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Diaz-Martin Z, Cisternas-Fuentes A, Kay KM, Raguso RA, Skogen K, Fant J. Reproductive strategies and their consequences for divergence, gene flow, and genetic diversity in three taxa of Clarkia. Heredity (Edinb) 2023; 131:338-349. [PMID: 37700028 PMCID: PMC10673949 DOI: 10.1038/s41437-023-00649-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/14/2023] Open
Abstract
Differences in reproductive strategies can have important implications for macro- and micro-evolutionary processes. We used a comparative approach through a population genetics lens to evaluate how three distinct reproductive strategies shape patterns of divergence among as well as gene flow and genetic diversity within three closely related taxa in the genus Clarkia. One taxon is a predominantly autonomous self-fertilizer and the other two taxa are predominantly outcrossing but vary in the primary pollinator they attract. In genotyping populations using genotyping-by-sequencing and comparing loci shared across taxa, our results suggest that differences in reproductive strategies in part promote evolutionary divergence among these closely related taxa. Contrary to expectations, we found that the selfing taxon had the highest levels of heterozygosity but a low rate of polymorphism. The high levels of fixed heterozygosity for a subset of loci suggests this pattern is driven by the presence of structural rearrangements in chromosomes common in other Clarkia taxa. In evaluating patterns within taxa, we found a complex interplay between reproductive strategy and geographic distribution. Differences in the mobility of primary pollinators did not translate to a difference in rates of genetic diversity and gene flow within taxa - a pattern likely due to one taxon having a patchier distribution and a less temporally and spatially reliable pollinator. Taken together, this work advances our understanding of the factors that shape gene flow and the distribution of genetic diversity within and among closely related taxa.
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Affiliation(s)
- Zoe Diaz-Martin
- Department of Biology, Spelman College, Atlanta, GA, 30314, USA.
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60035, USA.
| | - Anita Cisternas-Fuentes
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60035, USA
- Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, IL, 60208, USA
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, 130 McAllister Way, Santa Cruz, CA, 95060, USA
| | - Robert A Raguso
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Krissa Skogen
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60035, USA
- Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, IL, 60208, USA
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29631, USA
| | - Jeremie Fant
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60035, USA
- Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, IL, 60208, USA
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Lagunas M, Pálsson A, Jónsson B, Jóhannsson M, Jónsson ZO, Snorrason SS. Genetic structure and relatedness of brown trout ( Salmo trutta) populations in the drainage basin of the Ölfusá river, South-Western Iceland. PeerJ 2023; 11:e15985. [PMID: 37692111 PMCID: PMC10487600 DOI: 10.7717/peerj.15985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/08/2023] [Indexed: 09/12/2023] Open
Abstract
Background Lake Þingvallavatn in Iceland, a part of the river Ölfusá drainage basin, was presumably populated by brown trout soon after it formed at the end of the last Ice Age. The genetic relatedness of the brown trout in Þingvallavatn to other populations in the Ölfusá drainage basin is unknown. After the building of a dam at the outlet of the lake in 1959 brown trout catches declined, though numbers have now increased. The aim of this study was to assess effects of geographic isolation and potential downstream gene flow on the genetic structure and diversity in brown trout sampled in several locations in the western side of the watershed of River Ölfusá. We hypothesized that brown trout in Lake Þingvallavatn constituted several local spawning populations connected by occasional gene flow before the damming of the lake. We also estimated the effective population size (NE) of some of these populations and tested for signs of a recent population bottleneck in Lake Þingvallavatn. Methods We sampled brown trout inhabiting four lakes and 12 rivers within and near the watershed of River Ölfusá by means of electro- and net- fishing. After stringent data filtering, 2,597 polymorphic loci obtained from ddRADseq data from 317 individuals were ascertained as putative neutral markers. Results Overall, the genetic relatedness of brown trout in the Ölfusá watershed reflected the connectivity and topography of the waterways. Ancestry proportion analyses and a phylogenetic tree revealed seven distinct clusters, some of which corresponded to small populations with reduced genetic diversity. There was no evidence of downstream gene flow from Lake Þingvallavatn, although gene flow was observed from much smaller mountain populations. Most locations showed low NE values (i.e., ~14.6 on average) while the putative anadromous trout from River Sog and the spawning population from River Öxará, that flows into Lake Þingvallavatn, showed notably higher NE values (i.e., 71.2 and 56.5, respectively). No signals of recent population bottlenecks were detected in the brown trout of Lake Þingvallavatn. Discussion This is the first time that the genetic structure and diversity of brown trout in the watershed of River Ölfusá have been assessed. Our results point towards the presence of a metapopulation in the watershed of Lake Þingvallavatn, which has been influenced by restoration efforts and is now dominated by a genetic component originated in River Öxará. Many of the locations studied represent different populations. Those that are isolated in headwater streams and lakes are genetically distinct presenting low genetic diversity, yet they can be important in increasing the genetic variation in downstream populations. These populations should be considered for conservation and direct management.
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Affiliation(s)
- Marcos Lagunas
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Arnar Pálsson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Benóný Jónsson
- Marine and Freshwater Research Institute, Selfoss, Iceland
| | | | - Zophonías O. Jónsson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Sigurður S. Snorrason
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
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King E, McPhee MV, Vulstek SC, Cunningham CJ, Russell JR, Tallmon DA. Alternative life-history strategy contributions to effective population size in a naturally spawning salmon population. Evol Appl 2023; 16:1472-1482. [PMID: 37622095 PMCID: PMC10445090 DOI: 10.1111/eva.13580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 08/26/2023] Open
Abstract
Alternative life-history tactics are predicted to affect within-population genetic processes but have received little attention. For example, the impact of precocious males on effective population size (N e) has not been quantified directly in Pacific salmon Oncorhynchus spp., even though they can make up a large percentage of the total male spawners. We investigated the contribution of precocial males ("jacks") to N e in a naturally spawning population of Coho Salmon O. kisutch from the Auke Creek watershed in Juneau, Alaska. Mature adults that returned from 2009 to 2019 (~8000 individuals) were genotyped at 259 single-nucleotide polymorphism (SNP) loci for parentage analysis. We used demographic and genetic methods to estimate the effective number of breeders per year (N b). Jack contribution to N b was assessed by comparing values of N b calculated with and without jacks and their offspring. Over a range of N b values (108-406), the average jack contribution to N b from 2009 to 2015 was 12.9% (SE = 3.8%). Jacks consistently made up over 20% of the total male spawners. The presence of jacks did not seem to influence N b/N. The linkage disequilibrium N e estimate was lower than the demographic estimate, possibly due to immigration effects on population genetic processes: based on external marks and parentage data, we estimated that immigrant spawners produced 4.5% of all returning offspring. Our results demonstrate that jacks can influence N b and N e and can make a substantial contribution to population dynamics and conservation of threatened stocks.
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Affiliation(s)
- Erika King
- College of Fisheries and Ocean SciencesUniversity of AlaskaFairbanksAlaskaUSA
| | - Megan V. McPhee
- College of Fisheries and Ocean SciencesUniversity of AlaskaFairbanksAlaskaUSA
| | | | - Curry J. Cunningham
- College of Fisheries and Ocean SciencesUniversity of AlaskaFairbanksAlaskaUSA
| | | | - David A. Tallmon
- College of Fisheries and Ocean SciencesUniversity of AlaskaFairbanksAlaskaUSA
- Biology and Marine Biology ProgramUniversity of Alaska SoutheastJuneauAlaskaUSA
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Hemstrom W, Dauwalter D, Peacock M, Leasure D, Wenger S, Miller M, Neville. Population genomic monitoring provides insight into conservation status but no correlation with demographic estimates of extinction risk in a threatened trout. Evol Appl 2022; 15:1449-1468. [PMID: 36187186 PMCID: PMC9488680 DOI: 10.1111/eva.13473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/12/2022] [Indexed: 12/03/2022] Open
Abstract
The current extinction crisis requires effective assessment and monitoring tools. Genetic approaches are appealing given the relative ease of field sampling required to estimate genetic diversity characteristics assumed related to population size, evolutionary potential, and extinction risk, and to evaluate hybridization with non‐native species simultaneously. However, linkages between population genetic metrics of diversity from survey‐style field collections and demographic estimates of population size and extinction risk are still in need of empirical examples, especially for remotely distributed species of conservation concern where the approach might be most beneficial. We capitalized on an exceptional opportunity to evaluate congruence between genetic diversity metrics and demographic‐based estimates of abundance and extinction risk from a comprehensive Multiple Population Viability Analysis (MPVA) in a threatened fish, the Lahontan cutthroat trout (LCT). We sequenced non‐native trout reference samples and recently collected and archived tissue samples of most remaining populations of LCT (N = 60) and estimated common genetic assessment metrics, predicting minimal hybridization with non‐native trout, low diversity, and declining diversity over time. We further hypothesized genetic metrics would correlate positively with MPVA‐estimated abundance and negatively with extinction probability. We uncovered several instances of hybridization that pointed to immediate management needs. After removing hybridized individuals, cautious interpretation of low effective population sizes (2–63) suggested reduced evolutionary potential for many LCT populations. Other genetic metrics did not decline over time nor correlate with MPVA‐based estimates of harmonic mean abundance or 30‐year extinction probability. Our results demonstrate benefits of genetic monitoring for efficiently detecting hybridization and, though genetic results were disconnected from demographic assessment of conservation status, they suggest reduced evolutionary potential and likely a higher conservation risk than currently recognized for this threatened fish. We emphasize that genetic information provides essential complementary insight, in addition to demographic information, for evaluating species status.
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Affiliation(s)
- W. Hemstrom
- Department of Animal Science University of California Davis California U.S.A
| | | | - M. Peacock
- Department of Biology University of Nevada Reno Nevada U.S.A
| | - D. Leasure
- WorldPop, Geography and Environmental Science University of Southampton Southampton United Kingdom
| | - S. Wenger
- Odum School of Ecology University of Georgia Athens GA U.S.A
| | - M. Miller
- Department of Animal Science University of California Davis California U.S.A
| | - Neville
- Science Program, Trout Unlimited Boise ID U.S.A
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Gompert Z, Springer A, Brady M, Chaturvedi S, Lucas LK. Genomic time-series data show that gene flow maintains high genetic diversity despite substantial genetic drift in a butterfly species. Mol Ecol 2021; 30:4991-5008. [PMID: 34379852 DOI: 10.1111/mec.16111] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
Effective population size affects the efficacy of selection, rate of evolution by drift, and neutral diversity levels. When species are subdivided into multiple populations connected by gene flow, evolutionary processes can depend on global or local effective population sizes. Theory predicts that high levels of diversity might be maintained by gene flow, even very low levels of gene flow, consistent with species long-term effective population size, but tests of this idea are mostly lacking. Here, we show that Lycaeides buttery populations maintain low contemporary (variance) effective population sizes (e.g., ~200 individuals) and thus evolve rapidly by genetic drift. In contrast, populations harbored high levels of genetic diversity consistent with an effective population size several orders of magnitude larger. We hypothesized that the differences in the magnitude and variability of contemporary versus long-term effective population sizes were caused by gene flow of sufficient magnitude to maintain diversity but only subtly affect evolution on generational time scales. Consistent with this hypothesis, we detected low but non-trivial gene flow among populations. Furthermore, using short-term population-genomic time-series data, we documented patterns consistent with predictions from this hypothesis, including a weak but detectable excess of evolutionary change in the direction of the mean (migrant gene pool) allele frequencies across populations, and consistency in the direction of allele frequency change over time. The documented decoupling of diversity levels and short-term change by drift in Lycaeides has implications for our understanding of contemporary evolution and the maintenance of genetic variation in the wild.
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Affiliation(s)
- Zachariah Gompert
- Department of Biology, Utah State University, Logan, UT, 84322, USA.,Ecology Center, Utah State University, Logan, UT, 84322, USA
| | - Amy Springer
- Department of Biology, Utah State University, Logan, UT, 84322, USA
| | - Megan Brady
- Department of Biology, Utah State University, Logan, UT, 84322, USA
| | - Samridhi Chaturvedi
- Department of Biology, Utah State University, Logan, UT, 84322, USA.,Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Lauren K Lucas
- Department of Biology, Utah State University, Logan, UT, 84322, USA
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Duval E, Skaala Ø, Quintela M, Dahle G, Delaval A, Wennevik V, Glover KA, Hansen MM. Long-term monitoring of a brown trout (Salmo trutta) population reveals kin-associated migration patterns and contributions by resident trout to the anadromous run. BMC Ecol Evol 2021; 21:143. [PMID: 34256705 PMCID: PMC8276402 DOI: 10.1186/s12862-021-01876-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/02/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND In species showing partial migration, as is the case for many salmonid fishes, it is important to assess how anthropogenic pressure experienced by migrating individuals affects the total population. We focused on brown trout (Salmo trutta) from the Guddal River in the Norwegian Hardanger Fjord system, which encompasses both resident and anadromous individuals. Aquaculture has led to increased anthropogenic pressure on brown trout during the marine phase in this region. Fish traps in the Guddal River allow for sampling all ascending anadromous spawners and descending smolts. We analyzed microsatellite DNA markers from all individuals ascending in 2006-2016, along with all emigrating smolts in 2017. We investigated (1) if there was evidence for declines in census numbers and effective population size during that period, (2) if there was association between kinship and migration timing in smolts and anadromous adults, and (3) to what extent resident trout were parents of outmigrating smolts. RESULTS Census counts of anadromous spawners showed no evidence for a decline from 2006 to 2016, but were lower than in 2000-2005. Estimates of effective population size also showed no trends of declines during the study period. Sibship reconstruction of the 2017 smolt run showed significant association between kinship and migration timing, and a similar association was indicated in anadromous spawners. Parentage assignment of 2017 smolts with ascending anadromous trout as candidate parents, and assuming that unknown parents represented resident trout, showed that 70% of smolts had at least one resident parent and 24% had two resident parents. CONCLUSIONS The results bear evidence of a population that after an initial decline has stabilized at a lower number of anadromous spawners. The significant association between kinship and migration timing in smolts suggests that specific episodes of elevated mortality in the sea could disproportionally affect some families and reduce overall effective population size. Finally, the results based on parentage assignment demonstrate a strong buffering effect of resident trout in case of elevated marine mortality affecting anadromous trout, but also highlight that increased mortality of anadromous trout, most of which are females, may lower overall production in the system.
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Affiliation(s)
- Eloïse Duval
- Department of Biology, Aarhus University, Ny Munkegade 114, 8000, Aarhus C, Denmark.
- Theoretical and Experimental Ecology Station, UMR-5321, CNRS, University of Toulouse III Paul Sabatier, 2 route du CNRS, 09200, Moulis, France.
| | - Øystein Skaala
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway.
| | - María Quintela
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
| | - Geir Dahle
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
| | - Aurélien Delaval
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Vidar Wennevik
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
| | - Kevin A Glover
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
- Institute of Biology, University of Bergen, Bergen, Norway
| | - Michael M Hansen
- Department of Biology, Aarhus University, Ny Munkegade 114, 8000, Aarhus C, Denmark.
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway.
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Nadachowska-Brzyska K, Dutoit L, Smeds L, Kardos M, Gustafsson L, Ellegren H. Genomic inference of contemporary effective population size in a large island population of collared flycatchers (Ficedula albicollis). Mol Ecol 2021; 30:3965-3973. [PMID: 34145933 DOI: 10.1111/mec.16025] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/30/2022]
Abstract
Due to its central importance to many aspects of evolutionary biology and population genetics, the long-term effective population size (Ne ) has been estimated for numerous species and populations. However, estimating contemporary Ne is difficult and in practice this parameter is often unknown. In principle, contemporary Ne can be estimated using either analyses of temporal changes in allele frequencies, or the extent of linkage disequilibrium (LD) between unlinked markers. We applied these approaches to estimate contemporary Ne of a relatively recently founded island population of collared flycatchers (Ficedula albicollis). We sequenced the genomes of 85 birds sampled in 1993 and 2015, and applied several temporal methods to estimate Ne at a few thousand (4000-7000). The approach based on LD provided higher estimates of Ne (20,000-32,000) and was associated with high variance, often resulting in infinite Ne . We conclude that whole-genome sequencing data offers new possibilities to estimate high (>1000) contemporary Ne , but also note that such estimates remain challenging, in particular for LD-based methods for contemporary Ne estimation.
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Affiliation(s)
- Krystyna Nadachowska-Brzyska
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Ludovic Dutoit
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Martin Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Lars Gustafsson
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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Škraba Jurlina D, Marić A, Mrdak D, Kanjuh T, Špelić I, Nikolić V, Piria M, Simonović P. Alternative Life-History in Native Trout (Salmo spp.) Suppresses the Invasive Effect of Alien Trout Strains Introduced Into Streams in the Western Part of the Balkans. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Francisco SM, Robalo JI. Time matters: genetic composition and evaluation of effective population size in temperate coastal fish species. PeerJ 2020; 8:e9098. [PMID: 32391212 PMCID: PMC7197400 DOI: 10.7717/peerj.9098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/09/2020] [Indexed: 12/16/2022] Open
Abstract
Background Extensive knowledge on the genetic characterization of marine organisms has been assembled, mainly concerning the spatial distribution and structuring of populations. Temporal monitoring assesses not only the stability in genetic composition but also its trajectory over time, providing critical information for the accurate forecast of changes in genetic diversity of marine populations, particularly important for both fisheries and endangered species management. We assessed fluctuations in genetic composition among different sampling periods in the western Portuguese shore in three fish species. Methods White seabream Diplodus sargus, sand smelt Atherina presbyter and shanny Lipophrys pholis were chosen, because of their genetic patterns in distinct ecological environments, insight into historical and contemporary factors influencing population effective size (Ne), and degree of commercial exploitation. Samples were obtained near Lisbon between 2003 and 2014 and screened for genetic variation with mitochondrial and nuclear markers. Analyses included genealogies, genetic diversities, temporal structures and contemporary Ne. Results For mtDNA no temporal structure was detected, while for nDNA significant differences were recorded between some sampling periods for the shanny and the sand smelt. Haplotype networks revealed deep genealogies, with various levels of diversification. The shanny revealed a smaller Ne/generation when compared to the other species, which, in turn, revealed no evidence of genetic drift for most study periods. These results highlight the fact that temporal variations in genetic pool composition should be considered when evaluating the population structure of fish species with long distance dispersal, which are more vulnerable to recruitment fluctuations.
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Affiliation(s)
- Sara M Francisco
- MARE-Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, Lisbon, Portugal
| | - Joana I Robalo
- MARE-Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, Lisbon, Portugal
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Prodöhl PA, Ferguson A, Bradley CR, Ade R, Roberts C, Keay EJ, Costa AR, Hynes R. Impacts of acidification on brown trout Salmo trutta populations and the contribution of stocking to population recovery and genetic diversity. JOURNAL OF FISH BIOLOGY 2019; 95:719-742. [PMID: 31111501 PMCID: PMC6852074 DOI: 10.1111/jfb.14054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 05/20/2019] [Indexed: 05/25/2023]
Abstract
Anthropogenic acidification in SW-Scotland, from the early 19th Century onwards, led to the extinction of several loch (lake) brown trout (Salmo trutta) populations and substantial reductions in numbers in many others. Higher altitude populations with no stocking influence, which are isolated above natural and artificial barriers and subjected to the greatest effect of acidification, exhibited the least intrapopulation genetic diversity (34% of the allelic richness of the populations accessible to anadromous S. trutta). These, however, were characterised by the greatest interpopulation divergence (highest pairwise DEST 0.61 and FST 0.53 in contemporary samples) based on 16 microsatellite loci and are among the most differentiated S. trutta populations in NW-Europe. Five lochs above impassable waterfalls, where S. trutta were thought to be extinct, are documented as having been stocked in the late 1980s or 1990s. All five lochs now support self-sustaining S. trutta populations; three as a direct result of restoration stocking and two adjoining lochs largely arising from a small remnant wild population in one, but with some stocking input. The genetically unique Loch Grannoch S. trutta, which has been shown to have a heritable increased tolerance to acid conditions, was successfully used as a donor stock to restore populations in two acidic lochs. Loch Fleet S. trutta, which were re-established from four separate donor sources in the late 1980s, showed differential contribution from these ancestors and a higher genetic diversity than all 17 natural loch populations examined in the area. Genetically distinct inlet and outlet spawning S. trutta populations were found in this loch. Three genetically distinct sympatric populations of S. trutta were identified in Loch Grannoch, most likely representing recruitment from the three main spawning rivers. A distinct genetic signature of Loch Leven S. trutta, the progenitor of many Scottish farm strains, facilitated detection of stocking with these strains. One artificially created loch was shown to have a population genetically very similar to Loch Leven S. trutta. In spite of recorded historical supplemental stocking with Loch Leven derived farm strains, much of the indigenous S. trutta genetic diversity in the area remains intact, aside from the effects of acidification induced bottlenecks. Overall genetic diversity and extant populations have been increased by allochthonous stocking.
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Affiliation(s)
- Paulo A. Prodöhl
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
| | - Andrew Ferguson
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
| | - Caroline R. Bradley
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
| | - Robin Ade
- Dalry, Dumfries & GallowayScotlandUK
| | | | - E. J. Keay
- Marine Scotland, Freshwater Laboratory, FaskallyPitlochryUK
| | - Artur R. Costa
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
| | - Rosaleen Hynes
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
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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.
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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
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12
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The genetic characterization of an isolated remnant population of an endangered rodent (Cricetus cricetus L.) using comparative data: implications for conservation. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0925-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution. Genetics 2016; 204:723-735. [PMID: 27542959 PMCID: PMC5068858 DOI: 10.1534/genetics.116.191197] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/30/2016] [Indexed: 01/22/2023] Open
Abstract
The effective population size (Ne) is a major factor determining allele frequency changes in natural and experimental populations. Temporal methods provide a powerful and simple approach to estimate short-term Ne. They use allele frequency shifts between temporal samples to calculate the standardized variance, which is directly related to Ne. Here we focus on experimental evolution studies that often rely on repeated sequencing of samples in pools (Pool-seq). Pool-seq is cost-effective and often outperforms individual-based sequencing in estimating allele frequencies, but it is associated with atypical sampling properties: Additional to sampling individuals, sequencing DNA in pools leads to a second round of sampling, which increases the variance of allele frequency estimates. We propose a new estimator of Ne, which relies on allele frequency changes in temporal data and corrects for the variance in both sampling steps. In simulations, we obtain accurate Ne estimates, as long as the drift variance is not too small compared to the sampling and sequencing variance. In addition to genome-wide Ne estimates, we extend our method using a recursive partitioning approach to estimate Ne locally along the chromosome. Since the type I error is controlled, our method permits the identification of genomic regions that differ significantly in their Ne estimates. We present an application to Pool-seq data from experimental evolution with Drosophila and provide recommendations for whole-genome data. The estimator is computationally efficient and available as an R package at https://github.com/ThomasTaus/Nest.
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14
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Kamath PL, Haroldson MA, Luikart G, Paetkau D, Whitman C, Manen FT. Multiple estimates of effective population size for monitoring a long‐lived vertebrate: an application to
Y
ellowstone grizzly bears. Mol Ecol 2015; 24:5507-21. [DOI: 10.1111/mec.13398] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/17/2015] [Accepted: 09/17/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Pauline L. Kamath
- U.S. Geological Survey Northern Rocky Mountain Science Center 2327 University Way, Suite 2 Bozeman MT 59715 USA
| | - Mark A. Haroldson
- U.S. Geological Survey Northern Rocky Mountain Science Center 2327 University Way, Suite 2 Bozeman MT 59715 USA
| | - Gordon Luikart
- Flathead Lake Biological Station Fish and Wildlife Genomics Group Division of Biological Sciences University of Montana Missoula MT 59812 USA
| | - David Paetkau
- Wildlife Genetics International Box 274 Nelson British Columbia V1L 5P9 Canada
| | - Craig Whitman
- U.S. Geological Survey Northern Rocky Mountain Science Center 2327 University Way, Suite 2 Bozeman MT 59715 USA
| | - Frank T. Manen
- U.S. Geological Survey Northern Rocky Mountain Science Center 2327 University Way, Suite 2 Bozeman MT 59715 USA
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15
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McCartney-Melstad E, Shaffer HB. Amphibian molecular ecology and how it has informed conservation. Mol Ecol 2015; 24:5084-109. [PMID: 26437125 DOI: 10.1111/mec.13391] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 02/02/2023]
Abstract
Molecular ecology has become one of the key tools in the modern conservationist's kit. Here we review three areas where molecular ecology has been applied to amphibian conservation: genes on landscapes, within-population processes, and genes that matter. We summarize relevant analytical methods, recent important studies from the amphibian literature, and conservation implications for each section. Finally, we include five in-depth examples of how molecular ecology has been successfully applied to specific amphibian systems.
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Affiliation(s)
- Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
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16
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Ozerov M, Jürgenstein T, Aykanat T, Vasemägi A. Use of sibling relationship reconstruction to complement traditional monitoring in fisheries management and conservation of brown trout. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2015; 29:1164-1175. [PMID: 25773302 DOI: 10.1111/cobi.12480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/20/2014] [Indexed: 06/04/2023]
Abstract
Declining trends in the abundance of many fish urgently call for more efficient and informative monitoring methods that would provide necessary demographic data for the evaluation of existing conservation, restoration, and management actions. We investigated how genetic sibship reconstruction from young-of-the-year brown trout (Salmo trutta L.) juveniles provides valuable, complementary demographic information that allowed us to disentangle the effects of habitat quality and number of breeders on juvenile density. We studied restored (n = 15) and control (n = 15) spawning and nursery habitats in 16 brown trout rivers and streams over 2 consecutive years to evaluate the effectiveness of habitat restoration activities. Similar juvenile densities both in restored and control spawning and nursery grounds were observed. Similarly, no differences in the effective number of breeders, Nb(SA) , were detected between habitats, indicating that brown trout readily used recently restored spawning grounds. Only a weak relationship between the Nb(SA) and juvenile density was observed, suggesting that multiple factors affect juvenile abundance. In some areas, very low estimates of Nb(SA) were found at sites with high juvenile density, indicating that a small number of breeders can produce a high number of progeny in favorable conditions. In other sites, high Nb(SA) estimates were associated with low juvenile density, suggesting low habitat quality or lack of suitable spawning substrate in relation to available breeders. Based on these results, we recommend the incorporation of genetic sibship reconstruction to ongoing and future fish evaluation and monitoring programs to gain novel insights into local demographic and evolutionary processes relevant for fisheries management, habitat restoration, and conservation.
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Affiliation(s)
- Mikhail Ozerov
- Division of Genetics and Physiology, Department of Biology, University of Turku, 20014, Turku, Finland
| | - Tauno Jürgenstein
- Department of Aquaculture, Institute of Veterinary Medicine and Animal Science, Estonian University of Life Sciences, 51014, Tartu, Estonia
| | - Tutku Aykanat
- Division of Genetics and Physiology, Department of Biology, University of Turku, 20014, Turku, Finland
| | - Anti Vasemägi
- Division of Genetics and Physiology, Department of Biology, University of Turku, 20014, Turku, Finland
- Department of Aquaculture, Institute of Veterinary Medicine and Animal Science, Estonian University of Life Sciences, 51014, Tartu, Estonia
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17
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Gilbert KJ, Whitlock MC. Evaluating methods for estimating local effective population size with and without migration. Evolution 2015; 69:2154-66. [DOI: 10.1111/evo.12713] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 06/16/2015] [Accepted: 06/20/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Kimberly J. Gilbert
- Department of Zoology; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Michael C. Whitlock
- Department of Zoology; University of British Columbia; Vancouver BC V6T 1Z4 Canada
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18
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Arizmendi-Mejía R, Linares C, Garrabou J, Antunes A, Ballesteros E, Cebrian E, Díaz D, Ledoux JB. Combining genetic and demographic data for the conservation of a Mediterranean marine habitat-forming species. PLoS One 2015; 10:e0119585. [PMID: 25774522 PMCID: PMC4361678 DOI: 10.1371/journal.pone.0119585] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 01/14/2015] [Indexed: 11/19/2022] Open
Abstract
The integration of ecological and evolutionary data is highly valuable for conservation planning. However, it has been rarely used in the marine realm, where the adequate design of marine protected areas (MPAs) is urgently needed. Here, we examined the interacting processes underlying the patterns of genetic structure and demographic strucuture of a highly vulnerable Mediterranean habitat-forming species (i.e. Paramuricea clavata (Risso, 1826)), with particular emphasis on the processes of contemporary dispersal, genetic drift, and colonization of a new population. Isolation by distance and genetic discontinuities were found, and three genetic clusters were detected; each submitted to variations in the relative impact of drift and gene flow. No founder effect was found in the new population. The interplay of ecology and evolution revealed that drift is strongly impacting the smallest, most isolated populations, where partial mortality of individuals was highest. Moreover, the eco-evolutionary analyses entailed important conservation implications for P. clavata. Our study supports the inclusion of habitat-forming organisms in the design of MPAs and highlights the need to account for genetic drift in the development of MPAs. Moreover, it reinforces the importance of integrating genetic and demographic data in marine conservation.
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Affiliation(s)
- Rosana Arizmendi-Mejía
- Departament d´Ecologia, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028, Barcelona, Spain
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Cristina Linares
- Departament d´Ecologia, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028, Barcelona, Spain
| | - Joaquim Garrabou
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 177, 4050-123, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Enric Ballesteros
- Centre d’Estudis Avançats de Blanes (CSIC), Accés Cala St. Francesc 14, 17300, Blanes, Spain
| | - Emma Cebrian
- Centre d’Estudis Avançats de Blanes (CSIC), Accés Cala St. Francesc 14, 17300, Blanes, Spain
| | - David Díaz
- Instituto Español de Oceanografia, C/ Moll de Ponent s/n, 07015, Palma de Mallorca, Spain
| | - Jean-Baptiste Ledoux
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 177, 4050-123, Porto, Portugal
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19
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Estimation of the variance effective population size in age structured populations. Theor Popul Biol 2015; 101:9-23. [PMID: 25703299 DOI: 10.1016/j.tpb.2015.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 01/29/2015] [Accepted: 02/10/2015] [Indexed: 11/20/2022]
Abstract
The variance effective population size for age structured populations is generally hard to estimate and the temporal method often gives biased estimates. Here, we give an explicit expression for a correction factor which, combined with estimates from the temporal method, yield approximately unbiased estimates. The calculation of the correction factor requires knowledge of the age specific offspring distribution and survival probabilities as well as possible correlation between survival and reproductive success. In order to relax these requirements, we show that only first order moments of these distributions need to be known if the time between samples is large, or individuals from all age classes which reproduce are sampled. A very explicit approximate expression for the asymptotic coefficient of standard deviation of the estimator is derived, and it can be used to construct confidence intervals and optimal ways of weighting information from different markers. The asymptotic coefficient of standard deviation can also be used to design studies and we show that in order to maximize the precision for a given sample size, individuals from older age classes should be sampled since their expected variance of allele frequency change is higher and easier to estimate. However, for populations with fluctuating age class sizes, the accuracy of the method is reduced when samples are taken from older age classes with high demographic variation. We also present a method for simultaneous estimation of the variance effective and census population size.
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20
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Perrier C, Normandeau É, Dionne M, Richard A, Bernatchez L. Alternative reproductive tactics increase effective population size and decrease inbreeding in wild Atlantic salmon. Evol Appl 2014; 7:1094-106. [PMID: 25553070 PMCID: PMC4231598 DOI: 10.1111/eva.12172] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/06/2014] [Indexed: 01/07/2023] Open
Abstract
While nonanadromous males (stream-resident and/or mature male parr) contribute to reproduction in anadromous salmonids, little is known about their impacts on key population genetic parameters. Here, we evaluated the contribution of Atlantic salmon mature male parr to the effective number of breeders (Nb) using both demographic (variance in reproductive success) and genetic (linkage disequilibrium) methods, the number of alleles, and the relatedness among breeders. We used a recently published pedigree reconstruction of a wild anadromous Atlantic salmon population in which 2548 fry born in 2010 were assigned parentage to 144 anadromous female and 101 anadromous females that returned to the river to spawn in 2009 and to 462 mature male parr. Demographic and genetic methods revealed that mature male parr increased population Nb by 1.79 and 1.85 times, respectively. Moreover, mature male parr boosted the number of alleles found among progenies. Finally, mature male parr were in average less related to anadromous females than were anadromous males, likely because of asynchronous sexual maturation between mature male parr and anadromous fish of a given cohort. By increasing Nb and allelic richness, and by decreasing inbreeding, the reproductive contribution of mature male parr has important evolutionary and conservation implications for declining Atlantic salmon populations.
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Affiliation(s)
- Charles Perrier
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, Canada
| | - Éric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, Canada
| | - Mélanie Dionne
- Direction de la faune aquatique, Ministère du Développement durable, de l'Environnement, de la Faune et des Parcs du Québec Québec, Canada
| | - Antoine Richard
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, Canada
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21
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Capderrey C, Kaufmann B, Jean P, Malard F, Konecny-Dupré L, Lefébure T, Douady CJ. Microsatellite development and first population size estimates for the groundwater isopod Proasellus walteri. PLoS One 2013; 8:e76213. [PMID: 24086709 PMCID: PMC3785429 DOI: 10.1371/journal.pone.0076213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 08/17/2013] [Indexed: 11/18/2022] Open
Abstract
Effective population size (N e) is one of the most important parameters in, ecology, evolutionary and conservation biology; however, few studies of N e in surface freshwater organisms have been published to date. Even fewer studies have been carried out in groundwater organisms, although their evolution has long been considered to be particularly constrained by small N e. In this study, we estimated the contemporary effective population size of the obligate groundwater isopod: Proaselluswalteri (Chappuis, 1948). To this end, a genomic library was enriched for microsatellite motifs and sequenced using 454 GS-FLX technology. A total of 54,593 reads were assembled in 10,346 contigs or singlets, of which 245 contained candidate microsatellite sequences with suitable priming sites. Ninety-six loci were tested for amplification, polymorphism and multiplexing properties, of which seven were finally selected for N e estimation. Linkage disequilibrium and approximate Bayesian computation methods revealed that N e in this small interstitial groundwater isopod could reach large sizes (> 585 individuals). Our results suggest that environmental conditions in groundwater, while often referred to as extreme, are not necessarily associated with small N e.
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Affiliation(s)
- Cécile Capderrey
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Bernard Kaufmann
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Pauline Jean
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Florian Malard
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Lara Konecny-Dupré
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Tristan Lefébure
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Christophe J. Douady
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
- Institut Universitaire de France, Paris, France
- * E-mail:
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22
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Johnstone DL, O'Connell MF, Palstra FP, Ruzzante DE. Mature male parr contribution to the effective size of an anadromous Atlantic salmon (Salmo salar) population over 30 years. Mol Ecol 2013; 22:2394-407. [PMID: 23317429 DOI: 10.1111/mec.12186] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 11/13/2012] [Accepted: 11/21/2012] [Indexed: 11/26/2022]
Abstract
We describe temporal changes in the genetic composition of a small anadromous Atlantic salmon (Salmo salar) population from South Newfoundland, an area where salmon populations are considered threatened (COSEWIC 2010). We examined the genetic variability (13 microsatellite loci) in 869 out-migrating smolt and post-spawning kelt samples, collected from 1985 to 2011 for a total of 22 annual collections and a 30 year span of assigned cohorts. We estimated the annual effective number of breeders (Nb) and the generational effective population size (Ne) through genetic methods and demographically using the adult sex ratio. Comparisons between genetic and demographic estimates show that the adult spawners inadequately explain the observed Ne estimates, suggesting that mature male parr are significantly increasing Nb and Ne over the study period. Spawning as parr appears to be a viable and important strategy in the near absence of adult males.
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23
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Duong TY, Scribner KT, Forsythe PS, Crossman JA, Baker EA. Interannual variation in effective number of breeders and estimation of effective population size in long-lived iteroparous lake sturgeon (Acipenser fulvescens). Mol Ecol 2013; 22:1282-94. [DOI: 10.1111/mec.12167] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 11/26/2022]
Affiliation(s)
- Thuy Yen Duong
- Department of Fisheries and Wildlife; Michigan State University; 13 Natural Resources East Lansing MI 48824 USA
| | - Kim T. Scribner
- Department of Fisheries and Wildlife; Michigan State University; 13 Natural Resources East Lansing MI 48824 USA
- Department of Zoology; Michigan State University; 13 Natural Resources East Lansing MI 48824 USA
| | - Patrick S. Forsythe
- Department of Zoology; Michigan State University; 13 Natural Resources East Lansing MI 48824 USA
| | - James A. Crossman
- Department of Fisheries and Wildlife; Michigan State University; 13 Natural Resources East Lansing MI 48824 USA
| | - Edward A. Baker
- Michigan Department of Natural Resources; 488 Cherry Creek Road Marquette MI 49855 USA
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