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Liczner AR, Pither R, Bennett JR, Bowman J, Hall KR, Fletcher RJ, Ford AT, Michalak JL, Rayfield B, Wittische J, Pither J. Advances and challenges in ecological connectivity science. Ecol Evol 2024; 14:e70231. [PMID: 39224156 PMCID: PMC11366504 DOI: 10.1002/ece3.70231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 08/01/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
Maintaining and restoring ecological connectivity will be key in helping to prevent and reverse the loss of biodiversity. Fortunately, a growing body of research conducted over the last few decades has advanced our understanding of connectivity science, which will help inform evidence-based connectivity conservation actions. Increases in data availability and computing capacity have helped to dramatically increase our ability to model functional connectivity using more sophisticated models. Keeping track of these advances can be difficult, even for connectivity scientists and practitioners. In this article, we highlight some key advances from the past decade and outline many of the remaining challenges. We describe the efforts to increase the biological realism of connectivity models by, for example, isolating movement behaviors, population parameters, directional movements, and the effects of climate change. We also discuss considerations of when to model connectivity for focal or multiple species. Finally, we reflect on how to account for uncertainty and increase the transparency and reproducibility of connectivity research and discuss situations where decisions may require forgoing sophistication for more simple approaches.
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Affiliation(s)
- Amanda R. Liczner
- Okanagan Institute for Biodiversity, Resilience and Ecosystem ServicesUniversity of British ColumbiaKelownaBritish ColumbiaCanada
| | - Richard Pither
- National Wildlife Research CentreEnvironment and Climate Change CanadaOttawaOntarioCanada
| | | | - Jeff Bowman
- Wildlife Research and Monitoring SectionOntario Ministry of Natural Resources and ForestryPeterboroughOntarioCanada
| | | | - Robert J. Fletcher
- Department of Wildlife Ecology and ConservationUniversity of FloridaGainesvilleFloridaUSA
| | - Adam T. Ford
- Okanagan Institute for Biodiversity, Resilience and Ecosystem ServicesUniversity of British ColumbiaKelownaBritish ColumbiaCanada
- Department of Biology, Irving K. Barber Faculty of ScienceUniversity of British ColumbiaKelownaBritish ColumbiaCanada
| | - Julia L. Michalak
- School of Environmental and Forest SciencesUniversity of WashingtonSeattleWashingtonUSA
| | | | - Julian Wittische
- National Museum of Natural HistoryLuxembourgLuxembourg
- Fondation Faune‐FloreLuxembourgLuxembourg
- Department of Biological SciencesComplexe Des SciencesMontréalQuébecCanada
| | - Jason Pither
- Okanagan Institute for Biodiversity, Resilience and Ecosystem ServicesUniversity of British ColumbiaKelownaBritish ColumbiaCanada
- Department of Biology, Irving K. Barber Faculty of ScienceUniversity of British ColumbiaKelownaBritish ColumbiaCanada
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2
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Novo I, Ordás P, Moraga N, Santiago E, Quesada H, Caballero A. Impact of population structure in the estimation of recent historical effective population size by the software GONE. Genet Sel Evol 2023; 55:86. [PMID: 38049712 PMCID: PMC10694967 DOI: 10.1186/s12711-023-00859-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Effective population size (Ne) is a crucial parameter in conservation genetics and animal breeding. A recent method, implemented by the software GONE, has been shown to be rather accurate in estimating recent historical changes in Ne from a single sample of individuals. However, GONE estimations assume that the population being studied has remained isolated for a period of time, that is, without migration or confluence of other populations. If this occurs, the estimates of Ne can be heavily biased. In this paper, we evaluate the impact of migration and admixture on the estimates of historical Ne provided by GONE through a series of computer simulations considering several scenarios: (a) the mixture of two or more ancestral populations; (b) subpopulations that continuously exchange individuals through migration; (c) populations receiving migrants from a large source; and (d) populations with balanced systems of chromosomal inversions, which also generate genetic structure. RESULTS Our results indicate that the estimates of historical Ne provided by GONE may be substantially biased when there has been a recent mixture of populations that were previously separated for a long period of time. Similarly, biases may occur when the rate of continued migration between populations is low, or when chromosomal inversions are present at high frequencies. However, some biases due to population structuring can be eliminated by conducting population structure analyses and restricting the estimation to the differentiated groups. In addition, disregarding the genomic regions that are involved in inversions can also remove biases in the estimates of Ne. CONCLUSIONS Different kinds of deviations from isolation and panmixia of the populations can generate biases in the recent historical estimates of Ne. Therefore, estimation of past demography could benefit from performing population structure analyses beforehand, by mitigating the impact of these biases on historical Ne estimates.
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Affiliation(s)
- Irene Novo
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain.
| | - Pilar Ordás
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain
| | - Natalia Moraga
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain
| | - Enrique Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Humberto Quesada
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain
| | - Armando Caballero
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain
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3
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Prunier JG, Chevalier M, Raffard A, Loot G, Poulet N, Blanchet S. Genetic erosion reduces biomass temporal stability in wild fish populations. Nat Commun 2023; 14:4362. [PMID: 37474616 PMCID: PMC10359329 DOI: 10.1038/s41467-023-40104-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023] Open
Abstract
Genetic diversity sustains species adaptation. However, it may also support key ecosystems functions and services, for example biomass production, that can be altered by the worldwide loss of genetic diversity. Despite extensive experimental evidence, there have been few attempts to empirically test whether genetic diversity actually promotes biomass and biomass stability in wild populations. Here, using long-term demographic wild fish data from two large river basins in southwestern France, we demonstrate through causal modeling analyses that populations with high genetic diversity do not reach higher biomasses than populations with low genetic diversity. Nonetheless, populations with high genetic diversity have much more stable biomasses over recent decades than populations having suffered from genetic erosion, which has implications for the provision of ecosystem services and the risk of population extinction. Our results strengthen the importance of adopting prominent environmental policies to conserve this important biodiversity facet.
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Affiliation(s)
- Jérôme G Prunier
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UAR 2029, F-09200, Moulis, France.
| | - Mathieu Chevalier
- Department of Ecology and Evolution, University of Lausanne, Biophore, CH-1015, Lausanne, Switzerland
- Ifremer, DYNECO, F-29280, Plouzané, France
| | - Allan Raffard
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UAR 2029, F-09200, Moulis, France
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200, Thonon-les-Bains, France
| | - Géraldine Loot
- CNRS, UPS, École Nationale de Formation Agronomique (ENFA), UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, F-31062, Toulouse, cedex, 4, France
| | - Nicolas Poulet
- Pôle écohydraulique AFB-IMT, allée du Pr Camille Soula, 31400, Toulouse, France
| | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UAR 2029, F-09200, Moulis, France.
- CNRS, UPS, École Nationale de Formation Agronomique (ENFA), UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, F-31062, Toulouse, cedex, 4, France.
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4
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Deflem IS, Calboli FCF, Christiansen H, Hellemans B, Raeymaekers JAM, Volckaert FAM. Contrasting population genetic responses to migration barriers in two native and an invasive freshwater fish. Evol Appl 2022; 15:2010-2027. [PMID: 36540633 PMCID: PMC9753842 DOI: 10.1111/eva.13469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022] Open
Abstract
Habitat fragmentation impacts the distribution of genetic diversity and population genetic structure. Therefore, protecting the evolutionary potential of species, especially in the context of the current rate of human-induced environmental change, is an important goal. In riverine ecosystems, migration barriers affect the genetic structure of native species, while also influencing the spread of invasive species. In this study, we compare genetic patterns of two native and one highly invasive riverine fish species in a Belgian river basin, namely the native three-spined stickleback (Gasterosteus aculeatus) and stone loach (Barbatula barbatula), and the non-native and invasive topmouth gudgeon (Pseudorasbora parva). We aimed to characterize both natural and anthropogenic determinants of genetic diversity and population genetic connectivity. Genetic diversity was highest in topmouth gudgeon, followed by stone loach and three-spined stickleback. The correlation between downstream distance and genetic diversity, a pattern often observed in riverine systems, was only marginally significant in stone loach and three-spined stickleback, while genetic diversity strongly declined with increasing number of barriers in topmouth gudgeon. An Isolation-By-Distance pattern characterizes the population genetic structure of each species. Population differentiation was only associated with migration barriers in the invasive topmouth gudgeon, while genetic composition of all species seemed at least partially determined by the presence of migration barriers. Among the six barrier types considered (watermills, sluices, tunnels, weirs, riverbed obstructions, and others), the presence of watermills was the strongest driver of genetic structure and composition. Our results indicate that conservation and restoration actions, focusing on conserving genetic patterns, cannot be generalized across species. Moreover, measures might target either on restoring connectivity, while risking a rapid spread of the invasive topmouth gudgeon, or not restoring connectivity, while risking native species extinction in upstream populations.
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Affiliation(s)
- Io S. Deflem
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
| | - Federico C. F. Calboli
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
- Natural Resources Institute Finland (Luke)JokioinenFinland
| | | | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
| | - Joost A. M. Raeymaekers
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
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5
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Janecka MJ, Rovenolt F, Stephenson JF. How does host social behavior drive parasite non-selective evolution from the within-host to the landscape-scale? Behav Ecol Sociobiol 2021. [DOI: 10.1007/s00265-021-03089-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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Rougemont Q, Dolo V, Oger A, Besnard AL, Huteau D, Coutellec MA, Perrier C, Launey S, Evanno G. Riverscape genetics in brook lamprey: genetic diversity is less influenced by river fragmentation than by gene flow with the anadromous ecotype. Heredity (Edinb) 2021; 126:235-250. [PMID: 32989279 PMCID: PMC8027852 DOI: 10.1038/s41437-020-00367-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 01/05/2023] Open
Abstract
Understanding the effect of human-induced landscape fragmentation on gene flow and evolutionary potential of wild populations has become a major concern. Here, we investigated the effect of riverscape fragmentation on patterns of genetic diversity in the freshwater resident European brook lamprey (Lampetra planeri) that has a low ability to pass obstacles to migration. We tested the hypotheses of (i) asymmetric gene flow following water current and (ii) an effect of gene flow with the closely related anadromous river lamprey (L. fluviatilis) ecotype on L. planeri genetic diversity. We genotyped 2472 individuals, including 225 L. fluviatilis, sampled from 81 sites upstream and downstream barriers to migration, in 29 western European rivers. Linear modelling revealed a strong positive relationship between genetic diversity and the distance from the river source, consistent with expected patterns of decreased gene flow into upstream populations. However, the presence of anthropogenic barriers had a moderate effect on spatial genetic structure. Accordingly, we found evidence for downstream-directed gene flow, supporting the hypothesis that barriers do not limit dispersal mediated by water flow. Downstream L. planeri populations in sympatry with L. fluviatilis displayed consistently higher genetic diversity. We conclude that genetic drift and slight downstream gene flow drive the genetic make-up of upstream L. planeri populations whereas gene flow between ecotypes maintains higher levels of genetic diversity in L. planeri populations sympatric with L. fluviatilis. We discuss the implications of these results for the design of conservation strategies of lamprey, and other freshwater organisms with several ecotypes, in fragmented dendritic river networks.
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Affiliation(s)
- Quentin Rougemont
- ESE, Ecology and Ecosystem Health, INRAE, Agrocampus Ouest, 35042, Rennes, France.
- Département de biologie, Institut de Biologie Intégrative etsu des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada.
| | - Victoria Dolo
- ESE, Ecology and Ecosystem Health, INRAE, Agrocampus Ouest, 35042, Rennes, France
| | - Adrien Oger
- ESE, Ecology and Ecosystem Health, INRAE, Agrocampus Ouest, 35042, Rennes, France
| | - Anne-Laure Besnard
- ESE, Ecology and Ecosystem Health, INRAE, Agrocampus Ouest, 35042, Rennes, France
| | - Dominique Huteau
- ESE, Ecology and Ecosystem Health, INRAE, Agrocampus Ouest, 35042, Rennes, France
| | | | - Charles Perrier
- Centre de Biologie pour la Gestion des Populations UMR CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Sophie Launey
- ESE, Ecology and Ecosystem Health, INRAE, Agrocampus Ouest, 35042, Rennes, France
| | - Guillaume Evanno
- ESE, Ecology and Ecosystem Health, INRAE, Agrocampus Ouest, 35042, Rennes, France
- OFB, INRAE, Agrocampus Ouest, University Pau Pays Adour, Management of Diadromous Fish in their Environment, Rennes, France
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7
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Chiu M, Li B, Nukazawa K, Resh VH, Carvajal T, Watanabe K. Branching networks can have opposing influences on genetic variation in riverine metapopulations. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Ming‐Chih Chiu
- Center for Marine Environmental Studies (CMES) Ehime University Matsuyama Ehime Japan
- Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Bin Li
- Center for Marine Environmental Studies (CMES) Ehime University Matsuyama Ehime Japan
- Institute of Environment and Ecology Shandong Normal University Jinan China
| | - Kei Nukazawa
- Department of Civil and Environmental Engineering University of Miyazaki Miyazaki Japan
| | - Vincent H. Resh
- Department of Environmental Science, Policy & Management University of California Berkeley CA USA
| | - Thaddeus Carvajal
- Center for Marine Environmental Studies (CMES) Ehime University Matsuyama Ehime Japan
| | - Kozo Watanabe
- Center for Marine Environmental Studies (CMES) Ehime University Matsuyama Ehime Japan
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8
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Blanchet S, Prunier JG, Paz‐Vinas I, Saint‐Pé K, Rey O, Raffard A, Mathieu‐Bégné E, Loot G, Fourtune L, Dubut V. A river runs through it: The causes, consequences, and management of intraspecific diversity in river networks. Evol Appl 2020; 13:1195-1213. [PMID: 32684955 PMCID: PMC7359825 DOI: 10.1111/eva.12941] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 01/01/2023] Open
Abstract
Rivers are fascinating ecosystems in which the eco-evolutionary dynamics of organisms are constrained by particular features, and biologists have developed a wealth of knowledge about freshwater biodiversity patterns. Over the last 10 years, our group used a holistic approach to contribute to this knowledge by focusing on the causes and consequences of intraspecific diversity in rivers. We conducted empirical works on temperate permanent rivers from southern France, and we broadened the scope of our findings using experiments, meta-analyses, and simulations. We demonstrated that intraspecific (genetic) diversity follows a spatial pattern (downstream increase in diversity) that is repeatable across taxa (from plants to vertebrates) and river systems. This pattern can result from interactive processes that we teased apart using appropriate simulation approaches. We further experimentally showed that intraspecific diversity matters for the functioning of river ecosystems. It indeed affects not only community dynamics, but also key ecosystem functions such as litter degradation. This means that losing intraspecific diversity in rivers can yield major ecological effects. Our work on the impact of multiple human stressors on intraspecific diversity revealed that-in the studied river systems-stocking of domestic (fish) strains strongly and consistently alters natural spatial patterns of diversity. It also highlighted the need for specific analytical tools to tease apart spurious from actual relationships in the wild. Finally, we developed original conservation strategies at the basin scale based on the systematic conservation planning framework that appeared pertinent for preserving intraspecific diversity in rivers. We identified several important research avenues that should further facilitate our understanding of patterns of local adaptation in rivers, the identification of processes sustaining intraspecific biodiversity-ecosystem function relationships, and the setting of reliable conservation plans.
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Affiliation(s)
- Simon Blanchet
- Centre National pour la Recherche ScientifiqueStation d'Écologie Théorique et Expérimentale du CNRS à MoulisUniversité Toulouse III Paul SabatierUMR‐5321MoulisFrance
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
| | - Jérôme G. Prunier
- Centre National pour la Recherche ScientifiqueStation d'Écologie Théorique et Expérimentale du CNRS à MoulisUniversité Toulouse III Paul SabatierUMR‐5321MoulisFrance
| | - Ivan Paz‐Vinas
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
- Laboratoire Ecologie Fonctionnelle et EnvironnementUniversité de ToulouseUPSCNRSINPUMR‐5245 ECOLABToulouseFrance
| | - Keoni Saint‐Pé
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
| | - Olivier Rey
- IHPEUniv. MontpellierCNRSIfremerUniv. Perpignan Via DomitiaPerpignanFrance
| | - Allan Raffard
- Centre National pour la Recherche ScientifiqueStation d'Écologie Théorique et Expérimentale du CNRS à MoulisUniversité Toulouse III Paul SabatierUMR‐5321MoulisFrance
| | - Eglantine Mathieu‐Bégné
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
- IHPEUniv. MontpellierCNRSIfremerUniv. Perpignan Via DomitiaPerpignanFrance
| | - Géraldine Loot
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
| | - Lisa Fourtune
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
- PEIRENEEA 7500Université de LimogesLimogesFrance
| | - Vincent Dubut
- Aix Marseille UniversitéCNRSIRDAvignon UniversitéIMBEMarseilleFrance
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9
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Patton AH, Margres MJ, Stahlke AR, Hendricks S, Lewallen K, Hamede RK, Ruiz-Aravena M, Ryder O, McCallum HI, Jones ME, Hohenlohe PA, Storfer A. Contemporary Demographic Reconstruction Methods Are Robust to Genome Assembly Quality: A Case Study in Tasmanian Devils. Mol Biol Evol 2020; 36:2906-2921. [PMID: 31424552 PMCID: PMC6878949 DOI: 10.1093/molbev/msz191] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Reconstructing species’ demographic histories is a central focus of molecular ecology and evolution. Recently, an expanding suite of methods leveraging either the sequentially Markovian coalescent (SMC) or the site-frequency spectrum has been developed to reconstruct population size histories from genomic sequence data. However, few studies have investigated the robustness of these methods to genome assemblies of varying quality. In this study, we first present an improved genome assembly for the Tasmanian devil using the Chicago library method. Compared with the original reference genome, our new assembly reduces the number of scaffolds (from 35,975 to 10,010) and increases the scaffold N90 (from 0.101 to 2.164 Mb). Second, we assess the performance of four contemporary genomic methods for inferring population size history (PSMC, MSMC, SMC++, Stairway Plot), using the two devil genome assemblies as well as simulated, artificially fragmented genomes that approximate the hypothesized demographic history of Tasmanian devils. We demonstrate that each method is robust to assembly quality, producing similar estimates of Ne when simulated genomes were fragmented into up to 5,000 scaffolds. Overall, methods reliant on the SMC are most reliable between ∼300 generations before present (gbp) and 100 kgbp, whereas methods exclusively reliant on the site-frequency spectrum are most reliable between the present and 30 gbp. Our results suggest that when used in concert, genomic methods for reconstructing species’ effective population size histories 1) can be applied to nonmodel organisms without highly contiguous reference genomes, and 2) are capable of detecting independently documented effects of historical geological events.
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Affiliation(s)
- Austin H Patton
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Mark J Margres
- School of Biological Sciences, Washington State University, Pullman, WA.,Department of Organismic and Evolutionary Biology, Harvard University, MA
| | - Amanda R Stahlke
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Sarah Hendricks
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Kevin Lewallen
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Rodrigo K Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | | | - Oliver Ryder
- Institute for Conservation Research, San Diego, CA
| | | | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA
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10
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Paz-Vinas I, Loot G, Hermoso V, Veyssière C, Poulet N, Grenouillet G, Blanchet S. Systematic conservation planning for intraspecific genetic diversity. Proc Biol Sci 2019; 285:rspb.2017.2746. [PMID: 29695444 DOI: 10.1098/rspb.2017.2746] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 04/04/2018] [Indexed: 11/12/2022] Open
Abstract
Intraspecific diversity informs the demographic and evolutionary histories of populations, and should be a main conservation target. Although approaches exist for identifying relevant biological conservation units, attempts to identify priority conservation areas for intraspecific diversity are scarce, especially within a multi-specific framework. We used neutral molecular data on six European freshwater fish species (Squalius cephalus, Phoxinus phoxinus, Barbatula barbatula, Gobio occitaniae, Leuciscus burdigalensis and Parachondrostoma toxostoma) sampled at the riverscape scale (i.e. the Garonne-Dordogne river basin, France) to determine hot- and coldspots of genetic diversity, and to identify priority conservation areas using a systematic conservation planning approach. We demonstrate that systematic conservation planning is efficient for identifying priority areas representing a predefined part of the total genetic diversity of a whole landscape. With the exception of private allelic richness (PA), classical genetic diversity indices (allelic richness, genetic uniqueness) were poor predictors for identifying priority areas. Moreover, we identified weak surrogacies among conservation solutions found for each species, implying that conservation solutions are highly species-specific. Nonetheless, we showed that priority areas identified using intraspecific genetic data from multiple species provide more effective conservation solutions than areas identified for single species or on the basis of traditional taxonomic criteria.
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Affiliation(s)
- Ivan Paz-Vinas
- CNRS, UPS, IRD; UMR-5174 EDB, Université de Toulouse, 118 route de Narbonne, 31062 Toulouse cedex 4, France .,Aix-Marseille Université, CNRS, IRD, Avignon Université; UMR-7263 IMBE, 3 place Victor Hugo, 13331 Marseille cedex 3, France.,CNRS, ENTPE; UMR-5023 LEHNA, Université de Lyon, 6 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Géraldine Loot
- CNRS, UPS, IRD; UMR-5174 EDB, Université de Toulouse, 118 route de Narbonne, 31062 Toulouse cedex 4, France.,Institut Universitaire de France, Paris, France
| | - Virgilio Hermoso
- Centre Tecnologic Forestal de Catalunya, Crta. Sant Llorenc de Monunys, Km 2, 25280 Solsona, Lleida, Spain
| | - Charlotte Veyssière
- CNRS, UPS, IRD; UMR-5174 EDB, Université de Toulouse, 118 route de Narbonne, 31062 Toulouse cedex 4, France
| | - Nicolas Poulet
- French Biodiversity Agency, pôle écohydraulique, Allée du professeur Camille Soula, 31400 Toulouse, France
| | - Gaël Grenouillet
- CNRS, UPS, IRD; UMR-5174 EDB, Université de Toulouse, 118 route de Narbonne, 31062 Toulouse cedex 4, France.,Institut Universitaire de France, Paris, France
| | - Simon Blanchet
- CNRS, UPS, IRD; UMR-5174 EDB, Université de Toulouse, 118 route de Narbonne, 31062 Toulouse cedex 4, France.,CNRS, Station d'Écologie Théorique et Expérimentale, UMR-5321, 09200 Moulis, France
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11
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Bouchard C, Tessier N, Lapointe FJ. Watersheds influence the wood turtle’s (Glyptemys insculpta) genetic structure. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01169-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure. Heredity (Edinb) 2018; 121:663-678. [PMID: 30293985 PMCID: PMC6221895 DOI: 10.1038/s41437-018-0148-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 09/14/2018] [Accepted: 09/15/2018] [Indexed: 11/08/2022] Open
Abstract
In the last years, a wide range of methods allowing to reconstruct past population size changes from genome-wide data have been developed. At the same time, there has been an increasing recognition that population structure can generate genetic data similar to those produced under models of population size change. Recently, Mazet et al. (Heredity 116:362-371, 2016) showed that, for any model of population structure, it is always possible to find a panmictic model with a particular function of population size changes, having exactly the same distribution of T2 (the coalescence time for a sample of size two) as that of the structured model. They called this function IICR (Inverse Instantaneous Coalescence Rate) and showed that it does not necessarily correspond to population size changes under non-panmictic models. Besides, most of the methods used to analyse data under models of population structure tend to arbitrarily fix that structure and to minimise or neglect population size changes. Here, we extend the seminal work of Herbots (PhD thesis, University of London, 1994) on the structured coalescent and propose a new framework, the Non-Stationary Structured Coalescent (NSSC) that incorporates demographic events (changes in gene flow and/or deme sizes) to models of nearly any complexity. We show how to compute the IICR under a wide family of stationary and non-stationary models. As an example we address the question of human and Neanderthal evolution and discuss how the NSSC framework allows to interpret genomic data under this new perspective.
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Mathieu-Bégné E, Loot G, Chevalier M, Paz-Vinas I, Blanchet S. Demographic and genetic collapses in spatially structured populations: insights from a long-term survey in wild fish metapopulations. OIKOS 2018. [DOI: 10.1111/oik.05511] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eglantine Mathieu-Bégné
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
| | - Géraldine Loot
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
- Inst. Universitaire de France; Paris France
| | - Mathieu Chevalier
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
| | - Ivan Paz-Vinas
- Univ. de Lyon, Ecole Nationale des Travaux Publics de l'Etat (ENTPE), CNRS; UMR5023, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés; Villeurbanne France
- UPS, INP, CNRS, Univ. de Toulouse, UMR 5245 Laboratoire Écologie Fonctionnelle et Environnement; Ecolab Toulouse France
| | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
- CNRS, UPS; UMR5321, Station d'Ecologie Théorique et Expérimentale; Moulis France
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Pavinato VAC, Michel AP, de Campos JB, Omoto C, Zucchi MI. Influence of historical land use and modern agricultural expansion on the spatial and ecological divergence of sugarcane borer, Diatraea saccharalis (Lepidoptera: Crambidae) in Brazil. Heredity (Edinb) 2017; 120:25-37. [PMID: 29234172 DOI: 10.1038/s41437-017-0018-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/02/2017] [Accepted: 09/29/2017] [Indexed: 01/06/2023] Open
Abstract
Human-mediated changes in landscapes can facilitate niche expansion and accelerate the adaptation of insect species. The interaction between the evolutionary history of the sugarcane borer, Diatraea saccharalis Fabricius, and historical and modern agricultural activity in Brazil shaped its spatial genetic structure, facilitating ecological divergence and incipient host shifting. Based on microsatellite data, STRUCTURE analyses identified two (K = 2) and three (K = 3) significant genetic clusters that corresponded to: (a) a strong signal of spatial genetic structure and, (b) a cryptic signal of host differentiation. We inferred that K = 2 reflects the footprint of agricultural activity, such as expansion of crop production (sugarcane and maize), unintentional dispersion of pests, and management practices. In contrast, K = 3 indicated incipient host differentiation between larvae collected from sugarcane or maize. Our estimates of population size changes indicated that a historical bottleneck was associated with a reduction of sugarcane production ≈200 years ago. However, a more recent population expansion was detected (>1950s), associated with agricultural expansion of large crop production into previously unfarmed land. Partial Mantel tests supported our hypothesis of incipient host adaptation, and identified isolation-by-environment (e.g., host plant) in São Paulo and Minas Gerais states, where sugarcane has been traditionally produced in Brazil. The impact of agricultural production on D. saccharalis may continue, as the current population structure may hinder the efficacy of refuge plants in delaying insect resistance evolution to Bt toxin.
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Affiliation(s)
- Vitor A C Pavinato
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Avenida Bertrand Russel, s/n, Cidade Universitária Zeferino Vaz, 6109, Campinas, SP, Brazil. .,Department of Entomology, Ohio Agricultural Research and Development Center, Thorne Hall, The Ohio State University, 1680, Madison Avenue, Wooster, OH, USA.
| | - Andrew P Michel
- Department of Entomology, Ohio Agricultural Research and Development Center, Thorne Hall, The Ohio State University, 1680, Madison Avenue, Wooster, OH, USA
| | - Jaqueline B de Campos
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Avenida Bertrand Russel, s/n, Cidade Universitária Zeferino Vaz, 6109, Campinas, SP, Brazil
| | - Celso Omoto
- Department of Entomology and Acarology, University of São Paulo, Avenida Pádua Dias 11, CP 9, Piracicaba, SP, Brazil
| | - Maria I Zucchi
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Avenida Bertrand Russel, s/n, Cidade Universitária Zeferino Vaz, 6109, Campinas, SP, Brazil.,Agribusiness Technological Development of São Paulo (APTA), Laboratory of Conservation Genetics and Genomics, Rodovia SP 127 km 30, CP 28, Piracicaba, SP, Brazil
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15
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The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice. Heredity (Edinb) 2017; 120:13-24. [PMID: 29234166 PMCID: PMC5837117 DOI: 10.1038/s41437-017-0005-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 08/22/2017] [Accepted: 08/22/2017] [Indexed: 01/27/2023] Open
Abstract
Several inferential methods using genomic data have been proposed to quantify and date population size changes in the history of species. At the same time an increasing number of studies have shown that population structure can generate spurious signals of population size change. Recently, Mazet et al. (2016) introduced, for a sample size of two, a time-dependent parameter, which they called the IICR (inverse instantaneous coalescence rate). The IICR is equivalent to a population size in panmictic models, but not necessarily in structured models. It is characterised by a temporal trajectory that suggests population size changes, as a function of the sampling scheme, even when the total population size was constant. Here, we extend the work of Mazet et al. (2016) by (i) showing how the IICR can be computed for any demographic model of interest, under the coalescent, (ii) applying this approach to models of population structure (1D and 2D stepping stone, split models, two- and three-island asymmetric gene flow, continent-island models), (iii) stressing the importance of the sampling strategy in generating different histories, (iv) arguing that IICR plots can be seen as summaries of genomic information that can thus be used for model choice or model exclusion (v) applying this approach to the question of admixture between humans and Neanderthals. Altogether these results are potentially important given that the widely used PSMC (pairwise sequentially Markovian coalescent) method of Li and Durbin (2011) estimates the IICR of the sample, not necessarily the history of the populations.
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Laggis A, Baxevanis AD, Charalampidou A, Maniatsi S, Triantafyllidis A, Abatzopoulos TJ. Microevolution of the noble crayfish (Astacus astacus) in the Southern Balkan Peninsula. BMC Evol Biol 2017; 17:122. [PMID: 28558646 PMCID: PMC5450353 DOI: 10.1186/s12862-017-0971-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/17/2017] [Indexed: 12/02/2022] Open
Abstract
Background The noble crayfish (Astacus astacus) displays a complex historical and contemporary genetic status in Europe. The species divergence has been shaped by geological events (i.e. Pleistocene glaciations) and humanly induced impacts (i.e. translocations, pollution, etc.) on its populations due to species commercial value and its niche degradation. Until now, limited genetic information has been procured for the Balkan area and especially for the southernmost distribution of this species (i.e. Greece). It is well known that the rich habitat diversity of the Balkan Peninsula offers suitable conditions for genetically diversified populations. Thus, the present manuscript revisits the phylogenetic relationships of the noble crayfish in Europe and identifies the genetic make-up and the biogeographical patterns of the species in its southern range limit. Results Mitochondrial markers (i.e. COI and 16S) were used in order to elucidate the genetic structure and diversity of the noble crayfish in Europe. Two of the six European haplotypic lineages, were found exclusively in Greece. These two lineages exhibited greater haplotypic richness when compared with the rest four (of “Central European” origin) while they showed high genetic diversity. Divergence time analysis identified that the majority of this divergence was captured through Pleistocene, suggesting a southern glacial refugium (Greece, southern Balkans). Furthermore, six microsatellite markers were used in order to define the factors affecting the genetic structure and demographic history of the species in Greece. The population structure analysis revealed six to nine genetic clusters and eight putative genetic barriers. Evidence of bottleneck effects in the last ~5000 years (due to climatic and geological events and human activities) is also afforded. Findings from several other research fields (e.g. life sciences, geology or even archaeology) have been utilized to perceive the genetic make-up of the noble crayfish. Conclusions The southernmost part of Balkans has played a major role as a glacial refugium for A. astacus. Such refugia have served as centres of expansion to northern regions. Recent history of the noble crayfish in southern Balkans reveals the influence of environmental (climate, geology and/or topology) and anthropogenic factors. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0971-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anastasia Laggis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Athanasios D Baxevanis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Alexandra Charalampidou
- Scientific Computing Office, Information Technology (IT) Center, School of Sciences, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Macedonia, Greece
| | - Stefania Maniatsi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Alexander Triantafyllidis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Theodore J Abatzopoulos
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece.
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Limited Dispersal and Significant Fine - Scale Genetic Structure in a Tropical Montane Parrot Species. PLoS One 2016; 11:e0169165. [PMID: 28033364 PMCID: PMC5199109 DOI: 10.1371/journal.pone.0169165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 12/13/2016] [Indexed: 11/19/2022] Open
Abstract
Tropical montane ecosystems are biodiversity hotspots harbouring many endemics that are confined to specific habitat types within narrow altitudinal ranges. While deforestation put these ecosystems under threat, we still lack knowledge about how heterogeneous environments like the montane tropics promote population connectivity and persistence. We investigated the fine-scale genetic structure of the two largest subpopulations of the endangered El Oro parakeet (Pyrrhura orcesi) endemic to the Ecuadorian Andes. Specifically, we assessed the genetic divergence between three sites separated by small geographic distances but characterized by a heterogeneous habitat structure. Although geographical distances between sites are small (3-17 km), we found genetic differentiation between all sites. Even though dispersal capacity is generally high in parrots, our findings indicate that dispersal is limited even on this small geographic scale. Individual genotype assignment revealed similar genetic divergence across a valley (~ 3 km distance) compared to a continuous mountain range (~ 13 km distance). Our findings suggest that geographic barriers promote genetic divergence even on small spatial scales in this endangered endemic species. These results may have important implications for many other threatened and endemic species, particularly given the upslope shift of species predicted from climate change.
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Li X, Deng Y, Yang K, Gan W, Zeng R, Deng L, Song Z. Genetic Diversity and Structure Analysis of Percocypris pingi (Cypriniformes: Cyprinidae): Implications for Conservation and Hatchery Release in the Yalong River. PLoS One 2016; 11:e0166769. [PMID: 27911911 PMCID: PMC5135059 DOI: 10.1371/journal.pone.0166769] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 11/03/2016] [Indexed: 11/19/2022] Open
Abstract
Percocypris pingi is a near threatened cyprinid species, which has suffered a dramatic decline due to anthropogenic factors. As one response to this decline, hatchery release for P. pingi has been conducted in the lower reaches of the Yalong River since 2012. To understand the conservation status of this species and the potential impact of the release of hatchery-reared fish, we studied the genetic diversity and population structure of wild and hatchery populations of P. pingi. Two hatchery populations (Jinping [JPH] and Ya’an [YAH]) and two wild populations (Muli [MLW] and Woluo [WLW]) of P. pingi were analyzed based on microsatellite markers and the mitochondrial DNA control region. The results showed that P. pingi possesses moderate levels of genetic diversity, with observed heterozygosities ranging from 0.657 to 0.770 and nucleotide diversities ranging from 0.00212 to 0.00491. Our results also suggested WLW harbors considerable proportions of genetic diversity in this species and serves as a refuge for P. pingi during anthropogenic disturbance, thus playing an important role for the conservation of P. pingi populations. Microsatellite and mitochondrial markers both indicated close genetic relationships between YAH and MLW, JPH and WLW, respectively. The results to some extent reflected the geographical provenances for original broodstocks of the two hatchery populations, which provide some practical guidance for hatchery release of P. pingi. The existence of remarkable genetic divergence distributed along limited geographical range (approximately 10 kilometers) suggests the two wild populations should be regarded at least as two distinct evolutionary significant units (ESUs) and management units (MUs). Considering reduced intra-population genetic variation in hatchery population for release and significant genetic compositions of the two hatchery populations, some appropriate breeding strategies were proposed to benefit conservation of P. pingi.
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Affiliation(s)
- Xiaoyan Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yuanping Deng
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Kun Yang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Weixiong Gan
- Yalong River Hydropower Development Company, Ltd., Chengdu, China
| | - Rukui Zeng
- Yalong River Hydropower Development Company, Ltd., Chengdu, China
| | - Longjun Deng
- Yalong River Hydropower Development Company, Ltd., Chengdu, China
| | - Zhaobin Song
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- * E-mail:
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Hermes C, Döpper A, Schaefer HM, Segelbacher G. Effects of forest fragmentation on the morphological and genetic structure of a dispersal-limited, endangered bird species. NATURE CONSERVATION 2016. [DOI: 10.3897/natureconservation.16.10905] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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20
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Miranda EA, Batalha-Filho H, Congrains C, Carvalho AF, Ferreira KM, Del Lama MA. Phylogeography of Partamona rustica (Hymenoptera, Apidae), an Endemic Stingless Bee from the Neotropical Dry Forest Diagonal. PLoS One 2016; 11:e0164441. [PMID: 27723778 PMCID: PMC5056711 DOI: 10.1371/journal.pone.0164441] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/26/2016] [Indexed: 11/19/2022] Open
Abstract
The South America encompasses the highest levels of biodiversity found anywhere in the world and its rich biota is distributed among many different biogeographical regions. However, many regions of South America are still poorly studied, including its xeric environments, such as the threatened Caatinga and Cerrado phytogeographical domains. In particular, the effects of Quaternary climatic events on the demography of endemic species from xeric habitats are poorly understood. The present study uses an integrative approach to reconstruct the evolutionary history of Partamona rustica, an endemic stingless bee from dry forest diagonal in Brazil, in a spatial-temporal framework. In this sense, we sequenced four mitochondrial genes and genotyped eight microsatellite loci. Our results identified two population groups: one to the west and the other to the east of the São Francisco River Valley (SFRV). These groups split in the late Pleistocene, and the Approximate Bayesian Computation approach and phylogenetic reconstruction indicated that P. rustica originated in the west of the SFRV, subsequently colonising eastern region. Our tests of migration detected reduced gene flow between these groups. Finally, our results also indicated that the inferences both from the genetic data analyses and from the spatial distribution modelling are compatible with historical demographic stability.
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Affiliation(s)
- Elder Assis Miranda
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
- * E-mail:
| | - Henrique Batalha-Filho
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Carlos Congrains
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Antônio Freire Carvalho
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Kátia Maria Ferreira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Marco Antonio Del Lama
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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Sundqvist L, Keenan K, Zackrisson M, Prodöhl P, Kleinhans D. Directional genetic differentiation and relative migration. Ecol Evol 2016; 6:3461-3475. [PMID: 27127613 PMCID: PMC4842207 DOI: 10.1002/ece3.2096] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 12/18/2022] Open
Abstract
Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly used to gather this information. One potential caveat is that these measures assume gene flow to be symmetric. However, asymmetric gene flow is common in nature, especially in systems driven by physical processes such as wind or water currents. As information about levels of asymmetric gene flow among populations is essential for the correct interpretation of the distribution of contemporary genetic diversity within species, this should not be overlooked. To obtain information on asymmetric migration patterns from genetic data, complex models based on maximum-likelihood or Bayesian approaches generally need to be employed, often at great computational cost. Here, a new simpler and more efficient approach for understanding gene flow patterns is presented. This approach allows the estimation of directional components of genetic divergence between pairs of populations at low computational effort, using any of the classical or modern measures of genetic differentiation. These directional measures of genetic differentiation can further be used to calculate directional relative migration and to detect asymmetries in gene flow patterns. This can be done in a user-friendly web application called divMigrate-online introduced in this study. Using simulated data sets with known gene flow regimes, we demonstrate that the method is capable of resolving complex migration patterns under a range of study designs.
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Affiliation(s)
- Lisa Sundqvist
- Department of Marine SciencesUniversity of GothenburgSE‐405 30GothenburgSweden
| | - Kevin Keenan
- School of Biological SciencesInstitute for Global Food SecurityQueen's University BelfastBelfastBT9 7BLUK
| | - Martin Zackrisson
- Department for Chemistry and Molecular BiologyUniversity of GothenburgSE‐405 30GothenburgSweden
| | - Paulo Prodöhl
- School of Biological SciencesInstitute for Global Food SecurityQueen's University BelfastBelfastBT9 7BLUK
| | - David Kleinhans
- ForWind Center for Wind Energy ResearchInstitute of PhysicsCarl von Ossietzky UniversityDE‐26129OldenburgGermany
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Spatial patterns of genetic diversity, community composition and occurrence of native and non-native amphipods in naturally replicated tributary streams. BMC Ecol 2016; 16:23. [PMID: 27118474 PMCID: PMC4847240 DOI: 10.1186/s12898-016-0079-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 04/20/2016] [Indexed: 11/30/2022] Open
Abstract
Background Worldwide, natural communities are invaded by non-native species, with potentially devastating effects on the native communities. A large part of past research aimed at finding traits and characteristics of the invading species or the invaded community explaining observed invasions. Only recently, the focus shifted on the spatial patterns during invasions per se. Empirical data, however, are limited, as invasions are often unique incidences of a complex spatio-temporal process. In order to identify generalities of invasion patterns, we studied 13 naturally replicated tributary streams draining into Lake Constance, and studied the occurrence of native and non-native amphipods along linear transects from the stream outlets to the upstream headwater reaches. Results We found repeated spatial patterns of community composition and the occurrence of native and non-native amphipod species across two different years. Specifically, occurrence as well as abundance of two non-native amphipod species decreased from the stream outlets at the lake site towards upstream headwater reaches. Populations of the most common native amphipod species were largest at the uppermost headwater reaches. All populations of this native species, however, showed significant signals of recent genetic bottlenecks, irrespective of the stream position and occurrence of non-native species. Contrary to our expectations, this native species also showed no longitudinal genetic differentiation within individual tributaries as postulated for headwater versus outlet populations. Conclusions Our results indicate that invasions of river-systems may overall follow predictable patterns on the level of spatial distributions and community composition. However, effects of invading organisms on the genetic diversity and genetic structure of native populations observed at larger scales may not necessarily be directly reflected at the scale of smaller tributaries. Electronic supplementary material The online version of this article (doi:10.1186/s12898-016-0079-7) contains supplementary material, which is available to authorized users.
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Isolation by distance and non-identical patterns of gene flow within two river populations of the freshwater fish Rutilus rutilus (L. 1758). CONSERV GENET 2016; 17:861-874. [PMID: 32355467 PMCID: PMC7175732 DOI: 10.1007/s10592-016-0828-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 02/23/2016] [Indexed: 11/23/2022]
Abstract
The spatial distribution of organisms is maintained by a combination of in situ reproduction and dispersal of conspecifics from elsewhere within its habitable range. The determination of dispersal origin and sub-population connectivity has a vital role to play in forming effective management policies. The common roach (Rutilus rutilus) is an important component of the economically and socially valuable recreational fishery and represents a well-studied member of the Cyprinidae. Microsatellite allele data were used to investigate hypothetically variant levels of microevolutionary structuring and isolation-by-distance (IBD) in in the Rivers Stour and Thames. A strong signal of IBD was found in the Stour, probably due to the limited capacity for unrestricted bidirectional dispersal in this river compared with the Thames. A weak inference of IBD in the Thames is likely erroneous and effected by a strong localised genetic signal from a recent stocking event. Whilst we found significantly genetically divergent upstream areas in the River Stour, a strong signal of IBD remained when the headwater sub-population was removed, suggesting that that the signal is not biased by non-equilibrium conditions in upstream reaches. We discuss these results with reference to the management of aquatic bioresources and emphasise the idiosyncrasy that aquatic biota and hydrological complexity may imprint upon patterns of biodiversity within any given system.
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Thomaz AT, Christie MR, Knowles LL. The architecture of river networks can drive the evolutionary dynamics of aquatic populations. Evolution 2016; 70:731-9. [DOI: 10.1111/evo.12883] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 02/01/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Andréa T. Thomaz
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor Michigan 48109
| | - Mark R. Christie
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor Michigan 48109
- Department of Biological Science; Purdue University; West Lafayette Indiana 47907
- Department of Forestry and Natural Resources; Purdue University; West Lafayette Indiana 47907
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor Michigan 48109
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On the importance of being structured: instantaneous coalescence rates and human evolution--lessons for ancestral population size inference? Heredity (Edinb) 2015; 116:362-71. [PMID: 26647653 DOI: 10.1038/hdy.2015.104] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/07/2015] [Accepted: 10/28/2015] [Indexed: 11/09/2022] Open
Abstract
Most species are structured and influenced by processes that either increased or reduced gene flow between populations. However, most population genetic inference methods assume panmixia and reconstruct a history characterized by population size changes. This is potentially problematic as population structure can generate spurious signals of population size change through time. Moreover, when the model assumed for demographic inference is misspecified, genomic data will likely increase the precision of misleading if not meaningless parameters. For instance, if data were generated under an n-island model (characterized by the number of islands and migrants exchanged) inference based on a model of population size change would produce precise estimates of a bottleneck that would be meaningless. In addition, archaeological or climatic events around the bottleneck's timing might provide a reasonable but potentially misleading scenario. In a context of model uncertainty (panmixia versus structure) genomic data may thus not necessarily lead to improved statistical inference. We consider two haploid genomes and develop a theory that explains why any demographic model with structure will necessarily be interpreted as a series of changes in population size by inference methods ignoring structure. We formalize a parameter, the inverse instantaneous coalescence rate, and show that it is equivalent to a population size only in panmictic models, and is mostly misleading for structured models. We argue that this issue affects all population genetics methods ignoring population structure which may thus infer population size changes that never took place. We apply our approach to human genomic data.
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Dyer RJ. Population Graphs and Landscape Genetics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054150] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rodney J. Dyer
- Department of Biology and Center for Environmental Studies, Virginia Commonwealth University, Richmond, Virginia 23284-2012;
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Paz-Vinas I, Loot G, Stevens VM, Blanchet S. Evolutionary processes driving spatial patterns of intraspecific genetic diversity in river ecosystems. Mol Ecol 2015; 24:4586-604. [PMID: 26284462 DOI: 10.1111/mec.13345] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 07/30/2015] [Accepted: 08/13/2015] [Indexed: 01/17/2023]
Abstract
Describing, understanding and predicting the spatial distribution of genetic diversity is a central issue in biological sciences. In river landscapes, it is generally predicted that neutral genetic diversity should increase downstream, but there have been few attempts to test and validate this assumption across taxonomic groups. Moreover, it is still unclear what are the evolutionary processes that may generate this apparent spatial pattern of diversity. Here, we quantitatively synthesized published results from diverse taxa living in river ecosystems, and we performed a meta-analysis to show that a downstream increase in intraspecific genetic diversity (DIGD) actually constitutes a general spatial pattern of biodiversity that is repeatable across taxa. We further demonstrated that DIGD was stronger for strictly waterborne dispersing than for overland dispersing species. However, for a restricted data set focusing on fishes, there was no evidence that DIGD was related to particular species traits. We then searched for general processes underlying DIGD by simulating genetic data in dendritic-like river systems. Simulations revealed that the three processes we considered (downstream-biased dispersal, increase in habitat availability downstream and upstream-directed colonization) might generate DIGD. Using random forest models, we identified from simulations a set of highly informative summary statistics allowing discriminating among the processes causing DIGD. Finally, combining these discriminant statistics and approximate Bayesian computations on a set of twelve empirical case studies, we hypothesized that DIGD were most likely due to the interaction of two of these three processes and that contrary to expectation, they were not solely caused by downstream-biased dispersal.
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Affiliation(s)
- I Paz-Vinas
- Centre National de la Recherche Scientifique (CNRS), École Nationale de Formation Agronomique (ENFA), UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Paul Sabatier, 118 route de Narbonne, 31062, Toulouse Cedex 4, France.,UPS, UMR 5174 (EDB), Université de Toulouse, 118 route de Narbonne, 31062, Toulouse Cedex 4, France.,UMR 7263 - IMBE, Équipe EGE, Centre Saint-Charles, Aix-Marseille Université, CNRS, IRD, Université d'Avignon et des Pays de Vaucluse, Case 36, 3 place Victor Hugo, 13331, Marseille Cedex 3, France
| | - G Loot
- UPS, UMR 5174 (EDB), Université de Toulouse, 118 route de Narbonne, 31062, Toulouse Cedex 4, France.,Station d'Écologie Expérimentale du CNRS à Moulis, USR 2936, Centre National de la Recherche Scientifique (CNRS), 2 route du CNRS, 09200, Moulis, France
| | - V M Stevens
- Station d'Écologie Expérimentale du CNRS à Moulis, USR 2936, Centre National de la Recherche Scientifique (CNRS), 2 route du CNRS, 09200, Moulis, France
| | - S Blanchet
- Centre National de la Recherche Scientifique (CNRS), École Nationale de Formation Agronomique (ENFA), UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Paul Sabatier, 118 route de Narbonne, 31062, Toulouse Cedex 4, France.,Station d'Écologie Expérimentale du CNRS à Moulis, USR 2936, Centre National de la Recherche Scientifique (CNRS), 2 route du CNRS, 09200, Moulis, France
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Mazet O, Rodríguez W, Chikhi L. Demographic inference using genetic data from a single individual: Separating population size variation from population structure. Theor Popul Biol 2015; 104:46-58. [PMID: 26120083 DOI: 10.1016/j.tpb.2015.06.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 06/11/2015] [Accepted: 06/16/2015] [Indexed: 10/23/2022]
Abstract
The rapid development of sequencing technologies represents new opportunities for population genetics research. It is expected that genomic data will increase our ability to reconstruct the history of populations. While this increase in genetic information will likely help biologists and anthropologists to reconstruct the demographic history of populations, it also represents new challenges. Recent work has shown that structured populations generate signals of population size change. As a consequence it is often difficult to determine whether demographic events such as expansions or contractions (bottlenecks) inferred from genetic data are real or due to the fact that populations are structured in nature. Given that few inferential methods allow us to account for that structure, and that genomic data will necessarily increase the precision of parameter estimates, it is important to develop new approaches. In the present study we analyze two demographic models. The first is a model of instantaneous population size change whereas the second is the classical symmetric island model. We (i) re-derive the distribution of coalescence times under the two models for a sample of size two, (ii) use a maximum likelihood approach to estimate the parameters of these models (iii) validate this estimation procedure under a wide array of parameter combinations, (iv) implement and validate a model rejection procedure by using a Kolmogorov-Smirnov test, and a model choice procedure based on the AIC, and (v) derive the explicit distribution for the number of differences between two non-recombining sequences. Altogether we show that it is possible to estimate parameters under several models and perform efficient model choice using genetic data from a single diploid individual.
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Affiliation(s)
- Olivier Mazet
- UMR 5219, Institut de Mathématiques de Toulouse, Université de Toulouse & CNRS, France
| | - Willy Rodríguez
- UMR 5219, Institut de Mathématiques de Toulouse, Université de Toulouse & CNRS, France
| | - Lounès Chikhi
- CNRS, Université Paul Sabatier, ENFA, UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), F-31062 Toulouse, France; Université de Toulouse, UPS, EDB, F-31062 Toulouse, France; Instituto Gulbenkian de Ciência, P-2780-156 Oeiras, Portugal.
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Paz-Vinas I, Blanchet S. Dendritic connectivity shapes spatial patterns of genetic diversity: a simulation-based study. J Evol Biol 2015; 28:986-94. [PMID: 25808422 DOI: 10.1111/jeb.12626] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 03/12/2015] [Accepted: 03/19/2015] [Indexed: 01/18/2023]
Abstract
Landscape features notoriously affect spatial patterns of biodiversity. For instance, in dendritic ecological networks (such as river basins), dendritic connectivity has been proposed to create unique spatial patterns of biodiversity. Here, we compared genetic datasets simulated under a lattice-like, a dendritic and a circular landscape to test the influence of dendritic connectivity on neutral genetic diversity. The circular landscape had a level of connectivity similar to that of the dendritic landscape, so as to isolate the influence of dendricity on genetic diversity. We found that genetic diversity and differentiation varied strikingly among the three landscapes. For instance, the dendritic landscape generated higher total number of alleles and higher global Fst than the lattice-like landscape, and these indices also varied between the dendritic and the circular landscapes, suggesting an effect of dendricity. Furthermore, in the dendritic landscape, allelic richness was higher in highly connected demes (e.g. confluences in rivers) than in low-connected demes (e.g. upstream and downstream populations), which was not the case in the circular landscape, hence confirming the major role of dendricity. This led to bell-shaped distributions of allelic richness along an upstream-downstream gradient. Conversely, genetic differentiation (Fst ) was lower in highly than in low-connected demes (which was not observed in circular landscape), and significant patterns of isolation by distance (IBD) were also observed in the dendritic landscape. We conclude that in dendritic networks, the combined influence of dendricity and connectivity generates unique spatial patterns of neutral genetic diversity, which has implications for population geneticists and conservationists.
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Affiliation(s)
- I Paz-Vinas
- UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), Centre National de la Recherche Scientifique (CNRS), École Nationale de Formation Agronomique (ENFA), Université Paul Sabatier, Toulouse, France; UMR 5174 (EDB), Université de Toulouse, UPS, Toulouse, France; Aix-Marseille Université, CNRS, IRD, Université d'Avignon, UMR 7263 - IMBE, Équipe EGE, Centre Saint-Charles, Case 36, Marseille, France
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30
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Emerson BC, Hickerson MJ. Lack of support for the time-dependent molecular evolution hypothesis. Mol Ecol 2015; 24:702-9. [DOI: 10.1111/mec.13070] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 12/17/2014] [Accepted: 12/30/2014] [Indexed: 01/24/2023]
Affiliation(s)
- Brent C. Emerson
- Island Ecology and Evolution Research Group; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC); C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife, Canary Islands 38206 Spain
| | - Michael J. Hickerson
- Biology Department; City College of New York; New York NY 10031 USA
- The Graduate Center; City University of New York; New York NY 10016 USA
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31
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Putman AI, Carbone I. Challenges in analysis and interpretation of microsatellite data for population genetic studies. Ecol Evol 2014; 4:4399-428. [PMID: 25540699 PMCID: PMC4267876 DOI: 10.1002/ece3.1305] [Citation(s) in RCA: 237] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 10/02/2014] [Accepted: 10/03/2014] [Indexed: 12/14/2022] Open
Abstract
Advancing technologies have facilitated the ever-widening application of genetic markers such as microsatellites into new systems and research questions in biology. In light of the data and experience accumulated from several years of using microsatellites, we present here a literature review that synthesizes the limitations of microsatellites in population genetic studies. With a focus on population structure, we review the widely used fixation (F ST) statistics and Bayesian clustering algorithms and find that the former can be confusing and problematic for microsatellites and that the latter may be confounded by complex population models and lack power in certain cases. Clustering, multivariate analyses, and diversity-based statistics are increasingly being applied to infer population structure, but in some instances these methods lack formalization with microsatellites. Migration-specific methods perform well only under narrow constraints. We also examine the use of microsatellites for inferring effective population size, changes in population size, and deeper demographic history, and find that these methods are untested and/or highly context-dependent. Overall, each method possesses important weaknesses for use with microsatellites, and there are significant constraints on inferences commonly made using microsatellite markers in the areas of population structure, admixture, and effective population size. To ameliorate and better understand these constraints, researchers are encouraged to analyze simulated datasets both prior to and following data collection and analysis, the latter of which is formalized within the approximate Bayesian computation framework. We also examine trends in the literature and show that microsatellites continue to be widely used, especially in non-human subject areas. This review assists with study design and molecular marker selection, facilitates sound interpretation of microsatellite data while fostering respect for their practical limitations, and identifies lessons that could be applied toward emerging markers and high-throughput technologies in population genetics.
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Affiliation(s)
- Alexander I Putman
- Department of Plant Pathology, North Carolina State University Raleigh, North Carolina, 27695-7616
| | - Ignazio Carbone
- Department of Plant Pathology, North Carolina State University Raleigh, North Carolina, 27695-7616
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Streicher JW, Devitt TJ, Goldberg CS, Malone JH, Blackmon H, Fujita MK. Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs. Mol Ecol 2014; 23:3273-91. [DOI: 10.1111/mec.12814] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 05/20/2014] [Accepted: 05/23/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Jeffrey W. Streicher
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
| | - Thomas J. Devitt
- Department of Integrative Biology; The University of Texas at Austin; Austin TX 78712 USA
| | - Caren S. Goldberg
- Fish and Wildlife Sciences; University of Idaho; Moscow ID 83844 USA
| | - John H. Malone
- Department of Molecular and Cell Biology; University of Connecticut; Storrs CT 06269 USA
| | - Heath Blackmon
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
| | - Matthew K. Fujita
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
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Mok HF, Stepien CC, Kaczmarek M, Albelo LR, Sequeira AS. Genetic status and timing of a weevil introduction to Santa Cruz Island, Galapagos. J Hered 2014; 105:365-80. [PMID: 24399746 PMCID: PMC3984438 DOI: 10.1093/jhered/est096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 10/16/2013] [Accepted: 12/03/2013] [Indexed: 11/14/2022] Open
Abstract
Successful invasive species can overcome or circumvent the potential genetic loss caused by an introduction bottleneck through a rapid population expansion and admixture from multiple introductions. We explore the genetic makeup and the timing of a species introduction to Santa Cruz Island in the Galápagos archipelago. We investigate the presence of processes that can maintain genetic diversity in populations of the broad-nosed weevil Galapaganus howdenae howdenae. Analyses of combined genotypes for 8 microsatellite loci showed evidence of past population size reductions through moment and likelihood-based estimators. No evidence of admixture through multiple introductions was found, but substantial current population sizes (N0 298, 95% credible limits 50-2300), genetic diversity comparable with long-established endemics (Mean number of alleles = 3.875), and lack of genetic structure across the introduced range (F ST = 0.01359) could suggest that foundations are in place for populations to rapidly recover any loss of genetic variability. The time estimates for the introduction into Santa Cruz support an accidental transfer during the colonization period (1832-1959) predating the spurt in human population growth. Our evaluation of the genetic status of G. h. howdenae suggests potential for population growth in addition to our field observations of a concurrent expansion in range and feeding preferences towards protected areas and endemic host plants.
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Affiliation(s)
- Hoi-Fei Mok
- the Department of Biological Sciences, Wellesley College, Wellesley
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Hoban S. An overview of the utility of population simulation software in molecular ecology. Mol Ecol 2014; 23:2383-401. [DOI: 10.1111/mec.12741] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 03/22/2014] [Accepted: 03/26/2014] [Indexed: 01/12/2023]
Affiliation(s)
- Sean Hoban
- National Institute for Mathematical and Biological Synthesis; University of Tennessee; 1122 Volunteer Blvd. Suite 110A Knoxville TN 37996-3410 USA
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35
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Paz-Vinas I, Comte L, Chevalier M, Dubut V, Veyssiere C, Grenouillet G, Loot G, Blanchet S. Combining genetic and demographic data for prioritizing conservation actions: insights from a threatened fish species. Ecol Evol 2013; 3:2696-710. [PMID: 24567833 PMCID: PMC3930054 DOI: 10.1002/ece3.645] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 05/16/2013] [Accepted: 05/19/2013] [Indexed: 11/20/2022] Open
Abstract
Prioritizing and making efficient conservation plans for threatened populations requires information at both evolutionary and ecological timescales. Nevertheless, few studies integrate multidisciplinary approaches, mainly because of the difficulty for conservationists to assess simultaneously the evolutionary and ecological status of populations. Here, we sought to demonstrate how combining genetic and demographic analyses allows prioritizing and initiating conservation plans. To do so, we combined snapshot microsatellite data and a 30-year-long demographic survey on a threatened freshwater fish species (Parachondrostoma toxostoma) at the river basin scale. Our results revealed low levels of genetic diversity and weak effective population sizes (<63 individuals) in all populations. We further detected severe bottlenecks dating back to the last centuries (200–800 years ago), which may explain the differentiation of certain populations. The demographic survey revealed a general decrease in the spatial distribution and abundance of P. toxostoma over the last three decades. We conclude that demo-genetic approaches are essential for (1) identifying populations for which both evolutionary and ecological extinction risks are high; and (2) proposing conservation plans targeted toward these at risk populations, and accounting for the evolutionary history of populations. We suggest that demo-genetic approaches should be the norm in conservation practices. We combined genetic and demographic data from a threatened freshwater fish species (Parachondrostoma toxostoma) at the river basin scale for conservation purposes. Genetic diversity and effective population sizes are very low, probably due to the strong genetic bottlenecks detected in this study. The species spatial distribution and abundance also decreased during the last decades.
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Affiliation(s)
- Ivan Paz-Vinas
- UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Centre National de la Recherche Scientifique (CNRS), École Nationale de Formation Agronomique (ENFA), Université Paul Sabatier 118 route de Narbonne, F-31062, Toulouse Cedex 4, France ; UMR 5174 (EDB) UPS, Université de Toulouse 118 route de Narbonne, F-31062, Toulouse Cedex, France ; Centre National de la Recherche Scientifique (CNRS), Station d'Ecologie Expérimentale du CNRS à Moulis USR 2936, F-09200, Moulis, France
| | - Lise Comte
- UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Centre National de la Recherche Scientifique (CNRS), École Nationale de Formation Agronomique (ENFA), Université Paul Sabatier 118 route de Narbonne, F-31062, Toulouse Cedex 4, France ; UMR 5174 (EDB) UPS, Université de Toulouse 118 route de Narbonne, F-31062, Toulouse Cedex, France
| | - Mathieu Chevalier
- UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Centre National de la Recherche Scientifique (CNRS), École Nationale de Formation Agronomique (ENFA), Université Paul Sabatier 118 route de Narbonne, F-31062, Toulouse Cedex 4, France ; UMR 5174 (EDB) UPS, Université de Toulouse 118 route de Narbonne, F-31062, Toulouse Cedex, France ; UMR 5245 EcoLab (Laboratoire Ecologie Fonctionnelle et Environnement), CNRS F-31062, Toulouse, France
| | - Vincent Dubut
- IMBE - UMR 7263, Aix-Marseille Université, CNRS, IRD Centre Saint-Charles, Case 36, 3 place Victor Hugo, F-13331, Marseille Cedex 3, France
| | - Charlotte Veyssiere
- UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Centre National de la Recherche Scientifique (CNRS), École Nationale de Formation Agronomique (ENFA), Université Paul Sabatier 118 route de Narbonne, F-31062, Toulouse Cedex 4, France ; UMR 5174 (EDB) UPS, Université de Toulouse 118 route de Narbonne, F-31062, Toulouse Cedex, France
| | - Gaël Grenouillet
- UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Centre National de la Recherche Scientifique (CNRS), École Nationale de Formation Agronomique (ENFA), Université Paul Sabatier 118 route de Narbonne, F-31062, Toulouse Cedex 4, France ; UMR 5174 (EDB) UPS, Université de Toulouse 118 route de Narbonne, F-31062, Toulouse Cedex, France
| | - Geraldine Loot
- UMR 5174 (EDB) UPS, Université de Toulouse 118 route de Narbonne, F-31062, Toulouse Cedex, France ; Centre National de la Recherche Scientifique (CNRS), Station d'Ecologie Expérimentale du CNRS à Moulis USR 2936, F-09200, Moulis, France
| | - Simon Blanchet
- UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Centre National de la Recherche Scientifique (CNRS), École Nationale de Formation Agronomique (ENFA), Université Paul Sabatier 118 route de Narbonne, F-31062, Toulouse Cedex 4, France ; Centre National de la Recherche Scientifique (CNRS), Station d'Ecologie Expérimentale du CNRS à Moulis USR 2936, F-09200, Moulis, France
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