.
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Affiliation(s)
- Iseult Jackson
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- The SFI Centre for Research Training in Genomics Data Science, University of Galway, Galway, Ireland
| | - Peter Woodman
- Department of Archaeology, University College Cork, Cork, Ireland
| | - Marion Dowd
- Faculty of Science, Atlantic Technological University, Sligo, Ireland
| | - Linda Fibiger
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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174
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Rayos AL, Renner MAM, Ho SYW. The Neotropical endemic liverwort subfamily Micropterygioideae had circum-Antarctic links to the rest of the Lepidoziaceae during the early Cretaceous. Ecol Evol 2024; 14:e11066. [PMID: 38435016 PMCID: PMC10909501 DOI: 10.1002/ece3.11066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024] Open
Abstract
Lepidoziaceae are the third-largest family of liverworts, with about 860 species distributed on all continents. The evolutionary history of this family has not been satisfactorily resolved, with taxa such as Micropterygioideae yet to be included in phylogenetic analyses. We inferred a dated phylogeny of Lepidoziaceae using a data set consisting of 13 genetic markers, sampled from 147 species. Based on our phylogenetic estimate, we used statistical dispersal-vicariance analysis to reconstruct the biogeographic history of the family. We inferred a crown age of 197 Ma (95% credible interval 157-240 Ma) for the family in the Australian region, with most major lineages also originating in the same region. Micropterygioideae are placed as the sister group to Lembidioideae, with these two lineages diverging from each other about 132 Ma in the South American-Australian region. With South America and Australia being connected through Antarctica at the time, our results suggest a circum-Antarctic link between Micropterygioideae and the rest of the family. Crown Micropterygioideae were inferred to have arisen 45 Ma in South America before the continent separated from Antarctica. Extinction from southern temperate regions might explain the present-day restriction of Micropterygioideae to the Neotropics. Our study reveals the influence of past geological events, such as continental drift, on the evolution and distribution of a widespread and diverse family of liverworts.
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Affiliation(s)
- Antonio L Rayos
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
- Institute of Biological Sciences University of the Philippines Los Baños Los Baños Laguna Philippines
| | - Matthew A M Renner
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
- National Herbarium of New South Wales Royal Botanic Gardens Sydney Sydney New South Wales Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
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175
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Cunha Neto IL, Rossetto EFS, Gerolamo CS, Hernández-Gutiérrez R, Sukhorukov AP, Kushunina M, Melo-de-Pinna GFA, Angyalossy V. Medullary bundles in Caryophyllales: form, function, and evolution. THE NEW PHYTOLOGIST 2024; 241:2589-2605. [PMID: 37882322 DOI: 10.1111/nph.19342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/02/2023] [Indexed: 10/27/2023]
Abstract
The occurrence of conducting vascular tissue in the pith (CVTP) of tracheophytes is noteworthy. Medullary bundles, one of the remarkable examples of CVTP, evolved multiple times across angiosperms, notably in the Caryophyllales. Yet, information on the occurrence of medullary bundles is fragmented, hampering our understanding of their structure-function relationships, and evolutionary implications. Using three plastid molecular markers (matK, rbcL, and rps16 intron), a phylogeny is constructed for 561 species of Caryophyllales, and anatomical data are assembled for 856 species across 40 families to investigate the diversity of medullary bundles, their function, evolution, and diversification dynamics. Additionally, correlated evolution between medullary bundles and successive cambia was tested. Medullary bundles are ancestrally absent in Caryophyllales and evolved in core and noncore families. They are structurally diverse (e.g. number, arrangement, and types of bundles) and functionally active throughout the plant's lifespan, providing increased hydraulic conductivity, especially in herbaceous plants. Acquisition of medullary bundles does not explain diversification rate heterogeneity but is correlated to a higher diversification rate. Disparate developmental pathways were found leading to rampant convergent evolution of CVTP in Caryophyllales. These findings indicate the diversification of medullary bundles and vascular tissues as another central theme for functional and comparative molecular studies in Caryophyllales.
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Affiliation(s)
- Israel L Cunha Neto
- Department of Environmental Studies, New York University, New York, NY, 10012, USA
- Department of Botany, Institute of Biosciences, University of São Paulo, Cidade Universitária, São Paulo, SP, 05508-090, Brazil
| | - Elson Felipe S Rossetto
- Department of Animal and Plant Biology, Center of Biological Sciences, State University of Londrina, Campus Universitário, Londrina, PR, 86057-970, Brazil
| | - Caian S Gerolamo
- Department of Botany, Institute of Biosciences, University of São Paulo, Cidade Universitária, São Paulo, SP, 05508-090, Brazil
| | - Rebeca Hernández-Gutiérrez
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Alexander P Sukhorukov
- Department of Higher Plants, Biological Faculty, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
- Laboratory Herbarium (TK), Tomsk State University, Tomsk, 634050, Russia
| | - Maria Kushunina
- Laboratory Herbarium (TK), Tomsk State University, Tomsk, 634050, Russia
- Department of Plant Physiology, Biological Faculty, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Gladys F A Melo-de-Pinna
- Department of Botany, Institute of Biosciences, University of São Paulo, Cidade Universitária, São Paulo, SP, 05508-090, Brazil
| | - Veronica Angyalossy
- Department of Botany, Institute of Biosciences, University of São Paulo, Cidade Universitária, São Paulo, SP, 05508-090, Brazil
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176
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Chang SC, Ahyong ST, Tsang LM. Molecular phylogeny of deep-sea blind lobsters of the family Polychelidae (Decapoda: Polychelida), with implications for the origin and evolution of these "living fossils". Mol Phylogenet Evol 2024; 192:107998. [PMID: 38142793 DOI: 10.1016/j.ympev.2023.107998] [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: 08/10/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023]
Abstract
A comprehensive molecular analysis of the deep-sea blind lobsters of the family Polychelidae, often referred to as "living fossils", is conducted based on all six modern genera and 27 of the 38 extant species. Using six genetic markers from both mitochondrial and nuclear genomes, the molecular phylogenetic results differ considerably from previous morphological analyses and reveal the genera Polycheles and Pentacheles to be para- or polyphyletic. As the splitting of Polycheles has strong support from both molecular and morphological data, two new genera, Dianecheles and Neopolycheles, are erected for those species excluded from the clade containing the type species of Polycheles. The pattern of polyphyly of Pentacheles, however, is not robustly resolved, so it is retained as a single genus. Fossil evidence suggests that fossil polychelids inhabited deep-sea environments as early as the Early to Middle Jurassic, demonstrating the enduring adaptation of extant polychelid species to the deep-sea. Time-calibrated phylogeny suggested that modern polychelids probably had an Atlantic origin during the Jurassic period. Since their emergence, this ancient lobster group has continued to diversify, particularly in the West Pacific, and has colonized the abyssal zone, with the deepest genus, Willemoesia, representing the more 'derived' members among extant polychelids. Differences in eye reduction among extant polychelid genera highlight the necessity for ongoing investigations to ascertain the relative degree of functionality of their eyes, if they indeed retain any function.
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Affiliation(s)
- Su-Ching Chang
- Department of Biological Resources, National Chiayi University, Chiayi 600355, Taiwan, ROC
| | - Shane T Ahyong
- Australian Museum, 1 William St, Sydney, NSW 2010, Australia; School of Biological, Earth & Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia
| | - Ling-Ming Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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177
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Shao Y, Magee AF, Vasylyeva TI, Suchard MA. Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models. PLoS Comput Biol 2024; 20:e1011640. [PMID: 38551979 PMCID: PMC11006205 DOI: 10.1371/journal.pcbi.1011640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/10/2024] [Accepted: 03/10/2024] [Indexed: 04/09/2024] Open
Abstract
Birth-death models play a key role in phylodynamic analysis for their interpretation in terms of key epidemiological parameters. In particular, models with piecewise-constant rates varying at different epochs in time, to which we refer as episodic birth-death-sampling (EBDS) models, are valuable for their reflection of changing transmission dynamics over time. A challenge, however, that persists with current time-varying model inference procedures is their lack of computational efficiency. This limitation hinders the full utilization of these models in large-scale phylodynamic analyses, especially when dealing with high-dimensional parameter vectors that exhibit strong correlations. We present here a linear-time algorithm to compute the gradient of the birth-death model sampling density with respect to all time-varying parameters, and we implement this algorithm within a gradient-based Hamiltonian Monte Carlo (HMC) sampler to alleviate the computational burden of conducting inference under a wide variety of structures of, as well as priors for, EBDS processes. We assess this approach using three different real world data examples, including the HIV epidemic in Odesa, Ukraine, seasonal influenza A/H3N2 virus dynamics in New York state, America, and Ebola outbreak in West Africa. HMC sampling exhibits a substantial efficiency boost, delivering a 10- to 200-fold increase in minimum effective sample size per unit-time, in comparison to a Metropolis-Hastings-based approach. Additionally, we show the robustness of our implementation in both allowing for flexible prior choices and in modeling the transmission dynamics of various pathogens by accurately capturing the changing trend of viral effective reproductive number.
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Affiliation(s)
- Yucai Shao
- Department of Biostatistics, University of California, Los Angeles, California, United States of America
| | - Andrew F. Magee
- Department of Biomathematics, University of California, Los Angeles, California, United States of America
| | - Tetyana I. Vasylyeva
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Department of Population Health and Disease Prevention, University of California Irvine, Irvine, California, United States of America
| | - Marc A. Suchard
- Department of Biostatistics, University of California, Los Angeles, California, United States of America
- Department of Biomathematics, University of California, Los Angeles, California, United States of America
- Department of Human Genetics, Universtiy of California, Los Angeles, California, United States of America
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178
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Mannen K, Nagata T, Rozenberg A, Konno M, Del Carmen Marín M, Bagherzadeh R, Béjà O, Uchihashi T, Inoue K. Multiple Roles of a Conserved Glutamate Residue for Unique Biophysical Properties in a New Group of Microbial Rhodopsins Homologous to TAT Rhodopsin. J Mol Biol 2024; 436:168331. [PMID: 37898385 DOI: 10.1016/j.jmb.2023.168331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/02/2023] [Accepted: 10/21/2023] [Indexed: 10/30/2023]
Abstract
TAT rhodopsin, a microbial rhodopsin found in the marine SAR11 bacterium HIMB114, uniquely possesses a Thr-Ala-Thr (TAT) motif in the third transmembrane helix. Because of a low pKa value of the retinal Schiff base (RSB), TAT rhodopsin exhibits both a visible light-absorbing state with the protonated RSB and a UV-absorbing state with the deprotonated RSB at a neutral pH. The UV-absorbing state, in contrast to the visible light-absorbing one, converts to a long-lived photointermediate upon light absorption, implying that TAT rhodopsin functions as a pH-dependent light sensor. Despite detailed biophysical characterization and mechanistic studies on the TAT rhodopsin, it has been unknown whether other proteins with similarly unusual features exist. Here, we identified several new rhodopsin genes homologous to the TAT rhodopsin of HIMB114 (TATHIMB) from metagenomic data. Based on the absorption spectra of expressed proteins from these genes with visible and UV peaks similar to that of TATHIMB, they were classified as Twin-peaked Rhodopsin (TwR) family. TwR genes form a gene cluster with a set of 13 ORFs conserved in subclade IIIa of SAR11 bacteria. A glutamic acid in the second transmembrane helix, Glu54, is conserved in all of the TwRs. We investigated E54Q mutants of two TwRs and revealed that Glu54 plays critical roles in regulating the RSB pKa, oligomer formation, and the efficient photoreaction of the UV-absorbing state. The discovery of novel TwRs enables us to study the universality and individuality of the characteristics revealed so far in the original TATHIMB and contributes to further studies on mechanisms of unique properties of TwRs.
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Affiliation(s)
- Kentaro Mannen
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Andrey Rozenberg
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - María Del Carmen Marín
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Reza Bagherzadeh
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Nagoya 464-8602, Japan; Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan; Institute for Glyco-core Research, Nagoya University, Nagoya 464-8602, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan.
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179
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Paredes MI, Perofsky AC, Frisbie L, Moncla LH, Roychoudhury P, Xie H, Bakhash SAM, Kong K, Arnould I, Nguyen TV, Wendm ST, Hajian P, Ellis S, Mathias PC, Greninger AL, Starita LM, Frazar CD, Ryke E, Zhong W, Gamboa L, Threlkeld M, Lee J, Stone J, McDermot E, Truong M, Shendure J, Oltean HN, Viboud C, Chu H, Müller NF, Bedford T. Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county. PLoS Pathog 2024; 20:e1012117. [PMID: 38530853 PMCID: PMC10997136 DOI: 10.1371/journal.ppat.1012117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 04/05/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving local health departments to design interventions with limited information. We analyzed SARS-CoV-2 genomes sampled between February 2020 and March 2022 jointly with epidemiological and cell phone mobility data to investigate fine scale spatiotemporal SARS-CoV-2 transmission dynamics in King County, Washington, a diverse, metropolitan US county. We applied an approximate structured coalescent approach to model transmission within and between North King County and South King County alongside the rate of outside introductions into the county. Our phylodynamic analyses reveal that following stay-at-home orders, the epidemic trajectories of North and South King County began to diverge. We find that South King County consistently had more reported and estimated cases, COVID-19 hospitalizations, and longer persistence of local viral transmission when compared to North King County, where viral importations from outside drove a larger proportion of new cases. Using mobility and demographic data, we also find that South King County experienced a more modest and less sustained reduction in mobility following stay-at-home orders than North King County, while also bearing more socioeconomic inequities that might contribute to a disproportionate burden of SARS-CoV-2 transmission. Overall, our findings suggest a role for local-scale phylodynamics in understanding the heterogeneous transmission landscape.
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Affiliation(s)
- Miguel I. Paredes
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Amanda C. Perofsky
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lauren Frisbie
- Washington State Department of Health, Shoreline, Washington, United States of America
| | - Louise H. Moncla
- The University of Pennsylvania, Department of Pathobiology, Philadelphia, Pennsylvania, United States of America
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Shah A. Mohamed Bakhash
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Kevin Kong
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Isabel Arnould
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Tien V. Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Seffir T. Wendm
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Pooneh Hajian
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Sean Ellis
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Patrick C. Mathias
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Alexander L. Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Chris D. Frazar
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Erica Ryke
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Weizhi Zhong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America
| | - Luis Gamboa
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America
| | - Machiko Threlkeld
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Jeremy Stone
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America
| | - Evan McDermot
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America
| | - Melissa Truong
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
| | - Hanna N. Oltean
- Washington State Department of Health, Shoreline, Washington, United States of America
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Helen Chu
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Nicola F. Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Trevor Bedford
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
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180
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Kumar L, Rajpal R, Ahlawat B, Sehrawat JS, Spalzin S, Fonia RS, Thangaraj K, Rai N. The maternal genetic origin and diversity of the extant populations of the Ladakh region in India. Mitochondrion 2024; 75:101828. [PMID: 38128747 DOI: 10.1016/j.mito.2023.101828] [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: 10/12/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Ladakh lies at a strategic location between the Indus River valley and the Hindu Khush Mountains, which makes the "Land of high passes" one of the major routes of movement. Through the years the region has faced multi-layered cultural movements, genetic assimilation and demographic changes. The initial settlement in the years goes back to the early Neolithic age and still continues despite its harsh, unhospitable and cold climate. Previous studies mostly covered the patrilineal markers of the region and an in-depth study lacked to represent the matrilineal ancestry and possible genetic inflow in the region. Hence, our current study first time generated complete mitogenomes of 108 unrelated individuals from Ladakh belonging to three population groups namely, Changpa (n = 38), Brokpa (n = 32) and Monpa (n = 38). In the in-depth analysis, we found that the mitogenome of the three Ladakhi groups are highly diverse in terms of maternal haplogroup distribution carrying lineages specific to East Asia (M9a), Tibbet (A21) and South Asia (M3, M30, U2). In our analysis we found that Changpa and Monpa probably have shared maternal ancestry compared to Brokpa, which is very distinct and also later suffered possible historical Bottleneck. Bayesian evolutionary and Network analysis indicates more ancient maternal lineage of Changpa and Monpa in terms of M9a haplotypes, but they also share some genetic history with Tibeto-Burman speakers in past. These findings conclusively indicate possible matrilineal genetic inflow in Ladakh from three directions, primarily from East Asia or South East Asia during post-glacial, West Eurasia and also from South Asia.
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Affiliation(s)
- Lomous Kumar
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India
| | - Richa Rajpal
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bhavna Ahlawat
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; Department of Anthropology, Panjab University, Chandigarh 160014, India
| | | | - Sonam Spalzin
- Archaeological Survey of India, Mini Circle Leh, UT Ladakh, 180004, India
| | - Ramnath Singh Fonia
- Archaeological Survey of India, 144/1Kalidas Road, Dehradun, Uttrakhand, 248001, India
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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181
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Gojobori J, Arakawa N, Xiaokaiti X, Matsumoto Y, Matsumura S, Hongo H, Ishiguro N, Terai Y. Japanese wolves are most closely related to dogs and share DNA with East Eurasian dogs. Nat Commun 2024; 15:1680. [PMID: 38396028 PMCID: PMC10891106 DOI: 10.1038/s41467-024-46124-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Although the domestic dog's origin is still unclear, this lineage is believed to have been domesticated from an extinct population of gray wolves, which is expected to be more closely related to dogs than to other populations of gray wolves. Here, we sequence the whole genomes of nine Japanese wolves (7.5-100x: Edo to Meiji periods) and 11 modern Japanese dogs and analyze them together with those from other populations of dogs and wolves. A phylogenomic tree shows that, among the gray wolves, Japanese wolves are closest to the dog, suggesting that the ancestor of dogs is closely related to the ancestor of the Japanese wolf. Based on phylogenetic and geographic relationships, the dog lineage has most likely originated in East Asia, where it diverged from a common ancestor with the Japanese wolf. Since East Eurasian dogs possess Japanese wolf ancestry, we estimate an introgression event from the ancestor of the Japanese wolf to the ancestor of the East Eurasian dog that occurred before the dog's arrival in the Japanese archipelago.
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Affiliation(s)
- Jun Gojobori
- SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Shonan Village, Hayama, Kanagawa, 240-0193, Japan
| | - Nami Arakawa
- SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Shonan Village, Hayama, Kanagawa, 240-0193, Japan
| | - Xiayire Xiaokaiti
- SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Shonan Village, Hayama, Kanagawa, 240-0193, Japan
| | - Yuki Matsumoto
- Research and Development Section, Anicom Specialty Medical Institute, Naka-ku, Chojamachi, Yokohama, 231-0033, Japan
| | - Shuichi Matsumura
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu, 501-1193, Japan
| | - Hitomi Hongo
- SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Shonan Village, Hayama, Kanagawa, 240-0193, Japan
| | - Naotaka Ishiguro
- SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Shonan Village, Hayama, Kanagawa, 240-0193, Japan.
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu, 501-1193, Japan.
| | - Yohey Terai
- SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Shonan Village, Hayama, Kanagawa, 240-0193, Japan.
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182
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Palombo NE, Weiss-Schneeweiss H, Carrizo García C. Evolutionary relationships, hybridization and diversification under domestication of the locoto chile ( Capsicum pubescens) and its wild relatives. FRONTIERS IN PLANT SCIENCE 2024; 15:1353991. [PMID: 38463568 PMCID: PMC10924304 DOI: 10.3389/fpls.2024.1353991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/09/2024] [Indexed: 03/12/2024]
Abstract
Patterns of genetic variation in crops are the result of multiple processes that have occurred during their domestication and improvement, and are influenced by their wild progenitors that often remain understudied. The locoto chile, Capsicum pubescens, is a crop grown mainly in mid-highlands of South-Central America. This species is not known from the wild and exists only as a cultigen. The evolutionary affinities and exact origin of C. pubescens have still not been elucidated, with hypotheses suggesting its genetic relatedness and origin to two wild putative ancestral Capsicum species from the Central Andes, C. eximium and C. cardenasii. In the current study, RAD-sequencing was applied to obtain genome-wide data for 48 individuals of C. pubescens and its wild allies representing different geographical areas. Bayesian, Maximum Likelihood and coalescent-based analytical approaches were used to reconstruct population genetic patterns and phylogenetic relationships of the studied species. The results revealed that C. pubescens forms a well-defined monotypic lineage closely related to wild C. cardenasii and C. eximium, and also to C. eshbaughii. The primary lineages associated with the diversification under domestication of C. pubescens were also identified. Although direct ancestor-descendant relationship could not be inferred within this group of taxa, hybridization events were detected between C. pubescens and both C. cardenasii and C. eximium. Therefore, although hybrid origin of C. pubescens could not be inferred, gene flow involving its wild siblings was shown to be an important factor contributing to its contemporary genetic diversity. The data allowed for the inference of the center of origin of C. pubescens in central-western Bolivia highlands and for better understanding of the dynamics of its gene pool. The results of this study are essential for germplasm conservation and breeding purposes, and provide excellent basis for further research of the locoto chile and its wild relatives.
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Affiliation(s)
- Nahuel E. Palombo
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, CONICET, Córdoba, Argentina
| | | | - Carolina Carrizo García
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, CONICET, Córdoba, Argentina
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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183
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López-Cuamatzi IL, Ortega J, Ospina-Garcés SM, Zúñiga G, MacSwiney G. MC. Molecular and morphological data suggest a new species of big-eared bat (Vespertilionidae: Corynorhinus) endemic to northeastern Mexico. PLoS One 2024; 19:e0296275. [PMID: 38381712 PMCID: PMC10881012 DOI: 10.1371/journal.pone.0296275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/05/2023] [Indexed: 02/23/2024] Open
Abstract
Corynorhinus mexicanus is an insectivorous bat endemic to Mexico that inhabits the high and humid regions of the Sierra Madre Oriental (SMO), the Trans-Mexican Volcanic Belt (TMVB), and the Sierra Madre Occidental (SMOC). A previous study suggested that C. mexicanus could be a cryptic species complex due to the genetic divergence observed between specimens from the TMVB and SMOC. The present study implemented phylogenetic, population genetics, and morphological analyses to evaluate the hypothesis that C. mexicanus is a species complex. The phylogenetic analysis indicated that C. mexicanus is a polyphyletic species composed of three indirectly related lineages. The estimated divergence times for the lineages suggest that they first originated during the Pliocene, while the second and third shared a common ancestor with C. townsendii 1.55 million years ago, and diverged 600,000 years ago during the Middle Pleistocene. The population genetics analysis reveals the SMO lineage of C. mexicanus is an isolated genetic group and highly diverged from the rest of lineages (SMOC and TMVB). The morphological analyses showed variation in the skull and mandible associated with the lineages and sex of the specimens, highlighting a difference in mandible shape between the specimens of the SMO and the rest of C. mexicanus. The results of this study suggest the presence of an undescribed species of the genus Corynorhinus.
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Affiliation(s)
| | - Jorge Ortega
- Departamento de Zoología, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City, Mexico
| | - Sandra M. Ospina-Garcés
- Centro de Investigaciones Tropicales, Universidad Veracruzana, Xalapa de Enríquez, Veracruz, Mexico
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexic
| | - Gerardo Zúñiga
- Departamento de Zoología, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City, Mexico
| | - M. Cristina MacSwiney G.
- Centro de Investigaciones Tropicales, Universidad Veracruzana, Xalapa de Enríquez, Veracruz, Mexico
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184
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Roman-Reyna V, Sharma A, Toth H, Konkel Z, Omiotek N, Murthy S, Faith S, Slot J, Peduto Hand F, Goss EM, Jacobs JM. Live tracking of a plant pathogen outbreak reveals rapid and successive, multidecade plasmid reduction. mSystems 2024; 9:e0079523. [PMID: 38275768 PMCID: PMC10878067 DOI: 10.1128/msystems.00795-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Quickly understanding the genomic changes that lead to pathogen emergence is necessary to launch mitigation efforts and reduce harm. In this study, we tracked in real time a 2022 bacterial plant disease outbreak in U.S. geraniums (Pelargonium × hortorum) caused by Xhp2022, a novel lineage of Xanthomonas hortorum. Genomes from 31 Xhp2022 isolates from seven states showed limited chromosomal variation and all contained a single plasmid (p93). Time tree and single nucleotide polymorphism whole-genome analysis estimated that Xhp2022 emerged within the last decade. The phylogenomic analysis determined that p93 resulted from the cointegration of three plasmids (p31, p45, and p66) found sporadically across isolates from previous outbreaks. Although p93 had a 49 kb nucleotide reduction, it retained putative fitness genes, which became predominant in the 2022 outbreak. Overall, we demonstrated, through rapid whole-genome sequencing and analysis, a recent, traceable event of genome reduction for niche adaptation typically observed over millennia in obligate and fastidious pathogens.IMPORTANCEThe geranium industry, valued at $4 million annually, faces an ongoing Xanthomonas hortorum pv. pelargonii (Xhp) pathogen outbreak. To track and describe the outbreak, we compared the genome structure across historical and globally distributed isolates. Our research revealed Xhp population has not had chromosome rearrangements since 1974 and has three distinct plasmids. In 2012, we found all three plasmids in individual Xhp isolates. However, in 2022, the three plasmids co-integrated into one plasmid named p93. p93 retained putative fitness genes but lost extraneous genomic material. Our findings show that the 2022 strain group of the bacterial plant pathogen Xanthomonas hortorum underwent a plasmid reduction. We also observed several Xanthomonas species from different years, hosts, and continents have similar plasmids to p93, possibly due to shared agricultural settings. We noticed parallels between genome efficiency and reduction that we see across millennia with obligate parasites with increased niche specificity.
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Affiliation(s)
- Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Anuj Sharma
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Hannah Toth
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Zachary Konkel
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Nicolle Omiotek
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Shashanka Murthy
- Applied Microbiology Services Laboratory, The Ohio State University, Columbus, Ohio, USA
| | - Seth Faith
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Applied Microbiology Services Laboratory, The Ohio State University, Columbus, Ohio, USA
| | - Jason Slot
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
| | | | - Erica M. Goss
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Jonathan M. Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
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185
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Nimmo C, Ortiz AT, Tan CCS, Pang J, Acman M, Millard J, Padayatchi N, Grant AD, O'Donnell M, Pym A, Brynildsrud OB, Eldholm V, Grandjean L, Didelot X, Balloux F, van Dorp L. Detection of a historic reservoir of bedaquiline/clofazimine resistance-associated variants in Mycobacterium tuberculosis. Genome Med 2024; 16:34. [PMID: 38374151 PMCID: PMC10877763 DOI: 10.1186/s13073-024-01289-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/19/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Drug resistance in tuberculosis (TB) poses a major ongoing challenge to public health. The recent inclusion of bedaquiline into TB drug regimens has improved treatment outcomes, but this advance is threatened by the emergence of strains of Mycobacterium tuberculosis (Mtb) resistant to bedaquiline. Clinical bedaquiline resistance is most frequently conferred by off-target resistance-associated variants (RAVs) in the mmpR5 gene (Rv0678), the regulator of an efflux pump, which can also confer cross-resistance to clofazimine, another TB drug. METHODS We compiled a dataset of 3682 Mtb genomes, including 180 carrying variants in mmpR5, and its immediate background (i.e. mmpR5 promoter and adjacent mmpL5 gene), that have been associated to borderline (henceforth intermediate) or confirmed resistance to bedaquiline. We characterised the occurrence of all nonsynonymous mutations in mmpR5 in this dataset and estimated, using time-resolved phylogenetic methods, the age of their emergence. RESULTS We identified eight cases where RAVs were present in the genomes of strains collected prior to the use of bedaquiline in TB treatment regimes. Phylogenetic reconstruction points to multiple emergence events and circulation of RAVs in mmpR5, some estimated to predate the introduction of bedaquiline. However, epistatic interactions can complicate bedaquiline drug-susceptibility prediction from genetic sequence data. Indeed, in one clade, Ile67fs (a RAV when considered in isolation) was estimated to have emerged prior to the antibiotic era, together with a resistance reverting mmpL5 mutation. CONCLUSIONS The presence of a pre-existing reservoir of Mtb strains carrying bedaquiline RAVs prior to its clinical use augments the need for rapid drug susceptibility testing and individualised regimen selection to safeguard the use of bedaquiline in TB care and control.
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Affiliation(s)
- Camus Nimmo
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
- Division of Infection and Immunity, University College London, London, UK.
- Africa Health Research Institute, Durban, South Africa.
| | - Arturo Torres Ortiz
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Department of Medicine, Imperial College, London, UK
| | - Cedric C S Tan
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - Juanita Pang
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Mislav Acman
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - James Millard
- Africa Health Research Institute, Durban, South Africa
- Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, UK
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Nesri Padayatchi
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Alison D Grant
- Africa Health Research Institute, Durban, South Africa
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK
| | - Max O'Donnell
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
- Department of Medicine & Epidemiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Alex Pym
- Africa Health Research Institute, Durban, South Africa
| | - Ola B Brynildsrud
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Vegard Eldholm
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Louis Grandjean
- Division of Infection and Immunity, University College London, London, UK
- Laboratorio de Investigacion y Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | - François Balloux
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
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186
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Douglas J, Carter CW, Wills PR. HetMM: A Michaelis-Menten model for non-homogeneous enzyme mixtures. iScience 2024; 27:108977. [PMID: 38333698 PMCID: PMC10850774 DOI: 10.1016/j.isci.2024.108977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/21/2023] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
The Michaelis-Menten model requires its reaction velocities to come from a preparation of homogeneous enzymes, with identical or near-identical catalytic activities. However, this condition is not always met. We introduce a kinetic model that relaxes this requirement, by assuming there are an unknown number of enzyme species drawn from a probability distribution whose standard deviation is estimated. Through simulation studies, we demonstrate the method accurately discriminates between homogeneous and heterogeneous data, even with moderate levels of experimental error. We applied this model to three homogeneous and three heterogeneous biological systems, showing that the standard and heterogeneous models outperform respectively. Lastly, we show that heterogeneity is not readily distinguished from negatively cooperative binding under the Hill model. These two distinct attributes-inequality in catalytic ability and interference between binding sites-yield similar Michaelis-Menten curves that are not readily resolved without further experimentation. Our user-friendly software package allows homogeneity testing and parameter estimation.
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Affiliation(s)
- Jordan Douglas
- Department of Physics, The University of Auckland, Auckland 1010, New Zealand
- Centre for Computational Evolution, The University of Auckland, Auckland 1010, New Zealand
| | - Charles W. Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Peter R. Wills
- Department of Physics, The University of Auckland, Auckland 1010, New Zealand
- Centre for Computational Evolution, The University of Auckland, Auckland 1010, New Zealand
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187
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Sequeira JJ, Vinuthalakshmi K, Das R, van Driem G, Mustak MS. The maternal U1 haplogroup in the Koraga tribe as a correlate of their North Dravidian linguistic affinity. Front Genet 2024; 14:1303628. [PMID: 38384360 PMCID: PMC10880486 DOI: 10.3389/fgene.2023.1303628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/31/2023] [Indexed: 02/23/2024] Open
Abstract
Introduction: The Koraga tribe are an isolated endogamous tribal group found in the southwest coastal region of India. The Koraga language shares inherited grammatical features with North Dravidian languages. To seek a possible genetic basis for this exceptionality and understand the maternal lineage pattern, we have aimed to reconstruct the inter-population and intra-population relationships of the Koraga tribal population by using mtDNA markers for the hypervariable regions along with a partial coding region sequence analysis. Methods and Results: Amongst the 96 individuals studied, we observe 11 haplogroups, of which a few are shared and others are unique to the clans Soppu, Oṇṭi and Kuṇṭu. In addition to several deep rooted Indian-specific lineages of macrohaplogroups M and U, we observe a high frequency of the U1 lineage (∼38%), unique to the Koraga. A Bayesian analysis of the U1 clade shows that the Koraga tribe share their maternal lineage with ancestral populations of the Caucasus at the cusp of the Last Glacial Maximum. Discussion: Our study suggests that the U1 lineage found in the Indian subcontinent represents a remnant of a post-glacial dispersal. The presence of West Asian U1 when viewed along with historical linguistics leads us to hypothesise that Koraga represents a mother tongue retained by a vanquished population group that fled southward at the demise of the Indus civilisation as opposed to a father tongue, associated with a particular paternal lineage.
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Affiliation(s)
| | | | - Ranajit Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland
| | - Mohammed S. Mustak
- Department of Applied Zoology, Mangalore University, Mangalore, Karnataka, India
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188
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Xu XM, Xu H, Yang Z, Wei Z, Gu JY, Liu DH, Liu QR, Zhu SX. Phylogeny, biogeography, and character evolution of Anaphalis (Gnaphalieae, Asteraceae). FRONTIERS IN PLANT SCIENCE 2024; 15:1336229. [PMID: 38384761 PMCID: PMC10879626 DOI: 10.3389/fpls.2024.1336229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/24/2024] [Indexed: 02/23/2024]
Abstract
The HAP clade, mainly including Helichrysum Mill, Anaphalis DC., and Pseudognaphalium Kirp., is a major component of tribe Gnaphalieae (Asteraceae). In this clade, Anaphalis represents the largest genus of Asian Gnaphalieae. The intergeneric relationships among Anaphalis and its related genera and the infrageneric taxonomy of this genus are complex and remain controversial. However, there are few studies that have focused on these issues. Herein, based on the current most comprehensive sampling of the HAP clade, especially Anaphalis, we conducted phylogenetic analyses using chloroplast (cp) genome and nuclear ribosomal DNA (nrDNA) to evaluate the relationships within HAP clade, test the monophyly of Anaphalis, and examine the infrageneric taxonomy of this genus. Meanwhile, the morphological characters were verified to determine the circumscription and infrageneric taxonomy system of Anaphalis. Additionally, the biogeographical history, diversification processes, and evolution of crucial morphological characters were estimated and inferred. Our phylogenetic analyses suggested that Anaphalis is polyphyletic because it nested with Helichrysum and Pseudognaphalium. Two and four main clades of Anaphalis were identified in cp genome and nrDNA trees, respectively. Compared with nrDNA trees, the cp genome trees were more effective for phylogenetic resolution. After comprehensively analyzing morphological and phylogenetic evidence, it was concluded that the achene surface ornamentation and leaf base showed less homoplasy and supported the two Anaphalis lineages that were inferred from cp genome. Our biogeographical analyses based on cp genome indicated that HAP clade underwent rapid diversification from late Miocene to Pliocene. The two Anaphalis lineages appeared to have originated in Africa, then spread to Western and Southern Asia, and subsequently moved into Southwestern China forming a diversity center. The dispersal patterns of the two Anaphalis lineages were different. One dispersed around the world, except in Africa and South America. The other one dispersed to Eastern and Southeastern Asia from the ancestral origin region.
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Affiliation(s)
- Xue-Min Xu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - He Xu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zheng Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhen Wei
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Jun-Yu Gu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
- Resource Research Institute, Henan Provincial Third Institute of Resources and Environment Investigation, Zhengzhou, China
| | - Dan-Hui Liu
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumchi, China
| | - Quan-Ru Liu
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Shi-Xin Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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189
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Shao L, Qiao P, Wang J, Peng Y, Wang Y, Dong W, Li J. Comparative analysis of jujube and sour jujube gave insight into their difference in genetic diversity and suitable habitat. Front Genet 2024; 15:1322285. [PMID: 38380425 PMCID: PMC10878421 DOI: 10.3389/fgene.2024.1322285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Jujube (Ziziphus jujuba var. jujuba Mill.) and sour jujube (Z. jujuba var. spinosa (Bunge) Hu ex H.F.Chow.) are economically, nutritionally, and ecologically significant members of the Rhamnaceae family. Despite their importance, insufficient research on their genetics and habitats has impeded effective conservation and utilization. To address this knowledge gap, we conducted plastome sequencing, integrated distribution data from China, and assessed genetic diversity and suitable habitat. The plastomes of both species exhibited high conservation and low genetic diversity. A new-found 23 bp species-specific Indel in the petL-petG enabled us to develop a rapid Indel-based identification marker for species discrimination. Phylogenetic analysis and dating illuminated their genetic relationship, showing speciation occurred 6.9 million years ago, in a period of dramatic global temperature fluctuations. Substantial variations in suitable climatic conditions were observed, with the mean temperature of the coldest quarter as the primary factor influencing distributions (-3.16°C-12.73°C for jujube and -5.79°C to 4.11°C for sour jujube, suitability exceeding 0.6). Consequently, distinct conservation strategies are warranted due to differences in suitable habitats, with jujube having a broader distribution and sour jujube concentrated in Northern China. In conclusion, disparate habitats and climatic factors necessitate tailored conservation approaches. Comparing genetic diversity and developing rapid species-specific primers will further enhance the sustainable utilization of these valuable species.
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Affiliation(s)
- Lingzhi Shao
- School of Biology and Food Science, Hebei Normal University for Nationalities, Chengde, China
| | - Ping Qiao
- Dexing Research and Training Center of Chinese Medical Sciences, China Academy of Chinese Medical Sciences, Dexing, China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jingyi Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yanfang Peng
- School of Biology and Food Science, Hebei Normal University for Nationalities, Chengde, China
| | - Yiheng Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jie Li
- School of Biology and Food Science, Hebei Normal University for Nationalities, Chengde, China
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190
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Cirkovic V, Veinovic G, Stankovic D, Mihaljica D, Sukara R, Tomanovic S. Evolutionary dynamics and geographical dispersal of Borrelia lusitaniae. Front Microbiol 2024; 15:1330914. [PMID: 38380089 PMCID: PMC10877945 DOI: 10.3389/fmicb.2024.1330914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/03/2024] [Indexed: 02/22/2024] Open
Abstract
Background Borrelia lusitaniae is a species within the complex Borrelia burgdorferi sensu lato, associated with lizards as reservoirs and Ixodes ricinus as its main vector. Borrelia lusitaniae is predominantly distributed in Central and Southeast Europe, and in countries of the Mediterranean basin, such as Portugal, Morocco, Tunisia, and Italy where this spirochete appears to infect vector ticks more frequently than other genospecies. Evolution of this zoonotic tick-borne microparasite is shaped by different environmental factors. Comprehensive phylogenetic analysis may give insight into how B. lusitaniae spreads to new geographic locations. Aim We applied Bayesian statistical methods to B. lusitaniae multilocus sequence typing (MLST) data to study the migration routes of B. lusitaniae and its potential for further spread. Results The discrete phylogeographic analysis placed origins of B. lusitaniae in Southeast Europe and identified at least two introductions of B. lusitaniae from Europe to North Africa. Estimated effective reproductive potential (Re), as a key indicator for a pathogen spread, suggested potential for further spread. Conclusion The results of this study can provide beneficial information about the potential for further spread of B. lusitaniae in Europe and North Africa and estimation of necessity for the development of strategies to monitor and control Lyme borreliosis.
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Affiliation(s)
- Valentina Cirkovic
- Group for Medical Entomology, Centre of Excellence for Food- and Vector-Borne Zoonoses, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Gorana Veinovic
- Group for Medical Entomology, Centre of Excellence for Food- and Vector-Borne Zoonoses, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | - Darko Mihaljica
- Group for Medical Entomology, Centre of Excellence for Food- and Vector-Borne Zoonoses, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Ratko Sukara
- Group for Medical Entomology, Centre of Excellence for Food- and Vector-Borne Zoonoses, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Snezana Tomanovic
- Group for Medical Entomology, Centre of Excellence for Food- and Vector-Borne Zoonoses, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
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191
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Leaché AD, Davis HR, Feldman CR, Fujita MK, Singhal S. Repeated patterns of reptile diversification in Western North America supported by the Northern Alligator Lizard (Elgaria coerulea). J Hered 2024; 115:57-71. [PMID: 37982433 PMCID: PMC10838131 DOI: 10.1093/jhered/esad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023] Open
Abstract
Understanding the processes that shape genetic diversity by either promoting or preventing population divergence can help identify geographic areas that either facilitate or limit gene flow. Furthermore, broadly distributed species allow us to understand how biogeographic and ecogeographic transitions affect gene flow. We investigated these processes using genomic data in the Northern Alligator Lizard (Elgaria coerulea), which is widely distributed in Western North America across diverse ecoregions (California Floristic Province and Pacific Northwest) and mountain ranges (Sierra Nevada, Coastal Ranges, and Cascades). We collected single-nucleotide polymorphism data from 120 samples of E. coerulea. Biogeographic analyses of squamate reptiles with similar distributions have identified several shared diversification patterns that provide testable predictions for E. coerulea, including deep genetic divisions in the Sierra Nevada, demographic stability of southern populations, and recent post-Pleistocene expansion into the Pacific Northwest. We use genomic data to test these predictions by estimating the structure, connectivity, and phylogenetic history of populations. At least 10 distinct populations are supported, with mixed-ancestry individuals situated at most population boundaries. A species tree analysis provides strong support for the early divergence of populations in the Sierra Nevada Mountains and recent diversification into the Pacific Northwest. Admixture and migration analyses detect gene flow among populations in the Lower Cascades and Northern California, and a spatial analysis of gene flow identified significant barriers to gene flow across both the Sierra Nevada and Coast Ranges. The distribution of genetic diversity in E. coerulea is uneven, patchy, and interconnected at population boundaries. The biogeographic patterns seen in E. coerulea are consistent with predictions from co-distributed species.
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Affiliation(s)
- Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, United States
| | - Hayden R Davis
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, United States
| | - Chris R Feldman
- Department of Biology and Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, NV, United States
| | - Matthew K Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, TX, United States
| | - Sonal Singhal
- Department of Biology, California State University - Dominguez Hills, Carson, CA, United States
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192
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Hew YX, Ya'cob Z, Chen CD, Lau KW, Sofian-Azirun M, Muhammad-Rasul AH, Putt QY, Tan TK, Hadi UK, Suana IW, Takaoka H, Low VL. Co-occurrence of dual lineages within Simulium (Gomphostilbia) atratum De Meijere in the Indonesian Archipelago along Wallace's Line. Acta Trop 2024; 250:107097. [PMID: 38097150 DOI: 10.1016/j.actatropica.2023.107097] [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: 11/07/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
Mitochondrial cytochrome c oxidase subunit I (COI) sequences were utilized to infer the population genetic structure of Simulium (Gomphostilbia) atratum De Meijere, an endemic simulid species to Indonesia. Both median-joining haplotype network and maximum-likelihood tree revealed two genetic lineages (A and B) within the species, with an overlap distribution in Lombok, which is situated along Wallace's line. Genetic differentiation and gene flow with varying frequencies (FST = 0.02-0.967; Nm = 0.01-10.58) were observed between populations of S. (G.) atratum, of which population pairs of different lineages showed high genetic differentiation. Notably, the high genetic distance of up to 5.92 % observed within S. (G.) atratum in Lombok was attributed to the existence of two genetically distinct lineages. The co-occurrence of distinct lineages in Lombok indicated that Wallace's line did not act as faunistic border for S. (G.) atratum in the present study. Moreover, both lineages also exhibited unimodal distributions and negative values of neutrality tests, suggesting a pattern of population expansion. The expansion and divergence time estimation suggested that the two lineages of S. (G.) atratum diverged and expanded during the Pleistocene era in Indonesia.
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Affiliation(s)
- Yan Xin Hew
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia; Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Zubaidah Ya'cob
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Chee Dhang Chen
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Koon Weng Lau
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Mohd Sofian-Azirun
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | | | - Qi Yan Putt
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia; Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Tiong Kai Tan
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Upik Kesumawati Hadi
- Entomology Laboratory, Division of Parasitology and Medical Entomology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | - I Wayan Suana
- Faculty of Mathematics and Natural Science, University of Mataram (UNRAM), Mataram, Indonesia
| | - Hiroyuki Takaoka
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Van Lun Low
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia.
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193
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Bentz PC, Liu Z, Yang JB, Zhang L, Burrows S, Burrows J, Kanno A, Mao Z, Leebens-Mack J. Young evolutionary origins of dioecy in the genus Asparagus. AMERICAN JOURNAL OF BOTANY 2024; 111:e16276. [PMID: 38297448 DOI: 10.1002/ajb2.16276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 02/02/2024]
Abstract
PREMISE Dioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genus Asparagus (Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking. METHODS We use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genus Asparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature. RESULTS We estimate that dioecy evolved once or twice approximately 2.78-3.78 million years ago in Asparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers. CONCLUSIONS Our findings support previous work implicating a young age and the possibility of two origins of dioecy in Asparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy in Asparagus approximately 2.78-3.78 million years ago.
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Affiliation(s)
- Philip C Bentz
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
| | - Zhengjie Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | | | - Akira Kanno
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Zichao Mao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
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194
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Verry AJF, Mas-Carrió E, Gibb GC, Dutoit L, Robertson BC, Waters JM, Rawlence NJ. Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand's enigmatic takahē and moho. Mol Ecol 2024; 33:e17227. [PMID: 38018770 DOI: 10.1111/mec.17227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/05/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Many avian species endemic to Aotearoa New Zealand were driven to extinction or reduced to relict populations following successive waves of human arrival, due to hunting, habitat destruction and the introduction of mammalian predators. Among the affected species were the large flightless South Island takahē (Porphyrio hochstetteri) and the moho (North Island takahē; P. mantelli), with the latter rendered extinct and the former reduced to a single relictual population. Little is known about the evolutionary history of these species prior to their decline and/or extinction. Here we sequenced mitochondrial genomes from takahē and moho subfossils (12 takahē and 4 moho) and retrieved comparable sequence data from takahē museum skins (n = 5) and contemporary individuals (n = 17) to examine the phylogeny and recent evolutionary history of these species. Our analyses suggest that prehistoric takahē populations lacked deep phylogeographic structure, in contrast to moho, which exhibited significant spatial genetic structure, albeit based on limited sample sizes (n = 4). Temporal genetic comparisons show that takahē have lost much of their mitochondrial genetic diversity, likely due to a sudden demographic decline soon after human arrival (~750 years ago). Time-calibrated phylogenetic analyses strongly support a sister species relationship between takahē and moho, suggesting these flightless taxa diverged around 1.5 million years ago, following a single colonisation of New Zealand by a flighted Porphyrio ancestor approximately 4 million years ago. This study highlights the utility of palaeogenetic approaches for informing the conservation and systematic understanding of endangered species whose ranges have been severely restricted by anthropogenic impacts.
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Affiliation(s)
- Alexander J F Verry
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Eduard Mas-Carrió
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Gillian C Gibb
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Jonathan M Waters
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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195
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Mochales-Riaño G, Burriel-Carranza B, Barros MI, Velo-Antón G, Talavera A, Spilani L, Tejero-Cicuéndez H, Crochet PA, Piris A, García-Cardenete L, Busais S, Els J, Shobrak M, Brito JC, Šmíd J, Carranza S, Martínez-Freiría F. Hidden in the sand: Phylogenomics unravel an unexpected evolutionary history for the desert-adapted vipers of the genus Cerastes. Mol Phylogenet Evol 2024; 191:107979. [PMID: 38040070 DOI: 10.1016/j.ympev.2023.107979] [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: 10/05/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
The desert vipers of the genus Cerastes are a small clade of medically important venomous snakes within the family Viperidae. According to published morphological and molecular studies, the group is comprised by four species: two morphologically similar and phylogenetically sister taxa, the African horned viper (Cerastes cerastes) and the Arabian horned viper (Cerastes gasperettii); a more distantly related species, the Saharan sand viper (Cerastes vipera), and the enigmatic Böhme's sand viper (Cerastes boehmei), only known from a single specimen in captivity allegedly captured in Central Tunisia. In this study, we sequenced one mitochondrial marker (COI) as well as genome-wide data (ddRAD sequencing) from 28 and 41 samples, respectively, covering the entire distribution range of the genus to explore the population genomics, phylogenomic relationships and introgression patterns within the genus Cerastes. Additionally, and to provide insights into the mode of diversification of the group, we carried out niche overlap analyses considering climatic and habitat variables. Both nuclear phylogenomic reconstructions and population structure analyses have unveiled an unexpected evolutionary history for the genus Cerastes, which sharply contradicts the morphological similarities and previously published mitochondrial approaches. Cerastes cerastes and C. vipera are recovered as sister taxa whilst C. gasperettii is a sister taxon to the clade formed by these two species. We found a relatively high niche overlap (OI > 0.7) in both climatic and habitat variables between C. cerastes and C. vipera, contradicting a potential scenario of sympatric speciation. These results are in line with the introgression found between the northwestern African populations of C. cerastes and C. vipera. Finally, our genomic data confirms the existence of a lineage of C. cerastes in Arabia. All these results highlight the importance of genome-wide data over few genetic markers to study the evolutionary history of species.
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Affiliation(s)
| | - Bernat Burriel-Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; Museu de Ciències Naturals de Barcelona, P° Picasso s/n, Parc Ciutadella, 08003 Barcelona, Spain
| | - Margarida Isabel Barros
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Guillermo Velo-Antón
- Universidad de Vigo, Facultad de Biología, Edificio de Ciencias Experimentales, Bloque B, Planta 2, Laboratorio 39 (Grupo GEA), E-36310 Vigo, Spain
| | - Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Loukia Spilani
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Héctor Tejero-Cicuéndez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | | | - Alberto Piris
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Luis García-Cardenete
- Agencia de Medio Ambiente y Agua de Andalucía, C/Johan G. Gutenberg, 1, 41092 Seville, Spain
| | - Salem Busais
- Department of Biology, Faculty of Education, Aden University, Yemen
| | - Johannes Els
- Breeding Centre for Endangered Arabian Wildlife, Environment and Protected Areas Authority, Sharjah, United Arab Emirates
| | - Mohammed Shobrak
- National Center for Wildlife, Prince Saud Al Faisal Wildlife Research Centre, Taif, Saudi Arabia
| | - José Carlos Brito
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Jiří Šmíd
- Department of Zoology, Faculty of Science, Charles University, Vinicná 7, Prague, Czech Republic
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Fernando Martínez-Freiría
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.
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196
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Delicado D, Hauffe T, Wilke T. Fifth mass extinction event triggered the diversification of the largest family of freshwater gastropods (Caenogastropoda: Truncatelloidea: Hydrobiidae). Cladistics 2024; 40:82-96. [PMID: 37712584 DOI: 10.1111/cla.12558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/09/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023] Open
Abstract
The fifth mass extinction event (MEE) at the Cretaceous-Palaeogene (K-Pg) boundary 66 million years ago (Ma) led to massive species loss but also triggered the diversification of higher taxa. Five models have been proposed depending on whether this diversification occurred before, during or after the K-Pg boundary and the rate of species accumulation. While the effects of the K-Pg MEE on vertebrate evolution are relatively well understood, the impact on invertebrates, particularly in freshwater ecosystems, remains controversial. One example is the hyperdiverse Hydrobiidae-the most species-rich family of freshwater gastropods. Whereas some studies place its origin in the Jurassic or even Carboniferous, most fossil records postdate the K-Pg event. We therefore used robustly time-calibrated multi-locus phylogenies of >400 species representing >100 hydrobiid genera to unravel its evolutionary history and patterns of diversification. We found that the family started diversifying shortly after the K-Pg boundary (∼60 Ma; 95% highest posterior density 52-69 Ma). Lineage richness gradually increased to the present and phylogenetic diversity until ∼25 Ma. These findings suggest that diversification was not initially driven by ecological opportunity. Combining the two criteria of timing and rate of diversification, a soft-explosive diversification model of aquatic vertebrates best fits the patterns observed. We also show that most higher hydrobiid taxa (i.e. subfamilies) diversified from the Middle Oligocene to Middle Miocene (i.e. 12-28 Ma). Two of the 15 major clades delimited are described here as new subfamilies (i.e. Bullaregiinae n. subfam. and Pontobelgrandiellinae n. subfam.), whose members are restricted to subterranean waters. Our results are an important contribution to understanding how the fifth MEE has shaped evolution and patterns of biodiversity in continental aquatic systems. Given the high extinction risks faced by many hydrobiids today, they also emphasise the need to study the biodiversity of vulnerable ecosystems.
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Affiliation(s)
- Diana Delicado
- Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), D-35392, Giessen, Germany
| | - Torsten Hauffe
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Thomas Wilke
- Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), D-35392, Giessen, Germany
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197
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Dalapicolla J, Rodrigues do Prado J, Lacey Knowles L, Reis Percequillo A. Phylogenomics and species delimitation of an abundant and little-studied Amazonian forest spiny rat. Mol Phylogenet Evol 2024; 191:107992. [PMID: 38092321 DOI: 10.1016/j.ympev.2023.107992] [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: 03/31/2023] [Revised: 12/01/2023] [Accepted: 12/09/2023] [Indexed: 12/21/2023]
Abstract
Species delimitation studies based on integrating different datasets such as genomic, morphometric, and cytogenetics data are rare in studies focused on Neotropical rodents. As a consequence, the evolutionary history of most of these genera remains poorly understood. Proechimys is a highly diverse and widely distributed genus of Neotropical spiny rats with unique traits like multiple sympatry, micro-habitat segregation, and fuzzy species limits. Here, we applied RAD-Seq to infer the phylogenetic relationships, estimate the species boundaries, and estimate the divergence times for Proechimys, one of the most common and least studied small mammals in the Amazon. We tested whether inferred lineages in the phylogenetic trees could be considered distinct species based on the genomic dataset and morphometric data. Analyses revealed the genus is not monophyletic, with Proechimys hoplomyoides sister to a group of Hoplomys gymnurus + all other Proechimys species, contesting the generic status of Hoplomys. There are five main clades in Proechimys stricto sensu (excluding H. gymnurus and P. hoplomyoides). Species delimitation analyses supported 25 species within the genus Proechimys. The five main clades in Proechimys stricto sensu also showed similar ages for their origins, and two rapid diversification events were identified in the Early Pliocene and in the Early Pleistocene. Most cases of sympatry in Proechimys occur among species from the different main clades, and although Proechimys is an inhabitant of the Amazon, three species occupied the Cerrado biome during the Pleistocene. We could associate available nominal taxon, cytogenetics information, and DNA sequences in Genbank to most of the 25 species we hypothesized from our delimitation analyses. Based on our analyses, we estimate that eight forms represent putative new species that need a taxonomic revision.
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Affiliation(s)
- Jeronymo Dalapicolla
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil; Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, São Paulo, Brazil; Instituto Tecnológico Vale, Belém, Pará, Brazil.
| | | | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Alexandre Reis Percequillo
- Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, São Paulo, Brazil
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198
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Emami-Khoyi A. The complete mitogenome dataset of the Critically Endangered estuarine pipefish, Syngnathus watermeyeri. Data Brief 2024; 52:109864. [PMID: 38146291 PMCID: PMC10749243 DOI: 10.1016/j.dib.2023.109864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/27/2023] Open
Abstract
The Critically Endangered South African estuarine pipefish, Syngnathus watermeyeri, is one of the rarest teleost fish on the planet. In this analysed dataset, the complete mitochondrial genome of this species was assembled, annotated, and described. In addition, its evolutionary history was reconstructed in a Maximum Likelihood and a Bayesian framework. A circular mitochondrial contig 16 449 bp in length was assembled. A total of 13 protein-coding genes, 22 tRNAs and two rRNAs were annotated. The mitochondrial phylogenetic analysis showed that S. watermeyeri diverged from its widely distributed southern African sister species S. temminckii approximately 1.5 million years ago, and the ancestor of these two southern Afican pipefish species diverged from a clade of northern hemisphere pipefishes comprising S. acus, S. rostellatus, and S. typhle approximately 5.3 million years ago. The dataset presented here serves as the first step in understanding the evolutionary history of Africa's rarest pipefish.
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Affiliation(s)
- Arsalan Emami-Khoyi
- Centre for Ecological Genomics and Wildlife Conservation1, University of Johannesburg, Auckland Park 2006, South Africa
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199
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Cruaud A, Rasplus JY, Zhang J, Burks R, Delvare G, Fusu L, Gumovsky A, Huber JT, Janšta P, Mitroiu MD, Noyes JS, van Noort S, Baker A, Böhmová J, Baur H, Blaimer BB, Brady SG, Bubeníková K, Chartois M, Copeland RS, Dale-Skey Papilloud N, Dal Molin A, Dominguez C, Gebiola M, Guerrieri E, Kresslein RL, Krogmann L, Lemmon E, Murray EA, Nidelet S, Nieves-Aldrey JL, Perry RK, Peters RS, Polaszek A, Sauné L, Torréns J, Triapitsyn S, Tselikh EV, Yoder M, Lemmon AR, Woolley JB, Heraty JM. The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps. Cladistics 2024; 40:34-63. [PMID: 37919831 DOI: 10.1111/cla.12561] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 11/04/2023] Open
Abstract
Chalcidoidea are mostly parasitoid wasps that include as many as 500 000 estimated species. Capturing phylogenetic signal from such a massive radiation can be daunting. Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. We combined 1007 exons obtained with Anchored Hybrid Enrichment with 1048 ultra-conserved elements (UCEs) for 433 taxa including all extant families, >95% of all subfamilies, and 356 genera chosen to represent the vast diversity of the superfamily. Going back and forth between the molecular results and our collective knowledge of morphology and biology, we detected bias in the analyses that was driven by the saturation of nucleotide data. Our final results are based on a concatenated analysis of the least saturated exons and UCE datasets (2054 loci, 284 106 sites). Our analyses support an expected sister relationship with Mymarommatoidea. Seven previously recognized families were not monophyletic, so support for a new classification is discussed. Natural history in some cases would appear to be more informative than morphology, as illustrated by the elucidation of a clade of plant gall associates and a clade of taxa with planidial first-instar larvae. The phylogeny suggests a transition from smaller soft-bodied wasps to larger and more heavily sclerotized wasps, with egg parasitism as potentially ancestral for the entire superfamily. Deep divergences in Chalcidoidea coincide with an increase in insect families in the fossil record, and an early shift to phytophagy corresponds with the beginning of the "Angiosperm Terrestrial Revolution". Our dating analyses suggest a middle Jurassic origin of 174 Ma (167.3-180.5 Ma) and a crown age of 162.2 Ma (153.9-169.8 Ma) for Chalcidoidea. During the Cretaceous, Chalcidoidea may have undergone a rapid radiation in southern Gondwana with subsequent dispersals to the Northern Hemisphere. This scenario is discussed with regard to knowledge about the host taxa of chalcid wasps, their fossil record and Earth's palaeogeographic history.
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Affiliation(s)
- Astrid Cruaud
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Jean-Yves Rasplus
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Junxia Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, China
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Roger Burks
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Gérard Delvare
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Lucian Fusu
- Faculty of Biology, Alexandru Ioan Cuza University, Iasi, Romania
| | - Alex Gumovsky
- Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - John T Huber
- Natural Resources Canada, c/o Canadian National Collection of Insects, Ottawa, Ontario, Canada
| | - Petr Janšta
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Entomology, State Museum of Natural History, Stuttgart, Germany
| | | | - John S Noyes
- Insects Division, Natural History Museum, London, UK
| | - Simon van Noort
- Research and Exhibitions Department, South African Museum, Iziko Museums of South Africa, Cape Town, South Africa
- Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa
| | - Austin Baker
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Julie Böhmová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Hannes Baur
- Department of Invertebrates, Natural History Museum Bern, Bern, Switzerland
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Bonnie B Blaimer
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Seán G Brady
- Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Kristýna Bubeníková
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Marguerite Chartois
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Robert S Copeland
- Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
- International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | | | - Ana Dal Molin
- Departamento de Microbiologia e Parasitologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Chrysalyn Dominguez
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Marco Gebiola
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Emilio Guerrieri
- Insects Division, Natural History Museum, London, UK
- CNR-Institute for Sustainable Plant Protection (CNR-IPSP), National Research Council of Italy, Portici, Italy
| | - Robert L Kresslein
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Lars Krogmann
- Department of Entomology, State Museum of Natural History, Stuttgart, Germany
- Institute of Zoology, University of Hohenheim, Stuttgart, Germany
| | - Emily Lemmon
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Elizabeth A Murray
- Department of Entomology, Washington State University, Pullman, Washington, USA
| | - Sabine Nidelet
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | | | - Ryan K Perry
- Department of Plant Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Ralph S Peters
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | | | - Laure Sauné
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Javier Torréns
- Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja (CRILAR-CONICET), Anillaco, Argentina
| | - Serguei Triapitsyn
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | | | - Matthew Yoder
- Illinois Natural History Survey, University of Illinois, Champaign, Illinois, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, Florida, USA
| | - James B Woolley
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - John M Heraty
- Department of Entomology, University of California Riverside, Riverside, California, USA
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200
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Mylopotamitaki D, Weiss M, Fewlass H, Zavala EI, Rougier H, Sümer AP, Hajdinjak M, Smith GM, Ruebens K, Sinet-Mathiot V, Pederzani S, Essel E, Harking FS, Xia H, Hansen J, Kirchner A, Lauer T, Stahlschmidt M, Hein M, Talamo S, Wacker L, Meller H, Dietl H, Orschiedt J, Olsen JV, Zeberg H, Prüfer K, Krause J, Meyer M, Welker F, McPherron SP, Schüler T, Hublin JJ. Homo sapiens reached the higher latitudes of Europe by 45,000 years ago. Nature 2024; 626:341-346. [PMID: 38297117 PMCID: PMC10849966 DOI: 10.1038/s41586-023-06923-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/30/2023] [Indexed: 02/02/2024]
Abstract
The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe1. Local hybridization between the two groups occurred2, but not on all occasions3. Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups4. One such technocomplex for which the makers are unknown is the Lincombian-Ranisian-Jerzmanowician (LRJ), which has been described in northwestern and central Europe5-8. Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period.
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Affiliation(s)
- Dorothea Mylopotamitaki
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marcel Weiss
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institut für Ur- und Frühgeschichte, Erlangen, Germany.
| | - Helen Fewlass
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Ancient Genomics Lab, Francis Crick Institute, London, UK
| | - Elena Irene Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Hélène Rougier
- Department of Anthropology, California State University Northridge, Northridge, CA, USA
| | - Arev Pelin Sümer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Geoff M Smith
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Karen Ruebens
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Virginie Sinet-Mathiot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Univ. Bordeaux, CNRS, Ministère de la Culture, PACEA, UMR 5199, Bordeaux, France
| | - Sarah Pederzani
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Archaeological Micromorphology and Biomarker Lab, University of La Laguna, San Cristóbal de La Laguna, Spain
| | - Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Florian S Harking
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Huan Xia
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Jakob Hansen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - André Kirchner
- Department of Soil Protection and Soil Survey, State Authority for Mining, Energy and Geology of Lower Saxony (LBEG), Hannover, Germany
| | - Tobias Lauer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Terrestrial Sedimentology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Mareike Stahlschmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Evolutionary Anthropology and Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Michael Hein
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute of Ecology, Leuphana University, Lüneburg, Germany
- Historical Anthropospheres Working Group, Leipzig Lab, Leipzig University, Leipzig, Germany
| | - Sahra Talamo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry G. Ciamician, Bologna University, Bologna, Italy
| | - Lukas Wacker
- Ion Beam Physics, ETH Zurich, Zurich, Switzerland
| | - Harald Meller
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle, Germany
| | - Holger Dietl
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle, Germany
| | - Jörg Orschiedt
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle, Germany
| | - Jesper V Olsen
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Tim Schüler
- Thuringian State Office for the Preservation of Historical Monuments and Archaeology, Weimar, Germany
| | - Jean-Jacques Hublin
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France.
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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