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Oury N, Noël C, Mona S, Aurelle D, Magalon H. From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals. Mol Phylogenet Evol 2023; 184:107803. [PMID: 37120114 DOI: 10.1016/j.ympev.2023.107803] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/06/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data is available due to the small number of currently available markers and obscures species boundaries. Difficulties in inferring gene trees and morphological incongruences further blur the study and conservation of these organisms. Yet, can genomics alone be used to delimit species? Here, focusing on the coral genus Pocillopora, whose colonies play key roles in Indo-Pacific reef ecosystems but have challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNP) were first used to resolve Pocillopora phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to other lines of evidence based on genetic, morphology, biogeography and symbiont associations. Out of 21 species hypotheses delimited by genomics, 13 were strongly supported by all approaches, while six could represent either undescribed species or nominal species that have been synonymised incorrectly. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine Pocillopora species boundaries, (2) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, (3) the requirement of molecular identification when species identity of colonies is absolutely necessary to interpret results, as morphology can blur species identification in the field, and (4) the need for a taxonomic revision of the genus Pocillopora. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora, and more widely, scleractinian species boundaries, and will ultimately contribute to the taxonomic revision of this genus and the conservation of its species.
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Affiliation(s)
- Nicolas Oury
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, St Denis, La Réunion, France; Laboratoire Cogitamus, Paris, France.
| | - Cyril Noël
- IFREMER - IRSI - Service de Bioinformatique (SeBiMER), Plouzané, France
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE-PSL, Université PSL, CNRS, SU, UA, Paris, France; EPHE, PSL Research University, Paris, France; Laboratoire d'Excellence CORAIL, Perpignan, France
| | - Didier Aurelle
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE-PSL, Université PSL, CNRS, SU, UA, Paris, France; Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, St Denis, La Réunion, France; Laboratoire Cogitamus, Paris, France; Laboratoire d'Excellence CORAIL, Perpignan, France
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Eyer PA, Finand B, Mona S, Khimoun A, D'ettorre P, Fédérici P, Leroy C, Cornette R, Chifflet-Belle P, Monnin T, Doums C. Integrative characterization of genetic and phenotypic differentiation in an ant species complex with strong hierarchical population structure and low dispersal abilities. Heredity (Edinb) 2023; 130:163-176. [PMID: 36585503 PMCID: PMC9981590 DOI: 10.1038/s41437-022-00590-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
Low dispersal, occurrence of asexual reproduction and geographic discontinuity increase genetic differentiation between populations, which ultimately can lead to speciation. In this work, we used a multidisciplinary framework to characterize the genetic and phenotypic differentiation between and within two cryptic ant species with restricted dispersal, Cataglyphis cursor and C. piliscapa and used behavioral experiments to test for reproductive isolation. Their distribution is segregated by the Rhône River and they have been traditionally distinguished only by hair numbers, although a statistical assessment is still lacking. We found strong genetic (microsatellites, nuclear and mitochondrial sequences), morphological (number of hairs, tibia length, male genitalia) and chemical (cuticular hydrocarbons) differentiation not only between species but also among localities within species. However, inter-specific differentiation was slightly higher than intra-specific differentiation for most markers. Overall, this pattern could either reflect reproductive isolation or could result from a longer period of geographic isolation between species than among localities within species without necessarily involving reproductive isolation. Interestingly, our behavioral experiments showed an absence of mating between species associated to a higher aggressiveness of workers towards heterospecific males. This suggests that sexual selection may, at least partially, fuel reproductive isolation. We also showed that cuticular hydrocarbons, mtDNA sequences and number of hairs provide reliable criteria allowing species discrimination. Overall, this species complex offers a case study to further investigate varying stages of a speciation continuum by estimating reproductive isolation between pairs of localities varying by their level of genetic differentiation.
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Affiliation(s)
- P A Eyer
- Department of Entomology, 2143 TAMU, Texas A&M University, College Station, TX, 77843-2143, USA.
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE-PSL, Sorbonne Université, Université des Antilles, 75005, Paris, France.
- EPHE, PSL University, 75005, Paris, France.
| | - B Finand
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE-PSL, Sorbonne Université, Université des Antilles, 75005, Paris, France
| | - S Mona
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE-PSL, Sorbonne Université, Université des Antilles, 75005, Paris, France
- EPHE, PSL University, 75005, Paris, France
| | - A Khimoun
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE-PSL, Sorbonne Université, Université des Antilles, 75005, Paris, France
- EPHE, PSL University, 75005, Paris, France
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - P D'ettorre
- Laboratory of Experimental and Comparative Ethology, University of Paris 13, Sorbonne Paris Cité, 93430, Villetaneuse, France
| | - P Fédérici
- Sorbonne Université, Université Paris Est Créteil, CNRS, INRAe, IRD, Institute of Ecology and Environmental sciences of Paris, iEES-Paris, 75005, Paris, France
| | - C Leroy
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - R Cornette
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE-PSL, Sorbonne Université, Université des Antilles, 75005, Paris, France
| | - P Chifflet-Belle
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE-PSL, Sorbonne Université, Université des Antilles, 75005, Paris, France
- EPHE, PSL University, 75005, Paris, France
| | - T Monnin
- Sorbonne Université, Université Paris Est Créteil, CNRS, INRAe, IRD, Institute of Ecology and Environmental sciences of Paris, iEES-Paris, 75005, Paris, France
| | - C Doums
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE-PSL, Sorbonne Université, Université des Antilles, 75005, Paris, France
- EPHE, PSL University, 75005, Paris, France
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Devloo‐Delva F, Burridge CP, Kyne PM, Brunnschweiler JM, Chapman DD, Charvet P, Chen X, Cliff G, Daly R, Drymon JM, Espinoza M, Fernando D, Barcia LG, Glaus K, González‐Garza BI, Grant MI, Gunasekera RM, Hernandez S, Hyodo S, Jabado RW, Jaquemet S, Johnson G, Ketchum JT, Magalon H, Marthick JR, Mollen FH, Mona S, Naylor GJP, Nevill JEG, Phillips NM, Pillans RD, Postaire BD, Smoothey AF, Tachihara K, Tillet BJ, Valerio‐Vargas JA, Feutry P. From rivers to ocean basins: The role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator. Ecol Evol 2023; 13:e9837. [PMID: 36844667 PMCID: PMC9944188 DOI: 10.1002/ece3.9837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
The Bull Shark (Carcharhinus leucas) faces varying levels of exploitation around the world due to its coastal distribution. Information regarding population connectivity is crucial to evaluate its conservation status and local fishing impacts. In this study, we sampled 922 putative Bull Sharks from 19 locations in the first global assessment of population structure of this cosmopolitan species. Using a recently developed DNA-capture approach (DArTcap), samples were genotyped for 3400 nuclear markers. Additionally, full mitochondrial genomes of 384 Indo-Pacific samples were sequenced. Reproductive isolation was found between and across ocean basins (eastern Pacific, western Atlantic, eastern Atlantic, Indo-West Pacific) with distinct island populations in Japan and Fiji. Bull Sharks appear to maintain gene flow using shallow coastal waters as dispersal corridors, whereas large oceanic distances and historical land-bridges act as barriers. Females tend to return to the same area for reproduction, making them more susceptible to local threats and an important focus for management actions. Given these behaviors, the exploitation of Bull Sharks from insular populations, such as Japan and Fiji, may instigate local decline that cannot readily be replenished by immigration, which can in turn affect ecosystem dynamics and functions. These data also supported the development of a genetic panel to ascertain the population of origin, which will be useful in monitoring the trade of fisheries products and assessing population-level impacts of this harvest.
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Affiliation(s)
- Floriaan Devloo‐Delva
- Oceans and Atmosphere, CSIROHobartTasmaniaAustralia
- Quantitative Marine Science, Institute for Marine and Antarctic Studies, University of TasmaniaHobartTasmaniaAustralia
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Christopher P. Burridge
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Peter M. Kyne
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | | | - Demian D. Chapman
- Department of Biological SciencesFlorida International UniversityNorth MiamiFloridaUSA
| | - Patricia Charvet
- Programa de Pós‐graduação em Sistemática, Uso e Conservação da BiodiversidadeUniversidade Federal do Ceará (PPGSis ‐ UFC)FortalezaBrazil
| | - Xiao Chen
- College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
| | - Geremy Cliff
- KwaZulu‐Natal Sharks Board, Umhlanga 4320, South Africa and School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Ryan Daly
- Oceanographic Research Institute, South African Association for Marine Biological Research, PointDurbanSouth Africa
- South African Institute for Aquatic BiodiversityMkhandaSouth Africa
| | - J. Marcus Drymon
- Coastal Research and Extension CenterMississippi State UniversityBiloxiMississippiUSA
- Mississippi‐Alabama Sea Grant ConsortiumOcean SpringsMississippiUSA
| | - Mario Espinoza
- Centro de Investigación en Ciencias del Mar y Limnología & Escuela de BiologíaUniversidad de Costa Rica, San Pedro de Montes de OcaSan JoséCosta Rica
| | | | - Laura Garcia Barcia
- Department of Biological SciencesFlorida International UniversityNorth MiamiFloridaUSA
| | - Kerstin Glaus
- Faculty of Science, Technology and Environment, School of Marine StudiesThe University of the South PacificSuvaFiji
| | | | - Michael I. Grant
- College of Science and Engineering, Centre for Sustainable Tropical Fisheries and AquacultureJames Cook UniversityTownsvilleQueenslandAustralia
| | | | - Sebastian Hernandez
- Biomolecular Laboratory, Center for International ProgramsUniversidad VERITASSan JoséCosta Rica
- Sala de Colecciones, Facultad de Ciencias del MarUniversidad Católica del NorteCoquimboChile
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research InstituteUniversity of TokyoKashiwa, ChibaJapan
| | - Rima W. Jabado
- College of Science and Engineering, Centre for Sustainable Tropical Fisheries and AquacultureJames Cook UniversityTownsvilleQueenslandAustralia
- Elasmo ProjectDubaiUnited Arab Emirates
| | - Sébastien Jaquemet
- UMR ENTROPIE (Université de La Réunion, Université de Nouvelle‐Calédonie, IRD, CNRS, IFREMER), Faculté des Sciences et TechnologiesUniversité de La RéunionCedex 09, La RéunionFrance
| | - Grant Johnson
- Department of Industry, Tourism and Trade, Aquatic Resource Research UnitDarwinNorthern TerritoryAustralia
| | | | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, Université de Nouvelle‐Calédonie, IRD, CNRS, IFREMER), Faculté des Sciences et TechnologiesUniversité de La RéunionCedex 09, La RéunionFrance
| | - James R. Marthick
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | | | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB (UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHEUniversité des AntillesParisFrance
- EPHEPSL Research UniversityParisFrance
| | - Gavin J. P. Naylor
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | | | - Nicole M. Phillips
- School of Biological, Environmental and Earth SciencesThe University of Southern MississippiHattiesburgMississippiUSA
| | | | - Bautisse D. Postaire
- UMR ENTROPIE (Université de La Réunion, Université de Nouvelle‐Calédonie, IRD, CNRS, IFREMER), Faculté des Sciences et TechnologiesUniversité de La RéunionCedex 09, La RéunionFrance
| | - Amy F. Smoothey
- NSW Department of Primary Industries, Fisheries ResearchSydney Institute of Marine ScienceMosmanNew South WalesAustralia
| | - Katsunori Tachihara
- Laboratory of Fisheries Biology and Coral Reef Studies, Faculty of ScienceUniversity of Ryukyus, NishiharaOkinawaJapan
| | - Bree J. Tillet
- Translational Research Institute, University of Queensland Diamantina InstituteBrisbaneQueenslandAustralia
| | - Jorge A. Valerio‐Vargas
- Centro de Investigación en Ciencias del Mar y Limnología & Escuela de BiologíaUniversidad de Costa Rica, San Pedro de Montes de OcaSan JoséCosta Rica
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Lesturgie P, Braun CD, Clua E, Mourier J, Thorrold SR, Vignaud T, Planes S, Mona S. Like a rolling stone: Colonization and migration dynamics of the gray reef shark ( Carcharhinus amblyrhynchos). Ecol Evol 2023; 13:e9746. [PMID: 36644707 PMCID: PMC9831972 DOI: 10.1002/ece3.9746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/18/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023] Open
Abstract
Designing appropriate management plans requires knowledge of both the dispersal ability and what has shaped the current distribution of the species under consideration. Here, we investigated the evolutionary history of the endangered gray reef shark (Carcharhinus amblyrhynchos) across its range by sequencing thousands of RADseq loci in 173 individuals in the Indo-Pacific (IP). We first bring evidence of the occurrence of a range expansion (RE) originating close to the Indo-Australian Archipelago (IAA) where two stepping-stone waves (east and westward) colonized almost the entire IP. Coalescent modeling additionally highlighted a homogenous connectivity (Nm ~ 10 per generation) throughout the range, and isolation by distance model suggested the absence of barriers to dispersal despite the affinity of C. amblyrhynchos to coral reefs. This coincides with long-distance swims previously recorded, suggesting that the strong genetic structure at the IP scale (F ST ~ 0.56 between its ends) is the consequence of its broad current distribution and organization in a large number of demes. Our results strongly suggest that management plans for the gray reef shark should be designed on a range-wide rather than a local scale due to its continuous genetic structure. We further contrasted these results with those obtained previously for the sympatric but strictly lagoon-associated Carcharhinus melanopterus, known for its restricted dispersal ability. Carcharhinus melanopterus exhibits a similar RE dynamic but is characterized by a stronger genetic structure and a nonhomogeneous connectivity largely dependent on local coral reefs availability. This sheds new light on shark evolution, emphasizing the roles of IAA as source of biodiversity and of life-history traits in shaping the extent of genetic structure and diversity.
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Affiliation(s)
- Pierre Lesturgie
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE‐PSLUniversité PSL, CNRS, SU, UAParisFrance
| | - Camrin D. Braun
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Eric Clua
- Laboratoire d'Excellence CORAILPapetoaiFrench Polynesia
- EPHE, PSL Research UniversityParisFrance
| | - Johann Mourier
- Laboratoire d'Excellence CORAILPapetoaiFrench Polynesia
- Université de Corse Pasquale Paoli, UMS 3514 Plateforme Marine Stella MareBigugliaFrance
| | - Simon R. Thorrold
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | | | - Serge Planes
- Laboratoire d'Excellence CORAILPapetoaiFrench Polynesia
- EPHE, PSL Research UniversityParisFrance
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE‐PSLUniversité PSL, CNRS, SU, UAParisFrance
- EPHE, PSL Research UniversityParisFrance
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Lesturgie P, Lainé H, Suwalski A, Chifflet-Belle P, Maisano Delser P, Clua E, Jaquemet S, Magalon H, Mona S. Ecological and biogeographic features shaped the complex evolutionary history of an iconic apex predator (Galeocerdo cuvier). BMC Ecol Evol 2022; 22:147. [PMID: 36526977 PMCID: PMC9758794 DOI: 10.1186/s12862-022-02100-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The tiger shark (Galeocerdo cuvier) is a large iconic marine predator inhabiting worldwide tropical and subtropical waters. So far, only mitochondrial markers and microsatellites studies have investigated its worldwide historical demography with inconclusive outcomes. Here, we assessed for the first time the genomic variability of tiger shark based on RAD-seq data for 50 individuals from five sampling sites in the Indo-Pacific (IP) and one in the Atlantic Ocean (AO) to decipher the extent of the species' global connectivity and its demographic history. RESULTS Clustering algorithms (PCA and NMF), FST and an approximate Bayesian computation framework revealed the presence of two clusters corresponding to the two oceanic basins. By modelling the two-dimensional site frequency spectrum, we tested alternative isolation/migration scenarios between these two identified populations. We found the highest support for a divergence time between the two ocean basins of ~ 193,000 years before present (B.P) and an ongoing but limited asymmetric migration ~ 176 times larger from the IP to the AO (Nm ~ 3.9) than vice versa (Nm ~ 0.02). CONCLUSIONS The two oceanic regions are isolated by a strong barrier to dispersal more permeable from the IP to the AO through the Agulhas leakage. We finally emphasized contrasting recent demographic histories for the two regions, with the IP characterized by a recent bottleneck around 2000 years B.P. and the AO by an expansion starting 6000 years B.P. The large differentiation between the two oceanic regions and the absence of population structure within each ocean basin highlight the need for two large management units and call for future conservation programs at the oceanic rather than local scale, particularly in the Indo-Pacific where the population is declining.
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Affiliation(s)
- Pierre Lesturgie
- grid.503191.f0000 0001 0143 5055Institut de Systématique, Evolution, Biodiversité (ISYEB), EPHE-PSL, Université PSL, MNHN, CNRS, SU, UA, Paris, France
| | - Hugo Lainé
- grid.503191.f0000 0001 0143 5055Institut de Systématique, Evolution, Biodiversité (ISYEB), EPHE-PSL, Université PSL, MNHN, CNRS, SU, UA, Paris, France
| | - Arnaud Suwalski
- grid.503191.f0000 0001 0143 5055Institut de Systématique, Evolution, Biodiversité (ISYEB), EPHE-PSL, Université PSL, MNHN, CNRS, SU, UA, Paris, France ,grid.424469.90000 0001 2195 5365EPHE, PSL Research University, Paris, France
| | - Pascaline Chifflet-Belle
- grid.503191.f0000 0001 0143 5055Institut de Systématique, Evolution, Biodiversité (ISYEB), EPHE-PSL, Université PSL, MNHN, CNRS, SU, UA, Paris, France ,grid.424469.90000 0001 2195 5365EPHE, PSL Research University, Paris, France
| | | | - Eric Clua
- grid.424469.90000 0001 2195 5365EPHE, PSL Research University, Paris, France ,Laboratoire d’Excellence CORAIL, Papetoai, French Polynesia
| | - Sébastien Jaquemet
- grid.11642.300000 0001 2111 2608UMR ENTROPIE (Université de La Réunion/IRD/CNRS), Université de La Réunion, Saint Denis, France
| | - Hélène Magalon
- Laboratoire d’Excellence CORAIL, Papetoai, French Polynesia ,grid.11642.300000 0001 2111 2608UMR ENTROPIE (Université de La Réunion/IRD/CNRS), Université de La Réunion, Saint Denis, France
| | - Stefano Mona
- grid.503191.f0000 0001 0143 5055Institut de Systématique, Evolution, Biodiversité (ISYEB), EPHE-PSL, Université PSL, MNHN, CNRS, SU, UA, Paris, France ,grid.424469.90000 0001 2195 5365EPHE, PSL Research University, Paris, France ,Laboratoire d’Excellence CORAIL, Papetoai, French Polynesia
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abdelmoula A, Damak C, Chebbi D, Frikha F, Bouattour Y, Ben Hamad M, Chabchoub I, Ghribi M, Mona S, Ben Salah R, Marzouk S, Bahloul Z. La maladie de Still de l’adulte, une étiologie rare de l’insuffisance hépatique aiguë. Rev Med Interne 2022. [DOI: 10.1016/j.revmed.2022.10.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Lesturgie P, Planes S, Mona S. Coalescence times, life history traits and conservation concerns: An example from four coastal shark species from the Indo-Pacific. Mol Ecol Resour 2021; 22:554-566. [PMID: 34407294 DOI: 10.1111/1755-0998.13487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/27/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022]
Abstract
Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographical ranges and less mobile ones organized in metapopulations exchanging migrants to different degrees. In turn, population structure directly influences the coalescence pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (Ne ) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed Ne trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (metapopulation) and unstructured models and then inferred the Ne variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed Ne dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.
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Affiliation(s)
- Pierre Lesturgie
- Institut de Systématique, Evolution, Biodiversité, ISYEB (UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB (UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia.,EPHE, PSL Research University, Paris, France
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Mekki S, Damak C, Siddiqa S, Frikha F, Mona S, Ben Salah R, Marzouk S, Bahloul Z. Purpura vasculaire : série monocentrique de 73 cas suivis en médecine interne. Rev Med Interne 2021. [DOI: 10.1016/j.revmed.2021.03.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Derbel A, Mona S, Mouna G, Sahar M, Damak C, Ben Salah R, Frikha F, Sameh M, Bahloul Z. Thromboses veineuses au cours de la maladie de Behçet : à propos de 82 cas. Rev Med Interne 2021. [DOI: 10.1016/j.revmed.2021.03.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Chabchoub I, Dammak C, Ben Salah R, Frikha F, Mona S, Marzouk S, Bahloul Z. Un sarcome d’Ewing simulant une adénopathie sus claviculaire : à propos d’un cas. Rev Med Interne 2021. [DOI: 10.1016/j.revmed.2021.03.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Feutry P, Devloo-Delva F, Tran Lu Y A, Mona S, Gunasekera RM, Johnson G, Pillans RD, Jaccoud D, Kilian A, Morgan DL, Saunders T, Bax NJ, Kyne PM. One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark. Mol Ecol Resour 2020; 20:1470-1485. [PMID: 32492756 DOI: 10.1111/1755-0998.13204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 01/25/2023]
Abstract
With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close-Kin Mark-Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost-efficient method that combines DArTseq and sequence capture, and illustrate its use in a high resolution population analysis of Glyphis garricki, a rare, poorly known and threatened euryhaline shark. Clustering analyses and spatial distribution of kin pairs from four different regions across northern Australia and one in Papua New Guinea, representing its entire known range, revealed that each region hosts at least one distinct population. Further structuring is likely within Van Diemen Gulf, the region that included the most rivers sampled, suggesting additional population structuring would be found if other rivers were sampled. Coalescent analyses and spatially explicit modelling suggest that G. garricki experienced a recent range expansion during the opening of the Gulf of Carpentaria following the conclusion of the Last Glacial Maximum. The low migration rates between neighbouring populations of a species that is found only in restricted coastal and riverine habitats show the importance of managing each population separately, including careful monitoring of local and remote anthropogenic activities that may affect their environments. Overall we demonstrated how a carefully chosen SNP panel combined with DArTcap can provide highly accurate kinship inference and also support population structure and historical demography analyses, therefore maximising cost-effectiveness.
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Affiliation(s)
| | - Floriaan Devloo-Delva
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia.,School of Natural Sciences - Quantitative Marine Science, University of Tasmania, Hobart, TAS, Australia
| | - Adrien Tran Lu Y
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, Paris, France.,EPHE, PSL University, Paris, France
| | - Stefano Mona
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, Paris, France.,EPHE, PSL University, Paris, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | | | - Grant Johnson
- Department of Primary Industry and Fisheries, Aquatic Resource Research Unit, Darwin, NT, Australia
| | | | - Damian Jaccoud
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - David L Morgan
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Thor Saunders
- Department of Primary Industry and Fisheries, Aquatic Resource Research Unit, Darwin, NT, Australia
| | - Nicholas J Bax
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia.,Institute for Marine and Antarctic Science, University of Tasmania, Hobart, TAS, Australia
| | - Peter M Kyne
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
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12
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Delrieu-Trottin E, Hubert N, Giles EC, Chifflet-Belle P, Suwalski A, Neglia V, Rapu-Edmunds C, Mona S, Saenz-Agudelo P. Coping with Pleistocene climatic fluctuations: Demographic responses in remote endemic reef fishes. Mol Ecol 2020; 29:2218-2233. [PMID: 32428327 DOI: 10.1111/mec.15478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 12/28/2022]
Abstract
Elucidating demographic history during the settlement of ecological communities is crucial for properly inferring the mechanisms that shape patterns of species diversity and their persistence through time. Here, we used genomic data and coalescent-based approaches to elucidate for the first time the demographic dynamics associated with the settlement by endemic reef fish fauna of one of the most remote peripheral islands of the Pacific Ocean, Rapa Nui (Easter Island). We compared the demographic history of nine endemic species in order to explore their demographic responses to Pleistocene climatic fluctuations. We found that species endemic to Rapa Nui share a common demographic history, as signatures of population expansions were retrieved for almost all of the species studied here, and synchronous demographic expansions initiated during the last glacial period were recovered for more than half of the studied species. These results suggest that eustatic fluctuations associated with Milankovitch cycles have played a central role in species demographic histories and in the final stage of the community assembly of many Rapa Nui reef fishes. Specifically, sea level lowstands resulted in the maximum reef habitat extension for Rapa Nui endemic species; we discuss the potential role of seamounts in allowing endemic species to cope with Pleistocene climatic fluctuations, and we highlight the importance of local historical processes over regional ones. Overall, our results shed light on the mechanisms by which endemism arises and is maintained in peripheral reef fish fauna.
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Affiliation(s)
- Erwan Delrieu-Trottin
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Institut de Recherche pour le Développement, UMR 5554 (UM-CNRS-IRD-EPHE), ISEM, Montpellier, France.,Museum für Naturkunde, Leibniz-Institut für Evolutions-und Biodiversitätsforschung an der, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicolas Hubert
- Institut de Recherche pour le Développement, UMR 5554 (UM-CNRS-IRD-EPHE), ISEM, Montpellier, France
| | - Emily C Giles
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Programa de Doctorado en Ciencias mención Ecología y Evolución, Escuela de Graduados, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pascaline Chifflet-Belle
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Arnaud Suwalski
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Valentina Neglia
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | | | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
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13
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Khimoun A, Doums C, Molet M, Kaufmann B, Peronnet R, Eyer PA, Mona S. Urbanization without isolation: the absence of genetic structure among cities and forests in the tiny acorn ant Temnothorax nylanderi. Biol Lett 2020; 16:20190741. [PMID: 31992150 DOI: 10.1098/rsbl.2019.0741] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Urban alteration of neutral and adaptive evolutionary processes is still underexplored. Using a genome-wide SNP dataset, we investigated (i) urban-induced modifications of population demography, genetic diversity and population structure and (ii) signature of divergent selection between urban and forest populations in the ant species, Temnothorax nylanderi. Our results did not reveal an impact of urbanization on neutral processes since we observed: (i) analogous genetic diversity among paired urban/forest sites and two control populations; (ii) weak population genetic structure explained neither by habitat (urban versus forest) nor by geography; (iii) a remarkably similar demographic history across populations with an ancestral growth followed by a recent decline, regardless of their current habitat or geographical location. The micro-geographical home range of ants may explain their resilience to urbanization. Finally, we detected 19 candidate loci discriminating urban/forest populations and associated with core cellular components, molecular function or biological process. Two of these loci were associated with a gene ontology term that was previously found to belong to a module of co-expressed genes related to caste phenotype. These results call for transcriptomics analyses to identify genes associated with ant social traits and to infer their potential role in urban adaptation.
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Affiliation(s)
- A Khimoun
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000 Dijon, France
| | - C Doums
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, 75005 Paris, France.,EPHE, PSL University, 75005 Paris, France
| | - M Molet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), UMR 7618, Sorbonne Université, Université Paris Est Créteil, Université Paris Diderot, CNRS, INRA, IRD, 75005 Paris, France
| | - B Kaufmann
- Université de Lyon, UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Lyon 1, ENTPE, CNRS, Villeurbanne 69622, France
| | - R Peronnet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), UMR 7618, Sorbonne Université, Université Paris Est Créteil, Université Paris Diderot, CNRS, INRA, IRD, 75005 Paris, France
| | - P A Eyer
- Department of Entomology, Texas A&M University, 2143 TAMU, College Station, TX 77843-2143, USA
| | - S Mona
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, 75005 Paris, France.,EPHE, PSL University, 75005 Paris, France
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14
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Daher B, Bouyetse K, Haddaoui H, Rachida Z, Mona S, Karima M, Benamour J, Bourkadi J. Impact de l’observance sur le contrôle de l’asthme. Rev Mal Respir 2019. [DOI: 10.1016/j.rmr.2018.10.388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Lalis A, Mona S, Stoetzel E, Bonhomme F, Souttou K, Ouarour A, Aulagnier S, Denys C, Nicolas V. Out of Africa: demographic and colonization history of the Algerian mouse (Mus spretus Lataste). Heredity (Edinb) 2018; 122:150-171. [PMID: 29795180 DOI: 10.1038/s41437-018-0089-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/28/2018] [Accepted: 04/16/2018] [Indexed: 11/09/2022] Open
Abstract
North Africa is now recognized as a major area for the emergence and dispersal of anatomically modern humans from at least 315 kya. The Mediterranean Basin is thus particularly suited to study the role of climate versus human-mediated changes on the evolutionary history of species. The Algerian mouse (Mus spretus Lataste) is an endemic species from this basin, with its distribution restricted to North Africa (from Libya to Morocco), Iberian Peninsula and South of France. A rich paleontological record of M. spretus exists in North Africa, suggesting hypotheses concerning colonization pathways, and the demographic and morphologic history of this species. Here we combined genetic (3 mitochondrial DNA loci and 18 microsatellites) and climatic niche modeling data to infer the evolutionary history of the Algerian mouse. We collected 646 new individuals in 51 localities. Our results are consistent with an anthropogenic translocation of the Algerian mouse from North Africa to the Iberian Peninsula via Neolithic navigators, probably from the Tingitane Peninsula. Once arrived in Spain, suitable climatic conditions would then have favored the dispersion of the Algerian mice to France. The morphological differentiation observed between Spanish, French and North African populations could be explained by a founder effect and possibly local adaptation. This article helps to better understand the role of climate versus human-mediated changes on the evolutionary history of mammal species in the Mediterranean Basin.
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Affiliation(s)
- Aude Lalis
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Emmanuelle Stoetzel
- Histoire Naturelle de l'Homme Préhistorique, HNHP-UMR 7194-CNRS, MNHN, UPVD, Sorbonne Universités, Paris, France
| | - François Bonhomme
- Institut des Sciences de l'Evolution, ISEM-UMR 4554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Karim Souttou
- Department of Agronomy, Faculty of Natural Science and Life, University Ziane Achour, Djelfa, Algeria
| | - Ali Ouarour
- Laboratoire de Biologie et Santé, Faculté des Sciences, Université Abdelmalek Essâadi, Tétouan, Morocco
| | - Stéphane Aulagnier
- Institut National de la Recherche Agronomique, UR35 Comportement et Ecologie de la Faune Sauvage, Caytanet-Tolosan, France
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France.
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16
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Benazzo A, Trucchi E, Cahill JA, Maisano Delser P, Mona S, Fumagalli M, Bunnefeld L, Cornetti L, Ghirotto S, Girardi M, Ometto L, Panziera A, Rota-Stabelli O, Zanetti E, Karamanlidis A, Groff C, Paule L, Gentile L, Vilà C, Vicario S, Boitani L, Orlando L, Fuselli S, Vernesi C, Shapiro B, Ciucci P, Bertorelle G. Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers. Proc Natl Acad Sci U S A 2017; 114:E9589-E9597. [PMID: 29078308 PMCID: PMC5692547 DOI: 10.1073/pnas.1707279114] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
About 100 km east of Rome, in the central Apennine Mountains, a critically endangered population of ∼50 brown bears live in complete isolation. Mating outside this population is prevented by several 100 km of bear-free territories. We exploited this natural experiment to better understand the gene and genomic consequences of surviving at extremely small population size. We found that brown bear populations in Europe lost connectivity since Neolithic times, when farming communities expanded and forest burning was used for land clearance. In central Italy, this resulted in a 40-fold population decline. The overall genomic impact of this decline included the complete loss of variation in the mitochondrial genome and along long stretches of the nuclear genome. Several private and deleterious amino acid changes were fixed by random drift; predicted effects include energy deficit, muscle weakness, anomalies in cranial and skeletal development, and reduced aggressiveness. Despite this extreme loss of diversity, Apennine bear genomes show nonrandom peaks of high variation, possibly maintained by balancing selection, at genomic regions significantly enriched for genes associated with immune and olfactory systems. Challenging the paradigm of increased extinction risk in small populations, we suggest that random fixation of deleterious alleles (i) can be an important driver of divergence in isolation, (ii) can be tolerated when balancing selection prevents random loss of variation at important genes, and (iii) is followed by or results directly in favorable behavioral changes.
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Affiliation(s)
- Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Emiliano Trucchi
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo 1066, Norway
| | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Pierpaolo Maisano Delser
- Institute de Systematics, Evolution, Biodiversite, UMR 7205-CNRS, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, École Pratique des Hautes Études (EPHE), CP39, 75005 Paris, France
- EPHE, Paris Sciences & Lettres Research University, 75005 Paris, France
- Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin 2, Ireland
| | - Stefano Mona
- Institute de Systematics, Evolution, Biodiversite, UMR 7205-CNRS, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, École Pratique des Hautes Études (EPHE), CP39, 75005 Paris, France
- EPHE, Paris Sciences & Lettres Research University, 75005 Paris, France
| | - Matteo Fumagalli
- Department of Life Sciences, Imperial College London, Ascot SL5 7PY, United Kingdom
| | - Lynsey Bunnefeld
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
- Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom
| | - Luca Cornetti
- Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Matteo Girardi
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, 38010 San Michele all'Adige, Italy
| | - Lino Ometto
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all'Adige, Italy
- Independent Researcher, 38016 Mezzocorona, Italy
| | - Alex Panziera
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all'Adige, Italy
| | - Enrico Zanetti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Alexandros Karamanlidis
- Protection and Management of Wildlife and the Natural Environment, ARCTUROS, 53075 Aetos, Florina, Greece
| | - Claudio Groff
- Forest and Wildlife Service, Provincia Autonoma di Trento, 38100 Trento, Italy
| | - Ladislav Paule
- Department of Phytology, Faculty of Forestry, Technical University, 96053 Zvolen, Slovakia
| | - Leonardo Gentile
- Veterinary Service, National Park of Abruzzo Lazio and Molise, 67032 Pescasseroli, Italy
| | - Carles Vilà
- Department of Integrative Ecology, Doñana Biological Station, Consejo Superior de Investigaciones Científicas, 4102 Seville, Spain
| | - Saverio Vicario
- Institute of Atmospheric Pollution Research and Technologies, National Research Council, 70126 Bari, Italy
| | - Luigi Boitani
- Department of Biology and Biotechnologies "Charles Darwin," University of Rome La Sapienza, 00185 Rome, Italy
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 K Copenhagen, Denmark
| | - Silvia Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, 38010 San Michele all'Adige, Italy
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Paolo Ciucci
- Department of Biology and Biotechnologies "Charles Darwin," University of Rome La Sapienza, 00185 Rome, Italy
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy;
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Corrigan S, Maisano Delser P, Eddy C, Duffy C, Yang L, Li C, Bazinet AL, Mona S, Naylor GJ. Historical introgression drives pervasive mitochondrial admixture between two species of pelagic sharks. Mol Phylogenet Evol 2017; 110:122-126. [DOI: 10.1016/j.ympev.2017.03.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 02/16/2017] [Accepted: 03/08/2017] [Indexed: 11/26/2022]
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Delrieu-Trottin E, Mona S, Maynard J, Neglia V, Veuille M, Planes S. Population expansions dominate demographic histories of endemic and widespread Pacific reef fishes. Sci Rep 2017; 7:40519. [PMID: 28091580 PMCID: PMC5238389 DOI: 10.1038/srep40519] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 12/07/2016] [Indexed: 12/20/2022] Open
Abstract
Despite the unique nature of endemic species, their origin and population history remain poorly studied. We investigated the population history of 28 coral reef fish species, close related, from the Gambier and Marquesas Islands, from five families, with range size varying from widespread to small-range endemic. We analyzed both mitochondrial and nuclear sequence data using neutrality test and Bayesian analysis (EBSP and ABC). We found evidence for demographic expansions for most species (24 of 28), irrespective of range size, reproduction strategy or archipelago. The timing of the expansions varied greatly among species, from 8,000 to 2,000,000 years ago. The typical hypothesis for reef fish that links population expansions to the Last Glacial Maximum fit for 14 of the 24 demographic expansions. We propose two evolutionary processes that could lead to expansions older than the LGM: (a) we are retrieving the signature of an old colonization process for widespread, large-range endemic and paleoendemic species or (b) speciation; the expansion reflects the birth of the species for neoendemic species. We show for the first time that the demographic histories of endemic and widespread reef fish are not distinctly different and suggest that a number of processes drive endemism.
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Affiliation(s)
- Erwan Delrieu-Trottin
- Laboratoire d'Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France.,Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Stefano Mona
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 - CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, Paris Sorbonne Universités, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Jeffrey Maynard
- Laboratoire d'Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France.,SymbioSeas and Marine Applied Research Center, Wilmington NC 28411, United States of America
| | - Valentina Neglia
- Laboratoire d'Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France.,Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Michel Veuille
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 - CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, Paris Sorbonne Universités, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Serge Planes
- Laboratoire d'Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France
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Salah RB, Frikha F, Karima S, Damak C, Jallouli M, Mona S, Marzouk S, Bahloul Z. Les thromboses veineuses profondes du sujet âgé : à propos de 102 cas. Rev Med Interne 2016. [DOI: 10.1016/j.revmed.2016.10.154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Mona S. On the role played by the carrying capacity and the ancestral population size during a range expansion. Heredity (Edinb) 2016; 118:143-153. [PMID: 27599574 DOI: 10.1038/hdy.2016.73] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 07/19/2016] [Accepted: 07/26/2016] [Indexed: 01/05/2023] Open
Abstract
Most species are structured and various population genetics models have been proposed to investigate their history. For mathematical tractability, most of these models make the simplifying assumption of equilibrium. Here we focus on the properties of a nonequilibrium spatial explicit model, range expansions (REs). Despite their abundance, many details of their genetic consequences need yet to be fully investigated. The model we studied is characterized by four main parameters: the effective population size of each deme (N), the migration rate per generation per deme (m), the time of the expansion (Texp) and the effective size of the deme from which the expansion started (Nanc). By means of extensive coalescent simulations, we focused on two aspects of range expansions for fixed Nm: (1) the separate influence of N and m and (2) the role of Nanc. We compared our results with an equilibrium stepping stone model and found two main features typical of REs: an excess of rare variants for larger N and a complex interaction between N, Texp and Nanc in shaping the degree of population differentiation (which depends only on Nm in the stepping stone model). Finally, we developed an approximate Bayesian computation approach to jointly estimate N and m and to infer Nanc. When applied to pseudo-observed data sets, we could correctly recover both N and m (but not Nanc), provided a large number of demes were sampled. These findings highlight how it will be possible to estimate the dispersal rate in nonequilibrium metapopulations by using population genetics approaches.
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Affiliation(s)
- S Mona
- EPHE, PSL Research University, Paris, France.,Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 - CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, Paris Sorbonne Universités, Paris, France
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Boitard S, Rodríguez W, Jay F, Mona S, Austerlitz F. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach. PLoS Genet 2016; 12:e1005877. [PMID: 26943927 PMCID: PMC4778914 DOI: 10.1371/journal.pgen.1005877] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 01/27/2016] [Indexed: 12/02/2022] Open
Abstract
Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles. Molecular data sampled from extant individuals contains considerable information about their demographic history. In particular, one classical question in population genetics is to reconstruct past population size changes from such data. Relating these changes to various climatic, geological or anthropogenic events allows characterizing the main factors driving genetic diversity and can have major outcomes for conservation. Until recently, mostly very simple histories, including one or two population size changes, could be estimated from genetic data. This has changed with the sequencing of entire genomes in many species, and several methods allow now inferring complex histories consisting of several tens of population size changes. However, analyzing entire genomes, while accounting for recombination, remains a statistical and numerical challenge. These methods, therefore, can only be applied to small samples with a few diploid genomes. We overcome this limitation by using an approximate estimation approach, where observed genomes are summarized using a small number of statistics related to allele frequencies and linkage disequilibrium. In contrast to previous approaches, we show that our method allows us to reconstruct also the most recent part (the last 100 generations) of the population size history. As an illustration, we apply it to large samples of whole-genome sequences in four cattle breeds.
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Affiliation(s)
- Simon Boitard
- Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - CNRS & MNHN & UPMC & EPHE, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- * E-mail:
| | - Willy Rodríguez
- UMR CNRS 5219, Institut de Mathématiques de Toulouse, Université de Toulouse, Toulouse, France
| | - Flora Jay
- UMR 7206 Eco-anthropologie et Ethnobiologie, Muséum National d’Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France
- LRI, Paris-Sud University, CNRS UMR 8623, Orsay, France
| | - Stefano Mona
- Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - CNRS & MNHN & UPMC & EPHE, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
| | - Frédéric Austerlitz
- UMR 7206 Eco-anthropologie et Ethnobiologie, Muséum National d’Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France
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Marra A, Mona S, Sà RM, D’Onghia G, Maiorano P. Population genetic history of Aristeus antennatus (Crustacea: Decapoda) in the Western and Central Mediterranean Sea. PLoS One 2015; 10:e0117272. [PMID: 25775363 PMCID: PMC4361500 DOI: 10.1371/journal.pone.0117272] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/22/2014] [Indexed: 11/18/2022] Open
Abstract
Aristeus antennatus is an ecologically and economically important deep-water species in the Mediterranean Sea. In this study we investigated the genetic variability of A. antennatus sampled from 10 sampling stations in the Western and Central Mediterranean. By comparing our new samples with available data from the Western area, we aim to identify potential genetic stocks of A. antennatus and to reconstruct its historical demography in the Mediterranean. We analyzed two regions of mitochondrial DNA in 319 individuals, namely COI and 16S. We found two main results: i) the genetic diversity values consistent with previous data within the Mediterranean and the absence of barriers to gene flow within the Mediterranean Sea; ii) a constant long-term effective population size in almost all demes but a strong signature of population expansion in the pooled sample about 50,000 years B.P./ago. We propose two explanation for our results. The first is based on the ecology of A. antennatus. We suggest the existence of a complex meta-population structured into two layers: a deeper-dwelling stock, not affected by fishing, which preserves the pattern of historical demography; and genetically homogeneous demes inhabiting the fishing grounds. The larval dispersal, adult migration and continuous movements of individuals from “virgin” deeper grounds not affected by fishing to upper fishing areas support an effective ‘rescue effect’ contributing to the recovery of the exploited stocks and explain their genetic homogeneity throughout the Mediterranean Sea. The second is based on the reproduction model of this shrimp: the high variance in offspring production calls for a careful interpretation of the data observed under classical population genetics and Kingman’s coalescent. In both cases, management policies for A. antennatus will therefore require careful evaluation of the meta-population dynamics of all stocks in the Mediterranean. In the future, it will be particularly relevant to sample the deepest ones directly.
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Affiliation(s)
- Annamaria Marra
- Biology Department, University of Bari, Bari, Italy
- * E-mail:
| | - Stefano Mona
- Laboratoire Biologie intégrative des populations, Ecole Pratique des Hautes Etudes, Paris, France
| | - Rui M. Sà
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
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Merker M, Blin C, Mona S, Duforet-Frebourg N, Lecher S, Willery E, Blum MGB, Rüsch-Gerdes S, Mokrousov I, Aleksic E, Allix-Béguec C, Antierens A, Augustynowicz-Kopeć E, Ballif M, Barletta F, Beck HP, Barry CE, Bonnet M, Borroni E, Campos-Herrero I, Cirillo D, Cox H, Crowe S, Crudu V, Diel R, Drobniewski F, Fauville-Dufaux M, Gagneux S, Ghebremichael S, Hanekom M, Hoffner S, Jiao WW, Kalon S, Kohl TA, Kontsevaya I, Lillebæk T, Maeda S, Nikolayevskyy V, Rasmussen M, Rastogi N, Samper S, Sanchez-Padilla E, Savic B, Shamputa IC, Shen A, Sng LH, Stakenas P, Toit K, Varaine F, Vukovic D, Wahl C, Warren R, Supply P, Niemann S, Wirth T. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat Genet 2015; 47:242-9. [PMID: 25599400 PMCID: PMC11044984 DOI: 10.1038/ng.3195] [Citation(s) in RCA: 353] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/19/2014] [Indexed: 01/18/2023]
Abstract
Mycobacterium tuberculosis strains of the Beijing lineage are globally distributed and are associated with the massive spread of multidrug-resistant (MDR) tuberculosis in Eurasia. Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 110 representative isolates. We show that this lineage initially originated in the Far East, from where it radiated worldwide in several waves. We detected successive increases in population size for this pathogen over the last 200 years, practically coinciding with the Industrial Revolution, the First World War and HIV epidemics. Two MDR clones of this lineage started to spread throughout central Asia and Russia concomitantly with the collapse of the public health system in the former Soviet Union. Mutations identified in genes putatively under positive selection and associated with virulence might have favored the expansion of the most successful branches of the lineage.
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Affiliation(s)
- Matthias Merker
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Camille Blin
- 1] Laboratoire Biologie Intégrative des Population, Evolution Moléculaire, Ecole Pratique des Hautes Etudes, Paris, France. [2] Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
| | - Stefano Mona
- 1] Laboratoire Biologie Intégrative des Population, Evolution Moléculaire, Ecole Pratique des Hautes Etudes, Paris, France. [2] Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
| | - Nicolas Duforet-Frebourg
- Université Joseph Fourier, Centre National de la Recherche Scientifique, Laboratoire Techniques de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Grenoble, France
| | - Sophie Lecher
- 1] INSERM U1019, Center for Infection and Immunity of Lille, Lille, France. [2] Centre National de la Recherche Scientifique, UMR 8204, Lille, France. [3] Université Lille Nord, Center for Infection and Immunity of Lille, Lille, France. [4] Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Eve Willery
- 1] INSERM U1019, Center for Infection and Immunity of Lille, Lille, France. [2] Centre National de la Recherche Scientifique, UMR 8204, Lille, France. [3] Université Lille Nord, Center for Infection and Immunity of Lille, Lille, France. [4] Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Michael G B Blum
- Université Joseph Fourier, Centre National de la Recherche Scientifique, Laboratoire Techniques de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Grenoble, France
| | - Sabine Rüsch-Gerdes
- National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Igor Mokrousov
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Eman Aleksic
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
| | | | - Annick Antierens
- Medical Department, Médecins sans Frontières Switzerland, Geneva, Switzerland
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Marie Ballif
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Francesca Barletta
- Instituto de Medicina Tropical Alexander von Humboldt, Molecular Epidemiology Unit-Tuberculosis, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Hans Peter Beck
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Clifton E Barry
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | | | - Emanuele Borroni
- Emerging Bacterial Pathogens Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Isolina Campos-Herrero
- Department of Microbiology, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Daniela Cirillo
- Emerging Bacterial Pathogens Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Helen Cox
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Suzanne Crowe
- 1] Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia. [2] Department of Infectious Diseases, Alfred Hospital, Melbourne, Victoria, Australia. [3] Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Valeriu Crudu
- National Tuberculosis Reference Laboratory, Phthysiopneumology Institute, Chisinau, Republic of Moldova
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, Kiel, Germany
| | - Francis Drobniewski
- 1] Public Health England National Mycobacterial Reference Laboratory and Clinical Tuberculosis and Human Immunodeficiency Virus Group, Queen Mary's School of Medicine and Dentistry, London, UK. [2] Department of Infectious Diseases, Imperial College, London, UK
| | | | - Sébastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | | | - Madeleine Hanekom
- Department of Science and Technology/National Research Foundation, Centre of Excellence for Biomedical Tuberculosis Research/Medical Research Council, Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Sven Hoffner
- Department of Diagnostics and Vaccinology, Swedish Institute for Communicable Disease Control, Solna, Sweden
| | - Wei-wei Jiao
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Stobdan Kalon
- US Agency for International Development Quality Health Care Project, Bishkek, Kyrgyzstan
| | - Thomas A Kohl
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
| | | | - Troels Lillebæk
- Statens Serum Institute, International Reference Laboratory of Mycobacteriology, Copenhagen, Denmark
| | - Shinji Maeda
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Vladyslav Nikolayevskyy
- 1] Public Health England National Mycobacterial Reference Laboratory and Clinical Tuberculosis and Human Immunodeficiency Virus Group, Queen Mary's School of Medicine and Dentistry, London, UK. [2] Department of Infectious Diseases, Imperial College, London, UK
| | - Michael Rasmussen
- Statens Serum Institute, International Reference Laboratory of Mycobacteriology, Copenhagen, Denmark
| | - Nalin Rastogi
- World Health Organization Supranational Tuberculosis Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, France
| | - Sofia Samper
- Instituto de Investigación Sanitaria Aragón, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | | | - Branislava Savic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Isdore Chola Shamputa
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Adong Shen
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Li-Hwei Sng
- Central Tuberculosis Laboratory, Department of Pathology, Singapore General Hospital, Singapore
| | - Petras Stakenas
- Department of Immunology and Cell Biology, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Kadri Toit
- Tartu University Hospital United Laboratories, Mycobacteriology, Tartu, Estonia
| | | | - Dragana Vukovic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Robin Warren
- Department of Science and Technology/National Research Foundation, Centre of Excellence for Biomedical Tuberculosis Research/Medical Research Council, Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Philip Supply
- 1] INSERM U1019, Center for Infection and Immunity of Lille, Lille, France. [2] Centre National de la Recherche Scientifique, UMR 8204, Lille, France. [3] Université Lille Nord, Center for Infection and Immunity of Lille, Lille, France. [4] Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France. [5] Genoscreen, Lille, France
| | - Stefan Niemann
- 1] Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany. [2] German Center for Infection Research, Borstel Site, Borstel, Germany
| | - Thierry Wirth
- 1] Laboratoire Biologie Intégrative des Population, Evolution Moléculaire, Ecole Pratique des Hautes Etudes, Paris, France. [2] Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
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Mona S, Ray N, Arenas M, Excoffier L. Genetic consequences of habitat fragmentation during a range expansion. Heredity (Edinb) 2013; 112:291-9. [PMID: 24149654 DOI: 10.1038/hdy.2013.105] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 09/03/2013] [Accepted: 09/06/2013] [Indexed: 11/09/2022] Open
Abstract
We investigate the effect of habitat fragmentation on the genetic diversity of a species experiencing a range expansion. These two evolutionary processes have not been studied yet, at the same time, owing to the difficulties of deriving analytic results for non-equilibrium models. Here we provide a description of their interaction by using extensive spatial and temporal coalescent simulations and we suggest guidelines for a proper genetic sampling to detect fragmentation. To model habitat fragmentation, we simulated a two-dimensional lattice of demes partitioned into groups (patches) by adding barriers to dispersal. After letting a population expand on this grid, we sampled lineages from the lattice at several scales and studied their coalescent history. We find that in order to detect fragmentation, one needs to extensively sample at a local level rather than at a landscape level. This is because the gene genealogy of a scattered sample is less sensitive to the presence of genetic barriers. Considering the effect of temporal changes of fragmentation intensities, we find that at least 10, but often >100, generations are needed to affect local genetic diversity and population structure. This result explains why recent habitat fragmentation does not always lead to detectable signatures in the genetic structure of populations. Finally, as expected, long-distance dispersal increases local genetic diversity and decreases levels of population differentiation, efficiently counteracting the effects of fragmentation.
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Affiliation(s)
- S Mona
- 1] Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Berne, Berne, Switzerland [2] Swiss Institute of Bioinformatics, Lausanne, Switzerland [3] Department of Systematics and Evolution, Muséum National d'Histoire Naturelle, Ecole Pratique des Hautes Etudes, UMR-CNRS 7205, Paris, France
| | - N Ray
- EnviroSPACE Laboratory, Institute for Environmental Sciences, University of Geneva, Carouge, Switzerland
| | - M Arenas
- 1] Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Berne, Berne, Switzerland [2] Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - L Excoffier
- 1] Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Berne, Berne, Switzerland [2] Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Mona S, Mordret E, Veuille M, Tommaseo-Ponzetta M. Investigating sex-specific dynamics using uniparental markers: West New Guinea as a case study. Ecol Evol 2013; 3:2647-60. [PMID: 24567829 PMCID: PMC3930047 DOI: 10.1002/ece3.660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/27/2013] [Accepted: 05/31/2013] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial DNA (mtDNA) and Y chromosome (NRY) genetic markers have been often contrasted to investigate sex-specific dynamics. Traditionally, isolation by distance, intrapopulation genetic diversity and population differentiation are estimated from both markers and compared. Two possible sources of bias are often neglected. First, kilometric distances are frequently used as predictor of the connectivity between groups, hiding the role played by environmental features at a microgeographic scale. Second, the comparison of intrapopulation diversity and population differentiation between mtDNA and NRY is hampered by their different mutational mechanisms and rates. Here, we show how to account for these biases by analyzing from a different perspective a published dataset of eight West New Guinea (WNG) populations for which mtDNA control region sequences and seven linked NRY microsatellites had been typed. First, we modeled the connectivity among sampled populations by computing the number of days required to travel between groups. Then, we investigated the differences between the two sexes accounting for the molecular characteristics of the markers examined to obtain estimates on the product of the effective population size and the migration rate among demes (Nm). We achieved this goal by studying the shape of the gene genealogy at several sampling levels and using spatial explicit simulations. Both the direction and the rate of migration differ between male and females, with an Nm estimated to be >6 times higher in the latter under many evolutionary scenarios. We finally highlight the importance of applying metapopulation models when analyzing the genetic diversity of a species. We have applied the prediction of the sampling theory in a meta-population and we have corroborated our finding using spatial explicit simulations. Both approaches are fundamentally meant to deal with structured populations: we strongly believe in the importance of tacking structure into account when inferring the demographic history of a species.
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Affiliation(s)
- Stefano Mona
- Laboratoire Biologie intégrative des populations, Ecole Pratique des Hautes Etudes 46 rue de Lille, 75007, Paris, France ; CNRS UMR 7205, Muséum National d'Histoire Naturelle Rue Buffon, 75005, Paris, France
| | - Ernest Mordret
- Laboratoire Biologie intégrative des populations, Ecole Pratique des Hautes Etudes 46 rue de Lille, 75007, Paris, France ; CNRS UMR 7205, Muséum National d'Histoire Naturelle Rue Buffon, 75005, Paris, France
| | - Michel Veuille
- Laboratoire Biologie intégrative des populations, Ecole Pratique des Hautes Etudes 46 rue de Lille, 75007, Paris, France ; CNRS UMR 7205, Muséum National d'Histoire Naturelle Rue Buffon, 75005, Paris, France
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Tommaseo-Ponzetta M, Mona S, Calabrese F, Konrad G, Vacca E, Attimonelli M. Mountain Pygmies of Western New Guinea: A Morphological and Molecular Approach. Hum Biol 2013; 85:285-308. [DOI: 10.3378/027.085.0314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
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Porretta D, Mastrantonio V, Mona S, Epis S, Montagna M, Sassera D, Bandi C, Urbanelli S. The integration of multiple independent data reveals an unusual response to Pleistocene climatic changes in the hard tick Ixodes ricinus. Mol Ecol 2013; 22:1666-82. [PMID: 23398505 DOI: 10.1111/mec.12203] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 11/29/2012] [Accepted: 11/29/2012] [Indexed: 11/29/2022]
Abstract
In the last few years, improved analytical tools and the integration of genetic data with multiple sources of information have shown that temperate species exhibited more complex responses to ice ages than previously thought. In this study, we investigated how Pleistocene climatic changes affected the current distribution and genetic diversity of European populations of the tick Ixodes ricinus, an ectoparasite with high ecological plasticity. We first used mitochondrial and nuclear genetic markers to investigate the phylogeographic structure of the species and its Pleistocene history using coalescent-based methods; then we used species distribution modelling to infer the climatic niche of the species at last glacial maximum; finally, we reviewed the literature on the I. ricinus hosts to identify the locations of their glacial refugia. Our results support the scenario that during the last glacial phase, I. ricinus never experienced a prolonged allopatric divergence in separate glacial refugia, but persisted with interconnected populations across Southern and Central Europe. The generalist behaviour in host choice of I. ricinus would have played a major role in maintaining connections between its populations. Although most of the hosts persisted in separate refugia, from the point of view of I. ricinus, they represented a continuity of 'bridges' among populations. Our study highlights the importance of species-specific ecology in affecting responses to Pleistocene glacial-interglacial cycles. Together with other cases in Europe and elsewhere, it contributes to setting new hypotheses on how species with wide ecological plasticity coped with Pleistocene climatic changes.
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Affiliation(s)
- Daniele Porretta
- Department of Ecological and Biological Sciences, Tuscia University, Viterbo, Italy.
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Frezal L, Meli F, Mousset S, Mona S, Veuille M. Geographical delimitation of a partial selective sweep in African Drosophila melanogaster. Mol Ecol 2012; 21:5702-14. [PMID: 23110353 DOI: 10.1111/mec.12004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 06/23/2012] [Accepted: 07/10/2012] [Indexed: 11/30/2022]
Abstract
Positive selection leaves characteristic footprints on DNA variation but detecting such patterns is challenging as the age, the intensity and the mode of selection as well as demography and evolutionary parameters (mutation and recombination rates) all play roles and these are difficult to disentangle. We recorded nucleotide variation in a sample of isogenic chromosomes from a western African population of Drosophila melanogaster at a locus (Fbp2) for which a partial selective sweep had previously been reported. We compared this locus to four other genes from the same chromosomes and from a European and an East African population. Then, we assessed Fbp2 variation in a sample of 370 chromosomes covering a comprehensive geographic sampling of 16 African localities. The signature of selection was tested while accounting for the demographic history of the populations. We found a significant signal of selection in two West African localities including Ivory Coast. Variation at Fpb2 would thus represent a case of an ongoing selective sweep in the range of this species. A weaker, nonsignificant, signal of selection was, however, apparent in some other populations, thus leaving open several possibilities: (i) the selective sweep originated in Ivory Coast and has spread to the rest of the continent; (ii) several African populations report the signature of a selective event having occurred in an ancestral population; (iii) this genome region is subject to independent selective events in African populations; and (iv) A neutral scenario with population subdivision and local bottleneck cannot be fully excluded to explain the molecular patterns observed in some populations.
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Affiliation(s)
- L Frezal
- Laboratoire Biologie intégrative des populations, Ecole Pratique des Hautes Etudes, 46 rue de Lille, 75007, Paris, France
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Abstract
The analysis of genetic variation to estimate demographic and historical parameters and to quantitatively compare alternative scenarios recently gained a powerful and flexible approach: the Approximate Bayesian Computation (ABC). The likelihood functions does not need to be theoretically specified, but posterior distributions can be approximated by simulation even assuming very complex population models including both natural and human-induced processes. Prior information can be easily incorporated and the quality of the results can be analysed with rather limited additional effort. ABC is not a statistical analysis per se, but rather a statistical framework and any specific application is a sort of hybrid between a simulation and a data-analysis study. Complete software packages performing the necessary steps under a set of models and for specific genetic markers are already available, but the flexibility of the method is better exploited combining different programs. Many questions relevant in ecology can be addressed using ABC, but adequate amount of time should be dedicated to decide among alternative options and to evaluate the results. In this paper we will describe and critically comment on the different steps of an ABC analysis, analyse some of the published applications of ABC and provide user guidelines.
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Affiliation(s)
- G Bertorelle
- Department of Biology and Evolution, University of Ferrara, Via Borsari 46, 44100 Ferrara, Italy.
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Mona S, Catalano G, Lari M, Larson G, Boscato P, Casoli A, Sineo L, Di Patti C, Pecchioli E, Caramelli D, Bertorelle G. Population dynamic of the extinct European aurochs: genetic evidence of a north-south differentiation pattern and no evidence of post-glacial expansion. BMC Evol Biol 2010; 10:83. [PMID: 20346116 PMCID: PMC2858146 DOI: 10.1186/1471-2148-10-83] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 03/26/2010] [Indexed: 11/17/2022] Open
Abstract
Background The aurochs (Bos primigenius) was a large bovine that ranged over almost the entirety of the Eurasian continent and North Africa. It is the wild ancestor of the modern cattle (Bos taurus), and went extinct in 1627 probably as a consequence of human hunting and the progressive reduction of its habitat. To investigate in detail the genetic history of this species and to compare the population dynamics in different European areas, we analysed Bos primigenius remains from various sites across Italy. Results Fourteen samples provided ancient DNA fragments from the mitochondrial hypervariable region. Our data, jointly analysed with previously published sequences, support the view that Italian aurochsen were genetically similar to modern bovine breeds, but very different from northern/central European aurochsen. Bayesian analyses and coalescent simulations indicate that the genetic variation pattern in both Italian and northern/central European aurochsen is compatible with demographic stability after the last glaciation. We provide evidence that signatures of population expansion can erroneously arise in stable aurochsen populations when the different ages of the samples are not taken into account. Conclusions Distinct groups of aurochsen probably inhabited Italy and northern/central Europe after the last glaciation, respectively. On the contrary, Italian and Fertile Crescent aurochsen likely shared several mtDNA sequences, now common in modern breeds. We argue that a certain level of genetic homogeneity characterized aurochs populations in Southern Europe and the Middle East, and also that post-glacial recolonization of northern and central Europe advanced, without major demographic expansions, from eastern, and not southern, refugia.
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Affiliation(s)
- Stefano Mona
- Dipartimento di Biologia ed Evoluzione, Università di Ferrara, Ferrara, Italy
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Ghirotto S, Mona S, Benazzo A, Paparazzo F, Caramelli D, Barbujani G. Inferring Genealogical Processes from Patterns of Bronze-Age and Modern DNA Variation in Sardinia. Mol Biol Evol 2009; 27:875-86. [DOI: 10.1093/molbev/msp292] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Crestanello B, Pecchioli E, Vernesi C, Mona S, Martínková N, Janiga M, Hauffe HC, Bertorelle G. The genetic impact of translocations and habitat fragmentation in chamois (Rupicapra) spp. ACTA ACUST UNITED AC 2009; 100:691-708. [PMID: 19617524 DOI: 10.1093/jhered/esp053] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The chamois is a useful species with which to investigate the combined genetic impact of habitat fragmentation, over hunting, and translocations. Genetic variation within and between chamois (genus Rupicapra) populations was analyzed in 259 individuals from 16 sampling sites located in Italy, Spain, Slovakia, and the Czech Republic. Two mitochondrial DNA markers (control region and cytochrome b) and 11 nuclear microsatellites were typed. The principal results of this study can be summarized as follows: 1) high and significant differentiation between almost all chamois populations is observed even on a microgeographical scale, probably caused by the patchy distribution of this species, sharp geographical barriers to gene flow, and drift effects related to recent bottlenecks; 2) historical translocation events have left a clear genetic signature, including interspecific hybridization in some Alpine localities; 3) the Apennine subspecies of chamois, Rupicapra pyrenaica ornata, shows a high and similar level of divergence (about 1.5 My) from the Pyrenean (Rupicapra pyrenaica pyrenaica) and the Alpine (Rupicapra rupicapra) chamois; therefore, the specific status of these taxa should be revised. These results confirm the potential of population genetic analyses to dissect and interpret complex patterns of diversity in order to define factors important to conservation and management.
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Affiliation(s)
- Barbara Crestanello
- IASMA Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy
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Mona S, Grunz KE, Brauer S, Pakendorf B, Castrì L, Sudoyo H, Marzuki S, Barnes RH, Schmidtke J, Stoneking M, Kayser M. Genetic Admixture History of Eastern Indonesia as Revealed by Y-Chromosome and Mitochondrial DNA Analysis. Mol Biol Evol 2009; 26:1865-77. [PMID: 19414523 DOI: 10.1093/molbev/msp097] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Stefano Mona
- Department of Forensic Molecular Biology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
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Mona S, Crestanello B, Bankhead-Dronnet S, Pecchioli E, Ingrosso S, D'Amelio S, Rossi L, Meneguz PG, Bertorelle G. Disentangling the effects of recombination, selection, and demography on the genetic variation at a major histocompatibility complex class II gene in the alpine chamois. Mol Ecol 2009; 17:4053-67. [PMID: 19238706 DOI: 10.1111/j.1365-294x.2008.03892.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The major histocompatibility complex (MHC) harbours some of the most polymorphic loci in vertebrate genomes. MHC genes are thought to be subject to some form of balancing selection, most likely pathogen-mediated selection. Hence, MHC genes are excellent candidates for exploring adaptive processes. In this study, we investigated the genetic variation at exon 2 of the DRB class II MHC locus in 191 alpine chamois (Rupicapra rupicapra) from 10 populations in the eastern Alps of Italy. In particular, we were interested in distinguishing and estimating the relative impact of selective and demographic factors, while taking into account the confounding effect of recombination. The extremely high d(n)/d(s) ratio and the presence of trans-species polymorphisms suggest that a strong long-term balancing selection effect has been operating at this locus throughout the evolutionary history of this species. We analysed patterns of genetic variation within and between populations, and the mitochondrial D-loop polymorphism patterns were analysed to provide a baseline indicator of the effects of demographic processes. These analyses showed that (i) the chamois experienced a demographic decline in the last 5000-30 000 years, most likely related to the postglacial elevation in temperature; (ii) this demographic process can explain the results of neutrality tests applied to MHC variation within populations, but cannot justify the much weaker divergence between populations implied by MHC as opposed to mitochondrial DNA; (iii) similar sets of divergent alleles are probably maintained with similar frequencies by balancing selection in different populations, and this mechanism is also operating in small isolated populations, which are strongly affected by drift.
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Affiliation(s)
- S Mona
- Department of Biology and Evolution, University of Ferrara, Via Borsari 46, 44100 Ferrara, Italy
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Kayser M, Choi Y, van Oven M, Mona S, Brauer S, Trent RJ, Suarkia D, Schiefenhövel W, Stoneking M. The impact of the Austronesian expansion: evidence from mtDNA and Y chromosome diversity in the Admiralty Islands of Melanesia. Mol Biol Evol 2008; 25:1362-74. [PMID: 18390477 DOI: 10.1093/molbev/msn078] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The genetic ancestry of Polynesians can be traced to both Asia and Melanesia, which presumably reflects admixture occurring between incoming Austronesians and resident non-Austronesians in Melanesia before the subsequent occupation of the greater Pacific; however, the genetic impact of the Austronesian expansion to Melanesia remains largely unknown. We therefore studied the diversity of nonrecombining Y chromosomal (NRY) and mitochondrial (mt) DNA in the Admiralty Islands, located north of mainland Papua New Guinea, and updated our previous data from Asia, Melanesia, and Polynesia with new NRY markers. The Admiralties are occupied today solely by Austronesian-speaking groups, but their human settlement history goes back 20,000 years prior to the arrival of Austronesians about 3,400 years ago. On the Admiralties, we found substantial mtDNA and NRY variation of both Austronesian and non-Austronesian origins, with higher frequencies of Asian mtDNA and Melanesian NRY haplogroups, similar to previous findings in Polynesia and perhaps as a consequence of Austronesian matrilocality. Thus, the Austronesian language replacement on the Admiralties (and elsewhere in Island Melanesia and coastal New Guinea) was accompanied by an incomplete genetic replacement that is more associated with mtDNA than with NRY diversity. These results provide further support for the "Slow Boat" model of Polynesian origins, according to which Polynesian ancestors originated from East Asia but genetically mixed with Melanesians before colonizing the Pacific. We also observed that non-Austronesian groups of coastal New Guinea and Island Melanesia had significantly higher frequencies of Asian mtDNA haplogroups than of Asian NRY haplogroups, suggesting sex-biased admixture perhaps as a consequence of non-Austronesian patrilocality. We additionally found that the predominant NRY haplogroup of Asian origin in the Admiralties (O-M110) likely originated in Taiwan, thus providing the first direct Y chromosome evidence for a Taiwanese origin of the Austronesian expansion. Furthermore, we identified a NRY haplogroup (K-P79, also found on the Admiralties) in Polynesians that most likely arose in the Bismarck Archipelago, providing the first direct link between northern Island Melanesia and Polynesia. These results significantly advance our understanding of the impact of the Austronesian expansion and human history in the Pacific region.
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Affiliation(s)
- Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands.
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Mona S, Tommaseo-Ponzetta M, Brauer S, Sudoyo H, Marzuki S, Kayser M. Patterns of Y-Chromosome Diversity Intersect with the Trans-New Guinea Hypothesis. Mol Biol Evol 2007; 24:2546-55. [PMID: 17846104 DOI: 10.1093/molbev/msm187] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The island of New Guinea received part of the first human expansion out of Africa (>40,000 years ago), but its human genetic history remains poorly understood. In this study, we examined Y-chromosome diversity in 162 samples from the Bird's Head region of northwest New Guinea (NWNG) and compared the results with previously obtained data from other parts of the island. NWNG harbors a high level of cultural and linguistic diversity and is inhabited by non-Austronesian (i.e., Papuan)-speaking groups as well as harboring most of West New Guinea's (WNG) Austronesian-speaking groups. However, 97.5% of its Y-chromosomes belong to 5 haplogroups that originated in Melanesia; hence, the Y-chromosome diversity of NWNG (and, according to available data, of New Guinea as a whole) essentially reflects a local history. The remaining 2.5% belong to 2 haplogroups (O-M119 and O-M122) of East Asian origin, which were brought to New Guinea by Austronesian-speaking migrants around 3,500 years ago. Thus, the Austronesian expansion had only a small impact on shaping Y-chromosome diversity in NWNG, although the linguistic impact of this expansion to this region was much higher. In contrast, the expansion of Trans-New Guinea (TNG) speakers (non-Austronesian) starting about 6,000-10,000 years ago from the central highlands of what is now Papua New Guinea, presumably in combination with the expansion of agriculture, played a more important role in determining the Y-chromosome diversity of New Guinea. In particular, we identified 2 haplogroups (M-P34 and K-M254) as suggestive markers for the TNG expansion, whereas 2 other haplogroups (C-M38 and K-M9) most likely reflect the earlier local Y-chromosome diversity. We propose that sex-biased differences in the social structure and cultural heritage of the people involved in the Austronesian and the TNG expansions played an important role (among other factors) in shaping the New Guinean Y-chromosome landscape.
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Affiliation(s)
- Stefano Mona
- Department of Genetics and Microbiology, University of Bari, Bari, Italy
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Mona S, Randi E, Tommaseo-Ponzetta M. Evolutionary history of the genus Sus inferred from cytochrome b sequences. Mol Phylogenet Evol 2007; 45:757-62. [PMID: 17629713 DOI: 10.1016/j.ympev.2007.05.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Revised: 05/09/2007] [Accepted: 05/30/2007] [Indexed: 11/24/2022]
Affiliation(s)
- Stefano Mona
- Department of Genetics and Microbiology, University of Bari, Italy.
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