1
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Sard NM, Smith KR, Roth BM, Nathan LR, Herbst SJ, Scribner KT. Multiple sources implicated in the red swamp crayfish invasion in Michigan, USA. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02938-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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2
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Noninvasive Genetic Assessment Is an Effective Wildlife Research Tool When Compared with Other Approaches. Genes (Basel) 2021; 12:genes12111672. [PMID: 34828277 PMCID: PMC8625682 DOI: 10.3390/genes12111672] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/26/2022] Open
Abstract
Wildlife research has been indispensable for increasing our insight into ecosystem functioning as well as for designing effective conservation measures under the currently high rates of biodiversity loss. Genetic and genomic analyses might be able to yield the same information on, e.g., population size, health, or diet composition as other wildlife research methods, and even provide additional data that would not be possible to obtain by alternative means. Moreover, if DNA is collected non-invasively, this technique has only minimal or no impact on animal welfare. Nevertheless, the implementation rate of noninvasive genetic assessment in wildlife studies has been rather low. This might be caused by the perceived inefficiency of DNA material obtained non-invasively in comparison with DNA obtained from blood or tissues, or poorer performance in comparison with other approaches used in wildlife research. Therefore, the aim of this review was to evaluate the performance of noninvasive genetic assessment in comparison with other methods across different types of wildlife studies. Through a search of three scientific databases, 113 relevant studies were identified, published between the years 1997 and 2020. Overall, most of the studies (94%) reported equivalent or superior performance of noninvasive genetic assessment when compared with either invasive genetic sampling or another research method. It might be also cheaper and more time-efficient than other techniques. In conclusion, noninvasive genetic assessment is a highly effective research approach, whose efficacy and performance are likely to improve even further in the future with the development of optimized protocols.
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3
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Mayer M, Shine R, Brown GP. Rapid divergence of parasite infectivity and host resistance during a biological invasion. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa229] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Abstract
By perturbing co-evolved interactions, biological invasions provide an opportunity to study the evolution of interactions between hosts and their parasites on ecological timescales. We studied the interaction between the cane toad (Rhinella marina) and its direct-lifecycle lungworm (Rhabdias pseudosphaerocephala) that was brought from South America to Australia with the toads in 1935. Compared with infective parasite larvae from long-established (range-core) toad populations, parasite larvae from toads near the invasion front were larger, lived longer and were better able to resist exposure to toxin from the parotoid glands of toads. Experimentally, we infected the common-garden-reared progeny of toads from range-core and invasion-front populations within Australia with lungworms from both populations. Infective larvae from invasion-front (vs. range-core) populations of the parasite were more successful at entering toads (by skin penetration) and establishing infections in the lungs. Toads from invasion-front populations were less prone to infection by either type of larvae. Thus, within 84 years, parasites at an invasion front have increased infectivity, whereas hosts have increased resistance to parasite infection compared with range-core populations. Rapid evolution of traits might affect host–parasite interactions during biological invasions, generating unpredictable effects both on the invaders and on native ecosystems.
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Affiliation(s)
- Martin Mayer
- Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Richard Shine
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Gregory P Brown
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
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4
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Popovic I, Matias AMA, Bierne N, Riginos C. Twin introductions by independent invader mussel lineages are both associated with recent admixture with a native congener in Australia. Evol Appl 2020; 13:515-532. [PMID: 32431733 PMCID: PMC7045716 DOI: 10.1111/eva.12857] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 06/27/2019] [Accepted: 07/24/2019] [Indexed: 01/04/2023] Open
Abstract
Introduced species can impose profound impacts on the evolution of receiving communities with which they interact. If native and introduced taxa remain reproductively semi-isolated, human-mediated secondary contact may promote genetic exchange across newly created hybrid zones, potentially impacting native genetic diversity and invasive species spread. Here, we investigate the contributions of recent divergence histories and ongoing (post-introduction) gene flow between the invasive marine mussel, Mytilus galloprovincialis, and a morphologically indistinguishable and taxonomically contentious native Australian taxon, Mytilus planulatus. Using transcriptome-wide markers, we demonstrate that two contemporary M. galloprovincialis introductions into south-eastern Australia originate from genetically divergent lineages from its native range in the Mediterranean Sea and Atlantic Europe, where both introductions have led to repeated instances of admixture between introduced and endemic populations. Through increased genome-wide resolution of species relationships, combined with demographic modelling, we validate that mussels sampled in Tasmania are representative of the endemic Australian taxon (M. planulatus), but share strong genetic affinities to M. galloprovincialis. Demographic inferences indicate late-Pleistocene divergence times and historical gene flow between the Tasmanian endemic lineage and northern M. galloprovincialis, suggesting that native and introduced taxa have experienced a period of historical isolation of at least 100,000 years. Our results demonstrate that many genomic loci and sufficient sampling of closely related lineages in both sympatric (e.g. Australian populations) and allopatric (e.g. northern hemisphere Mytilus taxa) ranges are necessary to accurately (a) interpret patterns of intraspecific differentiation and to (b) distinguish contemporary invasive introgression from signatures left by recent divergence histories in high dispersal marine species. More broadly, our study fills a significant gap in systematic knowledge of native Australian biodiversity and sheds light on the intrinsic challenges for invasive species research when native and introduced species boundaries are not well defined.
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Affiliation(s)
- Iva Popovic
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
| | | | - Nicolas Bierne
- Institut des Sciences de l’EvolutionUMR 5554CNRS‐IRD‐EPHE‐UMUniversité de MontpellierMontpellierFrance
| | - Cynthia Riginos
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
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5
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Bélouard N, Paillisson J, Oger A, Besnard A, Petit EJ. Genetic drift during the spread phase of a biological invasion. Mol Ecol 2019; 28:4375-4387. [DOI: 10.1111/mec.15238] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Nadège Bélouard
- UMR ECOBIO CNRS Université de Rennes 1 Rennes France
- UMR ESE Ecology and Ecosystem Health INRA, Agrocampus Ouest Rennes France
| | | | - Adrien Oger
- UMR ECOBIO CNRS Université de Rennes 1 Rennes France
| | - Anne‐Laure Besnard
- UMR ESE Ecology and Ecosystem Health INRA, Agrocampus Ouest Rennes France
| | - Eric J. Petit
- UMR ESE Ecology and Ecosystem Health INRA, Agrocampus Ouest Rennes France
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6
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Dupuis JR, Ruiz‐Arce R, Barr NB, Thomas DB, Geib SM. Range-wide population genomics of the Mexican fruit fly: Toward development of pathway analysis tools. Evol Appl 2019; 12:1641-1660. [PMID: 31462920 PMCID: PMC6708432 DOI: 10.1111/eva.12824] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 11/30/2022] Open
Abstract
Recurrently invading pests provide unique challenges for pest management, but also present opportunities to utilize genomics to understand invasion dynamics and inform regulatory management through pathway analysis. In the southern United States, the Mexican fruit fly Anastrepha ludens is such a pest, and its incursions into Texas and California represent major threats to the agricultural systems of those regions. We developed a draft genome assembly for A. ludens, conducted range-wide population genomics using restriction site-associated DNA sequencing, and then developed and demonstrated a panel of highly differentiated diagnostic SNPs for source determination of intercepted flies in this system. Using 2,081 genomewide SNPs, we identified four populations across the range of A. ludens, corresponding to western Mexico, eastern Mexico/Texas, Guatemala/Belize/Honduras, and Costa Rica/Panama, with some intergradation present between clusters, particularly in Central America. From this population genomics framework, we developed a diagnostic panel of 28 highly differentiated SNPs that were able to recreate the genomewide population structure in this species. We demonstrated this panel on a set of test specimens, including specimens intercepted as part of regular trapping surveillance in Texas and California, and we were able to predict populations of origin for these specimens. This methodology presents a highly applied use of genomic techniques and can be implemented in any group of recurrently invading pests.
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Affiliation(s)
- Julian R. Dupuis
- U.S. Department of Agriculture‐Agricultural Research ServiceDaniel K. Inouye U.S. Pacific Basin Agricultural Research CenterHiloHawaii
- Department of Plant and Environmental Protection SciencesUniversity of Hawai’i at MānoaHonoluluHawaii
| | - Raul Ruiz‐Arce
- U.S. Department of Agriculture‐Animal and Plant Health Inspection Service, Plant Protection & Quarantine, Science and TechnologyMission LaboratoryEdinburgTexas
| | - Norman B. Barr
- U.S. Department of Agriculture‐Animal and Plant Health Inspection Service, Plant Protection & Quarantine, Science and TechnologyMission LaboratoryEdinburgTexas
| | - Donald B. Thomas
- U.S. Department of Agriculture‐Agricultural Research ServiceCattle Fever Tick Research LaboratoryEdinburgTexas
| | - Scott M. Geib
- U.S. Department of Agriculture‐Agricultural Research ServiceDaniel K. Inouye U.S. Pacific Basin Agricultural Research CenterHiloHawaii
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7
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Castellanos-Morales G, Ruiz-Mondragón KY, Hernández-Rosales HS, Sánchez-de la Vega G, Gámez N, Aguirre-Planter E, Montes-Hernández S, Lira-Saade R, Eguiarte LE. Tracing back the origin of pumpkins (Cucurbita pepo ssp. pepo L.) in Mexico. Proc Biol Sci 2019; 286:20191440. [PMID: 31409251 PMCID: PMC6710597 DOI: 10.1098/rspb.2019.1440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/23/2019] [Indexed: 11/12/2022] Open
Abstract
Cucurbita pepo is an economically important crop, which consists of cultivated C. pepo ssp. pepo, and two wild taxa (C. pepo ssp. fraterna and C. pepo ssp. ovifera). We aimed at understanding the domestication and the diversity of C. pepo in Mexico. We used two chloroplast regions and nine nuclear microsatellite loci to assess the levels of genetic variation and structure for C. pepo ssp. pepo's landraces sampled in 13 locations in Mexico, five improved varieties, one C. pepo ssp. fraterna population and ornamental C. pepo ssp. ovifera. We tested four hypotheses regarding the origin of C. pepo ssp. pepo's ancestor through approximate Bayesian computation: C. pepo ssp. ovifera as the ancestor; C. pepo ssp. fraterna as the ancestor; an unknown extinct lineage as the ancestor; and C. pepo ssp. pepo as hybrid from C. pepo ssp. ovifera and C. pepo ssp. fraterna ancestors. Cucurbita pepo ssp. pepo showed high genetic variation and low genetic differentiation. Cucurbita pepo ssp. fraterna and C. pepo ssp. pepo shared two chloroplast haplotypes. The three subspecies were well differentiated for microsatellite loci. Cucurbita pepo ssp. fraterna was probably C. pepo ssp. pepo's wild ancestor, but subsequent hybridization between taxa complicate defining C. pepo ssp. pepo's ancestor.
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Affiliation(s)
- Gabriela Castellanos-Morales
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Unidad Villahermosa, Villahermosa, Tabasco, Mexico
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
- UBIPRO, Facultad de Estudios Superiores, Iztacala, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Karen Y. Ruiz-Mondragón
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Helena S. Hernández-Rosales
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Guillermo Sánchez-de la Vega
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Niza Gámez
- Facultad de Estudios Superiores, Zaragoza, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarías (INIFAP), Celaya, Guanajuato, Mexico
| | - Rafael Lira-Saade
- UBIPRO, Facultad de Estudios Superiores, Iztacala, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
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8
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Pujol‐Buxó E, Garcia‐Cisneros A, Miaud C, Llorente GA. Genetic relationships and diversity patterns within the invasive range of the Mediterranean Painted Frog. J Zool (1987) 2019. [DOI: 10.1111/jzo.12703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E. Pujol‐Buxó
- Department of Evolutionary Biology, Ecology and Environmental Sciences University of Barcelona Barcelona Spain
- IrBio, Institut de Recerca de la Biodiversitat University of Barcelona Barcelona Spain
| | - A. Garcia‐Cisneros
- Department of Evolutionary Biology, Ecology and Environmental Sciences University of Barcelona Barcelona Spain
- Center for Advanced Studies of Blanes (CEAB‐CSIC) Blanes Spain
| | - C. Miaud
- EPHE, UMR 5175 CEFE, CNRS, UM, Univ. P. Valéry, SupAgro, IRD, INRA, Biogéographie et Écologie des Vertébrés PSL Research University Montpellier France
| | - G. A. Llorente
- Department of Evolutionary Biology, Ecology and Environmental Sciences University of Barcelona Barcelona Spain
- IrBio, Institut de Recerca de la Biodiversitat University of Barcelona Barcelona Spain
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9
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Sard N, Robinson J, Kanefsky J, Herbst S, Scribner K. Coalescent models characterize sources and demographic history of recent round goby colonization of Great Lakes and inland waters. Evol Appl 2019; 12:1034-1049. [PMID: 31080513 PMCID: PMC6503821 DOI: 10.1111/eva.12779] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 01/15/2019] [Indexed: 12/25/2022] Open
Abstract
The establishment and spread of aquatic invasive species are ecologically and economically harmful and a source of conservation concern internationally. Processes of species invasion have traditionally been inferred from observational data of species presence/absence and relative abundance. However, genetic-based approaches can provide valuable sources of inference. Restriction site-associated DNA sequencing was used to identify and genotype single nucleotide polymorphism (SNP) loci for Round Gobies (Neogobius melanostomus) (N = 440) from 18 sampling locations in the Great Lakes and in three Michigan, USA, drainages (Flint, Au Sable, and Cheboygan River basins). Sampled rivers differed in size, accessibility, and physical characteristics including man-made dispersal barriers. Population levels of genetic diversity and interpopulation variance in SNP allele frequency were used in coalescence-based approximate Bayesian computation (ABC) to statistically compare models representing competing hypotheses regarding source population, postcolonization dispersal, and demographic history in the Great Lakes and inland waters. Results indicate different patterns of colonization across the three drainages. In the Flint River, models indicate a strong population bottleneck (<3% of contemporary effective population size) and a single founding event from Saginaw Bay led to the colonization of inland river segments. In the Au Sable River, analyses could not distinguish potential source populations, but supported models indicated multiple introductions from one source population. In the Cheboygan River, supported models indicated that colonization likely proceeded from east (Lake Huron source) to west among inland locales sampled in the system. Despite the recent occupancy of Great Lakes and inland habitats, large numbers of loci analyzed in an ABC framework enable statistically supported identification of source populations and reconstruction of the direction of inland spread and demographic history following establishment. Information from analyses can direct management actions to limit the spread of invasive species from identified sources and most probable vectors into additional inland aquatic habitats.
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Affiliation(s)
- Nicholas Sard
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
- Present address:
Biology DepartmentSUNY OswegoOswegoNew York
| | - John Robinson
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
| | - Jeannette Kanefsky
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
| | - Seth Herbst
- Michigan Department of Natural ResourcesEast LansingMichigan
| | - Kim Scribner
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
- Department of Integrative BiologyMichigan State UniversityEast LansingMichigan
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10
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Vendrami DLJ, De Noia M, Telesca L, Handal W, Charrier G, Boudry P, Eberhart-Phillips L, Hoffman JI. RAD sequencing sheds new light on the genetic structure and local adaptation of European scallops and resolves their demographic histories. Sci Rep 2019; 9:7455. [PMID: 31092869 PMCID: PMC6520335 DOI: 10.1038/s41598-019-43939-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/30/2019] [Indexed: 12/25/2022] Open
Abstract
Recent developments in genomics are advancing our understanding of the processes shaping population structure in wild organisms. In particular, reduced representation sequencing has facilitated the generation of dense genetic marker datasets that provide greater power for resolving population structure, investigating the role of selection and reconstructing demographic histories. We therefore used RAD sequencing to study the great scallop Pecten maximus and its sister species P. jacobeus along a latitudinal cline in Europe. Analysis of 219 samples genotyped at 82,439 single nucleotide polymorphisms clearly resolved an Atlantic and a Norwegian group within P. maximus as well as P. jacobeus, in support of previous studies. Fine-scale structure was also detected, including pronounced differences involving Mulroy Bay in Ireland, where scallops are commercially cultured. Furthermore, we identified a suite of 279 environmentally associated loci that resolved a contrasting phylogenetic pattern to the remaining neutral loci, consistent with ecologically mediated divergence. Finally, demographic inference provided support for the two P. maximus groups having diverged during the last glacial maximum and subsequently expanded, whereas P. jacobeus diverged around 95,000 generations ago and experienced less pronounced expansion. Our results provide an integrative perspective on the factors shaping genome-wide differentiation in a commercially important marine invertebrate.
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Affiliation(s)
- David L J Vendrami
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, 33615, Bielefeld, Germany.
| | - Michele De Noia
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, 33615, Bielefeld, Germany.,Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Luca Telesca
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EQ, United Kingdom.,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, United Kingdom
| | - William Handal
- University of Brest, Laboratoire des Sciences de l'Environnement Marin (LEMAR, UMR 6539, UBO/CNRS/IRD/Ifremer), European University Institute for the Sea (IUEM), rue Dumont d'Urville, 29280, Plouzané, France
| | - Grégory Charrier
- University of Brest, Laboratoire des Sciences de l'Environnement Marin (LEMAR, UMR 6539, UBO/CNRS/IRD/Ifremer), European University Institute for the Sea (IUEM), rue Dumont d'Urville, 29280, Plouzané, France
| | - Pierre Boudry
- Ifremer, Laboratoire des Sciences de l'Environnement Marin (UBO/CNRS/IRD/Ifremer), Plouzané, France
| | - Luke Eberhart-Phillips
- Department of Evolutionary Ecology and Behavioural Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Joseph I Hoffman
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, 33615, Bielefeld, Germany.,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, United Kingdom
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11
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Barros T, Carvalho J, Fonseca C, Cushman SA. Assessing the complex relationship between landscape, gene flow, and range expansion of a Mediterranean carnivore. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1274-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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van Boheemen LA, Atwater DZ, Hodgins KA. Rapid and repeated local adaptation to climate in an invasive plant. THE NEW PHYTOLOGIST 2019; 222:614-627. [PMID: 30367474 DOI: 10.1111/nph.15564] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/18/2018] [Indexed: 06/08/2023]
Abstract
Biological invasions provide opportunities to study evolutionary processes occurring over contemporary timescales. To explore the speed and repeatability of adaptation, we examined the divergence of life-history traits to climate, using latitude as a proxy, in the native North American and introduced European and Australian ranges of the annual plant Ambrosia artemisiifolia. We explored niche changes following introductions using climate niche dynamic models. In a common garden, we examined trait divergence by growing seeds collected across three ranges with highly distinct demographic histories. Heterozygosity-fitness associations were used to explore the effect of invasion history on potential success. We accounted for nonadaptive population differentiation using 11 598 single nucleotide polymorphisms. We revealed a centroid shift to warmer, wetter climates in the introduced ranges. We identified repeated latitudinal divergence in life-history traits, with European and Australian populations positioned at either end of the native clines. Our data indicate rapid and repeated adaptation to local climates despite the recent introductions and a bottleneck limiting genetic variation in Australia. Centroid shifts in the introduced ranges suggest adaptation to more productive environments, potentially contributing to trait divergence between the ranges.
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Affiliation(s)
- Lotte A van Boheemen
- School of Biological Sciences, Monash University, Clayton, Vic., 3800, Australia
| | - Daniel Z Atwater
- Department of Biology, Earlham College, Richmond, IN, 47374, USA
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Clayton, Vic., 3800, Australia
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13
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Tingley R, Ward-Fear G, Schwarzkopf L, Greenlees MJ, Phillips BL, Brown G, Clulow S, Webb J, Capon R, Sheppard A, Strive T, Tizard M, Shine R. New Weapons in the Toad Toolkit: A Review of Methods to Control and Mitigate the Biodiversity Impacts of Invasive Cane Toads (Rhinella Marina). QUARTERLY REVIEW OF BIOLOGY 2018; 92:123-49. [PMID: 29562120 DOI: 10.1086/692167] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Our best hope of developing innovative methods to combat invasive species is likely to come from the study of high-profile invaders that have attracted intensive research not only into control, but also basic biology. Here we illustrate that point by reviewing current thinking about novel ways to control one of the world’s most well-studied invasions: that of the cane toad in Australia. Recently developed methods for population suppression include more effective traps based on the toad’s acoustic and pheromonal biology. New tools for containing spread include surveillance technologies (e.g., eDNA sampling and automated call detectors), as well as landscape-level barriers that exploit the toad’s vulnerability to desiccation—a strategy that could be significantly enhanced through the introduction of sedentary, range-core genotypes ahead of the invasion front. New methods to reduce the ecological impacts of toads include conditioned taste aversion in free-ranging predators, gene banking, and targeted gene flow. Lastly, recent advances in gene editing and gene drive technology hold the promise of modifying toad phenotypes in ways that may facilitate control or buffer impact. Synergies between these approaches hold great promise for novel and more effective means to combat the toad invasion and its consequent impacts on biodiversity.
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14
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Theodoridis S, Randin C, Szövényi P, Boucher FC, Patsiou TS, Conti E. How Do Cold-Adapted Plants Respond to Climatic Cycles? Interglacial Expansion Explains Current Distribution and Genomic Diversity in Primula farinosa L. Syst Biol 2018; 66:715-736. [PMID: 28334079 DOI: 10.1093/sysbio/syw114] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 12/14/2016] [Indexed: 12/16/2022] Open
Abstract
Understanding the effects of past climatic fluctuations on the distribution and population-size dynamics of cold-adapted species is essential for predicting their responses to ongoing global climate change. In spite of the heterogeneity of cold-adapted species, two main contrasting hypotheses have been proposed to explain their responses to Late Quaternary glacial cycles, namely, the interglacial contraction versus the interglacial expansion hypotheses. Here, we use the cold-adapted plant Primula farinosa to test two demographic models under each of the two alternative hypotheses and a fifth, null model. We first approximate the time and extent of demographic contractions and expansions during the Late Quaternary by projecting species distribution models across the last 72 ka. We also generate genome-wide sequence data using a Reduced Representation Library approach to reconstruct the spatial structure, genetic diversity, and phylogenetic relationships of lineages within P. farinosa. Finally, by integrating the results of climatic and genomic analyses in an Approximate Bayesian Computation framework, we propose the most likely model for the extent and direction of population-size changes in $P$. farinosa through the Late Quaternary. Our results support the interglacial expansion of $P$. farinosa, differing from the prevailing paradigm that the observed distribution of cold-adapted species currently fragmented in high altitude and latitude regions reflects the consequences of postglacial contraction processes.
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Affiliation(s)
- Spyros Theodoridis
- Department of Systematic and Evolutionary Botany, University of Zurich, CH-8008 Zurich, Switzerland.,Zurich-Basel Plant Science Center, CH-8092 Zurich, Switzerland
| | - Christophe Randin
- Institute of Botany, University of Basel, CH-4056 Basel, Switzerland.,Department of Ecology & Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Peter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, CH-8008 Zurich, Switzerland
| | - Florian C Boucher
- Department of Systematic and Evolutionary Botany, University of Zurich, CH-8008 Zurich, Switzerland.,Department of Botany and Zoology, University of Stellenbosch, 7602 Matieland, South Africa
| | - Theofania S Patsiou
- Department of Systematic and Evolutionary Botany, University of Zurich, CH-8008 Zurich, Switzerland.,Zurich-Basel Plant Science Center, CH-8092 Zurich, Switzerland.,Institute of Botany, University of Basel, CH-4056 Basel, Switzerland
| | - Elena Conti
- Department of Systematic and Evolutionary Botany, University of Zurich, CH-8008 Zurich, Switzerland.,Zurich-Basel Plant Science Center, CH-8092 Zurich, Switzerland
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15
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McCann SM, Kosmala GK, Greenlees MJ, Shine R. Physiological plasticity in a successful invader: rapid acclimation to cold occurs only in cool-climate populations of cane toads ( Rhinella marina). CONSERVATION PHYSIOLOGY 2018; 6:cox072. [PMID: 29399360 PMCID: PMC5786208 DOI: 10.1093/conphys/cox072] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/03/2017] [Accepted: 11/30/2017] [Indexed: 06/07/2023]
Abstract
Physiological plasticity may facilitate invasion of novel habitats; but is such plasticity present in all populations of the invader or is it elicited only by specific climatic challenges? In cold-climate areas of Australia, invasive cane toads (Rhinella marina) can rapidly acclimate to cool conditions. To investigate whether this physiological plasticity is found in all invasive cane toads or is only seen in cool climates, we measured the acclimation ability of toads from across Australia and the island of Hawai'i. We collected toads from the field and placed them at either 12 or 24°C for 12 h before measuring their righting response as a proxy for critical thermal minimum (CTmin). Toads from the coolest Australian region (New South Wales) demonstrated plasticity (as previously reported), with exposure to 12°C (vs. 24°C) decreasing CTmin by 2°C. In toads from other Australian populations, CTmins were unaffected by our thermal treatments. Hawai'ian toads from a cool, wet site also rapidly acclimated to cool conditions, whereas those from warmer and drier Hawai'ian sites did not. Thermal plasticity has diverged among populations of invasive cane toads, with rapid acclimation manifested only in two cool-climate populations from widely separated sites. Predictions about the potential range of invasive species thus must consider the possibility of geographic (intraspecific) heterogeneity in thermal plasticity; data from other parts of the species' range may fail to predict levels of plasticity elicited by thermal challenges.
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Affiliation(s)
- Samantha M McCann
- School of Life and Environmental Sciences, University of Sydney, Room 442, Heydon-Laurence Building (A08) Science Road, New South Wales 2006, Australia
| | - Georgia K Kosmala
- School of Life and Environmental Sciences, University of Sydney, Room 442, Heydon-Laurence Building (A08) Science Road, New South Wales 2006, Australia
| | - Matthew J Greenlees
- School of Life and Environmental Sciences, University of Sydney, Room 442, Heydon-Laurence Building (A08) Science Road, New South Wales 2006, Australia
| | - Richard Shine
- School of Life and Environmental Sciences, University of Sydney, Room 442, Heydon-Laurence Building (A08) Science Road, New South Wales 2006, Australia
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16
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Karabatsos G, Leisen F. An approximate likelihood perspective on ABC methods. STATISTICS SURVEYS 2018. [DOI: 10.1214/18-ss120] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Lillie M, Dubey S, Shine R, Belov K. Variation in Major Histocompatibility Complex diversity in invasive cane toad populations. WILDLIFE RESEARCH 2017. [DOI: 10.1071/wr17055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context The cane toad (Rhinella marina), a native species of central and southern America, was introduced to Australia in 1935 as a biocontrol agent after a complex history of prior introductions. The population rapidly expanded and has since spread through much of the Australian landmass, with severe impacts on the endemic wildlife, primarily via toxicity to predators. The invasion process has taken its toll on the cane toad, with changes in the immunological capacity across the Australian invasive population. Aims To investigate the immunogenetic underpinnings of these changes, we studied the diversity of the Major Histocompatiblity Complex (MHC) genes in introduced cane toad populations. Methods We studied the diversity of two MHC genes (the classical class I UA locus and a class II DAB locus) and compared these with neutral microsatellite markers in toads from the Australian site of introduction and the Australian invasion front. We also included toads from Hawai’i, the original source of the Australian toads, to infer founder effect. Key results Diversity across all markers was low across Australian and Hawai’ian samples, consistent with a reduction in genetic diversity through multiple founder effects during the course of the successive translocations. In Australia, allelic diversity at the microsatellite markers and the UA locus was reduced at the invasion front, whereas all three alleles at the DAB locus were maintained in the invasion-front toads. Conclusions Loss of allelic diversity observed at the microsatellite markers and the UA locus could be the result of drift and bottlenecking along the invasion process, however, the persistence of DAB diversity warrants further investigation to disentangle the evolutionary forces influencing this locus. Implications Through the use of different molecular markers, we provide a preliminary description of the adaptive genetic processes occurring in this invasive population. The extremely limited MHC diversity may represent low immunogenetic competence across the Australian population, which could be exploited for invasive species management.
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18
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Désamoré A, Patiño J, Mardulyn P, Mcdaniel SF, Zanatta F, Laenen B, Vanderpoorten A. High migration rates shape the postglacial history of amphi-Atlantic bryophytes. Mol Ecol 2016; 25:5568-5584. [PMID: 27661065 DOI: 10.1111/mec.13839] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 08/29/2016] [Accepted: 08/31/2016] [Indexed: 11/28/2022]
Abstract
Paleontological evidence and current patterns of angiosperm species richness suggest that European biota experienced more severe bottlenecks than North American ones during the last glacial maximum. How well this pattern fits other plant species is less clear. Bryophytes offer a unique opportunity to contrast the impact of the last glacial maximum in North America and Europe because about 60% of the European bryoflora is shared with North America. Here, we use population genetic analyses based on approximate Bayesian computation on eight amphi-Atlantic species to test the hypothesis that North American populations were less impacted by the last glacial maximum, exhibiting higher levels of genetic diversity than European ones and ultimately serving as a refugium for the postglacial recolonization of Europe. In contrast with this hypothesis, the best-fit demographic model involved similar patterns of population size contractions, comparable levels of genetic diversity and balanced migration rates between European and North American populations. Our results thus suggest that bryophytes have experienced comparable demographic glacial histories on both sides of the Atlantic. Although a weak, but significant genetic structure was systematically recovered between European and North American populations, evidence for migration from and towards both continents suggests that amphi-Atlantic bryophyte population may function as a metapopulation network. Reconstructing the biogeographic history of either North American or European bryophyte populations therefore requires a large, trans-Atlantic geographic framework.
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Affiliation(s)
- Aurélie Désamoré
- Institute of Botany, University of Liège, B22 Sart Tilman, Liège, Belgium. .,Department of Zoology, Swedish Museum of Natural History, Box 50007, SE-104 05, Stockholm, Sweden.
| | - Jairo Patiño
- Institute of Botany, University of Liège, B22 Sart Tilman, Liège, Belgium.,Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Tenerife, Canary Islands, 38206, Spain.,Centre for Ecology, Evolution and Environmental Changes and Platform for Enhancing Ecological Research & Sustainability, Universidade dos Açores, 9700-042, Angra do Heroísmo, Terceira, Açores, Portugal
| | - Patrick Mardulyn
- Department of Evolutionary Biology and Ecology, Université libre de Bruxelles, Campus du Solbosch, Avenue F.D. Roosevelt 50, 1050, Bruxelles, Belgium
| | - Stuart F Mcdaniel
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611-8525, USA
| | - Florian Zanatta
- Institute of Botany, University of Liège, B22 Sart Tilman, Liège, Belgium
| | - Benjamin Laenen
- Institute of Botany, University of Liège, B22 Sart Tilman, Liège, Belgium.,SciLifeLab Stockholm, Department of Ecology, Environment and Plant Sciences, Stockholm University, Tomtebodav. 23a, 171 21, Solna, Stockholm, Sweden
| | - Alain Vanderpoorten
- Institute of Botany, University of Liège, B22 Sart Tilman, Liège, Belgium.,Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Tenerife, Canary Islands, 38206, Spain
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19
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Garnier J, Lewis MA. Expansion Under Climate Change: The Genetic Consequences. Bull Math Biol 2016; 78:2165-2185. [PMID: 27743309 DOI: 10.1007/s11538-016-0213-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/26/2016] [Indexed: 11/27/2022]
Abstract
Range expansion and range shifts are crucial population responses to climate change. Genetic consequences are not well understood but are clearly coupled to ecological dynamics that, in turn, are driven by shifting climate conditions. We model a population with a deterministic reaction-diffusion model coupled to a heterogeneous environment that develops in time due to climate change. We decompose the resulting travelling wave solution into neutral genetic components to analyse the spatio-temporal dynamics of its genetic structure. Our analysis shows that range expansions and range shifts under slow climate change preserve genetic diversity. This is because slow climate change creates range boundaries that promote spatial mixing of genetic components. Mathematically, the mixing leads to so-called pushed travelling wave solutions. This mixing phenomenon is not seen in spatially homogeneous environments, where range expansion reduces genetic diversity through gene surfing arising from pulled travelling wave solutions. However, the preservation of diversity is diminished when climate change occurs too quickly. Using diversity indices, we show that fast expansions and range shifts erode genetic diversity more than slow range expansions and range shifts. Our study provides analytical insight into the dynamics of travelling wave solutions in heterogeneous environments.
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Affiliation(s)
- Jimmy Garnier
- LAMA, CNRS - Université Savoie Mont-Blanc, 73000, Chambéry, France.
| | - Mark A Lewis
- Department of Mathematical and Statistical Sciences, Centre for Mathematical Biology, University of Alberta, Edmonton, AB, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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20
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Trumbo DR, Epstein B, Hohenlohe PA, Alford RA, Schwarzkopf L, Storfer A. Mixed population genomics support for the central marginal hypothesis across the invasive range of the cane toad (Rhinella marina) in Australia. Mol Ecol 2016; 25:4161-76. [PMID: 27393238 PMCID: PMC5021610 DOI: 10.1111/mec.13754] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 06/17/2016] [Accepted: 06/27/2016] [Indexed: 12/26/2022]
Abstract
Understanding factors that cause species' geographic range limits is a major focus in ecology and evolution. The central marginal hypothesis (CMH) predicts that species cannot adapt to conditions beyond current geographic range edges because genetic diversity decreases from core to edge due to smaller, more isolated edge populations. We employed a population genomics framework using 24 235-33 112 SNP loci to test major predictions of the CMH in the ongoing invasion of the cane toad (Rhinella marina) in Australia. Cane toad tissue samples were collected along broad-scale, core-to-edge transects across their invasive range. Geographic and ecological core areas were identified using GIS and habitat suitability indices from ecological niche modelling. Bayesian clustering analyses revealed three genetic clusters, in the northwest invasion-front region, northeast precipitation-limited region and southeast cold temperature-limited region. Core-to-edge patterns of genetic diversity and differentiation were consistent with the CMH in the southeast, but were not supported in the northeast and showed mixed support in the northwest. Results suggest cold temperatures are a likely contributor to southeastern range limits, consistent with CMH predictions. In the northeast and northwest, ecological processes consisting of a steep physiological barrier and ongoing invasion dynamics, respectively, are more likely explanations for population genomic patterns than the CMH.
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Affiliation(s)
- Daryl R. Trumbo
- Washington State University; School of Biological Sciences; Abelson Hall, Room 305; Pullman, WA 990164, USA
| | - Brendan Epstein
- Washington State University; School of Biological Sciences; Abelson Hall, Room 305; Pullman, WA 990164, USA
| | - Paul A. Hohenlohe
- University of Idaho; Department of Biological Sciences; Life Sciences South 252; Moscow, ID 83844, USA
| | - Ross A. Alford
- James Cook University; College of Marine and Environmental Sciences; Building 28; Townsville, QLD 4811, Australia
| | - Lin Schwarzkopf
- James Cook University; College of Marine and Environmental Sciences; Building 28; Townsville, QLD 4811, Australia
| | - Andrew Storfer
- Washington State University; School of Biological Sciences; Abelson Hall, Room 305; Pullman, WA 990164, USA
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21
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Capblancq T, Després L, Rioux D, Mavárez J. Hybridization promotes speciation in Coenonympha butterflies. Mol Ecol 2016; 24:6209-22. [PMID: 26581657 DOI: 10.1111/mec.13479] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 11/09/2015] [Accepted: 11/12/2015] [Indexed: 01/16/2023]
Abstract
Hybridization has become a central element in theories of animal evolution during the last decade. New methods in population genomics and statistical model testing now allow the disentangling of the complexity that hybridization brings into key evolutionary processes such as local adaptation, colonization of new environments, species diversification and extinction. We evaluated the consequences of hybridization in a complex of three alpine butterflies in the genus Coenonympha, by combining morphological, genetic and ecological analyses. A series of approximate Bayesian computation procedures based on a large SNP data set strongly suggest that the Darwin's Heath (Coenonympha darwiniana) originated through hybridization between the Pearly Heath (Coenonympha arcania) and the Alpine Heath (Coenonympha gardetta) with different parental contributions. As a result of hybridization, the Darwin's Heath presents an intermediate morphology between the parental species, while its climatic niche seems more similar to the Alpine Heath. Our results also reveal a substantial genetic and morphologic differentiation between the two geographically disjoint Darwin's Heath lineages leading us to propose the splitting of this taxon into two different species.
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Affiliation(s)
- Thibaut Capblancq
- LECA, Université Grenoble Alpes, F-38000, Grenoble, France.,LECA, CNRS, F-38000, Grenoble, France
| | - Laurence Després
- LECA, Université Grenoble Alpes, F-38000, Grenoble, France.,LECA, CNRS, F-38000, Grenoble, France
| | - Delphine Rioux
- LECA, Université Grenoble Alpes, F-38000, Grenoble, France.,LECA, CNRS, F-38000, Grenoble, France
| | - Jesús Mavárez
- LECA, Université Grenoble Alpes, F-38000, Grenoble, France.,LECA, CNRS, F-38000, Grenoble, France
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22
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Barros T, Ferreira E, Rocha RG, Gaubert P, Bandeira V, Souto L, Mira A, Fonseca C. Genetic signature of the northward expansion of the Egyptian mongoose Herpestes ichneumon(Herpestidae) in the Iberian Peninsula. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12743] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tânia Barros
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
| | - Eduardo Ferreira
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
| | - Rita Gomes Rocha
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
- Departamento de Ciências Biológicas; Centro de Ciências Humanas e Naturais; Universidade Federal do Espírito Santo; Av. Fernando Ferrari 514, Goiabeiras 29075-910 Vitória ES Brazil
| | - Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UM-CNRS-IRD-CIRAD-EPHE; Université de Montpellier; Place Eugène Bataillon - CC 64; 34095 Montpellier, Cedex 05 France
| | - Victor Bandeira
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
| | - Luis Souto
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
| | - António Mira
- Unidade de Biologia da Conservação; Universidade de Évora; 7002-554 Évora Portugal
| | - Carlos Fonseca
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
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23
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Hagen SB, Kopatz A, Aspi J, Kojola I, Eiken HG. Evidence of rapid change in genetic structure and diversity during range expansion in a recovering large terrestrial carnivore. Proc Biol Sci 2016; 282:20150092. [PMID: 25904665 DOI: 10.1098/rspb.2015.0092] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recovery of natural populations occurs often with simultaneous or subsequent range expansions. According to population genetic theory, genetic structuring emerges at the expansion front together with decreasing genetic diversity, owing to multiple founder events. Thereupon, as the expansion proceeds and connectivity among populations is established, homogenization and a resurgence of genetic diversity are to be expected. Few studies have used a fine temporal scale combined with genetic sampling to track range expansions as they proceed in wild animal populations. As a natural experiment, the historical eradication of large terrestrial carnivores followed by their recovery and recolonization may facilitate empirical tests of these ideas. Here, using brown bear (Ursus arctos) as model species, we tested predictions from genetic theory of range expansion. Individuals from all over Finland were genotyped for every year between 1996 and 2010 using 12 validated autosomal microsatellite markers. A latitudinal shift of about 110 km was observed in the distribution and delineation of genetic clusters during this period. As the range expansion proceeded, we found, as theory predicts, that the degree of genetic structure decreased, and that both genetic variation and admixture increased. The genetic consequences of range expansions may first be detected after multiple generations, but we found major changes in genetic composition after just 1.5 generations, accompanied by population growth and increased migration. These rapid genetic changes suggest an ongoing concerted action of geographical and demographic expansion combined with substantial immigration of bears from Russia during the recovery of brown bears within the large ecosystem of northern Europe.
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Affiliation(s)
- Snorre B Hagen
- Bioforsk-Norwegian Institute for Agricultural and Environmental Research, 9925 Svanvik, Norway
| | - Alexander Kopatz
- Bioforsk-Norwegian Institute for Agricultural and Environmental Research, 9925 Svanvik, Norway
| | - Jouni Aspi
- Department of Biology, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Ilpo Kojola
- Luke-Natural Resources Institute, Viikinkaari 4, 00790 Helsinki, Finland
| | - Hans Geir Eiken
- Bioforsk-Norwegian Institute for Agricultural and Environmental Research, 9925 Svanvik, Norway
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24
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Turvey ST, Peters S, Brace S, Young RP, Crumpton N, Hansford J, Nuñez-Miño JM, King G, Tsalikidis K, Ottenwalder JA, Timpson A, Funk SM, Brocca JL, Thomas MG, Barnes I. Independent evolutionary histories in allopatric populations of a threatened Caribbean land mammal. DIVERS DISTRIB 2016. [DOI: 10.1111/ddi.12420] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Samuel T. Turvey
- Institute of Zoology; Zoological Society of London; Regent's Park London NW1 4RY UK
| | - Stuart Peters
- Research Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - Selina Brace
- Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Richard P. Young
- Durrell Wildlife Conservation Trust; Les Augrès Manor Trinity Jersey JE3 5BP Channel Islands
| | - Nick Crumpton
- Natural History Museum; Cromwell Road London SW7 5BD UK
- Research Department of Cell and Developmental Biology; University College London; Gower Street London WC1E 6BT UK
| | - James Hansford
- Institute of Zoology; Zoological Society of London; Regent's Park London NW1 4RY UK
- Ocean and Earth Science, National Oceanography Centre Southampton; University of Southampton Waterfront Campus; European Way Southampton UK
| | - Jose M. Nuñez-Miño
- Durrell Wildlife Conservation Trust; Les Augrès Manor Trinity Jersey JE3 5BP Channel Islands
| | - Gemma King
- School of Biological Sciences; Royal Holloway University of London; Egham Hill Egham TW20 OEX UK
| | - Katrina Tsalikidis
- School of Biological Sciences; Royal Holloway University of London; Egham Hill Egham TW20 OEX UK
| | | | - Adrian Timpson
- Institute of Archaeology; University College London; Gordon Square London WC1H 0PY UK
| | | | - Jorge L. Brocca
- Sociedad Ornitológica de la Hispaniola; Parque Zoologico Nacional; Avenida de la Vega Real Arroyo Hondo Santo Domingo Dominican Republic
| | - Mark G. Thomas
- Research Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - Ian Barnes
- Natural History Museum; Cromwell Road London SW7 5BD UK
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25
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McCartney-Melstad E, Shaffer HB. Amphibian molecular ecology and how it has informed conservation. Mol Ecol 2015; 24:5084-109. [PMID: 26437125 DOI: 10.1111/mec.13391] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 02/02/2023]
Abstract
Molecular ecology has become one of the key tools in the modern conservationist's kit. Here we review three areas where molecular ecology has been applied to amphibian conservation: genes on landscapes, within-population processes, and genes that matter. We summarize relevant analytical methods, recent important studies from the amphibian literature, and conservation implications for each section. Finally, we include five in-depth examples of how molecular ecology has been successfully applied to specific amphibian systems.
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Affiliation(s)
- Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
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26
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Reed JM, Stockwell CA. Evaluating an icon of population persistence: the Devil's Hole pupfish. Proc Biol Sci 2015; 281:20141648. [PMID: 25232135 DOI: 10.1098/rspb.2014.1648] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The Devil's Hole pupfish Cyprinodon diabolis has iconic status among conservation biologists because it is one of the World's most vulnerable species. Furthermore, C. diabolis is the most widely cited example of a persistent, small, isolated vertebrate population; a chronic exception to the rule that small populations do not persist long in isolation. It is widely asserted that this species has persisted in small numbers (less than 400 adults) for 10 000-20 000 years, but this assertion has never been evaluated. Here, we analyse the time series of count data for this species, and we estimate time to coalescence from microsatellite data to evaluate this hypothesis. We conclude that mean time to extinction is approximately 360-2900 years (median 410-1800), with less than a 2.1% probability of persisting 10 000 years. Median times to coalescence varied from 217 to 2530 years, but all five approximations had wide credible intervals. Our analyses suggest that Devil's Hole pupfish colonized this pool well after the Pleistocene Lakes receded, probably within the last few hundred to few thousand years; this could have occurred through human intervention.
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Affiliation(s)
- J Michael Reed
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Craig A Stockwell
- Department of Biological Sciences, North Dakota State University, Fargo, ND 58108, USA
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27
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Benazzo A, Ghirotto S, Vilaça ST, Hoban S. Using ABC and microsatellite data to detect multiple introductions of invasive species from a single source. Heredity (Edinb) 2015; 115:262-72. [PMID: 25920671 DOI: 10.1038/hdy.2015.38] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 03/12/2015] [Accepted: 03/14/2015] [Indexed: 11/09/2022] Open
Abstract
The introduction of invasive species to new locations (that is, biological invasions) can have major impact on biodiversity, agriculture and public health. As such, determining the routes and modality of introductions with genetic data has become a fundamental goal in molecular ecology. To assist with this goal, new statistical methods and frameworks have been developed, such as approximate Bayesian computation (ABC) for inferring invasion history. Here, we present a model of invasion accounting for multiple introductions from a single source (MISS), a heretofore largely unexplored model. We simulate microsatellite data to evaluate the power of ABC to distinguish between single and multiple introductions from the same source, under a range of demographic parameters. We also apply ABC to microsatellite data from three invasions of bumblebee in New Zealand. In addition, we assess the performance of several methods of summary statistics selection. Our simulated results suggested good ability to distinguish between one- and two-wave models over much but not all of the parameter space tested, independent of summary statistics used. Globally, parameter estimation was good except for bottleneck timing. For one of the bumblebee species, we clearly rejected the MISS model, while for the other two we found inconclusive results. Since a second wave may provide genetic reinforcement to initial colonists, help relieve inbreeding among founders, or increase the hazard of the invasion, its detection may be crucial for managing invasions; we suggest that the MISS model could be considered as a potential model in future theoretical and empirical studies of invasions.
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Affiliation(s)
- A Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - S Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - S T Vilaça
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - S Hoban
- 1] Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy [2] National Institute for Mathematical and Biological Synthesis (NIMBioS), University of Tennessee, Knoxville, TN, USA
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28
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Rollins LA, Richardson MF, Shine R. A genetic perspective on rapid evolution in cane toads (Rhinella marina). Mol Ecol 2015; 24:2264-76. [PMID: 25894012 DOI: 10.1111/mec.13184] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 12/12/2022]
Abstract
The process of biological invasion exposes a species to novel pressures, in terms of both the environments it encounters and the evolutionary consequences of range expansion. Several invaders have been shown to exhibit rapid evolutionary changes in response to those pressures, thus providing robust opportunities to clarify the processes at work during rapid phenotypic transitions. The accelerating pace of invasion of cane toads (Rhinella marina) in tropical Australia during its 80-year history has been well characterized at the phenotypic level, including common-garden experiments that demonstrate heritability of several dispersal-relevant traits. Individuals from the invasion front (and their progeny) show distinctive changes in morphology, physiology and behaviour that, in combination, result in far more rapid dispersal than is true of conspecifics from long-colonized areas. The extensive body of work on cane toad ecology enables us to place into context studies of the genetic basis of these traits. Our analyses of differential gene expression from toads from both ends of this invasion-history transect reveal substantial upregulation of many genes, notably those involved in metabolism and cellular repair. Clearly, then, the dramatically rapid phenotypic evolution of cane toads in Australia has been accompanied by substantial shifts in gene expression, suggesting that this system is well suited to investigating the genetic underpinnings of invasiveness.
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Affiliation(s)
- Lee A Rollins
- Centre for Integrative Ecology, School of Life & Environmental Sciences, Deakin University, Pigdons Road, Geelong, Vic., 3217, Australia
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Patiño J, Carine M, Mardulyn P, Devos N, Mateo RG, González-Mancebo JM, Shaw AJ, Vanderpoorten A. Approximate Bayesian Computation Reveals the Crucial Role of Oceanic Islands for the Assembly of Continental Biodiversity. Syst Biol 2015; 64:579-89. [DOI: 10.1093/sysbio/syv013] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/14/2015] [Indexed: 11/13/2022] Open
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Gotzek D, Axen HJ, Suarez AV, Helms Cahan S, Shoemaker D. Global invasion history of the tropical fire ant: a stowaway on the first global trade routes. Mol Ecol 2015; 24:374-88. [DOI: 10.1111/mec.13040] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 11/24/2014] [Accepted: 12/06/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Dietrich Gotzek
- Department of Animal Biology and Department of Entomology; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
- Department of Entomology; National Museum of Natural History; Smithsonian Institution; Washington DC 20013 USA
| | - Heather J. Axen
- Department of Biology; University of Vermont; Burlington VT 05405 USA
| | - Andrew V. Suarez
- Department of Animal Biology and Department of Entomology; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Sara Helms Cahan
- Department of Biology; University of Vermont; Burlington VT 05405 USA
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Lander TA, Klein EK, Oddou-Muratorio S, Candau JN, Gidoin C, Chalon A, Roig A, Fallour D, Auger-Rozenberg MA, Boivin T. Reconstruction of a windborne insect invasion using a particle dispersal model, historical wind data, and Bayesian analysis of genetic data. Ecol Evol 2014; 4:4609-25. [PMID: 25558356 PMCID: PMC4278814 DOI: 10.1002/ece3.1206] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/28/2014] [Accepted: 07/31/2014] [Indexed: 11/29/2022] Open
Abstract
Understanding how invasive species establish and spread is vital for developing effective management strategies for invaded areas and identifying new areas where the risk of invasion is highest. We investigated the explanatory power of dispersal histories reconstructed based on local-scale wind data and a regional-scale wind-dispersed particle trajectory model for the invasive seed chalcid wasp Megastigmus schimitscheki (Hymenoptera: Torymidae) in France. The explanatory power was tested by: (1) survival analysis of empirical data on M. schimitscheki presence, absence and year of arrival at 52 stands of the wasp's obligate hosts, Cedrus (true cedar trees); and (2) Approximate Bayesian analysis of M. schimitscheki genetic data using a coalescence model. The Bayesian demographic modeling and traditional population genetic analysis suggested that initial invasion across the range was the result of long-distance dispersal from the longest established sites. The survival analyses of the windborne expansion patterns derived from a particle dispersal model indicated that there was an informative correlation between the M. schimitscheki presence/absence data from the annual surveys and the scenarios based on regional-scale wind data. These three very different analyses produced highly congruent results supporting our proposal that wind is the most probable vector for passive long-distance dispersal of this invasive seed wasp. This result confirms that long-distance dispersal from introduction areas is a likely driver of secondary expansion of alien invasive species. Based on our results, management programs for this and other windborne invasive species may consider (1) focusing effort at the longest established sites and (2) monitoring outlying populations remains critically important due to their influence on rates of spread. We also suggest that there is a distinct need for new analysis methods that have the capacity to combine empirical spatiotemporal field data, genetic data, and environmental data to investigate dispersal and invasion.
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Affiliation(s)
- Tonya A Lander
- INRA, UR629 Ecologie des Forêts Méditerranéennes F-84914, Avignon, France
| | - Etienne K Klein
- INRA, UR546 Unité de Biostatistique et Processus Spatiaux F-84914, Avignon, France
| | | | - Jean-Noël Candau
- INRA, UR629 Ecologie des Forêts Méditerranéennes F-84914, Avignon, France ; National Resources Canada, Canadian Forest Service, Great Lakes Forestry Ctr Sault Ste Marie, Ontario, P6A 2E5, Canada
| | - Cindy Gidoin
- INRA, UR629 Ecologie des Forêts Méditerranéennes F-84914, Avignon, France
| | - Alain Chalon
- INRA, UR629 Ecologie des Forêts Méditerranéennes F-84914, Avignon, France
| | - Anne Roig
- INRA, UR629 Ecologie des Forêts Méditerranéennes F-84914, Avignon, France
| | - Delphine Fallour
- INRA, UR629 Ecologie des Forêts Méditerranéennes F-84914, Avignon, France
| | | | - Thomas Boivin
- INRA, UR629 Ecologie des Forêts Méditerranéennes F-84914, Avignon, France
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Antoniazza S, Kanitz R, Neuenschwander S, Burri R, Gaigher A, Roulin A, Goudet J. Natural selection in a postglacial range expansion: the case of the colour cline in the European barn owl. Mol Ecol 2014; 23:5508-23. [PMID: 25294501 DOI: 10.1111/mec.12957] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 09/30/2014] [Accepted: 10/03/2014] [Indexed: 12/13/2022]
Abstract
Gradients of variation--or clines--have always intrigued biologists. Classically, they have been interpreted as the outcomes of antagonistic interactions between selection and gene flow. Alternatively, clines may also establish neutrally with isolation by distance (IBD) or secondary contact between previously isolated populations. The relative importance of natural selection and these two neutral processes in the establishment of clinal variation can be tested by comparing genetic differentiation at neutral genetic markers and at the studied trait. A third neutral process, surfing of a newly arisen mutation during the colonization of a new habitat, is more difficult to test. Here, we designed a spatially explicit approximate Bayesian computation (ABC) simulation framework to evaluate whether the strong cline in the genetically based reddish coloration observed in the European barn owl (Tyto alba) arose as a by-product of a range expansion or whether selection has to be invoked to explain this colour cline, for which we have previously ruled out the actions of IBD or secondary contact. Using ABC simulations and genetic data on 390 individuals from 20 locations genotyped at 22 microsatellites loci, we first determined how barn owls colonized Europe after the last glaciation. Using these results in new simulations on the evolution of the colour phenotype, and assuming various genetic architectures for the colour trait, we demonstrate that the observed colour cline cannot be due to the surfing of a neutral mutation. Taking advantage of spatially explicit ABC, which proved to be a powerful method to disentangle the respective roles of selection and drift in range expansions, we conclude that the formation of the colour cline observed in the barn owl must be due to natural selection.
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Affiliation(s)
- Sylvain Antoniazza
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
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Buzbas EO, Rosenberg NA. AABC: approximate approximate Bayesian computation for inference in population-genetic models. Theor Popul Biol 2014; 99:31-42. [PMID: 25261426 DOI: 10.1016/j.tpb.2014.09.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 09/14/2014] [Accepted: 09/15/2014] [Indexed: 01/01/2023]
Abstract
Approximate Bayesian computation (ABC) methods perform inference on model-specific parameters of mechanistically motivated parametric models when evaluating likelihoods is difficult. Central to the success of ABC methods, which have been used frequently in biology, is computationally inexpensive simulation of data sets from the parametric model of interest. However, when simulating data sets from a model is so computationally expensive that the posterior distribution of parameters cannot be adequately sampled by ABC, inference is not straightforward. We present "approximate approximate Bayesian computation" (AABC), a class of computationally fast inference methods that extends ABC to models in which simulating data is expensive. In AABC, we first simulate a number of data sets small enough to be computationally feasible to simulate from the parametric model. Conditional on these data sets, we use a statistical model that approximates the correct parametric model and enables efficient simulation of a large number of data sets. We show that under mild assumptions, the posterior distribution obtained by AABC converges to the posterior distribution obtained by ABC, as the number of data sets simulated from the parametric model and the sample size of the observed data set increase. We demonstrate the performance of AABC on a population-genetic model of natural selection, as well as on a model of the admixture history of hybrid populations. This latter example illustrates how, in population genetics, AABC is of particular utility in scenarios that rely on conceptually straightforward but potentially slow forward-in-time simulations.
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Affiliation(s)
- Erkan O Buzbas
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Department of Statistical Science, University of Idaho, Moscow, ID 84844-1104, USA.
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA.
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Hansen MM, Limborg MT, Ferchaud AL, Pujolar JM. The effects of Medieval dams on genetic divergence and demographic history in brown trout populations. BMC Evol Biol 2014; 14:122. [PMID: 24903056 PMCID: PMC4106231 DOI: 10.1186/1471-2148-14-122] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 05/30/2014] [Indexed: 12/22/2022] Open
Abstract
Background Habitat fragmentation has accelerated within the last century, but may have been ongoing over longer time scales. We analyzed the timing and genetic consequences of fragmentation in two isolated lake-dwelling brown trout populations. They are from the same river system (the Gudenå River, Denmark) and have been isolated from downstream anadromous trout by dams established ca. 600–800 years ago. For reference, we included ten other anadromous populations and two hatchery strains. Based on analysis of 44 microsatellite loci we investigated if the lake populations have been naturally genetically differentiated from anadromous trout for thousands of years, or have diverged recently due to the establishment of dams. Results Divergence time estimates were based on 1) Approximate Bayesian Computation and 2) a coalescent-based isolation-with-gene-flow model. Both methods suggested divergence times ca. 600–800 years bp, providing strong evidence for establishment of dams in the Medieval as the factor causing divergence. Bayesian cluster analysis showed influence of stocked trout in several reference populations, but not in the focal lake and anadromous populations. Estimates of effective population size using a linkage disequilibrium method ranged from 244 to > 1,000 in all but one anadromous population, but were lower (153 and 252) in the lake populations. Conclusions We show that genetic divergence of lake-dwelling trout in two Danish lakes reflects establishment of water mills and impassable dams ca. 600–800 years ago rather than a natural genetic population structure. Although effective population sizes of the two lake populations are not critically low they may ultimately limit response to selection and thereby future adaptation. Our results demonstrate that populations may have been affected by anthropogenic disturbance over longer time scales than normally assumed.
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Affiliation(s)
- Michael M Hansen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
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Egizi A, Fonseca DM. Ecological limits can obscure expansion history: patterns of genetic diversity in a temperate mosquito in Hawaii. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0710-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Chapuis MP, Plantamp C, Blondin L, Pagès C, Vassal JM, Lecoq M. Demographic processes shaping genetic variation of the solitarious phase of the desert locust. Mol Ecol 2014; 23:1749-63. [PMID: 24502250 DOI: 10.1111/mec.12687] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 01/28/2014] [Accepted: 01/29/2014] [Indexed: 11/29/2022]
Abstract
Between plagues, the solitarious desert locust (Schistocerca gregaria) is generally thought to exist as small populations, which are particularly prone to extinction events in arid regions of Africa and Asia. Given the high genetic structuring observed in one geographical area (the Eritrean coast) by former authors, a metapopulation dynamics model involving repeated extinction and colonization events was favoured. In this study, we assessed the validity of a demographic scenario involving temporary populations of the solitarious phase of the desert locust by analysing large-scale population genetic data. We scored 24 microsatellites in 23 solitarious population samples collected over most of the species range during remission. We found very little genetic structuring and little evidence of declining genetic diversity. A Bayesian clustering method distinguished four genetically differentiated units. Three groups were largely consistent with three population samples which had undergone recent bottleneck events. Nevertheless, the last genetically homogeneous unit included all individuals from the remaining 18 population samples and did not show evidence of demographic disequilibrium. An approximate Bayesian computation treatment indicated a large population size for this main genetic group, moderately reduced between plague and remission but still containing tens of thousands of individuals. Our results diverge from the hypothesis of a classical metapopulation dynamics model. They instead support the scenario in which large populations persist in the solitarious phase of the desert locust.
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Fountain T, Duvaux L, Horsburgh G, Reinhardt K, Butlin RK. Human-facilitated metapopulation dynamics in an emerging pest species, Cimex lectularius. Mol Ecol 2014; 23:1071-84. [PMID: 24446663 PMCID: PMC4016754 DOI: 10.1111/mec.12673] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 01/06/2014] [Accepted: 01/13/2014] [Indexed: 12/01/2022]
Abstract
The number and demographic history of colonists can have dramatic consequences for the way in which genetic diversity is distributed and maintained in a metapopulation. The bed bug (Cimex lectularius) is a re-emerging pest species whose close association with humans has led to frequent local extinction and colonization, that is, to metapopulation dynamics. Pest control limits the lifespan of subpopulations, causing frequent local extinctions, and human-facilitated dispersal allows the colonization of empty patches. Founder events often result in drastic reductions in diversity and an increased influence of genetic drift. Coupled with restricted migration, this can lead to rapid population differentiation. We therefore predicted strong population structuring. Here, using 21 newly characterized microsatellite markers and approximate Bayesian computation (ABC), we investigate simplified versions of two classical models of metapopulation dynamics, in a coalescent framework, to estimate the number and genetic composition of founders in the common bed bug. We found very limited diversity within infestations but high degrees of structuring across the city of London, with extreme levels of genetic differentiation between infestations (FST = 0.59). ABC results suggest a common origin of all founders of a given subpopulation and that the numbers of colonists were low, implying that even a single mated female is enough to found a new infestation successfully. These patterns of colonization are close to the predictions of the propagule pool model, where all founders originate from the same parental infestation. These results show that aspects of metapopulation dynamics can be captured in simple models and provide insights that are valuable for the future targeted control of bed bug infestations.
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Affiliation(s)
- Toby Fountain
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK; Department of Biosciences, University of Helsinki, PO Box 65 (Viikinkaari 1), FI-00014, Helsinki, Finland
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Rico C, Normandeau E, Dion-Côté AM, Rico MI, Côté G, Bernatchez L. Combining next-generation sequencing and online databases for microsatellite development in non-model organisms. Sci Rep 2013; 3:3376. [PMID: 24296905 PMCID: PMC3847856 DOI: 10.1038/srep03376] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/30/2013] [Indexed: 12/02/2022] Open
Abstract
Next-generation sequencing (NGS) is revolutionising marker development and the rapidly increasing amount of transcriptomes published across a wide variety of taxa is providing valuable sequence databases for the identification of genetic markers without the need to generate new sequences. Microsatellites are still the most important source of polymorphic markers in ecology and evolution. Motivated by our long-term interest in the adaptive radiation of a non-model species complex of whitefishes (Coregonus spp.), in this study, we focus on microsatellite characterisation and multiplex optimisation using transcriptome sequences generated by Illumina® and Roche-454, as well as online databases of Expressed Sequence Tags (EST) for the study of whitefish evolution and demographic history. We identified and optimised 40 polymorphic loci in multiplex PCR reactions and validated the robustness of our analyses by testing several population genetics and phylogeographic predictions using 494 fish from five lakes and 2 distinct ecotypes.
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Affiliation(s)
- Ciro Rico
- 1] Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (EBD, CSIC), C/Américo Vespucio s/n, 41092 Sevilla, Spain [2] School of Marine Studies, University of the South Pacific, Lower Laucala Campus, Suva, Fiji Islands [3] Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Pavillon Charles-Eugène-Marchand, Québec G1V 0A6, Canada
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Schrey AW, Liebl AL, Richards CL, Martin LB. Range Expansion of House Sparrows (Passer domesticus) in Kenya: Evidence of Genetic Admixture and Human-Mediated Dispersal. J Hered 2013; 105:60-9. [DOI: 10.1093/jhered/est085] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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40
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Besnard G, Dupuy J, Larter M, Cuneo P, Cooke D, Chikhi L. History of the invasive African olive tree in Australia and Hawaii: evidence for sequential bottlenecks and hybridization with the Mediterranean olive. Evol Appl 2013; 7:195-211. [PMID: 24567742 PMCID: PMC3927883 DOI: 10.1111/eva.12110] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 09/04/2013] [Indexed: 11/30/2022] Open
Abstract
Humans have introduced plants and animals into new continents and islands with negative effects on local species. This has been the case of the olive that was introduced in Australia, New Zealand and Pacific islands where it became invasive. Two subspecies were introduced in Australia, and each successfully invaded a specific area: the African olive in New South Wales (NSW) and the Mediterranean olive in South Australia. Here, we examine their origins and spread and analyse a large sample of native and invasive accessions with chloroplast and nuclear microsatellites. African olive populations from the invaded range exhibit two South African chlorotypes hence supporting an introduction from South Africa, while populations from South Australia exhibit chlorotypes of Mediterranean cultivars. Congruently, nuclear markers support the occurrence of two lineages in Australia but demonstrate that admixture took place, attesting that they hybridized early after introduction. Furthermore, using an approximate Bayesian computation framework, we found strong support for the serial introduction of the African olive from South Africa to NSW and then from NSW to Hawaii. The taxon experienced successive bottlenecks that did not preclude invasion, meaning that rapid decisions need to be taken to avoid naturalization where it has not established a large population yet.
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Affiliation(s)
- Guillaume Besnard
- Laboratoire Evolution & Diversité Biologique, CNRS, UPS, ENFA, UMR 5174 Toulouse, France
| | - Jérémy Dupuy
- Laboratoire Evolution & Diversité Biologique, CNRS, UPS, ENFA, UMR 5174 Toulouse, France
| | | | - Peter Cuneo
- The Australian Botanic Garden, Mount Annan, Royal Botanic Gardens and Domain Trust Mount Annan, NSW, Australia
| | - David Cooke
- Department of Primary Industries and Resources PIRSA, Biosecurity SA Adelaide, SA, Australia
| | - Lounes Chikhi
- Laboratoire Evolution & Diversité Biologique, CNRS, UPS, ENFA, UMR 5174 Toulouse, France ; Instituto Gulbenkian de Ciência Oreiras, Portugal
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Glover KA, Pertoldi C, Besnier F, Wennevik V, Kent M, Skaala Ø. Atlantic salmon populations invaded by farmed escapees: quantifying genetic introgression with a Bayesian approach and SNPs. BMC Genet 2013; 14:74. [PMID: 23968202 PMCID: PMC3765417 DOI: 10.1186/1471-2156-14-74] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 08/15/2013] [Indexed: 11/12/2022] Open
Abstract
Background Many native Atlantic salmon populations have been invaded by domesticated escapees for three decades or longer. However, thus far, the cumulative level of gene-flow that has occurred from farmed to wild salmon has not been reported for any native Atlantic salmon population. The aim of the present study was to investigate temporal genetic stability in native populations, and, quantify gene-flow from farmed salmon that caused genetic changes where they were observed. This was achieved by genotyping historical and contemporary samples from 20 populations covering all of Norway with recently identified single nucleotide polymorphism markers that are collectively diagnostic for farmed and wild salmon. These analyses were combined with analysis of farmed salmon and implementation of Approximate Bayesian computation based simulations. Results Five of the populations displayed statistically significant temporal genetic changes. All five of these populations became more similar to a pool of farmed fish with time, strongly suggesting introgression of farmed fish as the primary cause. The remaining 15 populations displayed weak or non-significant temporal genetic changes. Estimated introgression of farmed fish ranged from 2-47% per population using approximate Bayesian computation. Thus, some populations exhibited high degrees of farmed salmon introgression while others were more or less unaffected. The observed frequency of escapees in each population was moderately correlated with estimated introgression per population R2 = 0.47 P < 0.001. Genetic isolation by distance existed within the historical and contemporary data sets, however, the among-population level of divergence decreased with time. Conclusions This is the first study to quantify cumulative introgression of farmed salmon in any native Atlantic salmon population. The estimations demonstrate that the level of introgression has been population-specific, and that the level of introgression is not solely predicted by the frequency of escapees observed in the population. However, some populations have been strongly admixed with farmed salmon, and these data provide policy makers with unique information to address this situation.
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Affiliation(s)
- Kevin Alan Glover
- Section of Population Genetics and Ecology, Institute of Marine Research, Bergen, Norway.
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Perkins TA, Phillips BL, Baskett ML, Hastings A. Evolution of dispersal and life history interact to drive accelerating spread of an invasive species. Ecol Lett 2013; 16:1079-87. [PMID: 23809102 DOI: 10.1111/ele.12136] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 01/28/2013] [Accepted: 05/12/2013] [Indexed: 11/29/2022]
Abstract
Populations on the edge of an expanding range are subject to unique evolutionary pressures acting on their life-history and dispersal traits. Empirical evidence and theory suggest that traits there can evolve rapidly enough to interact with ecological dynamics, potentially giving rise to accelerating spread. Nevertheless, which of several evolutionary mechanisms drive this interaction between evolution and spread remains an open question. We propose an integrated theoretical framework for partitioning the contributions of different evolutionary mechanisms to accelerating spread, and we apply this model to invasive cane toads in northern Australia. In doing so, we identify a previously unrecognised evolutionary process that involves an interaction between life-history and dispersal evolution during range shift. In roughly equal parts, life-history evolution, dispersal evolution and their interaction led to a doubling of distance spread by cane toads in our model, highlighting the potential importance of multiple evolutionary processes in the dynamics of range expansion.
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Affiliation(s)
- T Alex Perkins
- Center for Population Biology, University of California, Davis, CA, USA.
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White TA, Perkins SE, Heckel G, Searle JB. Adaptive evolution during an ongoing range expansion: the invasive bank vole (Myodes glareolus) in Ireland. Mol Ecol 2013; 22:2971-85. [PMID: 23701376 DOI: 10.1111/mec.12343] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 04/03/2013] [Indexed: 12/17/2022]
Abstract
Range expansions are extremely common, but have only recently begun to attract attention in terms of their genetic consequences. As populations expand, demes at the wave front experience strong genetic drift, which is expected to reduce genetic diversity and potentially cause 'allele surfing', where alleles may become fixed over a wide geographical area even if their effects are deleterious. Previous simulation models show that range expansions can generate very strong selective gradients on dispersal, reproduction, competition and immunity. To investigate the effects of range expansion on genetic diversity and adaptation, we studied the population genomics of the bank vole (Myodes glareolus) in Ireland. The bank vole was likely introduced in the late 1920s and is expanding its range at a rate of ~2.5 km/year. Using genotyping-by-sequencing, we genotyped 281 bank voles at 5979 SNP loci. Fourteen sample sites were arranged in three transects running from the introduction site to the wave front of the expansion. We found significant declines in genetic diversity along all three transects. However, there was no evidence that sites at the wave front had accumulated more deleterious mutations. We looked for outlier loci with strong correlations between allele frequency and distance from the introduction site, where the direction of correlation was the same in all three transects. Amongst these outliers, we found significant enrichment for genic SNPs, suggesting the action of selection. Candidates for selection included several genes with immunological functions and several genes that could influence behaviour.
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Affiliation(s)
- Thomas A White
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY 14853-2701, USA.
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Strong genetic differentiation due to multiple founder events during a recent range expansion of an introduced wall lizard population. Biol Invasions 2013. [DOI: 10.1007/s10530-013-0480-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
Approximate Bayesian computation has become an essential tool for the analysis of complex stochastic models when the likelihood function is numerically unavailable. However, the well-established statistical method of empirical likelihood provides another route to such settings that bypasses simulations from the model and the choices of the approximate Bayesian computation parameters (summary statistics, distance, tolerance), while being convergent in the number of observations. Furthermore, bypassing model simulations may lead to significant time savings in complex models, for instance those found in population genetics. The Bayesian computation with empirical likelihood algorithm we develop in this paper also provides an evaluation of its own performance through an associated effective sample size. The method is illustrated using several examples, including estimation of standard distributions, time series, and population genetics models.
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Affiliation(s)
- Kerrie L. Mengersen
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Pierre Pudlo
- Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier-sur-Lez Cedex, France
- Université Montpellier 2, Institut de Mathématiques et de Modélisation de Montpellier, 34095 Montpellier Cedex 5, France
- Institut de Biologie Computationnelle, Montpellier, France
| | - Christian P. Robert
- Université Paris Dauphine, Centre de Recherche en Mathematiques de la Decision, 75775 Paris Cedex 16, France
- Institut Universitaire de France, Paris, France; and
- Centre de Recherche en Statistique et Economie, 92245 Malakoff Cedex, France
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Stockwell CA, Heilveil JS, Purcell K. Estimating divergence time for two evolutionarily significant units of a protected fish species. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0447-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Aeschbacher S, Futschik A, Beaumont MA. Approximate
B
ayesian computation for modular inference problems with many parameters: the example of migration rates. Mol Ecol 2013; 22:987-1002. [DOI: 10.1111/mec.12165] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 11/08/2012] [Accepted: 11/08/2012] [Indexed: 12/01/2022]
Affiliation(s)
- S. Aeschbacher
- Institute of Evolutionary Biology University of Edinburgh Edinburgh EH9 3JTUK
- Institute of Science and Technology Austria (IST Austria) 3400Klosterneuburg Austria
| | - A. Futschik
- Institute of Statistics and Decision Support Systems University of Vienna 1010Vienna Austria
| | - M. A. Beaumont
- Department of Mathematics and School of Biological Sciences University of Bristol Bristol BS8 1TWUK
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48
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Phillips CD, Hoffman JI, George JC, Suydam RS, Huebinger RM, Patton JC, Bickham JW. Molecular insights into the historic demography of bowhead whales: understanding the evolutionary basis of contemporary management practices. Ecol Evol 2012; 3:18-37. [PMID: 23403722 PMCID: PMC3568839 DOI: 10.1002/ece3.374] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 08/07/2012] [Accepted: 08/08/2012] [Indexed: 11/12/2022] Open
Abstract
Patterns of genetic variation observed within species reflect evolutionary histories that include signatures of past demography. Understanding the demographic component of species' history is fundamental to informed management because changes in effective population size affect response to environmental change and evolvability, the strength of genetic drift, and maintenance of genetic variability. Species experiencing anthropogenic population reductions provide valuable case studies for understanding the genetic response to demographic change because historic changes in the census size are often well documented. A classic example is the bowhead whale, Balaena mysticetus, which experienced dramatic population depletion due to commercial whaling in the late 19th and early 20th centuries. Consequently, we analyzed a large multi-marker dataset of bowhead whales using a variety of analytical methods, including extended Bayesian skyline analysis and approximate Bayesian computation, to characterize genetic signatures of both ancient and contemporary demographic histories. No genetic signature of recent population depletion was recovered through any analysis incorporating realistic mutation assumptions, probably due to the combined influences of long generation time, short bottleneck duration, and the magnitude of population depletion. In contrast, a robust signal of population expansion was detected around 70,000 years ago, followed by a population decline around 15,000 years ago. The timing of these events coincides to a historic glacial period and the onset of warming at the end of the last glacial maximum, respectively. By implication, climate driven long-term variation in Arctic Ocean productivity, rather than recent anthropogenic disturbance, appears to have been the primary driver of historic bowhead whale demography.
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Affiliation(s)
- C D Phillips
- Department of Biological Sciences, Texas Tech University Lubbock, Texas
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49
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Keller SR, Gilbert KJ, Fields PD, Taylor DR. Bayesian inference of a complex invasion history revealed by nuclear and chloroplast genetic diversity in the colonizing plant, Silene latifolia. Mol Ecol 2012; 21:4721-34. [PMID: 22943057 DOI: 10.1111/j.1365-294x.2012.05751.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 06/12/2012] [Accepted: 06/20/2012] [Indexed: 01/07/2023]
Abstract
Species invading new ranges are subject to a series of demographic events that can strongly shape genetic diversity. Describing this demographic history is important for understanding where invasive species come from and how they spread, and is critical to testing hypotheses of postinvasion adaptation. Here, we analyse nuclear and chloroplast genetic diversity to study the invasion history of the widespread colonizing weed, Silene latifolia (Caryophyllaceae). Bayesian clustering and PCA revealed strong population structure in the native range of Europe, and although genotypes from multiple native sources were present in the introduced range of North America, the spatial distribution of genetic variance was dramatically reorganized. Using approximate Bayesian computation (ABC), we compared support for different invasion scenarios, including the number and size of independent introduction events and the amount of admixture occurring between sources of introduced genotypes. Our results supported independent introductions into eastern and western North America, with the latter forming a bridgehead for a secondary invasion into the Great Lakes region of central North America. Despite small estimated founder population sizes, the duration of the demographic bottleneck after the initial introduction appeared extremely short-lived. This pattern of repeated colonization and rapid expansion has effectively eroded the strong population structure and cytonuclear associations present in Europe, but has retained overall high genetic diversity since invasion. Our results highlight the flexibility of the ABC approach for constructing a narrative of the demographic history of species invasions and provide baseline for future studies of evolutionary changes in introduced S. latifolia populations.
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Affiliation(s)
- Stephen R Keller
- Appalachian Laboratory, University of Maryland Center for Environmental Science, 301 Braddock Road, Frostburg, MD 21532, USA.
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50
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Somaweera R, Shine R, Webb J, Dempster T, Letnic M. Why does vulnerability to toxic invasive cane toads vary among populations of Australian freshwater crocodiles? Anim Conserv 2012. [DOI: 10.1111/j.1469-1795.2012.00578.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. Somaweera
- School of Biological Sciences; The University of Sydney; Sydney; NSW; Australia
| | - R. Shine
- School of Biological Sciences; The University of Sydney; Sydney; NSW; Australia
| | | | - T. Dempster
- Department of Zoology; University of Melbourne; Melbourne; Vic.; Australia
| | - M. Letnic
- School of Biological, Earth and Environmental Sciences; University of New South Wales; Sydney; NSW; Australia
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