401
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Whipple AV, Holeski LM. Epigenetic Inheritance across the Landscape. Front Genet 2016; 7:189. [PMID: 27826318 PMCID: PMC5079072 DOI: 10.3389/fgene.2016.00189] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/10/2016] [Indexed: 12/12/2022] Open
Abstract
The study of epigenomic variation at the landscape-level in plants may add important insight to studies of adaptive variation. A major goal of landscape genomic studies is to identify genomic regions contributing to adaptive variation across the landscape. Heritable variation in epigenetic marks, resulting in transgenerational plasticity, can influence fitness-related traits. Epigenetic marks are influenced by the genome, the environment, and their interaction, and can be inherited independently of the genome. Thus, epigenomic variation likely influences the heritability of many adaptive traits, but the extent of this influence remains largely unknown. Here, we summarize the relevance of epigenetic inheritance to ecological and evolutionary processes, and review the literature on landscape-level patterns of epigenetic variation. Landscape-level patterns of epigenomic variation in plants generally show greater levels of isolation by distance and isolation by environment then is found for the genome, but the causes of these patterns are not yet clear. Linkage between the environment and epigenomic variation has been clearly shown within a single generation, but demonstrating transgenerational inheritance requires more complex breeding and/or experimental designs. Transgenerational epigenetic variation may alter the interpretation of landscape genomic studies that rely upon phenotypic analyses, but should have less influence on landscape genomic approaches that rely upon outlier analyses or genome–environment associations. We suggest that multi-generation common garden experiments conducted across multiple environments will allow researchers to understand which parts of the epigenome are inherited, as well as to parse out the relative contribution of heritable epigenetic variation to the phenotype.
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Affiliation(s)
- Amy V Whipple
- Department of Biological Sciences and Merriam-Powell Center for Environmental Research, Northern Arizona University Flagstaff, AZ, USA
| | - Liza M Holeski
- Department of Biological Sciences and Merriam-Powell Center for Environmental Research, Northern Arizona University Flagstaff, AZ, USA
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402
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Yardeni G, Tessler N, Imbert E, Sapir Y. Reproductive isolation between populations of Iris atropurpurea is associated with ecological differentiation. ANNALS OF BOTANY 2016; 118:971-982. [PMID: 27436798 PMCID: PMC5055820 DOI: 10.1093/aob/mcw139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/13/2016] [Accepted: 05/23/2016] [Indexed: 05/28/2023]
Abstract
Background and Aims Speciation is often described as a continuous dynamic process, expressed by different magnitudes of reproductive isolation (RI) among groups in different levels of divergence. Studying intraspecific partial RI can shed light on mechanisms underlying processes of population divergence. Intraspecific divergence can be driven by spatially stochastic accumulation of genetic differences following reduced gene flow, resulting in increased RI with increased geographical distance, or by local adaptation, resulting in increased RI with environmental difference. Methods We tested for RI as a function of both geographical distance and ecological differentiation in Iris atropurpurea, an endemic Israeli coastal plant. We crossed plants in the Netanya Iris Reserve population with plants from 14 populations across the species' full distribution, and calculated RI and reproductive success based on fruit set, seed set and fraction of seed viability. Key Results We found that total RI was not significantly associated with geographical distance, but significantly increased with ecological distance. Similarly, reproductive success of the crosses, estimated while controlling for the dependency of each component on the previous stage, significantly reduced with increased ecological distance. Conclusions Our results indicate that the rise of post-pollination reproductive barriers in I. atropurpurea is more affected by ecological differentiation between populations than by geographical distance, supporting the hypothesis that ecological differentiation is predominant over isolation by distance and by reduced gene flow in this species. These findings also affect conservation management, such as genetic rescue, in the highly fragmented and endangered I. atropurpurea.
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Affiliation(s)
- Gil Yardeni
- The Botanical Garden, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Naama Tessler
- Department of Biology, University of Haifa, Oranim, Tivon, Israel
| | - Eric Imbert
- Institut des Sciences de l’Evolution CNRS, IRD, University Montpellier 2, Montpellier, France
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403
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Piry S, Chapuis M, Gauffre B, Papaïx J, Cruaud A, Berthier K. Mapping Averaged Pairwise Information (MAPI): a new exploratory tool to uncover spatial structure. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12616] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | | | - Bertrand Gauffre
- UMR 7372, Centre d'Etudes Biologiques de Chizé CNRS – Université de La Rochelle 79360 Villiers‐en‐Bois France
- USC1339, Centre d'Etudes Biologiques de Chizé INRA 79360 Villiers‐en‐Bois France
| | - Julien Papaïx
- Biostatistique et Processus Spatiaux INRA 84914 Avignon France
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404
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Derkarabetian S, Burns M, Starrett J, Hedin M. Population genomic evidence for multiple Pliocene refugia in a montane‐restricted harvestman (Arachnida, Opiliones,
Sclerobunus robustus
) from the southwestern United States. Mol Ecol 2016; 25:4611-31. [DOI: 10.1111/mec.13789] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 07/11/2016] [Accepted: 07/19/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Shahan Derkarabetian
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
- Department of Biology University of California Riverside Riverside CA 92521 USA
| | - Mercedes Burns
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
| | - James Starrett
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
| | - Marshal Hedin
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
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405
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Harrisson KA, Yen JDL, Pavlova A, Rourke ML, Gilligan D, Ingram BA, Lyon J, Tonkin Z, Sunnucks P. Identifying environmental correlates of intraspecific genetic variation. Heredity (Edinb) 2016; 117:155-64. [PMID: 27273322 PMCID: PMC4981683 DOI: 10.1038/hdy.2016.37] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 04/14/2016] [Accepted: 04/18/2016] [Indexed: 11/08/2022] Open
Abstract
Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution).
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Affiliation(s)
- K A Harrisson
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - J D L Yen
- School of Physics & Astronomy, Monash University, Clayton, Victoria, Australia
| | - A Pavlova
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - M L Rourke
- Department of Primary Industries, DPI Fisheries, Narrandera, New South Wales, Australia
| | - D Gilligan
- Department of Primary Industries, DPI Fisheries, Batemans Bay Fisheries Office, Batemans Bay, New South Wales, Australia
| | - B A Ingram
- Fisheries Victoria, Department of Economic Development, Jobs, Transport and Resources, Alexandra, Victoria, Australia
| | - J Lyon
- Arthur Rylah Institute, Department of Environment, Land, Water & Planning, Heidelberg, Victoria, Australia
| | - Z Tonkin
- Arthur Rylah Institute, Department of Environment, Land, Water & Planning, Heidelberg, Victoria, Australia
| | - P Sunnucks
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
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406
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Abbasi S, Afsharzadeh S, Saeidi H, Triest L. Strong Genetic Differentiation of Submerged Plant Populations across Mountain Ranges: Evidence from Potamogeton pectinatus in Iran. PLoS One 2016; 11:e0161889. [PMID: 27560947 PMCID: PMC4999295 DOI: 10.1371/journal.pone.0161889] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/12/2016] [Indexed: 11/18/2022] Open
Abstract
Biogeographic barriers for freshwater biota can be effective at various spatial scales. At the largest spatial scale, freshwater organisms can become genetically isolated by their high mountain ranges, vast deserts, and inability to cross oceans. Isolation by distance of aquatic plants is expected to be stronger across than alongside mountain ridges whereas the heterogeneity of habitats among populations and temporary droughts may influence connectivity and hamper dispersal. Suitable aquatic plant habitats became reduced, even for the widespread submerged Potamogeton pectinatus L. (also named Stuckenia pectinata) giving structure to various aquatic habitats. We compared the level of genetic diversity in a heterogeneous series of aquatic habitats across Iran and tested their differentiation over distances and across mountain ranges (Alborz and Zagros) and desert zones (Kavir), with values obtained from temperate region populations. The diversity of aquatic ecosystems across and along large geographic barriers provided a unique ecological situation within Iran. P. pectinatus were considered from thirty-six sites across Iran at direct flight distances ranging from 20 to 1,200 km. Nine microsatellite loci revealed a very high number of alleles over all sites. A PCoA, NJT clustering and STRUCTURE analysis revealed a separate grouping of individuals of southeastern Iranian sites and was confirmed by their different nuclear ITS and cpDNA haplotypes thereby indicating an evolutionary significant unit (ESU). At the level of populations, a positive correlation between allelic differentiation Dest with geographic distance was found. Individual-based STRUCTURE analysis over 36 sites showed 7 genetic clusters. FST and RST values for ten populations reached 0.343 and 0.521, respectively thereby indicating that allele length differences are more important and contain evolutionary information. Overall, higher levels of diversity and a stronger differentiation was revealed among Iranian P. pectinatus than previously observed for temperate European regions, due to regional differences across mountain ranges over long distances.
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Affiliation(s)
- Shabnam Abbasi
- Department of Biology, Faculty of Science, University of Isfahan, 81746-73441, Isfahan, Iran
| | - Saeed Afsharzadeh
- Department of Biology, Faculty of Science, University of Isfahan, 81746-73441, Isfahan, Iran
| | - Hojjatollah Saeidi
- Department of Biology, Faculty of Science, University of Isfahan, 81746-73441, Isfahan, Iran
| | - Ludwig Triest
- Laboratory of Plant Biology and Nature Management (APNA), Department of Biology, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium
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407
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Gloss AD, Groen SC, Whiteman NK. A genomic perspective on the generation and maintenance of genetic diversity in herbivorous insects. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016; 47:165-187. [PMID: 28736510 DOI: 10.1146/annurev-ecolsys-121415-032220] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the processes that generate and maintain genetic variation within populations is a central goal in evolutionary biology. Theory predicts that some of this variation is maintained as a consequence of adapting to variable habitats. Studies in herbivorous insects have played a key role in confirming this prediction. Here, we highlight theoretical and conceptual models for the maintenance of genetic diversity in herbivorous insects, empirical genomic studies testing these models, and pressing questions within the realm of evolutionary and functional genomic studies. To address key gaps, we propose an integrative approach combining population genomic scans for adaptation, genome-wide characterization of targets of selection through experimental manipulations, mapping the genetic architecture of traits influencing fitness, and functional studies. We also stress the importance of studying the maintenance of genetic variation across biological scales-from variation within populations to divergence among populations-to form a comprehensive view of adaptation in herbivorous insects.
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Affiliation(s)
- Andrew D Gloss
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
| | - Simon C Groen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
| | - Noah K Whiteman
- Department of Integrative Biology, University of California-Berkeley, Berkeley, California
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408
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Szulkin M, Gagnaire PA, Bierne N, Charmantier A. Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits. Mol Ecol 2016; 25:542-58. [PMID: 26800038 DOI: 10.1111/mec.13486] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 12/20/2022]
Abstract
Linking population genetic variation to the spatial heterogeneity of the environment is of fundamental interest to evolutionary biology and ecology, in particular when phenotypic differences between populations are observed at biologically small spatial scales. Here, we applied restriction-site associated DNA sequencing (RAD-Seq) to test whether phenotypically differentiated populations of wild blue tits (Cyanistes caeruleus) breeding in a highly heterogeneous environment exhibit genetic structure related to habitat type. Using 12 106 SNPs in 197 individuals from deciduous and evergreen oak woodlands, we applied complementary population genomic analyses, which revealed that genetic variation is influenced by both geographical distance and habitat type. A fine-scale genetic differentiation supported by genome- and transcriptome-wide analyses was found within Corsica, between two adjacent habitats where blue tits exhibit marked differences in breeding time while nesting < 6 km apart. Using redundancy analysis (RDA), we show that genomic variation remains associated with habitat type when controlling for spatial and temporal effects. Finally, our results suggest that the observed patterns of genomic differentiation were not driven by a small proportion of highly differentiated loci, but rather emerged through a process such as habitat choice, which reduces gene flow between habitats across the entire genome. The pattern of genomic isolation-by-environment closely matches differentiation observed at the phenotypic level, thereby offering significant potential for future inference of phenotype-genotype associations in a heterogeneous environment.
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Affiliation(s)
- M Szulkin
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 Campus CNRS, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - P-A Gagnaire
- Université Montpellier 2, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France.,ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, 34200, Sète, France
| | - N Bierne
- Université Montpellier 2, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France.,ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, 34200, Sète, France
| | - A Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 Campus CNRS, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
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409
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Safran RJ, Scordato ESC, Wilkins MR, Hubbard JK, Jenkins BR, Albrecht T, Flaxman SM, Karaardıç H, Vortman Y, Lotem A, Nosil P, Pap P, Shen S, Chan S, Parchman T, Kane NC. Genome‐wide differentiation in closely related populations: the roles of selection and geographic isolation. Mol Ecol 2016; 25:3865-83. [DOI: 10.1111/mec.13740] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/08/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Affiliation(s)
- R. J. Safran
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - E. S. C. Scordato
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - M. R. Wilkins
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln NE USA
| | - J. K. Hubbard
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln NE USA
| | - B. R. Jenkins
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - T. Albrecht
- Department of Zoology Charles University in Prague and Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Prague Czech Republic
| | - S. M. Flaxman
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - H. Karaardıç
- Elementary Science Education Department Education Faculty Alanya Alaaddin Keykubat University Alanya Turkey
| | - Y. Vortman
- Department of Zoology Tel‐Aviv University Tel‐Aviv Israel
- Hula Research Center Department of Animal Sciences Tel‐Hai College Israel
| | - A. Lotem
- Department of Zoology Tel‐Aviv University Tel‐Aviv Israel
| | - P. Nosil
- Department of Animal and Plant Sciences University of Sheffield Sheffield UK
| | - P. Pap
- Department of Taxonomy and Ecology Babeş‐Bolyai University Cluj‐Napoca Romania
| | - S. Shen
- Biodiversity Research Center Academia Sinica Taipei Taiwan
| | - S.‐F. Chan
- Biodiversity Research Center Academia Sinica Taipei Taiwan
| | - T.L. Parchman
- Department of Biology University of Nevada Reno NV USA
| | - N. C. Kane
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
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410
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Richardson JL, Brady SP, Wang IJ, Spear SF. Navigating the pitfalls and promise of landscape genetics. Mol Ecol 2016; 25:849-63. [PMID: 26756865 DOI: 10.1111/mec.13527] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 12/12/2015] [Accepted: 01/07/2016] [Indexed: 12/17/2022]
Abstract
The field of landscape genetics has been evolving rapidly since its emergence in the early 2000s. New applications, techniques and criticisms of techniques appear like clockwork with each new journal issue. The developments are an encouraging, and at times bewildering, sign of progress in an exciting new field of study. However, we suggest that the rapid expansion of landscape genetics has belied important flaws in the development of the field, and we add an air of caution to this breakneck pace of expansion. Specifically, landscape genetic studies often lose sight of the fundamental principles and complex consequences of gene flow, instead favouring simplistic interpretations and broad inferences not necessarily warranted by the data. Here, we describe common pitfalls that characterize such studies, and provide practical guidance to improve landscape genetic investigation, with careful consideration of inferential limits, scale, replication, and the ecological and evolutionary context of spatial genetic patterns. Ultimately, the utility of landscape genetics will depend on translating the relationship between gene flow and landscape features into an understanding of long-term population outcomes. We hope the perspective presented here will steer landscape genetics down a more scientifically sound and productive path, garnering a field that is as informative in the future as it is popular now.
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Affiliation(s)
- Jonathan L Richardson
- Department of Biology, Providence College, 1 Cunningham Square, Providence, RI, 02918, USA
| | - Steven P Brady
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Ian J Wang
- Department of Environmental Science, Policy & Management, University of California, Berkeley, CA, 94720, USA
| | - Stephen F Spear
- The Orianne Society, 100 Phoenix Rd., Athens, GA, 30605, USA
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411
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Guo B, Lu D, Liao WB, Merilä J. Genomewide scan for adaptive differentiation along altitudinal gradient in the Andrew's toadBufo andrewsi. Mol Ecol 2016; 25:3884-900. [PMID: 27289071 DOI: 10.1111/mec.13722] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 06/02/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Baocheng Guo
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
| | - Di Lu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education); China West Normal University; Nanchong 637009 China
| | - Wen Bo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education); China West Normal University; Nanchong 637009 China
| | - Juha Merilä
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
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412
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Frei M, Csencsics D, Brodbeck S, Schweizer E, Bühler C, Gugerli F, Bolliger J. Combining landscape genetics, radio-tracking and long-term monitoring to derive management implications for Natterjack toads (Epidalea calamita) in agricultural landscapes. J Nat Conserv 2016. [DOI: 10.1016/j.jnc.2016.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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413
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Johansson MP, Quintela M, Laurila A. Genetic divergence and isolation by thermal environment in geothermal populations of an aquatic invertebrate. J Evol Biol 2016; 29:1701-12. [DOI: 10.1111/jeb.12902] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/13/2016] [Accepted: 05/18/2016] [Indexed: 12/14/2022]
Affiliation(s)
- M. P. Johansson
- Animal Ecology/Department of Ecology and Genetics; Uppsala University; Uppsala Sweden
| | - M. Quintela
- Animal Ecology/Department of Ecology and Genetics; Uppsala University; Uppsala Sweden
- Grupo de investigación BIOCOST; University of A Coruña; A Coruña Spain
| | - A. Laurila
- Animal Ecology/Department of Ecology and Genetics; Uppsala University; Uppsala Sweden
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414
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Noguerales V, Cordero PJ, Ortego J. Hierarchical genetic structure shaped by topography in a narrow-endemic montane grasshopper. BMC Evol Biol 2016; 16:96. [PMID: 27149952 PMCID: PMC4858822 DOI: 10.1186/s12862-016-0663-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/21/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Understanding the underlying processes shaping spatial patterns of genetic structure in free-ranging organisms is a central topic in evolutionary biology. Here, we aim to disentangle the relative importance of neutral (i.e. genetic drift) and local adaptation (i.e. ecological divergence) processes in the evolution of spatial genetic structure of the Morales grasshopper (Chorthippus saulcyi moralesi), a narrow-endemic taxon restricted to the Central Pyrenees. More specifically, we analysed range-wide patterns of genetic structure and tested whether they were shaped by geography (isolation-by-distance, IBD), topographic complexity and present and past habitat suitability models (isolation-by-resistance, IBR), and environmental dissimilarity (isolation-by-environment, IBE). RESULTS Different clustering analyses revealed a deep genetic structure that was best explained by IBR based on topographic complexity. Our analyses did not reveal a significant role of IBE, a fact that may be due to low environmental variation among populations and/or consequence of other ecological factors not considered in this study are involved in local adaptation processes. IBR scenarios informed by current and past climate distribution models did not show either a significant impact on genetic differentiation after controlling for the effects of topographic complexity, which may indicate that they are not capturing well microhabitat structure in the present or the genetic signal left by dispersal routes defined by habitat corridors in the past. CONCLUSIONS Overall, these results indicate that spatial patterns of genetic variation in our study system are primarily explained by neutral divergence and migration-drift equilibrium due to limited dispersal across abrupt reliefs, whereas environmental variation or spatial heterogeneity in habitat suitability associated with the complex topography of the region had no significant effect on genetic discontinuities after controlling for geography. Our study highlights the importance of considering a comprehensive suite of potential isolating mechanisms and analytical approaches in order to get robust inferences on the processes promoting genetic divergence of natural populations.
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Affiliation(s)
- Víctor Noguerales
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM), Ronda de Toledo 12, E-13071, Ciudad Real, Spain.
| | - Pedro J Cordero
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM), Ronda de Toledo 12, E-13071, Ciudad Real, Spain
| | - Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Avda. Américo Vespucio s/n, E-41092, Seville, Spain
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415
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Zhang YH, Wang IJ, Comes HP, Peng H, Qiu YX. Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae). Sci Rep 2016; 6:24041. [PMID: 27137438 PMCID: PMC4853719 DOI: 10.1038/srep24041] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/21/2016] [Indexed: 02/03/2023] Open
Abstract
Examining how historical and contemporary geographic and environmental factors contribute to genetic divergence at different evolutionary scales is a central yet largely unexplored question in ecology and evolution. Here, we examine this key question by investigating how environmental and geographic factors across different epochs have driven genetic divergence at deeper (phylogeographic) and shallower (landscape genetic) evolutionary scales in the Chinese Tertiary relict tree Emmenopterys henryi. We found that geography played a predominant role at all levels – phylogeographic clades are broadly geographically structured, the deepest levels of divergence are associated with major geological or pre-Quaternary climatic events, and isolation by distance (IBD) primarily explained population genetic structure. However, environmental factors are clearly also important – climatic fluctuations since the Last Interglacial (LIG) have likely contributed to phylogeographic structure, and the population genetic structure (in our AFLP dataset) was partly explained by isolation by environment (IBE), which may have resulted from natural selection in environments with divergent climates. Thus, historical and contemporary geography and historical and contemporary environments have all shaped patterns of genetic structure in E. henryi, and, in fact, changes in the landscape through time have also been critical factors.
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Affiliation(s)
- Yong-Hua Zhang
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
| | - Hans Peter Comes
- Department of Ecology &Evolution, Salzburg University, A-5020 Salzburg, Austria
| | - Hua Peng
- Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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416
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Munshi‐South J, Zolnik CP, Harris SE. Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations. Evol Appl 2016; 9:546-64. [PMID: 27099621 PMCID: PMC4831458 DOI: 10.1111/eva.12357] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/27/2015] [Indexed: 12/16/2022] Open
Abstract
Urbanization results in pervasive habitat fragmentation and reduces standing genetic variation through bottlenecks and drift. Loss of genomewide variation may ultimately reduce the evolutionary potential of animal populations experiencing rapidly changing conditions. In this study, we examined genomewide variation among 23 white-footed mouse (Peromyscus leucopus) populations sampled along an urbanization gradient in the New York City metropolitan area. Genomewide variation was estimated as a proxy for evolutionary potential using more than 10 000 single nucleotide polymorphism (SNP) markers generated by ddRAD-Seq. We found that genomewide variation is inversely related to urbanization as measured by percent impervious surface cover, and to a lesser extent, human population density. We also report that urbanization results in enhanced genomewide differentiation between populations in cities. There was no pattern of isolation by distance among these populations, but an isolation by resistance model based on impervious surface significantly explained patterns of genetic differentiation. Isolation by environment modeling also indicated that urban populations deviate much more strongly from global allele frequencies than suburban or rural populations. This study is the first to examine loss of genomewide SNP variation along an urban-to-rural gradient and quantify urbanization as a driver of population genomic patterns.
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Affiliation(s)
- Jason Munshi‐South
- Department of Biological Sciences and the Louis Calder Center—Biological Field StationFordham UniversityArmonkNYUSA
| | - Christine P. Zolnik
- Department of Biological Sciences and the Louis Calder Center—Biological Field StationFordham UniversityArmonkNYUSA
| | - Stephen E. Harris
- Ph.D. Program in EcologyEvolutionary Biology and Behaviorthe Graduate Center of the City University of New YorkNew YorkNYUSA
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417
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Durka W, Michalski SG, Berendzen KW, Bossdorf O, Bucharova A, Hermann JM, Hölzel N, Kollmann J. Genetic differentiation within multiple common grassland plants supports seed transfer zones for ecological restoration. J Appl Ecol 2016. [DOI: 10.1111/1365-2664.12636] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Walter Durka
- Department of Community Ecology (BZF); Helmholtz Centre for Environmental Research - UFZ; Theodor-Lieser-Str. 4 06120 Halle Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e 04103 Leipzig Germany
| | - Stefan G. Michalski
- Department of Community Ecology (BZF); Helmholtz Centre for Environmental Research - UFZ; Theodor-Lieser-Str. 4 06120 Halle Germany
| | - Kenneth W. Berendzen
- ZMBP - Central Facilities; University of Tübingen; Auf der Morgenstelle 32 72076 Tübingen Germany
| | - Oliver Bossdorf
- Plant Evolutionary Ecology; Institute of Evolution & Ecology; University of Tübingen; Auf der Morgenstelle 5 72076 Tübingen Germany
| | - Anna Bucharova
- Plant Evolutionary Ecology; Institute of Evolution & Ecology; University of Tübingen; Auf der Morgenstelle 5 72076 Tübingen Germany
| | - Julia-Maria Hermann
- Restoration Ecology; Department of Ecology & Ecosystem Management; Technical University Munich; Emil-Ramann-Str. 6 85354 Freising Germany
| | - Norbert Hölzel
- Biodiversity and Ecosystem Research Group; Institute of Landscape Ecology; University of Münster; Heisenbergstr. 2 48149 Münster Germany
| | - Johannes Kollmann
- Restoration Ecology; Department of Ecology & Ecosystem Management; Technical University Munich; Emil-Ramann-Str. 6 85354 Freising Germany
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418
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Kendrick GA, Orth RJ, Statton J, Hovey R, Ruiz Montoya L, Lowe RJ, Krauss SL, Sinclair EA. Demographic and genetic connectivity: the role and consequences of reproduction, dispersal and recruitment in seagrasses. Biol Rev Camb Philos Soc 2016; 92:921-938. [DOI: 10.1111/brv.12261] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 02/12/2016] [Accepted: 02/16/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Gary A. Kendrick
- School of Plant Biology, Faculty of Science; University of Western Australia; Crawley Western Australia 6009 Australia
- UWA Oceans Institute; University of Western Australia; Crawley Western Australia 6009 Australia
| | - Robert J. Orth
- Virginia Institute of Marine Science; College of William and Mary; Gloucester Point VA 23062 U.S.A
| | - John Statton
- School of Plant Biology, Faculty of Science; University of Western Australia; Crawley Western Australia 6009 Australia
- UWA Oceans Institute; University of Western Australia; Crawley Western Australia 6009 Australia
| | - Renae Hovey
- School of Plant Biology, Faculty of Science; University of Western Australia; Crawley Western Australia 6009 Australia
- UWA Oceans Institute; University of Western Australia; Crawley Western Australia 6009 Australia
| | - Leonardo Ruiz Montoya
- School of Plant Biology, Faculty of Science; University of Western Australia; Crawley Western Australia 6009 Australia
- UWA Oceans Institute; University of Western Australia; Crawley Western Australia 6009 Australia
| | - Ryan J. Lowe
- UWA Oceans Institute; University of Western Australia; Crawley Western Australia 6009 Australia
- School of Earth and Environment; University of Western Australia; Crawley Western Australia 6009 Australia
- ARC Centre of Excellence for Coral Reef Studies; James Cook University Townsville; Queensland 4811 Australia
| | - Siegfried L. Krauss
- School of Plant Biology, Faculty of Science; University of Western Australia; Crawley Western Australia 6009 Australia
- Kings Park and Botanic Garden; West Perth Western Australia 6005 Australia
| | - Elizabeth A. Sinclair
- School of Plant Biology, Faculty of Science; University of Western Australia; Crawley Western Australia 6009 Australia
- UWA Oceans Institute; University of Western Australia; Crawley Western Australia 6009 Australia
- Kings Park and Botanic Garden; West Perth Western Australia 6005 Australia
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419
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He SL, Wang YS, Li DZ, Yi TS. Environmental and Historical Determinants of Patterns of Genetic Differentiation in Wild Soybean (Glycine soja Sieb. et Zucc). Sci Rep 2016; 6:22795. [PMID: 26952904 PMCID: PMC4782138 DOI: 10.1038/srep22795] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/18/2016] [Indexed: 11/09/2022] Open
Abstract
Wild soybean, the direct progenitor of cultivated soybean, inhabits a wide distribution range across the mainland of East Asia and the Japanese archipelago. A multidisciplinary approach combining analyses of population genetics based on 20 nuclear microsatellites and one plastid locus were applied to reveal the genetic variation of wild soybean, and the contributions of geographical, environmental factors and historic climatic change on its patterns of genetic differentiation. High genetic diversity and significant genetic differentiation were revealed in wild soybean. Wild soybean was inferred to be limited to southern and central China during the Last Glacial Maximum (LGM) and experienced large-scale post-LGM range expansion into northern East Asia. A substantial northward range shift has been predicted to occur by the 2080s. A stronger effect of isolation by environment (IBE) versus isolation by geographical distance (IBD) was found for genetic differentiation in wild soybean, which suggested that environmental factors were responsible for the adaptive eco-geographical differentiation. This study indicated that IBE and historical climatic change together shaped patterns of genetic variation and differentiation of wild soybean. Different conservation measures should be implemented on different populations according to their adaptive potential to future changes in climate and human-induced environmental changes.
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Affiliation(s)
- Shui-Lian He
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, 650201, China
| | - Yun-Sheng Wang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- School of Environmental and life Science, Kaili University, Kaili, 650201, China
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Ting-Shuang Yi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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420
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Bai WN, Wang WT, Zhang DY. Phylogeographic breaks within Asian butternuts indicate the existence of a phytogeographic divide in East Asia. THE NEW PHYTOLOGIST 2016; 209:1757-72. [PMID: 26499508 DOI: 10.1111/nph.13711] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 09/15/2015] [Indexed: 05/16/2023]
Abstract
East Asia has been hypothesized to be subdivided into two distinct northern and southern areas, separated by a band of dry climate that was far more severe in the early Tertiary but still exists today. However, this biogeographic hypothesis has rarely been tested using a molecular phylogeographic approach. We genotyped 70 populations throughout the distributional range of Asian butternuts (Juglans section Cardiocaryon) using eight chloroplast DNA regions, one single-copy nuclear gene, and 17 nuclear microsatellite loci, supplemented with paleodistribution modeling of the major genetic clades. The genetic data consistently identified two clades, one northern, comprising Juglans mandshurica and Juglans ailantifolia, and one southern, comprising Juglans cathayensis. The two clades diverged through climate-induced vicariance of an ancestral northern range during the mid-Miocene and remained mostly separate thereafter, with geographical isolation of the Japanese Islands and refugial isolation or secondary contacts in the late Pleistocene producing further subdivision within the northern clade. But beyond all that, we also discovered a role of environmental adaptation in maintaining and/or reinforcing the north-south divergence. Asian butternuts offer a strong case for the existence of a biogeographic divide between the northern and southern parts of East Asia during the Neogene and into the Pleistocene.
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Affiliation(s)
- Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Wen-Ting Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
- School of Mathematics and Computer Science, Northwest University for Nationalities, Lanzhou, 730030, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
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421
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Population Genetic Structure of the Endangered Kaiser's Mountain Newt, Neurergus kaiseri (Amphibia: Salamandridae). PLoS One 2016; 11:e0149596. [PMID: 26918642 PMCID: PMC4769016 DOI: 10.1371/journal.pone.0149596] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 02/03/2016] [Indexed: 11/19/2022] Open
Abstract
Species often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in an endemic and critically endangered stream breeding mountain newt, Neurergus kaiseri, within its entire range in southwestern Iran. We identified two geographic regions based on phylogenetic relationships using Bayesian inference and maximum likelihood of 779 bp mtDNA (D-loop) in 111 individuals from ten of twelve known breeding populations. This analysis revealed a clear divergence between northern populations, located in more humid habitats at higher elevation, and southern populations, from drier habitats at lower elevations regions. From seven haplotypes found in these populations none was shared between the two regions. Analysis of molecular variance (AMOVA) of N. kaiseri indicates that 94.03% of sequence variation is distributed among newt populations and 5.97% within them. Moreover, a high degree of genetic subdivision, mainly attributable to the existence of significant variance among the two regions is shown (θCT = 0.94, P = 0.002). The positive and significant correlation between geographic and genetic distances (r = 0.61, P = 0.002) following controlling for environmental distance suggests an important influence of geographic divergence of the sites in shaping the genetic variation and may provide tools for a possible conservation based prioritization policy for the endangered species.
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422
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Sexton JP, Hufford MB, C.Bateman A, Lowry DB, Meimberg H, Strauss SY, Rice KJ. Climate structures genetic variation across a species' elevation range: a test of range limits hypotheses. Mol Ecol 2016; 25:911-28. [DOI: 10.1111/mec.13528] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 11/30/2015] [Accepted: 12/21/2015] [Indexed: 01/30/2023]
Affiliation(s)
- Jason P. Sexton
- School of Natural Sciences University of California 5200 North Lake Rd. Merced CA 95343 USA
| | - Matthew B. Hufford
- Department of Ecology, Evolution and Organismal Biology Iowa State University 339A Bessey Hall Ames IA 50011 USA
| | - Ashley C.Bateman
- Department of Biology Institute of Ecology and Evolution University of Oregon 77 Klamath Hall 1210 Eugene OR 97403 USA
| | - David B. Lowry
- Department of Plant Biology Michigan State University 612 Wilson Road East Lansing MI 48824 USA
| | - Harald Meimberg
- Institute of Integrative Nature Conservation Research University of Natural Resources and Life Sciences (Boku) Gregor Mendel‐Str. 33 1180 Vienna Austria
| | - Sharon Y. Strauss
- Department of Evolution and Ecology University of California One Shields Ave. Davis CA 95616 USA
| | - Kevin J. Rice
- Department of Plant Sciences University of California One Shields Ave. Davis CA 95616 USA
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423
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Benham PM, Witt CC. The dual role of Andean topography in primary divergence: functional and neutral variation among populations of the hummingbird, Metallura tyrianthina. BMC Evol Biol 2016; 16:22. [PMID: 26801894 PMCID: PMC4724075 DOI: 10.1186/s12862-016-0595-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/18/2016] [Indexed: 11/10/2022] Open
Abstract
Background The ridges and valleys of the Andes create physical barriers that limit animal dispersal and cause deterministic local variation in rainfall. This has resulted in physical isolation of animal populations and variation in habitats, each of which has likely contributed to the evolution of high species diversity in the region. However, the relative influences of geographic isolation, ecoclimatic conditions, and their potential interactions remain poorly understood. To address this, we compared patterns of genetic and morphological diversity in Peruvian populations of the hummingbird Metallura tyrianthina. Results Phylogenetic and variation partitioning analyses showed that geographic isolation rather than climatic dissimilarity explained the greatest proportion of genetic variance. In contrast, bill length variation was explained by climatic seasonality, but not by genetic divergence. We found that mutation-scaled migration rate (m) between persistently humid and semi-humid environments was nearly 20 times higher when the habitats were contiguous (m = 39.9) than when separated by a barrier, the Cordillera de Vilcanota (m = 2.1). Moreover, the population experiencing more gene flow exhibited a lesser degree of bill length divergence despite similar differences in climate. Conclusions Geographic isolation is necessary for genetic divergence. Ecological differences, represented here by climate characteristics, are necessary for functional divergence. Gene flow appears to hinder the evolution of functional traits toward local adaptive optima. This suggests that functional diversification requires geographic isolation followed or accompanied by a shift in ecological conditions. Andean topography causes both isolation and climatic variation, underscoring its dual role in biotic diversification. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0595-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Phred M Benham
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, 167 Castetter Hall MSC03 2020, 1 University of New Mexico, Albuquerque, NM, 87131, USA. .,Present address: Division of Biological Sciences, University of Montana, 32 Campus Dr. HS104, Missoula, MT, 59812, USA.
| | - Christopher C Witt
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, 167 Castetter Hall MSC03 2020, 1 University of New Mexico, Albuquerque, NM, 87131, USA.
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424
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Wu Z, Yu D, Li X, Xu X. Influence of geography and environment on patterns of genetic differentiation in a widespread submerged macrophyte, Eurasian watermilfoil (Myriophyllum spicatum L., Haloragaceae). Ecol Evol 2016; 6:460-8. [PMID: 26843930 PMCID: PMC4729246 DOI: 10.1002/ece3.1882] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/16/2015] [Accepted: 11/23/2015] [Indexed: 01/16/2023] Open
Abstract
The effects of geographic and environmental variables on the pattern of genetic differentiation have been thoroughly studied, whereas empirical studies on aquatic plants are rare. We examined the spatial genetic differentiation of 58 Myriophyllum spicatum populations distributed throughout China with 12 microsatellite loci, and we analyzed its association with geographic distance, geographic barriers, and environmental dissimilarity using causal modeling and multiple matrix regression with randomization (MMRR) analysis. Two genetic clusters were identified, and their geographic distribution suggested mountain ranges as a barrier to gene flow. The causal modeling revealed that both climate and geographic barriers significantly influenced genetic divergence among M. spicatum populations and that climate had the highest regression coefficient according to the MMRR analysis. This study showed that geography and environment together played roles in shaping the genetic structure of M. spicatum and that the influence of environment was greater. Our findings emphasized the potential importance of the environment in producing population genetic differentiation in aquatic plants at a large geographic scale.
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Affiliation(s)
- Zhigang Wu
- National Field Station of Freshwater Ecosystem of Liangzi Lake College of Life Sciences Wuhan University Wuhan China
| | - Dan Yu
- National Field Station of Freshwater Ecosystem of Liangzi Lake College of Life Sciences Wuhan University Wuhan China
| | - Xing Li
- National Field Station of Freshwater Ecosystem of Liangzi Lake College of Life Sciences Wuhan University Wuhan China
| | - Xinwei Xu
- National Field Station of Freshwater Ecosystem of Liangzi Lake College of Life Sciences Wuhan University Wuhan China
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425
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Guarnizo CE, Werneck FP, Giugliano LG, Santos MG, Fenker J, Sousa L, D’Angiolella AB, dos Santos AR, Strüssmann C, Rodrigues MT, Dorado-Rodrigues TF, Gamble T, Colli GR. Cryptic lineages and diversification of an endemic anole lizard (Squamata, Dactyloidae) of the Cerrado hotspot. Mol Phylogenet Evol 2016; 94:279-89. [DOI: 10.1016/j.ympev.2015.09.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/06/2015] [Accepted: 09/08/2015] [Indexed: 01/17/2023]
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426
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Riordan EC, Gugger PF, Ortego J, Smith C, Gaddis K, Thompson P, Sork VL. Association of genetic and phenotypic variability with geography and climate in three southern California oaks. AMERICAN JOURNAL OF BOTANY 2016; 103:73-85. [PMID: 26758886 DOI: 10.3732/ajb.1500135] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/10/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Geography and climate shape the distribution of organisms, their genotypes, and their phenotypes. To understand historical and future evolutionary and ecological responses to climate, we compared the association of geography and climate of three oak species (Quercus engelmannii, Quercus berberidifolia, and Quercus cornelius-mulleri) in an environmentally heterogeneous region of southern California at three organizational levels: regional species distributions, genetic variation, and phenotypic variation. METHODS We identified climatic variables influencing regional distribution patterns using species distribution models (SDMs), and then tested whether those individual variables are important in shaping genetic (microsatellite) and phenotypic (leaf morphology) variation. We estimated the relative contributions of geography and climate using multivariate redundancy analyses (RDA) with variance partitioning. KEY RESULTS The modeled distribution of each species was influenced by climate differently. Our analysis of genetic variation using RDA identified small but significant associations between genetic variation with climate and geography in Q. engelmannii and Q. cornelius-mulleri, but not in Q. berberidifolia, and climate explained more of the variation. Our analysis of phenotypic variation in Q. engelmannii indicated that climate had more impact than geography, but not in Q. berberidifolia. Throughout our analyses, we did not find a consistent pattern in effects of individual climatic variables. CONCLUSIONS Our comparative analysis illustrates that climate influences tree response at all organizational levels, but the important climate factors vary depending on the level and on the species. Because of these species-specific and level-specific responses, today's sympatric species are unlikely to have similar distributions in the future.
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Affiliation(s)
- Erin C Riordan
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Box 957239, Los Angeles, California 90095-7239 USA
| | - Paul F Gugger
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Box 957239, Los Angeles, California 90095-7239 USA
| | - Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Avenida Américo Vespucio s/n 41092 Seville, Spain
| | - Carrie Smith
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Box 957239, Los Angeles, California 90095-7239 USA
| | - Keith Gaddis
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Box 957239, Los Angeles, California 90095-7239 USA
| | - Pam Thompson
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Box 957239, Los Angeles, California 90095-7239 USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Box 957239, Los Angeles, California 90095-7239 USA Institute of the Environment and Sustainability, University of California Los Angeles, Box 951496, Los Angeles, California 90095-1496 USA
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427
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Sexton JP, Dickman EE. What can local and geographic population limits tell us about distributions? AMERICAN JOURNAL OF BOTANY 2016; 103:129-139. [PMID: 26772307 DOI: 10.3732/ajb.1500224] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 12/28/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Understanding the evolutionary and ecological factors that determine plant distributions is of primary importance in botanical research. These factors may vary in predictable ways across different spatial scales, and thus, we can leverage scale to reveal the underlying processes limiting plant distributions. METHODS We review various research considerations across local and geographic scales, including the investigation of dispersal and habitat limitation, evolutionary factors, abiotic and biotic factors, and research logistics. We also present two case studies, slender monkeyflower (Mimulus leptaleus) and cut-leaf monkeyflower (Mimulus laciniatus), in the California Sierra Nevada. KEY RESULTS At a local spatial scale (within 50 m), no seeds were produced from plants sown at sites located just beyond known patches of M. leptaleus, but within the species' geographic range. At a much broader spatial scale (kilometers), at the highest and lowest elevations of the species' range, we found greatly reduced abundance and fecundity in plants sown outside of the geographic range limits of M. laciniatus. CONCLUSIONS These cases illustrate two contrasting spatial scales, yet agree in their illustration of strong habitat limitation. We end by discussing future avenues of research and by suggesting ways botanical researchers can frame their studies to maximize information gained on species requirements, distribution limits, and conservation among varying spatial scales.
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Affiliation(s)
- Jason P Sexton
- School of Natural Sciences, 5200 North Lake Road, University of California, Merced, California 95343 USA
| | - Erin E Dickman
- School of Natural Sciences, 5200 North Lake Road, University of California, Merced, California 95343 USA
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428
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Bontrager M, Angert AL. Effects of range-wide variation in climate and isolation on floral traits and reproductive output of Clarkia pulchella. AMERICAN JOURNAL OF BOTANY 2016; 103:10-21. [PMID: 26362193 DOI: 10.3732/ajb.1500091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 05/28/2015] [Indexed: 05/11/2023]
Abstract
PREMISE OF THE STUDY Plant mating systems and geographic range limits are conceptually linked by shared underlying drivers, including landscape-level heterogeneity in climate and in species' abundance. Studies of how geography and climate interact to affect plant traits that influence mating system and population dynamics can lend insight to ecological and evolutionary processes shaping ranges. Here, we examined how spatiotemporal variation in climate affects reproductive output of a mixed-mating annual, Clarkia pulchella. We also tested the effects of population isolation and climate on mating-system-related floral traits across the range. METHODS We measured reproductive output and floral traits on herbarium specimens collected across the range of C. pulchella. We extracted climate data associated with specimens and derived a population isolation metric from a species distribution model. We then examined how predictors of reproductive output and floral traits vary among populations of increasing distance from the range center. Finally, we tested whether reproductive output and floral traits vary with increasing distance from the center of the range. KEY RESULTS Reproductive output decreased as summer precipitation decreased, and low precipitation may contribute to limiting the southern and western range edges of C. pulchella. High spring and summer temperatures are correlated with low herkogamy, but these climatic factors show contrasting spatial patterns in different quadrants of the range. CONCLUSIONS Limiting factors differ among different parts of the range. Due to the partial decoupling of geography and environment, examining relationships between climate, reproductive output, and mating-system-related floral traits reveals spatial patterns that might be missed when focusing solely on geographic position.
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Affiliation(s)
- Megan Bontrager
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Amy L Angert
- Departments of Botany and Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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429
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Saenz-Agudelo P, Dibattista JD, Piatek MJ, Gaither MR, Harrison HB, Nanninga GB, Berumen ML. Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes. Mol Ecol 2015; 24:6241-55. [DOI: 10.1111/mec.13471] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 11/09/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Pablo Saenz-Agudelo
- Division of Biological and Environmental Science and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Saudi Arabia
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Valdivia Chile
| | - Joseph D. Dibattista
- Division of Biological and Environmental Science and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Saudi Arabia
- Department of Environment and Agriculture; Curtin University; PO Box U1987 Perth WA 6845 Australia
| | - Marek J. Piatek
- Computational Bioscience Research Center; King Abdullah University of Science and Technology; Thuwal 23955 Saudi Arabia
| | - Michelle R. Gaither
- School of Biological and Biomedical Sciences; Durham University; South Road Durham DH1 3LE UK
- Section of Ichthyology; California Academy of Sciences; 55 Music Concourse Drive San Francisco CA 94118 USA
| | - Hugo B. Harrison
- Australian Research Council Centre of Excellence for Coral Reef Studies; James Cook University; Townsville QLD 4811 Australia
| | - Gerrit B. Nanninga
- Division of Biological and Environmental Science and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Saudi Arabia
- USR 3278 CRIOBE CNRS-EPHE; CRIOBE BP 1013 Papetoai 98729 Moorea French Polynesia
| | - Michael L. Berumen
- Division of Biological and Environmental Science and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Saudi Arabia
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430
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Forester BR, Jones MR, Joost S, Landguth EL, Lasky JR. Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes. Mol Ecol 2015; 25:104-20. [PMID: 26576498 DOI: 10.1111/mec.13476] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 11/10/2015] [Accepted: 11/10/2015] [Indexed: 12/18/2022]
Abstract
The spatial structure of the environment (e.g. the configuration of habitat patches) may play an important role in determining the strength of local adaptation. However, previous studies of habitat heterogeneity and local adaptation have largely been limited to simple landscapes, which poorly represent the multiscale habitat structure common in nature. Here, we use simulations to pursue two goals: (i) we explore how landscape heterogeneity, dispersal ability and selection affect the strength of local adaptation, and (ii) we evaluate the performance of several genotype-environment association (GEA) methods for detecting loci involved in local adaptation. We found that the strength of local adaptation increased in spatially aggregated selection regimes, but remained strong in patchy landscapes when selection was moderate to strong. Weak selection resulted in weak local adaptation that was relatively unaffected by landscape heterogeneity. In general, the power of detection methods closely reflected levels of local adaptation. False-positive rates (FPRs), however, showed distinct differences across GEA methods based on levels of population structure. The univariate GEA approach had high FPRs (up to 55%) under limited dispersal scenarios, due to strong isolation by distance. By contrast, multivariate, ordination-based methods had uniformly low FPRs (0-2%), suggesting these approaches can effectively control for population structure. Specifically, constrained ordinations had the best balance of high detection and low FPRs and will be a useful addition to the GEA toolkit. Our results provide both theoretical and practical insights into the conditions that shape local adaptation and how these conditions impact our ability to detect selection.
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Affiliation(s)
- Brenna R Forester
- Nicholas School of the Environment, University Program in Ecology, Duke University, Durham, NC, 27708, USA
| | - Matthew R Jones
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Stéphane Joost
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), Laboratory of Geographic Information Systems (LASIG), CH-1015, Lausanne, Switzerland
| | - Erin L Landguth
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Jesse R Lasky
- Earth Institute, and Department of Ecology, Evolution & Environmental Biology, Columbia University, New York, NY, 10027, USA.,Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
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431
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Clowers KJ, Will JL, Gasch AP. A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae. Mol Ecol 2015; 24:5886-98. [PMID: 26518477 PMCID: PMC4824287 DOI: 10.1111/mec.13439] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/24/2015] [Accepted: 10/27/2015] [Indexed: 12/24/2022]
Abstract
Differential adaptation to distinct niches can restrict gene flow and promote population differentiation within a species. However, in some cases the distinction between niches can collapse, forming a hybrid niche with features of both environments. We previously reported that distinctions between vineyards and oak soil present an ecological barrier that restricts gene flow between lineages of Saccharomyces cerevisiae. Vineyard isolates are tolerant to stresses associated with grapes while North American oak strains are particularly tolerant to freeze-thaw cycles. Here, we report the isolation of S. cerevisiae strains from Wisconsin cherry trees, which display features common to vineyards (e.g. high sugar concentrations) and frequent freeze-thaw cycles. Genome sequencing revealed that the isolated strains are highly heterozygous and represent recent hybrids of the oak × vineyard lineages. We found that the hybrid strains are phenotypically similar to vineyard strains for some traits, but are more similar to oak strains for other traits. The cherry strains were exceptionally good at growing in cherry juice, raising the possibility that they have adapted to this niche. We performed transcriptome profiling in cherry, oak and vineyard strains and show that the cherry-tree hybrids display vineyard-like or oak-like expression, depending on the gene sets, and in some cases, the expression patterns linked back to shared stress tolerances. Allele-specific expression in these natural hybrids suggested concerted cis-regulatory evolution at sets of functionally regulated genes. Our results raise the possibility that hybridization of the two lineages provides a genetic solution to the thriving in this unique niche.
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Affiliation(s)
- Katie J Clowers
- Laboratory of Genetics, University of Wisconsin-Madison, 425-G Henry Mall, Madison, WI, 53706, USA
| | - Jessica L Will
- Laboratory of Genetics, University of Wisconsin-Madison, 425-G Henry Mall, Madison, WI, 53706, USA
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, 425-G Henry Mall, Madison, WI, 53706, USA
- Great Lakes Bioenergy Research Center, 1552 University Ave., Madison, WI, 53704, USA
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432
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Ferrer ES, García-Navas V, Bueno-Enciso J, Barrientos R, Serrano-Davies E, Cáliz-Campal C, Sanz JJ, Ortego J. The influence of landscape configuration and environment on population genetic structure in a sedentary passerine: insights from loci located in different genomic regions. J Evol Biol 2015; 29:205-19. [DOI: 10.1111/jeb.12776] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/07/2015] [Accepted: 10/12/2015] [Indexed: 11/29/2022]
Affiliation(s)
- E. S. Ferrer
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - V. García-Navas
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
| | - J. Bueno-Enciso
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - R. Barrientos
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - E. Serrano-Davies
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - C. Cáliz-Campal
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
| | - J. J. Sanz
- Departamento de Ecología Evolutiva; Museo Nacional de Ciencias Naturales (CSIC); Madrid Spain
| | - J. Ortego
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
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433
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Hecht BC, Matala AP, Hess JE, Narum SR. Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range. Mol Ecol 2015; 24:5573-95. [DOI: 10.1111/mec.13409] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 09/29/2015] [Accepted: 10/01/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Benjamin C. Hecht
- Columbia River Inter-Tribal Fish Commission; Hagerman Fish Culture Experiment Station; 3059F National Fish Hatchery Road Hagerman ID 83332 USA
- Aquaculture Research Institute; University of Idaho; Hagerman Fish Culture Experiment Station; 3059F National Fish Hatchery Road Hagerman ID 83332 USA
| | - Andrew P. Matala
- Columbia River Inter-Tribal Fish Commission; Hagerman Fish Culture Experiment Station; 3059F National Fish Hatchery Road Hagerman ID 83332 USA
| | - Jon E. Hess
- Columbia River Inter-Tribal Fish Commission; Hagerman Fish Culture Experiment Station; 3059F National Fish Hatchery Road Hagerman ID 83332 USA
| | - Shawn R. Narum
- Columbia River Inter-Tribal Fish Commission; Hagerman Fish Culture Experiment Station; 3059F National Fish Hatchery Road Hagerman ID 83332 USA
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434
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Murphy AL, Pavlova A, Thompson R, Davis J, Sunnucks P. Swimming through sand: connectivity of aquatic fauna in deserts. Ecol Evol 2015; 5:5252-5264. [PMID: 30151128 PMCID: PMC6102528 DOI: 10.1002/ece3.1741] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 08/11/2015] [Accepted: 08/22/2015] [Indexed: 01/15/2023] Open
Abstract
Freshwater ecosystems in arid regions range from highly fragmented to highly connected, and connectivity has been assumed to be a major factor in the persistence of aquatic biota in arid environments. This review sought to synthesize existing research on genetic estimation of population connectivity in desert freshwaters, identify knowledge gaps, and set priorities for future studies of connectivity in these environments. From an extensive literature search, we synthesized the approaches applied, systems studied, and conclusions about connectivity reached in population genetic research concerning desert freshwater connectivity globally. We restrict our scope to obligate aquatic fauna that disperse largely via freshwaters and exclude those with active aerial dispersal abilities. We examined 92 papers, comprising 133 studies, published from 1987 to 2014. Most described studies of fishes and invertebrates in the deserts of Australia and North America. Connectivity declined with increasing scale, but did not differ significantly among arid regions or taxonomic classes. There were significant differences in connectivity patterns between species with different dispersal abilities, and between spring and riverine habitats at local scales. Population connectivity in desert freshwaters is typically most influenced by the ecology of the species concerned and hydrological connectivity. Most studies did not assess predefined models of connectivity, but described gene flow and/or genetic structure. Climate change and anthropogenic impacts worldwide are likely to increase the incidence and impact of habitat fragmentation in already threatened desert freshwaters. To reduce this risk, biodiversity conservation and environmental management must address connectivity, but often the required information does not exist. Researchers can provide this by explicitly considering the effects of hydrology and species' ecology on connectivity, and incorporating these into connectivity models, which are vital for understanding connectivity in desert freshwaters.
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Affiliation(s)
- Ashley L Murphy
- School of Biological Sciences Monash University Melbourne Victoria 3800 Australia
| | - Alexandra Pavlova
- School of Biological Sciences Monash University Melbourne Victoria 3800 Australia
| | - Ross Thompson
- Institute for Applied Ecology University of Canberra Canberra Australian Capital Territory 2617 Australia
| | - Jenny Davis
- Institute for Applied Ecology University of Canberra Canberra Australian Capital Territory 2617 Australia
| | - Paul Sunnucks
- School of Biological Sciences Monash University Melbourne Victoria 3800 Australia
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435
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Charmantier A, Doutrelant C, Dubuc-Messier G, Fargevieille A, Szulkin M. Mediterranean blue tits as a case study of local adaptation. Evol Appl 2015; 9:135-52. [PMID: 27087844 PMCID: PMC4780380 DOI: 10.1111/eva.12282] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/27/2015] [Indexed: 02/01/2023] Open
Abstract
While the study of the origins of biological diversity across species has provided numerous examples of adaptive divergence, the realization that it can occur at microgeographic scales despite gene flow is recent, and scarcely illustrated. We review here evidence suggesting that the striking phenotypic differentiation in ecologically relevant traits exhibited by blue tits Cyanistes caeruleus in their southern range‐edge putatively reflects adaptation to the heterogeneity of the Mediterranean habitats. We first summarize the phenotypic divergence for a series of life history, morphological, behavioural, acoustic and colour ornament traits in blue tit populations of evergreen and deciduous forests. For each divergent trait, we review the evidence obtained from common garden experiments regarding a possible genetic origin of the observed phenotypic differentiation as well as evidence for heterogeneous selection. Second, we argue that most phenotypically differentiated traits display heritable variation, a fundamental requirement for evolution to occur. Third, we discuss nonrandom dispersal, selective barriers and assortative mating as processes that could reinforce local adaptation. Finally, we show how population genomics supports isolation – by – environment across landscapes. Overall, the combination of approaches converges to the conclusion that the strong phenotypic differentiation observed in Mediterranean blue tits is a fascinating case of local adaptation.
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Affiliation(s)
- Anne Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive Campus CNRS Montpellier France
| | - Claire Doutrelant
- Centre d'Ecologie Fonctionnelle et Evolutive Campus CNRS Montpellier France
| | - Gabrielle Dubuc-Messier
- Centre d'Ecologie Fonctionnelle et Evolutive Campus CNRS Montpellier France; Département des sciences biologiques Université du Québec à Montréal Succursalle centre-ville QC Canada
| | | | - Marta Szulkin
- Centre d'Ecologie Fonctionnelle et Evolutive Campus CNRS Montpellier France
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436
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Wu Z, Yu D, Wang Z, Li X, Xu X. Great influence of geographic isolation on the genetic differentiation of Myriophyllum spicatum under a steep environmental gradient. Sci Rep 2015; 5:15618. [PMID: 26494202 PMCID: PMC4616052 DOI: 10.1038/srep15618] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/28/2015] [Indexed: 11/01/2022] Open
Abstract
Understanding how natural processes affect population genetic structures is an important issue in evolutionary biology. One effective method is to assess the relative importance of environmental and geographical factors in the genetic structure of populations. In this study, we examined the spatial genetic variation of thirteen Myriophyllum spicatum populations from the Qinghai-Tibetan Plateau (QTP) and adjacent highlands (Yunnan-Guizhou Plateau, YGP) by using microsatellite loci and environmental and geographical factors. Bioclim layers, hydrological properties and elevation were considered as environmental variables and reduced by principal component analysis. The genetic isolation by geographic distance (IBD) was tested by Mantel tests and the relative importance of environmental variables on population genetic differentiation was determined by a partial Mantel test and multiple matrix regression with randomization (MMRR). Two genetic clusters corresponding to the QTP and YGP were identified. Both tests and MMRR revealed a significant and strong correlation between genetic divergence and geographic isolation under the influence of environmental heterogeneity at the overall and finer spatial scales. Our findings suggested the dominant role of geography on the evolution of M. spicatum under a steep environmental gradient in the alpine landscape as a result of dispersal limitation and genetic drift.
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Affiliation(s)
- Zhigang Wu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Dan Yu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Zhong Wang
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xing Li
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xinwei Xu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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437
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Harter DEV, Thiv M, Weig A, Jentsch A, Beierkuhnlein C. Spatial and ecological population genetic structures within two island-endemic Aeonium species of different niche width. Ecol Evol 2015; 5:4327-44. [PMID: 26664682 PMCID: PMC4667834 DOI: 10.1002/ece3.1682] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 07/13/2015] [Accepted: 07/22/2015] [Indexed: 01/21/2023] Open
Abstract
The Crassulacean genus Aeonium is a well-known example for plant species radiation on oceanic archipelagos. However, while allopatric speciation among islands is documented for this genus, the role of intra-island speciation due to population divergence by topographical isolation or ecological heterogeneity has not yet been addressed. The aim of this study was to investigate intraspecific genetic structures and to identify spatial and ecological drivers of genetic population differentiation on the island scale. We analyzed inter simple sequence repeat variation within two island-endemic Aeonium species of La Palma: one widespread generalist that covers a large variety of different habitat types (Ae. davidbramwellii) and one narrow ecological specialist (Ae. nobile), in order to assess evolutionary potentials on this island. Gene pool differentiation and genetic diversity patterns were associated with major landscape structures in both species, with phylogeographic implications. However, overall levels of genetic differentiation were low. For the generalist species, outlier loci detection and loci-environment correlation approaches indicated moderate signatures of divergent selection pressures linked to temperature and precipitation variables, while the specialist species missed such patterns. Our data point to incipient differentiation among populations, emphasizing that ecological heterogeneity and topographical structuring within the small scales of an island can foster evolutionary processes. Very likely, such processes have contributed to the radiation of Aeonium on the Canary Islands. There is also support for different evolutionary mechanisms between generalist and specialist species.
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Affiliation(s)
| | - Mike Thiv
- State Museum of Natural History StuttgartStuttgartGermany
| | - Alfons Weig
- DNA Analytics and EcoinformaticsBayCEERUniversity of BayreuthBayreuthGermany
| | - Anke Jentsch
- Disturbance EcologyBayCEERUniversity of BayreuthBayreuthGermany
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438
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Johansson ML, Alberto F, Reed DC, Raimondi PT, Coelho NC, Young MA, Drake PT, Edwards CA, Cavanaugh K, Assis J, Ladah LB, Bell TW, Coyer JA, Siegel DA, Serrão EA. Seascape drivers of Macrocystis pyrifera population genetic structure in the northeast Pacific. Mol Ecol 2015; 24:4866-85. [PMID: 26339775 DOI: 10.1111/mec.13371] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/26/2015] [Accepted: 09/01/2015] [Indexed: 01/10/2023]
Abstract
At small spatial and temporal scales, genetic differentiation is largely controlled by constraints on gene flow, while genetic diversity across a species' distribution is shaped on longer temporal and spatial scales. We assess the hypothesis that oceanographic transport and other seascape features explain different scales of genetic structure of giant kelp, Macrocystis pyrifera. We followed a hierarchical approach to perform a microsatellite-based analysis of genetic differentiation in Macrocystis across its distribution in the northeast Pacific. We used seascape genetic approaches to identify large-scale biogeographic population clusters and investigate whether they could be explained by oceanographic transport and other environmental drivers. We then modelled population genetic differentiation within clusters as a function of oceanographic transport and other environmental factors. Five geographic clusters were identified: Alaska/Canada, central California, continental Santa Barbara, California Channel Islands and mainland southern California/Baja California peninsula. The strongest break occurred between central and southern California, with mainland Santa Barbara sites forming a transition zone between the two. Breaks between clusters corresponded approximately to previously identified biogeographic breaks, but were not solely explained by oceanographic transport. An isolation-by-environment (IBE) pattern was observed where the northern and southern Channel Islands clustered together, but not with closer mainland sites, despite the greater distance between them. The strongest environmental association with this IBE pattern was observed with light extinction coefficient, which extends suitable habitat to deeper areas. Within clusters, we found support for previous results showing that oceanographic connectivity plays an important role in the population genetic structure of Macrocystis in the Northern hemisphere.
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Affiliation(s)
- Mattias L Johansson
- Department of Biological Sciences, University of Wisconsin - Milwaukee, PO Box 413, Milwaukee, WI, 53201, USA
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Filipe Alberto
- Department of Biological Sciences, University of Wisconsin - Milwaukee, PO Box 413, Milwaukee, WI, 53201, USA
| | - Daniel C Reed
- Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Peter T Raimondi
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95064, USA
| | - Nelson C Coelho
- Department of Biological Sciences, University of Wisconsin - Milwaukee, PO Box 413, Milwaukee, WI, 53201, USA
| | - Mary A Young
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95064, USA
| | - Patrick T Drake
- Ocean Sciences Department, University of California, Santa Cruz, CA, 95064, USA
| | | | - Kyle Cavanaugh
- Department of Geography, University of California, Los Angeles, CA, 90095, USA
| | - Jorge Assis
- Center of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Lydia B Ladah
- Department of Biological Oceanography, CISESE, Ensenada, C.P. 22860, Baja California, México
| | - Tom W Bell
- Earth Research Institute, University of California, Santa Barbara, CA, 93106, USA
| | - James A Coyer
- Shoals Marine Laboratory, Cornell University, Portsmouth, NH, 03801, USA
| | - David A Siegel
- Earth Research Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Ester A Serrão
- Center of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
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439
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Deacon NJ, Cavender-Bares J. Limited Pollen Dispersal Contributes to Population Genetic Structure but Not Local Adaptation in Quercus oleoides Forests of Costa Rica. PLoS One 2015; 10:e0138783. [PMID: 26407244 PMCID: PMC4583504 DOI: 10.1371/journal.pone.0138783] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/03/2015] [Indexed: 11/25/2022] Open
Abstract
Background Quercus oleoides Cham. and Schlect., tropical live oak, is a species of conservation importance in its southern range limit of northwestern Costa Rica. It occurs in high-density stands across a fragmented landscape spanning a contrasting elevation and precipitation gradient. We examined genetic diversity and spatial genetic structure in this geographically isolated and genetically distinct population. We characterized population genetic diversity at 11 nuclear microsatellite loci in 260 individuals from 13 sites. We monitored flowering time at 10 sites, and characterized the local environment in order to compare observed spatial genetic structure to hypotheses of isolation-by-distance and isolation-by-environment. Finally, we quantified pollen dispersal distances and tested for local adaptation through a reciprocal transplant experiment in order to experimentally address these hypotheses. Results High genetic diversity is maintained in the population and the genetic variation is significantly structured among sampled sites. We identified 5 distinct genetic clusters and average pollen dispersal predominately occurred over short distances. Differences among sites in flowering phenology and environmental factors, however, were not strictly associated with genetic differentiation. Growth and survival of upland and lowland progeny in their native and foreign environments was expected to exhibit evidence of local adaptation due to the more extreme dry season in the lowlands. Seedlings planted in the lowland garden experienced much higher mortality than seedlings in the upland garden, but we did not identify evidence for local adaptation. Conclusion Overall, this study indicates that the Costa Rican Q. oleoides population has a rich population genetic history. Despite environmental heterogeneity and habitat fragmentation, isolation-by-distance and isolation-by-environment alone do not explain spatial genetic structure. These results add to studies of genetic structure by examining a common, tropical tree over multiple habitats and provide information for managers of a successional forest in a protected area.
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Affiliation(s)
- Nicholas John Deacon
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- Plant Biological Sciences Graduate Program, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
| | - Jeannine Cavender-Bares
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
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440
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Mosaic genetic differentiation along environmental and geographic gradients indicate divergent selection in a white pine species complex. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9785-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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441
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Botta F, Eriksen C, Fontaine MC, Guillot G. Enhanced computational methods for quantifying the effect of geographic and environmental isolation on genetic differentiation. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12424] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Filippo Botta
- Applied Mathematics and Computer Science Department Technical University of Denmark Copenhagen Denmark
- Now at Centre for Macro‐Ecology Copenhagen University Copenhagen Denmark
| | - Casper Eriksen
- Applied Mathematics and Computer Science Department Technical University of Denmark Copenhagen Denmark
| | - Michaël C. Fontaine
- Marine Evolution and Conservation Groningen Institute for Evolutionary Life Sciences University of Groningen The Netherlands
| | - Gilles Guillot
- Applied Mathematics and Computer Science Department Technical University of Denmark Copenhagen Denmark
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442
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Collin H, Fumagalli L. The role of geography and ecology in shaping repeated patterns of morphological and genetic differentiation between European minnows (Phoxinus phoxinus) from the Pyrenees and the Alps. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12611] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hélène Collin
- Département d'Ecologie et Evolution; Laboratoire de Biologie de la Conservation, Biophore; Université de Lausanne; Lausanne 1015 Switzerland
- Institute of Integrative Biology; Department of Evolution; Ecology and Behaviour; University of Liverpool; Liverpool L69 7ZB UK
| | - Luca Fumagalli
- Département d'Ecologie et Evolution; Laboratoire de Biologie de la Conservation, Biophore; Université de Lausanne; Lausanne 1015 Switzerland
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443
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Giles EC, Saenz-Agudelo P, Hussey NE, Ravasi T, Berumen ML. Exploring seascape genetics and kinship in the reef sponge Stylissa carteri in the Red Sea. Ecol Evol 2015; 5:2487-502. [PMID: 26257865 PMCID: PMC4523348 DOI: 10.1002/ece3.1511] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 03/27/2015] [Accepted: 03/30/2015] [Indexed: 01/21/2023] Open
Abstract
A main goal of population geneticists is to study patterns of gene flow to gain a better understanding of the population structure in a given organism. To date most efforts have been focused on studying gene flow at either broad scales to identify barriers to gene flow and isolation by distance or at fine spatial scales in order to gain inferences regarding reproduction and local dispersal. Few studies have measured connectivity at multiple spatial scales and have utilized novel tools to test the influence of both environment and geography on shaping gene flow in an organism. Here a seascape genetics approach was used to gain insight regarding geographic and ecological barriers to gene flow of a common reef sponge, Stylissa carteri in the Red Sea. Furthermore, a small-scale (<1 km) analysis was also conducted to infer reproductive potential in this organism. At the broad scale, we found that sponge connectivity is not structured by geography alone, but rather, genetic isolation in the southern Red Sea correlates strongly with environmental heterogeneity. At the scale of a 50-m transect, spatial autocorrelation analyses and estimates of full-siblings revealed that there is no deviation from random mating. However, at slightly larger scales (100–200 m) encompassing multiple transects at a given site, a greater proportion of full-siblings was found within sites versus among sites in a given location suggesting that mating and/or dispersal are constrained to some extent at this spatial scale. This study adds to the growing body of literature suggesting that environmental and ecological variables play a major role in the genetic structure of marine invertebrate populations.
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Affiliation(s)
- Emily C Giles
- Red Sea Research Center, King Abdullah University of Science and Technology Thuwal, 23599-6900, Saudi Arabia
| | - Pablo Saenz-Agudelo
- Red Sea Research Center, King Abdullah University of Science and Technology Thuwal, 23599-6900, Saudi Arabia ; Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile Valdivia, Chile
| | | | - Timothy Ravasi
- Division of Biological and Environmental Sciences and Engineering, Division of Applied Mathematics and Computer Science, King Abdullah University of Science and Technology Thuwal, 23599-6900, Saudi Arabia
| | - Michael L Berumen
- Red Sea Research Center, King Abdullah University of Science and Technology Thuwal, 23599-6900, Saudi Arabia
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Berg PR, Jentoft S, Star B, Ring KH, Knutsen H, Lien S, Jakobsen KS, André C. Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.). Genome Biol Evol 2015; 7:1644-63. [PMID: 25994933 PMCID: PMC4494048 DOI: 10.1093/gbe/evv093] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
How genomic selection enables species to adapt to divergent environments is a fundamental question in ecology and evolution. We investigated the genomic signatures of local adaptation in Atlantic cod (Gadus morhua L.) along a natural salinity gradient, ranging from 35‰ in the North Sea to 7‰ within the Baltic Sea. By utilizing a 12 K SNPchip, we simultaneously assessed neutral and adaptive genetic divergence across the Atlantic cod genome. Combining outlier analyses with a landscape genomic approach, we identified a set of directionally selected loci that are strongly correlated with habitat differences in salinity, oxygen, and temperature. Our results show that discrete regions within the Atlantic cod genome are subject to directional selection and associated with adaptation to the local environmental conditions in the Baltic- and the North Sea, indicating divergence hitchhiking and the presence of genomic islands of divergence. We report a suite of outlier single nucleotide polymorphisms within or closely located to genes associated with osmoregulation, as well as genes known to play important roles in the hydration and development of oocytes. These genes are likely to have key functions within a general osmoregulatory framework and are important for the survival of eggs and larvae, contributing to the buildup of reproductive isolation between the low-salinity adapted Baltic cod and the adjacent cod populations. Hence, our data suggest that adaptive responses to the environmental conditions in the Baltic Sea may contribute to a strong and effective reproductive barrier, and that Baltic cod can be viewed as an example of ongoing speciation.
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Affiliation(s)
- Paul R Berg
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Kristoffer H Ring
- Centre for Development and the Environment (SUM), University of Oslo, Norway
| | - Halvor Knutsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway Institute of Marine Research (IMR), Flødevigen, His, Norway University of Agder, Kristiansand, Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Carl André
- Department of Biology and Environmental Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
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445
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Lonsinger RC, Schweizer RM, Pollinger JP, Wayne RK, Roemer GW. Fine-scale genetic structure of the ringtail (Bassariscus astutus) in a Sky Island mountain range. J Mammal 2015. [DOI: 10.1093/jmammal/gyv050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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446
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Barley AJ, Monnahan PJ, Thomson RC, Grismer LL, Brown RM. Sun skink landscape genomics: assessing the roles of micro-evolutionary processes in shaping genetic and phenotypic diversity across a heterogeneous and fragmented landscape. Mol Ecol 2015; 24:1696-712. [DOI: 10.1111/mec.13151] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 02/27/2015] [Accepted: 03/10/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Anthony J. Barley
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
| | - Patrick J. Monnahan
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
| | - Robert C. Thomson
- Department of Biology; University of Hawai'i at Mānoa; Honolulu HI 96822 USA
| | - L. Lee Grismer
- Department of Biology; La Sierra University; Riverside CA 92515 USA
| | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
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447
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Mitchell MW, Locatelli S, Sesink Clee PR, Thomassen HA, Gonder MK. Environmental variation and rivers govern the structure of chimpanzee genetic diversity in a biodiversity hotspot. BMC Evol Biol 2015; 15:1. [PMID: 25608511 PMCID: PMC4314796 DOI: 10.1186/s12862-014-0274-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/15/2014] [Indexed: 11/13/2022] Open
Abstract
Background The mechanisms that underlie the diversification of tropical animals remain poorly understood, but new approaches that combine geo-spatial modeling with spatially explicit genetic data are providing fresh insights on this topic. Data about the diversification of tropical mammals remain particularly sparse, and vanishingly few opportunities exist to study endangered large mammals that increasingly exist only in isolated pockets. The chimpanzees of Cameroon represent a unique opportunity to examine the mechanisms that promote genetic differentiation in tropical mammals because the region is home to two chimpanzee subspecies: Pan troglodytes ellioti and P. t. trogolodytes. Their ranges converge in central Cameroon, which is a geographically, climatically and environmentally complex region that presents an unparalleled opportunity to examine the roles of rivers and/or environmental variation in influencing the evolution of chimpanzee populations. Results We analyzed microsatellite genotypes and mtDNA HVRI sequencing data from wild chimpanzees sampled at a fine geographic scale across Cameroon and eastern Nigeria using a spatially explicit approach based upon Generalized Dissimilarity Modeling. Both the Sanaga River and environmental variation were found to contribute to driving separation of the subspecies. The importance of environmental variation differed among subspecies. Gene-environment associations were weak in P. t. troglodytes, whereas environmental variation was found to play a much larger role in shaping patterns of genetic differentiation in P. t. ellioti. Conclusions We found that both the Sanaga River and environmental variation likely play a role in shaping patterns of chimpanzee genetic diversity. Future studies using single nucleotide polymorphism (SNP) data are necessary to further understand how rivers and environmental variation contribute to shaping patterns of genetic variation in chimpanzees. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0274-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew W Mitchell
- Department of Biology, Drexel University, Philadelphia 19104, Pennsylvania, USA.
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Sesink Clee PR, Abwe EE, Ambahe RD, Anthony NM, Fotso R, Locatelli S, Maisels F, Mitchell MW, Morgan BJ, Pokempner AA, Gonder MK. Chimpanzee population structure in Cameroon and Nigeria is associated with habitat variation that may be lost under climate change. BMC Evol Biol 2015; 15:2. [PMID: 25608567 PMCID: PMC4314735 DOI: 10.1186/s12862-014-0275-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/15/2014] [Indexed: 01/23/2023] Open
Abstract
Background The Nigeria-Cameroon chimpanzee (Pan troglodytes ellioti) is found in the Gulf of Guinea biodiversity hotspot located in western equatorial Africa. This subspecies is threatened by habitat fragmentation due to logging and agricultural development, hunting for the bushmeat trade, and possibly climate change. Although P. t. ellioti appears to be geographically separated from the neighboring central chimpanzee (P. t. troglodytes) by the Sanaga River, recent population genetics studies of chimpanzees from across this region suggest that additional factors may also be important in their separation. The main aims of this study were: 1) to model the distribution of suitable habitat for P. t. ellioti across Cameroon and Nigeria, and P. t. troglodytes in southern Cameroon, 2) to determine which environmental factors best predict their optimal habitats, and 3) to compare modeled niches and test for their levels of divergence from one another. A final aim of this study was to examine the ways that climate change might impact suitable chimpanzee habitat across the region under various scenarios. Results Ecological niche models (ENMs) were created using the software package Maxent for the three populations of chimpanzees that have been inferred to exist in Cameroon and eastern Nigeria: (i) P. t. troglodytes in southern Cameroon, (ii) P. t. ellioti in northwestern Cameroon, and (iii) P. t. ellioti in central Cameroon. ENMs for each population were compared using the niche comparison test in ENMtools, which revealed complete niche divergence with very little geographic overlap of suitable habitat between populations. Conclusions These findings suggest that a positive relationship may exist between environmental variation and the partitioning of genetic variation found in chimpanzees across this region. ENMs for each population were also projected under three different climate change scenarios for years 2020, 2050, and 2080. Suitable habitat of P. t. ellioti in northwest Cameroon / eastern Nigeria is expected to remain largely unchanged through 2080 in all considered scenarios. In contrast, P. t. ellioti in central Cameroon, which represents half of the population of this subspecies, is expected to experience drastic reductions in its ecotone habitat over the coming century. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0275-z) contains supplementary material, which is available to authorized users.
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449
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The population genetics of wild chimpanzees in Cameroon and Nigeria suggests a positive role for selection in the evolution of chimpanzee subspecies. BMC Evol Biol 2015; 15:3. [PMID: 25608610 PMCID: PMC4314757 DOI: 10.1186/s12862-014-0276-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/15/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chimpanzees (Pan troglodytes) can be divided into four subspecies. Substantial phylogenetic evidence suggests that these subspecies can be grouped into two distinct lineages: a western African group that includes P. t. verus and P. t. ellioti and a central/eastern African group that includes P. t. troglodytes and P. t. schweinfurthii. The geographic division of these two lineages occurs in Cameroon, where the rages of P. t. ellioti and P. t. troglodytes appear to converge at the Sanaga River. Remarkably, few population genetic studies have included wild chimpanzees from this region. RESULTS We analyzed microsatellite genotypes of 187 wild, unrelated chimpanzees, and mitochondrial control region sequencing data from 604 chimpanzees. We found that chimpanzees in Cameroon and eastern Nigeria comprise at least two, and likely three populations. Both the mtDNA and microsatellite data suggest that there is a primary separation of P. t. troglodytes in southern Cameroon from P. t. ellioti north and west of the Sanaga River. These two populations split ~200-250 thousand years ago (kya), but have exchanged one migrant per generation since separating. In addition, P. t. ellioti consists of two populations that split from one another ~4 kya. One population is located in the rainforests of western Cameroon and eastern Nigeria, whereas the second population appears to be confined to a savannah-woodland mosaic in central Cameroon. CONCLUSIONS Our findings suggest that there are as many as three genetically distinct populations of chimpanzees in Cameroon and eastern Nigeria. P. t. troglodytes in southern Cameroon comprises one population that is separated from two populations of P. t. ellioti in western and central Cameroon, respectively. P. t. ellioti and P. t. troglodytes appear to be characterized by a pattern of isolation-with-migration, and thus, we propose that neutral processes alone can not explain the differentiation of P. t. ellioti and P. t. troglodytes.
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450
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Rieseberg L, Vines T, Gow J, Geraldes A. Editorial 2015. Mol Ecol 2015; 24:1-17. [DOI: 10.1111/mec.12997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/10/2014] [Indexed: 11/30/2022]
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