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Fukutani K, Matsui M, Tran DV, Nishikawa K. Genetic diversity and demography of Bufo japonicus and B. torrenticola (Amphibia: Anura: Bufonidae) influenced by the Quaternary climate. PeerJ 2022; 10:e13452. [PMID: 35698618 PMCID: PMC9188313 DOI: 10.7717/peerj.13452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/27/2022] [Indexed: 01/14/2023] Open
Abstract
The Quaternary climate affected the present species richness and geographic distribution patterns of amphibians by limiting their activities during the glacial period. The present study examined the phylogenetic relationships of Japanese toads (Bufo japonicus and B. torrenticola) and the demography of each lineage from the past to the present based on mitochondrial sequences and ecological niche models. Japanese toads are a monophyletic group with two main clades (clades A and B). Clade A represents B. j. formosus, including three clades (clades A1, A2, and A3). Clade B contains three clades, two of which corresponded to B. j. japonicus (clades B1 and B2) and the other to B. torrenticola. Clade B2 and B. torrenticola made a sister group, and, thus, B. j. japonicus is paraphyletic. Clades A and B diverged in the late Miocene 5.7 million years ago (Mya) during the period when the Japanese archipelago was constructed. The earliest divergence between the three clades of clade A was estimated at 1.8 Mya. Clades A1 and A2 may have diverged at 0.8 Mya, resulting from the isolation in the multiple different refugia; however, the effects of the glacial climate on the divergence events of clade A3 are unclear. Divergences within clade B occurred from the late Pliocene to the early Pleistocene (3.2-2.2 Mya). Niche similarity between the parapatric clade in clade B (clades B1 and B2) indicated their allopatric divergence. It was suggested that niche segregation between B. japonicus and B. torrenticola contributed to a rapid adaptation of B. torrenticola for lotic breeding. All clade of Japanese toads retreated to each refugium at a low elevation in the glacial period, and effective population sizes increased to construct the current populations after the Last Glacial Maximum. Furthermore, we highlight the areas of climate stability from the last glacial maximum to the present that have served as the refugia of Japanese toads and, thus, affected their present distribution patterns.
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Affiliation(s)
- Kazumi Fukutani
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Dung Van Tran
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan,Wildlife Department, Vietnam National University of Forestry, Hanoi, Vietnam
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan,Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
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Niwa K, Tran DV, Nishikawa K. Differentiated historical demography and ecological niche forming present distribution and genetic structure in coexisting two salamanders (Amphibia, Urodela, Hynobiidae) in a small island, Japan. PeerJ 2022; 10:e13202. [PMID: 35505683 PMCID: PMC9057287 DOI: 10.7717/peerj.13202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/09/2022] [Indexed: 01/12/2023] Open
Abstract
Background The climatic oscillations in the Quaternary period considerably shaped the distribution and population genetic structure of organisms. Studies on the historical dynamics of distribution and demography not only reflect the current geographic distribution but also allow us to understand the adaption and genetic differentiation of species. However, the process and factors affecting the present distribution and genetic structure of many taxa are still poorly understood, especially for endemic organisms to small islands. Methods Here, we integrated population genetic and ecological niche modelling approaches to investigate the historical distribution and demographic dynamics of two co-existing salamanders on Tsushima Island, Japan: the true H. tsuensis (Group A), and Hynobius sp. (Group B). We also examined the hypothesis on the equivalency and similarity of niches of these groups by identity and background tests for ecological niche space. Results Our result showed that Group A is considered to have undergone a recent population expansion after the Last Glacial Maximum while it is unlikely to have occurred in Group B. The highest suitability was predicted for Group A in southern Tsushima Island, whereas the northern part of Tsushima Island was the potential distribution of Group B. The results also suggested a restricted range of both salamanders during the Last Interglacial and Last Glacial Maximum, and recent expansion in Mid-Holocene. The genetic landscape-shape interpolation analysis and historical suitable area of ecological niche modelling were consistent, and suggested refugia used during glacial ages in southern part for Group A, and in northern part of Tsushima Island for Group B. Additionally, we found evidence of nonequivalence for the ecological niche of the two groups of the salamanders, although our test could not show either niche divergence or conservatism based on the background tests. The environmental predictors affecting the potential distribution of each group also showed distinctiveness, leading to differences in selecting suitable areas. Finally, the combination of population genetics and ecological modeling has revealed the differential demographic/historical response between coexisting two salamanders on a small island.
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Affiliation(s)
- Keita Niwa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan,Akita Prefectural Office, Akita, Japan
| | - Dung Van Tran
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan,Wildlife Department, Faculty of Forest Resources and Environmental Management, Vietnam National University of Forestry, Hanoi, Vietnam
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan,Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
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4
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Wham BE, Rahman SR, Martinez‐Correa M, Hines HM. Mito-nuclear discordance at a mimicry color transition zone in bumble bee Bombus melanopygus. Ecol Evol 2021; 11:18151-18168. [PMID: 35003664 PMCID: PMC8717287 DOI: 10.1002/ece3.8412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 10/24/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022] Open
Abstract
As hybrid zones exhibit selective patterns of gene flow between otherwise distinct lineages, they can be especially valuable for informing processes of microevolution and speciation. The bumble bee, Bombus melanopygus, displays two distinct color forms generated by Müllerian mimicry: a northern "Rocky Mountain'' color form with ferruginous mid-abdominal segments (B. m. melanopygus) and a southern "Pacific'' form with black mid-abdominal segments (B. m. edwardsii). These morphs meet in a mimetic transition zone in northern California and southern Oregon that is more narrow and transitions further west than comimetic bumble bee species. To understand the historical formation of this mimicry zone, we assessed color distribution data for B. melanopygus from the last 100 years. We then examined gene flow among the color forms in the transition zone by comparing sequences from mitochondrial COI barcode sequences, color-controlling loci, and the rest of the nuclear genome. These data support two geographically distinct mitochondrial haplogroups aligned to the ancestrally ferruginous and black forms that meet within the color transition zone. This clustering is also supported by the nuclear genome, which, while showing strong admixture across individuals, distinguishes individuals most by their mitochondrial haplotype, followed by geography. These data suggest the two lineages most likely were historically isolated, acquired fixed color differences, and then came into secondary contact with ongoing gene flow. The transition zone, however, exhibits asymmetries: mitochondrial haplotypes transition further south than color pattern, and both transition over shorter distances in the south. This system thus demonstrates alternative patterns of gene flow that occur in contact zones, presenting another example of mito-nuclear discordance. Discordant gene flow is inferred to most likely be driven by a combination of mimetic selection, dominance effects, and assortative mating.
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Affiliation(s)
- Briana E. Wham
- Department of EntomologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
- The Pennsylvania State University LibrariesUniversity ParkPennsylvaniaUSA
| | - Sarthok Rasique Rahman
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
- Department of Biological SciencesThe University of AlabamaTuscaloosaAlabamaUSA
| | | | - Heather M. Hines
- Department of EntomologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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Yao H, Zhang Y, Wang Z, Liu G, Ran Q, Zhang Z, Guo K, Yang A, Wang N, Wang P. Inter-glacial isolation caused divergence of cold-adapted species: the case of the snow partridge. Curr Zool 2021; 68:489-498. [PMID: 36090147 PMCID: PMC9450178 DOI: 10.1093/cz/zoab075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
Deciphering the role of climatic oscillations in species divergence helps us understand the mechanisms that shape global biodiversity. The cold-adapted species may have expanded their distribution with the development of glaciers during glacial period. With the retreat of glaciers, these species were discontinuously distributed in the high-altitude mountains and isolated by geographical barriers. However, the study that focuses on the speciation process of cold-adapted species is scant. To fill this gap, we combined population genetic data and ecological niche models (ENMs) to explore divergence process of snow partridge (Lerwa lerwa). Lerwa lerwa is a cold-adapted bird that is distributed from 4,000 to 5,500 m. We found 2 genetic populations within L. lerwa, and they diverged from each other at about 0.40–0.44 million years ago (inter-glacial period after Zhongliangan glaciation). The ENMs suggested that L. lerwa expanded to the low elevations of the Himalayas and Hengduan mountains during glacial period, whereas it contracted to the high elevations, southern of Himalayas, and Hengduan mountains during inter-glacial periods. Effective population size trajectory also suggested that L. lerwa expanded its population size during the glacial period. Consistent with our expectation, the results support that inter-glacial isolation contributed to the divergence of cold-adapted L. lerwa on Qinghai-Tibetan Plateau. This study deepens our understanding of how climatic oscillations have driven divergence process of cold-adapted Phasianidae species distributed on mountains.
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Affiliation(s)
- Hongyan Yao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yanan Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Zhen Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Hangzhou Xi’ao Environmental Science Technique Company Limited, Zhejiang 310011, China
| | - Gaoming Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Quan Ran
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Yancheng Wetland and World Natural Heritage Conservation and Management Center, Jiangsu 224000, China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Keji Guo
- Central South Inventory and Planning Institute of National Forestry and Grassland Administration, Changsha 410014, China
| | - Ailin Yang
- Chinese Institute for Brain Research, Beijing 102206, China
| | - Nan Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Pengcheng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Pliocene origins, Pleistocene refugia, and postglacial range expansions in southern devil scorpions (Vaejovidae: Vaejovis carolinianus). ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00505-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Schwartz MK, Walters AD, Pilgrim KL, Moriarty KM, Slauson KM, Zielinski WJ, Aubry KB, Sacks BN, Zarn KE, Quinn CB, Young MK. Pliocene-Early Pleistocene Geological Events Structure Pacific Martens (Martes caurina). J Hered 2021; 111:169-181. [PMID: 32161974 DOI: 10.1093/jhered/esaa005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 02/10/2020] [Indexed: 11/15/2022] Open
Abstract
The complex topography, climate, and geological history of Western North America have shaped contemporary patterns of biodiversity and species distributions in the region. Pacific martens (Martes caurina) are distributed along the northern Pacific Coast of North America with disjunct populations found throughout the Northwestern Forested Mountains and Marine West Coast Forest ecoregions of the West Coast. Martes in this region have been classified into subspecies; however, the subspecific designation has been extensively debated. In this study, we use genomic data to delineate conservation units of Pacific marten in the Sierra-Cascade-Coastal montane belt in the western United States. We analyzed the mitochondrial genome for 94 individuals to evaluate the spatial distribution and divergence times of major lineages. We further genotyped 401 individuals at 13 microsatellite loci to investigate major patterns of population structure. Both nuclear and mitochondrial DNA suggest substantial genetic substructure concordant with historical subspecies designations. Our results revealed that the region contains 2 distinct mitochondrial lineages: a Cascades/Sierra lineage that diverged from the Cascades/coastal lineage 2.23 (1.48-3.14 mya), consistent with orogeny of the Cascade Mountain chain. Interestingly, Pacific Martes share phylogeographic patterns similar with other sympatric taxa, suggesting that the complex geological history has shaped the biota of this region. The information is critical for conservation and management efforts, and further investigation of adaptive diversity is warranted following appropriate revision of conservation management designations.
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Affiliation(s)
- Michael K Schwartz
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Ashley D Walters
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Kristine L Pilgrim
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Katie M Moriarty
- National Council for Air and Stream Improvement, Inc., Corvallis, OR
| | - Keith M Slauson
- USDA Forest Service, Pacific Southwest Research Station, Arcata, CA
| | - William J Zielinski
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT.,USDA Forest Service, Pacific Southwest Research Station, Arcata, CA
| | - Keith B Aubry
- USDA Forest Service, Pacific Northwest Research Station, Olympia, WA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Katherine E Zarn
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Michael K Young
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
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Bagley JC, Heming NM, Gutiérrez EE, Devisetty UK, Mock KE, Eckert AJ, Strauss SH. Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen ( Populus tremuloides). Ecol Evol 2020; 10:4609-4629. [PMID: 32551047 PMCID: PMC7297775 DOI: 10.1002/ece3.6214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 01/01/2023] Open
Abstract
Populus tremuloides is the widest-ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome-wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, ploidy levels, admixture, and Pleistocene range dynamics of P. tremuloides, and tested several historical biogeographical hypotheses. We found three genetic lineages located mainly in coastal-Cascades (cluster 1), east-slope Cascades-Sierra Nevadas-Northern Rockies (cluster 2), and U.S. Rocky Mountains through southern Canadian (cluster 3) regions of the P. tremuloides range, with tree graph relationships of the form ((cluster 1, cluster 2), cluster 3). Populations consisted mainly of diploids (86%) but also small numbers of triploids (12%) and tetraploids (1%), and ploidy did not adversely affect our genetic inferences. The main vector of admixture was from cluster 3 into cluster 2, with the admixture zone trending northwest through the Rocky Mountains along a recognized phenotypic cline (Utah to Idaho). Clusters 1 and 2 provided strong support for the "stable-edge hypothesis" that unglaciated southwestern populations persisted in situ since the last glaciation. By contrast, despite a lack of clinal genetic variation, cluster 3 exhibited "trailing-edge" dynamics from niche suitability predictions signifying complete northward postglacial expansion. Results were also consistent with the "inland dispersal hypothesis" predicting postglacial assembly of Pacific Northwestern forest ecosystems, but rejected the hypothesis that Pacific-coastal populations were colonized during outburst flooding from glacial Lake Missoula. Overall, congruent patterns between our phylogeographic and ecological niche modeling results and fossil pollen data demonstrate complex mixtures of stable-edge, refugial locations, and postglacial expansion within P. tremuloides. These findings confirm and refine previous genetic studies, while strongly supporting a distinct Pacific-coastal genetic lineage of quaking aspen.
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Affiliation(s)
- Justin C. Bagley
- Plant Evolutionary Genomics LaboratoryDepartment of BiologyVirginia Commonwealth UniversityRichmondVAUSA
- Departamento de ZoologiaInstituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrazil
| | - Neander M. Heming
- Departamento de ZoologiaInstituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrazil
| | - Eliécer E. Gutiérrez
- Departamento de ZoologiaInstituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrazil
- Programa de Pos‐Graduação em Biodiversidade AnimalCentro de Ciências Naturais e ExatasUniversidade Federal de Santa MariaSanta MariaBrazil
| | | | - Karen E. Mock
- Department of Wildland Resources and Ecology CenterUtah State UniversityLoganUTUSA
| | - Andrew J. Eckert
- Plant Evolutionary Genomics LaboratoryDepartment of BiologyVirginia Commonwealth UniversityRichmondVAUSA
| | - Steven H. Strauss
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisORUSA
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Liu Y, Pham HT, He Z, Wei C. Phylogeography of the cicada Platypleura hilpa in subtropical and tropical East Asia based on mitochondrial and nuclear genes and microsatellite markers. Int J Biol Macromol 2020; 151:529-544. [PMID: 32084484 DOI: 10.1016/j.ijbiomac.2020.02.183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/16/2020] [Accepted: 02/16/2020] [Indexed: 10/25/2022]
Abstract
Climate change and geographical events play key roles in driving population genetic structure of organisms, but different scenarios were suggested for species occurring in tropical and subtropical areas. We investigated the population genetic structure, diversity and demographic history of the cicada Platypleura hilpa which occurs in coastal areas of southern China and northeastern Indo-Burma, and analysed the potential impact of climate change and geological events on its evolutionary history. Our data imply that P. hilpa comprises five main lineages with nearly unique sets of haplotypes and distinct geographic distributions. A major split of the lineages occurred in the Pleistocene. Geographic distance and geomorphic barriers serve as the primary factors shaping the genetic population structure, and several climatic factors are associated with the divergence. The potential range during the Last Glacial Maximum has apparently increased in south China and the exposed South China Sea Shelf. The Pleistocene sea-level fluctuations had profound effects on the regional genetic structure. The Beibu Gulf represents a more important geographic barrier than the Qiongzhou Strait in blocking gene flow among populations. These results contribute to a better understanding of the pressure climatic change and geographical events impose on insects in coastal areas of East Asia.
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Affiliation(s)
- Yunxiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hong Thai Pham
- Vietnam National Museum of Nature Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Street, Cau Giay, Hanoi, Viet Nam
| | - Zhiqiang He
- College of Plant Science, Tarim University, Alar, Xinjiang 843300, China
| | - Cong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Oh KP, Aldridge CL, Forbey JS, Dadabay CY, Oyler-McCance SJ. Conservation Genomics in the Sagebrush Sea: Population Divergence, Demographic History, and Local Adaptation in Sage-Grouse (Centrocercus spp.). Genome Biol Evol 2020; 11:2023-2034. [PMID: 31135036 DOI: 10.1093/gbe/evz112] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2019] [Indexed: 02/06/2023] Open
Abstract
Sage-grouse are two closely related iconic species of the North American West, with historically broad distributions across sagebrush-steppe habitat. Both species are dietary specialists on sagebrush during winter, with presumed adaptations to tolerate the high concentrations of toxic secondary metabolites that function as plant chemical defenses. Marked range contraction and declining population sizes since European settlement have motivated efforts to identify distinct population genetic variation, particularly that which might be associated with local genetic adaptation and dietary specialization of sage-grouse. We assembled a reference genome and performed whole-genome sequencing across sage-grouse from six populations, encompassing both species and including several populations on the periphery of the species ranges. Population genomic analyses reaffirmed genome-wide differentiation between greater and Gunnison sage-grouse, revealed pronounced intraspecific population structure, and highlighted important differentiation of a small isolated population of greater sage-grouse in the northwest of the range. Patterns of genome-wide differentiation were largely consistent with a hypothesized role of genetic drift due to limited gene flow among populations. Inferred ancient population demography suggested persistent declines in effective population sizes that have likely contributed to differentiation within and among species. Several genomic regions with single-nucleotide polymorphisms exhibiting extreme population differentiation were associated with candidate genes linked to metabolism of xenobiotic compounds. In vitro activity of enzymes isolated from sage-grouse livers supported a role for these genes in detoxification of sagebrush, suggesting that the observed interpopulation variation may underlie important local dietary adaptations, warranting close consideration for conservation strategies that link sage-grouse to the chemistry of local sagebrush.
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Affiliation(s)
- Kevin P Oh
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado
| | - Cameron L Aldridge
- Natural Resource Ecology Laboratory and Department of Ecosystem Sciences, Colorado State University in cooperation with U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado
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Jordan MA, Mumaw V, Millspaw N, Mockford SW, Janzen FJ. Range-wide phylogeography of Blanding’s Turtle [Emys (= Emydoidea) blandingii]. CONSERV GENET 2019. [DOI: 10.1007/s10592-018-01140-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Tarroso P, Carvalho SB, Velo‐Antón G. Phylin 2.0: Extending the phylogeographical interpolation method to include uncertainty and user‐defined distance metrics. Mol Ecol Resour 2019; 19:1081-1094. [DOI: 10.1111/1755-0998.13010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 02/18/2019] [Accepted: 03/01/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Pedro Tarroso
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| | - Sílvia B. Carvalho
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Guillermo Velo‐Antón
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
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Miller MP, Davis RJ, Forsman ED, Mullins TD, Haig SM. Isolation by distance versus landscape resistance: Understanding dominant patterns of genetic structure in Northern Spotted Owls (Strix occidentalis caurina). PLoS One 2018; 13:e0201720. [PMID: 30071083 PMCID: PMC6072037 DOI: 10.1371/journal.pone.0201720] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 07/21/2018] [Indexed: 11/25/2022] Open
Abstract
Landscape genetics investigations examine how the availability and configuration of habitat influence genetic structure of plants and animals. We used landscape genetics to evaluate the role that forest connectivity plays in determining genetic structure of the federally-threatened Northern Spotted Owl (Strix occidentalis caurina) using genotypes of 339 Northern Spotted Owls obtained for 10 microsatellite loci. Spatial clustering analyses identified a distinct genetic cluster at the southern extent of the region examined. This cluster could not be linked to landscape connectivity patterns and suggested that post-Pleistocene processes were involved with its development rather than contemporary landscape configuration. We also compared matrices of pairwise inter-individual genetic distances with resistance distances derived from a circuit-theory based framework. Resistance distances were obtained for an idealized raster map that reflected continuous unimpeded dispersal habitat across the landscape along with five empirically-derived raster maps reflecting the 1870’s, 1940’s, 1986, 1994, and 2012. Resistance distances from the idealized map served as surrogates for linear geographic distances. Relative to idealized conditions, resistance distances were ~250% higher in the 1940’s and ~200% higher from 1986 onward. Resistance distances from the 1870’s were ~40% higher than idealized conditions. Inter-individual genetic distances were most highly correlated with resistance distances from the idealized map rather than any of the empirical maps. Two hypotheses explain our results. First, our results may reflect temporal lags between the onset of large-scale habitat alterations and their novel effects on genetic structure in long-lived species such as Northern Spotted Owls. Second, because Northern Spotted Owls disperse over long distances, our results may indicate that forest habitat has never been sufficiently fragmented to the point where connectivity was disrupted. The second hypothesis could indicate that forest management practices mandated by the Northwest Forest Plan succeeded with one of its primary goals. However, our results do not represent a complete portrayal of the status of Northern Spotted Owls given detection of significant population declines and bottlenecks in other studies. Future investigations based on computer simulations may help distinguish between hypotheses.
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Affiliation(s)
- Mark P. Miller
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, Corvallis, Oregon, United States of America
- * E-mail:
| | - Raymond J. Davis
- U.S. Department of Agriculture Forest Service, Pacific Northwest Region, Corvallis, Oregon, United States of America
| | - Eric D. Forsman
- U.S. Department of Agriculture Forest Service, Pacific Northwest Region, Corvallis, Oregon, United States of America
| | - Thomas D. Mullins
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, Corvallis, Oregon, United States of America
| | - Susan M. Haig
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, Corvallis, Oregon, United States of America
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Ferreira CM, Sabino-Marques H, Barbosa S, Costa P, Encarnação C, Alpizar-Jara R, Pita R, Beja P, Mira A, Searle JB, Paupério J, Alves PC. Genetic non-invasive sampling (gNIS) as a cost-effective tool for monitoring elusive small mammals. EUR J WILDLIFE RES 2018. [DOI: 10.1007/s10344-018-1188-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Morgan-Richards M, Bulgarella M, Sivyer L, Dowle EJ, Hale M, McKean NE, Trewick SA. Explaining large mitochondrial sequence differences within a population sample. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170730. [PMID: 29291063 PMCID: PMC5717637 DOI: 10.1098/rsos.170730] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/26/2017] [Indexed: 06/07/2023]
Abstract
Mitochondrial DNA sequence is frequently used to infer species' boundaries, as divergence is relatively rapid when populations are reproductively isolated. However, the shared history of a non-recombining gene naturally leads to correlation of pairwise differences, resulting in mtDNA clusters that might be mistaken for evidence of multiple species. There are four distinct processes that can explain high levels of mtDNA sequence difference within a single sample. Here, we examine one case in detail as an exemplar to distinguish among competing hypotheses. Within our sample of tree wētā (Hemideina crassidens; Orthoptera), we found multiple mtDNA haplotypes for a protein-coding region (cytb/ND1) that differed by a maximum of 7.9%. From sequencing the whole mitochondrial genome of two representative individuals, we found evidence of constraining selection. Heterozygotes were as common as expected under random mating at five nuclear loci. Morphological traits and nuclear markers did not resolve the mtDNA groupings of individuals. We concluded that the large differences found among our sample of mtDNA sequences were simply owing to a large population size over an extended period of time allowing an equilibrium between mutation and drift to retain a great deal of genetic diversity within a single species.
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Affiliation(s)
| | - Mariana Bulgarella
- Ecology, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - Louisa Sivyer
- Ecology, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - Edwina J. Dowle
- Department of Integrative Biology, University of Colorado, 1151 Arapahoe, SI 2071, Denver, CO 80204, USA
| | - Marie Hale
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Natasha E. McKean
- Ecology, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - Steven A. Trewick
- Ecology, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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16
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Graham MR, Wood DA, Henault JA, Valois ZJ, Cushing PE. Ancient lakes, Pleistocene climates and river avulsions structure the phylogeography of a large but little-known rock scorpion from the Mojave and Sonoran deserts. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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17
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Dellicour S, Gerard M, Prunier JG, Dewulf A, Kuhlmann M, Michez D. Distribution and predictors of wing shape and size variability in three sister species of solitary bees. PLoS One 2017; 12:e0173109. [PMID: 28273178 PMCID: PMC5342212 DOI: 10.1371/journal.pone.0173109] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 02/15/2017] [Indexed: 12/02/2022] Open
Abstract
Morphological traits can be highly variable over time in a particular geographical area. Different selective pressures shape those traits, which is crucial in evolutionary biology. Among these traits, insect wing morphometry has already been widely used to describe phenotypic variability at the inter-specific level. On the contrary, fewer studies have focused on intra-specific wing morphometric variability. Yet, such investigations are relevant to study potential convergences of variation that could highlight micro-evolutionary processes. The recent sampling and sequencing of three solitary bees of the genus Melitta across their entire species range provides an excellent opportunity to jointly analyse genetic and morphometric variability. In the present study, we first aim to analyse the spatial distribution of the wing shape and centroid size (used as a proxy for body size) variability. Secondly, we aim to test different potential predictors of this variability at both the intra- and inter-population levels, which includes genetic variability, but also geographic locations and distances, elevation, annual mean temperature and precipitation. The comparison of spatial distribution of intra-population morphometric diversity does not reveal any convergent pattern between species, thus undermining the assumption of a potential local and selective adaptation at the population level. Regarding intra-specific wing shape differentiation, our results reveal that some tested predictors, such as geographic and genetic distances, are associated with a significant correlation for some species. However, none of these predictors are systematically identified for the three species as an important factor that could explain the intra-specific morphometric variability. As a conclusion, for the three solitary bee species and at the scale of this study, our results clearly tend to discard the assumption of the existence of a common pattern of intra-specific signal/structure within the intra-specific wing shape and body size variability.
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Affiliation(s)
- Simon Dellicour
- Rega Institute for Medical Research, Clinical and Epidemiological Virology, Department of Microbiology and Immunology, KU Leuven—University of Leuven, Minderbroedersstaat 10, Leuven, Belgium
- * E-mail:
| | - Maxence Gerard
- Laboratoire de Zoologie, Research institute of Biosciences, University of Mons, Place du Parc 23, Mons, Belgium
| | - Jérôme G. Prunier
- Station d'Écologie Théorique et Expérimentale, Université de Toulouse, CNRS, Moulis, France
| | - Alexandre Dewulf
- Laboratoire de Zoologie, Research institute of Biosciences, University of Mons, Place du Parc 23, Mons, Belgium
| | - Michael Kuhlmann
- Zoological Museum, University of Kiel, Hegewischstr. 3, Kiel, Germany
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, United Kingdom
| | - Denis Michez
- Laboratoire de Zoologie, Research institute of Biosciences, University of Mons, Place du Parc 23, Mons, Belgium
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18
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Rosenberg DK, Davis RJ, Van Norman KJ, Dunk JR, Forsman ED, Huff RD. Patterns of red tree vole distribution and habitat suitability: implications for surveys and conservation planning. Ecosphere 2016. [DOI: 10.1002/ecs2.1630] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Daniel K. Rosenberg
- Oregon Wildlife Institute Box 1061 Corvallis Oregon 97330 USA
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon 97331 USA
| | - Raymond J. Davis
- U.S. Forest Service Pacific Northwest Research Station 3200 SW Jefferson Way Corvallis Oregon 97331 USA
| | - Kelli J. Van Norman
- Interagency Special Status/Sensitive Species Program OR/WA BLM and Region 6 Forest Service 1220 SW 3rd Avenue Portland Oregon 97204 USA
| | - Jeffrey R. Dunk
- Department of Environmental Science and Management Humboldt State University Arcata California 95521 USA
| | - Eric D. Forsman
- U.S. Forest Service Pacific Northwest Research Station 3200 SW Jefferson Way Corvallis Oregon 97331 USA
| | - Robert D. Huff
- Interagency Special Status/Sensitive Species Program OR/WA BLM and Region 6 Forest Service 1220 SW 3rd Avenue Portland Oregon 97204 USA
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19
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Ceccarelli FS, Pizarro-Araya J, Ojanguren-Affilastro AA. Phylogeography and population structure of twoBrachistosternusspecies (Scorpiones: Bothriuridae) from the Chilean coastal desert - the perils of coastal living. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12877] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- F. Sara Ceccarelli
- División de Aracnología; Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; Av. Ángel Gallardo 470; C1405DJR Buenos Aires Argentina
| | - Jaime Pizarro-Araya
- Laboratorio de Entomología Ecológica; Departamento de Biología; Facultad de Ciencias; Universidad de La Serena; Casilla 599 La Serena Chile
| | - Andrés A. Ojanguren-Affilastro
- División de Aracnología; Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; Av. Ángel Gallardo 470; C1405DJR Buenos Aires Argentina
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20
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Wan JZ, Wang CJ, Liu CX, Li HL. Climate change may alter genetic diversity of Duchesnea indica, a clonal plant species. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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Haig SM, Miller MP, Bellinger R, Draheim HM, Mercer DM, Mullins TD. The conservation genetics juggling act: integrating genetics and ecology, science and policy. Evol Appl 2015; 9:181-95. [PMID: 27087847 PMCID: PMC4780381 DOI: 10.1111/eva.12337] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/27/2015] [Indexed: 01/08/2023] Open
Abstract
The field of conservation genetics, when properly implemented, is a constant juggling act integrating molecular genetics, ecology, and demography with applied aspects concerning managing declining species or implementing conservation laws and policies. This young field has grown substantially since the 1980s following the development of polymerase chain reaction and now into the genomics era. Our laboratory has ‘grown up’ with the field, having worked on these issues for over three decades. Our multidisciplinary approach entails understanding the behavior and ecology of species as well as the underlying processes that contribute to genetic viability. Taking this holistic approach provides a comprehensive understanding of factors that influence species persistence and evolutionary potential while considering annual challenges that occur throughout their life cycle. As a federal laboratory, we are often addressing the needs of the U.S. Fish and Wildlife Service in their efforts to list, de‐list, or recover species. Nevertheless, there remains an overall communication gap between research geneticists and biologists who are charged with implementing their results. Therefore, we outline the need for a National Center for Small Population Biology to ameliorate this problem and provide organizations charged with making status decisions firmer ground from which to make their critical decisions.
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Affiliation(s)
- Susan M Haig
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR USA
| | - Mark P Miller
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR USA
| | - Renee Bellinger
- Department of Biology, Tropical Conservation Biology and Environmental Science University of Hawaii Hilo HI USA
| | - Hope M Draheim
- Pacific States Marine Fisheries Commission Eagle Fish Genetics Laboratory Eagle ID USA
| | - Dacey M Mercer
- Hatfield Marine Science Center Oregon State University Newport OR USA
| | - Thomas D Mullins
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR USA
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22
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Koblmüller S, Steinwender B, Weiß S, Sefc KM. Gene flow, population growth and a novel substitution rate estimate in a subtidal rock specialist, the black-faced blenny Tripterygion delaisi (Perciformes, Blennioidei, Tripterygiidae) from the Adriatic Sea. J ZOOL SYST EVOL RES 2015; 53:291-299. [PMID: 26617435 PMCID: PMC4658704 DOI: 10.1111/jzs.12110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2015] [Indexed: 11/27/2022]
Abstract
Population histories depend on the interplay between exogeneous and endogeneous factors. In marine species, phylogeographic and demographic patterns are often shaped by sea level fluctuations, water currents and dispersal ability. Using mitochondrial control region sequences (n = 120), we infer phylogeographic structure and historic population size changes of a common littoral fish species, the black-faced blenny Tripterygion delaisi (Perciformes, Blennioidei, Tripterygiidae) from the north-eastern Adriatic Sea. We find that Adriatic T. delaisi are differentiated from conspecific populations in the remaining Mediterranean, but display little phylogeographic structure within the Adriatic basin. The pattern is consistent with passive dispersal of planktonic larvae along cyclonic currents within the Adriatic Sea, but limited active dispersal of adults. Demographic reconstructions are consistent with recent population expansion, probably triggered by rising sea levels after the last glacial maximum (LGM). Placing the onset of population growth between the LGM and the warming of surface waters (18 000-13 000 years BP) and employing a novel expansion dating approach, we inferred a substitution rate of 2.61-3.61% per site per MY. Our study is one of only few existing investigations of the genetic structure of animals within the Adriatic basin and is the first to provide an estimate for mitochondrial control region substitution rates in blennioid fishes.
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Affiliation(s)
| | | | - Sara Weiß
- Institute of ZoologyUniversity of GrazGrazAustria
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23
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Fang F, Ji Y, Zhao Q, Wang Y, Gao W, Chu K, Sun H. Phylogeography of the Chinese endemic freshwater crabSinopotamon acutum(Brachyura, Potamidae). ZOOL SCR 2015. [DOI: 10.1111/zsc.12131] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fang Fang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Yongkun Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Qiang Zhao
- College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Yujuan Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Wei Gao
- College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Kelin Chu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Hongying Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
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24
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Dellicour S, Michez D, Rasplus JY, Mardulyn P. Impact of past climatic changes and resource availability on the population demography of three food-specialist bees. Mol Ecol 2015; 24:1074-90. [PMID: 25612734 DOI: 10.1111/mec.13085] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 12/24/2014] [Accepted: 01/15/2015] [Indexed: 12/01/2022]
Abstract
Past climate change is known to have strongly impacted current patterns of genetic variation of animals and plants in Europe. However, ecological factors also have the potential to influence demographic history and thus patterns of genetic variation. In this study, we investigated the impact of past climate, and also the potential impact of host plant species abundance, on intraspecific genetic variation in three codistributed and related specialized solitary bees of the genus Melitta with very similar life history traits and dispersal capacities. We sequenced five independent loci in samples collected from the three species. Our analyses revealed that the species associated with the most abundant host plant species (Melitta leporina) displays unusually high genetic variation, to an extent that is seldom reported in phylogeographic studies of animals and plants. This suggests a potential role of food resource abundance in determining current patterns of genetic variation in specialized herbivorous insects. Patterns of genetic variation in the two other species indicated lower overall levels of diversity, and that M. nigricans could have experienced a recent range expansion. Ecological niche modelling of the three Melitta species and their main host plant species suggested a strong reduction in range size during the last glacial maximum. Comparing observed sequence data with data simulated using spatially explicit models of coalescence suggests that M. leporina recovered a range and population size close to their current levels at the end of the last glaciation, and confirms recent range expansion as the most likely scenario for M. nigricans. Overall, this study illustrates that both demographic history and ecological factors may have contributed to shape current phylogeographic patterns.
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Affiliation(s)
- Simon Dellicour
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, av. FD Roosevelt 50, 1050, Brussels, Belgium
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25
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Schield DR, Card DC, Adams RH, Jezkova T, Reyes-Velasco J, Proctor FN, Spencer CL, Herrmann HW, Mackessy SP, Castoe TA. Incipient speciation with biased gene flow between two lineages of the Western Diamondback Rattlesnake (Crotalus atrox). Mol Phylogenet Evol 2014; 83:213-23. [PMID: 25534232 DOI: 10.1016/j.ympev.2014.12.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 12/03/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
We used mitochondrial DNA sequence data from 151 individuals to estimate population genetic structure across the range of the Western Diamondback Rattlesnake (Crotalus atrox), a widely distributed North American pit viper. We also tested hypotheses of population structure using double-digest restriction site associated DNA (ddRADseq) data, incorporating thousands of nuclear genome-wide SNPs from 42 individuals. We found strong mitochondrial support for a deep divergence between eastern and western C. atrox populations, and subsequent intermixing of these populations in the Inter-Pecos region of the United States and Mexico. Our nuclear RADseq data also identify these two distinct lineages of C. atrox, and provide evidence for nuclear admixture of eastern and western alleles across a broad geographic region. We identified contrasting patterns of mitochondrial and nuclear genetic variation across this genetic fusion zone that indicate partially restricted patterns of gene flow, which may be due to either pre- or post-zygotic isolating mechanisms. The failure of these two lineages to maintain complete genetic isolation, and evidence for partially-restricted gene flow, imply that these lineages were in the early stages of speciation prior to secondary contact.
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Affiliation(s)
- Drew R Schield
- Department of Biology & Amphibian and Reptile Diversity Research Center, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Daren C Card
- Department of Biology & Amphibian and Reptile Diversity Research Center, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Richard H Adams
- Department of Biology & Amphibian and Reptile Diversity Research Center, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Tereza Jezkova
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV 89154, USA
| | - Jacobo Reyes-Velasco
- Department of Biology & Amphibian and Reptile Diversity Research Center, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - F Nicole Proctor
- Department of Biology & Amphibian and Reptile Diversity Research Center, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Carol L Spencer
- Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, Berkeley, CA 94720, USA
| | - Hans-Werner Herrmann
- School of Natural Resources and the Environment, 1041 E Lowell Street, University of Arizona, Tuscon, AZ 85721, USA
| | - Stephen P Mackessy
- School of Biological Sciences, 501 20(th) Street, University of Northern Colorado, Greeley, CO 80639, USA
| | - Todd A Castoe
- Department of Biology & Amphibian and Reptile Diversity Research Center, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA.
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26
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Tarroso P, Velo-Antón G, Carvalho SB. phylin: anrpackage for phylogeographic interpolation. Mol Ecol Resour 2014; 15:349-57. [DOI: 10.1111/1755-0998.12312] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/28/2014] [Accepted: 08/01/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Pedro Tarroso
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - Guillermo Velo-Antón
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - Sílvia B. Carvalho
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
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27
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Benguigui M, Arenas M. Spatial and temporal simulation of human evolution. Methods, frameworks and applications. Curr Genomics 2014; 15:245-55. [PMID: 25132795 PMCID: PMC4133948 DOI: 10.2174/1389202915666140506223639] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/05/2014] [Accepted: 05/04/2014] [Indexed: 01/29/2023] Open
Abstract
Analyses of human evolution are fundamental to understand the current gradients of human diversity. In this concern, genetic samples collected from current populations together with archaeological data are the most important resources to study human evolution. However, they are often insufficient to properly evaluate a variety of evolutionary scenarios, leading to continuous debates and discussions. A commonly applied strategy consists of the use of computer simulations based on, as realistic as possible, evolutionary models, to evaluate alternative evolutionary scenarios through statistical correlations with the real data. Computer simulations can also be applied to estimate evolutionary parameters or to study the role of each parameter on the evolutionary process. Here we review the mainly used methods and evolutionary frameworks to perform realistic spatially explicit computer simulations of human evolution. Although we focus on human evolution, most of the methods and software we describe can also be used to study other species. We also describe the importance of considering spatially explicit models to better mimic human evolutionary scenarios based on a variety of phenomena such as range expansions, range shifts, range contractions, sex-biased dispersal, long-distance dispersal or admixtures of populations. We finally discuss future implementations to improve current spatially explicit simulations and their derived applications in human evolution.
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Affiliation(s)
- Macarena Benguigui
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Miguel Arenas
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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28
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Houston DD, Shiozawa DK, Smith BT, Riddle BR. Investigating the effects of Pleistocene events on genetic divergence within Richardsonius balteatus, a widely distributed western North American minnow. BMC Evol Biol 2014; 14:111. [PMID: 24885371 PMCID: PMC4038058 DOI: 10.1186/1471-2148-14-111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/12/2014] [Indexed: 11/29/2022] Open
Abstract
Background Biogeographers seek to understand the influences of global climate shifts and geologic changes to the landscape on the ecology and evolution of organisms. Across both longer and shorter timeframes, the western North American landscape has experienced dynamic transformations related to various geologic processes and climatic oscillations, including events as recently as the Last Glacial Maximum (LGM; ~20 Ka) that have impacted the evolution of the North American biota. Redside shiner is a cyprinid species that is widely distributed throughout western North America. The species’ native range includes several well-documented Pleistocene refugia. Here we use mitochondrial DNA sequence data to assess phylogeography, and to test two biogeographic hypotheses regarding post-glacial colonization by redside shiner: 1) Redside shiner entered the Bonneville Basin at the time of the Bonneville Flood (Late Pleistocene; 14.5 Ka), and 2) redside shiner colonized British Columbia post-glacially from a single refugium in the Upper Columbia River drainage. Results Genetic diversification in redside shiner began in the mid to late Pleistocene, but was not associated with LGM. Different clades of redside shiner were distributed in multiple glacial age refugia, and each clade retains a signature of population expansion, with clades having secondary contact in some areas. Conclusions Divergence times between redside shiner populations in the Bonneville Basin and the Upper Snake/Columbia River drainage precedes the Bonneville Flood, thus it is unlikely that redside shiner invaded the Bonneville Basin during this flooding event. All but one British Columbia population of redside shiner are associated with the Upper Columbia River drainage with the lone exception being a population near the coast, suggesting that the province as a whole was colonized from multiple refugia, but the inland British Columbia redside shiner populations are affiliated with a refugium in the Upper Columbia River drainage.
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Affiliation(s)
- Derek D Houston
- School of Life Sciences, University of Nevada-Las Vegas, Las Vegas, NV 89154-4004, USA.
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29
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Olafsson K, Pampoulie C, Hjorleifsdottir S, Gudjonsson S, Hreggvidsson GO. Present-day genetic structure of Atlantic salmon (Salmo salar) in Icelandic rivers and ice-cap retreat models. PLoS One 2014; 9:e86809. [PMID: 24498283 PMCID: PMC3911922 DOI: 10.1371/journal.pone.0086809] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 12/18/2013] [Indexed: 12/04/2022] Open
Abstract
Due to an improved understanding of past climatological conditions, it has now become possible to study the potential concordance between former climatological models and present-day genetic structure. Genetic variability was assessed in 26 samples from different rivers of Atlantic salmon in Iceland (total of 2,352 individuals), using 15 microsatellite loci. F-statistics revealed significant differences between the majority of the populations that were sampled. Bayesian cluster analyses using both prior information and no prior information on sampling location revealed the presence of two distinguishable genetic pools - namely, the Northern (Group 1) and Southern (Group 2) regions of Iceland. Furthermore, the random permutation of different allele sizes among allelic states revealed a significant mutational component to the genetic differentiation at four microsatellite loci (SsaD144, Ssa171, SSsp2201 and SsaF3), and supported the proposition of a historical origin behind the observed variation. The estimated time of divergence, using two different ABC methods, suggested that the observed genetic pattern originated from between the Last Glacial Maximum to the Younger Dryas, which serves as additional evidence of the relative immaturity of Icelandic fish populations, on account of the re-colonisation of this young environment following the Last Glacial Maximum. Additional analyses suggested the presence of several genetic entities which were likely to originate from the original groups detected.
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Affiliation(s)
- Kristinn Olafsson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
- Genetics, Matis Ltd., Reykjavík, Iceland
- * E-mail:
| | | | | | | | - Gudmundur O. Hreggvidsson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
- Genetics, Matis Ltd., Reykjavík, Iceland
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30
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Dellicour S, Mardulyn P. spads 1.0: a toolbox to perform spatial analyses on DNA sequence data sets. Mol Ecol Resour 2013; 14:647-51. [PMID: 24215429 DOI: 10.1111/1755-0998.12200] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 10/21/2013] [Accepted: 11/07/2013] [Indexed: 11/27/2022]
Abstract
SPADS 1.0 (for 'Spatial and Population Analysis of DNA Sequences') is a population genetic toolbox for characterizing genetic variability within and among populations from DNA sequences. In view of the drastic increase in genetic information available through sequencing methods, spads was specifically designed to deal with multilocus data sets of DNA sequences. It computes several summary statistics from populations or groups of populations, performs input file conversions for other population genetic programs and implements locus-by-locus and multilocus versions of two clustering algorithms to study the genetic structure of populations. The toolbox also includes two MATLAB and r functions, GDISPAL and GDIVPAL, to display differentiation and diversity patterns across landscapes. These functions aim to generate interpolating surfaces based on multilocus distance and diversity indices. In the case of multiple loci, such surfaces can represent a useful alternative to multiple pie charts maps traditionally used in phylogeography to represent the spatial distribution of genetic diversity. These coloured surfaces can also be used to compare different data sets or different diversity and/or distance measures estimated on the same data set.
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Affiliation(s)
- Simon Dellicour
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, av. FD Roosevelt 50, Brussels, 1050, Belgium
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Graham MR, Jaeger JR, Prendini L, Riddle BR. Phylogeography of Beck’s Desert Scorpion, Paruroctonus becki, reveals Pliocene diversification in the Eastern California Shear Zone and postglacial expansion in the Great Basin Desert. Mol Phylogenet Evol 2013; 69:502-13. [DOI: 10.1016/j.ympev.2013.07.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 07/10/2013] [Accepted: 07/29/2013] [Indexed: 11/28/2022]
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Rapson SA, Goldizen AW, Seddon JM. Gene flow in mongooses endemic to Namibia's granite inselbergs despite past climatic fluctuations and isolating landscape features. J Mammal 2013. [DOI: 10.1644/11-mamm-a-379.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Lizards on ice: evidence for multiple refugia in Liolaemus pictus (Liolaemidae) during the last glacial maximum in the Southern Andean beech forests. PLoS One 2012; 7:e48358. [PMID: 23209552 PMCID: PMC3507886 DOI: 10.1371/journal.pone.0048358] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 09/24/2012] [Indexed: 11/23/2022] Open
Abstract
Historical climate changes and orogenesis are two important factors that have shaped intraspecific biodiversity patterns worldwide. Although southern South America has experienced such complex events, there is a paucity of studies examining the effects on intraspecific diversification in this part of the world. Liolaemus pictus is the southernmost distributed lizard in the Chilean temperate forest, whose genetic structure has likely been influenced by Pleistocene glaciations. We conducted a phylogeographic study of L. pictus in Chile and Argentina based on one mitochondrial and two nuclear genes recovering two strongly divergent groups, Northern and Southern clades. The first group is distributed from the northernmost limit of the species to the Araucanía region while the second group is distributed throughout the Andes and the Chiloé archipelago in Southern Chile. Our results suggest that L. pictus originated 751 Kya, with divergence between the two clades occurring in the late Pleistocene. Demographic reconstructions for the Northern and Southern clades indicate a decrease in effective population sizes likely associated with Pleistocene glaciations. Surprisingly, patterns of genetic variation, clades age and historical gene flow in populations distributed within the limits of the Last Glacial Maximum (LGM) are not explained by recent colonization. We propose an “intra-Andean multiple refuge” hypothesis, along with the classical refuge hypothesis previously proposed for the biota of the Chilean Coastal range and Eastern Andean Cordillera. Our hypothesis is supported by niche modelling analysis suggesting the persistence of fragments of suitable habitat for the species within the limits of the LGM ice shield. This type of refuge hypothesis is proposed for the first time for an ectothermic species.
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Leppänen J, Vepsäläinen K, Savolainen R. Phylogeography of the ant Myrmica rubra and its inquiline social parasite. Ecol Evol 2012; 1:46-62. [PMID: 22393482 PMCID: PMC3287377 DOI: 10.1002/ece3.6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 06/06/2011] [Accepted: 06/07/2011] [Indexed: 11/30/2022] Open
Abstract
Widely distributed Palearctic insects are ideal to study phylogeographic patterns owing to their high potential to survive in many Pleistocene refugia and—after the glaciation—to recolonize vast, continuous areas. Nevertheless, such species have received little phylogeographic attention. Here, we investigated the Pleistocene refugia and subsequent postglacial colonization of the common, abundant, and widely distributed ant Myrmica rubra over most of its Palearctic area, using mitochondrial DNA (mtDNA). The western and eastern populations of M. rubra belonged predominantly to separate haplogroups, which formed a broad secondary contact zone in Central Europe. The distribution of genetic diversity and haplogroups implied that M. rubra survived the last glaciation in multiple refugia located over an extensive area from Iberia in the west to Siberia in the east, and colonized its present areas of distribution along several routes. The matrilineal genetic structure of M. rubra was probably formed during the last glaciation and subsequent postglacial expansion. Additionally, because M. rubra has two queen morphs, the obligately socially parasitic microgyne and its macrogyne host, we tested the suggested speciation of the parasite. Locally, the parasite and host usually belonged to the same haplogroup but differed in haplotype frequencies. This indicates that genetic differentiation between the morphs is a universal pattern and thus incipient, sympatric speciation of the parasite from its host is possible. If speciation is taking place, however, it is not yet visible as lineage sorting of the mtDNA between the morphs.
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Affiliation(s)
- Jenni Leppänen
- Department of Biosciences P.O. Box 65, 00014 University of Helsinki Finland
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Lévy-Hartmann L, Roussel V, Letourneur Y, Sellos DY. Global and New Caledonian patterns of population genetic variation in the deep-sea splendid alfonsino, Beryx splendens, inferred from mtDNA. Genetica 2012; 139:1349-65. [PMID: 22527688 DOI: 10.1007/s10709-012-9628-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 01/02/2012] [Indexed: 10/28/2022]
Abstract
Splendid alfonsino Beryx splendens is a commercial species in several countries, but is not currently exploited in New Caledonia. Information on species biology and genetics can influence the development of fisheries and assist in their management, but the genetic structuring and diversity of B. splendens populations remain largely unknown. To improve knowledge of genetic parameters, we used mitochondrial DNA sequences to conduct a comparative study of populations from throughout the world. Fragments of 815 bp of cytochrome b gene were sequenced and used to interpret the species history. We analyzed 204 individuals representing 14 geographical populations worldwide. A special focus was put on populations from New Caledonia. Analysis of variation between sequences, based on pairwise F statistics and AMOVA, demonstrated a population subdivision between the Atlantic and Indo-Pacific Oceans (Fst = 0.11-0.32; P < 0.05). Minimum-spanning network analysis revealed a mainly star-shaped pattern, with two lineages that may represent population expansion following a bottleneck/founder event and/or suggest colonization by migratory events over large distances. Our observations demonstrated that the species seems to follow the oceanic currents. Analysis of the nucleotide sequences revealed 122 variable sites, which defined numerous haplotypes, some associated with particular geographical regions. These data suggest an extremely high intra-specific genetic diversity, even at small scales. Focusing on the New Caledonia area, statistical analysis did not reveal sub-structuring among samples, suggesting again that at least a fraction of individuals migrate. No significant isolation by distance pattern was observed in this species (R = -0.22; P = 0.79) among seamount populations in the EEZ.
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Affiliation(s)
- Lauriana Lévy-Hartmann
- Laboratoire Insulaire du Vivant et de l'Environnement, Université de la Nouvelle-Calédonie, BP R4, 98851, Nouméa Cedex, New Caledonia, France.
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Rosales-Castillo JA, Vázquez-Garcidueñas MS, Álvarez-Hernández H, Chassin-Noria O, Varela-Murillo AI, Zavala-Páramo MG, Cano-Camacho H, Vázquez-Marrufo G. Genetic diversity and population structure of Escherichia coli from neighboring small-scale dairy farms. J Microbiol 2011; 49:693-702. [DOI: 10.1007/s12275-011-0461-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 04/21/2011] [Indexed: 10/15/2022]
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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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Arenas M, Ray N, Currat M, Excoffier L. Consequences of range contractions and range shifts on molecular diversity. Mol Biol Evol 2011; 29:207-18. [PMID: 21778191 DOI: 10.1093/molbev/msr187] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Due to past and current climatic changes, range contractions and range shifts are essential stages in the history of a species. However, unlike range expansions, the molecular consequences of these processes have been little investigated. In order to fill this gap, we simulated patterns of molecular diversity within and between populations for various types of range contractions and range shifts. We show that range contractions tend to decrease genetic diversity as compared with population with stable ranges but quite counterintuitively fast range contractions preserve higher levels of diversity and induce lower levels of genetic differentiation among refuge areas than slow contractions. Contrastingly, fast range shifts lead to lower levels of diversity than slow range shifts. At odds with our expectations, we find that species actively migrating toward refuge areas can only preserve higher levels of diversity in refugia if the contraction is rapid. Under slow range contraction or slow range shift, active migration toward refugia lead to a larger loss of diversity as compared with scenarios with isotropic migration and may thus not be a good evolutionary strategy. These results suggest that the levels of diversity preserved after a climate change both within and between refuge areas will not only depend on the dispersal abilities of a species but also on the speed of the change. It also implies that a given episode of climatic change will impact differently species with different generation times.
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Affiliation(s)
- Miguel Arenas
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Berne, Switzerland.
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CABANNE GUSTAVOS, D'HORTA FERNANDOM, MEYER DIOGO, SILVA JOSÉMC, MIYAKI CRISTINAY. Evolution of Dendrocolaptes platyrostris (Aves: Furnariidae) between the South American open vegetation corridor and the Atlantic forest. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01678.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gaither MR, Bowen BW, Bordenave TR, Rocha LA, Newman SJ, Gomez JA, van Herwerden L, Craig MT. Phylogeography of the reef fish Cephalopholis argus (Epinephelidae) indicates Pleistocene isolation across the Indo-Pacific Barrier with contemporary overlap in The Coral Triangle. BMC Evol Biol 2011; 11:189. [PMID: 21722383 PMCID: PMC3145601 DOI: 10.1186/1471-2148-11-189] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Accepted: 07/01/2011] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The Coral Triangle (CT), bounded by the Philippines, the Malay Peninsula, and New Guinea, is the epicenter of marine biodiversity. Hypotheses that explain the source of this rich biodiversity include 1) the center of origin, 2) the center of accumulation, and 3) the region of overlap. Here we contribute to the debate with a phylogeographic survey of a widely distributed reef fish, the Peacock Grouper (Cephalopholis argus; Epinephelidae) at 21 locations (N = 550) using DNA sequence data from mtDNA cytochrome b and two nuclear introns (gonadotropin-releasing hormone and S7 ribosomal protein). RESULTS Population structure was significant (ΦST = 0.297, P < 0.001; FST = 0.078, P < 0.001; FST = 0.099, P < 0.001 for the three loci, respectively) among five regions: French Polynesia, the central-west Pacific (Line Islands to northeastern Australia), Indo-Pacific boundary (Bali and Rowley Shoals), eastern Indian Ocean (Cocos/Keeling and Christmas Island), and western Indian Ocean (Diego Garcia, Oman, and Seychelles). A strong signal of isolation by distance was detected in both mtDNA (r = 0.749, P = 0.001) and the combined nuclear loci (r = 0.715, P < 0.001). We detected evidence of population expansion with migration toward the CT. Two clusters of haplotypes were detected in the mtDNA data (d = 0.008), corresponding to the Pacific and Indian Oceans, with a low level of introgression observed outside a mixing zone at the Pacific-Indian boundary. CONCLUSIONS We conclude that the Indo-Pacific Barrier, operating during low sea level associated with glaciation, defines the primary phylogeographic pattern in this species. These data support a scenario of isolation on the scale of 105 year glacial cycles, followed by population expansion toward the CT, and overlap of divergent lineages at the Pacific-Indian boundary. This pattern of isolation, divergence, and subsequent overlap likely contributes to species richness at the adjacent CT and is consistent with the region of overlap hypothesis.
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Affiliation(s)
- Michelle R Gaither
- Hawaii Institute of Marine Biology University of Hawaii PO Box 1346, Kaneohe, HI 96744, USA
| | - Brian W Bowen
- Hawaii Institute of Marine Biology University of Hawaii PO Box 1346, Kaneohe, HI 96744, USA
| | - Tiana-Rae Bordenave
- Hawaii Institute of Marine Biology University of Hawaii PO Box 1346, Kaneohe, HI 96744, USA
| | - Luiz A Rocha
- Department of Ichthyology California Academy of Sciences 55 Music Concourse Drive San Francisco, CA 94118, USA
| | - Stephen J Newman
- Western Australian Fisheries and Marine Research Laboratories Department of Fisheries Government of Western Australia P.O. Box 20, North Beach, WA 6920, Australia
| | - Juan A Gomez
- School of Marine & Tropical Biology James Cook University Townsville, QLD 4811, Australia
| | - Lynne van Herwerden
- School of Marine & Tropical Biology James Cook University Townsville, QLD 4811, Australia
| | - Matthew T Craig
- Department of Marine Sciences University of Puerto Rico Mayagüez P.O. Box 9000, Mayagüez PR 00681, USA
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BUTLER JASONM, DODD jr CKENNETH, ARESCO MATT, AUSTIN JAMESD. Morphological and molecular evidence indicates that the Gulf Coast box turtle (Terrapene carolina major) is not a distinct evolutionary lineage in the Florida Panhandle. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01625.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Safner T, Miller MP, McRae BH, Fortin MJ, Manel S. Comparison of Bayesian clustering and edge detection methods for inferring boundaries in landscape genetics. Int J Mol Sci 2011; 12:865-89. [PMID: 21541031 PMCID: PMC3083678 DOI: 10.3390/ijms12020865] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 01/18/2011] [Accepted: 01/19/2011] [Indexed: 11/25/2022] Open
Abstract
Recently, techniques available for identifying clusters of individuals or boundaries between clusters using genetic data from natural populations have expanded rapidly. Consequently, there is a need to evaluate these different techniques. We used spatially-explicit simulation models to compare three spatial Bayesian clustering programs and two edge detection methods. Spatially-structured populations were simulated where a continuous population was subdivided by barriers. We evaluated the ability of each method to correctly identify boundary locations while varying: (i) time after divergence, (ii) strength of isolation by distance, (iii) level of genetic diversity, and (iv) amount of gene flow across barriers. To further evaluate the methods' effectiveness to detect genetic clusters in natural populations, we used previously published data on North American pumas and a European shrub. Our results show that with simulated and empirical data, the Bayesian spatial clustering algorithms outperformed direct edge detection methods. All methods incorrectly detected boundaries in the presence of strong patterns of isolation by distance. Based on this finding, we support the application of Bayesian spatial clustering algorithms for boundary detection in empirical datasets, with necessary tests for the influence of isolation by distance.
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Affiliation(s)
- Toni Safner
- Laboratory of Alpine Ecology, Equipe Population Genomics and Biodiversity, UMR CNRS 5553, BP 53, University Joseph Fourier, 38041 Grenoble Cedex 9, France; E-Mail:
- Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Svetosimunska 25, 10000 Zagreb, Croatia
| | - Mark P. Miller
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84321, USA; E-Mail:
| | - Brad H. McRae
- The Nature Conservancy, 1917 1st Ave, Seattle, WA 98101, USA; E-Mail:
| | - Marie-Josée Fortin
- Department of Ecology & Evolutionary Biology, University of Toronto, Ontario, M6R 2R8, Canada; E-Mail:
| | - Stéphanie Manel
- Laboratory of Alpine Ecology, Equipe Population Genomics and Biodiversity, UMR CNRS 5553, BP 53, University Joseph Fourier, 38041 Grenoble Cedex 9, France; E-Mail:
- Laboratory of Population Environment Development, UMR 151 UP/IRD, University Aix-Marseille I, 3 place Victor Hugo, 13331 Marseille Cedex 03, France
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Godbout J, Beaulieu J, Bousquet J. Phylogeographic structure of jack pine (Pinus banksiana; Pinaceae) supports the existence of a coastal glacial refugium in northeastern North America. AMERICAN JOURNAL OF BOTANY 2010; 97:1903-1912. [PMID: 21616829 DOI: 10.3732/ajb.1000148] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
PREMISE OF THE STUDY The genetic structure of jack pine (Pinus banksiana Lamb.), a North American boreal conifer with large longitudinal distribution, was investigated to test for the possible existence of a genetically distinct lineage in the Maritimes region in northeastern North America, which could be indicative of a mid-latitude coastal refuge during the last glaciation. • METHODS One maternally inherited mitochondrial DNA (mtDNA) minisatellite marker and four paternally inherited chloroplast DNA (cpDNA) microsatellite markers were used to assess the range-wide geographical structure of jack pine populations with particular focus on northeastern North America. • KEY RESULTS The populations from the Maritimes region presented a unique mtDNA background characterized by very low diversity and the preponderance of a distinctive mitotype. The distribution of cpDNA diversity was not spatially structured, though three chlorotypes were restricted to the east. • CONCLUSIONS MtDNA data suggest that populations from the Maritimes region derive from a genetically depauperated north-coastal refugium. Contrastingly, the much higher geographical uniformity observed for cpDNA variation indicates that gene flow by pollen had been much more effective than seed gene flow at homogenizing population structure.
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Affiliation(s)
- Julie Godbout
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, 1030 Avenue de la Médecine, Université Laval, Quebec, Quebec G1V 0A6 Canada
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Miller MP, Haig SM. Identifying shared genetic structure patterns among Pacific Northwest forest taxa: insights from use of visualization tools and computer simulations. PLoS One 2010; 5:e13683. [PMID: 21060824 PMCID: PMC2966394 DOI: 10.1371/journal.pone.0013683] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 10/05/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Identifying causal relationships in phylogeographic and landscape genetic investigations is notoriously difficult, but can be facilitated by use of multispecies comparisons. METHODOLOGY/PRINCIPAL FINDINGS We used data visualizations to identify common spatial patterns within single lineages of four taxa inhabiting Pacific Northwest forests (northern spotted owl: Strix occidentalis caurina; red tree vole: Arborimus longicaudus; southern torrent salamander: Rhyacotriton variegatus; and western white pine: Pinus monticola). Visualizations suggested that, despite occupying the same geographical region and habitats, species responded differently to prevailing historical processes. S. o. caurina and P. monticola demonstrated directional patterns of spatial genetic structure where genetic distances and diversity were greater in southern versus northern locales. A. longicaudus and R. variegatus displayed opposite patterns where genetic distances were greater in northern versus southern regions. Statistical analyses of directional patterns subsequently confirmed observations from visualizations. Based upon regional climatological history, we hypothesized that observed latitudinal patterns may have been produced by range expansions. Subsequent computer simulations confirmed that directional patterns can be produced by expansion events. CONCLUSIONS/SIGNIFICANCE We discuss phylogeographic hypotheses regarding historical processes that may have produced observed patterns. Inferential methods used here may become increasingly powerful as detailed simulations of organisms and historical scenarios become plausible. We further suggest that inter-specific comparisons of historical patterns take place prior to drawing conclusions regarding effects of current anthropogenic change within landscapes.
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Affiliation(s)
- Mark P Miller
- Department of Biology and Center for High Performance Computing, Utah State University, Logan, Utah, United States of America.
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SHAFER AARONBA, CULLINGHAM CATHERINEI, CÔTÉ STEEVED, COLTMAN DAVIDW. Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Mol Ecol 2010; 19:4589-621. [PMID: 20849561 DOI: 10.1111/j.1365-294x.2010.04828.x] [Citation(s) in RCA: 260] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- AARON B. A. SHAFER
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - CATHERINE I. CULLINGHAM
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - STEEVE D. CÔTÉ
- Département de Biologie and Centre for Northern Studies, Université Laval, Québec, Québec G1V 0A6, Canada
| | - DAVID W. COLTMAN
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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VANDERGAST AMYG, PERRY WILLIAMM, LUGO ROBERTOV, HATHAWAY STACIEA. Genetic landscapes GIS Toolbox: tools to map patterns of genetic divergence and diversity. Mol Ecol Resour 2010; 11:158-61. [DOI: 10.1111/j.1755-0998.2010.02904.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- AMY G. VANDERGAST
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, 4165 Spruance Road Suite 200, San Diego, CA 92101, USA
| | - WILLIAM M. PERRY
- U.S. Geological Survey, Dixon Field Station, 6924 Tremont Road, Dixon, CA 95620, USA
| | - ROBERTO V. LUGO
- U.S. Geological Survey, Western Region Geospatial Information Office, 3020 State University Drive East, Modoc Hall, Suite 4003, Sacramento CA 95819, USA
| | - STACIE A. HATHAWAY
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, 4165 Spruance Road Suite 200, San Diego, CA 92101, USA
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Chavez AS, Kenagy GJ. Historical biogeography of western heather voles (Phenacomys intermedius) in montane systems of the Pacific Northwest. J Mammal 2010. [DOI: 10.1644/09-mamm-a-303.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Himes CM, Kenagy GJ. Influence of montane isolation and refugia on population structure ofSorex palustrisin western North America. J Mammal 2010. [DOI: 10.1644/09-mamm-a-378.1] [Citation(s) in RCA: 9] [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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Gortat T, Gryczyńska-Siemiątkowska A, Rutkowski R, Kozakiewicz A, Mikoszewski A, Kozakiewicz M. Landscape pattern and genetic structure of a yellow-necked mouse Apodemus flavicollis population in north-eastern Poland. ACTA ACUST UNITED AC 2010. [DOI: 10.4098/j.at.0001-7051.102.2009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Rodríguez-Robles JA, Jezkova T, Leal M. Climatic stability and genetic divergence in the tropical insular lizard Anolis krugi, the Puerto Rican 'Lagartijo Jardinero de la Montaña'. Mol Ecol 2010; 19:1860-76. [PMID: 20374489 DOI: 10.1111/j.1365-294x.2010.04616.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Two factors that can lead to geographic structuring in conspecific populations are barriers to dispersal and climatic stability. Populations that occur in different physiographic regions may be restricted to those areas by physical and/or ecological barriers, which may facilitate the formation of phylogeographic clades. Long-term climatic stability can also promote genetic diversification, because new clades are more likely to evolve in areas that experience lesser climatic shifts. We conducted a phylogeographic study of the Puerto Rican lizard Anolis krugi to assess whether populations of this anole show genetic discontinuities across the species' range, and if they do, whether these breaks coincide with the boundaries of the five physiographic regions of Puerto Rico. We also assessed whether interpopulation genetic distances in A. krugi are positively correlated with relative climatic stability in the island. Anolis krugi exhibits genetic structuring, but the phylogroups do not correspond to the physiographic regions of Puerto Rico. We used climatic reconstructions of two environmental extremes of the Quaternary period, the present conditions and those during the last glacial maximum (LGM), to quantify the degree of climatic stability between sampling locations. We documented positive correlations between genetic distances and relative climatic stability, although these associations were not significant when corrected for autocorrelation. Principal component analyses indicated the existence of climatic niche differences between some phylogeographic clades of A. krugi. The approach that we employed to assess the relationship between climatic stability and the genetic architecture of A. krugi can also be used to investigate the impact of factors such as the spatial distribution of food sources, parasites, predators or competitors on the genetic landscape of a species.
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