1
|
Vertacnik KL, Vernygora OV, Dupuis JR. snpAIMeR: R package for evaluating ancestry informative marker contributions in non-model population diagnostics. Bioinformatics 2024; 40:btae377. [PMID: 38885407 PMCID: PMC11194479 DOI: 10.1093/bioinformatics/btae377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 05/07/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
MOTIVATION Single nucleotide polymorphism (SNP) markers are increasingly popular for population genomics and inferring ancestry for individuals of unknown origin. Because large SNP datasets are impractical for rapid and routine analysis, diagnostics rely on panels of highly informative markers. Strategies exist for selecting these markers, however, resources for efficiently evaluating their performance are limited for non-model systems. RESULTS snpAIMeR is a user-friendly R package that evaluates the efficacy of genomic markers for the cluster assignment of unknown individuals. It is intended to help minimize panel size and genotyping effort by determining the informativeness of candidate diagnostic markers. Provided genotype data from individuals of known origin, it uses leave-one-out cross-validation to determine population assignment rates for individual markers and marker combinations. AVAILABILITY AND IMPLEMENTATION snpAIMeR is available on CRAN (https://CRAN.R-project.org/package=snpAIMeR).
Collapse
Affiliation(s)
- Kim L Vertacnik
- Department of Entomology, University of Kentucky, Lexington, KY 40546, United States
| | - Oksana V Vernygora
- Department of Entomology, University of Kentucky, Lexington, KY 40546, United States
| | - Julian R Dupuis
- Department of Entomology, University of Kentucky, Lexington, KY 40546, United States
| |
Collapse
|
2
|
White SL, Rash JM, Kazyak DC. Is now the time? Review of genetic rescue as a conservation tool for brook trout. Ecol Evol 2023; 13:e10142. [PMID: 37250443 PMCID: PMC10213484 DOI: 10.1002/ece3.10142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/04/2023] [Accepted: 05/11/2023] [Indexed: 05/31/2023] Open
Abstract
Brook trout populations have been declining throughout their native range in the east coast of the United States. Many populations are now distributed in small, isolated habitat patches where low genetic diversity and high rates of inbreeding reduce contemporary viability and long-term adaptive potential. Although human-assisted gene flow could theoretically improve conservation outcomes through genetic rescue, there is widespread hesitancy to use this tool to support brook trout conservation. Here, we review the major uncertainties that have limited genetic rescue from being considered as a viable conservation tool for isolated brook trout populations and compare the risks of genetic rescue with other management alternatives. Drawing on theoretical and empirical studies, we discuss methods for implementing genetic rescue in brook trout that could yield long-term evolutionary benefits while avoiding negative fitness effects associated with outbreeding depression and the spread of maladapted alleles. We also highlight the potential for future collaborative efforts to accelerate our understanding of genetic rescue as a viable tool for conservation. Ultimately, while we acknowledge that genetic rescue is not without risk, we emphasize the merits that this tool offers for protecting and propagating adaptive potential and improving species' resilience to rapid environmental change.
Collapse
Affiliation(s)
- Shannon L. White
- U.S. Geological Survey Eastern Ecological Science CenterKearneysvilleWest VirginiaUSA
| | - Jacob M. Rash
- North Carolina Wildlife Resources CommissionMarionNorth CarolinaUSA
| | - David C. Kazyak
- U.S. Geological Survey Eastern Ecological Science CenterKearneysvilleWest VirginiaUSA
| |
Collapse
|
3
|
Lam DK, Frantz AC, Burke T, Geffen E, Sin SYW. Both selection and drift drive the spatial pattern of adaptive genetic variation in a wild mammal. Evolution 2023; 77:221-238. [PMID: 36626810 DOI: 10.1093/evolut/qpac014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 10/03/2022] [Accepted: 11/04/2022] [Indexed: 01/12/2023]
Abstract
The major histocompatibility complex (MHC) has been intensively studied for the relative effects of different evolutionary forces in recent decades. Pathogen-mediated balancing selection is generally thought to explain the high polymorphism observed in MHC genes, but it is still unclear to what extent MHC diversity is shaped by selection relative to neutral drift. In this study, we genotyped MHC class II DRB genes and 15 neutral microsatellite loci across 26 geographic populations of European badgers (Meles meles) covering most of their geographic range. By comparing variation of microsatellite and diversity of MHC at different levels, we demonstrate that both balancing selection and drift have shaped the evolution of MHC genes. When only MHC allelic identity was investigated, the spatial pattern of MHC variation was similar to that of microsatellites. By contrast, when functional aspects of the MHC diversity (e.g., immunological supertypes) were considered, balancing selection appears to decrease genetic structuring across populations. Our comprehensive sampling and analytical approach enable us to conclude that the likely mechanisms of selection are heterozygote advantage and/or rare-allele advantage. This study is a clear demonstration of how both balancing selection and genetic drift simultaneously affect the evolution of MHC genes in a widely distributed wild mammal.
Collapse
Affiliation(s)
- Derek Kong Lam
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Alain C Frantz
- Musée National d'Histoire Naturelle, Luxembourg, Luxembourg
| | - Terry Burke
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Eli Geffen
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
4
|
Phylogeography and population genetics of a headwater-stream adapted crayfish, Cambarus pristinus (Decapoda: Cambaridae), from the Cumberland Plateau in Tennessee. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01477-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
5
|
Nakajima S, Sueyoshi M, Hirota SK, Ishiyama N, Matsuo A, Suyama Y, Nakamura F. A strategic sampling design revealed the local genetic structure of cold-water fluvial sculpin: a focus on groundwater-dependent water temperature heterogeneity. Heredity (Edinb) 2021; 127:413-422. [PMID: 34417564 PMCID: PMC8478981 DOI: 10.1038/s41437-021-00468-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023] Open
Abstract
A key piece of information for ecosystem management is the relationship between the environment and population genetic structure. However, it is difficult to clearly quantify the effects of environmental factors on genetic differentiation because of spatial autocorrelation and analytical problems. In this study, we focused on stream ecosystems and the environmental heterogeneity caused by groundwater and constructed a sampling design in which geographic distance and environmental differences are not correlated. Using multiplexed ISSR genotyping by sequencing (MIG-seq) method, a fine-scale population genetics study was conducted in fluvial sculpin Cottus nozawae, for which summer water temperature is the determinant factor in distribution and survival. There was a clear genetic structure in the watershed. Although a significant isolation-by-distance pattern was detected in the watershed, there was no association between genetic differentiation and water temperature. Instead, asymmetric gene flow from relatively low-temperature streams to high-temperature streams was detected, indicating the importance of low-temperature streams and continuous habitats. The groundwater-focused sampling strategy yielded insightful results for conservation.
Collapse
Affiliation(s)
- Souta Nakajima
- grid.39158.360000 0001 2173 7691Laboratory of Ecosystem Management, Graduate School of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo, Hokkaido Japan
| | - Masanao Sueyoshi
- grid.472015.50000 0000 9513 8387Aqua Restoration Research Center, Public Works Research Institute, KawashimaKasada-machi, Kakamigahara, Gifu Japan
| | - Shun K. Hirota
- grid.69566.3a0000 0001 2248 6943Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi Japan
| | - Nobuo Ishiyama
- grid.452441.2Forest Research Institute, Hokkaido Research Organization, Koshunai, Bibai, Hokkaido Japan
| | - Ayumi Matsuo
- grid.69566.3a0000 0001 2248 6943Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi Japan
| | - Yoshihisa Suyama
- grid.69566.3a0000 0001 2248 6943Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi Japan
| | - Futoshi Nakamura
- grid.39158.360000 0001 2173 7691Laboratory of Ecosystem Management, Graduate School of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo, Hokkaido Japan
| |
Collapse
|
6
|
Prentice MB, Vye SR, Jenkins SR, Shaw PW, Ironside JE. Genetic diversity and relatedness in aquaculture and marina populations of the invasive tunicate Didemnum vexillum in the British Isles. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02615-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractIntroductions of invasive, non-native species in the marine environment are increasing as human activity within coastal areas rises. Genetic datasets are useful tools to identify source populations, track routes of invasions, and illuminate the role of genetic variation in the establishment and subsequent spread of novel introductions. Here, a microsatellite dataset is used to estimate the genetic diversity and population structure of 7 introduced Didemnum vexillum populations in Britain and Ireland, 4 of which are associated with aquaculture and 3 with marinas. Genetic differentiation observed between these populations indicates human-mediated transport as the main mechanism underlying the population structure of D. vexillum in Britain and Ireland. In addition to elucidating patterns of population structure we found that aquaculture sites showed significantly higher genetic diversity (measured as allelic richness) in comparison to the marina sites. We discuss these findings in relation to the history of each invasion, the complex life history of D. vexillum, and available evidence of the relative invasiveness of these populations. Our results show numerous interesting patterns which highlight further research avenues to elucidate the complex factors underlying the global spread of this successful invader.
Collapse
|
7
|
Yamazaki Y, Kitamura JI, Ikeya K, Mori S. Fine-scale genetic structure of the endangered bitterling in the middle river basin of the Kiso River, Japan. Genetica 2021; 149:179-190. [PMID: 33934258 DOI: 10.1007/s10709-021-00123-9] [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: 02/09/2021] [Accepted: 04/27/2021] [Indexed: 11/28/2022]
Abstract
Recently, anthropogenic alterations have had severe and negative impacts on the terrestrial and aquatic species and environments. To conserve species that have a small and limited habitat, it is necessary to focus on fine-scale population structure and its effects on persistence. The deepbodied bitterling Acheilognathus longipinnis is an endangered freshwater fish that occupies ponds scattered in lateral bars in the Kiso River. In this study, we conducted multi-locus microsatellite DNA analysis to evaluate both fine-scale population structure and genetic diversity, in order to conserve A. longipinnis. The smaller number of loci deviating from the Hardy-Weinberg equilibrium in ponds scattered in individual lateral bars compared to the whole river system suggests that A. longipinnis forms a local breeding population in units of ponds. The population was roughly split between the river banks and the local population located in ponds in the mid-channel bar showed intermediate relationships with the river bank populations. Gene flow between local populations was not always homogeneous and was not influenced by geographical distances between local populations or the direction of river flow. The dispersal of A. longipinnis across both river bank sides may be constrained and is probably affected by the ecological characteristics of A. longipinnis and the hydrological regimes. Consequently, A. longipinnis in the Kiso River is maintained as a complex of multiple local populations with appropriate gene flow among them. To conserve A. longipinnis, both the persistence of the unstable ponds and moderate genetic exchanges by individual migration are required.
Collapse
Affiliation(s)
- Yuji Yamazaki
- Faculty of Science, University of Toyama, Toyama, 930-8555, Japan.
| | - Jyun-Ichi Kitamura
- Mie Prefectural Museum, 3060 Isshinden-kouzubeta, Tsu, Mie, 514-0061, Japan
| | - Koki Ikeya
- Gifu World Fresh Water Aquarium, 1453 Kawashimakasada, Kakamigahara, Gifu, 501-6021, Japan
| | - Seiichi Mori
- Gifu-Kyoritsu University, Ogaki 5-50, Gifu, 503-8550, Japan
| |
Collapse
|
8
|
River drying influences genetic variation and population structure in an Arctic freshwater fish. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01339-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
9
|
Zhang Z, Yu D, Liu F, Chen S, Liu H. Gene Flow and Individual Relatedness Suggest Population Spatial Connectivity of Sinogastromyzon sichangensis (Cypriniformes: Balitoridae) in the Chishui River, China. Zoolog Sci 2021; 37:434-443. [PMID: 32972084 DOI: 10.2108/zs190137] [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: 11/14/2019] [Accepted: 05/31/2020] [Indexed: 11/17/2022]
Abstract
Sinogastromyzon sichangensis is a hillstream loach endemic to the upper Yangtze River, China. It is unclear whether this fish lives in a very restricted area or may be dispersed over a long distance. In the present study spatial connectivity of populations of S. sichangensis was investigated based on 343 individuals collected from 12 sites of Chishui River and employing 22 microsatellite loci. The results of genetic diversity analysis showed that observed heterozygosity (HO) and polymorphism information content (PIC) ranged from 0.5653 to 0.6999 and 0.8513 to 0.8819, respectively. Population structure analysis suggested that S. sichangensis had an unclear genetic structure. AMOVA showed that 69.36% of genetic variation was attributed to differentiation within individuals and all the pairwise genetic differentiation indices (FST) were low (mean FST = 0.0344), indicating weak differentiation among these populations. Estimation of gene flow showed frequent flow among populations, and contemporary levels (mean contemporary migration rate, mc = 0.0131) were approximately equal to historical levels (mean historical migration rate, mh = 0.0147). Individual relatedness analysis revealed a high level of sibship within and among different populations. The frequent gene flow and widespread sibship were due to S. sichangensis laying drifting eggs which travel for a long distance until hatching, after which the juveniles or adults migrate upstream. The results of unclear geographic structure and frequent exchange also indicate that it is necessary to decrease the negative impacts of anthropogenic activities on the connectivity of rivers to protect the migration routes of S. sichangensis.
Collapse
Affiliation(s)
- Zhi Zhang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China.,University of Chinese Academy of Sciences, Beijing 100039, P.R. China
| | - Dan Yu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China
| | - Fei Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China
| | - Sha Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China.,College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, P.R. China
| | - Huanzhang Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China,
| |
Collapse
|
10
|
White SL, Hanks EM, Wagner T. A novel quantitative framework for riverscape genetics. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02147. [PMID: 32338800 DOI: 10.1002/eap.2147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/08/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Riverscape genetics, which applies concepts in landscape genetics to riverine ecosystems, lack appropriate quantitative methods that address the spatial autocorrelation structure of linear stream networks and account for bidirectional geneflow. To address these challenges, we present a general framework for the design and analysis of riverscape genetic studies. Our framework starts with the estimation of pairwise genetic distance at sample sites and the development of a spatially structured ecological network (SSEN) on which riverscape covariates are measured. We then introduce the novel bidirectional geneflow in riverscapes (BGR) model that uses principles of isolation-by-resistance to quantify the effects of environmental covariates on genetic connectivity, with spatial covariance defined using simultaneous autoregressive models on the SSEN and the generalized Wishart distribution to model pairwise distance matrices arising through a random walk model of geneflow. We highlight the utility of this framework in an analysis of riverscape genetics for brook trout (Salvelinus fontinalis) in north central Pennsylvania, USA. Using the fixation index (FST ) as the measure of genetic distance, we estimated the effects of 12 riverscape covariates on geneflow by evaluating the relative support of eight competing BGR models. We then compared the performance of the top-ranked BGR model to results obtained from comparable analyses using multiple regression on distance matrices (MRM) and the program STRUCTURE. We found that the BGR model had more power to detect covariate effects, particularly for variables that were only partial barriers to geneflow and/or uncommon in the riverscape, making it more informative for assessing patterns of population connectivity and identifying threats to species conservation. This case study highlights the utility of our modeling framework over other quantitative methods in riverscape genetics, particularly the ability to rigorously test hypotheses about factors that influence geneflow and probabilistically estimate the effect of riverscape covariates, including stream flow direction. This framework is flexible across taxa and riverine networks, is easily executable, and provides intuitive results that can be used to investigate the likely outcomes of current and future management scenarios.
Collapse
Affiliation(s)
- Shannon L White
- Pennsylvania Cooperative Fish and Wildlife Research Unit, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Ephraim M Hanks
- Department of Statistics, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Tyler Wagner
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research Unit, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| |
Collapse
|
11
|
Genetic Structure and Population Demography of White-Spotted Charr in the Upstream Watershed of a Large Dam. WATER 2020. [DOI: 10.3390/w12092406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
White-spotted charr (Salvelinus leucomaenis leucomaenis) is an anadromous fish that has been severely harmed by human land-use development, particularly through habitat fragmentation. However, the anthropogenic impacts on populations of this species have not been evaluated, except those on small dammed-off populations. Using multiplexed ISSR genotyping by sequencing, we investigated the genetic structure of white-spotted charr in four tributaries in the upper section of the Kanayama Dam in the Sorachi River, Hokkaido Island, Japan. There were no distinct genetic structures (FST = 0.014), probably because some active individuals migrate frequently among tributaries. By model-flexible demographic simulation, historical changes in the effective population size were inferred. The result indicates that the population size has decreased since the end of the last glacial period, with three major population decline events, including recent declines that were probably associated with recent human activities. Nevertheless, populations in the watershed upstream of the Kanayama Dam are still expected to be at low risk of immediate extinction, owing to the large watershed size and the limited number of small check dams. An effective conservation measure for sustaining the white-spotted charr population is to maintain high connectivity between tributaries, such as by providing fishways in check dams during construction.
Collapse
|
12
|
Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01297-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
13
|
Righi T, Splendiani A, Fioravanti T, Petetta A, Candelma M, Gioacchini G, Gillespie K, Hanke A, Carnevali O, Caputo Barucchi V. Mediterranean swordfish ( Xiphias gladius Linnaeus, 1758) population structure revealed by microsatellite DNA: genetic diversity masked by population mixing in shared areas. PeerJ 2020; 8:e9518. [PMID: 33194325 PMCID: PMC7394060 DOI: 10.7717/peerj.9518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 06/19/2020] [Indexed: 11/20/2022] Open
Abstract
Background The Mediterranean swordfish stock is overfished and considered not correctly managed. Elucidating the patterns of the Mediterranean swordfish population structure constitutes an essential prerequisite for effective management of this fishery resource. To date, few studies have investigated intra-Mediterranean swordfish population structure, and their conclusions are controversial. Methods A panel of 20 microsatellites DNA was used to investigate fine-scale population structuring of swordfish from six main fishing areas of the Mediterranean Sea. Results This study provides evidence to reject the hypothesis of a single swordfish population within the Mediterranean Sea. DAPC analysis revealed the presence of three genetic clusters and a high level of admixture within the Mediterranean Sea. Genetic structure was supported by significant FST values while mixing was endorsed by the heterozygosity deficit observed in sampling localities indicative of a possible Wahlund effect, by sampling admixture individuals. Overall, our tests reject the hypothesis of a single swordfish population within the Mediterranean Sea. Homing towards the Mediterranean breeding areas may have generated a weak degree of genetic differentiation between populations even at the intra-basin scale.
Collapse
Affiliation(s)
- Tommaso Righi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Andrea Splendiani
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Tatiana Fioravanti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Andrea Petetta
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Michela Candelma
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Giorgia Gioacchini
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Kyle Gillespie
- Fisheries and Oceans Canada, St. Andrews Biological Station, Ottawa, Canada
| | - Alex Hanke
- Fisheries and Oceans Canada, St. Andrews Biological Station, Ottawa, Canada
| | - Oliana Carnevali
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Vincenzo Caputo Barucchi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| |
Collapse
|
14
|
Gallo O, Castillo DF, Godinho R, Casanave EB. Genetic diversity, population structure, and immigration, in a partially hunted puma population of south-central Argentina. J Mammal 2020. [DOI: 10.1093/jmammal/gyaa039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AbstractCarnivores are decreasing globally due in part to anthropogenic ecological disturbances. In Argentina, human activities have fragmented wildlife habitat, thereby intensifying puma–livestock conflict and leading to population control of the predator species by hunting. We investigated genetic variability and population structure of pumas (Puma concolor) from three south-central Argentine provinces with two different management policies for the species: full protection versus legal hunting. All genetic estimates were based on 83 individuals genotyped at 25 species-specific microsatellite loci. The overall genetic diversity was high (observed heterozygosity = 0.63), but lower than in other South American populations. Spatial analyses revealed the presence of two bottlenecked genetic clusters with very similar diversity and low gene flow (3% per generation) between them. However, analyses based on a priori separated groups showed that gene flow follows increasing values of hunting pressure, converging to the area with the greatest number of individuals harvested. Our results suggest that hunting pressure likely is contributing to the gene flow pattern, limiting pumas’ movements and creating a metapopulation dynamic among geographic subpopulations. Integrated demographic and genetic approaches are needed to better understand pumas’ movements across the landscape and adopt successful management plans to achieve long-term population viability.
Collapse
Affiliation(s)
- Orlando Gallo
- Instituto de Ciencias Biológicas y Biomédicas del Sur (INBIOSUR)-CONICET, Dpto. de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 671, Bahía Blanca, Argentina
| | - Diego F Castillo
- Instituto de Ciencias Biológicas y Biomédicas del Sur (INBIOSUR)-CONICET, Dpto. de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 671, Bahía Blanca, Argentina
| | - Raquel Godinho
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO/InBio), Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas 7, Vairão, Portugal
| | - Emma B Casanave
- Instituto de Ciencias Biológicas y Biomédicas del Sur (INBIOSUR)-CONICET, Dpto. de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 671, Bahía Blanca, Argentina
| |
Collapse
|
15
|
Population genomic and phenotype diversity of invasive Drosophila suzukii in Hawai‘i. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02217-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
16
|
Lehnert SJ, Baillie SM, MacMillan J, Paterson IG, Buhariwalla CF, Bradbury IR, Bentzen P. Multiple decades of stocking has resulted in limited hatchery introgression in wild brook trout ( Salvelinus fontinalis) populations of Nova Scotia. Evol Appl 2020; 13:1069-1089. [PMID: 32431753 PMCID: PMC7232767 DOI: 10.1111/eva.12923] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 12/06/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022] Open
Abstract
Many populations of freshwater fishes are threatened with losses, and increasingly, the release of hatchery individuals is one strategy being implemented to support wild populations. However, stocking of hatchery individuals may pose long-term threats to wild populations, particularly if genetic interactions occur between wild and hatchery individuals. One highly prized sport fish that has been heavily stocked throughout its range is the brook trout (Salvelinus fontinalis). In Nova Scotia, Canada, hatchery brook trout have been stocked since the early 1900s, and despite continued stocking efforts, populations have suffered declines in recent decades. Before this study, the genetic structure of brook trout populations in the province was unknown; however, given the potential negative consequences associated with hatchery stocking, it is possible that hatchery programs have adversely affected the genetic integrity of wild populations. To assess the influence of hatchery supplementation on wild populations, we genotyped wild brook trout from 12 river systems and hatchery brook trout from two major hatcheries using 100 microsatellite loci. Genetic analyses of wild trout revealed extensive population genetic structure among and within river systems and significant isolation-by-distance. Hatchery stocks were genetically distinct from wild populations, and most populations showed limited to no evidence of hatchery introgression (<5% hatchery ancestry). Only a single location had a substantial number of hatchery-derived trout and was located in the only river where a local strain is used for supplementation. The amount of hatchery stocking within a watershed did not influence the level of hatchery introgression. Neutral genetic structure of wild populations was influenced by geography with some influence of climate and stocking indices. Overall, our study suggests that long-term stocking has not significantly affected the genetic integrity of wild trout populations, highlighting the variable outcomes of stocking and the need to evaluate the consequences on a case-by-case basis.
Collapse
Affiliation(s)
- Sarah J. Lehnert
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Shauna M. Baillie
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
| | - John MacMillan
- Inland Fisheries DivisionNova Scotia Department of Fisheries and AquaculturePictouNSCanada
| | - Ian G. Paterson
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
| | - Colin F. Buhariwalla
- Inland Fisheries DivisionNova Scotia Department of Fisheries and AquaculturePictouNSCanada
| | - Ian R. Bradbury
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
| | - Paul Bentzen
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
| |
Collapse
|
17
|
Washburn BA, Cashner MF, Blanton RE. Small fish, large river: Surprisingly minimal genetic structure in a dispersal-limited, habitat specialist fish. Ecol Evol 2020; 10:2253-2268. [PMID: 32128153 PMCID: PMC7042738 DOI: 10.1002/ece3.6064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/23/2019] [Accepted: 01/02/2020] [Indexed: 11/08/2022] Open
Abstract
Genetic connectivity is expected to be lower in species with limited dispersal ability and a high degree of habitat specialization (intrinsic factors). Also, gene flow is predicted to be limited by habitat conditions such as physical barriers and geographic distance (extrinsic factors). We investigated the effects of distance, intervening pools, and rapids on gene flow in a species, the Tuxedo Darter (Etheostoma lemniscatum), a habitat specialist that is presumed to be dispersal-limited. We predicted that the interplay between these intrinsic and extrinsic factors would limit dispersal and lead to genetic structure even at the small spatial scale of the species range (a 38.6 km river reach). The simple linear distribution of E. lemniscatum allowed for an ideal test of how these factors acted on gene flow and allowed us to test expectations (e.g., isolation-by-distance) of linearly distributed species. Using 20 microsatellites from 163 individuals collected from 18 habitat patches, we observed low levels of genetic structure that were related to geographic distance and rapids, though these factors were not barriers to gene flow. Pools separating habitat patches did not contribute to any observed genetic structure. Overall, E. lemniscatum maintains gene flow across its range and is comprised of a single population. Due to the linear distribution of the species, a stepping-stone model of dispersal best explains the maintenance of gene flow across its small range. In general, our observation of higher-than-expected connectivity likely stems from an adaptation to disperse due to temporally unstable and patchy habitat.
Collapse
Affiliation(s)
- Brooke A. Washburn
- Department of BiologyCenter of Excellence for Field BiologyAustin Peay State UniversityClarksvilleTNUSA
- Present address:
Department of Biological SciencesUniversity of DenverDenverCOUSA
| | - Mollie F. Cashner
- Department of BiologyCenter of Excellence for Field BiologyAustin Peay State UniversityClarksvilleTNUSA
| | - Rebecca E. Blanton
- Department of BiologyCenter of Excellence for Field BiologyAustin Peay State UniversityClarksvilleTNUSA
| |
Collapse
|
18
|
Beer SD, Cornett S, Austerman P, Trometer B, Hoffman T, Bartron ML. Genetic diversity, admixture, and hatchery influence in Brook Trout ( Salvelinus fontinalis) throughout western New York State. Ecol Evol 2019; 9:7455-7479. [PMID: 31346416 PMCID: PMC6635958 DOI: 10.1002/ece3.5237] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/22/2019] [Accepted: 04/16/2019] [Indexed: 02/06/2023] Open
Abstract
Although Brook Trout are distributed across most of eastern North America, population numbers have declined in many regions due to habitat loss, climate change, and competition with non-native species. In New York State, Brook Trout habitat has been substantially reduced, with many areas showing complete extirpation of Brook Trout populations, predominantly in the western portion of the state. Small, fragmented populations are at risk of genetic diversity loss, inbreeding depression, and reduced fitness, leading to a greater potential for local extirpation. Genetic monitoring is a practical tool that can facilitate further conservation-decision making regarding small populations. In this study, we used 12 microsatellite loci to examine 3,436 sampled Brook Trout, representing 75 sites from the Allegheny, Erie/Niagara, Genesee, Oswego, Lake Ontario, and Susquehanna drainage basins throughout western New York State. Three Brook Trout hatchery strains were also genetically characterized to evaluate the degree of hatchery introgression between wild populations and hatchery strains stocked in the region. Overall, estimates of genetic diversity varied widely: Allelic richness ranged from 2.23 to 7.485, and expected heterozygosity ranged from 0.402 to 0.766. As observed for Brook Trout in other regions, we found a high degree of genetic differentiation among populations, with all comparisons except one showing significant F ST values. Hatchery introgression was found to be minimal, with estimates ranging from 1.96% to 3.10% of wild individuals exhibiting membership proportions to a hatchery strain cluster exceeding 10% (q ≥ 0.10). Results from this investigation can be used to prioritize management efforts for Brook Trout in western New York State and act as a baseline to monitor future population trends.
Collapse
Affiliation(s)
| | - Scott Cornett
- New York State Department of Environmental ConservationAlleganyNew York
| | - Peter Austerman
- New York State Department of Environmental ConservationAvonNew York
| | - Betsy Trometer
- U.S. Fish and Wildlife ServiceLower Great Lakes Fish and Wildlife Conservation OfficeBasomNew York
| | - Thomas Hoffman
- U.S. Fish and Wildlife ServiceLower Great Lakes Fish and Wildlife Conservation OfficeBasomNew York
| | | |
Collapse
|
19
|
Oliveira JDA, Farias IP, Costa GC, Werneck FP. Model-based riverscape genetics: disentangling the roles of local and connectivity factors in shaping spatial genetic patterns of two Amazonian turtles with different dispersal abilities. Evol Ecol 2019. [DOI: 10.1007/s10682-019-09973-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
20
|
Pregler KC, Kanno Y, Rankin D, Coombs JA, Whiteley AR. Characterizing genetic integrity of rear-edge trout populations in the southern Appalachians. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1116-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
21
|
White SL, Miller WL, Dowell SA, Bartron ML, Wagner T. Limited hatchery introgression into wild brook trout ( Salvelinus fontinalis) populations despite reoccurring stocking. Evol Appl 2018; 11:1567-1581. [PMID: 30344628 PMCID: PMC6183464 DOI: 10.1111/eva.12646] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 01/17/2023] Open
Abstract
Due to increased anthropogenic pressures on many fish populations, supplementing wild populations with captive-raised individuals has become an increasingly common management practice. Stocking programs can be controversial due to uncertainty about the long-term fitness effects of genetic introgression on wild populations. In particular, introgression between hatchery and wild individuals can cause declines in wild population fitness, resiliency, and adaptive potential and contribute to local population extirpation. However, low survival and fitness of captive-raised individuals can minimize the long-term genetic consequences of stocking in wild populations, and to date the prevalence of introgression in actively stocked ecosystems has not been rigorously evaluated. We quantified the extent of introgression in 30 populations of wild brook trout (Salvelinus fontinalis) in a Pennsylvania watershed and examined the correlation between introgression and 11 environmental covariates. Genetic assignment tests were used to determine the origin (wild vs. captive-raised) for 1,742 wild-caught and 300 hatchery brook trout. To avoid assignment biases, individuals were assigned to two simulated populations that represented the average allele frequencies in wild and hatchery groups. Fish with intermediate probabilities of wild ancestry were classified as introgressed, with threshold values determined through simulation. Even with reoccurring stocking at most sites, over 93% of wild-caught individuals probabilistically assigned to wild origin, and only 5.6% of wild-caught fish assigned to introgressed. Models examining environmental drivers of introgression explained <3% of the among-population variability, and all estimated effects were highly uncertain. This was not surprising given overall low introgression observed in this study. Our results suggest that introgression of hatchery-derived genotypes can occur at low rates, even in actively stocked ecosystems and across a range of habitats. However, a cautious approach to stocking may still be warranted, as the potential effects of stocking on wild population fitness and the mechanisms limiting introgression are not known.
Collapse
Affiliation(s)
- Shannon L. White
- Pennsylvania Cooperative Fish and Wildlife Research UnitPennsylvania State UniversityUniversity ParkPennsylvania
- Department of Ecosystem Science and ManagementPennsylvania State UniversityUniversity ParkPennsylvania
| | - William L. Miller
- Pennsylvania Cooperative Fish and Wildlife Research UnitPennsylvania State UniversityUniversity ParkPennsylvania
- Department of Ecosystem Science and ManagementPennsylvania State UniversityUniversity ParkPennsylvania
| | | | | | - Tyler Wagner
- U.S. Geological SurveyPennsylvania Cooperative Fish and Wildlife Research UnitPennsylvania State UniversityUniversity ParkPennsylvania
| |
Collapse
|
22
|
Phenotypic assortment by body shape in wild-caught fish shoals. Naturwissenschaften 2018; 105:53. [DOI: 10.1007/s00114-018-1581-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/15/2018] [Accepted: 08/20/2018] [Indexed: 12/14/2022]
|
23
|
Blum AG, Kanno Y, Letcher BH. Seasonal streamflow extremes are key drivers of Brook Trout young‐of‐the‐year abundance. Ecosphere 2018. [DOI: 10.1002/ecs2.2356] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Annalise G. Blum
- Department of Civil and Environmental Engineering Tufts University 200 College Avenue Medford Massachusetts 02155 USA
- U.S. Geological Survey 12201 Sunrise Valley Drive Reston Virginia 20192 USA
| | - Yoichiro Kanno
- Department of Fish, Wildlife, and Conservation Biology, and Graduate Degree Program in Ecology Colorado State University Fort Collins Colorado 80523 USA
| | - Benjamin H. Letcher
- Leetown Science Center S. O. Conte Anadromous Fish Research Center U.S. Geological Survey One Migratory Way, Turners Falls Massachusetts 01376 USA
| |
Collapse
|
24
|
Dam trout: Genetic variability in Oncorhynchus mykiss above and below barriers in three Columbia River systems prior to restoring migrational access. PLoS One 2018; 13:e0197571. [PMID: 29851979 PMCID: PMC5979028 DOI: 10.1371/journal.pone.0197571] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/06/2018] [Indexed: 12/03/2022] Open
Abstract
Restoration of access to lost habitat for threatened and endangered fishes above currently impassable dams represents a major undertaking. Biological monitoring is critical to understand the dynamics and success of anadromous recolonization as, in the case of Oncorhynchus mykiss, anadromous steelhead populations are reconnected with their conspecific resident rainbow trout counterparts. We evaluate three river systems in the Lower Columbia River basin: the White Salmon, Sandy, and Lewis rivers that are in the process of removing and/or providing passage around existing human-made barriers in O. mykiss riverine habitat. In these instances, now isolated resident rainbow trout populations will be exposed to competition and/or genetic introgression with steelhead and vice versa. Our genetic analyses of 2,158 fish using 13 DNA microsatellite (mSAT) loci indicated that within each basin anadromous O. mykiss were genetically distinct from and significantly more diverse than their resident above-dam trout counterparts. Above long-standing natural impassable barriers, each of these watersheds also harbors unique rainbow trout gene pools with reduced levels of genetic diversity. Despite frequent releases of non-native steelhead and rainbow trout in each river, hatchery releases do not appear to have had a significant genetic effect on the population structure of O. mykiss in any of these watersheds. Simulation results suggest there is a high likelihood of identifying anadromous x resident individuals in the Lewis and White Salmon rivers, and slightly less so in the Sandy River. These genetic data are a prerequisite for informed monitoring, managing, and conserving the different life history forms during upstream recolonization when sympatry of life history forms of O. mykiss is restored.
Collapse
|
25
|
Jaisuk C, Senanan W. Effects of landscape features on population genetic variation of a tropical stream fish, Stone lapping minnow, Garra cambodgiensis, in the upper Nan River drainage basin, northern Thailand. PeerJ 2018; 6:e4487. [PMID: 29568710 PMCID: PMC5845392 DOI: 10.7717/peerj.4487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/20/2018] [Indexed: 11/20/2022] Open
Abstract
Spatial genetic variation of river-dwelling freshwater fishes is typically affected by the historical and contemporary river landscape as well as life-history traits. Tropical river and stream landscapes have endured extended geological change, shaping the existing pattern of genetic diversity, but were not directly affected by glaciation. Thus, spatial genetic variation of tropical fish populations should look very different from the pattern observed in temperate fish populations. These data are becoming important for designing appropriate management and conservation plans, as these aquatic systems are undergoing intense development and exploitation. This study evaluated the effects of landscape features on population genetic diversity of Garra cambodgiensis, a stream cyprinid, in eight tributary streams in the upper Nan River drainage basin (n = 30–100 individuals/location), Nan Province, Thailand. These populations are under intense fishing pressure from local communities. Based on 11 microsatellite loci, we detected moderate genetic diversity within eight population samples (average number of alleles per locus = 10.99 ± 3.00; allelic richness = 10.12 ± 2.44). Allelic richness within samples and stream order of the sampling location were negatively correlated (P < 0.05). We did not detect recent bottleneck events in these populations, but we did detect genetic divergence among populations (Global FST = 0.022, P < 0.01). The Bayesian clustering algorithms (TESS and STRUCTURE) suggested that four to five genetic clusters roughly coincide with sub-basins: (1) headwater streams/main stem of the Nan River, (2) a middle tributary, (3) a southeastern tributary and (4) a southwestern tributary. We observed positive correlation between geographic distance and linearized FST (P < 0.05), and the genetic differentiation pattern can be moderately explained by the contemporary stream network (STREAMTREE analysis, R2 = 0.75). The MEMGENE analysis suggested genetic division between northern (genetic clusters 1 and 2) and southern (clusters 3 and 4) sub-basins. We observed a high degree of genetic admixture in each location, highlighting the importance of natural flooding patterns and possible genetic impacts of supplementary stocking. Insights obtained from this research advance our knowledge of the complexity of a tropical stream system, and guide current conservation and restoration efforts for this species in Thailand.
Collapse
Affiliation(s)
- Chaowalee Jaisuk
- Department of Aquatic Science, Faculty of Science, Burapha University, Chon Buri, Thailand.,Department of Animal Science and Fisheries, Faculty of Science and Agricultural Technology, Rajamangala University of Technology Lanna Nan Campus, Nan, Thailand
| | - Wansuk Senanan
- Department of Aquatic Science, Faculty of Science, Burapha University, Chon Buri, Thailand
| |
Collapse
|
26
|
Robinson ZL, Coombs JA, Hudy M, Nislow KH, Letcher BH, Whiteley AR. Experimental test of genetic rescue in isolated populations of brook trout. Mol Ecol 2017; 26:4418-4433. [PMID: 28664980 DOI: 10.1111/mec.14225] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/21/2017] [Accepted: 06/05/2017] [Indexed: 12/27/2022]
Abstract
Genetic rescue is an increasingly considered conservation measure to address genetic erosion associated with habitat loss and fragmentation. The resulting gene flow from facilitating migration may improve fitness and adaptive potential, but is not without risks (e.g., outbreeding depression). Here, we conducted a test of genetic rescue by translocating ten (five of each sex) brook trout (Salvelinus fontinalis) from a single source to four nearby and isolated stream populations. To control for the demographic contribution of translocated individuals, ten resident individuals (five of each sex) were removed from each recipient population. Prior to the introduction of translocated individuals, the two smallest above-barrier populations had substantially lower genetic diversity, and all populations had reduced effective number of breeders relative to adjacent below-barrier populations. In the first reproductive bout following translocation, 31 of 40 (78%) translocated individuals reproduced successfully. Translocated individuals contributed to more families than expected under random mating and generally produced larger full-sibling families. We observed relatively high (>20%) introgression in three of the four recipient populations. The translocations increased genetic diversity of recipient populations by 45% in allelic richness and 25% in expected heterozygosity. Additionally, strong evidence of hybrid vigour was observed through significantly larger body sizes of hybrid offspring relative to resident offspring in all recipient populations. Continued monitoring of these populations will test for negative fitness effects beyond the first generation. However, these results provide much-needed experimental data to inform the potential effectiveness of genetic rescue-motivated translocations.
Collapse
Affiliation(s)
- Zachary L Robinson
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | - Jason A Coombs
- U.S. Forest Service, Northern Research Station, University of Massachusetts, Amherst, MA, USA
| | | | - Keith H Nislow
- U.S. Forest Service, Northern Research Station, University of Massachusetts, Amherst, MA, USA
| | - Benjamin H Letcher
- U.S. Geological Survey, Leetown Science Center, S.O. Conte Anadromous Fish Research Center, Turners Falls, MA, USA
| | - Andrew R Whiteley
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| |
Collapse
|
27
|
Hanks EM. Modeling Spatial Covariance Using the Limiting Distribution of Spatio-Temporal Random Walks. J Am Stat Assoc 2017. [DOI: 10.1080/01621459.2016.1224714] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Ephraim M. Hanks
- Department of Statistics, The Pennsylvania State University, State College, PA
| |
Collapse
|
28
|
Pascoal S, Kilner RM. Development and application of 14 microsatellite markers in the burying beetle Nicrophorus vespilloides reveals population genetic differentiation at local spatial scales. PeerJ 2017; 5:e3278. [PMID: 28480146 PMCID: PMC5417058 DOI: 10.7717/peerj.3278] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/06/2017] [Indexed: 11/20/2022] Open
Abstract
Burying beetles (genus Nicrophorus) are relatively rare among insects in providing sophisticated parental care. Consequently, they have become model species in research analysing social evolution, the evolution of parental care and mating systems. We used the recently published N. vespilloides genome and transcriptome to develop microsatellite markers. Specifically, we developed 14 polymorphic markers with five to 13 alleles per locus and used them to investigate levels of genetic differentiation in four south Cambridgeshire (UK) populations of N. vespilloides, separated by 21 km at most. The markers revealed significant genetic structuring among populations (global FST = 0.023) with all but one of the pairwise comparisons among populations being significant. The single exception was the comparison between the two closest populations, which are approximately 2.5 km apart. In general, the microsatellite markers showed lower observed heterozygosity than expected. We infer that there is limited dispersal between populations and potentially also some inbreeding within them and suggest that this may be due to habitat fragmentation. We discuss these results in the context of recent laboratory experiments on inbreeding and beetle flight.
Collapse
Affiliation(s)
- Sonia Pascoal
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Rebecca M Kilner
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
29
|
Ciofi C, Levato S, Manfredi T, Natali C, Nazirides T, Tepsich A, Crivelli AJ, Chelazzi G. Patterns of gene flow along linear habitats: population genetics of the European pond turtle (Emys orbicularis) in floodplain ponds. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
30
|
Whiteley AR, Coombs JA, O'Donnell MJ, Nislow KH, Letcher BH. Keeping things local: Subpopulation Nb and Ne in a stream network with partial barriers to fish migration. Evol Appl 2017; 10:348-365. [PMID: 28352295 PMCID: PMC5367083 DOI: 10.1111/eva.12454] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 12/11/2016] [Indexed: 01/17/2023] Open
Abstract
For organisms with overlapping generations that occur in metapopulations, uncertainty remains regarding the spatiotemporal scale of inference of estimates of the effective number of breeders (N^b) and whether these estimates can be used to predict generational Ne. We conducted a series of tests of the spatiotemporal scale of inference of estimates of Nb in nine consecutive cohorts within a long‐term study of brook trout (Salvelinus fontinalis). We also tested a recently developed approach to estimate generational Ne from N^b and compared this to an alternative approach for estimating N^e that also accounts for age structure. Multiple lines of evidence were consistent with N^b corresponding to the local (subpopulation) spatial scale and the cohort‐specific temporal scale. We found that at least four consecutive cohort‐specific estimates of N^b were necessary to obtain reliable estimates of harmonic mean N^b for a subpopulation. Generational N^e derived from cohort‐specific N^b was within 7%–50% of an alternative approach to obtain N^e, suggesting some population specificity for concordance between approaches. Our results regarding the spatiotemporal scale of inference for Nb should apply broadly to many taxa that exhibit overlapping generations and metapopulation structure and point to promising avenues for using cohort‐specific N^b for local‐scale genetic monitoring.
Collapse
Affiliation(s)
- Andrew R Whiteley
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences College of Forestry and Conservation University of Montana Missoula MT USA
| | - Jason A Coombs
- Department of Environmental Conservation University of Massachusetts Amherst Amherst MA USA; U.S. Forest Service Northern Research Station University of Massachusetts Amherst MA USA
| | - Matthew J O'Donnell
- U.S. Geological Survey Leetown Science Center S.O. Conte Anadromous Fish Research Center Turners Falls MA USA
| | - Keith H Nislow
- U.S. Forest Service Northern Research Station University of Massachusetts Amherst MA USA
| | - Benjamin H Letcher
- U.S. Geological Survey Leetown Science Center S.O. Conte Anadromous Fish Research Center Turners Falls MA USA
| |
Collapse
|
31
|
Salisbury SJ, McCracken GR, Keefe D, Perry R, Ruzzante DE. A portrait of a sucker using landscape genetics: how colonization and life history undermine the idealized dendritic metapopulation. Mol Ecol 2016; 25:4126-45. [PMID: 27393723 DOI: 10.1111/mec.13757] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/28/2016] [Accepted: 06/28/2016] [Indexed: 01/19/2023]
Abstract
Dendritic metapopulations have been attributed unique properties by in silico studies, including an elevated genetic diversity relative to a panmictic population of equal total size. These predictions have not been rigorously tested in nature, nor has there been full consideration of the interacting effects among contemporary landscape features, colonization history and life history traits of the target species. We tested for the effects of dendritic structure as well as the relative importance of life history, environmental barriers and historical colonization on the neutral genetic structure of a longnose sucker (Catostomus catostomus) metapopulation in the Kogaluk watershed of northern Labrador, Canada. Samples were collected from eight lakes, genotyped with 17 microsatellites, and aged using opercula. Lakes varied in differentiation, historical and contemporary connectivity, and life history traits. Isolation by distance was detected only by removing two highly genetically differentiated lakes, suggesting a lack of migration-drift equilibrium and the lingering influence of historical factors on genetic structure. Bayesian analyses supported colonization via the Kogaluk's headwaters. The historical concentration of genetic diversity in headwaters inferred by this result was supported by high historical and contemporary effective sizes of the headwater lake, T-Bone. Alternatively, reduced allelic richness in headwaters confirmed the dendritic structure's influence on gene flow, but this did not translate to an elevated metapopulation effective size. A lack of equilibrium and upstream migration may have dampened the effects of dendritic structure. We suggest that interacting historical and contemporary factors prevent the achievement of the idealized traits of a dendritic metapopulation in nature.
Collapse
Affiliation(s)
- Sarah J Salisbury
- Department of Biology, Dalhousie University, Halifax, NS, B3H4R2, Canada
| | | | - Donald Keefe
- Department of Environment and Conservation, Newfoundland and Labrador, Corner Brook, NL, Canada
| | - Robert Perry
- Department of Environment and Conservation, Newfoundland and Labrador, Corner Brook, NL, Canada
| | - Daniel E Ruzzante
- Department of Biology, Dalhousie University, Halifax, NS, B3H4R2, Canada
| |
Collapse
|
32
|
Benestan LM, Ferchaud A, Hohenlohe PA, Garner BA, Naylor GJP, Baums IB, Schwartz MK, Kelley JL, Luikart G. Conservation genomics of natural and managed populations: building a conceptual and practical framework. Mol Ecol 2016; 25:2967-77. [DOI: 10.1111/mec.13647] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/12/2016] [Accepted: 04/06/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Laura Marilyn Benestan
- Departement de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec G1V 0A6 Canada
| | - Anne‐Laure Ferchaud
- Departement de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec G1V 0A6 Canada
| | - Paul A. Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow ID 83844 USA
| | - Brittany A. Garner
- Flathead Lake Biological Station Fish and Wildlife Genomic Group Division of Biological Science University of Montana Missoula MT 59812 USA
- Wildlife Program Fish and Wildlife Genomic Group College of Forestry and Conservation University of Montana Missoula MT 59812 USA
| | - Gavin J. P. Naylor
- Hollings Marine Lab College of Charleston and Medical University of South Carolina 331 Fort Johnson Rd. Charleston SC 29412 USA
| | - Iliana Brigitta Baums
- Department of Biology Pennsylvania State University 208 Mueller Lab University Park PA 1680 USA
| | - Michael K. Schwartz
- USDA Forest Service National Genomics Center for Wildlife and Fish Conservation 800 E. Beckwith Ave. Missoula MT 59801 USA
| | - Joanna L. Kelley
- School of Biological Sciences Washington State University Pullman WA 99164 USA
| | - Gordon Luikart
- Flathead Lake Biological Station Fish and Wildlife Genomic Group Division of Biological Science University of Montana Missoula MT 59812 USA
- Wildlife Program Fish and Wildlife Genomic Group College of Forestry and Conservation University of Montana Missoula MT 59812 USA
| |
Collapse
|
33
|
Ruzzante DE, McCracken GR, Parmelee S, Hill K, Corrigan A, MacMillan J, Walde SJ. Effective number of breeders, effective population size and their relationship with census size in an iteroparous species, Salvelinus fontinalis. Proc Biol Sci 2016; 283:20152601. [PMID: 26817773 PMCID: PMC4795031 DOI: 10.1098/rspb.2015.2601] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/07/2016] [Indexed: 11/12/2022] Open
Abstract
The relationship between the effective number of breeders (Nb) and the generational effective size (Ne) has rarely been examined empirically in species with overlapping generations and iteroparity. Based on a suite of 11 microsatellite markers, we examine the relationship between Nb, Ne and census population size (Nc) in 14 brook trout (Salvelinus fontinalis) populations inhabiting 12 small streams in Nova Scotia and sampled at least twice between 2009 and 2015. Unbiased estimates of Nb obtained with individuals of a single cohort, adjusted on the basis of age at first maturation (α) and adult lifespan (AL), were from 1.66 to 0.24 times the average estimates of Ne obtained with random samples of individuals of mixed ages (i.e. [Formula: see text]). In turn, these differences led to adjusted Ne estimates that were from nearly five to 0.7 times the estimates derived from mixed-aged individuals. These differences translate into the same range of variation in the ratio of effective to census population size [Formula: see text] within populations. Adopting [Formula: see text] as the more precise and unbiased estimates, we found that these brook trout populations differ markedly in their effective to census population sizes (range approx. 0.3 to approx. 0.01). Using AgeNe, we then showed that the variance in reproductive success or reproductive skew varied among populations by a factor of 40, from Vk/k ≈ 5 to 200. These results suggest wide differences in population dynamics, probably resulting from differences in productivity affecting the intensity of competition for access to mates or redds, and thus reproductive skew. Understanding the relationship between Ne, Nb and Nc, and how these relate to population dynamics and fluctuations in population size, are important for the design of robust conservation strategies in small populations with overlapping generations and iteroparity.
Collapse
Affiliation(s)
- Daniel E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Gregory R McCracken
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Samantha Parmelee
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Kristen Hill
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Amelia Corrigan
- Inland Fisheries Division, Nova Scotia Department of Fisheries and Aquaculture, Halifax, Nova Scotia, Canada B3J 2R5
| | - John MacMillan
- Inland Fisheries Division, Nova Scotia Department of Fisheries and Aquaculture, Halifax, Nova Scotia, Canada B3J 2R5
| | - Sandra J Walde
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| |
Collapse
|
34
|
Graham CF, Eberts RL, Morgan TD, Boreham DR, Lance SL, Manzon RG, Martino JA, Rogers SM, Wilson JY, Somers CM. Fine-Scale Ecological and Genetic Population Structure of Two Whitefish (Coregoninae) Species in the Vicinity of Industrial Thermal Emissions. PLoS One 2016; 11:e0146656. [PMID: 26807722 PMCID: PMC4726566 DOI: 10.1371/journal.pone.0146656] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 12/21/2015] [Indexed: 12/19/2022] Open
Abstract
Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species (Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ13C and δ15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearby reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (Fst, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Thus, future research should focus on the potential impacts of thermal emissions on development and recruitment.
Collapse
Affiliation(s)
- Carly F. Graham
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Rebecca L. Eberts
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Thomas D. Morgan
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Douglas R. Boreham
- Medical Sciences, Northern Ontario School of Medicine, Greater Sudbury, Ontario, Canada
| | - Stacey L. Lance
- Savannah River Ecology Laboratory, University of Georgia, Athens, Georgia, United States of America
| | - Richard G. Manzon
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Jessica A. Martino
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Sean M. Rogers
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Joanna Y. Wilson
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | | |
Collapse
|
35
|
Gouskov A, Reyes M, Wirthner-Bitterlin L, Vorburger C. Fish population genetic structure shaped by hydroelectric power plants in the upper Rhine catchment. Evol Appl 2016; 9:394-408. [PMID: 26834832 PMCID: PMC4721079 DOI: 10.1111/eva.12339] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/02/2015] [Indexed: 01/20/2023] Open
Abstract
The Rhine catchment in Switzerland has been transformed by a chain of hydroelectric power stations. We addressed the impact of fragmentation on the genetic structure of fish populations by focusing on the European chub (Squalius cephalus). This fish species is not stocked and copes well with altered habitats, enabling an assessment of the effects of fragmentation per se. Using microsatellites, we genotyped 2133 chub from 47 sites within the catchment fragmented by 37 hydroelectric power stations, two weirs and the Rhine Falls. The shallow genetic population structure reflected drainage topology and was affected significantly by barriers to migration. The effect of power stations equipped with fishpasses on genetic differentiation was detectable, albeit weaker than that of man‐made barriers without fishpasses. The Rhine Falls as the only long‐standing natural obstacle (formed 14 000 to 17 000 years ago) also had a strong effect. Man‐made barriers also exacerbated the upstream decrease in allelic diversity in the catchment, particularly when lacking fishpasses. Thus, existing fishpasses do have the desired effect of mitigating fragmentation, but barriers still reduce population connectivity in a fish that traverses fishpasses better than many other species. Less mobile species are likely to be affected more severely.
Collapse
Affiliation(s)
- Alexandre Gouskov
- Institute of Integrative Biology ETH Zürich Zürich Switzerland; Aquatic Ecology Eawag Dübendorf Switzerland
| | | | | | - Christoph Vorburger
- Institute of Integrative Biology ETH Zürich Zürich Switzerland; Aquatic Ecology Eawag Dübendorf Switzerland
| |
Collapse
|
36
|
Kazyak DC, Hilderbrand RH, King TL, Keller SR, Chhatre VE. Hiding in Plain Sight: A Case for Cryptic Metapopulations in Brook Trout (Salvelinus fontinalis). PLoS One 2016; 11:e0146295. [PMID: 26730588 PMCID: PMC4701135 DOI: 10.1371/journal.pone.0146295] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 12/15/2015] [Indexed: 11/19/2022] Open
Abstract
A fundamental issue in the management and conservation of biodiversity is how to define a population. Spatially contiguous fish occupying a stream network have often been considered to represent a single, homogenous population. However, they may also represent multiple discrete populations, a single population with genetic isolation-by-distance, or a metapopulation. We used microsatellite DNA and a large-scale mark-recapture study to assess population structure in a spatially contiguous sample of Brook Trout (Salvelinus fontinalis), a species of conservation concern. We found evidence for limited genetic exchange across small spatial scales and in the absence of barriers to physical movement. Mark-recapture and stationary passive integrated transponder antenna records demonstrated that fish from two tributaries very seldom moved into the opposite tributary, but movements between the tributaries and mainstem were more common. Using Bayesian genetic clustering, we identified two genetic groups that exhibited significantly different growth rates over three years of study, yet survival rates were very similar. Our study highlights the importance of considering the possibility of multiple genetically distinct populations occurring within spatially contiguous habitats, and suggests the existence of a cryptic metapopulation: a spatially continuous distribution of organisms exhibiting metapopulation-like behaviors.
Collapse
Affiliation(s)
- David C. Kazyak
- University of Maryland Center for Environmental Science, Appalachian Laboratory, Frostburg, Maryland, United States of America
- U.S. Geological Survey, Leetown Science Center, Aquatic Ecology Branch, Kearneysville, West Virginia, United States of America
- * E-mail:
| | - Robert H. Hilderbrand
- University of Maryland Center for Environmental Science, Appalachian Laboratory, Frostburg, Maryland, United States of America
| | - Tim L. King
- U.S. Geological Survey, Leetown Science Center, Aquatic Ecology Branch, Kearneysville, West Virginia, United States of America
| | - Stephen R. Keller
- University of Vermont, Department of Plant Biology, Burlington, Vermont, United States of America
| | - Vikram E. Chhatre
- University of Vermont, Department of Plant Biology, Burlington, Vermont, United States of America
| |
Collapse
|
37
|
Dupuis JR, Sperling FAH. Repeated Reticulate Evolution in North American Papilio machaon Group Swallowtail Butterflies. PLoS One 2015; 10:e0141882. [PMID: 26517268 PMCID: PMC4627828 DOI: 10.1371/journal.pone.0141882] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 10/14/2015] [Indexed: 01/07/2023] Open
Abstract
Hybridization between distinct populations or species is increasingly recognized as an important process for generating biodiversity. However, the interaction between hybridization and speciation is complex, and the diverse evolutionary outcomes of hybridization are difficult to differentiate. Here we characterize potential hybridization in a species group of swallowtail butterflies using microsatellites, DNA sequences, and morphology, and assess whether adaptive introgression or homoploid hybrid speciation was the primary process leading to each putative hybrid lineage. Four geographically separated hybrid populations were identified in the Papilio machaon species group. One distinct mitochondrial DNA clade from P. machaon was fixed in three hybrid taxa (P. brevicauda, P. joanae, and P. m. kahli), while one hybrid swarm (P. zelicaon x machaon) exhibited this hybrid mtDNA clade as well as widespread parental mtDNA haplotypes from both parental species. Microsatellite markers and morphology showed variable admixture and intermediacy, ranging from signatures of prolonged differential introgression from the paternal species (P. polyxenes/P. zelicaon) to current gene flow with both parental species. Divergences of the hybrid lineages dated to early- to mid-Pleistocene, suggesting that repeated glaciations and subsequent range shifts of parental species, particularly P. machaon hudsonianus, facilitated initial hybridization. Although each lineage is distinct, P. joanae is the only taxon with sufficient evidence (ecological separation from parental species) to define it as a homoploid hybrid species. The repetition of hybridization in this group provides a valuable foundation for future research on hybridization, and these results emphasize the potential for hybridization to drive speciation in diverse ways.
Collapse
Affiliation(s)
- Julian R. Dupuis
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Felix A. H. Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
38
|
Whiteley AR, Coombs JA, Cembrola M, O'Donnell MJ, Hudy M, Nislow KH, Letcher BH. Effective number of breeders provides a link between interannual variation in stream flow and individual reproductive contribution in a stream salmonid. Mol Ecol 2015; 24:3585-602. [DOI: 10.1111/mec.13273] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/03/2015] [Accepted: 06/10/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Andrew R. Whiteley
- Department of Environmental Conservation University of Massachusetts Amherst MA 01003 USA
- U.S. Forest Service Northern Research Station University of Massachusetts Amherst MA 01003 USA
| | - Jason A. Coombs
- Department of Environmental Conservation University of Massachusetts Amherst MA 01003 USA
- U.S. Forest Service Northern Research Station University of Massachusetts Amherst MA 01003 USA
| | - Matthew Cembrola
- Department of Environmental Conservation University of Massachusetts Amherst MA 01003 USA
| | - Matthew J. O'Donnell
- U.S. Geological Survey Leetown Science Center S.O. Conte Anadromous Fish Research Center Turners Falls MA 01376 USA
| | - Mark Hudy
- U.S. Geological Survey, Ecosystems 12201 Sunrise Valley Drive Reston VA 20192 USA
| | - Keith H. Nislow
- U.S. Forest Service Northern Research Station University of Massachusetts Amherst MA 01003 USA
| | - Benjamin H. Letcher
- U.S. Geological Survey Leetown Science Center S.O. Conte Anadromous Fish Research Center Turners Falls MA 01376 USA
| |
Collapse
|
39
|
Ishiyama N, Sueyoshi M, Nakamura F. To what extent do human-altered landscapes retain population connectivity? Historical changes in gene flow of wetland fish Pungitius pungitius. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150033. [PMID: 26587264 PMCID: PMC4632577 DOI: 10.1098/rsos.150033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/08/2015] [Indexed: 06/05/2023]
Abstract
Understanding how human-altered landscapes affect population connectivity is valuable for conservation planning. Natural connectivity among wetlands, which is maintained by floods, is disappearing owing to farmland expansion. Using genetic data, we assessed historical changes in the population connectivity of the ninespine stickleback within a human-altered wetland system. We predicted that: (i) the contemporary gene flow maintained by the artificial watercourse network may be restricted to a smaller spatial scale compared with the gene flow preceding alteration, and (ii) the contemporary gene flow is dominated by the downstream direction owing to the construction of low-head barriers. We evaluated the potential source population in both timescales. Seventeen studied populations were grouped into four genetically different clusters, and we estimated the migration rates among these clusters. Contemporary migration was restricted to between neighbouring clusters, although a directional change was not detected. Furthermore, we consistently found the same potential source cluster, from past to present, characterized by large amounts of remnant habitats connected by artificial watercourses. These findings highlight that: (i) artificial connectivity can sustain the short-distance connectivity of the ninespine stickleback, which contributes to maintaining the potential source populations; however, (ii) population connectivity throughout the landscape has been prevented by agricultural developments.
Collapse
Affiliation(s)
- N. Ishiyama
- Author for correspondence: N. Ishiyama e-mail:
| | | | | |
Collapse
|
40
|
Benestan L, Gosselin T, Perrier C, Sainte-Marie B, Rochette R, Bernatchez L. RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus). Mol Ecol 2015; 24:3299-315. [DOI: 10.1111/mec.13245] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 05/09/2015] [Accepted: 05/12/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Laura Benestan
- Institut de Biologie Intégrative des Systèmes (IBIS); Université Laval; Québec Quebec Canada G1V0A6
| | - Thierry Gosselin
- Institut de Biologie Intégrative des Systèmes (IBIS); Université Laval; Québec Quebec Canada G1V0A6
| | - Charles Perrier
- Institut de Biologie Intégrative des Systèmes (IBIS); Université Laval; Québec Quebec Canada G1V0A6
| | - Bernard Sainte-Marie
- Pêches et Océans Canada; Institut Maurice-Lamontagne; CP 1000 Mont-Joli Quebec Canada G5H 3Z4
| | - Rémy Rochette
- Department of Biology; University of New Brunswick; PO Box 5050 Saint John New Brunswick Canada E2L 4L5
| | - Louis Bernatchez
- Institut de Biologie Intégrative des Systèmes (IBIS); Université Laval; Québec Quebec Canada G1V0A6
| |
Collapse
|
41
|
Kanno Y, Letcher BH, Hitt NP, Boughton DA, Wofford JEB, Zipkin EF. Seasonal weather patterns drive population vital rates and persistence in a stream fish. GLOBAL CHANGE BIOLOGY 2015; 21:1856-1870. [PMID: 25523515 DOI: 10.1111/gcb.12837] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 10/24/2014] [Indexed: 06/04/2023]
Abstract
Climate change affects seasonal weather patterns, but little is known about the relative importance of seasonal weather patterns on animal population vital rates. Even when such information exists, data are typically only available from intensive fieldwork (e.g., mark-recapture studies) at a limited spatial extent. Here, we investigated effects of seasonal air temperature and precipitation (fall, winter, and spring) on survival and recruitment of brook trout (Salvelinus fontinalis) at a broad spatial scale using a novel stage-structured population model. The data were a 15-year record of brook trout abundance from 72 sites distributed across a 170-km-long mountain range in Shenandoah National Park, Virginia, USA. Population vital rates responded differently to weather and site-specific conditions. Specifically, young-of-year survival was most strongly affected by spring temperature, adult survival by elevation and per-capita recruitment by winter precipitation. Low fall precipitation and high winter precipitation, the latter of which is predicted to increase under climate change for the study region, had the strongest negative effects on trout populations. Simulations show that trout abundance could be greatly reduced under constant high winter precipitation, consistent with the expected effects of gravel-scouring flows on eggs and newly hatched individuals. However, high-elevation sites would be less vulnerable to local extinction because they supported higher adult survival. Furthermore, the majority of brook trout populations are projected to persist if high winter precipitation occurs only intermittently (≤3 of 5 years) due to density-dependent recruitment. Variable drivers of vital rates should be commonly found in animal populations characterized by ontogenetic changes in habitat, and such stage-structured effects may increase population persistence to changing climate by not affecting all life stages simultaneously. Yet, our results also demonstrate that weather patterns during seemingly less consequential seasons (e.g., winter precipitation) can have major impacts on animal population dynamics.
Collapse
Affiliation(s)
- Yoichiro Kanno
- Department of Forestry and Environmental Conservation, Clemson University, 261 Lehotsky Hall, Clemson, SC 29634, USA
| | | | | | | | | | | |
Collapse
|
42
|
Cristofari R, Trucchi E, Whittington JD, Vigetta S, Gachot-Neveu H, Stenseth NC, Le Maho Y, Le Bohec C. Spatial heterogeneity as a genetic mixing mechanism in highly philopatric colonial seabirds. PLoS One 2015; 10:e0117981. [PMID: 25680103 PMCID: PMC4332635 DOI: 10.1371/journal.pone.0117981] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 01/06/2015] [Indexed: 11/25/2022] Open
Abstract
How genetic diversity is maintained in philopatric colonial systems remains unclear, and understanding the dynamic balance of philopatry and dispersal at all spatial scales is essential to the study of the evolution of coloniality. In the King penguin, Aptenodytes patagonicus, return rates of post-fledging chicks to their natal sub-colony are remarkably high. Empirical studies have shown that adults return year after year to their previous breeding territories within a radius of a few meters. Yet, little reliable data are available on intra- and inter-colonial dispersal in this species. Here, we present the first fine-scale study of the genetic structure in a king penguin colony in the Crozet Archipelago. Samples were collected from individual chicks and analysed at 8 microsatellite loci. Precise geolocation data of hatching sites and selective pressures associated with habitat features were recorded for all sampling locations. We found that despite strong natal and breeding site fidelity, king penguins retain a high degree of panmixia and genetic diversity. Yet, genetic structure appears markedly heterogeneous across the colony, with higher-than-expected inbreeding levels, and local inbreeding and relatedness hotspots that overlap predicted higher-quality nesting locations. This points towards heterogeneous population structure at the sub-colony level, in which fine-scale environmental features drive local philopatric behaviour, while lower-quality patches may act as genetic mixing mechanisms at the colony level. These findings show how a lack of global genetic structuring can emerge from small-scale heterogeneity in ecological parameters, as opposed to the classical model of homogeneous dispersal. Our results also emphasize the importance of sampling design for estimation of population parameters in colonial seabirds, as at high spatial resolution, basic genetic features are shown to be location-dependent. Finally, this study stresses the importance of understanding intra-colonial dispersal and genetic mixing mechanisms in order to better estimate species-wide gene flows and population dynamics.
Collapse
Affiliation(s)
- Robin Cristofari
- Université de Strasbourg (UdS), Institut Pluridisciplinaire Hubert Curien, Laboratoire International Associé LIA-647 BioSensib (CSM-CNRS-UdS), Strasbourg Cedex 02, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7178, LIA-647 BioSensib, Strasbourg Cedex 02, France
- Centre Scientifique de Monaco (CSM), LIA-647 BioSensib, 8, Quai Antoine 1er, Monaco, Principality of Monaco
- University of Oslo, Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, Postboks 1066, Blindern, Oslo, Norway
| | - Emiliano Trucchi
- University of Oslo, Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, Postboks 1066, Blindern, Oslo, Norway
| | - Jason D. Whittington
- Université de Strasbourg (UdS), Institut Pluridisciplinaire Hubert Curien, Laboratoire International Associé LIA-647 BioSensib (CSM-CNRS-UdS), Strasbourg Cedex 02, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7178, LIA-647 BioSensib, Strasbourg Cedex 02, France
- Centre Scientifique de Monaco (CSM), LIA-647 BioSensib, 8, Quai Antoine 1er, Monaco, Principality of Monaco
- University of Oslo, Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, Postboks 1066, Blindern, Oslo, Norway
| | - Stéphanie Vigetta
- Université de Strasbourg (UdS), Institut Pluridisciplinaire Hubert Curien, Laboratoire International Associé LIA-647 BioSensib (CSM-CNRS-UdS), Strasbourg Cedex 02, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7178, LIA-647 BioSensib, Strasbourg Cedex 02, France
| | - Hélène Gachot-Neveu
- Université de Strasbourg (UdS), Institut Pluridisciplinaire Hubert Curien, Laboratoire International Associé LIA-647 BioSensib (CSM-CNRS-UdS), Strasbourg Cedex 02, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7178, LIA-647 BioSensib, Strasbourg Cedex 02, France
| | - Nils Christian Stenseth
- University of Oslo, Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, Postboks 1066, Blindern, Oslo, Norway
| | - Yvon Le Maho
- Université de Strasbourg (UdS), Institut Pluridisciplinaire Hubert Curien, Laboratoire International Associé LIA-647 BioSensib (CSM-CNRS-UdS), Strasbourg Cedex 02, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7178, LIA-647 BioSensib, Strasbourg Cedex 02, France
- Centre Scientifique de Monaco (CSM), LIA-647 BioSensib, 8, Quai Antoine 1er, Monaco, Principality of Monaco
| | - Céline Le Bohec
- Centre Scientifique de Monaco (CSM), LIA-647 BioSensib, 8, Quai Antoine 1er, Monaco, Principality of Monaco
- University of Oslo, Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, Postboks 1066, Blindern, Oslo, Norway
| |
Collapse
|
43
|
Winans GA, Gayeski N, Timmins-Schiffman E. All dam-affected trout populations are not alike: fine scale geographic variability in resident rainbow trout in Icicle Creek, WA, USA. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0659-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
44
|
River mainstem thermal regimes influence population structuring within an appalachian brook trout population. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0636-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
45
|
|
46
|
Fitzpatrick SW, Crockett H, Funk WC. Water availability strongly impacts population genetic patterns of an imperiled Great Plains endemic fish. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0577-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
47
|
Unger SD, Rhodes OE, Sutton TM, Williams RN. Population genetics of the Eastern Hellbender (Cryptobranchus alleganiensis alleganiensis) across multiple spatial scales. PLoS One 2013; 8:e74180. [PMID: 24204565 PMCID: PMC3800131 DOI: 10.1371/journal.pone.0074180] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/28/2013] [Indexed: 02/07/2023] Open
Abstract
Conservation genetics is a powerful tool to assess the population structure of species and provides a framework for informing management of freshwater ecosystems. As lotic habitats become fragmented, the need to assess gene flow for species of conservation management becomes a priority. The eastern hellbender (Cryptobranchus alleganiensis alleganiensis) is a large, fully aquatic paedamorphic salamander. Many populations are experiencing declines throughout their geographic range, yet the genetic ramifications of these declines are currently unknown. To this end, we examined levels of genetic variation and genetic structure at both range-wide and drainage (hierarchical) scales. We collected 1,203 individuals from 77 rivers throughout nine states from June 2007 to August 2011. Levels of genetic diversity were relatively high among all sampling locations. We detected significant genetic structure across populations (Fst values ranged from 0.001 between rivers within a single watershed to 0.218 between states). We identified two genetically differentiated groups at the range-wide scale: 1) the Ohio River drainage and 2) the Tennessee River drainage. An analysis of molecular variance (AMOVA) based on landscape-scale sampling of basins within the Tennessee River drainage revealed the majority of genetic variation (∼94-98%) occurs within rivers. Eastern hellbenders show a strong pattern of isolation by stream distance (IBSD) at the drainage level. Understanding levels of genetic variation and differentiation at multiple spatial and biological scales will enable natural resource managers to make more informed decisions and plan effective conservation strategies for cryptic, lotic species.
Collapse
Affiliation(s)
- Shem D. Unger
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, United States of America
- * E-mail:
| | - Olin E. Rhodes
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, United States of America
| | - Trent M. Sutton
- School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Rod N. Williams
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| |
Collapse
|
48
|
Perrier C, Guyomard R, Bagliniere JL, Nikolic N, Evanno G. Changes in the genetic structure of Atlantic salmon populations over four decades reveal substantial impacts of stocking and potential resiliency. Ecol Evol 2013; 3:2334-49. [PMID: 23919174 PMCID: PMC3728969 DOI: 10.1002/ece3.629] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 04/28/2013] [Accepted: 05/06/2013] [Indexed: 01/08/2023] Open
Abstract
While the stocking of captive-bred fish has been occurring for decades and has had substantial immediate genetic and evolutionary impacts on wild populations, its long-term consequences have only been weakly investigated. Here, we conducted a spatiotemporal analysis of 1428 Atlantic salmon sampled from 1965 to 2006 in 25 populations throughout France to investigate the influence of stocking on the neutral genetic structure in wild Atlantic salmon (Salmo salar) populations. On the basis of the analysis of 11 microsatellite loci, we found that the overall genetic structure among populations dramatically decreased over the period studied. Admixture rates among populations were highly variable, ranging from a nearly undetectable contribution from donor stocks to total replacement of the native gene pool, suggesting extremely variable impacts of stocking. Depending on population, admixture rates either increased, remained stable, or decreased in samples collected between 1998 and 2006 compared to samples from 1965 to 1987, suggesting either rising, long-lasting or short-term impacts of stocking. We discuss the potential mechanisms contributing to this variability, including the reduced fitness of stocked fish and persistence of wild locally adapted individuals.
Collapse
Affiliation(s)
- Charles Perrier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, Canada ; INRA, UMR 0985 Ecology and Health of Ecosystems 35042, Rennes, France ; Agrocampus Ouest 65 rue de Saint-Brieuc, 35042, Rennes, France ; INRA, UMR 1313 Génétique Animale et Biologie Intégrative F-78350, Jouy-en-Josas, France
| | | | | | | | | |
Collapse
|
49
|
Henry P, Sim Z, Russello MA. Genetic evidence for restricted dispersal along continuous altitudinal gradients in a climate change-sensitive mammal: the American Pika. PLoS One 2012; 7:e39077. [PMID: 22720034 PMCID: PMC3376113 DOI: 10.1371/journal.pone.0039077] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 05/15/2012] [Indexed: 11/24/2022] Open
Abstract
When faced with rapidly changing environments, wildlife species are left to adapt, disperse or disappear. Consequently, there is value in investigating the connectivity of populations of species inhabiting different environments in order to evaluate dispersal as a potential strategy for persistence in the face of climate change. Here, we begin to investigate the processes that shape genetic variation within American pika populations from the northern periphery of their range, the central Coast Mountains of British Columbia, Canada. At these latitudes, pikas inhabit sharp elevation gradients ranging from sea level to 1500 m, providing an excellent system for studying the effects of local environmental conditions on pika population genetic structure and gene flow. We found low levels of neutral genetic variation compared to previous studies from more southerly latitudes, consistent with the relatively recent post-glacial colonization of the study location. Moreover, significant levels of inbreeding and marked genetic structure were detected within and among sites. Although low levels of recent gene flow were revealed among elevations within a transect, potentially admixed individuals and first generation migrants were identified using discriminant analysis of principal components between populations separated by less than five kilometers at the same elevations. There was no evidence for historical population decline, yet there was signal for recent demographic contractions, possibly resulting from environmental stochasticity. Correlative analyses revealed an association between patterns of genetic variation and annual heat-to-moisture ratio, mean annual precipitation, precipitation as snow and mean maximum summer temperature. Changes in climatic regimes forecasted for the region may thus potentially increase the rate of population extirpation by further reducing dispersal between sites. Consequently, American pika may have to rely on local adaptations or phenotypic plasticity in order to survive predicted climate changes, although additional studies are required to investigate the evolutionary potential of this climate change sensitive species.
Collapse
Affiliation(s)
- Philippe Henry
- Department of Biology, University of British Columbia, Okanagan campus, Kelowna, British Columbia, Canada
- * E-mail:
| | - Zijian Sim
- Department of Biology, University of British Columbia, Okanagan campus, Kelowna, British Columbia, Canada
| | - Michael A. Russello
- Department of Biology, University of British Columbia, Okanagan campus, Kelowna, British Columbia, Canada
| |
Collapse
|
50
|
STELKENS RIKEB, JAFFUEL GEOFFREY, ESCHER MATTHIAS, WEDEKIND CLAUS. Genetic and phenotypic population divergence on a microgeographic scale in brown trout. Mol Ecol 2012; 21:2896-915. [DOI: 10.1111/j.1365-294x.2012.05581.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|