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White KS, Hood E, Wolken GJ, Peitzsch EH, Bühler Y, Wikstrom Jones K, Darimont CT. Snow avalanches are a primary climate-linked driver of mountain ungulate populations. Commun Biol 2024; 7:423. [PMID: 38684895 PMCID: PMC11058775 DOI: 10.1038/s42003-024-06073-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 03/19/2024] [Indexed: 05/02/2024] Open
Abstract
Snow is a major, climate-sensitive feature of the Earth's surface and catalyst of fundamentally important ecosystem processes. Understanding how snow influences sentinel species in rapidly changing mountain ecosystems is particularly critical. Whereas effects of snow on food availability, energy expenditure, and predation are well documented, we report how avalanches exert major impacts on an ecologically significant mountain ungulate - the coastal Alaskan mountain goat (Oreamnos americanus). Using long-term GPS data and field observations across four populations (421 individuals over 17 years), we show that avalanches caused 23-65% of all mortality, depending on area. Deaths varied seasonally and were directly linked to spatial movement patterns and avalanche terrain use. Population-level avalanche mortality, 61% of which comprised reproductively important prime-aged individuals, averaged 8% annually and exceeded 22% when avalanche conditions were severe. Our findings reveal a widespread but previously undescribed pathway by which snow can elicit major population-level impacts and shape demographic characteristics of slow-growing populations of mountain-adapted animals.
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Affiliation(s)
- Kevin S White
- Department of Natural Sciences, Program on the Environment, University of Alaska Southeast, Juneau, AK, 99801, USA.
- Department of Geography, University of Victoria, Victoria, BC, V8W 2Y2, Canada.
- Division of Wildlife Conservation (ret.), Alaska Department of Fish and Game, Juneau, AK, 99811, USA.
| | - Eran Hood
- Department of Natural Sciences, Program on the Environment, University of Alaska Southeast, Juneau, AK, 99801, USA
| | - Gabriel J Wolken
- Alaska Division of Geological and Geophysical Surveys, Climate and Cryosphere Hazards Program, Fairbanks, AK, 99709, USA
- Alaska Climate Adaptation Science Center, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Erich H Peitzsch
- U.S. Geological Survey, Northern Rocky Mountain Science Center, West Glacier, Montana, MT, 59936, USA
| | - Yves Bühler
- WSL Institute for Snow and Avalanche Research SLF, Davos CH-7260, Davos, Switzerland
- Climate Change, Extremes and Natural Hazards in Alpine Regions Research Centre CERC, Davos CH-7260, Davos, Switzerland
| | - Katreen Wikstrom Jones
- Alaska Climate Adaptation Science Center, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Chris T Darimont
- Department of Geography, University of Victoria, Victoria, BC, V8W 2Y2, Canada
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2
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Wang S, Girardello M, Zhang W. Potential and progress of studying mountain biodiversity by means of butterfly genetics and genomics. J Genet Genomics 2024; 51:292-301. [PMID: 37302475 DOI: 10.1016/j.jgg.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023]
Abstract
Mountains are rich in biodiversity, and butterflies are species-rich and have a good ecological and evolutionary research foundation. This review addresses the potential and progress of studying mountain biodiversity using butterflies as a model. We discuss the uniqueness of mountain ecosystems, factors influencing the distribution of mountain butterflies, representative genetic and evolutionary models in butterfly research, and evolutionary studies of mountain biodiversity involving butterfly genetics and genomics. Finally, we demonstrate the necessity of studying mountain butterflies and propose future perspectives. This review provides insights for studying the biodiversity of mountain butterflies as well as a summary of research methods for reference.
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Affiliation(s)
- Shuting Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Marco Girardello
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group, Faculdade de Ciências Agrárias e do Ambiente, Universidade dos Açores, 9700-042 Angra do Heroísmo, Terceira, Portugal
| | - Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
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3
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Steffen ML. New age constraints for human entry into the Americas on the north Pacific coast. Sci Rep 2024; 14:4291. [PMID: 38383701 PMCID: PMC10881565 DOI: 10.1038/s41598-024-54592-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 02/14/2024] [Indexed: 02/23/2024] Open
Abstract
The timing of the initial peopling of the Americas is unresolved. Because the archaeological record necessitates discussion of human entry from Beringia into southern North America during the last glaciation, addressing this problem routinely involves evaluating environmental parameters then targeting areas suitable for human settlement. Vertebrate remains indicate landscape quality and are a key dataset for assessing coastal migration theories and the viability of coastal routes. Here, radiocarbon dates on vertebrate specimens and archaeological sites are calibrated to document species occurrences and the ages of human settlements across the western expansion and decay of the Cordilleran Ice Sheet (CIS) during the Late Wisconsin Fraser Glaciation in four subregions of the north Pacific coast of North America. The results show archaeological sites occur after glacial maxima and are generally consistent with the age of other securely dated earliest sites in southern North America. They also highlight gaps in the vertebrate chronologies around CIS maxima in each of the subregions that point to species redistributions and extirpations and signal times of low potential for human settlement and subsistence in a key portion of the proposed coastal migration route. This study, therefore, defines new age constraints for human coastal migration theories in the peopling of the Americas debate.
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4
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Martchenko D, Shafer ABA. Contrasting whole-genome and reduced representation sequencing for population demographic and adaptive inference: an alpine mammal case study. Heredity (Edinb) 2023; 131:273-281. [PMID: 37532838 PMCID: PMC10539292 DOI: 10.1038/s41437-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 07/22/2023] [Accepted: 07/22/2023] [Indexed: 08/04/2023] Open
Abstract
Genomes capture the adaptive and demographic history of a species, but the choice of sequencing strategy and sample size can impact such inferences. We compared whole genome and reduced representation sequencing approaches to study the population demographic and adaptive signals of the North American mountain goat (Oreamnos americanus). We applied the restriction site-associated DNA sequencing (RADseq) approach to 254 individuals and whole genome resequencing (WGS) approach to 35 individuals across the species range at mid-level coverage (9X) and to 5 individuals at high coverage (30X). We used ANGSD to estimate the genotype likelihoods and estimated the effective population size (Ne), population structure, and explicitly modelled the demographic history with δaδi and MSMC2. The data sets were overall concordant in supporting a glacial induced vicariance and extremely low Ne in mountain goats. We evaluated a set of climatic variables and geographic location as predictors of genetic diversity using redundancy analysis. A moderate proportion of total variance (36% for WGS and 21% for RADseq data sets) was explained by geography and climate variables; both data sets support a large impact of drift and some degree of local adaptation. The empirical similarities of WGS and RADseq presented herein reassuringly suggest that both approaches will recover large demographic and adaptive signals in a population; however, WGS offers several advantages over RADseq, such as inferring adaptive processes and calculating runs-of-homozygosity estimates. Considering the predicted climate-induced changes in alpine environments and the genetically depauperate mountain goat, the long-term adaptive capabilities of this enigmatic species are questionable.
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Affiliation(s)
- Daria Martchenko
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada.
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
- Department of Forensics & Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
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5
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Rice C, Larue B, Festa-Bianchet M. Variation in age of primiparity in mountain goats (Oreamnos americanus) estimated from horn growth increments. CAN J ZOOL 2021. [DOI: 10.1139/cjz-2021-0166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Variation in age of primiparity is important for population dynamics and wildlife management because it can affect population growth. Using a novel technique based on the trade-off between annual horn growth and reproduction, we estimated the age of primiparity for 2274 female mountain goats (Oreamnos americanus (Blainville, 1816)) harvested across British Columbia, Canada, from 1976 to 2019. We then investigated spatio-temporal variation in the probability that harvested females were primiparous when aged 3, 4, or 5 years and older using Bayesian ordinal regressions. We found that the probability of primiparity at 3 years decreased over time in nearly all mountain ranges. In the Coastal Mountain range, however, the probability of primiparity at age 3 significantly increased. These results suggest that the large coastal populations of mountain goats could be more resilient to harvest than other populations in British Columbia, which may be experiencing environmental effects promoting later primiparity. Models predicting age of primiparity from annual growth measures are a valuable tool for wildlife management and could help conservation of many species.
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Affiliation(s)
- Chad Rice
- Département de biologie et Centre d’Études Nordiques, Université de Sherbrooke, 2500, boulevard de l’Université, Sherbrooke, QC J1K 2R1, Canada
- Département de biologie et Centre d’Études Nordiques, Université de Sherbrooke, 2500, boulevard de l’Université, Sherbrooke, QC J1K 2R1, Canada
| | - Benjamin Larue
- Département de biologie et Centre d’Études Nordiques, Université de Sherbrooke, 2500, boulevard de l’Université, Sherbrooke, QC J1K 2R1, Canada
- Département de biologie et Centre d’Études Nordiques, Université de Sherbrooke, 2500, boulevard de l’Université, Sherbrooke, QC J1K 2R1, Canada
| | - Marco Festa-Bianchet
- Département de biologie et Centre d’Études Nordiques, Université de Sherbrooke, 2500, boulevard de l’Université, Sherbrooke, QC J1K 2R1, Canada
- Département de biologie et Centre d’Études Nordiques, Université de Sherbrooke, 2500, boulevard de l’Université, Sherbrooke, QC J1K 2R1, Canada
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6
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Huxley JD, Spasojevic MJ. Area Not Geographic Isolation Mediates Biodiversity Responses of Alpine Refugia to Climate Change. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.633697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Climate refugia, where local populations of species can persist through periods of unfavorable regional climate, play a key role in the maintenance of regional biodiversity during times of environmental change. However, the ability of refugia to buffer biodiversity change may be mediated by the landscape context of refugial habitats. Here, we examined how plant communities restricted to refugial sky islands of alpine tundra in the Colorado Rockies are changing in response to rapid climate change in the region (increased temperature, declining snowpack, and earlier snow melt-out) and if these biodiversity changes are mediated by the area or geographic isolation of the sky island. We resampled plant communities in 153 plots at seven sky islands distributed across the Colorado Rockies at two time points separated by 12 years (2007/2008–2019/2020) and found changes in taxonomic, phylogenetic, and functional diversity over time. Specifically, we found an increase in species richness, a trend toward increased phylogenetic diversity, a shift toward leaf traits associated with the stress-tolerant end of leaf economics spectrum (e.g., lower specific leaf area, higher leaf dry matter content), and a decrease in the functional dispersion of specific leaf area. Importantly, these changes were partially mediated by refugial area but not by geographic isolation, suggesting that dispersal from nearby areas of tundra does not play a strong role in mediating these changes, while site characteristics associated with a larger area (e.g., environmental heterogeneity, larger community size) may be relatively more important. Taken together, these results suggest that considering the landscape context (area and geographic isolation) of refugia may be critical for prioritizing the conservation of specific refugial sites that provide the most conservation value.
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7
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Graham BA, Cicero C, Strickland D, Woods JG, Coneybeare H, Dohms KM, Szabo I, Burg TM. Cryptic genetic diversity and cytonuclear discordance characterize contact among Canada jay ( Perisoreus canadensis) morphotypes in western North America. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abstract
Three distinct Canada jay (Perisoreus canadensis) morphotypes with easily recognizable plumage traits come into contact in western North America. Recent work demonstrated high genetic structure across the species’ range; however, patterns of genetic variation in these contact zones remain unknown. We categorized 605 individuals into one of three morphotypes (Pacific, Rocky Mountain, and Boreal) based on plumage, and genotyped individuals at the mtDNA control region and 12 microsatellite loci to assess the extent of hybridization between morphotypes. Our data showed cryptic genetic diversity and high cytonuclear discordance among morphotypes within contact zones, which is likely the result of recent and historical admixture. The distributions of the Boreal and Pacific morphotypes each showed a strong association with a single, distinct genetic group, whereas the Rocky Mountain morphotype exhibited higher genetic diversity and was associated with multiple genotypes. Our analyses show the importance of considering both plumage and genetic traits when examining contact zones between closely related taxa. Finally the data presented in this study reaffirm that the Pacific morphotype is distinct from the Boreal and Rocky Mountain morphotypes based on genetic, phenotypic and ecological data, indicating that the Pacific morphotype should be re-elevated to a full species.
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Affiliation(s)
- Brendan A Graham
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | | | - John G Woods
- 41221 23rd Avenue SW, Salmon Arm, BC, V1E 0A9, Canada
| | | | - Kimberly M Dohms
- Canadian Wildlife Services, Environment and Climate Change Canada, Delta, BC, Canada
| | - Ildiko Szabo
- Beaty Biodiversity Museum, University of British Columbia, Vancouver, BC, Canada
| | - Theresa M Burg
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
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8
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White KS, Levi T, Breen J, Britt M, Meröndun J, Martchenko D, Shakeri YN, Porter B, Shafer ABA. Integrating Genetic Data and Demographic Modeling to Facilitate Conservation of Small, Isolated Mountain Goat Populations. J Wildl Manage 2021. [DOI: 10.1002/jwmg.21978] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kevin S. White
- Division of Wildlife Conservation Alaska Department of Fish and Game Juneau AK 99811 USA
| | - Taal Levi
- Department of Fish and Wildlife Oregon State University Corvallis OR 97331 USA
| | - Jessica Breen
- Forensics Program, Trent University Peterborough ON K9J 7B8 Canada
| | - Meghan Britt
- Forensics Program, Trent University Peterborough ON K9J 7B8 Canada
| | - Justin Meröndun
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON K9J 7B8 Canada
| | - Daria Martchenko
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON K9J 7B8 Canada
| | - Yasaman N. Shakeri
- Division of Wildlife Conservation Alaska Department of Fish and Game Juneau AK 99811 USA
| | - Boyd Porter
- Division of Wildlife Conservation Alaska Department of Fish and Game Juneau AK 99811 USA
| | - Aaron B. A. Shafer
- Forensic Science Program and Environmental and Life Sciences Graduate Program Trent University Peterborough ON K9J 7B8 Canada
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9
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Cullingham CI, Peery RM, Dao A, McKenzie DI, Coltman DW. Predicting the spread-risk potential of chronic wasting disease to sympatric ungulate species. Prion 2020; 14:56-66. [PMID: 32008428 PMCID: PMC7009333 DOI: 10.1080/19336896.2020.1720486] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 02/08/2023] Open
Abstract
Wildlife disease incidence is increasing, resulting in negative impacts on the economy, biodiversity, and potentially human health. Chronic wasting disease (CWD) is a fatal, transmissible spongiform encephalopathy of cervids (wild and captive) which continues to spread geographically resulting in exposure to potential new host species. The disease agent (PrPCWD) is a misfolded conformer of the cellular prion protein (PrPC). In Canada, the disease is endemic in Alberta and Saskatchewan, affecting mule and white-tail deer, with lesser impact on elk and moose. As the disease continues to expand, additional wild ungulate species including bison, bighorn sheep, mountain goat, and pronghorn antelope may be exposed. To better understand the species-barrier, we reviewed the current literature on taxa naturally or experimentally exposed to CWD to identify susceptible and resistant species. We created a phylogeny of these taxa using cytochrome B and found that CWD susceptibility followed the species phylogeny. Using this phylogeny we estimated the probability of CWD susceptibility for wild ungulate species. We then compared PrPC amino acid polymorphisms among these species to identify which sites segregated between susceptible and resistant species. We identified sites that were significantly associated with susceptibility, but they were not fully discriminating. Finally, we sequenced Prnp from 578 wild ungulates to further evaluate their potential susceptibility. Together, these data suggest the host-range for CWD will potentially include pronghorn, mountain goat and bighorn sheep, but bison are likely to be more resistant. These findings highlight the need for monitoring potentially susceptible species as CWD continues to expand.
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Affiliation(s)
- Catherine I. Cullingham
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
- Department of Biology, Carleton University, Ottawa, Canada
| | - Rhiannon M. Peery
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Anh Dao
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Debbie I. McKenzie
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - David W. Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
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10
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Lynch LM, Felice R, O'Brien HD. Appendicular skeletal morphology of North American Martes reflect independent modes of evolution in conjunction with Pleistocene glacial cycles. Anat Rec (Hoboken) 2020; 304:1439-1462. [PMID: 33099887 DOI: 10.1002/ar.24545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 11/12/2022]
Abstract
Pleistocene glacial cycles are thought to have driven ecological niche shifts, including novel niche formation. North American pine martens, Martes americana and M. caurina, are exemplar taxa thought to have diverged molecularly and morphologically during Pleistocene glaciation. Previous research found correlations between Martes limb morphology with biome and climate, suggesting that appendicular evolution may have occurred via adaptation to selective pressures imposed by novel and shifting habitats. Such variation can also be achieved through non-adaptive means such as genetic drift. Here, we evaluate whether regional genetic differences reflect limb morphology differences among populations of M. americana and M. caurina by analyzing evolutionary tempo and mode of six limb elements. Our comparative phylogenetic models indicate that genetic structure predicts limb shape better than size. Marten limb size has low phylogenetic signal, and the best supported model of evolution is punctuational (kappa), with morphological and genetic divergence occurring simultaneously. Disparity through time analysis suggests that the tempo of limb evolution in Martes tracks Pleistocene glacial cycles, such that limb size may be responding to shifting climates rather than population genetic structure. Contrarily, we find that limb shape is strongly tied to genetic relationships, with high phylogenetic signal and a lambda mode of evolution. Overall, this pattern of limb size and shape variation may be the result of geographic isolation during Pleistocene glacial advance, while declines in disparity suggest hybridization during interglacial periods. Future inclusion of extinct populations of Martes, which were more morphologically and ecologically diverse, may further clarify Martes phenotypic evolution.
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Affiliation(s)
- Leigha M Lynch
- Anatomy and Cell Biology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma, USA.,Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Ryan Felice
- Cell and Developmental Biology, University College London, London, United Kingdom
| | - Haley D O'Brien
- Anatomy and Cell Biology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma, USA
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11
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Ford BM, Cornellas A, Leonard JA, Weir RD, Russello MA. Spatiotemporal analyses suggest the role of glacial history and the ice-free corridor in shaping American badger population genetic variation. Ecol Evol 2020; 10:8345-8357. [PMID: 32788984 PMCID: PMC7417222 DOI: 10.1002/ece3.6541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/03/2020] [Accepted: 06/10/2020] [Indexed: 11/07/2022] Open
Abstract
Recurring glacial cycles through the Quaternary period drastically altered the size and distribution of natural populations of North American flora and fauna. The "southerly refugia model" has been the longstanding framework for testing the effects of glaciation on contemporary genetic patterns; however, insights from ancient DNA have contributed to the reconstruction of more complex histories for some species. The American badger, Taxidea taxus, provides an interesting species for exploring the genetic legacy of glacial history, having been hypothesized to have postglacially emerged from a single, southerly refugium to recolonize northern latitudes. However, previous studies have lacked genetic sampling from areas where distinct glacial refugia have been hypothesized, including the Pacific Northwest and American Far North (Yukon, Alaska). In order to further investigate the phylogeographic history of American badgers, we collected mitochondrial DNA sequence data from ancient subfossil material collected within the historical range (Alaska, Yukon) and combined them with new and previously published data from across the species' contemporary distribution (n = 1,207). We reconstructed a mostly unresolved phylogenetic tree and star-like haplotype network indicative of emergence from a largely panmictic glacial refugium and recent population expansion, the latter further punctuated by significantly negative Tajima's D and Fu's Fs values. Although directionality of migration cannot be unequivocally inferred, the moderate to high levels of genetic variation exhibited by American badgers, alongside the low frequency of haplotypes with indels in the Midwest, suggest a potential recolonization into central North America after the hypothesized ice-free corridor reopened ~13,000 years ago. Overall, the expanded reconstruction of phylogeographic history of American badgers offers a broader understanding of contemporary range-wide patterns and identifies unique genetic units that can likely be used to inform conservation of at-risk populations at the northern periphery.
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Affiliation(s)
- Brett M. Ford
- Department of BiologyUniversity of British ColumbiaKelownaBCCanada
| | - Anna Cornellas
- Conservation and Evolutionary Genetics GroupEstación Biológica de Doñana (EBD‐CSIC)SevilleSpain
| | - Jennifer A. Leonard
- Conservation and Evolutionary Genetics GroupEstación Biológica de Doñana (EBD‐CSIC)SevilleSpain
| | - Richard D. Weir
- British Columbia Ministry of Environment and Climate Change StrategyVictoriaBCCanada
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12
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Deakin S, Gorrell JC, Kneteman J, Hik DS, Jobin RM, Coltman DW. Spatial genetic structure of Rocky Mountain bighorn sheep (Ovis canadensis canadensis) at the northern limit of their native range. CAN J ZOOL 2020. [DOI: 10.1139/cjz-2019-0183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Canadian Rocky Mountains are one of the few places on Earth where the spatial genetic structure of wide-ranging species has been relatively unaffected by anthropogenic disturbance. We characterized the spatial genetic structure of Rocky Mountain bighorn sheep (Ovis canadensis canadensis Shaw, 1804) in the northern portion of their range. Using microsatellites from 1495 individuals and mitochondrial DNA sequences from 188 individuals, we examined both broad- and fine-scale spatial genetic structure, assessed sex-biased gene flow within the northern portion of the species range, and identified geographic patterns of genetic diversity. We found that broad-scale spatial genetic structure was consistent with barriers to movement created by major river valleys. The fine-scale spatial genetic structure was characterized by a strong isolation-by-distance pattern, and analysis of neighborhood size using spatial autocorrelation indicated gene flow frequently occurred over distances of up to 100 km. However, analysis of sex-specific spatial autocorrelation and analysis of mitochondrial haplotype distributions failed to detect any evidence of sex-biased gene flow. Finally, our analyses reveal decreasing genetic diversity with increasing latitude, consistent with patterns of post-glacial recolonization of the Rocky Mountains.
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Affiliation(s)
- Samuel Deakin
- Department of Biological Sciences, University of Alberta, CW 405, Biological Sciences Building, Edmonton, AB T6G 2E9, Canada
| | - Jamieson C. Gorrell
- Department of Biological Sciences, Vancouver Island University, 900 Fifth Street, Nanaimo, BC V9R 5S5, Canada
| | - Jeffery Kneteman
- Alberta Environment and Parks, 131 Civic Centre Road, Hinton, AB T7V 2E6, Canada
| | - David S. Hik
- Department of Biological Sciences, University of Alberta, CW 405, Biological Sciences Building, Edmonton, AB T6G 2E9, Canada; Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Richard M. Jobin
- Alberta Fish and Wildlife Enforcement Branch, 6909 – 116 Street, Edmonton, AB T6H 4P2, Canada
| | - David W. Coltman
- Department of Biological Sciences, University of Alberta, CW 405, Biological Sciences Building, Edmonton, AB T6G 2E9, Canada
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13
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Wolf JF, Kriss KD, MacAulay KM, Shafer ABA. Panmictic population genetic structure of northern British Columbia mountain goats (Oreamnos americanus) has implications for harvest management. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01274-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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14
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Genome Assembly and Analysis of the North American Mountain Goat ( Oreamnos americanus) Reveals Species-Level Responses to Extreme Environments. G3-GENES GENOMES GENETICS 2020; 10:437-442. [PMID: 31806764 PMCID: PMC7003085 DOI: 10.1534/g3.119.400747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The North American mountain goat (Oreamnos americanus) is an iconic alpine species that faces stressors from climate change, industrial development, and recreational activities. This species’ phylogenetic position within the Caprinae lineage has not been resolved and their phylogeographic history is dynamic and controversial. Genomic data could be used to address these questions and provide valuable insights to conservation and management initiatives. We sequenced short-read genomic libraries constructed from a DNA sample of a 2.5-year-old female mountain goat at 80X coverage. We improved the short-read assembly by generating Chicago library data and scaffolding using the HiRise approach. The final assembly was 2,506 Mbp in length with an N50 of 66.6 Mbp, which is within the length range and in the upper quartile for N50 published ungulate genome assemblies. Comparative analysis identified 84 gene families unique to the mountain goat. The species demographic history in terms of effective population size generally mirrored climatic trends over the past one hundred thousand years and showed a sharp decline during the last glacial maximum. This genome assembly will provide a reference basis for future population and comparative genomic analyses.
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15
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Horreo JL, Griffiths AM, Machado-Schiaffino G, Stevens JR, Garcia-Vazquez E. Northern areas as refugia for temperate species under current climate warming: Atlantic salmon (Salmo salar L.) as a model in northern Europe. JOURNAL OF FISH BIOLOGY 2019; 95:304-310. [PMID: 30281146 DOI: 10.1111/jfb.13825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/26/2018] [Indexed: 06/08/2023]
Abstract
In this work, patterns of geographical genetic diversity in Atlantic salmon Salmo salar were studied across the whole Atlantic Arc; whether these patterns (and thus genetic population structure) were affected by water temperatures was also evaluated. Salmo salar populations were characterized using microsatellite loci and then analysed with reference to ocean surface temperature data from across the region. Analysis showed the presence of a latitudinal cline of genetic variability (higher in northern areas) and water temperatures (sea surface temperatures) determining genetic population structure (the latter in combination with genetic drift in southern populations). Under the current global change scenario, northern areas of Europe would constitute refugia for diversity in the future. This is effectively the inverse of what appears to have happened in glacial refugia during the last glacial maximum. From this perspective, the still abundant and large northern populations S. salar should be considered as precious as the small almost relict southern ones and given appropriate protection. Careful management of the species, coordinated across countries and latitudes, is needed in order to avoid its extinction in Europe.
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Affiliation(s)
- Jose L Horreo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Andrew M Griffiths
- Department of Biosciences, Hatherly Laboratories, University of Exeter, Exeter, UK
| | | | - Jamie R Stevens
- Department of Biosciences, Hatherly Laboratories, University of Exeter, Exeter, UK
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Zha X, Tian Y, Gao X, Wang W, Yu C. Quantitatively evaluate the environmental impact factors of the life expectancy in Tibet, China. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2019; 41:1507-1520. [PMID: 30599055 DOI: 10.1007/s10653-018-0211-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Life expectancy is influenced by both innate human self-factors and external environmental factors. Due to the individual difference of self-factors, the external environment impacts on life expectancy are especially important under the geoscience perspective. However, few studies discussed impacts of various socioeconomic and environmental factors comprehensively, and quantitative analysis of multi-factors is lacking. We chose 13 potential factors of socio-economy, ecological environment, geological environment and geographical environment to quantitatively analyze their impacts and their interactive influences on Tibet's life expectancy in 2010 by using geographical detector (Geodetector) algorithm, and figure out their suitable ranges or types. Our results indicated that the high life expectancy at birth in Tibet are distributed like a strip; the main control factor of life expectancy in Tibet is socioeconomy, followed by geological environment; furthermore, the highest range of socioeconomic factors and the igneous rock exposed areas correspond to the maximum value of life expectancy at birth; factors of ecological environment have a certain impact on the life expectancy of Tibetan residents, while factors of geographical environment have few effects on the life expectancy. Lower radiation, moderate temperature and rainfall may have favorable effects on the increase in the life expectancy. The life expectancy of Tibet is mainly affected by socioeconomy, geological and ecological environment; interactions between these factors can increase the impact on the life expectancy of Tibet. Consequently, this study can better understand the impact factors of the life expectancy in Tibet and could provide a reference basis for local government's policy making of relocation and population management.
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Affiliation(s)
- Xinjie Zha
- State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Tian
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xing Gao
- State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wei Wang
- State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chengqun Yu
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
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Jahner JP, Matocq MD, Malaney JL, Cox M, Wolff P, Gritts MA, Parchman TL. The genetic legacy of 50 years of desert bighorn sheep translocations. Evol Appl 2019; 12:198-213. [PMID: 30697334 PMCID: PMC6346675 DOI: 10.1111/eva.12708] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/16/2018] [Accepted: 08/18/2018] [Indexed: 12/20/2022] Open
Abstract
Conservation biologists have increasingly used translocations to mitigate population declines and restore locally extirpated populations. Genetic data can guide the selection of source populations for translocations and help evaluate restoration success. Bighorn sheep (Ovis canadensis) are a managed big game species that suffered widespread population extirpations across western North America throughout the early 1900s. Subsequent translocation programs have successfully re-established many formally extirpated bighorn herds, but most of these programs pre-date genetically informed management practices. The state of Nevada presents a particularly well-documented case of decline followed by restoration of extirpated herds. Desert bighorn sheep (O. c. nelsoni) populations declined to less than 3,000 individuals restricted to remnant herds in the Mojave Desert and a few locations in the Great Basin Desert. Beginning in 1968, the Nevada Department of Wildlife translocated ~2,000 individuals from remnant populations to restore previously extirpated areas, possibly establishing herds with mixed ancestries. Here, we examined genetic diversity and structure among remnant herds and the genetic consequences of translocation from these herds using a genotyping-by-sequencing approach to genotype 17,095 loci in 303 desert bighorn sheep. We found a signal of population genetic structure among remnant Mojave Desert populations, even across geographically proximate mountain ranges. Further, we found evidence of a genetically distinct, potential relict herd from a previously hypothesized Great Basin lineage of desert bighorn sheep. The genetic structure of source herds was clearly reflected in translocated populations. In most cases, herds retained genetic evidence of multiple translocation events and subsequent admixture when founded from multiple remnant source herds. Our results add to a growing literature on how population genomic data can be used to guide and monitor restoration programs.
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Affiliation(s)
| | - Marjorie D. Matocq
- Department of Natural Resources and Environmental Science, and Program in Ecology, Evolution, and Conservation BiologyUniversity of NevadaRenoNevada
| | - Jason L. Malaney
- Department of BiologyAustin Peay State UniversityClarksvilleTennessee
| | - Mike Cox
- Nevada Department of Wildlife, and Wild Sheep Working GroupWestern Association of Fish and Wildlife AgenciesRenoNevada
| | | | | | - Thomas L. Parchman
- Department of Biology, and Program in Ecology, Evolution, and Conservation BiologyUniversity of NevadaRenoNevada
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18
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Sim Z, Davis CS, Jex B, Hegel T, Coltman DW. Management implications of highly resolved hierarchical population genetic structure in thinhorn sheep. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1123-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Shirane Y, Shimozuru M, Yamanaka M, Tsuruga H, Hirano S, Nagano N, Moriwaki J, Nakanishi M, Ishinazaka T, Nose T, Kasai S, Shirayanagi M, Masuda Y, Fujimoto Y, Osada M, Akaishi M, Mano T, Masuda R, Sashika M, Tsubota T. Sex-biased natal dispersal in Hokkaido brown bears revealed through mitochondrial DNA analysis. EUR J WILDLIFE RES 2018. [DOI: 10.1007/s10344-018-1222-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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20
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Riquelme C, Estay SA, López R, Pastore H, Soto-Gamboa M, Corti P. Protected areas' effectiveness under climate change: a latitudinal distribution projection of an endangered mountain ungulate along the Andes Range. PeerJ 2018; 6:e5222. [PMID: 30013852 PMCID: PMC6046192 DOI: 10.7717/peerj.5222] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/21/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Climate change is one of the greatest threats to biodiversity, pushing species to shift their distribution ranges and making existing protected areas inadequate. Estimating species distribution and potential modifications under climate change are then necessary for adjusting conservation and management plans; this is especially true for endangered species. An example of this issue is the huemul (Hippocamelus bisulcus), an endemic endangered deer from the southern Andes Range, with less than 2,000 individuals. It is distributed in fragmented populations along a 2,000 km latitudinal gradient, in Chile and Argentina. Several threats have reduced its distribution to <50% of its former range. METHODS To estimate its potential distribution and protected areas effectiveness, we constructed a species distribution model using 2,813 huemul presence points throughout its whole distribution range, together with 19 bioclimatic layers and altitude information from Worldclim. Its current distribution was projected for years 2050 and 2070 using five different Global Climate Models estimated for scenarios representing two carbon Representative Concentration Routes (RCP)-RCP4.5 and RCP6.0. RESULTS Based on current huemul habitat variables, we estimated 91,617 km2 of suitable habitat. In future scenarios of climate change, there was a loss of suitable habitat due to altitudinal and latitudinal variation. Future projections showed a decrease of 59.86-60.26% for the year 2050 and 58.57-64.34% for the year 2070 according to RCP4.5 and RCP6.0, respectively. Protected areas only covered only 36.18% of the present distribution, 38.57-34.94% for the year 2050 and 30.79-31.94% for 2070 under climate change scenarios. DISCUSSION Modeling current and future huemul distributions should allow the establishment of priority conservation areas in which to focus efforts and funds, especially areas without official protection. In this way, we can improve management in areas heavily affected by climate change to help ensure the persistence of this deer and other species under similar circumstances worldwide.
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Affiliation(s)
- Carlos Riquelme
- Programa de Magíster en Ecología Aplicada, Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Laboratorio de Manejo y Conservación de Vida Silvestre, Instituto de Ciencia Animal y Programa de Investigación Aplicada en Fauna Silvestre, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Sergio A. Estay
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Hernán Pastore
- Dirección Regional Patagonia Norte, Administración de Parques Nacionales, San Carlos de Bariloche, Argentina
| | - Mauricio Soto-Gamboa
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Paulo Corti
- Laboratorio de Manejo y Conservación de Vida Silvestre, Instituto de Ciencia Animal y Programa de Investigación Aplicada en Fauna Silvestre, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
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21
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Dohms KM, Graham BA, Burg TM. Multilocus genetic analyses and spatial modeling reveal complex population structure and history in a widespread resident North American passerine ( Perisoreus canadensis). Ecol Evol 2017; 7:9869-9889. [PMID: 29238522 PMCID: PMC5723591 DOI: 10.1002/ece3.3478] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 08/08/2017] [Accepted: 08/19/2017] [Indexed: 11/29/2022] Open
Abstract
An increasing body of studies of widely distributed, high latitude species shows a variety of refugial locations and population genetic patterns. We examined the effects of glaciations and dispersal barriers on the population genetic patterns of a widely distributed, high latitude, resident corvid, the gray jay (Perisoreus canadensis), using the highly variable mitochondrial DNA (mtDNA) control region and microsatellite markers combined with species distribution modeling. We sequenced 914 bp of mtDNA control region for 375 individuals from 37 populations and screened seven loci for 402 individuals from 27 populations across the gray jay range. We used species distribution modeling and a range of phylogeographic analyses (haplotype diversity, ΦST, SAMOVA, FST, Bayesian clustering analyses) to examine evolutionary history and population genetic structure. MtDNA and microsatellite markers revealed significant genetic differentiation among populations with high concordance between markers. Paleodistribution models supported at least five potential areas of suitable gray jay habitat during the last glacial maximum and revealed distributions similar to the gray jay's contemporary during the last interglacial. Colonization from and prolonged isolation in multiple refugia is evident. Historical climatic fluctuations, the presence of multiple dispersal barriers, and highly restricted gene flow appear to be responsible for strong genetic diversification and differentiation in gray jays.
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Affiliation(s)
- Kimberly M Dohms
- Department of Biological Sciences University of Lethbridge Lethbridge AB Canada.,Present address: Canadian Wildlife Service, Environment and Climate Change Canada Delta BC Canada
| | - Brendan A Graham
- Department of Biological Sciences University of Windsor Windsor ON Canada
| | - Theresa M Burg
- Department of Biological Sciences University of Lethbridge Lethbridge AB Canada
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22
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Pu H, Li J, Wang P, Cui L, Wang H. The death of the circulatory system diseases in China: provincial socioeconomic and environmental perspective. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:10381-10390. [PMID: 28281057 DOI: 10.1007/s11356-017-8677-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/20/2017] [Indexed: 06/06/2023]
Abstract
Few studies have explored the association between circulatory system diseases (CSDs) and provincial socioeconomic and environmental factors from spatial perspective, although large literature have focused on CSD. The numbers of death of hypertension disease (HD), ischemic heart disease (IHD), and cerebrovascular disease (CVD) are investigated, and 14 representative socioeconomic and environmental factors are collected. Stepwise regression model (SRM) and geographically weighted regression model (GWRM) are applied to determine the spatial correlation between the number of death of those diseases and selected factors. The results are the following: (1) diseases exhibit a pattern of zonal distribution. Higher HD is mostly distributed in south district, whereas higher IHD and CVD are observed in the north area. (2) SO2 emission amount (SO2 EA) is significantly positively related with HD, while coal consumption (CC) and PM2.5 are notably positively correlated with IHD and CVD. (3) A 10,000 tons increase in SO2 EA results in three increases in the numbers of death of HD. For every 100 ten thousand tons (TTTs) increase in CC, the death of IHD and CVD increases by 11.1 and 15.7, while for every 1 μg/m3 increase in ambient PM2.5 concentration, the numbers of death of IHD and CVD increase by 34.773 and 43.222, respectively. (4) Our findings show that there exist spatial differences for SO2 EA, CC, and PM2.5 influencing HD, IHD, and CVD. This study is expected to provide a reference for HD, IHD, and CVD control in different regions.
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Affiliation(s)
- Haixia Pu
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiatian Li
- Faculty of Land Resource Engineering, Kunming University of Science and Technology, Wenchang Road, 121 street, Kunming, 650093, China.
| | - Pin Wang
- Design and Research Institute of the Yellow River Water Conservancy Committee, Zhengzhou, 450003, China
| | - Linlin Cui
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Huaxin Wang
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
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23
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Pironon S, Papuga G, Villellas J, Angert AL, García MB, Thompson JD. Geographic variation in genetic and demographic performance: new insights from an old biogeographical paradigm. Biol Rev Camb Philos Soc 2016; 92:1877-1909. [DOI: 10.1111/brv.12313] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 10/07/2016] [Accepted: 10/17/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Samuel Pironon
- Instituto Pirenaico de Ecología (IPE-CSIC); Box 1005 avenida Montañana 50059 Zaragoza, Spain
| | - Guillaume Papuga
- UMR 5175 Centre d'Ecologie Fonctionnelle et Evolutive, CNRS; Box 1019 route de Mende 34090 Montpellier France
- Dipartimento di Scienze della Natura e del Territorio; Università degli Studi di Sassari; Box 21 Piazza Universitá 07100 Sassari Italy
| | - Jesús Villellas
- Department of Biology; Duke University; Box 90338 Durham NC 27708-0338 U.S.A
| | - Amy L. Angert
- Departments of Botany and Zoology; University of British Columbia; Box 4200-6270 University Boulevard, Vancouver V6T 1Z4 Canada
| | - María B. García
- Instituto Pirenaico de Ecología (IPE-CSIC); Box 1005 avenida Montañana 50059 Zaragoza, Spain
| | - John D. Thompson
- UMR 5175 Centre d'Ecologie Fonctionnelle et Evolutive, CNRS; Box 1019 route de Mende 34090 Montpellier France
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24
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Macfarlane CBA, Natola L, Brown MW, Burg TM. Population genetic isolation and limited connectivity in the purple finch ( Haemorhous purpureus). Ecol Evol 2016; 6:8304-8317. [PMID: 27878097 PMCID: PMC5108279 DOI: 10.1002/ece3.2524] [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: 03/11/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 11/11/2022] Open
Abstract
Using a combination of mitochondrial and z-linked sequences, microsatellite data, and spatio-geographic modeling, we examined historical and contemporary factors influencing the population genetic structure of the purple finch (Haemorhous purpureus). Mitochondrial DNA data show the presence of two distinct groups corresponding to the two subspecies, H. p. purpureus and H. p. californicus. The two subspecies likely survived in separate refugia during the last glacial maximum, one on the Pacific Coast and one east of the Rocky Mountains, and now remain distinct lineages with little evidence of gene flow between them. Southwestern British Columbia is a notable exception, as subspecies mixing between central British Columbia and Vancouver Island populations suggests a possible contact zone in this region. Z-linked data support two mitochondrial groups; however, Coastal Oregon and central British Columbia sites show evidence of mixing. Contemporary population structure based on microsatellite data identified at least six genetic clusters: three H. p. purpureus clusters, two H. p. californicus clusters, and one mixed cluster, which likely resulted from high site fidelity and isolation by distance, combined with sexual selection on morphological characters reinforcing subspecies differences.
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25
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Bell KC, Calhoun KL, Hoberg EP, Demboski JR, Cook JA. Temporal and spatial mosaics: deep host association and shallow geographic drivers shape genetic structure in a widespread pinworm, Rauschtineria eutamii. Biol J Linn Soc Lond 2016; 119:397-413. [PMID: 27725785 PMCID: PMC5055073 DOI: 10.1111/bij.12833] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Climate and host demographic cycling often shape both parasite genetic diversity and host distributions, processes that transcend a history of strict host-parasite association. We explored host associations and histories based on an evaluation of mitochondrial and nuclear sequences to reveal the underlying history and genetic structure of a pinworm, Rauschtineria eutamii, infecting 10 species of western North American chipmunks (Rodentia:Tamias, subgenus Neotamias). Rauschtineria eutamii contains divergent lineages influenced by the diversity of hosts and variation across the complex topography of western North America. We recovered six reciprocally monophyletic R. eutamii mitochondrial clades, largely supported by nuclear gene trees, exhibiting divergence levels comparable to intraspecific variation reported for other nematodes. Phylogenetic relationships among pinworm clades suggest that R. eutamii colonized an ancestral lineage of western chipmunks and lineages persisted during historical isolation in diverging Neotamias species or species groups. Pinworm diversification, however, is incongruent and asynchronous relative to host diversification. Secondarily, patterns of shallow divergence were shaped by geography through events of episodic colonization reflecting an interaction of taxon pulses and ecological fitting among assemblages in recurrent sympatry. Pinworms occasionally infect geographically proximal host species; however, host switching may be unstable or ephemeral, as there is no signal of host switching in the deeper history of R. eutamii.
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Affiliation(s)
- Kayce C. Bell
- Department of Biology, Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87108, USA
| | - Kendall L. Calhoun
- Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, California 94720, USA
| | - Eric P. Hoberg
- US National Parasite Collection, USDA, Agricultural Research Service, Beltsville Area Research Center, BARC East 1180, 10300 Baltimore Avenue, Beltsville, Maryland 20715, USA
| | - John R. Demboski
- Department of Zoology, Denver Museum of Nature & Science, 2001 Colorado Boulevard, Denver, Colorado 80205, USA
| | - Joseph A. Cook
- Department of Biology, Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87108, USA
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26
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Xu Z, Zhang ML, Cohen JI. Phylogeographic History of Atraphaxis Plants in Arid Northern China and the Origin of A. bracteata in the Loess Plateau. PLoS One 2016; 11:e0163243. [PMID: 27656885 PMCID: PMC5033255 DOI: 10.1371/journal.pone.0163243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 09/05/2016] [Indexed: 12/02/2022] Open
Abstract
In China, species of Atraphaxis (Polygonaceae) primarily inhabit arid zones across temperate steppe and desert regions. The complex geologic history (e.g., expansion of deserts) and extreme climate shifts of the region appear to have played an important role in shaping the phylogeography of Atraphaxis. The present study focuses on species-level phylogeographic patterns of Atraphaxis in China, with the goal of determining the impact of past environmental changes, in northern China, on the evolutionary history of the genus. Five hundred and sixty-four individuals distributed among 71 populations of 11 species of Atraphaxis from across the geographic range of the genus were studied using sequence data from two plastid spacers, psbK-psbI and psbB-psbH. The results demonstrate that most chloroplast haplotypes are species-specific, except for some present among widespread species. The phylogeny of Atraphaxis was well structured, and molecular dating analyses suggest that the main divergence events occurred during the late Pliocene and Pleistocene (5.73–0.03 million years ago). The statistical dispersal-vicariance analysis (S-DIVA) results provide evidence that phylogeographic patterns for the genus were characterized by both vicariance events and regional dispersal. The presented data suggest that the rapid expansion of deserts and climatic changes in northern China during the late Pliocene and Pleistocene have driven the diversification and spread of Atraphaxis in the region. The expansion of the Tengger Desert provided appropriate conditions for the origin of A. bracteata. Additionally, a contact zone in the north of the Hexi Corridor was identified as having played a significant role as a migratory route for species in adjacent areas.
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Affiliation(s)
- Zhe Xu
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Ming-Li Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - James I Cohen
- Applied Biology, Kettering University, 1700 University Ave., Flint, MI, 48504, United States of America
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Sim Z, Hall JC, Jex B, Hegel TM, Coltman DW. Genome-wide set of SNPs reveals evidence for two glacial refugia and admixture from postglacial recolonization in an alpine ungulate. Mol Ecol 2016; 25:3696-705. [DOI: 10.1111/mec.13701] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 04/16/2016] [Accepted: 05/02/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Zijian Sim
- Department of Biological Sciences; University of Alberta; Edmonton Alberta Canada
| | - Jocelyn C. Hall
- Department of Biological Sciences; University of Alberta; Edmonton Alberta Canada
| | - Bill Jex
- Ministry of Forests, Lands and Natural Resource Operations; Bag 5000 - 3726 Alfred Ave Smithers British Columbia Canada
| | - Troy M. Hegel
- Yukon Department of Environment; PO Box 2703 Whitehorse Yukon Canada Y1A2C6
| | - David W. Coltman
- Department of Biological Sciences; University of Alberta; Edmonton Alberta Canada
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28
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Adams RV, Lazerte SE, Otter KA, Burg TM. Influence of landscape features on the microgeographic genetic structure of a resident songbird. Heredity (Edinb) 2016; 117:63-72. [PMID: 26905462 DOI: 10.1038/hdy.2016.12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 01/16/2016] [Accepted: 01/18/2016] [Indexed: 11/09/2022] Open
Abstract
Landscape features influence individual dispersal and as a result can affect both gene flow and genetic variation within and between populations. The landscape of British Columbia, Canada, is already highly heterogeneous because of natural ecological and geological transitions, but disturbance from human-mediated processes has further fragmented continuous habitat, particularly in the central plateau region. In this study, we evaluated the effects of landscape heterogeneity on the genetic structure of a common resident songbird, the black-capped chickadee (Poecile atricapillus). Previous work revealed significant population structuring in British Columbia that could not be explained by physical barriers, so our aim was to assess the pattern of genetic structure at a microgeographic scale and determine the effect of different landscape features on genetic differentiation. A total of 399 individuals from 15 populations were genotyped for fourteen microsatellite loci revealing significant population structuring in this species. Individual- and population-based analyses revealed as many as nine genetic clusters with isolation in the north, the central plateau and the south. Moreover, a mixed modelling approach that accounted for non-independence of pairwise distance values revealed a significant effect of land cover and elevation resistance on genetic differentiation. These results suggest that barriers in the landscape influence dispersal which has led to the unexpectedly high levels of population isolation. Our study demonstrates the importance of incorporating landscape features when interpreting patterns of population differentiation. Despite taking a microgeographic approach, our results have opened up additional questions concerning the processes influencing dispersal and gene flow at the local scale.
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Affiliation(s)
- R V Adams
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - S E Lazerte
- Natural Resources and Environmental Studies, University of Northern British Columbia, Prince George, British Columbia, Canada
| | - K A Otter
- Natural Resources and Environmental Studies, University of Northern British Columbia, Prince George, British Columbia, Canada
| | - T M Burg
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
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Stojak J, Wójcik JM, Ruczyńska I, Searle JB, McDevitt AD. Contrasting and congruent patterns of genetic structuring in two Microtus vole species using museum specimens. MAMMAL RES 2016. [DOI: 10.1007/s13364-015-0260-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Campbell MA, Takebayashi N, López JA. Beringian sub-refugia revealed in blackfish (Dallia): implications for understanding the effects of Pleistocene glaciations on Beringian taxa and other Arctic aquatic fauna. BMC Evol Biol 2015; 15:144. [PMID: 26187279 PMCID: PMC4506597 DOI: 10.1186/s12862-015-0413-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 06/08/2015] [Indexed: 12/03/2022] Open
Abstract
Background Pleistocene climatic instability had profound and diverse effects on the distribution and abundance of Arctic organisms revealed by variation in phylogeographic patterns documented in extant Arctic populations. To better understand the effects of geography and paleoclimate on Beringian freshwater fishes, we examined genetic variability in the genus Dallia (blackfish: Esociformes: Esocidae). The genus Dallia groups between one and three nominal species of small, cold- and hypoxia-tolerant freshwater fishes restricted entirely in distribution to Beringia from the Yukon River basin near Fairbanks, Alaska westward including the Kuskokwim River basin and low-lying areas of Western Alaska to the Amguema River on the north side of the Chukotka Peninsula and Mechigmen Bay on the south side of the Chukotka Peninsula. The genus has a non-continuous distribution divided by the Bering Strait and the Brooks Range. We examined the distribution of genetic variation across this range to determine the number and location of potential sub-refugia within the greater Beringian refugium as well as the roles of the Bering land bridge, Brooks Range, and large rivers within Beringia in shaping the current distribution of populations of Dallia. Our analyses were based on DNA sequence data from two nuclear gene introns (S7 and RAG1) and two mitochondrial genome fragments from nineteen sampling locations. These data were examined under genetic clustering and coalescent frameworks to identify sub-refugia within the greater Beringia refugium and to infer the demographic history of different populations of Dallia. Results We identified up to five distinct genetic clusters of Dallia. Four of these genetic clusters are present in Alaska: (1) Arctic Coastal Plain genetic cluster found north of the Brooks Range, (2) interior Alaska genetic cluster placed in upstream locations in the Kuskokwim and Yukon river basins, (3) a genetic cluster found on the Seward Peninsula, and (4) a coastal Alaska genetic cluster encompassing downstream Kuskokwim River and Yukon River basin sample locations and samples from Southwest Alaska not in either of these drainages. The Chukotka samples are assigned to their own genetic cluster (5) similar to the coastal Alaska genetic cluster. The clustering and ordination analyses implemented in Discriminant Analysis of Principal Components (DAPC) and STRUCTURE showed mostly concordant groupings and a high degree of differentiation among groups. The groups of sampling locations identified as genetic clusters correspond to geographic areas divided by likely biogeographic barriers including the Brooks Range and the Bering Strait. Estimates of sequence diversity (θ) are highest in the Yukon River and Kuskokwim River drainages near the Bering Sea. We also infer asymmetric migration rates between genetic clusters. The isolation of Dallia on the Arctic Coastal Plain of Alaska is associated with very low estimated migration rates between the coastal Alaska genetic cluster and the Arctic Coastal Plain genetic cluster. Conclusions Our results support a scenario with multiple aquatic sub-refugia in Beringia during the Pleistocene and the preservation of that structure in extant populations of Dallia. An inferred historical presence of Dallia across the Bering land bridge explains the similarities in the genetic composition of Dallia in West Beringia and western coastal Alaska. In contrast, historic and contemporary isolation across the Brooks Range shaped the distinctiveness of present day Arctic Coastal Plain Dallia. Overall this study uncovered a high degree of genetic structuring among populations of Dallia supporting the idea of multiple Beringian sub-refugia during the Pleistocene and which appears to be maintained to the present due to the strictly freshwater nature and low dispersal ability of this genus. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0413-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew A Campbell
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA. .,Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand.
| | - Naoki Takebayashi
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA. .,Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA.
| | - J Andrés López
- School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA. .,University of Alaska Museum, Fairbanks, AK, 99775, USA.
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Lanier HC, Massatti R, He Q, Olson LE, Knowles LL. Colonization from divergent ancestors: glaciation signatures on contemporary patterns of genomic variation in Collared Pikas (Ochotona collaris). Mol Ecol 2015; 24:3688-705. [DOI: 10.1111/mec.13270] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 05/27/2015] [Accepted: 05/29/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Hayley C. Lanier
- Department of Zoology and Physiology; University of Wyoming at Casper; Casper WY 82601 USA
| | - Rob Massatti
- Department of Ecology and Evolutionary Biology; The University of Michigan; Ann Arbor MI 41809-1079 USA
| | - Qixin He
- Department of Ecology and Evolutionary Biology; The University of Michigan; Ann Arbor MI 41809-1079 USA
| | - Link E. Olson
- University of Alaska Museum; University of Alaska Fairbanks; Fairbanks AK 99775 USA
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology; The University of Michigan; Ann Arbor MI 41809-1079 USA
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Parks LC, Wallin DO, Cushman SA, McRae BH. Landscape-level analysis of mountain goat population connectivity in Washington and southern British Columbia. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0732-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Edwards T, Berry KH, Inman RD, Esque TC, Nussear KE, Jones CA, Culver M. Testing Taxon Tenacity of Tortoises: evidence for a geographical selection gradient at a secondary contact zone. Ecol Evol 2015; 5:2095-114. [PMID: 26045959 PMCID: PMC4449762 DOI: 10.1002/ece3.1500] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 11/30/2022] Open
Abstract
We examined a secondary contact zone between two species of desert tortoise, Gopherus agassizii and G. morafkai. The taxa were isolated from a common ancestor during the formation of the Colorado River (4–8 mya) and are a classic example of allopatric speciation. However, an anomalous population of G. agassizii comes into secondary contact with G. morafkai east of the Colorado River in the Black Mountains of Arizona and provides an opportunity to examine reinforcement of species' boundaries under natural conditions. We sampled 234 tortoises representing G. agassizii in California (n - 103), G. morafkai in Arizona (n - 78), and 53 individuals of undetermined assignment in the contact zone including and surrounding the Black Mountains. We genotyped individuals for 25 STR loci and determined maternal lineage using mtDNA sequence data. We performed multilocus genetic clustering analyses and used multiple statistical methods to detect levels of hybridization. We tested hypotheses about habitat use between G. agassizii and G. morafkai in the region where they co-occur using habitat suitability models. Gopherus agassizii and G. morafkai maintain independent taxonomic identities likely due to ecological niche partitioning, and the maintenance of the hybrid zone is best described by a geographical selection gradient model.
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Affiliation(s)
- Taylor Edwards
- School of Natural Resources and the Environment, The University of Arizona Tucson, Arizona, 85721 ; University of Arizona Genetics Core, University of Arizona 1657 E. Helen Street, Tucson, Arizona, 85721
| | - Kristin H Berry
- Western Ecological Research Center, U.S. Geological Survey Falcon Business Park, 21803 Cactus Avenue, Suite F, Riverside, California, 92518
| | - Richard D Inman
- Western Ecological Research Center, U.S. Geological Survey 160 North Stephanie St., Henderson, Nevada, 89074
| | - Todd C Esque
- Western Ecological Research Center, U.S. Geological Survey 160 North Stephanie St., Henderson, Nevada, 89074
| | - Kenneth E Nussear
- Western Ecological Research Center, U.S. Geological Survey 160 North Stephanie St., Henderson, Nevada, 89074
| | - Cristina A Jones
- School of Natural Resources and the Environment, The University of Arizona Tucson, Arizona, 85721 ; Arizona Game and Fish Department, Nongame Wildlife Branch Phoenix, Arizona, 85086
| | - Melanie Culver
- School of Natural Resources and the Environment, The University of Arizona Tucson, Arizona, 85721 ; Arizona Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, University of Arizona Tucson, Arizona, 85721
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Lanier HC, Gunderson AM, Weksler M, Fedorov VB, Olson LE. Comparative phylogeography highlights the double-edged sword of climate change faced by arctic- and alpine-adapted mammals. PLoS One 2015; 10:e0118396. [PMID: 25734275 PMCID: PMC4348485 DOI: 10.1371/journal.pone.0118396] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 01/15/2015] [Indexed: 11/23/2022] Open
Abstract
Recent studies suggest that alpine and arctic organisms may have distinctly different phylogeographic histories from temperate or tropical taxa, with recent range contraction into interglacial refugia as opposed to post-glacial expansion out of refugia. We use a combination of phylogeographic inference, demographic reconstructions, and hierarchical Approximate Bayesian Computation to test for phylodemographic concordance among five species of alpine-adapted small mammals in eastern Beringia. These species (Collared Pikas, Hoary Marmots, Brown Lemmings, Arctic Ground Squirrels, and Singing Voles) vary in specificity to alpine and boreal-tundra habitat but share commonalities (e.g., cold tolerance and nunatak survival) that might result in concordant responses to Pleistocene glaciations. All five species contain a similar phylogeographic disjunction separating eastern and Beringian lineages, which we show to be the result of simultaneous divergence. Genetic diversity is similar within each haplogroup for each species, and there is no support for a post-Pleistocene population expansion in eastern lineages relative to those from Beringia. Bayesian skyline plots for four of the five species do not support Pleistocene population contraction. Brown Lemmings show evidence of late Quaternary demographic expansion without subsequent population decline. The Wrangell-St. Elias region of eastern Alaska appears to be an important zone of recent secondary contact for nearctic alpine mammals. Despite differences in natural history and ecology, similar phylogeographic histories are supported for all species, suggesting that these, and likely other, alpine- and arctic-adapted taxa are already experiencing population and/or range declines that are likely to synergistically accelerate in the face of rapid climate change. Climate change may therefore be acting as a double-edged sword that erodes genetic diversity within populations but promotes divergence and the generation of biodiversity.
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Affiliation(s)
- Hayley C. Lanier
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
- * E-mail:
| | - Aren M. Gunderson
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
| | - Marcelo Weksler
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
| | - Vadim B. Fedorov
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
| | - Link E. Olson
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
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Richard JH, White KS, Côté SD. Mating effort and space use of an alpine ungulate during the rut. Behav Ecol Sociobiol 2014. [DOI: 10.1007/s00265-014-1772-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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De Kort H, Vandepitte K, Bruun HH, Closset-Kopp D, Honnay O, Mergeay J. Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree speciesAlnus glutinosa. Mol Ecol 2014; 23:4709-21. [DOI: 10.1111/mec.12813] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/24/2014] [Accepted: 04/25/2014] [Indexed: 01/17/2023]
Affiliation(s)
- Hanne De Kort
- Plant Conservation and Population Biology; Department of Biology; University of Leuven; Kasteelpark Arenberg 31 Heverlee B-3001 Belgium
| | - Katrien Vandepitte
- Plant Conservation and Population Biology; Department of Biology; University of Leuven; Kasteelpark Arenberg 31 Heverlee B-3001 Belgium
| | - Hans Henrik Bruun
- Ecology and Evolution Section; Department of Biology; University of Copenhagen; Universitetsparken 15 København 2100 Denmark
| | - Déborah Closset-Kopp
- Research unit of “Ecologie et Dynamique des Systèmes Anthropisés”; Jules Vernes University of Picardy; 1 Rue des Louvels Amiens F-80037 France
| | - Olivier Honnay
- Plant Conservation and Population Biology; Department of Biology; University of Leuven; Kasteelpark Arenberg 31 Heverlee B-3001 Belgium
| | - Joachim Mergeay
- Research Institute for Nature and Forest; Gaverstraat 4 Geraardsbergen B-9500 Belgium
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Cheng E, Hodges KE, Melo-Ferreira J, Alves PC, Mills LS. Conservation implications of the evolutionary history and genetic diversity hotspots of the snowshoe hare. Mol Ecol 2014; 23:2929-42. [PMID: 24814937 DOI: 10.1111/mec.12790] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 05/05/2014] [Accepted: 05/05/2014] [Indexed: 11/27/2022]
Abstract
With climate warming, the ranges of many boreal species are expected to shift northward and to fragment in southern peripheral ranges. To understand the conservation implications of losing southern populations, we examined range-wide genetic diversity of the snowshoe hare (Lepus americanus), an important prey species that drives boreal ecosystem dynamics. We analysed microsatellite (8 loci) and mitochondrial DNA sequence (cytochrome b and control region) variation in almost 1000 snowshoe hares. A hierarchical structure analysis of the microsatellite data suggests initial subdivision in two groups, Boreal and southwestern. The southwestern group further splits into Greater Pacific Northwest and U.S. Rockies. The genealogical information retrieved from mtDNA is congruent with the three highly differentiated and divergent groups of snowshoe hares. These groups can correspond with evolutionarily significant units that might have evolved in separate refugia south and east of the Pleistocene ice sheets. Genetic diversity was highest at mid-latitudes of the species' range, and genetic uniqueness was greatest in southern populations, consistent with substructuring inferred from both mtDNA and microsatellite analyses at finer levels of analysis. Surprisingly, snowshoe hares in the Greater Pacific Northwest mtDNA lineage were more closely related to black-tailed jackrabbits (Lepus californicus) than to other snowshoe hares, which may result from secondary introgression or shared ancestral polymorphism. Given the genetic distinctiveness of southern populations and minimal gene flow with their northern neighbours, fragmentation and loss of southern boreal habitats could mean loss of many unique alleles and reduced evolutionary potential.
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Affiliation(s)
- Ellen Cheng
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
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Roffler GH, Talbot SL, Luikart G, Sage GK, Pilgrim KL, Adams LG, Schwartz MK. Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0583-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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When east meets west: population structure of a high-latitude resident species, the boreal chickadee (Poecile hudsonicus). Heredity (Edinb) 2013; 111:321-9. [PMID: 23759728 DOI: 10.1038/hdy.2013.54] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 04/16/2013] [Accepted: 04/30/2013] [Indexed: 11/09/2022] Open
Abstract
The population genetic structure of northern boreal species has been strongly influenced both by the Quaternary glaciations and the presence of contemporary barriers, such as mountain ranges and rivers. We used a combination of mitochondrial DNA (mtDNA), nuclear microsatellites and spatial distribution modelling to study the population genetic structure of the boreal chickadee (Poecile hudsonicus), a resident passerine, and to investigate whether historical or contemporary barriers have influenced this northern species. MtDNA data showed evidence of eastern and western groups, with secondary admixture occurring in central Canada. This suggests that the boreal chickadee probably persisted in multiple glacial refugia, one in Beringia and at least one in the east. Palaeo-distribution modelling identified suitable habitat in Beringia (Alaska), Atlantic Canada and the southern United States, and correspond to divergence dates of 60-96 kya. Pairwise FST values for both mtDNA and microsatellites were significant for all comparisons involving Newfoundland, though mtDNA data suggest a more recent separation. Furthermore, unlike mtDNA data, nuclear data support population connectivity among the continental populations, possibly due to male-biased dispersal. Although both are significant, the isolation-by-distance signal is much stronger for mtDNA (r(2)=0.51) than for microsatellites (r(2)=0.05), supporting the hypothesis of male-biased dispersal. The population structure of the boreal chickadee was influenced by isolation in multiple refugia and contemporary barriers. In addition to geographical distance, physical barriers such as the Strait of Belle Isle and northern mountains in Alaska are restricting gene flow, whereas the Rocky Mountains in the west are a porous barrier.
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Igea J, Aymerich P, Fernández-González A, González-Esteban J, Gómez A, Alonso R, Gosálbez J, Castresana J. Phylogeography and postglacial expansion of the endangered semi-aquatic mammal Galemys pyrenaicus. BMC Evol Biol 2013; 13:115. [PMID: 23738626 PMCID: PMC3682870 DOI: 10.1186/1471-2148-13-115] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 05/28/2013] [Indexed: 01/20/2023] Open
Abstract
Background Species with strict ecological requirements may provide new insights into the forces that shaped the geographic variation of genetic diversity. The Pyrenean desman, Galemys pyrenaicus, is a small semi-aquatic mammal that inhabits clean streams of the northern half of the Iberian Peninsula and is endangered in most of its geographic range, but its genetic structure is currently unknown. While the stringent ecological demands derived from its aquatic habitat might have caused a partition of the genetic diversity among river basins, Pleistocene glaciations would have generated a genetic pattern related to glacial refugia. Results To study the relative importance of historical and ecological factors in the genetic structure of G. pyrenaicus, we used mitochondrial and intronic sequences of specimens covering most of the species range. We show, first, that the Pyrenean desman has very low levels of genetic diversity compared to other mammals. In addition, phylogenetic and dating analyses of the mitochondrial sequences reveal a strong phylogeographic structure of a Middle Pleistocene origin, suggesting that the main lineages arose during periods of glacial isolation. Furthermore, both the spatial distribution of nuclear and mitochondrial diversity and the results of species distribution modeling suggest the existence of a major glacial refugium in the northwestern part of the Iberian Peninsula. Finally, the main mitochondrial lineages show a striking parapatric distribution without any apparent exchange of mitochondrial haplotypes between the lineages that came into secondary contact (although with certain permeability to nuclear genes), indicating incomplete mixing after the post-glacial recolonization. On the other hand, when we analyzed the partition of the genetic diversity among river basins, the Pyrenean desman showed a lower than expected genetic differentiation among main rivers. Conclusions The analysis of mitochondrial and intronic markers in G. pyrenaicus showed the predominant effects of Pleistocene glaciations on the genetic structure of this species, while the distribution of the genetic diversity was not greatly influenced by the main river systems. These results and, particularly, the discovery of a marked phylogeographic structure, may have important implications for the conservation of the Pyrenean desman.
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Affiliation(s)
- Javier Igea
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37, Barcelona 08003, Spain
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Godsoe W, Larson MA, Glennon KL, Segraves KA. Polyploidization in Heuchera cylindrica (Saxifragaceae) did not result in a shift in climatic requirements. AMERICAN JOURNAL OF BOTANY 2013; 100:496-508. [PMID: 23400493 DOI: 10.3732/ajb.1200275] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
PREMISE OF THE STUDY Polyploidization is a key factor involved in the diversification of plants. Although polyploids are commonly found, there remains controversy on the mechanisms that lead to their successful establishment. One major problem that has been identified is that newly formed polyploids lack mates of the appropriate ploidy level and may experience severely reduced fertility due to nonproductive intercytotype crosses. Niche differentiation has been proposed as a primary mechanism that can alleviate this reproductive disadvantage and facilitate polyploid establishment. Here we test whether the establishment of tetraploid cytotypes of Heuchera cylindrica (Saxifragaceae) is consistent with climatic niche differentiation. • METHODS We use a combination of field surveys, flow cytometry and species distribution models to: (1) examine the distribution of diploid and tetraploid cytotypes; and (2) determine whether tetraploid Heuchera cylindrica occupy climates that differ from those of its diploid progenitors. • KEY RESULTS The geographic distributions of diploid and tetraploid cytotypes are largely allopatric as an extensive survey of 636 plants from 43 locations failed to detect any populations with both cytotypes. Although diploids and tetraploids occur in different geographic areas, polyploid Heuchera cylindrica occur almost exclusively in environments that are predicted to be suitable to diploid populations. • CONCLUSIONS Climatic niche differentiation does not explain the geographic distribution of tetraploid Heuchera cylindrica. We propose instead that tetraploid lineages were able to establish by taking advantage of glacial retreat and expanding into previously unoccupied sites.
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Affiliation(s)
- William Godsoe
- Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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Parasites in ungulates of Arctic North America and Greenland: a view of contemporary diversity, ecology, and impact in a world under change. ADVANCES IN PARASITOLOGY 2012; 79:99-252. [PMID: 22726643 DOI: 10.1016/b978-0-12-398457-9.00002-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Parasites play an important role in the structure and function of arctic ecosystems, systems that are currently experiencing an unprecedented rate of change due to various anthropogenic perturbations, including climate change. Ungulates such as muskoxen, caribou, moose and Dall's sheep are also important components of northern ecosystems and are a source of food and income, as well as a focus for maintenance of cultural traditions, for northerners. Parasites of ungulates can influence host health, population dynamics and the quality, quantity and safety of meat and other products of animal origin consumed by people. In this article, we provide a contemporary view of the diversity of nematode, cestode, trematode, protozoan and arthropod parasites of ungulates in arctic and subarctic North America and Greenland. We explore the intricate associations among host and parasite assemblages and identify key issues and gaps in knowledge that emerge in a regime of accelerating environmental transition.
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Allen GA, Marr KL, McCormick LJ, Hebda RJ. The impact of Pleistocene climate change on an ancient arctic-alpine plant: multiple lineages of disparate history in Oxyria digyna. Ecol Evol 2012; 2:649-65. [PMID: 22822441 PMCID: PMC3399151 DOI: 10.1002/ece3.213] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 12/20/2011] [Accepted: 12/28/2011] [Indexed: 11/08/2022] Open
Abstract
The ranges of arctic-alpine species have shifted extensively with Pleistocene climate changes and glaciations. Using sequence data from the trnH-psbA and trnT-trnL chloroplast DNA spacer regions, we investigated the phylogeography of the widespread, ancient (>3 million years) arctic-alpine plant Oxyria digyna (Polygonaceae). We identified 45 haplotypes and six highly divergent major lineages; estimated ages of these lineages (time to most recent common ancestor, T(MRCA)) ranged from ∼0.5 to 2.5 million years. One lineage is widespread in the arctic, a second is restricted to the southern Rocky Mountains of the western United States, and a third was found only in the Himalayan and Altai regions of Asia. Three other lineages are widespread in western North America, where they overlap extensively. The high genetic diversity and the presence of divergent major cpDNA lineages within Oxyria digyna reflect its age and suggest that it was widespread during much of its history. The distributions of individual lineages indicate repeated spread of Oxyria digyna through North America over multiple glacial cycles. During the Last Glacial Maximum it persisted in multiple refugia in western North America, including Beringia, south of the continental ice, and within the northern limits of the Cordilleran ice sheet. Our data contribute to a growing body of evidence that arctic-alpine species have migrated from different source regions over multiple glacial cycles and that cryptic refugia contributed to persistence through the Last Glacial Maximum.
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SCHOVILLE SEAND, LAM ATHENAW, RODERICK GEORGEK. A range-wide genetic bottleneck overwhelms contemporary landscape factors and local abundance in shaping genetic patterns of an alpine butterfly (Lepidoptera: Pieridae:Colias behrii). Mol Ecol 2012; 21:4242-56. [DOI: 10.1111/j.1365-294x.2012.05696.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Shafer ABA, Northrup JM, White KS, Boyce MS, Côté SD, Coltman DW. Habitat selection predicts genetic relatedness in an alpine ungulate. Ecology 2012; 93:1317-29. [DOI: 10.1890/11-0815.1] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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VERKUIL YVONNEI, PIERSMA THEUNIS, JUKEMA JOOP, HOOIJMEIJER JOSCEW, ZWARTS LEO, BAKER ALLANJ. The interplay between habitat availability and population differentiation: a case study on genetic and morphological structure in an inland wader (Charadriiformes). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01878.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ortego J, Riordan EC, Gugger PF, Sork VL. Influence of environmental heterogeneity on genetic diversity and structure in an endemic southern Californian oak. Mol Ecol 2012; 21:3210-23. [PMID: 22548448 DOI: 10.1111/j.1365-294x.2012.05591.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding how specific environmental factors shape gene flow while disentangling their importance relative to the effects of geographical isolation is a major question in evolutionary biology and a specific goal of landscape genetics. Here, we combine information from nuclear microsatellite markers and ecological niche modelling to study the association between climate and spatial genetic structure and variability in Engelmann oak (Quercus engelmannii), a wind-pollinated species with high potential for gene flow. We first test whether genetic diversity is associated with climatic niche suitability and stability since the Last Glacial Maximum (LGM). Second, we use causal modelling to analyse the potential influence of climatic factors (current and LGM niche suitability) and altitude in the observed patterns of genetic structure. We found that genetic diversity is negatively associated with local climatic stability since the LGM, which may be due to higher immigration rates in unstable patches during favourable climatic periods and/or temporally varying selection. Analyses of spatial genetic structure revealed the presence of three main genetic clusters, a pattern that is mainly driven by two highly differentiated populations located in the northern edge of the species distribution range. After controlling for geographic distance, causal modelling analyses showed that genetic relatedness decreases with the environmental divergence among sampling sites estimated as altitude and current and LGM niche suitability. Natural selection against nonlocal genotypes and/or asynchrony in reproductive phenology may explain this pattern. Overall, this study suggests that local environmental conditions can shape patterns of genetic structure and variability even in species with high potential for gene flow and relatively small distribution ranges.
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Affiliation(s)
- Joaquín Ortego
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Box 957239, Los Angeles, CA 90095-7239, USA.
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YANNIC GLENN, PELLISSIER LOÏC, DUBEY SYLVAIN, VEGA RODRIGO, BASSET PATRICK, MAZZOTTI STEFANO, PECCHIOLI ELENA, VERNESI CRISTIANO, HAUFFE HEIDIC, SEARLE JEREMYB, HAUSSER JACQUES. Multiple refugia and barriers explain the phylogeography of the Valais shrew, Sorex antinorii (Mammalia: Soricomorpha). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2011.01824.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Hoberg EP, Abrams A, Pilitt PA, Jenkins EJ. Discovery and description of a new trichostrongyloid species (Nematoda: Ostertagiinae), abomasal parasites in mountain goat, Oreamnos americanus, from the Western Cordillera of North America. J Parasitol 2012; 98:817-46. [PMID: 22316219 DOI: 10.1645/ge-3047.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Marshallagia lichtenfelsi sp. n. is a dimorphic ostertagiine nematode occurring in the abomasum of mountain goats, Oreamnos americanus, from the Western Cordillera of North America. Major and minor morphotype males and females are characterized and distinguished relative to the morphologically similar Marshallagia marshalli / Marshallagia occidentalis from North America and Marshallagia dentispicularis, along with other congeners, from the Palearctic region. The configuration of the convoluted and irregular synlophe in the cervical region of males and females of M. lichtenfelsi is apparently unique, contrasting with a continuous and parallel system of ridges among those species of Marshallagia, including M. marshalli/M. occidentalis, which have been evaluated. Specimens of M. lichtenfelsi are further defined by the rectangular form of the accessory bursal membrane (width > length) in the major morphotype and by the trapezoidal Sjöberg's organ in the minor morphotype, in addition to specific attributes of the spicules and spicule tips. We regard 12 species, including the proposed new taxon, to be valid. Primary diagnostic characters are reviewed for Marshallagia and a framework is presented for standardization of future descriptions incorporating the synlophe in males and females and the structure of the spicules and genital cone in major and minor morphotype males. The center of diversity for species of Marshallagia is the mountain-steppe region of central Eurasia where 11 species (including the Holarctic M. marshalli) are recognized in association with Caprini, Rupicaprini, and Antelopinae; only 2 species occur in the Nearctic. In this assemblage, M. lichtenfelsi is endemic to North America and limited in host distribution to mountain goats. An intricate history for refugial isolation and population fragmentation demonstrated for mountain goats and wild sheep indicates the potential for considerable cryptic diversity for Marshallagia and other nematodes. Shifting patterns of contact and sympatry among assemblages of ungulates during the Pleistocene are consistent with geographic and host colonization as a process involved in diversification of these parasites.
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Affiliation(s)
- Eric P Hoberg
- U.S. National Parasite Collection and Animal Parasitic Disease Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA.
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Hoberg EP, Galbreath KE, Cook JA, Kutz SJ, Polley L. Northern host-parasite assemblages: history and biogeography on the borderlands of episodic climate and environmental transition. ADVANCES IN PARASITOLOGY 2012; 79:1-97. [PMID: 22726642 DOI: 10.1016/b978-0-12-398457-9.00001-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Diversity among assemblages of mammalian hosts and parasites in northern terrestrial ecosystems was structured by a deep history of biotic and abiotic change that overlies a complex geographic arena. Since the Pliocene, Holarctic ecosystems assembled in response to shifting climates (glacial and interglacial stages). Cycles of episodic dispersal/isolation and diversification defined northern diversity on landscape to regional scales. Episodes of geographic expansion and colonisation linked Eurasia and North America across Beringia and drove macroevolutionary structure of host and parasite associations. Asynchronous dispersal from centres of origin in Eurasia into the Nearctic resulted in gradients in parasite diversity in the carnivoran, lagomorph, rodent and artiodactyl assemblages we reviewed. Recurrent faunal interchange and isolation in conjunction with episodes of host colonisation have produced a mosaic structure for parasite faunas and considerable cryptic diversity among nematodes and cestodes. Mechanisms of invasion and geographic colonisation leading to the establishment of complex faunal assemblages are equivalent in evolutionary and ecological time, as demonstrated by various explorations of diversity in these high-latitude systems. Our ability to determine historical responses to episodic shifts in global climate may provide a framework for predicting the cascading effects of contemporary environmental change.
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