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Brasil SNR, Kelemen EP, Rehan SM. Historic DNA uncovers genetic effects of climate change and landscape alteration in two wild bee species. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01488-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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2
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Clarke SH, McCracken GR, Humphries S, Ruzzante D, Grant JWA, Fraser DJ. Demographic resilience of brook trout populations subjected to experimental size-selective harvesting. Evol Appl 2022; 15:1792-1805. [PMID: 36426123 PMCID: PMC9679253 DOI: 10.1111/eva.13478] [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: 01/02/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022] Open
Abstract
Sustainable management of exploited populations benefits from integrating demographic and genetic considerations into assessments, as both play a role in determining harvest yields and population persistence. This is especially important in populations subject to size-selective harvest, because size selective harvesting has the potential to result in significant demographic, life-history, and genetic changes. We investigated harvest-induced changes in the effective number of breeders (N ^ b ) for introduced brook trout populations (Salvelinus fontinalis) in alpine lakes from western Canada. Three populations were subject to 3 years of size-selective harvesting, while three control populations experienced no harvest. TheN ^ c decreased consistently across all harvested populations (on average 60.8%) but fluctuated in control populations. There were no consistent changes inN ^ b between control or harvest populations, but one harvest population experienced a decrease inN ^ b of 63.2%. TheN ^ b /N ^ c ratio increased consistently across harvest lakes; however we found no evidence of genetic compensation (where variance in reproductive success decreases at lower abundance) based on changes in family evenness (FE ^ ) and the number of full-sibling families (N ^ fam ). We found no relationship betweenFE ^ andN ^ c or betweenN ^ fam /N ^ c andFE ^ . We posit that change inN ^ b was buffered by constraints on breeding habitat prior to harvest, such that the same number of breeding sites were occupied before and after harvest. These results suggest that effective size in harvested populations may be resilient to considerable changes in Nc in the short-term, but it is still important to monitor exploited populations to assess the risk of inbreeding and ensure their long-term survival.
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Affiliation(s)
| | | | - Shelley Humphries
- Lake Louise, Yoho, and Kootenay Field Unit, Parks CanadaRadium Hot SpringsBritish ColumbiaCanada
| | | | | | - Dylan J. Fraser
- Department of BiologyConcordia UniversityMontrealQuebecCanada
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3
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Dyson CJ, Piscano OL, Durham RM, Thompson VJ, Johnson CH, Goodisman MAD. Temporal Analysis of Effective Population Size and Mating System in a Social Wasp. J Hered 2021; 112:626-634. [PMID: 34558622 DOI: 10.1093/jhered/esab057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 09/20/2021] [Indexed: 02/07/2023] Open
Abstract
Highly social species are successful because they cooperate in obligately integrated societies. We examined temporal genetic variation in the eusocial wasp Vespula maculifrons to gain a greater understanding of evolution in highly social taxa. First, we wished to test if effective population sizes of eusocial species were relatively low due to the reproductive division of labor that characterizes eusocial taxa. We thus estimated the effective population size of V. maculifrons by examining temporal changes in population allele frequencies. We sampled the genetic composition of a V. maculifrons population at 3 separate timepoints spanning a 13-year period. We found that effective population size ranged in the hundreds of individuals, which is similar to estimates in other, non-eusocial taxa. Second, we estimated levels of polyandry in V. maculifrons in different years to determine if queen mating system varied over time. We found no significant change in the number or skew of males mated to queens. In addition, mating skew was not significant within V. maculifrons colonies. Therefore, our data suggest that queen mate number may be subject to stabilizing selection in this taxon. Overall, our study provides novel insight into the selective processes operating in eusocial species by analyzing temporal genetic changes within populations.
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Affiliation(s)
- Carl J Dyson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Olivia L Piscano
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rebecca M Durham
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Veronica J Thompson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Catherine H Johnson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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4
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Using Noninvasive Genetic Sampling to Survey Rare Butterfly Populations. INSECTS 2019; 10:insects10100311. [PMID: 31547512 PMCID: PMC6835262 DOI: 10.3390/insects10100311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 11/17/2022]
Abstract
Advances in nondestructive genetic sampling techniques continue to offer new opportunities for studying organisms, particularly those of conservation concern where more traditional invasive sampling methods are often not available. As part of a proof-of-concept, we investigated the effectiveness of using the chorion from residual butterfly egg debris as a source of viable genetic material for analysis. Laboratory material from a captive breeding population of the federally endangered Miami blue butterfly (Cyclargus thomasi bethunebakeri) was used to test efficacy and refine the methodology. The resulting best practices were subsequently evaluated using field-collected material from extant north Florida populations of the at-risk frosted elfin butterfly (Callophyrs irus). Our results demonstrated that it is possible to extract DNA of sufficiently high quantity and quality for successful gene sequencing. We additionally describe a simple, low-cost, and reliable method of collecting and storing egg debris samples that can be consistently adopted for field or laboratory work as well as deployed with projects that have a larger geographic scope and/or involve citizen scientists. Potential limitations related to field sample collection are discussed as well as needs for future evaluation.
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5
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Kent CF, Dey A, Patel H, Tsvetkov N, Tiwari T, MacPhail VJ, Gobeil Y, Harpur BA, Gurtowski J, Schatz MC, Colla SR, Zayed A. Conservation Genomics of the Declining North American Bumblebee Bombus terricola Reveals Inbreeding and Selection on Immune Genes. Front Genet 2018; 9:316. [PMID: 30147708 PMCID: PMC6095975 DOI: 10.3389/fgene.2018.00316] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/24/2018] [Indexed: 01/23/2023] Open
Abstract
The yellow-banded bumblebee Bombus terricola was common in North America but has recently declined and is now on the IUCN Red List of threatened species. The causes of B. terricola's decline are not well understood. Our objectives were to create a partial genome and then use this to estimate population data of conservation interest, and to determine whether genes showing signs of recent selection suggest a specific cause of decline. First, we generated a draft partial genome (contig set) for B. terricola, sequenced using Pacific Biosciences RS II at an average depth of 35×. Second, we sequenced the individual genomes of 22 bumblebee gynes from Ontario and Quebec using Illumina HiSeq 2500, each at an average depth of 20×, which were used to improve the PacBio genome calls and for population genetic analyses. The latter revealed that several samples had long runs of homozygosity, and individuals had high inbreeding coefficient F, consistent with low effective population size. Our data suggest that B. terricola's effective population size has decreased orders of magnitude from pre-Holocene levels. We carried out tests of selection to identify genes that may have played a role in ameliorating environmental stressors underlying B. terricola's decline. Several immune-related genes have signatures of recent positive selection, which is consistent with the pathogen-spillover hypothesis for B. terricola's decline. The new B. terricola contig set can help solve the mystery of bumblebee decline by enabling functional genomics research to directly assess the health of pollinators and identify the stressors causing declines.
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Affiliation(s)
- Clement F Kent
- Department of Biology, York University, Toronto, ON, Canada
| | - Alivia Dey
- Department of Biology, York University, Toronto, ON, Canada
| | | | | | | | - Victoria J MacPhail
- Wildlife Preservation Canada, Guelp, ON, Canada.,Faculty of Environmental Studies, York University, Toronto, ON, Canada
| | | | - Brock A Harpur
- Department of Biology, York University, Toronto, ON, Canada.,Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - James Gurtowski
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Michael C Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States.,Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Sheila R Colla
- Wildlife Preservation Canada, Guelp, ON, Canada.,Faculty of Environmental Studies, York University, Toronto, ON, Canada
| | - Amro Zayed
- Department of Biology, York University, Toronto, ON, Canada
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6
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Waples RS, Grewe PM, Bravington MW, Hillary R, Feutry P. Robust estimates of a high Ne/ N ratio in a top marine predator, southern bluefin tuna. SCIENCE ADVANCES 2018; 4:eaar7759. [PMID: 30035218 PMCID: PMC6051734 DOI: 10.1126/sciadv.aar7759] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
Genetic studies of several marine species with high fecundity have produced "tiny" estimates (≤10-3) of the ratio of effective population size (Ne) to adult census size (N), suggesting that even very large populations might be at genetic risk. A recent study using close-kin mark-recapture methods estimated adult abundance at N ≈ 2 × 106 for southern bluefin tuna (SBT), a highly fecund top predator that supports a lucrative (~$1 billion/year) fishery. We used the same genetic and life history data (almost 13,000 fish collected over 5 years) to generate genetic and demographic estimates of Ne per generation and Nb (effective number of breeders) per year and the Ne/N ratio. Demographic estimates, which accounted for age-specific vital rates, skip breeding, variation in fecundity at age, and persistent individual differences in reproductive success, suggest that Ne/N is >0.1 and perhaps about 0.5. The genetic estimates supported this conclusion. Simulations using true Ne = 5 × 105 (Ne/N = 0.25) produced results statistically consistent with the empirical genetic estimates, whereas simulations using Ne = 2 × 104 (Ne/N = 0.01) did not. Our results show that robust estimates of Ne and Ne/N can be obtained for large populations, provided sufficiently large numbers of individuals and genetic markers are used and temporal replication (here, 5 years of adult and juvenile samples) is sufficient to provide a distribution of estimates. The high estimated Ne/N ratio in SBT is encouraging and suggests that the species will not be compromised by a lack of genetic diversity in responding to environmental change and harvest.
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Affiliation(s)
- Robin S. Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, USA
| | - Peter M. Grewe
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Oceans and Atmosphere, G.P.O. Box 1538, Hobart 7001, Tasmania, Australia
| | - Mark W. Bravington
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Oceans and Atmosphere, G.P.O. Box 1538, Hobart 7001, Tasmania, Australia
| | - Richard Hillary
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Oceans and Atmosphere, G.P.O. Box 1538, Hobart 7001, Tasmania, Australia
| | - Pierre Feutry
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Oceans and Atmosphere, G.P.O. Box 1538, Hobart 7001, Tasmania, Australia
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7
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Myhre AM, Engen S, SAEther BE. Effective size of density-dependent two-sex populations: the effect of mating systems. J Evol Biol 2017; 30:1561-1575. [PMID: 28594470 DOI: 10.1111/jeb.13126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 05/10/2017] [Accepted: 06/01/2017] [Indexed: 12/01/2022]
Abstract
Density dependence in vital rates is a key feature affecting temporal fluctuations of natural populations. This has important implications for the rate of random genetic drift. Mating systems also greatly affect effective population sizes, but knowledge of how mating system and density regulation interact to affect random genetic drift is poor. Using theoretical models and simulations, we compare Ne in short-lived, density-dependent animal populations with different mating systems. We study the impact of a fluctuating, density-dependent sex ratio and consider both a stable and a fluctuating environment. We find a negative relationship between annual Ne /N and adult population size N due to density dependence, suggesting that loss of genetic variation is reduced at small densities. The magnitude of this decrease was affected by mating system and life history. A male-biased, density-dependent sex ratio reduces the rate of genetic drift compared to an equal, density-independent sex ratio, but a stochastic change towards male bias reduces the Ne /N ratio. Environmental stochasticity amplifies temporal fluctuations in population size and is thus vital to consider in estimation of effective population sizes over longer time periods. Our results on the reduced loss of genetic variation at small densities, particularly in polygamous populations, indicate that density regulation may facilitate adaptive evolution at small population sizes.
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Affiliation(s)
- A M Myhre
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - S Engen
- Centre for Biodiversity Dynamics, Department of Mathematical Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - B-E SAEther
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
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8
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Greene DU, Gore JA, Austin JD. Reintroduction of captive-born beach mice: the importance of demographic and genetic monitoring. J Mammal 2017. [DOI: 10.1093/jmammal/gyw229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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9
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Myhre AM, Engen S, Saether BE. Effective size of density-dependent populations in fluctuating environments. Evolution 2016; 70:2431-2446. [DOI: 10.1111/evo.13063] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 09/07/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Ane Marlene Myhre
- Department of Biology, Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; N-7491 Trondheim Norway
| | - Steinar Engen
- Department of Mathematical Sciences, Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; N-7491 Trondheim Norway
| | - Bernt-Erik Saether
- Department of Biology, Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; N-7491 Trondheim Norway
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10
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Hinkson KM, Richter SC. Temporal trends in genetic data and effective population size support efficacy of management practices in critically endangered dusky gopher frogs (Lithobates sevosus). Ecol Evol 2016; 6:2667-78. [PMID: 27066242 PMCID: PMC4798149 DOI: 10.1002/ece3.2084] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 02/14/2016] [Accepted: 02/22/2016] [Indexed: 11/09/2022] Open
Abstract
Monitoring temporal changes in population genetic diversity and effective population size can provide vital information on future viability. The dusky gopher frog, Lithobates sevosus, is a critically endangered species found only in coastal Mississippi, with low genetic variability as a consequence of isolation and population size reduction. Conservation management practices have been implemented, but their efficacy has not been addressed. We genotyped individuals collected 1997-2014 to determine temporal trends in population genetic variation, structure, and effective size. Observed and expected heterozygosity and allelic richness revealed temporally stable, but low, levels of genetic variation. Positive levels of inbreeding were found in each year. There was weak genetic structure among years, which can be attributed to increased effects of genetic drift and inbreeding in small populations. L. sevosus exhibited an increase in effective population size, and currently has an estimated effective size of 33.0-58.6 individuals, which is approximately half the census size. This large ratio could possibly be explained by genetic compensation. We found that management practices have been effective at maintaining and improving effective size and genetic diversity, but that additional strategies need to be implemented to enhance viability of the species.
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Affiliation(s)
- Kristin M. Hinkson
- Department of Biological SciencesEastern Kentucky UniversityRichmondKentucky40475
| | - Stephen C. Richter
- Department of Biological SciencesEastern Kentucky UniversityRichmondKentucky40475
- Division of Natural AreasEastern Kentucky UniversityRichmondKentucky40475
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11
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Kuparinen A, Hutchings JA, Waples RS. Harvest-induced evolution and effective population size. Evol Appl 2016; 9:658-72. [PMID: 27247617 PMCID: PMC4869408 DOI: 10.1111/eva.12373] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/17/2016] [Indexed: 01/18/2023] Open
Abstract
Much has been written about fishery‐induced evolution (FIE) in exploited species, but relatively little attention has been paid to the consequences for one of the most important parameters in evolutionary biology—effective population size (Ne). We use a combination of simulations of Atlantic cod populations experiencing harvest, artificial manipulation of cod life tables, and analytical methods to explore how adding harvest to natural mortality affects Ne, census size (N), and the ratio Ne/N. We show that harvest‐mediated reductions in Ne are due entirely to reductions in recruitment, because increasing adult mortality actually increases the Ne/N ratio. This means that proportional reductions in abundance caused by harvest represent an upper limit to the proportional reductions in Ne, and that in some cases Ne can even increase with increased harvest. This result is a quite general consequence of increased adult mortality and does not depend on harvest selectivity or FIE, although both of these influence the results in a quantitative way. In scenarios that allowed evolution, Ne recovered quickly after harvest ended and remained higher than in the preharvest population for well over a century, which indicates that evolution can help provide a long‐term buffer against loss of genetic variability.
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Affiliation(s)
- Anna Kuparinen
- Department of Environmental Sciences University of Helsinki Helsinki Finland
| | - Jeffrey A Hutchings
- Department of Biology Dalhousie University Halifax NS Canada; Department of Biosciences Centre For Ecological and Evolutionary Synthesis University of Oslo Oslo Norway; Department of Natural Sciences University of Agder Kristiansand Norway
| | - Robin S Waples
- National Marine Fisheries Service National Oceanic and Atmospheric Administration Northwest Fisheries Science Center Seattle WA USA
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12
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Turlure C, Vandewoestijne S, Baguette M. Conservation genetics of a threatened butterfly: comparison of allozymes, RAPDs and microsatellites. BMC Genet 2014; 15:114. [PMID: 25367292 PMCID: PMC4234837 DOI: 10.1186/s12863-014-0114-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 10/16/2014] [Indexed: 11/21/2022] Open
Abstract
Background Addressing genetic issues in the management of fragmented wild populations of threatened species is one of the most important challenges in conservation biology. Nowadays, a diverse array of molecular methods exists to assess genetic diversity and differentiation of wild populations such as allozymes, dominant markers and co-dominant markers. However it remains worthwhile i) to compare the genetic estimates obtained using those several markers in order to ii) test their relative utility, reliability and relevance and iii) the impact of these results for the design of species-specific conservation measures. Results Following the successful isolation of 15 microsatellites loci for the cranberry fritillary butterfly, Boloria aquilonaris, we analyzed the genetic diversity and structure of eight populations located in four different landscapes, at both the regional and the landscape scales. We confront results based on microsatellites to those obtained using allozymes and RAPDs on the same samples. Genetic population analyses using different molecular markers indicate that the B. aquilonaris populations are characterized by a weak genetic variation, likely due to low effective population size and low dispersal at the regional scale. This results in inbreeding in some populations, which may have detrimental consequences on their long term viability. However, gene flow within landscape is limited but not inexistent, with some long range movements resulting in low or no isolation by distance. Spatial structuring was detected among the most isolated populations. Conclusions The use of allozymes and RAPD are of very limited value to determine population structuring at small spatial (i.e. landscape) scales, microsatellites giving much higher estimate resolution. The use of RAPD data is also limited for evidencing inbreeding. However, coarse-grain spatial structure (i.e. regional scale), and gene flow estimates based on RAPD and microsatellites data gave congruent results. At a time with increasing development of new molecular methods and markers, dominant markers may still be worthwhile to consider in organisms for which no genomic information is available, and for which limited resources are available.
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Affiliation(s)
- Camille Turlure
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain, Place Croix du Sud 4, Louvain-la-Neuve, B-1348, Belgium.
| | - Sofie Vandewoestijne
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain, Place Croix du Sud 4, Louvain-la-Neuve, B-1348, Belgium.
| | - Michel Baguette
- CNRS USR 2936 Station d'Ecologie Expérimentale du CNRS à Moulis, F-09200, Moulis, France. .,Muséum National d'Histoire Naturelle, Institut de Systématique, Evolution et Biodiversité, UMR 7205, 57 rue Cuvier, Paris cedex 5, F-75005, France.
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13
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Local extinction event despite high levels of gene flow and genetic diversity in the federally-endangered Miami blue butterfly. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0580-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Duong TY, Scribner KT, Forsythe PS, Crossman JA, Baker EA. Interannual variation in effective number of breeders and estimation of effective population size in long-lived iteroparous lake sturgeon (Acipenser fulvescens). Mol Ecol 2013; 22:1282-94. [DOI: 10.1111/mec.12167] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 11/26/2022]
Affiliation(s)
- Thuy Yen Duong
- Department of Fisheries and Wildlife; Michigan State University; 13 Natural Resources East Lansing MI 48824 USA
| | - Kim T. Scribner
- Department of Fisheries and Wildlife; Michigan State University; 13 Natural Resources East Lansing MI 48824 USA
- Department of Zoology; Michigan State University; 13 Natural Resources East Lansing MI 48824 USA
| | - Patrick S. Forsythe
- Department of Zoology; Michigan State University; 13 Natural Resources East Lansing MI 48824 USA
| | - James A. Crossman
- Department of Fisheries and Wildlife; Michigan State University; 13 Natural Resources East Lansing MI 48824 USA
| | - Edward A. Baker
- Michigan Department of Natural Resources; 488 Cherry Creek Road Marquette MI 49855 USA
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15
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Tucker KP, Hunter ME, Bonde RK, Austin JD, Clark AM, Beck CA, McGuire PM, Oli MK. Low genetic diversity and minimal population substructure in the endangered Florida manatee: implications for conservation. J Mammal 2012. [DOI: 10.1644/12-mamm-a-048.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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16
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Influences of habitat fragmentation by damming on the genetic structure of masu salmon populations in Hokkaido, Japan. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0349-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Osborne MJ, Carson EW, Turner TF. Genetic monitoring and complex population dynamics: insights from a 12-year study of the Rio Grande silvery minnow. Evol Appl 2012; 5:553-74. [PMID: 23028397 PMCID: PMC3461139 DOI: 10.1111/j.1752-4571.2011.00235.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 12/12/2011] [Indexed: 11/30/2022] Open
Abstract
The endangered Rio Grande silvery minnow persists as a remnant population in a highly fragmented and regulated arid-land river system. The species is subject to dramatic annual fluctuations in density. Since 2003, the wild population has been supplemented by hatchery-reared fish. We report on a 12-year (1999–2010) monitoring study of genetic diversity and effective population size (Ne) of wild and hatchery stocks. Our goals were to evaluate how genetic metrics responded to changes in wild fish density and whether they corresponded to the number and levels of diversity of hatchery-reared repatriates. Genetic diversity and all measures of Ne in the wild population did not correlate with wild fish density until hatchery supplementation began in earnest. Estimates of variance and inbreeding effective size were not correlated. Our results suggest source–sink dynamics where captive stocks form a genetically diverse source and the wild population behaves as a sink. Nevertheless, overall genetic diversity of silvery minnow has been maintained over the last decade, and we attribute this to a well-designed and executed propagation management plan. When multiple factors like environmental fluctuation and hatchery supplementation act simultaneously on a population, interpretation of genetic monitoring data may be equally complex and require considerable ecological data.
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Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, University of New Mexico Albuquerque, New Mexico, USA
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18
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Saarinen EV, Daniels JC. Using museum specimens to assess historical distribution and genetic diversity in an endangered butterfly. ANIM BIOL 2012. [DOI: 10.1163/157075612x624176] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The Miami blue butterfly,Cyclargus thomasi bethunebakeri, is a state-endangered taxon in Florida and a candidate for federal listing. This once common butterfly saw a dramatic decline in population number and abundance in the 1970s and 1980s, but significant collections of individuals prior to this decline are deposited in natural history museums. Using museum specimens, we quantified the genetic diversity in a historical population present in Key Largo, Florida in 1940, 1960, and 1980. Genetic diversity was consistently high within this historical population, but diversity was observed to decrease over the decades sampled. A comparison of historical diversity from the Key Largo population with the extant populations on Bahia Honda State Park (BHSP) and Key West National Wildlife Refuge (KWNWR) revealed differences in allelic frequencies, but only minor differences in the overall number of alleles. The historical distribution of butterflies throughout the Florida Keys further suggests a metapopulation structure. This structure involved partially-isolated populations ofC. t. bethunebakerithat were loosely connected via gene flow and that underwent localized extinction and colonization events along the chain of suitable habitat in the Florida Keys. It appears that a “mini-metapopulation” currently exists on BHSP and KWNWR; structures that are similar to the historical metapopulation structure and distribution of populations on a larger scale. Knowledge of historical distribution helps to plan future reintroduction events with captive-bred butterflies. Additional populations of butterflies may represent undiscovered genetic diversity that, if appropriate, may be further incorporated into captive-breeding efforts.
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Affiliation(s)
- Emily V. Saarinen
- Department of Natural Sciences, University of Michigan-Dearborn, 4901 Evergreen Road, Dearborn, MI 48128, USA
| | - Jaret C. Daniels
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, P.O. Box 112710, Gainesville, FL 32611-2710, USA
- Department of Entomology and Nematology, University of Florida, P.O. Box 110620, Gainesville, FL 32611-0620, USA
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Barker JSF. Effective population size of natural populations of Drosophila buzzatii, with a comparative evaluation of nine methods of estimation. Mol Ecol 2011; 20:4452-71. [PMID: 21951766 DOI: 10.1111/j.1365-294x.2011.05324.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Allozyme and microsatellite data from numerous populations of Drosophila buzzatii have been used (i) to determine to what degree N(e) varies among generations within populations, and among populations, and (ii) to evaluate the congruence of four temporal and five single-sample estimators of N(e) . Effective size of different populations varied over two orders of magnitude, most populations are not temporally stable in genetic composition, and N(e) showed large variation over generations in some populations. Short-term N(e) estimates from the temporal methods were highly correlated, but the smallest estimates were the most precise for all four methods, and the most consistent across methods. Except for one population, N(e) estimates were lower when assuming gene flow than when assuming populations that were closed. However, attempts to jointly estimate N(e) and immigration rate were of little value because the source of migrants was unknown. Correlations among the estimates from the single-sample methods generally were not significant although, as for the temporal methods, estimates were most consistent when they were small. These single-sample estimates of current N(e) are generally smaller than the short-term temporal estimates. Nevertheless, population genetic variation is not being depleted, presumably because of past or ongoing migration. A clearer picture of current and short-term effective population sizes will only follow with better knowledge of migration rates between populations. Different methods are not necessarily estimating the same N(e) , they are subject to different bias, and the biology, demography and history of the population(s) may affect different estimators differently.
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Affiliation(s)
- J S F Barker
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.
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Endersby NM, Hoffmann AA, White VL, Ritchie SA, Johnson PH, Weeks AR. Changes in the genetic structure of Aedes aegypti (Diptera: Culicidae) populations in Queensland, Australia, across two seasons: implications for potential mosquito releases. JOURNAL OF MEDICAL ENTOMOLOGY 2011; 48:999-1007. [PMID: 21936318 PMCID: PMC3290397 DOI: 10.1603/me10264] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Diseases transmitted by mosquitoes could be controlled if vector populations were replaced with strains that have reduced vector competency. Such a strategy is being developed for control of dengue virus which is transmitted by Aedes aegypti (L.) (Diptera: Culicidae). Mosquitoes artificially infected with the bacterium, Wolbachia pipientis Hertig, are being assessed as candidates for release at the adult stage with the aim of replacement of the wild population. Wolbachia can reduce the capacity of Ae. aegypti to transmit dengue virus and has potential to be driven through the natural population via a system of cytoplasmic incompatibility. Deployment of benign mosquito strains will be influenced by population size and structure of wild-type Ae. aegypti in proposed release areas, as well as rates of gene flow among populations in the wet and dry tropical seasons. Mosquitoes from northern Queensland were screened with genetic markers to find an optimal locality for release of a benign strain of Ae. aegypti. The inland towns of Chillagoe and Charters Towers and the coastal town of Ingham had mosquito populations that were partly genetically isolated from mosquitoes in other areas across both seasons. These locations may be suitable release sites if it is important for the released strain to be restricted during initial phases of implementation. Smaller genetic differences were also evident among other regions and were consistent over two seasons (wet and dry).
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Affiliation(s)
- N M Endersby
- Centre for Environmental Stress and Adaptation Research, Department of Genetics, Bio21 Institute, The University of Melbourne, Victoria 3010, Australia.
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21
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Bernatchez L, Tseng M. Evolutionary applications summer 2011. Evol Appl 2011; 4:617-20. [PMID: 25568009 PMCID: PMC3352538 DOI: 10.1111/j.1752-4571.2011.00205.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
- Louis Bernatchez
- Département de biologie, Université Laval Québec, QC, Canada e-mail:
| | - Michelle Tseng
- Department of Zoology, University of British Columbia Vancouver, BC, Canada e-mail:
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Arnaud JF, Cuguen J, Fénart S. Metapopulation structure and fine-scaled genetic structuring in crop-wild hybrid weed beets. Heredity (Edinb) 2011; 107:395-404. [PMID: 21448229 DOI: 10.1038/hdy.2011.23] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
This study explores the microspatial and temporal genetic variation in crop-wild hybrid weed beets that emerged from the seed bank in a cultivated field surveyed over two successive years. We demonstrate the occurrence of demes highly genetically differentiated, kin-structured, characterized by moderate effective population sizes, differing in propensity for selfing, and arising from nonrandom genetic subsets of the seed bank. Only one deme identified in the first survey year significantly contributed to the weed beets that emerged in the second year. Spatial structuring appears to be primarily due to gravity seed dispersal and limited pollen flow among weed beet demes. Within each genetic cluster identified by Bayesian assignments and multivariate analyses, F(IS) estimates and level of biparental inbreeding--revealed by progeny analyses--dropped to non-significant values. This suggests that random mating occurs at the scale of genetically distinct demes over a very short scale. Our results highlight the need to carefully depict genetic discontinuities in weed species, when attempting to describe their local genetic neighborhoods within which genetic drift and selective processes occur.
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Affiliation(s)
- J-F Arnaud
- Laboratoire de Génétique et Évolution des Populations Végétales, FRE CNRS 3268, Bâtiment SN2, Université des Sciences et Technologies de Lille-Lille 1, Villeneuve d'Ascq cedex, France.
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Osborne MJ, Davenport SR, Hoagstrom CW, Turner TF. Genetic effective size, N(e), tracks density in a small freshwater cyprinid, Pecos bluntnose shiner (Notropis simus pecosensis). Mol Ecol 2010; 19:2832-44. [PMID: 20579288 DOI: 10.1111/j.1365-294x.2010.04695.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Genetic monitoring tracks changes in measures of diversity including allelic richness, heterozygosity and genetic effective size over time, and has emerged as an important tool for understanding evolutionary consequences of population management. One proposed application of genetic monitoring has been to estimate abundance and its trajectory through time. Here, genetic monitoring was conducted across five consecutive year for the Pecos bluntnose shiner, a federally threatened minnow. Temporal changes in allele frequencies at seven microsatellite DNA loci were used to estimate variance effective size (N(eV)) across adjacent years in the time series. Likewise, effective size was computed using the linkage disequilibrium method (N(eD)) for each sample. Estimates of N(e) were then compared to estimates of adult fish density obtained from traditional demographic monitoring. For Pecos bluntnose shiner, density (catch-per-unit-effort), N(eV) and N(eD) were positively associated across this time series. Results for Pecos bluntnose shiner were compared to a related and ecologically similar species, the Rio Grande silvery minnow. In this species, density and N(eV) were negatively associated, which suggested decoupling of abundance and effective size trajectories. Conversely, density and N(eD) were positively associated. For Rio Grande silvery minnow, discrepancies among estimates of N(e) and their relationships with adult fish density could be related to effects of high variance in reproductive success in the wild and/or effects of supplementation of the wild population with captive-bred and reared fish. The efficacy of N(e) as a predictor of density and abundance may depend on intrinsic population dynamics of the species and how these dynamics are influenced by the landscape features, management protocols and other factors.
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Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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