1
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Nakajima S, Sueyoshi M, Hirota SK, Ishiyama N, Matsuo A, Suyama Y, Nakamura F. A strategic sampling design revealed the local genetic structure of cold-water fluvial sculpin: a focus on groundwater-dependent water temperature heterogeneity. Heredity (Edinb) 2021; 127:413-422. [PMID: 34417564 PMCID: PMC8478981 DOI: 10.1038/s41437-021-00468-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023] Open
Abstract
A key piece of information for ecosystem management is the relationship between the environment and population genetic structure. However, it is difficult to clearly quantify the effects of environmental factors on genetic differentiation because of spatial autocorrelation and analytical problems. In this study, we focused on stream ecosystems and the environmental heterogeneity caused by groundwater and constructed a sampling design in which geographic distance and environmental differences are not correlated. Using multiplexed ISSR genotyping by sequencing (MIG-seq) method, a fine-scale population genetics study was conducted in fluvial sculpin Cottus nozawae, for which summer water temperature is the determinant factor in distribution and survival. There was a clear genetic structure in the watershed. Although a significant isolation-by-distance pattern was detected in the watershed, there was no association between genetic differentiation and water temperature. Instead, asymmetric gene flow from relatively low-temperature streams to high-temperature streams was detected, indicating the importance of low-temperature streams and continuous habitats. The groundwater-focused sampling strategy yielded insightful results for conservation.
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Affiliation(s)
- Souta Nakajima
- grid.39158.360000 0001 2173 7691Laboratory of Ecosystem Management, Graduate School of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo, Hokkaido Japan
| | - Masanao Sueyoshi
- grid.472015.50000 0000 9513 8387Aqua Restoration Research Center, Public Works Research Institute, KawashimaKasada-machi, Kakamigahara, Gifu Japan
| | - Shun K. Hirota
- grid.69566.3a0000 0001 2248 6943Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi Japan
| | - Nobuo Ishiyama
- grid.452441.2Forest Research Institute, Hokkaido Research Organization, Koshunai, Bibai, Hokkaido Japan
| | - Ayumi Matsuo
- grid.69566.3a0000 0001 2248 6943Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi Japan
| | - Yoshihisa Suyama
- grid.69566.3a0000 0001 2248 6943Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi Japan
| | - Futoshi Nakamura
- grid.39158.360000 0001 2173 7691Laboratory of Ecosystem Management, Graduate School of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo, Hokkaido Japan
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2
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Semenova AV, Stroganov AN, Rubtsova GA, Rybakov MO. Genetic Structure of the Pacific Herring Clupea pallasii Valenciennes, 1847 on a Macrogeographic Scale. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421060090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Semenova AV, Stroganov AN, Ponomareva EV, Afanas’ev KI, Vilkina OV. Large-scale genetic structure and diversity of Arctic rainbow smelt Osmerus dentex Steindachner et Kner, 1870 throughout its distributional range based on microsatellites. Polar Biol 2021. [DOI: 10.1007/s00300-021-02848-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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4
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Valenzuela‐Aguayo F, McCracken GR, Manosalva A, Habit E, Ruzzante DE. Human-induced habitat fragmentation effects on connectivity, diversity, and population persistence of an endemic fish, Percilia irwini, in the Biobío River basin (Chile). Evol Appl 2020; 13:794-807. [PMID: 32211068 PMCID: PMC7086057 DOI: 10.1111/eva.12901] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/14/2019] [Accepted: 11/05/2019] [Indexed: 01/15/2023] Open
Abstract
An understanding of how genetic variability is distributed in space is fundamental for the conservation and maintenance of diversity in spatially fragmented and vulnerable populations. While fragmentation can occur from natural barriers, it can also be exacerbated by anthropogenic activities such as hydroelectric power plant development. Whatever the source, fragmentation can have significant ecological effects, including disruptions of migratory processes and gene flow among populations. In Chile, the Biobío River basin exhibits a high degree of habitat fragmentation due to the numerous hydroelectric power plants in operation, the number of which is expected to increase following new renewable energy use strategies. Here, we assessed the effects of different kinds of barriers on the genetic structure of the endemic freshwater fish Percilia irwini, knowledge that is critically needed to inform conservation strategies in light of current and anticipated further fragmentation initiatives in the system. We identified eight genetic units throughout the entire Biobío system with high effective sizes. A reduced effective size estimate was, however, observed in a single population located between two impassable barriers. Both natural waterfalls and human-made dams were important drivers of population differentiation in this system; however, dams affect genetic diversity differentially depending on their mode of operation. Evidence of population extirpation was found in two river stretches limited by upstream and downstream dams. Significant gene flow in both directions was found among populations not separated by natural or anthropogenic barriers. Our results suggest a significant vulnerability of P. irwini populations to future dam development and demonstrate the importance of studying basin-wide data sets with genetic metrics to understand the strength and direction of anthropogenic impacts on fish populations.
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Affiliation(s)
- Francisca Valenzuela‐Aguayo
- Laboratorio de Ecología y Conservación de PecesDepartamento de Sistemas AcuáticosFacultad de Ciencias Ambientales y Centro EULAUniversidad de ConcepciónConcepciónChile
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| | | | - Aliro Manosalva
- Laboratorio de Ecología y Conservación de PecesDepartamento de Sistemas AcuáticosFacultad de Ciencias Ambientales y Centro EULAUniversidad de ConcepciónConcepciónChile
| | - Evelyn Habit
- Laboratorio de Ecología y Conservación de PecesDepartamento de Sistemas AcuáticosFacultad de Ciencias Ambientales y Centro EULAUniversidad de ConcepciónConcepciónChile
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5
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Nakano S, Fausch KD, Koizumi I, Kanno Y, Taniguchi Y, Kitano S, Miyake Y. Evaluating a pattern of ecological character displacement: charr jaw morphology and diet diverge in sympatry versus allopatry across catchments in Hokkaido, Japan. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
AbstractSimilar species that overlap in sympatry may diverge in characters related to resource use as a result of evolution or phenotypic plasticity. Dolly Varden charr (Salvelinus malma) and whitespotted charr (S. leucomaenis) overlap along streams in Hokkaido, Japan, and compete by interference for invertebrate drift-foraging positions. Previous research has shown that as drift declines during summer, Dolly Varden shift foraging modes to capture benthic prey, a behaviour facilitated by their subterminal jaw morphology. We compare body and jaw morphology of Dolly Varden in sympatry vs. allopatry in two locations to test for character displacement. Statistical analysis showed significant divergence in characters related to foraging, which was correlated with variation in individual charr diets. Dolly Varden in sympatry had shorter heads and lower jaws than in allopatry, and even within sites charr with these characteristics fed less on drifting terrestrial invertebrates but more on benthic aquatic invertebrates. Those in allopatry had longer heads and lower jaws, and fed more on terrestrial invertebrates. The close proximity of sites in one stream suggests that Dolly Varden may display phenotypic plasticity similar to other charr, allowing rapid responses in morphology to the presence of competitors. These morphological shifts probably help them maintain positive fitness when competing with whitespotted charr in Hokkaido streams.
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Affiliation(s)
- Shigeru Nakano
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan, and Tomakomai Forest Research Station, Hokkaido University Forests, Tomakomai, Hokkaido, Japan
| | - Kurt D Fausch
- Department of Fish, Wildlife, and Conservation Biology, and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | - Itsuro Koizumi
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yoichiro Kanno
- Department of Fish, Wildlife, and Conservation Biology, and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | | | - Satoshi Kitano
- Nagano Environmental Conservation Research Institute, Kitago, Nagano, Japan
| | - Yo Miyake
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan
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6
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Homola JJ, Loftin CS, Kinnison MT. Landscape genetics reveals unique and shared effects of urbanization for two sympatric pool-breeding amphibians. Ecol Evol 2019; 9:11799-11823. [PMID: 31695889 PMCID: PMC6822048 DOI: 10.1002/ece3.5685] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/26/2019] [Accepted: 08/30/2019] [Indexed: 01/05/2023] Open
Abstract
Metapopulation-structured species can be negatively affected when landscape fragmentation impairs connectivity. We investigated the effects of urbanization on genetic diversity and gene flow for two sympatric amphibian species, spotted salamanders (Ambystoma maculatum) and wood frogs (Lithobates sylvaticus), across a large (>35,000 km2) landscape in Maine, USA, containing numerous natural and anthropogenic gradients. Isolation-by-distance (IBD) patterns differed between the species. Spotted salamanders showed a linear and relatively high variance relationship between genetic and geographic distances (r = .057, p < .001), whereas wood frogs exhibited a strongly nonlinear and lower variance relationship (r = 0.429, p < .001). Scale dependence analysis of IBD found gene flow has its most predictable influence (strongest IBD correlations) at distances up to 9 km for spotted salamanders and up to 6 km for wood frogs. Estimated effective migration surfaces revealed contrasting patterns of high and low genetic diversity and gene flow between the two species. Population isolation, quantified as the mean IBD residuals for each population, was associated with local urbanization and less genetic diversity in both species. The influence of geographic proximity and urbanization on population connectivity was further supported by distance-based redundancy analysis and multiple matrix regression with randomization. Resistance surface modeling found interpopulation connectivity to be influenced by developed land cover, light roads, interstates, and topography for both species, plus secondary roads and rivers for wood frogs. Our results highlight the influence of anthropogenic landscape features within the context of natural features and broad spatial genetic patterns, in turn supporting the premise that while urbanization significantly restricts interpopulation connectivity for wood frogs and spotted salamanders, specific landscape elements have unique effects on these two sympatric species.
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Affiliation(s)
| | - Cynthia S. Loftin
- Maine Cooperative Fish and Wildlife Research UnitU.S. Geological SurveyOronoMEUSA
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7
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Sahashi G, Morita K. Adoption of alternative migratory tactics: a view from the ultimate mechanism and threshold trait changes in a salmonid fish. OIKOS 2017. [DOI: 10.1111/oik.03715] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Genki Sahashi
- Div. of Biosphere Science; Graduate School of Environmental Sciences, Hokkaido Univ., Hakodate; Hokkaido Japan
- Dept of Aquatic Life Science; Graduate School of Agriculture and Life Sciences, The Univ. of Tokyo, 1-1-1 Yayoi, Bunkyo-ku; JP-113-8657 Tokyo Japan
| | - Kentaro Morita
- Hokkaido National Fisheries Research Institute, Japan Fisheries Research and Education Agency; Sapporo Japan
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8
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Marion ZH, Fordyce JA, Fitzpatrick BM. Pairwise beta diversity resolves an underappreciated source of confusion in calculating species turnover. Ecology 2017; 98:933-939. [DOI: 10.1002/ecy.1753] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 01/11/2017] [Accepted: 01/17/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Zachary H. Marion
- Department of Ecology & Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
| | - James A. Fordyce
- Department of Ecology & Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
| | - Benjamin M. Fitzpatrick
- Department of Ecology & Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
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9
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Sultana N, Igawa T, Islam MM, Hasan M, Alam MS, Komaki S, Kawamura K, Khan MMR, Sumida M. Inter- and intra-specific genetic divergence of Asian tiger frogs (genus Hoplobatrachus), with special reference to the population structure of H. tigerinus in Bangladesh. Genes Genet Syst 2017; 91:217-227. [PMID: 27452042 DOI: 10.1266/ggs.16-00006] [Citation(s) in RCA: 2] [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 five frog species of the genus Hoplobatrachus are widely distributed in Asia and Africa, with Asia being considered the genus' origin. However, the evolutionary relationships of Asian Hoplobatrachus species remain ambiguous. Additionally, genetic diversity and fundamental differentiation processes within species have not been studied. We conducted molecular phylogenetic analysis on Asian Hoplobatrachus frogs and population genetic analysis on H. tigerinus in Bangladesh using the mitochondrial CYTB gene and 21 microsatellite markers. The resultant phylogenetic tree revealed monophyly in each species, notwithstanding the involvement of cryptic species in H. chinensis and H. tigerinus, which are evident from the higher genetic divergence between populations. Bayesian inference of population structure revealed genetic divergence between western and eastern H. tigerinus populations in Bangladesh, suggesting restricted gene flow caused by barriers posed by major rivers. However, genetic distances among populations were generally low. A discrete population is located in the low riverine delta region, which likely reflects long-distance dispersal. These results strongly suggest that the environment specific to this river system has maintained the population structure of H. tigerinus in this region.
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Affiliation(s)
- Nasrin Sultana
- Institute for amphibian Biology, Graduate School of Science, Hiroshima University
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10
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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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11
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Li X, Deng Y, Yang K, Gan W, Zeng R, Deng L, Song Z. Genetic Diversity and Structure Analysis of Percocypris pingi (Cypriniformes: Cyprinidae): Implications for Conservation and Hatchery Release in the Yalong River. PLoS One 2016; 11:e0166769. [PMID: 27911911 PMCID: PMC5135059 DOI: 10.1371/journal.pone.0166769] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 11/03/2016] [Indexed: 11/19/2022] Open
Abstract
Percocypris pingi is a near threatened cyprinid species, which has suffered a dramatic decline due to anthropogenic factors. As one response to this decline, hatchery release for P. pingi has been conducted in the lower reaches of the Yalong River since 2012. To understand the conservation status of this species and the potential impact of the release of hatchery-reared fish, we studied the genetic diversity and population structure of wild and hatchery populations of P. pingi. Two hatchery populations (Jinping [JPH] and Ya’an [YAH]) and two wild populations (Muli [MLW] and Woluo [WLW]) of P. pingi were analyzed based on microsatellite markers and the mitochondrial DNA control region. The results showed that P. pingi possesses moderate levels of genetic diversity, with observed heterozygosities ranging from 0.657 to 0.770 and nucleotide diversities ranging from 0.00212 to 0.00491. Our results also suggested WLW harbors considerable proportions of genetic diversity in this species and serves as a refuge for P. pingi during anthropogenic disturbance, thus playing an important role for the conservation of P. pingi populations. Microsatellite and mitochondrial markers both indicated close genetic relationships between YAH and MLW, JPH and WLW, respectively. The results to some extent reflected the geographical provenances for original broodstocks of the two hatchery populations, which provide some practical guidance for hatchery release of P. pingi. The existence of remarkable genetic divergence distributed along limited geographical range (approximately 10 kilometers) suggests the two wild populations should be regarded at least as two distinct evolutionary significant units (ESUs) and management units (MUs). Considering reduced intra-population genetic variation in hatchery population for release and significant genetic compositions of the two hatchery populations, some appropriate breeding strategies were proposed to benefit conservation of P. pingi.
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Affiliation(s)
- Xiaoyan Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yuanping Deng
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Kun Yang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Weixiong Gan
- Yalong River Hydropower Development Company, Ltd., Chengdu, China
| | - Rukui Zeng
- Yalong River Hydropower Development Company, Ltd., Chengdu, China
| | - Longjun Deng
- Yalong River Hydropower Development Company, Ltd., Chengdu, China
| | - Zhaobin Song
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- * E-mail:
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12
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Inostroza PA, Vera-Escalona I, Wicht AJ, Krauss M, Brack W, Norf H. Anthropogenic Stressors Shape Genetic Structure: Insights from a Model Freshwater Population along a Land Use Gradient. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:11346-11356. [PMID: 27643810 DOI: 10.1021/acs.est.6b04629] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Environmental pollution including mutagens from wastewater effluents and discontinuity by man-made barriers are considered typical anthropogenic pressures on microevolutionary processes that are responsible for the loss of biodiversity in aquatic ecosystems. Here, we tested for the effects of wastewater treatment plants (WWTPs), weirs and other stressors on the invertebrate species Gammarus pulex at the population genetic level combining evolutionary ecotoxicology, body burden analysis and testing for exposure to mutagens. Exposure to chemical pollution alone and in combination with the presence of weirs resulted in a depression of allelic richness in native G. pulex populations. Our results suggest that the input of a mutagenic effluent from a WWTP resulted in a strong increase in private alleles over the affected populations. In addition, the presence of weirs along the river disrupted the migration across the river and thus the gene flow between G. pulex upstream and downstream. This study provides strong evidence that the assessment of genetic variation including private alleles together with the contamination of mutagenic and nonmutagenic chemical pollution offers new insights into the regulation of genetic population structure and highlights the relevance of emerging anthropogenic pressures at the genetic level.
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Affiliation(s)
- Pedro A Inostroza
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ , Permoserstraße 15, Leipzig, Germany
- Department of Ecosystem Analyses, RWTH Aachen University, Institute for Environmental Research , Worringerweg 1, Aachen, Germany
| | - Iván Vera-Escalona
- Department of Biology, Dalhousie University , 1355 Oxford St., Halifax, Canada
| | - Anna-Jorina Wicht
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ , Permoserstraße 15, Leipzig, Germany
- Department of Ecosystem Analyses, RWTH Aachen University, Institute for Environmental Research , Worringerweg 1, Aachen, Germany
| | - Martin Krauss
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ , Permoserstraße 15, Leipzig, Germany
| | - Werner Brack
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ , Permoserstraße 15, Leipzig, Germany
- Department of Ecosystem Analyses, RWTH Aachen University, Institute for Environmental Research , Worringerweg 1, Aachen, Germany
| | - Helge Norf
- Department of Aquatic Ecosystem Analysis and Management, Helmholtz Centre for Environmental Research - UFZ , Brückstraße 3A, Magdeburg, Germany
- Department of River Ecology, Helmholtz Centre for Environmental Research - UFZ , Brückstraße 3A, Magdeburg, Germany
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13
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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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14
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Koizumi I, Shimatani IK. Socially induced reproductive synchrony in a salmonid: an approximate Bayesian computation approach. Behav Ecol 2016. [DOI: 10.1093/beheco/arw056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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15
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Lemoine M, Lucek K, Perrier C, Saladin V, Adriaensen F, Barba E, Belda EJ, Charmantier A, Cichoń M, Eeva T, Grégoire A, Hinde CA, Johnsen A, Komdeur J, Mänd R, Matthysen E, Norte AC, Pitala N, Sheldon BC, Slagsvold T, Tinbergen JM, Török J, Ubels R, van Oers K, Visser ME, Doligez B, Richner H. Low but contrasting neutral genetic differentiation shaped by winter temperature in European great tits. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12745] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Mélissa Lemoine
- Institute for Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 CH-8057 Zurich Switzerland
| | - Kay Lucek
- Aquatic Ecology and Evolution; Institute of Ecology and Evolution; University of Bern; Baltzerstrasse 6 CH-3012 Bern Switzerland
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
| | - Charles Perrier
- Centre d'Ecologie Fonctionnelle et Evolutive; Unité Mixte de Recherche 5175; 1919 Route de Mende FR-34293 Montpellier Cedex 5 France
| | - Verena Saladin
- Division of Evolutionary Ecology; Institute of Ecology and Evolution; University of Bern; Baltzerstrasse 6 CH-3012 Bern Switzerland
| | - Frank Adriaensen
- Evolutionary Ecology Group; Department of Biology; University of Antwerp; BE-2020 Antwerp Belgium
| | - Emilio Barba
- Cavanilles’ Institute of Biodiversity and Evolutionary Biology; University of Valencia; C/Catedrático José Beltrán 2 46980 Paterna Spain
| | - Eduardo J. Belda
- Instituto de Investigación para la Gestión Integrada de Zonas Costeras-IGIC; U.P.V.; C/Paranínfo n° 1 ES-46730 Gandia Valencia Spain
| | - Anne Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive; Unité Mixte de Recherche 5175; 1919 Route de Mende FR-34293 Montpellier Cedex 5 France
| | - Mariusz Cichoń
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - Tapio Eeva
- Department of Biology; University of Turku; FI-20014 Turku Finland
| | - Arnaud Grégoire
- Centre d'Ecologie Fonctionnelle et Evolutive; Unité Mixte de Recherche 5175; 1919 Route de Mende FR-34293 Montpellier Cedex 5 France
| | - Camilla A. Hinde
- Behavioural Ecology Group; Department of Animal Sciences; Wageningen University; 6700 AH Wageningen The Netherlands
| | - Arild Johnsen
- Natural History Museum; University of Oslo; PO Box 1172 Blindern NO-0318 Oslo Norway
| | - Jan Komdeur
- Behavioural Ecology and Self-organization; Centre for Ecological and Evolutionary studies; University of Groningen; PO Box 11103 NL-9747 AG Groningen The Netherlands
| | - Raivo Mänd
- Department of Zoology; Institute of Ecology and Earth Sciences; University of Tartu; Vanemuise 46 Tartu EE-51014 Estonia
| | - Erik Matthysen
- Evolutionary Ecology Group; Department of Biology; University of Antwerp; BE-2020 Antwerp Belgium
| | - Ana Cláudia Norte
- Department of Life Sciences; Largo Marquês de Pombal; Faculty of Sciences and Technology; Marine and Environmental Sciences Centre (MARE); University of Coimbra; 3004-517 Coimbra Portugal
| | - Natalia Pitala
- Department of Biological and Environmental Science; University of Jyväskylä; PO Box 35 FI-40014 Finland
| | - Ben C. Sheldon
- Edward Grey Institute of Field Ornithology; Department of Zoology; University of Oxford; South Parks Road Oxford OX1 3PS England
| | - Tore Slagsvold
- Centre for Ecological and Evolutionary Synthesis (CEES); Department of Biosciences; University of Oslo; PO Box 1066 Blindern NO-0316 Oslo Norway
| | - Joost M. Tinbergen
- Animal Ecology Group; Centre for Ecological and Evolutionary Studies; University of Groningen; PO Box 11103 NL-9747 AG Groningen The Netherlands
| | - János Török
- Behavioural Ecology Group; Department of Systematic Zoology and Ecology; Eötvös Loránd University; Pázmány Péter sétány 1/c 1117 Budapest Hungary
| | - Richard Ubels
- Animal Ecology Group; Centre for Ecological and Evolutionary Studies; University of Groningen; PO Box 11103 NL-9747 AG Groningen The Netherlands
| | - Kees van Oers
- Department of Animal Ecology; Netherlands Institute of Ecology (NIOO-KNAW); PO Box 50; 6700 AB Wageningen The Netherlands
| | - Marcel E. Visser
- Department of Animal Ecology; Netherlands Institute of Ecology (NIOO-KNAW); PO Box 50; 6700 AB Wageningen The Netherlands
| | - Blandine Doligez
- Department of Biometry and Evolutionary Biology; CNRS, University of Lyon, UMR 5558; F-69622 Villeurbanne Cedex France
- Animal Ecology/Department of Ecology and Genetics; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18d SE-752 36 Uppsala Sweden
| | - Heinz Richner
- Division of Evolutionary Ecology; Institute of Ecology and Evolution; University of Bern; Baltzerstrasse 6 CH-3012 Bern Switzerland
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16
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Ruzzante DE, McCracken GR, Parmelee S, Hill K, Corrigan A, MacMillan J, Walde SJ. Effective number of breeders, effective population size and their relationship with census size in an iteroparous species, Salvelinus fontinalis. Proc Biol Sci 2016; 283:20152601. [PMID: 26817773 PMCID: PMC4795031 DOI: 10.1098/rspb.2015.2601] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/07/2016] [Indexed: 11/12/2022] Open
Abstract
The relationship between the effective number of breeders (Nb) and the generational effective size (Ne) has rarely been examined empirically in species with overlapping generations and iteroparity. Based on a suite of 11 microsatellite markers, we examine the relationship between Nb, Ne and census population size (Nc) in 14 brook trout (Salvelinus fontinalis) populations inhabiting 12 small streams in Nova Scotia and sampled at least twice between 2009 and 2015. Unbiased estimates of Nb obtained with individuals of a single cohort, adjusted on the basis of age at first maturation (α) and adult lifespan (AL), were from 1.66 to 0.24 times the average estimates of Ne obtained with random samples of individuals of mixed ages (i.e. [Formula: see text]). In turn, these differences led to adjusted Ne estimates that were from nearly five to 0.7 times the estimates derived from mixed-aged individuals. These differences translate into the same range of variation in the ratio of effective to census population size [Formula: see text] within populations. Adopting [Formula: see text] as the more precise and unbiased estimates, we found that these brook trout populations differ markedly in their effective to census population sizes (range approx. 0.3 to approx. 0.01). Using AgeNe, we then showed that the variance in reproductive success or reproductive skew varied among populations by a factor of 40, from Vk/k ≈ 5 to 200. These results suggest wide differences in population dynamics, probably resulting from differences in productivity affecting the intensity of competition for access to mates or redds, and thus reproductive skew. Understanding the relationship between Ne, Nb and Nc, and how these relate to population dynamics and fluctuations in population size, are important for the design of robust conservation strategies in small populations with overlapping generations and iteroparity.
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Affiliation(s)
- Daniel E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Gregory R McCracken
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Samantha Parmelee
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Kristen Hill
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Amelia Corrigan
- Inland Fisheries Division, Nova Scotia Department of Fisheries and Aquaculture, Halifax, Nova Scotia, Canada B3J 2R5
| | - John MacMillan
- Inland Fisheries Division, Nova Scotia Department of Fisheries and Aquaculture, Halifax, Nova Scotia, Canada B3J 2R5
| | - Sandra J Walde
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
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17
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Gouskov A, Reyes M, Wirthner-Bitterlin L, Vorburger C. Fish population genetic structure shaped by hydroelectric power plants in the upper Rhine catchment. Evol Appl 2016; 9:394-408. [PMID: 26834832 PMCID: PMC4721079 DOI: 10.1111/eva.12339] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/02/2015] [Indexed: 01/20/2023] Open
Abstract
The Rhine catchment in Switzerland has been transformed by a chain of hydroelectric power stations. We addressed the impact of fragmentation on the genetic structure of fish populations by focusing on the European chub (Squalius cephalus). This fish species is not stocked and copes well with altered habitats, enabling an assessment of the effects of fragmentation per se. Using microsatellites, we genotyped 2133 chub from 47 sites within the catchment fragmented by 37 hydroelectric power stations, two weirs and the Rhine Falls. The shallow genetic population structure reflected drainage topology and was affected significantly by barriers to migration. The effect of power stations equipped with fishpasses on genetic differentiation was detectable, albeit weaker than that of man‐made barriers without fishpasses. The Rhine Falls as the only long‐standing natural obstacle (formed 14 000 to 17 000 years ago) also had a strong effect. Man‐made barriers also exacerbated the upstream decrease in allelic diversity in the catchment, particularly when lacking fishpasses. Thus, existing fishpasses do have the desired effect of mitigating fragmentation, but barriers still reduce population connectivity in a fish that traverses fishpasses better than many other species. Less mobile species are likely to be affected more severely.
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Affiliation(s)
- Alexandre Gouskov
- Institute of Integrative Biology ETH Zürich Zürich Switzerland; Aquatic Ecology Eawag Dübendorf Switzerland
| | | | | | - Christoph Vorburger
- Institute of Integrative Biology ETH Zürich Zürich Switzerland; Aquatic Ecology Eawag Dübendorf Switzerland
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18
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Klinga P, Mikoláš M, Zhelev P, Höglund J, Paule L. Genetic differentiation of western capercaillie in the Carpathian Mountains: the importance of post glacial expansions and habitat connectivity. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12643] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Peter Klinga
- Faculty of Forestry; Technical University; SK-96053 Zvolen Slovakia
| | - Martin Mikoláš
- Faculty of Forestry and Wood Sciences; Czech University of Life Sciences; Kamýcka cesta 1176 CZ-165 21 Praha 6-Suchdol Czech Republic
- PRALES; Odtrnovie 563 SK-013 22 Rosina Slovakia
| | - Petar Zhelev
- Faculty of Forestry; University of Forestry; Kliment Ohridski Blvd. 10 BG-17456 Sofia Bulgaria
| | - Jacob Höglund
- Department of Ecology and Genetics; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - Ladislav Paule
- Faculty of Forestry; Technical University; SK-96053 Zvolen Slovakia
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19
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Population structure and variability of Pacific herring (Clupea pallasii) in the White Sea, Barents and Kara Seas revealed by microsatellite DNA analyses. Polar Biol 2015. [DOI: 10.1007/s00300-015-1653-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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20
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Raeymaekers JAM, Maes GE, Geldof S, Hontis I, Nackaerts K, Volckaert FAM. Modeling genetic connectivity in sticklebacks as a guideline for river restoration. Evol Appl 2015; 1:475-88. [PMID: 25567729 PMCID: PMC3352376 DOI: 10.1111/j.1752-4571.2008.00019.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Accepted: 01/28/2008] [Indexed: 11/27/2022] Open
Abstract
Estimating genetic connectivity in disturbed riverine landscapes is of key importance for river restoration. However, few species of the disturbed riverine fauna may provide a detailed and basin-wide picture of the human impact on the population genetics of riverine organisms. Here we used the most abundant native fish, the three-spined stickleback (Gasterosteus aculeatus L.), to detect the geographical determinants of genetic connectivity in the eastern part of the Scheldt basin in Belgium. Anthropogenic structures came out as the strongest determinant of population structure, when evaluated against a geographically well-documented baseline model accounting for natural effects. These barriers not only affected genetic diversity, but they also controlled the balance between gene flow and genetic drift, and therefore may crucially disrupt the population structure of sticklebacks. Landscape models explained a high percentage of variation (allelic richness: adjusted R (2) = 0.78; pairwise F ST: adjusted R (2) = 0.60), and likely apply to other species as well. River restoration and conservation genetics may highly benefit from riverine landscape genetics, including model building, the detection of outlier populations, and a specific test for the geographical factors controlling the balance between gene flow and genetic drift.
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Affiliation(s)
- Joost A M Raeymaekers
- Laboratory for Animal Biodiversity and Systematics, Katholieke Universiteit Leuven Leuven, Belgium
| | - Gregory E Maes
- Laboratory for Animal Biodiversity and Systematics, Katholieke Universiteit Leuven Leuven, Belgium
| | - Sarah Geldof
- Laboratory for Animal Biodiversity and Systematics, Katholieke Universiteit Leuven Leuven, Belgium
| | - Ingrid Hontis
- Laboratory for Animal Biodiversity and Systematics, Katholieke Universiteit Leuven Leuven, Belgium
| | - Kris Nackaerts
- InterGraph Belgium NV, Tennessee House, Riverside Business Park Brussels, Belgium
| | - Filip A M Volckaert
- Laboratory for Animal Biodiversity and Systematics, Katholieke Universiteit Leuven Leuven, Belgium
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21
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Aycrigg JL, Garton EO. Linking metapopulation structure to elk population management in Idaho: a genetic approach. J Mammal 2014. [DOI: 10.1644/12-mamm-a-300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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22
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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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23
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Petrou EL, Hauser L, Waples RS, Seeb JE, Templin WD, Gomez-Uchida D, Seeb LW. Secondary contact and changes in coastal habitat availability influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta). Mol Ecol 2013; 22:5848-60. [PMID: 24118255 PMCID: PMC4265302 DOI: 10.1111/mec.12543] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 09/18/2013] [Accepted: 09/23/2013] [Indexed: 02/03/2023]
Abstract
Numerous empirical studies have reported lack of migration–drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ∼13 000 years ago. The chum salmon's (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years.
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Affiliation(s)
- E L Petrou
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, WA, 98112, USA
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24
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Petrou EL, Seeb JE, Hauser L, Witteveen MJ, Templin WD, Seeb LW. Fine-scale sampling reveals distinct isolation by distance patterns in chum salmon (Oncorhynchus keta) populations occupying a glacially dynamic environment. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0534-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Shimono Y, Hayakawa H, Kurokawa S, Nishida T, Ikeda H, Futagami N. Phylogeography of mugwort (Artemisia indica), a native pioneer herb in Japan. J Hered 2013; 104:830-41. [PMID: 24023252 DOI: 10.1093/jhered/est054] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many phylogeographic studies of various tree species have been conducted to elucidate the locations of refugia and the colonization patterns during the Pleistocene. However, only a few large-scale phylogeographic studies have been conducted on herbaceous plants, especially scarce on herbs that are adapted to disturbance. Artemisia indica is a fast-growing perennial herb found in open habitats. To examine the basic information on the genetic structure of this species, we investigated the chloroplast DNA variation within and among populations across Japan. We detected 26 haplotypes in 604 individuals from 28 Japanese populations. The haplotype A1 had wide geographic distribution, and its close relatives were locally present. Some putative ancestral lineages were found mainly in the Kyushu region. This may be because several lineages migrated from the Eurasian continent to the northern coast in Kyushu via the Korean peninsula during the Pleistocene, and the A1 haplotype expanded northward, whereas others remained in southern areas. Phylogenetic distant haplotypes were present mainly in the Kanto region. Because the geographic distribution pattern of these haplotypes in this region is believed to be unnatural, these haplotypes may be derived from commercial sources for re-vegetation during the last few decades.
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Affiliation(s)
- Yoshiko Shimono
- the National Institute for Agro-Environmental Sciences, Tsukuba, Japan
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26
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Reynolds RG, Fitzpatrick BM. Tests of two methods for identifying founder effects in metapopulations reveal substantial type II error. Genetica 2013; 141:119-31. [DOI: 10.1007/s10709-013-9711-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 03/09/2013] [Indexed: 10/27/2022]
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27
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Gomez-Uchida D, Palstra FP, Knight TW, Ruzzante DE. Contemporary effective population and metapopulation size (N e and meta-N e): comparison among three salmonids inhabiting a fragmented system and differing in gene flow and its asymmetries. Ecol Evol 2013; 3:569-80. [PMID: 23532448 PMCID: PMC3605847 DOI: 10.1002/ece3.485] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 12/14/2012] [Accepted: 12/24/2012] [Indexed: 11/15/2022] Open
Abstract
We estimated local and metapopulation effective sizes ([Formula: see text] and meta-[Formula: see text]) for three coexisting salmonid species (Salmo salar, Salvelinus fontinalis, Salvelinus alpinus) inhabiting a freshwater system comprising seven interconnected lakes. First, we hypothesized that [Formula: see text] might be inversely related to within-species population divergence as reported in an earlier study (i.e., FST: S. salar> S. fontinalis> S. alpinus). Using the approximate Bayesian computation method implemented in ONeSAMP, we found significant differences in [Formula: see text] ([Formula: see text]) between species, consistent with a hierarchy of adult population sizes ([Formula: see text]). Using another method based on a measure of linkage disequilibrium (LDNE: [Formula: see text]), we found more finite [Formula: see text] values for S. salar than for the other two salmonids, in line with the results above that indicate that S. salar exhibits the lowest [Formula: see text] among the three species. Considering subpopulations as open to migration (i.e., removing putative immigrants) led to only marginal and non-significant changes in [Formula: see text], suggesting that migration may be at equilibrium between genetically similar sources. Second, we hypothesized that meta-[Formula: see text] might be significantly smaller than the sum of local [Formula: see text]s (null model) if gene flow is asymmetric, varies among subpopulations, and is driven by common landscape features such as waterfalls. One 'bottom-up' or numerical approach that explicitly incorporates variable and asymmetric migration rates showed this very pattern, while a number of analytical models provided meta-[Formula: see text] estimates that were not significantly different from the null model or from each other. Our study of three species inhabiting a shared environment highlights the importance and utility of differentiating species-specific and landscape effects, not only on dispersal but also in the demography of wild populations as assessed through local [Formula: see text]s and meta-[Formula: see text]s and their relevance in ecology, evolution and conservation.
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28
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Scharsack JP, Schweyen H, Schmidt AM, Dittmar J, Reusch TB, Kurtz J. Population genetic dynamics of three-spined sticklebacks (Gasterosteus aculeatus) in anthropogenic altered habitats. Ecol Evol 2012; 2:1122-43. [PMID: 22833789 PMCID: PMC3402189 DOI: 10.1002/ece3.232] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 01/18/2012] [Indexed: 01/26/2023] Open
Abstract
In industrialized and/or agriculturally used landscapes, inhabiting species are exposed to a variety of anthropogenic changes in their environments. Genetic diversity may be reduced if populations encounter founder events, bottlenecks, or isolation. Conversely, genetic diversity may increase if populations adapt to changes in selective regimes in newly created habitats. With the present study, genetic variability of 918 sticklebacks from 43 samplings (21.3 ± 3.8 per sample) at 36 locations from cultivated landscapes in Northwest Germany was analyzed at nine neutral microsatellite loci. To test if differentiation is influenced by habitat alterations, sticklebacks were collected from ancient running waters and adjacent artificial stagnant waters, from brooks with salt water inflow of anthropogenic and natural origin and adjacent freshwater sites. Overall population structure was dominated by isolation by distance (IBD), which was significant across all populations, and analysis of molecular variance (AMOVA) revealed that 10.6% of the variation was explained by river catchment area. Populations in anthropogenic modified habitats deviated from the general IBD structure and in the AMOVA, grouping by habitat type running/stagnant water explained 4.9% of variation and 1.4% of the variation was explained by salt-/freshwater habitat. Sticklebacks in salt-polluted water systems seem to exhibit elevated migratory activity between fresh- and saltwater habitats, reducing IBD. In other situations, populations showed distinct signs of genetic isolation, which in some locations was attributed to mechanical migration barriers, but in others to potential anthropogenic induced bottleneck or founder effects. The present study shows that anthropogenic habitat alterations may have diverse effects on the population genetic structure of inhabiting species. Depending on the type of habitat change, increased genetic differentiation, diversification, or isolation are possible consequences.
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29
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carrea C, Barriga JP, Cussac VE, Ruzzante DE. Genetic and phenotypic differentiation among Galaxias maculatus populations in a Patagonian postglacial lake system. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01939.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Juan P. Barriga
- INIBIOMA (Universidad Nacional del Comahue-CONICET) Quintral; 1250 (8400); Bariloche; RN; Argentina
| | - Victor E. Cussac
- INIBIOMA (Universidad Nacional del Comahue-CONICET) Quintral; 1250 (8400); Bariloche; RN; Argentina
| | - Daniel E. Ruzzante
- Department of Biology; Dalhousie University; Halifax; NS; B3H 4R2; Canada
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30
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Toju H, Ueno S, Taniguchi F, Sota T. Metapopulation structure of a seed-predator weevil and its host plant in arms race coevolution. Evolution 2011; 65:1707-22. [PMID: 21644958 DOI: 10.1111/j.1558-5646.2011.01243.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Although the importance of gene flow in the geographic structuring of host-parasite interactions has been well discussed, little is known about how dispersal drives the spatial dynamics of other types of coevolutionary interactions in nature. We evaluated the roles of gene flow in the geographically structured processes of a predator-prey arms race involving a seed-predatory weevil with a long mouthpart and its host camellia plant with a thick fruit coat. Molecular genetic analyses showed that both weevil and camellia populations were structured at a spatial scale of several kilometers. Importantly, the spatial pattern of the migration of weevils, but not that of camellias, imposed significant effects on the geographic configuration of the levels of coevolutionary escalation. This result suggests that even if migration is limited in one species (camellia), local coevolution with the other species that migrates between neighboring localities (weevil) can reduce the interpopulation difference in the local adaptive optima of the former species. Thus, gene flow of a species potentially homogenizes the local biological environments provided by the species and thereby promotes the evolutionary convergence of its coevolving counterparts. Consequently, by focusing on coevolutionary interactions in natural communities, "indirect" effects of gene flow on the adaptive divergence of organisms could be identified.
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Affiliation(s)
- Hirokazu Toju
- Division of Biological Science, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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31
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Junge C, Vøllestad LA, Barson NJ, Haugen TO, Otero J, Sætre GP, Leder EH, Primmer CR. Strong gene flow and lack of stable population structure in the face of rapid adaptation to local temperature in a spring-spawning salmonid, the European grayling (Thymallus thymallus). Heredity (Edinb) 2011; 106:460-71. [PMID: 21224882 PMCID: PMC3131973 DOI: 10.1038/hdy.2010.160] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 11/19/2010] [Accepted: 11/22/2010] [Indexed: 11/09/2022] Open
Abstract
Gene flow has the potential to both constrain and facilitate adaptation to local environmental conditions. The early stages of population divergence can be unstable because of fluctuating levels of gene flow. Investigating temporal variation in gene flow during the initial stages of population divergence can therefore provide insights to the role of gene flow in adaptive evolution. Since the recent colonization of Lake Lesjaskogsvatnet in Norway by European grayling (Thymallus thymallus), local populations have been established in over 20 tributaries. Multiple founder events appear to have resulted in reduced neutral variation. Nevertheless, there is evidence for local adaptation in early life-history traits to different temperature regimes. In this study, microsatellite data from almost a decade of sampling were assessed to infer population structuring and its temporal stability. Several alternative analyses indicated that spatial variation explained 2-3 times more of the divergence in the system than temporal variation. Over all samples and years, there was a significant correlation between genetic and geographic distance. However, decomposed pairwise regression analysis revealed differing patterns of genetic structure among local populations and indicated that migration outweighs genetic drift in the majority of populations. In addition, isolation by distance was observable in only three of the six years, and signals of population bottlenecks were observed in the majority of samples. Combined, the results suggest that habitat-specific adaptation in this system has preceded the development of consistent population substructuring in the face of high levels of gene flow from divergent environments.
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Affiliation(s)
- C Junge
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.
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32
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The influence of historical geneflow, bathymetry and distribution patterns on the population genetics of morphologically diverse Galápagos' Opuntia echios. J Mol Evol 2011; 72:315-25. [PMID: 21336620 DOI: 10.1007/s00239-011-9434-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 01/28/2011] [Indexed: 10/18/2022]
Abstract
Throughout history, remote archipelagos have repeatedly been designated natural laboratories to study evolutionary processes. The extensive, geographically structured, morphological variation within Galápagos' Opuntia cacti has been presumed to be another example of how such processes shape diversity. However, recent genetic studies on speciation and potential effects of plasticity within this system failed to confirm earlier classification and hypothesized radiation on both global and single island levels. Detailed population genetic information, however, is crucial in conserving these semi-arid ecosystem keystone species. In this article, we re-evaluate the genetics of Opuntia echios inhabiting one of the most taxon rich places on the archipelago: Santa Cruz and its surrounding satellite islands, using microsatellite data. Our analysis revealed high genetic variability within all sampled locations, providing little support for the hypothesis of clonal reproduction. Inter-island gene flow patterns appear to be largely influenced by bathymetry and sea levels during last ice ages. Although O. echios from Seymour Norte are morphologically recognized as being a separate taxon, Daphné Major's cacti are the most differentiated. In addition, we found a potential barrier for gene flow along the ring-like distribution of Opuntias at the western side of Santa Cruz, suggesting potential links with geology.
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Savage WK, Fremier AK, Shaffer HB. Landscape genetics of alpine Sierra Nevada salamanders reveal extreme population subdivision in space and time. Mol Ecol 2010; 19:3301-14. [PMID: 20701683 DOI: 10.1111/j.1365-294x.2010.04718.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Quantifying the influence of the landscape on the genetic structure of natural populations remains an important empirical challenge, particularly for poorly studied, ecologically cryptic species. We conducted an extensive microsatellite analysis to examine the population genetics of the southern long-toed salamander (Ambystoma macrodactylum sigillatum) in a naturally complex landscape. Using spatially explicit modelling, we investigated the influence of the Sierra Nevada topography on potential dispersal corridors between sampled populations. Our results indicate very high-genetic divergence among populations, high within-deme relatedness, and little evidence of recent migration or population admixture. We also discovered unexpectedly high between-year genetic differentiation (F(ST)) for breeding sites, suggesting that breeding groups vary over localized space and time. While environmental factors associated with high-elevation montane habitats apparently play an important role in shaping population differentiation, additional, species-specific biological processes must also be operating to account for observed deviations from temporal, among-year panmixia. Our study emphasizes the population-level insights that can be gained from high-density sampling in space and time, and the highly substructured population biology that may characterize amphibians in extreme montane habitats.
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Affiliation(s)
- Wesley K Savage
- Department of Evolution and Ecology, and Center for Population Biology, University of California, Davis, CA 95616-8755, USA.
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MEEUWIG MICHAELH, GUY CHRISTOPHERS, KALINOWSKI STEVENT, FREDENBERG WADEA. Landscape influences on genetic differentiation among bull trout populations in a stream-lake network. Mol Ecol 2010; 19:3620-33. [DOI: 10.1111/j.1365-294x.2010.04655.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Olsen JB, Beacham TD, Wetklo M, Seeb LW, Smith CT, Flannery BG, Wenburg JK. The influence of hydrology and waterway distance on population structure of Chinook salmon Oncorhynchus tshawytscha in a large river. JOURNAL OF FISH BIOLOGY 2010; 76:1128-1148. [PMID: 20409166 DOI: 10.1111/j.1095-8649.2010.02554.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Adult Chinook salmon Oncorhynchus tshawytscha navigate in river systems using olfactory cues that may be influenced by hydrologic factors such as flow and the number, size and spatial distribution of tributaries. Thus, river hydrology may influence both homing success and the level of straying (gene flow), which in turn influences population structure. In this study, two methods of multivariate analysis were used to examine the extent to which four indicators of hydrology and waterway distance explained population structure of O. tshawytscha in the Yukon River. A partial Mantel test showed that the indicators of hydrology were positively associated with broad-scale (Yukon basin) population structure, when controlling for the influence of waterway distance. Multivariate multiple regression showed that waterway distance, supplemented with the number and flow of major drainage basins, explained more variation in broad-scale population structure than any single indicator. At an intermediate spatial scale, indicators of hydrology did not appear to influence population structure after accounting for waterway distance. These results suggest that habitat changes in the Yukon River, which alter hydrology, may influence the basin-wide pattern of population structure in O. tshawytscha. Further research is warranted on the role of hydrology in concert with waterway distance in influencing population structure in Pacific salmon.
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Affiliation(s)
- J B Olsen
- Conservation Genetics Laboratory, US Fish and Wildlife Service Alaska Region, Anchorage, AK 99503, USA. jeffrey
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SHIKANO TAKAHITO, SHIMADA YUKINORI, HERCZEG GÁBOR, MERILÄ JUHA. History vs. habitat type: explaining the genetic structure of European nine-spined stickleback (Pungitius pungitius) populations. Mol Ecol 2010; 19:1147-61. [DOI: 10.1111/j.1365-294x.2010.04553.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Griffiths AM, Koizumi I, Bright D, Stevens JR. A case of isolation by distance and short-term temporal stability of population structure in brown trout (Salmo trutta) within the River Dart, southwest England. Evol Appl 2009; 2:537-54. [PMID: 25567897 PMCID: PMC3352451 DOI: 10.1111/j.1752-4571.2009.00092.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Accepted: 06/09/2009] [Indexed: 11/29/2022] Open
Abstract
Salmonid fishes exhibit high levels of population differentiation. In particular, the brown trout (Salmo trutta L.) demonstrates complex within river drainage genetic structure. Increasingly, these patterns can be related to the underlying evolutionary models, of which three scenarios (member-vagrant hypothesis, metapopulation model and panmixia) facilitate testable predictions for investigations into population structure. We analysed 1225 trout collected from the River Dart, a 75 km long river located in southwest England. Specimens were collected from 22 sample sites across three consecutive summers (2001-2003) and genetic variation was examined at nine microsatellite loci. A hierarchical analysis of molecular variance revealed that negligible genetic variation was attributed among temporal samples. The highest levels of differentiation occurred among samples isolated above barriers to fish movement, and once these samples were removed, a significant effect of isolation-by-distance was observed. These results suggest that, at least in the short-term, ecological events are more important in shaping the population structure of Dart trout than stochastic extinction events, and certainly do not contradict the expectations of a member-vagrant hypothesis. Furthermore, individual-level spatial autocorrelation analyses support previous recommendations for the preservation of a number of spawning sites spaced throughout the tributary system to conserve the high levels of genetic variation identified in salmonid species.
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Affiliation(s)
- Andrew M Griffiths
- Hatherly Laboratories, School of Biosciences, University of Exeter Devon, UK
| | - Itsuro Koizumi
- Division of Environmental Science Development, Graduate School of Environmental Science, Hokkaido University Hokkaido, Japan
| | | | - Jamie R Stevens
- Hatherly Laboratories, School of Biosciences, University of Exeter Devon, UK
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Gomez-Uchida D, Knight TW, Ruzzante DE. Interaction of landscape and life history attributes on genetic diversity, neutral divergence and gene flow in a pristine community of salmonids. Mol Ecol 2009; 18:4854-69. [PMID: 19878451 DOI: 10.1111/j.1365-294x.2009.04409.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Landscape genetics holds promise for the forecasting of spatial patterns of genetic diversity based on key environmental features. Yet, the degree to which inferences based on single species can be extended to whole communities is not fully understood. We used a pristine and spatially structured community of three landlocked salmonids (Salvelinus fontinalis, Salmo salar, and Salvelinus alpinus) from Gros Morne National Park (Newfoundland, Canada) to test several predictions on the interacting effects of landscape and life history variation on genetic diversity, neutral divergence, and gene flow (m, migration rate). Landscape factors consistently influenced multispecies genetic patterns: (i) waterfalls created strong dichotomies in genetic diversity and divergence between populations above and below them in all three salmonids; (ii) contemporary m decreased with waterway distance in all three species, while neutral genetic divergence (theta) increased with waterway distance, albeit in only two taxa; (iii) river flow generally produced downstream-biased m between populations when waterfalls separated these, but not otherwise. In contrast, we expected differential life history to result in a hierarchy of neutral divergence (S. salar > S. fontinalis > S. alpinus) based on disparities in dispersal abilities and population size from previous mark-recapture studies. Such hierarchy additionally matched varying degrees of spatial genetic structure among species revealed through individual-based analyses. We conclude that, whereas key landscape attributes hold power to predict multispecies genetic patterns in equivalent communities, they are likely to interact with species-specific life history attributes such as dispersal, demography, and ecology, which will in turn affect holistic conservation strategies.
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Affiliation(s)
- Daniel Gomez-Uchida
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS B3H4J1, Canada.
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Raeymaekers JAM, Raeymaekers D, Koizumi I, Geldof S, Volckaert FAM. Guidelines for restoring connectivity around water mills: a population genetic approach to the management of riverine fish. J Appl Ecol 2009. [DOI: 10.1111/j.1365-2664.2009.01652.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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ZAMUDIO KELLYR, ROBERTSON JEANNEM, CHAN LAURENM, SAZIMA IVAN. Population structure in the catfish Trichogenes longipinnis: drift offset by asymmetrical migration in a tiny geographic range. Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2009.01209.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wagner CE, McCune AR. Contrasting patterns of spatial genetic structure in sympatric rock-dwelling cichlid fishes. Evolution 2009; 63:1312-26. [PMID: 19154384 DOI: 10.1111/j.1558-5646.2009.00612.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cichlid fish of Lake Tanganyika in Eastern Africa are a celebrated example of both ecological and species diversification. Because population subdivision is likely to play an important role in the speciation process, understanding how habitat features interact with species' demographic, behavioral and ecological attributes to influence gene flow and population divergence may help explain the causes of high species richness in this and other systems. Here, we test the roles of isolation-by-habitat and isolation-by-distance in generating fine-scale population genetic structure in three sympatric species of habitat-restricted cichlids in Lake Tanganyika. Using multilocus microsatellite genotypes, we contrast patterns of population differentiation in these habitat specialists along a mosaic coastline of both favorable and unfavorable habitat. Despite their close phylogenetic relationship and shared habitat affinity, these species show striking differences in their pattern of genetic subdivision within the same geographical region, suggesting substantially different patterns of gene flow. In particular, two trophically specialized species exhibit much more restricted gene flow over sandy habitat than a trophically opportunistic species. This result suggests that ecological and behavioral traits have a strong influence on the scale and degree of population subdivision, a finding that has potentially important implications for understanding differential propensities for diversification among lineages and phylogenetic patterns of diversity.
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Affiliation(s)
- Catherine E Wagner
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA.
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Koizumi I, Yamamoto S, Nomoto K, Maekawa K. Synchrony in local population dynamics of stream-dwelling Dolly Varden: do genetically similar groups show similar demography? POPUL ECOL 2008. [DOI: 10.1007/s10144-008-0108-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Barr KR, Lindsay DL, Athrey G, Lance RF, Hayden TJ, Tweddale SA, Leberg PL. Population structure in an endangered songbird: maintenance of genetic differentiation despite high vagility and significant population recovery. Mol Ecol 2008; 17:3628-39. [PMID: 18643883 DOI: 10.1111/j.1365-294x.2008.03868.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Black-capped vireos (Vireo atricapilla), an endangered, migratory species dependent upon early successional habitat, have experienced significant recovery since its protection. In light of its vagility and known increase in population size and range, limited genetic differentiation would be expected in the species. Using 15 microsatellite loci and an extensive sampling regime, we detected significant overall genetic differentiation (F(ST) = 0.021) and high interpopulation differentiation compared to other migratory birds. Although proximate sites (separated by < 20 km) tended to be genetically similar, there was no apparent association of either geographical distance or landscape attributes with differentiation between sites. Evidence of a population bottleneck was also detected in a site located near other large concentrations of birds. Although black-capped vireos are capable of large-scale movements and the population has experienced a recent expansion, dispersal appears too insufficient to eliminate the genetic differentiation resulting from restricted colonization of ephemeral habitats.
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Affiliation(s)
- Kelly R Barr
- Department of Biology, University of Louisiana, Lafayette, LA 70504, USA.
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MÄKINEN TUULI, PANOVA MARINA, JOHANNESSON KERSTIN, TATARENKOV ANDREY, APPELQVIST CHRISTIN, ANDRÉ CARL. Genetic differentiation on multiple spatial scales in an ecotype-forming marine snail with limited dispersal: Littorina saxatilis. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.00960.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Effects of population size and forest management on genetic diversity and structure of the tuberous orchid Orchis mascula. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9543-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Tomas C, Sanchez JJ, Barbaro A, Brandt-Casadevall C, Hernandez A, Ben Dhiab M, Ramon M, Morling N. X-chromosome SNP analyses in 11 human Mediterranean populations show a high overall genetic homogeneity except in North-west Africans (Moroccans). BMC Evol Biol 2008; 8:75. [PMID: 18312628 PMCID: PMC2315647 DOI: 10.1186/1471-2148-8-75] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Accepted: 02/29/2008] [Indexed: 11/20/2022] Open
Abstract
Background Due to its history, with a high number of migration events, the Mediterranean basin represents a challenging area for population genetic studies. A large number of genetic studies have been carried out in the Mediterranean area using different markers but no consensus has been reached on the genetic landscape of the Mediterranean populations. In order to further investigate the genetics of the human Mediterranean populations, we typed 894 individuals from 11 Mediterranean populations with 25 single-nucleotide polymorphisms (SNPs) located on the X-chromosome. Results A high overall homogeneity was found among the Mediterranean populations except for the population from Morocco, which seemed to differ genetically from the rest of the populations in the Mediterranean area. A very low genetic distance was found between populations in the Middle East and most of the western part of the Mediterranean Sea. A higher migration rate in females versus males was observed by comparing data from X-chromosome, mt-DNA and Y-chromosome SNPs both in the Mediterranean and a wider geographic area. Multilocus association was observed among the 25 SNPs on the X-chromosome in the populations from Ibiza and Cosenza. Conclusion Our results support both the hypothesis of (1) a reduced impact of the Neolithic Wave and more recent migration movements in NW-Africa, and (2) the importance of the Strait of Gibraltar as a geographic barrier. In contrast, the high genetic homogeneity observed in the Mediterranean area could be interpreted as the result of the Neolithic wave caused by a large demic diffusion and/or more recent migration events. A differentiated contribution of males and females to the genetic landscape of the Mediterranean area was observed with a higher migration rate in females than in males. A certain level of background linkage disequilibrium in populations in Ibiza and Cosenza could be attributed to their demographic background.
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Affiliation(s)
- Carmen Tomas
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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Gonzalez EG, Zardoya R. Relative role of life-history traits and historical factors in shaping genetic population structure of sardines (Sardina pilchardus). BMC Evol Biol 2007; 7:197. [PMID: 17953768 PMCID: PMC2204010 DOI: 10.1186/1471-2148-7-197] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Accepted: 10/22/2007] [Indexed: 12/04/2022] Open
Abstract
Background Marine pelagic fishes exhibit rather complex patterns of genetic differentiation, which are the result of both historical processes and present day gene flow. Comparative multi-locus analyses based on both nuclear and mitochondrial genetic markers are probably the most efficient and informative approach to discerning the relative role of historical events and life-history traits in shaping genetic heterogeneity. The European sardine (Sardina pilchardus) is a small pelagic fish with a relatively high migratory capability that is expected to show low levels of genetic differentiation among populations. Previous genetic studies based on meristic and mitochondrial control region haplotype frequency data supported the existence of two sardine subspecies (S. p. pilchardus and S. p. sardina). Results We investigated genetic structure of sardine among nine locations in the Atlantic Ocean and Mediterranean Sea using allelic size variation of eight specific microsatellite loci. Bayesian clustering and assignment tests, maximum likelihood estimates of migration rates, as well as classical genetic-variance-based methods (hierarchical AMOVA test and RST pairwise comparisons) supported a single evolutionary unit for sardines. These analyses only detected weak but significant genetic differentiation, which followed an isolation-by-distance pattern according to Mantel test. Conclusion We suggest that the discordant genetic structuring patterns inferred based on mitochondrial and microsatellite data might indicate that the two different classes of molecular markers may be reflecting different and complementary aspects of the evolutionary history of sardine. Mitochondrial data might be reflecting past isolation of sardine populations into two distinct groupings during Pleistocene whereas microsatellite data reveal the existence of present day gene flow among populations, and a pattern of isolation by distance.
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Affiliation(s)
- Elena G Gonzalez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2; 28006 Madrid, Spain.
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