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Chen B, Bai Y, Wang J, Ke Q, Zhou Z, Zhou T, Pan Y, Wu R, Wu X, Zheng W, Xu P. Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:141-154. [PMID: 37275538 PMCID: PMC10232709 DOI: 10.1007/s42995-023-00165-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 01/25/2023] [Indexed: 06/07/2023]
Abstract
The large yellow croaker (Larimichthys crocea) is one of the most economically valuable marine fish in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few decades. The stock division and species distribution, which have important implications for ecological protection, germplasm recovery, and fishery resource management, have been debated since the 1960s. However, it is still uncertain even how many stocks exist in this species. To address this, we evaluated the fine-scale genetic structure of large yellow croaker populations distributed along the eastern and southern Chinese coastline based on 7.64 million SNP markers. Compared with the widely accepted stock boundaries proposed in the 1960s, our results revealed that a climate-driven habitat change probably occurred between the Naozhou (Nanhai) Stock and the Ming-Yuedong (Mindong) Stock. The boundary between these two stocks might have shifted northwards from the Pearl River Estuary to the northern area of the Taiwan Strait, accompanied by highly asymmetric introgression. In addition, we found divergent landscapes of natural selection between the stocks inhabiting northern and southern areas. The northern population exhibited highly agminated signatures of strong natural selection in genes related to developmental processes, whereas moderate and interspersed selective signatures were detected in many immune-related genes in the southern populations. These findings establish the stock status and genome-wide evolutionary landscapes of large yellow croaker, providing a basis for conservation, fisheries management and further evolutionary biology studies. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00165-2.
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Affiliation(s)
- Baohua Chen
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102 China
| | - Yulin Bai
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Jiaying Wang
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Qiaozhen Ke
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
| | - Zhixiong Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Ying Pan
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, 350000 China
| | - Renxie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088 China
| | - Xiongfei Wu
- Ningbo Academy of Oceanology and Fishery, Ningbo, 315012 China
| | - Weiqiang Zheng
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
| | - Peng Xu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102 China
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2
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Lowell N, Suhrbier A, Tarpey C, May S, Carson H, Hauser L. Population structure and adaptive differentiation in the sea cucumber Apostichopus californicus and implications for spatial resource management. PLoS One 2023; 18:e0280500. [PMID: 36928497 PMCID: PMC10019739 DOI: 10.1371/journal.pone.0280500] [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: 08/08/2022] [Accepted: 01/03/2023] [Indexed: 03/18/2023] Open
Abstract
A growing body of evidence suggests that spatial population structure can develop in marine species despite large population sizes and high gene flow. Characterizing population structure is important for the effective management of exploited species, as it can be used to identify appropriate scales of management in fishery and aquaculture contexts. The California sea cucumber, Apostichopus californicus, is one such exploited species whose management could benefit from further characterization of population structure. Using restriction site-associated DNA (RAD) sequencing, we developed 2075 single nucleotide polymorphisms (SNPs) to quantify genetic structure over a broad section of the species' range along the North American west coast and within the Salish Sea, a region supporting the Washington State A. californicus fishery and developing aquaculture production of the species. We found evidence for population structure (global fixation index (FST) = 0.0068) with limited dispersal driving two patterns of differentiation: isolation-by-distance and a latitudinal gradient of differentiation. Notably, we found detectable population differences among collection sites within the Salish Sea (pairwise FST = 0.001-0.006). Using FST outlier detection and gene-environment association, we identified 10.2% of total SNPs as putatively adaptive. Environmental variables (e.g., temperature, salinity) from the sea surface were more correlated with genetic variation than those same variables measured near the benthos, suggesting that selection on pelagic larvae may drive adaptive differentiation to a greater degree than selection on adults. Our results were consistent with previous estimates of and patterns in population structure for this species in other extents of the range. Additionally, we found that patterns of neutral and adaptive differentiation co-varied, suggesting that adaptive barriers may limit dispersal. Our study provides guidance to decision-makers regarding the designation of management units for A. californicus and adds to the growing body of literature identifying genetic population differentiation in marine species despite large, nominally connected populations.
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Affiliation(s)
- Natalie Lowell
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Andy Suhrbier
- Pacific Shellfish Institute, Olympia, Washington, United States of America
| | - Carolyn Tarpey
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Samuel May
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Henry Carson
- Washington Department of Fish and Wildlife, Olympia, Washington, United States of America
| | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
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3
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Walisch TJ, Colling G, Hermant S, Matthies D. Molecular and quantitative genetic variation within and between populations of the declining grassland species Saxifraga granulata. Ecol Evol 2022; 12:e9462. [PMID: 36415877 PMCID: PMC9674452 DOI: 10.1002/ece3.9462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 09/06/2022] [Accepted: 10/04/2022] [Indexed: 11/21/2022] Open
Abstract
Formerly common plant species are expected to be particularly susceptible to recent habitat fragmentation. We studied the population genetics of 19 recently fragmented Saxifraga granulata populations (max. distance 61 km) in Luxembourg and neighboring Germany using RAPD markers and a common garden experiment. We assessed (1) the relationships between plant fitness, quantitative genetic variation, molecular genetic variation, and population size; and (2) the relative importance of genetic drift and selection in shaping genetic variation. Molecular genetic diversity was high but did not correlate with population size, habitat conditions, or plant performance. Genetic differentiation was low (F ST = 0.079 ± 0.135), and there was no isolation by distance. Longevity, clonality, and the long-lived seed bank of S. granulata may have prevented strong genetic erosion and genetic differentiation among populations. However, genetic distinctness increased with decreasing genetic diversity indicating that random genetic drift occurred in the studied populations. Quantitative and molecular genetic variations were correlated, and their differentiation (Q ST vs. F ST) among S. granulata populations was similar, suggesting that mainly random processes have shaped the quantitative genetic differentiation among populations. However, pairwise quantitative genetic distances increased with geographic and climatic distances, even when adjusted for molecular genetic distances, indicating diversifying selection. Our results indicate that long-lived clonal species may be buffered at least temporarily against the negative effects of fragmentation. The relationship between quantitative genetic and geographic distance may be a more sensitive indicator of selection than Q ST-F ST differences.
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Affiliation(s)
- Tania J. Walisch
- Musée National d'Histoire NaturelleLuxembourg CityLuxembourg
- Department of BiologyPhilipps‐Universität MarburgMarburgGermany
| | - Guy Colling
- Musée National d'Histoire NaturelleLuxembourg CityLuxembourg
| | - Sylvie Hermant
- Musée National d'Histoire NaturelleLuxembourg CityLuxembourg
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4
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Blondel L, Paterson IG, Bentzen P, Hendry AP. Resistance and resilience of genetic and phenotypic diversity to "black swan" flood events: A retrospective analysis with historical samples of guppies. Mol Ecol 2021; 30:1017-1028. [PMID: 33346935 DOI: 10.1111/mec.15782] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/04/2020] [Accepted: 12/14/2020] [Indexed: 01/05/2023]
Abstract
Rare extreme "black swan" disturbances can impact ecosystems in many ways, such as destroying habitats, depleting resources, and causing high mortality. In rivers, for instance, exceptional floods that occur infrequently (e.g., so-called "50-year floods") can strongly impact the abundance of fishes and other aquatic organisms. Beyond such ecological effects, these floods could also impact intraspecific diversity by elevating genetic drift or dispersal and by imposing strong selection, which could then influence the population's ability to recover from disturbance. And yet, natural systems might be resistant (show little change) or resilient (show rapid recovery) even to rare extreme events - perhaps as a result of selection due to past events. We considered these possibilities in two rivers where native guppies experienced two extreme floods - one in 2005 and another in 2016. For each river, we selected four sites and used archived "historical" samples to compare levels of genetic and phenotypic diversity before vs. after floods. Genetic diversity was represented by 33 neutral microsatellite markers, and phenotypic diversity was represented by body length and male melanic (black) colour. We found that genetic diversity and population structure was mostly "resistant" to even these extreme floods; whereas the larger impacts on phenotypic diversity were short-lived, suggesting additional "resilience". We discuss the determinants of these two outcomes for guppies facing floods, and then consider the general implications for the resistance and resilience of intraspecific variation to black swan disturbances.
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Affiliation(s)
- Léa Blondel
- Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
| | - Ian G Paterson
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Paul Bentzen
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
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5
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Jha A, Vasudevan K. Demographic history of the fragmented yellowthroated bulbul (Pycnonotus xantholaemus) population in the Deccan Peninsula, India. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The yellow-throated bulbul (YTB) is an endemic passerine restricted to scrub forests along hill slopes with exposed rocky outcrops in the Deccan Peninsula, India. It is found in small, discontinuous populations and is vulnerable to extinction due to ongoing habitat loss and subsequent population decline. To assess the genetic connectivity and past demography, we sequenced 1050 nucleotide base pairs of the mitochondrial control region of 60 individuals that represent distinct populations in the geographic range of the species. We recovered 39 haplotypes defined by 81 variable sites. Haplotype diversity was high with low nucleotide diversity, suggesting rapid population growth from a founder population with a small effective population size. The negative values of Tajima’sDand Fu’sFsand small positive value of Ramos-Onsins and Rozas’R2suggest deviation from neutrality and population expansion. The haplotype network and demographic expansion parameters further suggest historical population expansion. Mismatch analysis statistics and Bayesian skyline plots estimate population expansion during the late Pleistocene. Although the species presently occurs in small, disconnected we found no structuring of the population. Dispersal events are the most likely explanation for the absence of genetic structuring in the YTB population. These results represent important data for the design of a conservation plan for this endemic and globally threatened species.
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Affiliation(s)
- A Jha
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500048, India
| | - K Vasudevan
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500048, India
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6
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Lima-Rezende CA, Rocha AV, Júnior AFC, Martins ÉDS, Vasconcelos V, Caparroz R. Late Pleistocene climatic changes promoted demographic expansion and population reconnection of a Neotropical savanna-adapted bird, Neothraupis fasciata (Aves: Thraupidae). PLoS One 2019; 14:e0212876. [PMID: 30893330 PMCID: PMC6426193 DOI: 10.1371/journal.pone.0212876] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 02/11/2019] [Indexed: 11/19/2022] Open
Abstract
We performed phylogeographic and genetic structure analyses of Neothraupis fasciata joined with species distribution modelling to evaluate whether: (1) the distribution of genetic variability shows a pattern expected by the isolation-by-distance model; (2) the influence of the Pleistocene climate changes on species distribution; and (3) climate/climatic stability (hypothesis of climatic stability) as a predictor of population genetic diversity. Based on two molecular datasets (ND2 and FIB-5), the isolation-by-distance hypothesis was not supported. The mitochondrial haplotype network indicated the existence of historically isolated populations at the southern range of the species distribution, and recent population expansion was identified by both neutrality tests and extended Bayesian skyline plot analysis. Thus, the climatic changes during the Pleistocene might have promoted the reconnection of the partially isolated southern populations, which may have persisted in the plateaus during the cycles of savanna contractions. Subsequently, this species (re)colonized northern areas of the species present distribution, following the continuous vegetation on the São Francisco and Central plateaus about 60 kyr, and also reached the Amazonian savannas likely via the central corridor. Thus, our results indicated that the intrinsic relationship between the relief heterogeneity (plateaus and depressions) and the climatic fluctuations, mainly in the Pleistocene, promoted population reconnection and demographic expansion of N. fasciata.
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Affiliation(s)
- Cássia Alves Lima-Rezende
- Laboratório de Genética e Biodiversidade, Departamento de Genética e Morfologia-IB, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Amanda Vaz Rocha
- Laboratório de Genética e Biodiversidade, Departamento de Genética e Morfologia-IB, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | | | | | - Vinicius Vasconcelos
- Laboratório de Solos e Vegetação, Departamento de Ecologia-IB, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Renato Caparroz
- Laboratório de Genética e Biodiversidade, Departamento de Genética e Morfologia-IB, Universidade de Brasília, Brasília, Distrito Federal, Brazil
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7
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Genetic diversity and population structure of two endemic Cupressus (Cupressaceae) species on the Qinghai-Tibetan plateau. J Genet 2019. [DOI: 10.1007/s12041-019-1059-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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8
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Ishida Y, Gugala NA, Georgiadis NJ, Roca AL. Evolutionary and demographic processes shaping geographic patterns of genetic diversity in a keystone species, the African forest elephant ( Loxodonta cyclotis). Ecol Evol 2018; 8:4919-4931. [PMID: 29876070 PMCID: PMC5980461 DOI: 10.1002/ece3.4062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 03/15/2018] [Accepted: 03/19/2018] [Indexed: 11/08/2022] Open
Abstract
The past processes that have shaped geographic patterns of genetic diversity may be difficult to infer from current patterns. However, in species with sex differences in dispersal, differing phylogeographic patterns between mitochondrial (mt) and nuclear (nu) DNA may provide contrasting insights into past events. Forest elephants (Loxodonta cyclotis) were impacted by climate and habitat change during the Pleistocene, which likely shaped phylogeographic patterns in mitochondrial (mt) DNA that have persisted due to limited female dispersal. By contrast, the nuclear (nu) DNA phylogeography of forest elephants in Central Africa has not been determined. We therefore examined the population structure of Central African forest elephants by genotyping 94 individuals from six localities at 21 microsatellite loci. Between forest elephants in western and eastern Congolian forests, there was only modest genetic differentiation, a pattern highly discordant with that of mtDNA. Nuclear genetic patterns are consistent with isolation by distance. Alternatively, male-mediated gene flow may have reduced the previous regional differentiation in Central Africa suggested by mtDNA patterns, which likely reflect forest fragmentation during the Pleistocene. In species like elephants, male-mediated gene flow erases the nuclear genetic signatures of past climate and habitat changes, but these continue to persist as patterns in mtDNA because females do not disperse. Conservation implications of these results are discussed.
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Affiliation(s)
- Yasuko Ishida
- Department of Animal SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois
| | - Natalie A. Gugala
- Department of Animal SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois
| | | | - Alfred L. Roca
- Department of Animal SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois
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9
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Scribner KT, Soiseth C, McGuire J, Sage GK, Thorsteinson L, Nielsen JL, Knudsen E. Genetic assessment of the effects of streamscape succession on coho salmon Oncorhynchus kisutch colonization in recently deglaciated streams. JOURNAL OF FISH BIOLOGY 2017; 91:195-218. [PMID: 28523791 DOI: 10.1111/jfb.13337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 04/20/2017] [Indexed: 06/07/2023]
Abstract
Measures of genetic diversity within and among populations and historical geomorphological data on stream landscapes were used in model simulations based on approximate Bayesian computation (ABC) to examine hypotheses of the relative importance of stream features (geomorphology and age) associated with colonization events and gene flow for coho salmon Oncorhynchus kisutch breeding in recently deglaciated streams (50-240 years b.p.) in Glacier Bay National Park (GBNP), Alaska. Population estimates of genetic diversity including heterozygosity and allelic richness declined significantly and monotonically from the oldest and largest to youngest and smallest GBNP streams. Interpopulation variance in allele frequency increased with increasing distance between streams (r = 0·435, P < 0·01) and was inversely related to stream age (r = -0·281, P < 0·01). The most supported model of colonization involved ongoing or recent (<10 generations before sampling) colonization originating from large populations outside Glacier Bay proper into all other GBNP streams sampled. Results here show that sustained gene flow from large source populations is important to recently established O. kisutch metapopulations. Studies that document how genetic and demographic characteristics of newly founded populations vary associated with successional changes in stream habitat are of particular importance to and have significant implications for, restoration of declining or repatriation of extirpated populations in other regions of the species' native range.
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Affiliation(s)
- K T Scribner
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824-1222, U.S.A
- Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824-1222, U.S.A
| | - C Soiseth
- Glacier Bay National Park and Preserve, P. O. Box 140, Gustavus, AK, 99826, U.S.A
| | - J McGuire
- Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824-1222, U.S.A
| | - G K Sage
- U. S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, U.S.A
| | - L Thorsteinson
- Alaska Region, U. S. Geological Survey, 250 Egan Drive, Juneau, AK, 99801, U.S.A
| | - J L Nielsen
- U. S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, U.S.A
| | - E Knudsen
- U. S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, U.S.A
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10
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Bagley RK, Sousa VC, Niemiller ML, Linnen CR. History, geography and host use shape genomewide patterns of genetic variation in the redheaded pine sawfly (
Neodiprion lecontei
). Mol Ecol 2017; 26:1022-1044. [DOI: 10.1111/mec.13972] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/10/2016] [Accepted: 12/01/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Robin K. Bagley
- Department of Biology University of Kentucky Lexington KY 40506 USA
| | - Vitor C. Sousa
- cE3c ‐ Centre for Ecology, Evolution and Environmental Changes Faculdade de Ciências Universidade de Lisboa 1749‐016 Lisboa Portugal
| | - Matthew L. Niemiller
- Illinois Natural History Survey Prairie Research Institute University of Illinois Urbana‐Champaign Champaign IL 61820 USA
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11
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Lecocq T, Gérard M, Michez D, Dellicour S. Conservation genetics of European bees: new insights from the continental scale. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0917-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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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.
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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
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13
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Young EF, Belchier M, Hauser L, Horsburgh GJ, Meredith MP, Murphy EJ, Pascoal S, Rock J, Tysklind N, Carvalho GR. Oceanography and life history predict contrasting genetic population structure in two Antarctic fish species. Evol Appl 2015; 8:486-509. [PMID: 26029262 PMCID: PMC4430772 DOI: 10.1111/eva.12259] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 02/27/2015] [Indexed: 01/27/2023] Open
Abstract
Understanding the key drivers of population connectivity in the marine environment is essential for the effective management of natural resources. Although several different approaches to evaluating connectivity have been used, they are rarely integrated quantitatively. Here, we use a 'seascape genetics' approach, by combining oceanographic modelling and microsatellite analyses, to understand the dominant influences on the population genetic structure of two Antarctic fishes with contrasting life histories, Champsocephalus gunnari and Notothenia rossii. The close accord between the model projections and empirical genetic structure demonstrated that passive dispersal during the planktonic early life stages is the dominant influence on patterns and extent of genetic structuring in both species. The shorter planktonic phase of C. gunnari restricts direct transport of larvae between distant populations, leading to stronger regional differentiation. By contrast, geographic distance did not affect differentiation in N. rossii, whose longer larval period promotes long-distance dispersal. Interannual variability in oceanographic flows strongly influenced the projected genetic structure, suggesting that shifts in circulation patterns due to climate change are likely to impact future genetic connectivity and opportunities for local adaptation, resilience and recovery from perturbations. Further development of realistic climate models is required to fully assess such potential impacts.
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Affiliation(s)
| | | | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Gavin J Horsburgh
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield Sheffield, UK
| | | | | | - Sonia Pascoal
- School of Biological Sciences, Bangor University Bangor, Gwynedd, UK
| | - Jennifer Rock
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield Sheffield, UK ; School of Biological Sciences, Bangor University Bangor, Gwynedd, UK ; Present address: Department of Zoology, University of Otago Dunedin, 9054, New Zealand
| | - Niklas Tysklind
- School of Biological Sciences, Bangor University Bangor, Gwynedd, UK ; Present address: Campus Agronomique BP 709-97387, Kourou Cedex, France
| | - Gary R Carvalho
- School of Biological Sciences, Bangor University Bangor, Gwynedd, UK
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14
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Barley AJ, Monnahan PJ, Thomson RC, Grismer LL, Brown RM. Sun skink landscape genomics: assessing the roles of micro-evolutionary processes in shaping genetic and phenotypic diversity across a heterogeneous and fragmented landscape. Mol Ecol 2015; 24:1696-712. [DOI: 10.1111/mec.13151] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 02/27/2015] [Accepted: 03/10/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Anthony J. Barley
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
| | - Patrick J. Monnahan
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
| | - Robert C. Thomson
- Department of Biology; University of Hawai'i at Mānoa; Honolulu HI 96822 USA
| | - L. Lee Grismer
- Department of Biology; La Sierra University; Riverside CA 92515 USA
| | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
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15
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Toward the genetic origins of a potentially non-native population of threespine stickleback (Gasterosteus aculeatus) in Alberta. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0706-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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van Strien MJ, Holderegger R, Van Heck HJ. Isolation-by-distance in landscapes: considerations for landscape genetics. Heredity (Edinb) 2015; 114:27-37. [PMID: 25052412 PMCID: PMC4815601 DOI: 10.1038/hdy.2014.62] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 05/13/2014] [Accepted: 05/27/2014] [Indexed: 11/08/2022] Open
Abstract
In landscape genetics, isolation-by-distance (IBD) is regarded as a baseline pattern that is obtained without additional effects of landscape elements on gene flow. However, the configuration of suitable habitat patches determines deme topology, which in turn should affect rates of gene flow. IBD patterns can be characterized either by monotonically increasing pairwise genetic differentiation (for example, FST) with increasing interdeme geographic distance (case-I pattern) or by monotonically increasing pairwise genetic differentiation up to a certain geographical distance beyond which no correlation is detectable anymore (case-IV pattern). We investigated if landscape configuration influenced the rate at which a case-IV pattern changed to a case-I pattern. We also determined at what interdeme distance the highest correlation was measured between genetic differentiation and geographic distance and whether this distance corresponded to the maximum migration distance. We set up a population genetic simulation study and assessed the development of IBD patterns for several habitat configurations and maximum migration distances. We show that the rate and likelihood of the transition of case-IV to case-I FST-distance relationships was strongly influenced by habitat configuration and maximum migration distance. We also found that the maximum correlation between genetic differentiation and geographic distance was not related to the maximum migration distance and was measured across all deme pairs in a case-I pattern and, for a case-IV pattern, at the distance where the FST-distance curve flattens out. We argue that in landscape genetics, separate analyses should be performed to either assess IBD or the landscape effects on gene flow.
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Affiliation(s)
- M J van Strien
- Planning of Landscape and Urban Systems, ETH Zurich, Stefano-Franscini-Platz 5, Zurich, Switzerland
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, Birmensdorf, Switzerland
| | - R Holderegger
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, Birmensdorf, Switzerland
- Department of Environmental System Sciences, ETH Zurich, Universitätsstrasse 16, Zurich, Switzerland
| | - H J Van Heck
- Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff, UK
- Institute of Earth Sciences, Utrecht University, Budapestlaan 4, Utrecht, The Netherlands
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17
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Salmenkova EA, Omelchenko VT. Factors responsible for spatial population genetic structure in white-spotted char Salvelinus leucomaensis (Pallas). RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414120102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Hennessy C, Tsai CC, Beasley JC, Beatty WS, Zollner PA, Rhodes OE. Elucidation of population connectivity in synanthropic mesopredators: Using genes to define relevant spatial scales for management of raccoons and Virginia opossums. J Wildl Manage 2014. [DOI: 10.1002/jwmg.812] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Cecilia Hennessy
- Department of Forestry and Natural Resources; Purdue University; 715 W State Street West Lafayette 47907 IN USA
| | - Chia-Chun Tsai
- Department of Forestry and Natural Resources; Purdue University; 715 W State Street West Lafayette 47907 IN USA
| | - James C. Beasley
- Savannah River Ecology Lab; University of Georgia; Drawer E Aiken 29802 SC USA
| | - William S. Beatty
- Department of Forestry and Natural Resources; Purdue University; 715 W State Street West Lafayette 47907 IN USA
| | - Patrick A. Zollner
- Department of Forestry and Natural Resources; Purdue University; 715 W State Street West Lafayette 47907 IN USA
| | - Olin E. Rhodes
- Savannah River Ecology Lab; University of Georgia; Drawer E Aiken 29802 SC USA
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19
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Falahati-Anbaran M, Lundemo S, Ansell SW, Stenøien HK. Contrasting patterns of genetic structuring in natural populations of Arabidopsis lyrata Subsp. petraea across different regions in northern Europe. PLoS One 2014; 9:e107479. [PMID: 25226024 PMCID: PMC4166467 DOI: 10.1371/journal.pone.0107479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/11/2014] [Indexed: 01/08/2023] Open
Abstract
Level and partitioning of genetic diversity is expected to vary between contrasting habitats, reflecting differences in strength of ecological and evolutionary processes. Therefore, it is necessary to consider processes acting on different time scales when trying to explain diversity patterns in different parts of species' distributions. To explore how historical and contemporary factors jointly may influence patterns of genetic diversity and population differentiation, we compared genetic composition in the perennial herb Arabidopsis lyrata ssp. petraea from the northernmost parts of its distribution range on Iceland to that previously documented in Scandinavia. Leaf tissue and soil were sampled from ten Icelandic populations of A. lyrata. Seedlings were grown from soil samples, and tissue from above-ground and seed bank individuals were genotyped with 21 microsatellite markers. Seed bank density in Icelandic populations was low but not significantly different from that observed in Norwegian populations. While within-population genetic diversity was relatively high on Iceland (H(E) = 0.35), among-population differentiation was low (F(ST) = 0.10) compared to Norwegian and Swedish populations. Population differentiation was positively associated with geographical distance in both Iceland and Scandinavia, but the strength of this relationship varied between regions. Although topography and a larger distribution range may explain the higher differentiation between mountainous Norwegian relative to lowland populations in Sweden, these factors cannot explain the lower differentiation in Icelandic compared to Swedish populations. We propose that low genetic differentiation among Icelandic populations is not caused by differences in connectivity, but is rather due to large historical effective population sizes. Thus, rather than contemporary processes, historical factors such as survival of Icelandic lineages in northern refugia during the last glacial period may have contributed to the observed pattern.
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Affiliation(s)
- Mohsen Falahati-Anbaran
- Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway; School of Biology and Center of Excellence in Phylogeny of Living Organisms, University of Tehran, Tehran, Iran
| | - Sverre Lundemo
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway; Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Stephen W Ansell
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Hans K Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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20
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Ponce-Reyes R, Clegg SM, Carvalho SB, McDonald-Madden E, Possingham HP. Geographical surrogates of genetic variation for selecting island populations for conservation. DIVERS DISTRIB 2014. [DOI: 10.1111/ddi.12195] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Rocío Ponce-Reyes
- The School of Biological Sciences; University of Queensland; St Lucia Qld 4072 Australia
| | - Sonya M. Clegg
- Environmental Futures Research Institute; Griffith School of Environment; Griffith University; Gold Coast Campus Gold Coast Qld 4222 Australia
- Biodiversity and Geosciences Program; Queensland Museum; PO Box 3300 South Brisbane Qld 4101 Australia
- Division of Life Sciences; Imperial College London; Silwood Park Ascot Berkshire SL5 7PY UK
| | - Silvia B. Carvalho
- The School of Biological Sciences; University of Queensland; St Lucia Qld 4072 Australia
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - Eve McDonald-Madden
- The School of Biological Sciences; University of Queensland; St Lucia Qld 4072 Australia
- ARC Centre of Excellence for Environmental Decisions; University of Queensland; St Lucia Qld 4072 Australia
- Climate Adaptation Flagship; CSIRO Ecosystem Sciences; 41 Boggo Rd Dutton Park Qld 4102 Australia
| | - Hugh P. Possingham
- The School of Biological Sciences; University of Queensland; St Lucia Qld 4072 Australia
- Division of Life Sciences; Imperial College London; Silwood Park Ascot Berkshire SL5 7PY UK
- ARC Centre of Excellence for Environmental Decisions; University of Queensland; St Lucia Qld 4072 Australia
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21
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de Lafontaine G, Ducousso A, Lefèvre S, Magnanou E, Petit RJ. Stronger spatial genetic structure in recolonized areas than in refugia in the European beech. Mol Ecol 2014; 22:4397-412. [PMID: 23980761 DOI: 10.1111/mec.12403] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 05/17/2013] [Accepted: 05/21/2013] [Indexed: 11/29/2022]
Abstract
Extant rear-edge populations located in former glacial refugia remain understudied despite their high conservation value. These populations should have experienced strong genetic drift due to their small size and long isolation. Moreover, the prolonged action of isolation by distance in refugial areas should result in stronger regional spatial genetic structure (SGS) than in recolonized areas, but empirical tests of this prediction are scarce. To fill this gap, we first used a set of 16 microsatellite markers to investigate the genetic structure of European beech in France in 65 populations from three refugial areas and one control recolonized (nonrefugial) area. Then, using the same approach, we reanalysed published isozyme data from 375 populations distributed across the entire species range. We found stronger genetic differentiation among populations in refugia than in recolonized areas. However, contrary to expectations, regional SGS was lower within refugia than within recolonized areas. Published studies presenting similar analyses suggest that our results could have generality across different biogeographical settings and types of organisms. Strong and prolonged genetic drift in refugial areas could have erased the signature of range expansions that is still visible in recolonized areas. Our results therefore suggest that Pleistocene population isolation has played a key role in increasing the genetic complexity of extant rear-edge populations.
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22
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Prinz K, Weising K, Hensen I. Habitat fragmentation and recent bottlenecks influence genetic diversity and differentiation of the Central European halophyte Suaeda maritima (Chenopodiaceae). AMERICAN JOURNAL OF BOTANY 2013; 100:2210-2218. [PMID: 24148614 DOI: 10.3732/ajb.1300097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Central European salt habitats are mainly restricted to the maritime coast but scattered occurrences can also be found inland. In inland habitats, human activities have caused losses and reductions in the size of natural salt sites but have also created new anthropogenic habitats around potash mining dumps colonized by halophytic species in the last 30 yr. We aimed to investigate the effects of bottlenecks, isolation, and ongoing habitat fragmentation on the genetic variation of a species commonly growing in these special habitats. METHODS We used 10 microsatellite markers to compare genetic diversity and differentiation of 31 populations of Suaeda maritima (Chenopodiaceae) from Central European coasts and inland habitats. Two approaches were applied to analyze the tetraploid data based on allele frequencies directly derived from microsatellite data and from transformed binary data. KEY RESULTS In comparison to the coastal populations from the North Sea and the English Channel, significantly reduced genetic variation and increased between-population differentiation was revealed for populations from the German inland and the Baltic Sea coast. Genetic structure analyses clearly separated coastal and inland populations. CONCLUSIONS Our results indicate that gene flow is restricted among populations from inland salt sites and the Baltic Sea coast, presumably due to their isolation, small sizes, genetic bottlenecks and/or founder events. Patterns of allele distribution indicate some occasional genetic exchange among habitat types in the past. Anthropogenic salt sites may facilitate gene flow among inland salt habitats preventing endangered inland halophyte populations from genetic erosion.
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Affiliation(s)
- Kathleen Prinz
- Institute for Systematic Botany with Herbarium Haussknecht and Botanical Garden, Friedrich-Schiller-University Jena, Philosophenweg 16, D-07743 Jena, Germany
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23
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Vetter D, Rücker G, Storch I. Meta‐analysis: A need for well‐defined usage in ecology and conservation biology. Ecosphere 2013. [DOI: 10.1890/es13-00062.1] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Daniela Vetter
- Wildlife Ecology and Management, Faculty of Environment and Natural Resources, University of Freiburg, Tennenbacher Str. 4, 79106 Freiburg, Germany
| | - Gerta Rücker
- Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Str. 26, 79104 Freiburg, Germany
| | - Ilse Storch
- Wildlife Ecology and Management, Faculty of Environment and Natural Resources, University of Freiburg, Tennenbacher Str. 4, 79106 Freiburg, Germany
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24
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High urban population density of birds reflects their timing of urbanization. Oecologia 2012; 170:867-75. [DOI: 10.1007/s00442-012-2355-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 04/26/2012] [Indexed: 10/28/2022]
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25
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Torres-Pérez F, Palma RE, Hjelle B, Holmes EC, Cook JA. Spatial but not temporal co-divergence of a virus and its mammalian host. Mol Ecol 2011; 20:4109-22. [PMID: 21880089 DOI: 10.1111/j.1365-294x.2011.05241.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Co-divergence between host and parasites suggests that evolutionary processes act across similar spatial and temporal scales. Although there has been considerable work on the extent and correlates of co-divergence of RNA viruses and their mammalian hosts, relatively little is known about the extent to which virus evolution is determined by the phylogeographic history of host species. To test hypotheses related to co-divergence across a variety of spatial and temporal scales, we explored phylogenetic signatures in Andes virus (ANDV) sampled from Chile and its host rodent, Oligoryzomys longicaudatus. ANDV showed strong spatial subdivision, a phylogeographic pattern also recovered in the host using both spatial and genealogical approaches, and despite incomplete lineage sorting. Lineage structure in the virus seemed to be a response to current population dynamics in the host at the spatial scale of ecoregions. However, finer scale analyses revealed contrasting patterns of genetic structure across a latitudinal gradient. As predicted by their higher substitution rates, ANDV showed greater genealogical resolution than the rodent, with topological congruence influenced by the degree of lineage sorting within the host. However, despite these major differences in evolutionary dynamics, the geographic structure of host and virus converged across large spatial scales.
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Affiliation(s)
- Fernando Torres-Pérez
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.
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26
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Chambers JL, Garant D. Determinants of Population Genetic Structure in Eastern Chipmunks (Tamias striatus): The Role of Landscape Barriers and Sex-Biased Dispersal. J Hered 2010; 101:413-22. [DOI: 10.1093/jhered/esq029] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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27
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HARRIS LN, TAYLOR EB. Pleistocene glaciations and contemporary genetic diversity in a Beringian fish, the broad whitefish,Coregonus nasus(Pallas): inferences from microsatellite DNA variation. J Evol Biol 2010; 23:72-86. [DOI: 10.1111/j.1420-9101.2009.01858.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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ÓLAFSDÓTTIR GUÐBJÖRGÁ, SNORRASON SIGURÐURS. Parallels, nonparallels, and plasticity in population differentiation of threespine stickleback within a lake. Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2009.01318.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Genetic diversity, phenotypic variation and local adaptation in the alpine landscape: case studies with alpine plant species. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s00035-009-0065-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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30
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Neaves LE, Zenger KR, Prince RIT, Eldridge MDB, Cooper DW. Landscape discontinuities influence gene flow and genetic structure in a large, vagile Australian mammal, Macropus fuliginosus. Mol Ecol 2009; 18:3363-78. [PMID: 19659477 DOI: 10.1111/j.1365-294x.2009.04293.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Large vagile mammals typically exhibit little genetic structuring across their range, particularly when their habitat is essentially continuous. We investigated the population genetic structure of a large vagile Australian macropodid, Macropus fuliginosus, which is continuously distributed across most of southern Australia, using nine highly polymorphic nuclear microsatellite loci. Five distinct genetic units were identified across the range, four on the mainland and one on Kangaroo Island. In addition to the predicted historic Nullarbor Plain Barrier, two unexpected mainland barriers to gene flow were identified. Both were associated with landscape discontinuities (Swan River, Flinders Ranges), which appear within the dispersal capabilities of M. fuliginosus. Typical of large vagile mammals, M. fuliginosus displays high genetic diversity (with the exception of an insular population) and weak genetic structuring (within genetic units). However, the expansion of M. fuliginosus from southwestern Australia during the Pleistocene has resulted in significantly reduced genetic diversity in eastern populations. No significant sex-biased dispersal was detected, although differences in habitat, densities and climatic conditions between the eastern and western regions of the range appear to influence dispersal with the effects of isolation by distance only evident in the west. These results suggest that the biogeography of southern Australia is more complex than previously thought and reveal that seemingly minor landscape features can significantly impact genetic structuring in large vagile mammals.
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Affiliation(s)
- Linda E Neaves
- Department of Biological Sciences, Macquarie University, NSW, Australia.
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31
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Lee-Yaw JA, Davidson A, McRae BH, Green DM. Do landscape processes predict phylogeographic patterns in the wood frog? Mol Ecol 2009; 18:1863-74. [PMID: 19302465 DOI: 10.1111/j.1365-294x.2009.04152.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Understanding factors that influence population connectivity and the spatial distribution of genetic variation is a major goal in molecular ecology. Improvements in the availability of high-resolution geographic data have made it increasingly possible to quantify the effects of landscape features on dispersal and genetic structure. However, most studies examining such landscape effects have been conducted at very fine (e.g. landscape genetics) or broad (e.g. phylogeography) spatial scales. Thus, the extent to which processes operating at fine spatial scales are linked to patterns at larger scales remains unclear. Here, we test whether factors impacting wood frog dispersal at fine spatial scales are correlated with genetic structure at regional scales. Using recently developed methods borrowed from electrical circuit theory, we generated landscape resistance matrices among wood frog populations in eastern North America based on slope, a wetness index, land cover and absolute barriers to wood frog dispersal. We then determined whether these matrices are correlated with genetic structure based on six microsatellite markers and whether such correlations outperform a landscape-free model of isolation by resistance. We observed significant genetic structure at regional spatial scales. However, topography and landscape variables associated with the intervening habitat between sites provide little explanation for patterns of genetic structure. Instead, absolute dispersal barriers appear to be the best predictor of regional genetic structure in this species. Our results suggest that landscape variables that influence dispersal, microhabitat selection and population structure at fine spatial scales do not necessarily explain patterns of genetic structure at broader scales.
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Affiliation(s)
- Julie A Lee-Yaw
- Department of Zoology, University of British Columbia, BC, Canada.
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32
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Barson NJ, Haugen TO, Vøllestad LA, Primmer CR. Contemporary isolation-by-distance, but not isolation-by-time, among demes of European Grayling (Thymallus thymallus, Linnaeus) with recent common ancestors. Evolution 2009; 63:549-56. [PMID: 19154368 DOI: 10.1111/j.1558-5646.2008.00554.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of isolation by distance (IBD) and isolation by time (IBT) was contrasted among demes of European grayling (Thymallus thymallus) that have diverged within the last 25 generations following colonization of a lake (Lesjaskogsvatnet). We find low but significant levels of genetic differentiation among spawning tributaries and a pattern of IBD among them. We do not, however, find evidence for IBT despite an up to four-week difference in spawning date between "warm/early" and "cold/late" spawning demes and differences in the incubation temperatures experienced by offspring. It appears that IBD has developed more rapidly than IBT in this system and that adaptive divergence has been initiated in the absence of IBT. Although analysis of selected loci could reveal reduced recombination in parts of the genome associated with temporal divergence, our analysis of neutral genetic data suggests that IBD is a more important isolating mechanism in the early stages of adaptive divergence in European grayling.
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Affiliation(s)
- Nicola J Barson
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, P.O. Box 1066 Blindern, N-0316 Oslo, Norway
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33
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Combined analysis of nuclear and mitochondrial markers provide new insight into the genetic structure of North European Picea abies. Heredity (Edinb) 2009; 102:549-62. [DOI: 10.1038/hdy.2009.16] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Bradbury IR, Laurel B, Snelgrove PVR, Bentzen P, Campana SE. Global patterns in marine dispersal estimates: the influence of geography, taxonomic category and life history. Proc Biol Sci 2008; 275:1803-9. [PMID: 18445556 DOI: 10.1098/rspb.2008.0216] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We examine estimates of dispersal in a broad range of marine species through an analysis of published values, and evaluate how well these values represent global patterns through a comparison with correlates of dispersal. Our analysis indicates a historical focus in dispersal studies on low-dispersal/low-latitude species, and we hypothesize that these studies are not generally applicable and representative of global patterns. Large-scale patterns in dispersal were examined using a database of correlates of dispersal such as planktonic larval duration (PLD, 318 species) and genetic differentiation (FST, 246 species). We observed significant differences in FST (p<0.001) and PLD (p<0.001) between taxonomic groups (e.g. fishes, cnidarians, etc.). Within marine fishes (more than 50% of datasets), the prevalence of demersal eggs was negatively associated with PLD (R2=0.80, p<0.001) and positively associated with genetic structure (R2=0.74, p<0.001). Furthermore, dispersal within marine fishes (i.e. PLD and FST) increased with latitude, adult body size and water depth. Of these variables, multiple regression identified latitude and body size as persistent predictors across taxonomic levels. These global patterns of dispersal represent a first step towards understanding and predicting species-level and regional differences in dispersal, and will be improved as more comprehensive data become available.
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Affiliation(s)
- Ian R Bradbury
- Marine Gene Probe Laboratory, Biology Department, Life Sciences Centre, Dalhousie University, Halifax, NS, Canada B3H 4J1.
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Dionne M, Caron F, Dodson JJ, Bernatchez L. Landscape genetics and hierarchical genetic structure in Atlantic salmon: the interaction of gene flow and local adaptation. Mol Ecol 2008; 17:2382-96. [PMID: 18430145 DOI: 10.1111/j.1365-294x.2008.03771.x] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Disentangling evolutionary forces that may interact to determine the patterns of genetic differentiation within and among wild populations is a major challenge in evolutionary biology. The objective of this study was to assess the genetic structure and the potential influence of several ecological variables on the extent of genetic differentiation at multiple spatial scales in a widely distributed species, the Atlantic salmon, Salmo salar. A total of 2775 anadromous fish were sampled from 51 rivers along the North American Atlantic coast and were genotyped using 13 microsatellites. A Bayesian analysis clustered these populations into seven genetically and geographically distinct groups, characterized by different environmental and ecological factors, mainly temperature. These groups were also characterized by different extent of genetic differentiation among populations. Dispersal was relatively high and of the same magnitude within compared to among regional groups, which contrasted with the maintenance of a regional genetic structure. However, genetic differentiation was lower among populations exchanging similar rates of local as opposed to inter-regional migrants, over the same geographical scale. This raised the hypothesis that gene flow could be constrained by local adaptation at the regional scale. Both coastal distance and temperature regime were found to influence the observed genetic structure according to landscape genetic analyses. The influence of other factors such as latitude, river length and altitude, migration tactic, and stocking was not significant at any spatial scale. Overall, these results suggested that the interaction between gene flow and thermal regime adaptation mainly explained the hierarchical genetic structure observed among Atlantic salmon populations.
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Affiliation(s)
- Mélanie Dionne
- Département de Biologie, Université Laval, Québec, Canada G1V 0A6.
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36
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Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9367-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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37
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Koizumi I, Yamamoto S, Maekawa K. Decomposed pairwise regression analysis of genetic and geographic distances reveals a metapopulation structure of stream-dwelling Dolly Varden charr. Mol Ecol 2006; 15:3175-89. [PMID: 16968263 DOI: 10.1111/j.1365-294x.2006.03019.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isolation by distance is usually tested by the correlation of genetic and geographic distances separating all pairwise populations' combinations. However, this method can be significantly biased by only a few highly diverged populations and lose the information of individual population. To detect outlier populations and investigate the relative strengths of gene flow and genetic drift for each population, we propose a decomposed pairwise regression analysis. This analysis was applied to the well-described one-dimensional stepping-stone system of stream-dwelling Dolly Varden charr (Salvelinus malma). When genetic and geographic distances were plotted for all pairs of 17 tributary populations, the correlation was significant but weak (r(2) = 0.184). Seven outlier populations were determined based on the systematic bias of the regression residuals, followed by Akaike's information criteria. The best model, 10 populations included, showed a strong pattern of isolation by distance (r(2) = 0.758), suggesting equilibrium between gene flow and genetic drift in these populations. Each outlier population was also analysed by plotting pairwise genetic and geographic distances against the 10 nonoutlier populations, and categorized into one of the three patterns: strong genetic drift, genetic drift with a limited gene flow and a high level of gene flow. These classifications were generally consistent with a priori predictions for each population (physical barrier, population size, anthropogenic impacts). Combined the genetic analysis with field observations, Dolly Varden in this river appeared to form a mainland-island or source-sink metapopulation structure. The generality of the method will merit many types of spatial genetic analyses.
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Affiliation(s)
- Itsuro Koizumi
- Department of Biological and Environmental Sciences, PO Box 65 (Viikinkaari 1), FIN-00014, University of Helsinki, Finland. itsuro@
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