1
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Beer MA, Proft KM, Veillet A, Kozakiewicz CP, Hamilton DG, Hamede R, McCallum H, Hohenlohe PA, Burridge CP, Margres MJ, Jones ME, Storfer A. Disease-driven top predator decline affects mesopredator population genomic structure. Nat Ecol Evol 2024; 8:293-303. [PMID: 38191839 DOI: 10.1038/s41559-023-02265-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/02/2023] [Indexed: 01/10/2024]
Abstract
Top predator declines are pervasive and often have dramatic effects on ecological communities via changes in food web dynamics, but their evolutionary consequences are virtually unknown. Tasmania's top terrestrial predator, the Tasmanian devil, is declining due to a lethal transmissible cancer. Spotted-tailed quolls benefit via mesopredator release, and they alter their behaviour and resource use concomitant with devil declines and increased disease duration. Here, using a landscape community genomics framework to identify environmental drivers of population genomic structure and signatures of selection, we show that these biotic factors are consistently among the top variables explaining genomic structure of the quoll. Landscape resistance negatively correlates with devil density, suggesting that devil declines will increase quoll genetic subdivision over time, despite no change in quoll densities detected by camera trap studies. Devil density also contributes to signatures of selection in the quoll genome, including genes associated with muscle development and locomotion. Our results provide some of the first evidence of the evolutionary impacts of competition between a top predator and a mesopredator species in the context of a trophic cascade. As top predator declines are increasing globally, our framework can serve as a model for future studies of evolutionary impacts of altered ecological interactions.
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Affiliation(s)
- Marc A Beer
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Kirstin M Proft
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Anne Veillet
- Hilo Core Genomics Facility, University of Hawaii at Hilo, Hilo, HI, USA
| | - Christopher P Kozakiewicz
- Department of Integrative Biology, Michigan State University, W.K. Kellogg Biological Station, Hickory Corners, MI, USA
| | - David G Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le Cancer, Montpellier, France
| | - Hamish McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | | | - Mark J Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, USA.
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2
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Waples RS. Practical application of the linkage disequilibrium method for estimating contemporary effective population size: A review. Mol Ecol Resour 2024; 24:e13879. [PMID: 37873672 DOI: 10.1111/1755-0998.13879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/25/2023]
Abstract
The method to estimate contemporary effective population size (Ne ) based on patterns of linkage disequilibrium (LD) at unlinked loci has been widely applied to natural and managed populations. The underlying model makes many simplifying assumptions, most of which have been evaluated in numerous studies published over the last two decades. Here, these performance evaluations are reviewed and summarized, with a focus on information that facilitates practical application to real populations in nature. Potential sources of bias that are discussed include calculation of r2 (a measure of LD), adjustments for sampling error, physical linkage, age structure, migration and spatial structure, mutation and selection, mating systems, changes in abundance, rare alleles, missing data, genotyping errors, data filtering choices and methods for combining multiple Ne estimates. Factors that affect precision are reviewed, including pseudoreplication that limits the information gained from large genomics datasets, constraints imposed by small samples of individuals, and the challenges in obtaining robust estimates for large populations. Topics that merit further research include the potential to weight r2 values by allele frequency, lump samples of individuals, use genotypic likelihoods rather than called genotypes, prune large LD values and apply the method to species practising partial monogamy.
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Affiliation(s)
- Robin S Waples
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
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3
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Mancini AN, Chandrashekar A, Lahitsara JP, Ogbeta DG, Rajaonarivelo JA, Ranaivorazo NR, Rasoazanakolona J, Safwat M, Solo J, Razafindraibe JG, Razafindrakoto G, Baden AL. Terrain Ruggedness and Canopy Height Predict Short-Range Dispersal in the Critically Endangered Black-and-White Ruffed Lemur. Genes (Basel) 2023; 14:746. [PMID: 36981017 PMCID: PMC10048730 DOI: 10.3390/genes14030746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 03/30/2023] Open
Abstract
Dispersal is a fundamental aspect of primates' lives and influences both population and community structuring, as well as species evolution. Primates disperse within an environmental context, where both local and intervening environmental factors affect all phases of dispersal. To date, research has primarily focused on how the intervening landscape influences primate dispersal, with few assessing the effects of local habitat characteristics. Here, we use a landscape genetics approach to examine between- and within-site environmental drivers of short-range black-and-white ruffed lemur (Varecia variegata) dispersal in the Ranomafana region of southeastern Madagascar. We identified the most influential drivers of short-range ruffed lemur dispersal as being between-site terrain ruggedness and canopy height, more so than any within-site habitat characteristic evaluated. Our results suggest that ruffed lemurs disperse through the least rugged terrain that enables them to remain within their preferred tall-canopied forest habitat. Furthermore, we noted a scale-dependent environmental effect when comparing our results to earlier landscape characteristics identified as driving long-range ruffed lemur dispersal. We found that forest structure drives short-range dispersal events, whereas forest presence facilitates long-range dispersal and multigenerational gene flow. Together, our findings highlight the importance of retaining high-quality forests and forest continuity to facilitate dispersal and maintain functional connectivity in ruffed lemurs.
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Affiliation(s)
- Amanda N. Mancini
- Department of Anthropology, The Graduate Center, City University of New York, New York, NY 10016, USA
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, NY 10065, USA
| | - Aparna Chandrashekar
- Department of Anthropology, The Graduate Center, City University of New York, New York, NY 10016, USA
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, NY 10065, USA
| | | | - Daisy Gold Ogbeta
- Department of Nursing, Helene Fuld College of Nursing, New York, NY 10035, USA
- Department of Chemistry, Hunter College, New York, NY 10065, USA
| | - Jeanne Arline Rajaonarivelo
- UMI 233 TransVIHMI, Institut de Recherche pour le Développement (IRD), University of Montpellier, Inserm U 1175, 34000 Montpellier, France
| | | | - Joseane Rasoazanakolona
- Department of Zoology and Animal Biodiversity, Faculty of Science, University of Antananarivo, Antananarivo 101, Madagascar
| | - Mayar Safwat
- Department of Chemistry, Hunter College, New York, NY 10065, USA
| | - Justin Solo
- Centre ValBio Research Center, Ranomafana, Ifanadiana 312, Madagascar (J.G.R.)
| | | | | | - Andrea L. Baden
- Department of Anthropology, The Graduate Center, City University of New York, New York, NY 10016, USA
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, NY 10065, USA
- Department of Anthropology, Hunter College, New York, NY 10065, USA
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4
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Reed EMX, Reiskind MH, Burford Reiskind MO. Life-history stage and the population genetics of the tiger mosquito Aedes albopictus at a fine spatial scale. MEDICAL AND VETERINARY ENTOMOLOGY 2023; 37:132-142. [PMID: 36300547 DOI: 10.1111/mve.12618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
As a widespread vector of disease with an expanding range, the mosquito Aedes albopictus Skuse (Diptera: Culicidae) is a high priority for research and management. A. albopictus has a complex life history with aquatic egg, larval and pupal stages, and a terrestrial adult stage. This requires targeted management strategies for each life stage, coordinated across time and space. Population genetics can aid in A. albopictus control by evaluating patterns of genetic diversity and dispersal. However, how life stage impacts population genetic characteristics is unknown. We examined whether patterns of A. albopictus genetic diversity and differentiation changed with life stage at a spatial scale relevant to management efforts. We first conducted a literature review of field-caught A. albopictus population genetic papers and identified 101 peer-reviewed publications, none of which compared results between life stages. Our study uniquely examines population genomic patterns of egg and adult A. albopictus at five sites in Wake County, North Carolina, USA, using 8425 single nucleotide polymorphisms. We found that the level of genetic diversity and connectivity between sites varied between adults and eggs. This warrants further study and is critical for research aimed at informing local management.
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Affiliation(s)
- Emily M X Reed
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Michael H Reiskind
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
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5
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Alvarez-Aleman A, Hunter ME, Frazer TK, Powell JA, Alfonso EG, Austin JD. The first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba. Genetica 2022; 150:327-341. [PMID: 36271978 DOI: 10.1007/s10709-022-00172-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/04/2022] [Indexed: 11/04/2022]
Abstract
The coastal waters of Cuba are home to a small, endangered population of West Indian manatee, which would benefit from a comprehensive characterization of the population's genetic variation. We conducted the first genetic assessment of Cuban manatees to determine the extent of the population's genetic structure and characterize the neutral genetic diversity among regions within the archipelago. We genotyped 49 manatees at 18 microsatellite loci, a subset of 27 samples on 1703 single nucleotide polymorphisms (SNPs), and sequenced 59 manatees at the mitochondrial control region. The Cuba manatee population had low nuclear (microsatellites HE = 0.44, and SNP HE = 0.29) and mitochondrial genetic diversity (h = 0.068 and π = 0.00025), and displayed moderate departures from random mating (microsatellite FIS = 0.12, SNP FIS = 0.10). Our results suggest that the western portion of the archipelago undergoes periodic exchange of alleles based on the evidence of shared ancestry and low but significant differentiation. The southeast Guantanamo Bay region and the western portion of the archipelago were more differentiated than southwest and northwest manatees. The genetic distinctiveness observed in the southeast supports its recognition as a demographically independent unit for natural resource management regardless of whether it is due to historical isolation or isolation by distance. Estimates of the regional effective population sizes, with the microsatellite and SNP datasets, were small (all Ne < 60). Subsequent analyses using additional samples could better examine how the observed structure is masking simple isolation by distance patterns or whether ecological or biogeographic forces shape genetic patterns.
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Affiliation(s)
- Anmari Alvarez-Aleman
- School of Natural Resources and Environment, University of Florida, 2035 McCarty hall D, Gainesville, FL, 32611, USA. .,Centro de Investigaciones Marinas, Universidad de La Habana, Calle 16 # 114 Entre 1ra y 3ra Plaza, Havana, Cuba. .,Clearwater Marine Aquarium Research Institute, Clearwater Marine Aquarium, Clearwater, FL, USA.
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
| | - Thomas K Frazer
- School of Natural Resources and Environment, University of Florida, 2035 McCarty hall D, Gainesville, FL, 32611, USA.,College of Marine Science, University of South Florida, 140 Seventh Avenue South, KRC 3109, St. Petersburg, FL, 33701, USA
| | - James A Powell
- Clearwater Marine Aquarium Research Institute, Clearwater Marine Aquarium, Clearwater, FL, USA
| | - Eddy Garcia Alfonso
- Refugio de Fauna Lanzanillo-Pajonal-Fragoso, Empresa Provincial para la Protección de la Flora y la Fauna, Villa Clara, Cuba
| | - James D Austin
- School of Natural Resources and Environment, University of Florida, 2035 McCarty hall D, Gainesville, FL, 32611, USA.,Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL, 32611, USA
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6
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Maier PA, Vandergast AG, Ostoja SM, Aguilar A, Bohonak AJ. Gene Pool Boundaries for the Yosemite Toad (Anaxyrus canorus) Reveal Asymmetrical Migration Within Meadow Neighborhoods. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.851676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Yosemite toad (Anaxyrus [Bufo] canorus) is a federally threatened species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. The species is one of the first amphibians to undergo a large demographic collapse that was well-documented, and is reputed to remain in low abundance throughout its range. Recent phylogeographic work has demonstrated that Pleistocene toad lineages diverged and then admixed to differing extents across an elevational gradient. Although lineage divisions may have significant effects on evolutionary trajectories over large spatial and temporal scales, present-day population dynamics must be delineated in order to manage and conserve the species effectively. In this study, we used a double-digest RADseq dataset to address three primary questions: (1) Are single meadows or neighborhoods of nearby meadows most correlated with population boundaries? (2) Does asymmetrical migration occur among neighborhoods of nearby meadows? (3) What topographic or hydrological variables predict such asymmetrical migration in these meadow neighborhoods? Hierarchical STRUCTURE and AMOVA analyses suggested that populations are typically circumscribed by a single meadow, although 84% of meadows exist in neighborhoods of at least two meadows connected by low levels of migration, and over half (53%) of neighborhoods examined display strong asymmetrical migration. Meadow neighborhoods often contain one or more large and flat “hub” meadows that experience net immigration, surrounded by smaller and topographically rugged “satellite” meadows with net emigration. Hubs tend to contain more genetic diversity and could be prioritized for conservation and habitat management and as potential sources for reestablishment efforts.
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7
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Srivastava DS, Coristine L, Angert AL, Bontrager M, Amundrud SL, Williams JL, Yeung ACY, Zwaan DR, Thompson PL, Aitken SN, Sunday JM, O'Connor MI, Whitton J, Brown NEM, MacLeod CD, Parfrey LW, Bernhardt JR, Carrillo J, Harley CDG, Martone PT, Freeman BG, Tseng M, Donner SD. Wildcards in climate change biology. ECOL MONOGR 2021. [DOI: 10.1002/ecm.1471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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Bernard AM, Finnegan KA, Pavinski Bitar P, Stanhope MJ, Shivji MS. Genomic assessment of global population structure in a highly migratory and habitat versatile apex predator, the tiger shark (Galeocerdo cuvier). J Hered 2021; 112:497-507. [PMID: 34374783 DOI: 10.1093/jhered/esab046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/09/2021] [Indexed: 11/12/2022] Open
Abstract
Understanding the population dynamics of highly mobile, widely distributed, oceanic sharks, many of which are overexploited, is necessary to aid their conservation management. We investigated the global population genomics of tiger sharks (Galeocerdo cuvier), a circumglobally distributed, apex predator displaying remarkable behavioral versatility in its diet, habitat use (near coastal, coral reef, pelagic), and individual movement patterns (spatially resident to long-distance migrations). We genotyped 242 tiger sharks from 10 globally distributed locations at more than 2000 single nucleotide polymorphisms. Although this species often conducts massive distance migrations, the data show strong genetic differentiation at both neutral (FST=0.125-0.144) and candidate outlier loci (FST=0.570-0.761) between western Atlantic and Indo-Pacific sharks, suggesting the potential for adaptation to the environments specific to these oceanic regions. Within these regions, there was mixed support for population differentiation between northern and southern hemispheres in the western Atlantic, and none for structure within the Indian Ocean. Notably, the results demonstrate a low level of population differentiation of tiger sharks from the remote Hawaiian archipelago compared to sharks from the Indian Ocean (FST=0.003-0.005, P<0.01). Given concerns about biodiversity loss and marine ecosystem impacts caused by overfishing of oceanic sharks in the midst of rapid environmental change, our results suggest it imperative that international fishery management prioritize conservation of the evolutionary potential of the highly genetically differentiated Atlantic and Indo-Pacific populations of this unique apex predator. Furthermore, we suggest targeted management attention to tiger sharks in the Hawaiian archipelago based on a precautionary biodiversity conservation perspective.
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Affiliation(s)
- Andrea M Bernard
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, Florida, USA
| | - Kimberly A Finnegan
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, Florida, USA.,Guy Harvey Research Institute, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, Florida, USA
| | - Paulina Pavinski Bitar
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Michael J Stanhope
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Mahmood S Shivji
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, Florida, USA.,Guy Harvey Research Institute, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, Florida, USA
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9
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Metapopulation genetics of endangered reticulated flatwoods salamanders (Ambystoma bishopi) in a dynamic and fragmented landscape. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01360-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Boissin E, Neglia V, Baksay S, Micu D, Bat L, Topaloglu B, Todorova V, Panayotova M, Kruschel C, Milchakova N, Voutsinas E, Beqiraj S, Nasto I, Aglieri G, Taviani M, Zane L, Planes S. Chaotic genetic structure and past demographic expansion of the invasive gastropod Tritia neritea in its native range, the Mediterranean Sea. Sci Rep 2020; 10:21624. [PMID: 33303767 PMCID: PMC7730386 DOI: 10.1038/s41598-020-77742-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 11/16/2020] [Indexed: 11/21/2022] Open
Abstract
To better predict population evolution of invasive species in introduced areas it is critical to identify and understand the mechanisms driving genetic diversity and structure in their native range. Here, we combined analyses of the mitochondrial COI gene and 11 microsatellite markers to investigate both past demographic history and contemporaneous genetic structure in the native area of the gastropod Tritia neritea, using Bayesian skyline plots (BSP), multivariate analyses and Bayesian clustering. The BSP framework revealed population expansions, dated after the last glacial maximum. The haplotype network revealed a strong geographic clustering. Multivariate analyses and Bayesian clustering highlighted the strong genetic structure at all scales, between the Black Sea and the Adriatic Sea, but also within basins. Within basins, a random pattern of genetic patchiness was observed, suggesting a superimposition of processes involving natural biological effects (no larval phase and thus limited larval dispersal) and putative anthropogenic transport of specimens. Contrary to the introduced area, no isolation-by-distance patterns were recovered in the Mediterranean or the Black Seas, highlighting different mechanisms at play on both native and introduced areas, triggering unknown consequences for species’ evolutionary trajectories. These results of Tritia neritea populations on its native range highlight a mixture of ancient and recent processes, with the effects of paleoclimates and life history traits likely tangled with the effects of human-mediated dispersal.
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Affiliation(s)
- Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence « CORAIL », Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.
| | - Valentina Neglia
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence « CORAIL », Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Sandra Baksay
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence « CORAIL », Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.,Laboratoire Evolution & Diversite Biologique, University TOULOUSE III - Paul Sabatier, 118 route de Narbonne, 31062, Toulouse Cedex 09, France
| | - Dragos Micu
- Romanian Waters National Authority, 127 Mircea cel Batran Blvd., 900592, Constanţa, Romania
| | - Levent Bat
- Department of Hydrobiology, Sinop University Faculty of Fisheries, 57000, Sinop, Turkey
| | - Bulent Topaloglu
- Faculty of Aquatic Sciences, Istanbul University, Ordu St No: 8, 34134, Istanbul, Turkey
| | - Valentina Todorova
- Institute of Oceanology-BAS (IO-BAS), P.O. Box 152, 9000, Varna, Bulgaria
| | - Marina Panayotova
- Institute of Oceanology-BAS (IO-BAS), P.O. Box 152, 9000, Varna, Bulgaria
| | - Claudia Kruschel
- University of Zadar, Ul. Mihovila Pavlinovića, 23000, Zadar, Croatia
| | - Nataliya Milchakova
- Institute of Biology of the Southern Seas, 2 Nakhimov Ave., Sevastopol, Russia, 299011
| | - Emanuela Voutsinas
- Institute of Oceanography, Hellenic Centre for Marine Research, P.O. Box 712, 19013, Anavyssos, Greece
| | - Sajmir Beqiraj
- Faculty of Natural Sciences, Department of Biology, University of Tirana, Bulevardi "Zogu I Parë", 25/1, 1001, Tiranë, Albania
| | - Ina Nasto
- Department of Biology, Faculty of Technical Sciences, Vlora University, 9401, Vlora, Albania
| | - Giorgio Aglieri
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, via Archirafi 28, 90123, Palermo, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Rome, Italy
| | - Marco Taviani
- Institute of Marine Sciences (ISMAR), CNR, via Gobetti 101, 40129, Bologna, Italy.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.,Department of Biology, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA, 02543, USA
| | - Lorenzo Zane
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Rome, Italy.,Dipartimento di Biologia, Università di Padova, via U. Bassi/58B, 35121, Padua, Italy
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence « CORAIL », Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
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11
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Aguirre-Liguori JA, Luna-Sánchez JA, Gasca-Pineda J, Eguiarte LE. Evaluation of the Minimum Sampling Design for Population Genomic and Microsatellite Studies: An Analysis Based on Wild Maize. Front Genet 2020; 11:870. [PMID: 33193568 PMCID: PMC7531271 DOI: 10.3389/fgene.2020.00870] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/16/2020] [Indexed: 12/21/2022] Open
Abstract
Massive parallel sequencing (MPS) is revolutionizing the field of molecular ecology by allowing us to understand better the evolutionary history of populations and species, and to detect genomic regions that could be under selection. However, the economic and computational resources needed generate a tradeoff between the amount of loci that can be obtained and the number of populations or individuals that can be sequenced. In this work, we analyzed and compared two simulated genomic datasets fitting a hierarchical structure, two extensive empirical genomic datasets, and a dataset comprising microsatellite information. For all datasets, we generated different subsampling designs by changing the number of loci, individuals, populations, and individuals per population to test for deviations in classic population genetics parameters (HS, FIS, FST). For the empirical datasets we also analyzed the effect of sampling design on landscape genetic tests (isolation by distance and environment, central abundance hypothesis). We also tested the effect of sampling a different number of populations in the detection of outlier SNPs. We found that the microsatellite dataset is very sensitive to the number of individuals sampled when obtaining summary statistics. FIS was particularly sensitive to a low sampling of individuals in the simulated, genomic, and microsatellite datasets. For the empirical and simulated genomic datasets, we found that as long as many populations are sampled, few individuals and loci are needed. For the empirical datasets, we found that increasing the number of populations sampled was important in obtaining precise landscape genetic estimates. Finally, we corroborated that outlier tests are sensitive to the number of populations sampled. We conclude by proposing different sampling designs depending on the objectives.
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Affiliation(s)
- Jonás A Aguirre-Liguori
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, United States
| | - Javier A Luna-Sánchez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jaime Gasca-Pineda
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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12
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Genetic consequences of social structure in the golden-crowned sifaka. Heredity (Edinb) 2020; 125:328-339. [PMID: 32792649 PMCID: PMC7555495 DOI: 10.1038/s41437-020-0345-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 11/08/2022] Open
Abstract
Many species are structured in social groups (SGs) where individuals exhibit complex mating strategies. Yet, most population genetic studies ignore SGs either treating them as small random-mating units or focusing on a higher hierarchical level (the population). Empirical studies acknowledging SGs have found an overall excess of heterozygotes within SGs and usually invoke inbreeding avoidance strategies to explain this finding. However, there is a lack of null models against which ecological theories can be tested and inbreeding avoidance quantified. Here, we investigate inbreeding (deviation from random mating) in an endangered forest-dwelling pair-living lemur species (Propithecus tattersalli). In particular, we measure the inbreeding coefficient (FIS) in empirical data at different scales: SGs, sampling sites and forest patches. We observe high excess of heterozygotes within SGs. The magnitude of this excess is highly dependent on the sampling scheme: while offspring are characterised by a high excess of heterozygotes (FIS < 0), the reproductive pair does not show dramatic departures from Hardy-Weinberg expectations. Moreover, the heterozygosity excess disappears at larger geographic scales (sites and forests). We use a modelling framework that incorporates details of the sifaka mating system but does not include active inbreeding avoidance mechanisms. The simulated data show that, although apparent "random mating" or even inbreeding may occur at the "population" level, outbreeding is maintained within SGs. Altogether our results suggest that social structure leads to high levels of outbreeding without the need for active inbreeding avoidance mechanisms. Thus, demonstrating and measuring the existence of active inbreeding avoidance mechanisms may be more difficult than usually assumed.
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Homola JJ, Loftin CS, Cammen KM, Helbing CC, Birol I, Schultz TF, Kinnison MT. Replicated Landscape Genomics Identifies Evidence of Local Adaptation to Urbanization in Wood Frogs. J Hered 2020; 110:707-719. [PMID: 31278891 PMCID: PMC6785938 DOI: 10.1093/jhered/esz041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/28/2019] [Indexed: 12/20/2022] Open
Abstract
Native species that persist in urban environments may benefit from local adaptation to novel selection factors. We used double-digest restriction-side associated DNA (RAD) sequencing to evaluate shifts in genome-wide genetic diversity and investigate the presence of parallel evolution associated with urban-specific selection factors in wood frogs (Lithobates sylvaticus). Our replicated paired study design involved 12 individuals from each of 4 rural and urban populations to improve our confidence that detected signals of selection are indeed associated with urbanization. Genetic diversity measures were less for urban populations; however, the effect size was small, suggesting little biological consequence. Using an FST outlier approach, we identified 37 of 8344 genotyped single nucleotide polymorphisms with consistent evidence of directional selection across replicates. A genome-wide association study analysis detected modest support for an association between environment type and 12 of the 37 FST outlier loci. Discriminant analysis of principal components using the 37 FST outlier loci produced correct reassignment for 87.5% of rural samples and 93.8% of urban samples. Eighteen of the 37 FST outlier loci mapped to the American bullfrog (Rana [Lithobates] catesbeiana) genome, although none were in coding regions. This evidence of parallel evolution to urban environments provides a powerful example of the ability of urban landscapes to direct evolutionary processes.
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Affiliation(s)
- Jared J Homola
- School of Biology and Ecology, University of Maine, Orono, ME.,Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI
| | - Cynthia S Loftin
- the US Geological Survey, Maine Cooperative Fish and Wildlife Research Unit, Orono, ME
| | | | - Caren C Helbing
- the Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Inanc Birol
- the Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Thomas F Schultz
- the Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, NC
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14
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Carvajal TM, Ogishi K, Yaegeshi S, Hernandez LFT, Viacrusis KM, Ho HT, Amalin DM, Watanabe K. Fine-scale population genetic structure of dengue mosquito vector, Aedes aegypti, in Metropolitan Manila, Philippines. PLoS Negl Trop Dis 2020; 14:e0008279. [PMID: 32365059 PMCID: PMC7224578 DOI: 10.1371/journal.pntd.0008279] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/14/2020] [Accepted: 04/08/2020] [Indexed: 11/25/2022] Open
Abstract
Dengue is a highly endemic disease in Southeast Asia and is transmitted primarily by the mosquito, Aedes aegypti. The National Capital Region (NCR) of the Philippines, or Metropolitan Manila, is a highly urbanized area that is greatly affected by this arboviral disease. Urbanization has been shown to increase the dispersal of this mosquito vector. For this reason, we conducted a fine-scale population genetic study of Ae. aegypti in this region. We collected adult Ae. aegypti mosquitoes (n = 526 individuals) within the region (n = 21 study areas) and characterized the present population structure and the genetic relatedness among mosquito populations. We genotyped 11 microsatellite loci from all sampled mosquito individuals and analyzed their genetic diversity, differentiation and structure. The results revealed low genetic differentiation across mosquito populations which suggest high gene flow and/or weak genetic drift among mosquito populations. Bayesian analysis indicated multiple genetic structures (K = 3-6), with no clear genetically distinct population structures. This result implies the passive or long-distance dispersal capability nature Ae. aegypti possibly through human-mediated transportation. The constructed dendrogram in this study describes the potential passive dispersal patterns across Metropolitan Manila. Furthermore, spatial autocorrelation analysis showed the limited and active dispersal capability (<1km) of the mosquito vector. Our findings are consistent with previous studies that investigated the genetic structure and dual (active and passive) dispersal capability of Ae. aegypti in a fine-scale highly urbanized area.
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Affiliation(s)
- Thaddeus M. Carvajal
- Center for Marine Environmental Studies (CMES)–Ehime University, Matsuyama, Japan
- Department of Civil and Environmental Engineering—Ehime University, Matsuyama, Japan
- Biology Department–De La Salle University, Taft Ave Manila, Philippines
- Biological Control Research Unit, Center for Natural Science and Environmental Research—De La Salle University, Taft Ave Manila, Philippines
| | - Kohei Ogishi
- Department of Civil and Environmental Engineering—Ehime University, Matsuyama, Japan
| | - Sakiko Yaegeshi
- Department of Civil and Environmental Engineering—Ehime University, Matsuyama, Japan
- Department of Civil and Environmental Engineering, University of Yamanashi, Kofu, Japan
| | | | | | - Howell T. Ho
- Department of Biological Sciences, Trinity University of Asia, Quezon City, Philippines
| | - Divina M. Amalin
- Biology Department–De La Salle University, Taft Ave Manila, Philippines
- Biological Control Research Unit, Center for Natural Science and Environmental Research—De La Salle University, Taft Ave Manila, Philippines
| | - Kozo Watanabe
- Center for Marine Environmental Studies (CMES)–Ehime University, Matsuyama, Japan
- Department of Civil and Environmental Engineering—Ehime University, Matsuyama, Japan
- Biology Department–De La Salle University, Taft Ave Manila, Philippines
- Biological Control Research Unit, Center for Natural Science and Environmental Research—De La Salle University, Taft Ave Manila, Philippines
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15
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Homola JJ, Loftin CS, Kinnison MT. Landscape genetics reveals unique and shared effects of urbanization for two sympatric pool-breeding amphibians. Ecol Evol 2019; 9:11799-11823. [PMID: 31695889 PMCID: PMC6822048 DOI: 10.1002/ece3.5685] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/26/2019] [Accepted: 08/30/2019] [Indexed: 01/05/2023] Open
Abstract
Metapopulation-structured species can be negatively affected when landscape fragmentation impairs connectivity. We investigated the effects of urbanization on genetic diversity and gene flow for two sympatric amphibian species, spotted salamanders (Ambystoma maculatum) and wood frogs (Lithobates sylvaticus), across a large (>35,000 km2) landscape in Maine, USA, containing numerous natural and anthropogenic gradients. Isolation-by-distance (IBD) patterns differed between the species. Spotted salamanders showed a linear and relatively high variance relationship between genetic and geographic distances (r = .057, p < .001), whereas wood frogs exhibited a strongly nonlinear and lower variance relationship (r = 0.429, p < .001). Scale dependence analysis of IBD found gene flow has its most predictable influence (strongest IBD correlations) at distances up to 9 km for spotted salamanders and up to 6 km for wood frogs. Estimated effective migration surfaces revealed contrasting patterns of high and low genetic diversity and gene flow between the two species. Population isolation, quantified as the mean IBD residuals for each population, was associated with local urbanization and less genetic diversity in both species. The influence of geographic proximity and urbanization on population connectivity was further supported by distance-based redundancy analysis and multiple matrix regression with randomization. Resistance surface modeling found interpopulation connectivity to be influenced by developed land cover, light roads, interstates, and topography for both species, plus secondary roads and rivers for wood frogs. Our results highlight the influence of anthropogenic landscape features within the context of natural features and broad spatial genetic patterns, in turn supporting the premise that while urbanization significantly restricts interpopulation connectivity for wood frogs and spotted salamanders, specific landscape elements have unique effects on these two sympatric species.
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Affiliation(s)
| | - Cynthia S. Loftin
- Maine Cooperative Fish and Wildlife Research UnitU.S. Geological SurveyOronoMEUSA
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16
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Burkhart JJ, Puckett EE, Beringer CJ, Sholy CN, Semlitsch RD, Eggert LS. Post-Pleistocene differentiation in a Central Interior Highlands endemic salamander. Ecol Evol 2019; 9:11171-11184. [PMID: 31641463 PMCID: PMC6802018 DOI: 10.1002/ece3.5619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 11/07/2022] Open
Abstract
AIM For many endemic species with limited dispersal capacities, the relationship between landscape changes and species distributions is still unclear. We characterized the population structure of the endemic ringed salamander (Ambystoma annulatum) across its distribution in the Central Interior Highlands (CIH) of North America, an area of high species endemism, to infer the ecological and evolutionary history of the species. METHODS We sampled 498 individuals across the species distribution and characterized the population genetic structure using nuclear microsatellite and mitochondrial DNA (mtDNA) markers. RESULTS Ambystoma annulatum exist in two strongly supported nuclear genetic clusters across the CIH that correspond to a northern cluster that includes the Missouri Ozark populations and a southern cluster that includes the Arkansas and Oklahoma Ozarks and the Ouachita Mountains. Our demographic models estimated that these populations diverged approximately 2,700 years ago. Pairwise estimates of genetic differentiation at microsatellite and mtDNA markers indicated limited contemporary gene flow and suggest that genetic differentiation was primarily influenced by changes in the post-Pleistocene landscape of the CIH. MAIN CONCLUSIONS Both the geologic history and post-European settlement history of the CIH have influenced the population genetic structure of A. annulatum. The low mtDNA diversity suggests a retraction into and expansion out of refugial areas in the south-central Ozarks, during temperature fluctuations of the Pleistocene and Holocene epochs. Similarly, the estimated divergence time for the two nuclear clusters corresponds to changes in the post-Pleistocene landscape. More recently, decreased A. annulatum gene flow may be a result of increased habitat fragmentation and alteration post-European settlement.
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Affiliation(s)
| | - Emily E. Puckett
- Department of Biological SciencesUniversity of MemphisMemphisTNUSA
| | | | | | | | - Lori S. Eggert
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
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17
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Winiarski KJ, Peterman WE, Whiteley AR, McGarigal K. Multiscale resistant kernel surfaces derived from inferred gene flow: An application with vernal pool breeding salamanders. Mol Ecol Resour 2019; 20:97-113. [DOI: 10.1111/1755-0998.13089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Kristopher J. Winiarski
- Department of Environmental Conservation University of Massachusetts Amherst MA USA
- Northeast Climate Adaptation Science Center University of Massachusetts Amherst MA USA
| | - William E. Peterman
- School of Environment and Natural Resources Ohio State University Columbus OH USA
| | - Andrew R. Whiteley
- W.A. Franke College of Forestry and Conservation Wildlife Biology Program University of Montana Missoula MT USA
| | - Kevin McGarigal
- Department of Environmental Conservation University of Massachusetts Amherst MA USA
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18
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Hamilton MG, Mekkawy W, Kilian A, Benzie JAH. Single Nucleotide Polymorphisms (SNPs) Reveal Sibship Among Founders of a Bangladeshi Rohu ( Labeo rohita) Breeding Population. Front Genet 2019; 10:597. [PMID: 31275363 PMCID: PMC6593075 DOI: 10.3389/fgene.2019.00597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 06/05/2019] [Indexed: 01/04/2023] Open
Abstract
Rohu (Labeo rohita) is a significant freshwater aquaculture species with approximately 1.8 Mt produced annually. Fin clips obtained from the founders of a newly established Bangladesh-based breeding population (∼140 fish from each of the Halda, Jamuna, and Padma rivers) were used to identify 9157 SNPs and 14 411 silicoDArT markers using the Diversity Arrays Technology (DArT) genotyping-by-sequencing platform known as DArTseq. After quality control, 1985 SNPs were retained and used to examine population structure within and among river systems. Examination of genomic relationships revealed evidence of full- and half-sibling relationships among founders. Accordingly, sibship and dummy parents were assigned within each river population using a maximum likelihood approach with COLONY software. Founders that had no dummy parents in common were then identified for population genetic analyses. Only 40 unique dummy parents and 17 founders with no common dummy parents were identified from the Halda river, compared with 206 (96) from the Jamuna and 184 (83) from the Padma. Overall pairwise FST estimates among rivers were low (<0.005) and the optimum number of clusters using unsupervised K-means clustering was one, indicating little genetic divergence among the river populations in our SNPs. These results suggest that observed sibship among founders should be accounted for in future pedigree-based analyses and it cannot be assumed that fertilized spawn collections are representative samples of river populations.
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Affiliation(s)
| | - Wagdy Mekkawy
- WorldFish, Penang, Malaysia
- Animal Production Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd., (DArT P/L), University of Canberra, Bruce, ACT, Australia
| | - John A. H. Benzie
- WorldFish, Penang, Malaysia
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
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19
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O'Connell KA, Mulder KP, Maldonado J, Currie KL, Ferraro DM. Sampling related individuals within ponds biases estimates of population structure in a pond-breeding amphibian. Ecol Evol 2019; 9:3620-3636. [PMID: 30962914 PMCID: PMC6434569 DOI: 10.1002/ece3.4994] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/28/2019] [Accepted: 01/28/2019] [Indexed: 12/20/2022] Open
Abstract
Effective conservation and management of pond-breeding amphibians depends on the accurate estimation of population structure, demographic parameters, and the influence of landscape features on breeding-site connectivity. Population-level studies of pond-breeding amphibians typically sample larval life stages because they are easily captured and can be sampled nondestructively. These studies often identify high levels of relatedness between individuals from the same pond, which can be exacerbated by sampling the larval stage. Yet, the effect of these related individuals on population genetic studies using genomic data is not yet fully understood. Here, we assess the effect of within-pond relatedness on population and landscape genetic analyses by focusing on the barred tiger salamanders (Ambystoma mavortium) from the Nebraska Sandhills. Utilizing genome-wide SNPs generated using a double-digest RADseq approach, we conducted standard population and landscape genetic analyses using datasets with and without siblings. We found that reduced sample sizes influenced parameter estimates more than the inclusion of siblings, but that within-pond relatedness led to the inference of spurious population structure when analyses depended on allele frequencies. Our landscape genetic analyses also supported different models across datasets depending on the spatial resolution analyzed. We recommend that future studies not only test for relatedness among larval samples but also remove siblings before conducting population or landscape genetic analyses. We also recommend alternative sampling strategies to reduce sampling siblings before sequencing takes place. Biases introduced by unknowingly including siblings can have significant implications for population and landscape genetic analyses, and in turn, for species conservation strategies and outcomes.
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Affiliation(s)
- Kyle A. O'Connell
- Department of Vertebrate ZoologyNational Museum of Natural History, Smithsonian InstitutionWashingtonDistrict of Columbia
- Global Genome InitiativeNational Museum of Natural History, Smithsonian InstitutionWashingtonDistrict of Columbia
- Department of BiologyThe University of Texas at ArlingtonArlingtonTexas
| | - Kevin P. Mulder
- Department of Vertebrate ZoologyNational Museum of Natural History, Smithsonian InstitutionWashingtonDistrict of Columbia
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO)PortoPortugal
| | - Jose Maldonado
- Department of BiologyThe University of Texas at ArlingtonArlingtonTexas
| | | | - Dennis M. Ferraro
- School of Natural ResourcesUniversity of Nebraska LincolnLincolnNebraska
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20
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Combining phylogeography and landscape genetics to infer the evolutionary history of a short-range Mediterranean relict, Salamandra salamandra longirostris. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1110-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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21
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Fonseca PAS, Leal TP, Santos FC, Gouveia MH, Id-Lahoucine S, Rosse IC, Ventura RV, Bruneli FAT, Machado MA, Peixoto MGCD, Tarazona-Santos E, Carvalho MRS. Reducing cryptic relatedness in genomic data sets via a central node exclusion algorithm. Mol Ecol Resour 2017; 18:435-447. [PMID: 29271609 DOI: 10.1111/1755-0998.12746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 12/04/2017] [Accepted: 12/14/2017] [Indexed: 11/30/2022]
Abstract
Cryptic relatedness is a confounding factor in genetic diversity and genetic association studies. Development of strategies to reduce cryptic relatedness in a sample is a crucial step for downstream genetic analyses. This study uses a node selection algorithm, based on network degrees of centrality, to evaluate its applicability and impact on evaluation of genetic diversity and population stratification. 1,036 Guzerá (Bos indicus) females were genotyped using Illumina Bovine SNP50 v2 BeadChip. Four strategies were compared. The first and second strategies consist on a iterative exclusion of most related individuals based on PLINK kinship coefficient (φij) and VanRaden's φij, respectively. The third and fourth strategies were based on a node selection algorithm. The fourth strategy, Network G matrix, preserved the larger number of individuals with a better diversity and representation from the initial sample. Determining the most probable number of populations was directly affected by the kinship metric. Network G matrix was the better strategy for reducing relatedness due to producing a larger sample, with more distant individuals, a more similar distribution when compared with the full data set in the MDS plots and keeping a better representation of the population structure. Resampling strategies using VanRaden's φij as a relationship metric was better to infer the relationships among individuals. Moreover, the resampling strategies directly impact the genomic inflation values in genomewide association studies. The use of the node selection algorithm also implies better selection of the most central individuals to be removed, providing a more representative sample.
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Affiliation(s)
- Pablo A S Fonseca
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Thiago P Leal
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Fernanda C Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Mateus H Gouveia
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Samir Id-Lahoucine
- Center for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Izinara C Rosse
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ricardo V Ventura
- Center for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada.,Beef Improvement Opportunities, Guelph, ON, Canada
| | | | | | | | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maria Raquel S Carvalho
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Lenhardt PP, Brühl CA, Leeb C, Theissinger K. Amphibian population genetics in agricultural landscapes: does viniculture drive the population structuring of the European common frog ( Rana temporaria)? PeerJ 2017; 5:e3520. [PMID: 28713651 PMCID: PMC5508807 DOI: 10.7717/peerj.3520] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/08/2017] [Indexed: 01/22/2023] Open
Abstract
Amphibian populations have been declining globally over the past decades. The intensification of agriculture, habitat loss, fragmentation of populations and toxic substances in the environment are considered as driving factors for this decline. Today, about 50% of the area of Germany is used for agriculture and is inhabited by a diverse variety of 20 amphibian species. Of these, 19 are exhibiting declining populations. Due to the protection status of native amphibian species, it is important to evaluate the effect of land use and associated stressors (such as road mortality and pesticide toxicity) on the genetic population structure of amphibians in agricultural landscapes. We investigated the effects of viniculture on the genetic differentiation of European common frog (Rana temporaria) populations in Southern Palatinate (Germany). We analyzed microsatellite data of ten loci from ten breeding pond populations located within viniculture landscape and in the adjacent forest block and compared these results with a previously developed landscape permeability model. We tested for significant correlation of genetic population differentiation and landscape elements, including land use as well as roads and their associated traffic intensity, to explain the genetic structure in the study area. Genetic differentiation among forest populations was significantly lower (median pairwise FST = 0.0041 at 5.39 km to 0.0159 at 9.40 km distance) than between viniculture populations (median pairwise FST = 0.0215 at 2.34 km to 0.0987 at 2.39 km distance). Our analyses rejected isolation by distance based on roads and associated traffic intensity as the sole explanation of the genetic differentiation and suggest that the viniculture landscape has to be considered as a limiting barrier for R. temporaria migration, partially confirming the isolation of breeding ponds predicted by the landscape permeability model. Therefore, arable land may act as a sink habitat, inhibiting genetic exchange and causing genetic differentiation of pond populations in agricultural areas. In viniculture, pesticides could be a driving factor for the observed genetic impoverishment, since pesticides are more frequently applied than any other management measure and can be highly toxic for terrestrial life stages of amphibians.
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Affiliation(s)
- Patrick P Lenhardt
- Institute for Environmental Science, Universität Koblenz-Landau, Germany
| | - Carsten A Brühl
- Institute for Environmental Science, Universität Koblenz-Landau, Germany
| | - Christoph Leeb
- Institute for Environmental Science, Universität Koblenz-Landau, Germany
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23
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Waples RS, Anderson EC. Purging putative siblings from population genetic data sets: a cautionary view. Mol Ecol 2017; 26:1211-1224. [DOI: 10.1111/mec.14022] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Robin S. Waples
- NOAA Fisheries; Northwest Fisheries Science Center; 2725 Montlake Blvd. East Seattle WA 98112 USA
| | - Eric C. Anderson
- NOAA Fisheries; Southwest Fisheries Science Center; 110 McAllister Way Santa Cruz CA 95060 USA
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