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Veale A, Reudink MW, Burg TM. Neutral markers reveal complex population structure across the range of a widespread songbird. Ecol Evol 2024; 14:e11638. [PMID: 38979005 PMCID: PMC11228359 DOI: 10.1002/ece3.11638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/17/2024] [Accepted: 06/13/2024] [Indexed: 07/10/2024] Open
Abstract
Understanding how both contemporary and historical physical barriers influence gene flow is key to reconstructing evolutionary histories and can allow us to predict species' resilience to changing environmental conditions. During the last glacial maximum (LGM), many high latitude North American bird species were forced into glacial refugia, including mountain bluebirds (Silia currucoides). Within their current breeding range, mountain bluebirds still experience a wide variety of environmental conditions and barriers that may disrupt gene flow and isolate populations. Using single nucleotide polymorphisms (SNPs) obtained through restriction site-associated DNA sequencing, we detected at least four genetically distinct mountain bluebird populations. Based on this structure, we determined that isolation-by-distance, the northern Rocky Mountains, and discontinuous habitat are responsible for the low connectivity and the overall history of each population going back to the last glacial maximum. Finally, we identified five candidate genes under balancing selection and three loci under diversifying selection. This study provides the first look at connectivity and gene flow across the range of these high-altitude and high latitude songbirds.
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Affiliation(s)
- Aaron Veale
- Department of Biological SciencesUniversity of LethbridgeLethbridgeAlbertaCanada
| | - Matthew W. Reudink
- Department of Biological SciencesThompson Rivers UniversityKamloopsBritish ColumbiaCanada
| | - Theresa M. Burg
- Department of Biological SciencesUniversity of LethbridgeLethbridgeAlbertaCanada
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Imwattana K, Aguero B, Nieto-Lugilde M, Duffy A, Jaramillo-Chico J, Hassel K, Afonina O, Lamkowski P, Jonathan Shaw A. Parallel patterns of genetic diversity and structure in circumboreal species of the Sphagnum capillifolium complex. AMERICAN JOURNAL OF BOTANY 2024; 111:e16348. [PMID: 38764292 DOI: 10.1002/ajb2.16348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 05/21/2024]
Abstract
PREMISE Shared geographical patterns of population genetic variation among related species is a powerful means to identify the historical events that drive diversification. The Sphagnum capillifolium complex is a group of closely related peat mosses within the Sphagnum subgenus Acutifolia and contains several circumboreal species whose ranges encompass both glaciated and unglaciated regions across the northern hemisphere. In this paper, we (1) inferred the phylogeny of subg. Acutifolia and (2) investigated patterns of population structure and genetic diversity among five circumboreal species within the S. capillifolium complex. METHODS We generated RAD sequencing data from most species of the subg. Acutifolia and samples from across the distribution ranges of circumboreal species within the S. capillifolium complex. RESULTS We resolved at least 14 phylogenetic clusters within the S. capillifolium complex. Five circumboreal species show some common patterns: One population system comprises plants in eastern North America and Europe, and another comprises plants in the Pacific Northwest or around the Beringian and Arctic regions. Alaska appears to be a hotspot for genetic admixture, genetic diversity, and sometimes endemic subclades. CONCLUSIONS Our results support the hypothesis that populations of five circumboreal species within the S. capillifolium complex survived in multiple refugia during the last glacial maximum. Long-distance dispersal out of refugia, population bottlenecks, and possible adaptations to conditions unique to each refugium could have contributed to current geographic patterns. These results indicate the important role of historical events in shaping the complex population structure of plants with broad distribution ranges.
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Affiliation(s)
- Karn Imwattana
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, USA
- Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Blanka Aguero
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, USA
| | - Marta Nieto-Lugilde
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, USA
| | - Aaron Duffy
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, USA
| | - Juan Jaramillo-Chico
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, USA
| | - Kristian Hassel
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Olga Afonina
- Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Paul Lamkowski
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
- University of Applied Science Neubrandenburg
| | - A Jonathan Shaw
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, USA
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D’Ercole J, Dapporto L, Opler P, Schmidt CB, Ho C, Menchetti M, Zakharov EV, Burns JM, Hebert PDN. A genetic atlas for the butterflies of continental Canada and United States. PLoS One 2024; 19:e0300811. [PMID: 38568891 PMCID: PMC10990199 DOI: 10.1371/journal.pone.0300811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024] Open
Abstract
Multi-locus genetic data for phylogeographic studies is generally limited in geographic and taxonomic scope as most studies only examine a few related species. The strong adoption of DNA barcoding has generated large datasets of mtDNA COI sequences. This work examines the butterfly fauna of Canada and United States based on 13,236 COI barcode records derived from 619 species. It compiles i) geographic maps depicting the spatial distribution of haplotypes, ii) haplotype networks (minimum spanning trees), and iii) standard indices of genetic diversity such as nucleotide diversity (π), haplotype richness (H), and a measure of spatial genetic structure (GST). High intraspecific genetic diversity and marked spatial structure were observed in the northwestern and southern North America, as well as in proximity to mountain chains. While species generally displayed concordance between genetic diversity and spatial structure, some revealed incongruence between these two metrics. Interestingly, most species falling in this category shared their barcode sequences with one at least other species. Aside from revealing large-scale phylogeographic patterns and shedding light on the processes underlying these patterns, this work also exposed cases of potential synonymy and hybridization.
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Affiliation(s)
- Jacopo D’Ercole
- Centre for Biodiversity Genomics, Guelph, Ontario, Canada
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Leonardo Dapporto
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Paul Opler
- Colorado State University, Fort Collins, Colorado, United States of America
| | - Christian B. Schmidt
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Chris Ho
- Centre for Biodiversity Genomics, Guelph, Ontario, Canada
| | | | | | - John M. Burns
- Department of Entomology, Smithsonian Institution, Washington, DC, United States of America
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Guelph, Ontario, Canada
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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Wefferling KM, Castro M, Castro S, Holmlund H, Loureiro J, Rothfels CJ, Schuettpelz E. Polyploid goldback and silverback ferns (Pentagramma) occupy a wider, colder, and wetter bioclimatic niche than diploid counterparts. AMERICAN JOURNAL OF BOTANY 2024; 111:e16305. [PMID: 38517199 DOI: 10.1002/ajb2.16305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 03/23/2024]
Abstract
PREMISE The western North American fern genus Pentagramma (Pteridaceae) is characterized by complex patterns of ploidy variation, an understanding of which is critical to comprehending both the evolutionary processes within the genus and its current diversity. METHODS We undertook a cytogeographic study across the range of the genus, using a combination of chromosome counts and flow cytometry to infer ploidy level. Bioclimatic variables and elevation were used to compare niches. RESULTS We found that diploids and tetraploids are common and widespread, and triploids are rare and sporadic; in contrast with genome size inferences in earlier studies, no hexaploids were found. Diploids and tetraploids show different geographic ranges: only tetraploids were found in the northernmost portion of the range (Washington, Oregon, and British Columbia) and only diploids were found in the Sierra Nevada of California. Diploid, triploid, and tetraploid cytotypes were found to co-occur in relatively few localities: in the southern (San Diego County, California) and desert Southwest (Arizona) parts of the range, and along the Pacific Coast of California. CONCLUSIONS Tetraploids occupy a wider bioclimatic niche than diploids both within P. triangularis and at the genus-wide scale. It is unknown whether the wider niche of tetraploids is due to their expansion upon the diploid niche, if diploids have contracted their niche due to competition or changing abiotic conditions, or if this wider niche occupancy is due to multiple origins of tetraploids.
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Affiliation(s)
- Keir M Wefferling
- Department of Biology, Gary A. Fewless Herbarium, Cofrin Center for Biodiversity, University of Wisconsin-Green Bay, Green Bay, 54311, Wisconsin, USA
| | - Mariana Castro
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Sílvia Castro
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Helen Holmlund
- Natural Science Division, Pepperdine University, Malibu, 90263, California, USA
| | - João Loureiro
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Carl J Rothfels
- Department of Biology, Ecology Center, and Intermountain Herbarium, Utah State University, Logan, 84322, Utah, USA
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, 20560, DC, USA
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Kessler C, Shafer ABA. Genomic Analyses Capture the Human-Induced Demographic Collapse and Recovery in a Wide-Ranging Cervid. Mol Biol Evol 2024; 41:msae038. [PMID: 38378172 PMCID: PMC10917209 DOI: 10.1093/molbev/msae038] [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: 08/15/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024] Open
Abstract
The glacial cycles of the Quaternary heavily impacted species through successions of population contractions and expansions. Similarly, populations have been intensely shaped by human pressures such as unregulated hunting and land use changes. White-tailed and mule deer survived in different refugia through the Last Glacial Maximum, and their populations were severely reduced after the European colonization. Here, we analyzed 73 resequenced deer genomes from across their North American range to understand the consequences of climatic and anthropogenic pressures on deer demographic and adaptive history. We found strong signals of climate-induced vicariance and demographic decline; notably, multiple sequentially Markovian coalescent recovers a severe decline in mainland white-tailed deer effective population size (Ne) at the end of the Last Glacial Maximum. We found robust evidence for colonial overharvest in the form of a recent and dramatic drop in Ne in all analyzed populations. Historical census size and restocking data show a clear parallel to historical Ne estimates, and temporal Ne/Nc ratio shows patterns of conservation concern for mule deer. Signatures of selection highlight genes related to temperature, including a cold receptor previously highlighted in woolly mammoth. We also detected immune genes that we surmise reflect the changing land use patterns in North America. Our study provides a detailed picture of anthropogenic and climatic-induced decline in deer diversity and clues to understanding the conservation concerns of mule deer and the successful demographic recovery of white-tailed deer.
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Affiliation(s)
- Camille Kessler
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada
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Hold K, Lord E, Brealey JC, Le Moullec M, Bieker VC, Ellegaard MR, Rasmussen JA, Kellner FL, Guschanski K, Yannic G, Røed KH, Hansen BB, Dalén L, Martin MD, Dussex N. Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos. Sci Rep 2024; 14:4143. [PMID: 38374421 PMCID: PMC10876933 DOI: 10.1038/s41598-024-54296-2] [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: 09/25/2023] [Accepted: 02/11/2024] [Indexed: 02/21/2024] Open
Abstract
Climate warming at the end of the last glacial period had profound effects on the distribution of cold-adapted species. As their range shifted towards northern latitudes, they were able to colonise previously glaciated areas, including remote Arctic islands. However, there is still uncertainty about the routes and timing of colonisation. At the end of the last ice age, reindeer/caribou (Rangifer tarandus) expanded to the Holarctic region and colonised the archipelagos of Svalbard and Franz Josef Land. Earlier studies have proposed two possible colonisation routes, either from the Eurasian mainland or from Canada via Greenland. Here, we used 174 ancient, historical and modern mitogenomes to reconstruct the phylogeny of reindeer across its whole range and to infer the colonisation route of the Arctic islands. Our data shows a close affinity among Svalbard, Franz Josef Land and Novaya Zemlya reindeer. We also found tentative evidence for positive selection in the mitochondrial gene ND4, which is possibly associated with increased heat production. Our results thus support a colonisation of the Eurasian Arctic archipelagos from the Eurasian mainland and provide some insights into the evolutionary history and adaptation of the species to its High Arctic habitat.
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Affiliation(s)
- Katharina Hold
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway.
| | - Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405, Stockholm, Sweden
- Department of Zoology, Stockholm University, 10691, Stockholm, Sweden
| | - Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway
- Department of Terrestrial Ecology, Norwegian Institute of Nature Research (NINA), Høgskoleringen 9, 7034, Trondheim, Norway
| | - Mathilde Le Moullec
- Gjærevoll Centre for Biodiversity Foresight Analyses, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
- Department of Mammals and Birds, Greenland, Institute of Natural Resources, Kivioq 2, 3900, Nuuk, Greenland
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway
| | - Martin R Ellegaard
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway
| | - Jacob A Rasmussen
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Fabian L Kellner
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway
| | - Katerina Guschanski
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Glenn Yannic
- Univ. Savoie Mont Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, 38000, Grenoble, France
| | - Knut H Røed
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Brage B Hansen
- Gjærevoll Centre for Biodiversity Foresight Analyses, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
- Department of Terrestrial Ecology, Norwegian Institute of Nature Research (NINA), Høgskoleringen 9, 7034, Trondheim, Norway
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405, Stockholm, Sweden
- Department of Zoology, Stockholm University, 10691, Stockholm, Sweden
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway.
| | - Nicolas Dussex
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway.
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Faske TM, Agneray AC, Jahner JP, Osuna-Mascaró C, Sheta LM, Richardson BA, Leger EA, Parchman TL. Environment predicts the maintenance of reproductive isolation in a mosaic hybrid zone of rubber rabbitbrush. Evolution 2024; 78:300-314. [PMID: 37962379 DOI: 10.1093/evolut/qpad207] [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: 07/31/2023] [Revised: 10/23/2023] [Accepted: 11/09/2023] [Indexed: 11/15/2023]
Abstract
Widely distributed plants of western North America experience divergent selection across environmental gradients, have complex histories shaped by biogeographic barriers and distributional shifts and often illustrate continuums of reproductive isolation. Rubber rabbitbrush (Ericameria nauseosa) is a foundational shrub species that occurs across diverse environments of western North America. Its remarkable phenotypic diversity is currently ascribed to two subspecies-Ericameria nauseosa nauseosa and Ericameria nauseosa consimilis-and 22 named varieties. To understand how genetic variation is partitioned across subspecies, varieties, and environments, we used high throughput sequencing of reduced representation libraries. We found clear evidence for divergence between the two subspecies, despite largely sympatric distributions. Numerous locations exhibiting admixed ancestry were not geographically localized but were widely distributed across a mosaic hybrid zone. The occurrence of hybrid and subspecific ancestries was strongly predicted by environmental variables as well as the proximity to major ecotones between ecoregions. Although this repeatability illustrates the importance of environmental factors in shaping reproductive isolation, variability in the prevalence of hybridization also indicates these factors likely differ across ecological contexts. There was mixed evidence for the evolutionary cohesiveness of varieties, but several genetically distinct and narrow endemic varieties exhibited admixed subspecific ancestries, hinting at the possibility for transgressive hybridization to contribute to phenotypic novelty and the colonization of new environments in E. nauseosa.
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Affiliation(s)
- Trevor M Faske
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
- Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV 89557, United States
| | - Alison C Agneray
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
- Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV 89557, United States
- Bureau of Land Management, Nevada State Office, Reno, NV 89502, United States
| | - Joshua P Jahner
- Department of Botany, University of Wyoming, Laramie, WY, 82071, United States
| | | | - Lana M Sheta
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
| | - Bryce A Richardson
- Rocky Mountain Research Station, USDA Forest Service, Moscow, ID 83843, United States
| | - Elizabeth A Leger
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
- Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV 89557, United States
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
- Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV 89557, United States
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Aleuy OA, Peacock SJ, Molnár PK, Ruckstuhl KE, Kutz SJ. Local thermal adaptation and local temperature regimes drive the performance of a parasitic helminth under climate change: The case of Marshallagia marshalli from wild ungulates. GLOBAL CHANGE BIOLOGY 2023; 29:6217-6233. [PMID: 37615247 DOI: 10.1111/gcb.16918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/25/2023]
Abstract
Across a species' range, populations are exposed to their local thermal environments, which on an evolutionary scale, may cause adaptative differences among populations. Helminths often have broad geographic ranges and temperature-sensitive life stages but little is known about whether and how local thermal adaptation can influence their response to climate change. We studied the thermal responses of the free-living stages of Marshallagia marshalli, a parasitic nematode of wild ungulates, along a latitudinal gradient. We first determine its distribution in wild sheep species in North America. Then we cultured M. marshalli eggs from different locations at temperatures from 5 to 38°C. We fit performance curves based on the metabolic theory of ecology to determine whether development and mortality showed evidence of local thermal adaptation. We used parameter estimates in life-cycle-based host-parasite models to understand how local thermal responses may influence parasite performance under general and location-specific climate-change projections. We found that M. marshalli has a wide latitudinal and host range, infecting wild sheep species from New Mexico to Yukon. Increases in mortality and development time at higher temperatures were most evident for isolates from northern locations. Accounting for location-specific parasite parameters primarily influenced the magnitude of climate change parasite performance, while accounting for location-specific climates primarily influenced the phenology of parasite performance. Despite differences in development and mortality among M. marshalli populations, when using site-specific climate change projections, there was a similar magnitude of impact on the relative performance of M. marshalli among populations. Climate change is predicted to decrease the expected lifetime reproductive output of M. marshalli in all populations while delaying its seasonal peak by approximately 1 month. Our research suggests that accurate projections of the impacts of climate change on broadly distributed species need to consider local adaptations of organisms together with local temperature profiles and climate projections.
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Affiliation(s)
- O Alejandro Aleuy
- Department of Biological Sciences, University of Calgary, Alberta, Calgary, Canada
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Alberta, Calgary, Canada
| | - Stephanie J Peacock
- Department of Biological Sciences, University of Calgary, Alberta, Calgary, Canada
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Alberta, Calgary, Canada
| | - Péter K Molnár
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Toronto, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Ontario, Toronto, Canada
| | - Kathreen E Ruckstuhl
- Department of Biological Sciences, University of Calgary, Alberta, Calgary, Canada
| | - Susan J Kutz
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Alberta, Calgary, Canada
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Fu J, Wen L. Impacts of Quaternary glaciation, geological history and geography on animal species history in continental East Asia: A phylogeographic review. Mol Ecol 2023; 32:4497-4514. [PMID: 37332105 DOI: 10.1111/mec.17053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/20/2023]
Abstract
Continental East Asia has a mild Pleistocene climate and a complex recent geological history. Phylogeographic studies of animals over the last 30 years have produced several distinctive patterns. Glaciation refugia are numerous and are not restricted to any particular regions. Most of them are localized and species-specific, although several large refugia, for example the mountains of SW China, are shared by multiple species and have refugia-within-refugia. Furthermore, postglaciation range expansion events vary greatly in time, scale and direction. Large-scale south-to-north post-LGM expansions are few and mostly occurred in the northern regions. Additionally, several unique geographic features, including the three-step terrain of China and the northern arid belt, have significant impacts on many species histories. Overall, the impacts of Pleistocene glaciations, particularly the LGM, on species history vary drastically from nondetectable to significant. The impacts are the least for species from the southwestern region and are most dominant for species from the north. Geological events play a more significant role in shaping species history than Pleistocene climatic changes. Phylogeographic patterns among animals species are highly consistent with those of plants. Future phylogeographic endeavour in East Asia should be hypothesis-driven and seek processes that underlie common patterns. The wide use of genomic data allow accurate estimates of historical population processes and exploration of older history beyond the Pleistocene.
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Affiliation(s)
- Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Longying Wen
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Key Laboratory of Sichuan Institute for Protecting Endangered Birds in the Southwest Mountains, College of Life Sciences, Leshan Normal University, Leshan, China
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10
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Winker K, Withrow JJ, Gibson DD, Pruett CL. Beringia as a high-latitude engine of avian speciation. Biol Rev Camb Philos Soc 2023; 98:1081-1099. [PMID: 36879465 DOI: 10.1111/brv.12945] [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: 04/23/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023]
Abstract
Beringia is a biogeographically dynamic region that extends from northeastern Asia into northwestern North America. This region has affected avian divergence and speciation in three important ways: (i) by serving as a route for intercontinental colonisation between Asia and the Americas; (ii) by cyclically splitting (and often reuniting) populations, subspecies, and species between these continents; and (iii) by providing isolated refugia through glacial cycles. The effects of these processes can be seen in taxonomic splits of shallow to increasing depths and in the presence of regional endemics. We review the taxa involved in the latter two processes (splitting-reuniting and isolation), with a focus on three research topics: avian diversity, time estimates of the generation of that diversity, and the regions within Beringia that might have been especially important. We find that these processes have generated substantial amounts of avian diversity, including 49 pairs of avian subspecies or species whose breeding distributions largely replace one another across the divide between the Old World and the New World in Beringia, and 103 avian species and subspecies endemic to this region. Among endemics, about one in three is recognised as a full biological species. Endemic taxa in the orders Charadriiformes (shorebirds, alcids, gulls, and terns) and Passeriformes (perching birds) are particularly well represented, although they show very different levels of diversity through evolutionary time. Endemic Beringian Charadriiformes have a 1.31:1 ratio of species to subspecies. In Passeriformes, endemic taxa have a 0.09:1 species-to-subspecies ratio, suggesting that passerine (and thus terrestrial) endemism might be more prone to long-term extinction in this region, although such 'losses' could occur through their being reconnected with wider continental populations during favourable climatic cycles (e.g. subspecies reintegration with other populations). Genetic evidence suggests that most Beringian avian taxa originated over the past 3 million years, confirming the importance of Quaternary processes. There seems to be no obvious clustering in their formation through time, although there might be temporal gaps with lower rates of diversity generation. For at least 62 species, taxonomically undifferentiated populations occupy this region, providing ample potential for future evolutionary diversification.
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Affiliation(s)
- Kevin Winker
- University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
| | - Jack J Withrow
- University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
| | - Daniel D Gibson
- University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
| | - Christin L Pruett
- Department of Biology, Ouachita Baptist University, 410 Ouachita St, Arkadelphia, AR, 71998, USA
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Potter BA, Halffman CM, McKinney HJ, Reuther JD, Finney BP, Lanoë FB, López JA, Holmes CE, Palmer E, Capps M, Kemp BM. Freshwater and anadromous fishing in Ice Age Beringia. SCIENCE ADVANCES 2023; 9:eadg6802. [PMID: 37267368 PMCID: PMC10413661 DOI: 10.1126/sciadv.adg6802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/01/2023] [Indexed: 06/04/2023]
Abstract
While freshwater and anadromous fish have been critical economic resources for late prehistoric and modern Native Americans, the origin and development of fishing is not well understood. We document the earliest known human use of freshwater and anadromous fish in North America by 13,000 and 11,800 years ago, respectively, from primary anthropogenic contexts in central Alaska (eastern Beringia). Fish use appears conditioned by broad climatic factors, as all occurrences but one are within the Younger Dryas chronozone. Earlier Bølling-Allerød and later early Holocene components, while exhibiting similar organic preservation, did not yield evidence of fishing, suggesting that this was a response to changing environmental factors, perhaps reductions in higher ranked resources such as large terrestrial mammals. Late Pleistocene and recent Indigenous peoples harvested similar fish taxa in the region (salmon, burbot, whitefish, and pike). We characterize late Pleistocene fishing in interior Beringia as an important element of broad-spectrum foraging rather than the intensive communal fishing and storage common among recent peoples.
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Affiliation(s)
- Ben A. Potter
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Carrin M. Halffman
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Holly J. McKinney
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Joshua D. Reuther
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA
- Archaeology Department, University of Alaska Museum of the North, Fairbanks, AK, USA
| | - Bruce P. Finney
- Department of Biological Sciences and Geosciences, Idaho State University, Pocatello, ID, USA
| | - François B. Lanoë
- Archaeology Department, University of Alaska Museum of the North, Fairbanks, AK, USA
- Bureau of Applied Research in Anthropology, University of Arizona, Tucson AZ, USA
| | - J. Andrés López
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, USA
- Department of Fishes and Marine Invertebrates, University of Alaska Museum of the North, Fairbanks, AK, USA
| | - Charles E. Holmes
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Erica Palmer
- Laboratories of Molecular Anthropology and Microbiome Research, Norman, OK, USA
| | - Marie Capps
- Laboratories of Molecular Anthropology and Microbiome Research, Norman, OK, USA
| | - Brian M. Kemp
- Laboratories of Molecular Anthropology and Microbiome Research, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
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12
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Boria RA, Blois JL. Phylogeography within the Peromyscus maniculatus species group: Understanding past distribution of genetic diversity and areas of refugia in western North America. Mol Phylogenet Evol 2023; 180:107701. [PMID: 36623612 DOI: 10.1016/j.ympev.2023.107701] [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: 06/30/2022] [Revised: 12/09/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
The effects of anthropogenic climate change on biodiversity have been recognized on every continent, ocean, and across different taxonomic groups. Here, we study the range dynamics and demography of a cosmopolitan species: the deer mouse, Peromyscus maniculatus. We generated a multilocus SNP dataset using the ddRADseq protocol for 218 individuals across the geographic range within three western North American lineages of this species group. We evaluated population structure using several methods and explored the correlation between geographic and genetic distances. We modeled the demographic history using a site frequency spectrum approach and used a machine learning algorithm to infer current and past (Last Glacial Maximum; LGM) environmental suitability. Lastly, we explored the origin of population expansion for the identified lineages. The genome-wide SNP dataset was able to identify-three regionally distinct groups- 1) P. m. gambelii (southern California); 2) P. keeni (Pacific Northwest); 3) P. m. sonoriensis (a broad population spanning the Pacific Northwest through central California and across the Rocky Mountains into the Great Plains). Demographic analysis indicated the splits between the three populations occurred within the last 500 thousand years, with one very recent (late Holocene) split. Ecological niche models for each of these lineages predicted suitable environment present throughout their known ranges for current conditions, and a severe reduction of northern habitat in the past. The deer mouse has responded to past climate changes by expanding its range during interglacial periods and contracting its range during glacial periods leading to strong population differentiation. But lower magnitude climate change or other processes within the Holocene interglacial period led to population differentiation as well, which is likely still ongoing today given the substantial anthropogenic climate change and other landscape transformations caused by humans during the Anthropocene. By understanding the historical processes that led to the contemporary geographic distribution of biodiversity, we can determine the relative importance of different factors that shape biodiversity, now and into the future.
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Affiliation(s)
- Robert A Boria
- School of Natural Sciences, University of California- Merced, Merced, CA 95343, USA; Present address: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Jessica L Blois
- School of Natural Sciences, University of California- Merced, Merced, CA 95343, USA
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13
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Malanson GP, Pansing ER, Testolin R, Jiménez-Alfaro B. Simulations reveal climate and legacy effects underlying regional beta diversity in alpine vegetation. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1053017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
IntroductionWhether the distribution and assembly of plant species are adapted to current climates or legacy effects poses a problem for their conservation during ongoing climate change. The alpine regions of southern and central Europe are compared to those of the western United States and Canada because they differ in their geographies and histories.MethodsIndividual-based simulation experiments disentangled the role of geography in species adaptations and legacy effects in four combinations: approximations of observed alpine geographies vs. regular lattices with the same number of regions (realistic and null representations), and virtual species with responses to either climatic or simple spatial gradients (adaptations or legacy effects). Additionally, dispersal distances were varied using five Gaussian kernels. Because the similarity of pairs of regional species pools indicated the processes of assembly at extensive spatiotemporal scales and is a measure of beta diversity, this output of the simulations was correlated to observed similarity for Europe and North America.ResultsIn North America, correlations were highest for simulations with approximated geography and location-adapted species; those in Europe had their highest correlation with the lattice pattern and climate-adapted species. Only SACEU correlations were sensitive to dispersal limitation.DiscussionThe southern and central European alpine areas are more isolated and with more distinct climates to which species are adapted. In the western United States and Canada, less isolation and more mixing of species from refugia has caused location to mask climate adaptation. Among continents, the balance of explanatory factors for the assembly of regional species pools will vary with their unique historical biogeographies, with isolation lessening disequilibria.
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14
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Kimmitt AA, Pegan TM, Jones AW, Wacker KS, Brennan CL, Hudon J, Kirchman JJ, Ruegg K, Benz BW, Herman R, Winger BM. Genetic evidence for widespread population size expansion in North American boreal birds prior to the Last Glacial Maximum. Proc Biol Sci 2023; 290:20221334. [PMID: 36695033 PMCID: PMC9874272 DOI: 10.1098/rspb.2022.1334] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/19/2022] [Indexed: 01/26/2023] Open
Abstract
Pleistocene climate cycles are well documented to have shaped contemporary species distributions and genetic diversity. Northward range expansions in response to deglaciation following the Last Glacial Maximum (LGM; approximately 21 000 years ago) are surmised to have led to population size expansions in terrestrial taxa and changes in seasonal migratory behaviour. Recent findings, however, suggest that some northern temperate populations may have been more stable than expected through the LGM. We modelled the demographic history of 19 co-distributed boreal-breeding North American bird species from full mitochondrial gene sets and species-specific molecular rates. We used these demographic reconstructions to test how species with different migratory strategies were affected by glacial cycles. Our results suggest that effective population sizes increased in response to Pleistocene deglaciation earlier than the LGM, whereas genetic diversity was maintained throughout the LGM despite shifts in geographical range. We conclude that glacial cycles prior to the LGM have most strongly shaped contemporary genetic diversity in these species. We did not find a relationship between historic population dynamics and migratory strategy, contributing to growing evidence that major switches in migratory strategy during the LGM are unnecessary to explain contemporary migratory patterns.
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Affiliation(s)
- Abigail A. Kimmitt
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Teresa M. Pegan
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew W. Jones
- Department of Ornithology, Cleveland Museum of Natural History, Cleveland, OH 44106, USA
| | - Kristen S. Wacker
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Courtney L. Brennan
- Department of Ornithology, Cleveland Museum of Natural History, Cleveland, OH 44106, USA
| | - Jocelyn Hudon
- Royal Alberta Museum, Edmonton, Alberta Canada, T5J 0G2
| | | | - Kristen Ruegg
- Biology Department, Colorado State University, Fort Collins, CO 80521, USA
| | - Brett W. Benz
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rachael Herman
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Benjamin M. Winger
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
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15
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Moreira LR, Klicka J, Smith BT. Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age. Mol Ecol 2023; 32:1739-1759. [PMID: 36617622 DOI: 10.1111/mec.16841] [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: 03/08/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 01/10/2023]
Abstract
The influence of genetic drift on population dynamics during Pleistocene glacial cycles is well understood, but the role of selection in shaping patterns of genomic variation during these events is less explored. We resequenced whole genomes to investigate how demography and natural selection interact to generate the genomic landscapes of Downy and Hairy Woodpecker, species codistributed in previously glaciated North America. First, we explored the spatial and temporal patterns of genomic diversity produced by neutral evolution. Next, we tested (i) whether levels of nucleotide diversity along the genome are correlated with intrinsic genomic properties, such as recombination rate and gene density, and (ii) whether different demographic trajectories impacted the efficacy of selection. Our results revealed cycles of bottleneck and expansion, and genetic structure associated with glacial refugia. Nucleotide diversity varied widely along the genome, but this variation was highly correlated between the species, suggesting the presence of conserved genomic features. In both taxa, nucleotide diversity was positively correlated with recombination rate and negatively correlated with gene density, suggesting that linked selection played a role in reducing diversity. Despite strong fluctuations in effective population size, the maintenance of relatively large populations during glaciations may have facilitated selection. Under these conditions, we found evidence that the individual demographic trajectory of populations modulated linked selection, with purifying selection being more efficient in removing deleterious alleles in large populations. These results highlight that while genome-wide variation reflects the expected signature of demographic change during climatic perturbations, the interaction of multiple processes produces a predictable and highly heterogeneous genomic landscape.
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Affiliation(s)
- Lucas R Moreira
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, New York, USA.,Department of Ornithology, American Museum of Natural History, New York City, New York, USA.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - John Klicka
- Burke Museum of Natural History and Culture and Department of Biology, University of Washington, Seattle, Washington, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York City, New York, USA
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16
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Mitochondrial genomes reveal mid-Pleistocene population divergence, and post-glacial expansion, in Australasian snapper (Chrysophrys auratus). Heredity (Edinb) 2023; 130:30-39. [PMID: 36463371 DOI: 10.1038/s41437-022-00579-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Glacial cycles play important roles in determining the phylogeographic structure of terrestrial species, however, relatively little is known about their impacts on the distribution of marine biota. This study utilised modern (n = 350) and ancient (n = 26) mitochondrial genomes from Australasian snapper (Chrysophrys auratus) sampled in New Zealand to assess their demographic and phylogeographic history. We also tested for changes in genetic diversity using the up to 750-year-old mitochondrial genomes from pre-European archaeological sites to assess the potential impacts of human exploitation. Nucleotide diversity and haplotype diversity was high (π = 0.005, h = 0.972). There was no significant change in nucleotide diversity over the last 750 years (p = 0.343), with no detectable loss of diversity as a result of indigenous and industrial-scale fishing activity. While there was no evidence for contemporary population structure (AMOVA, p = 0.764), phylogeographic analyses identified two distinct mitochondrial clades that diverged approximately 650,000 years ago during the mid-Pleistocene, suggesting the species experienced barriers to gene flow when sea levels dropped over 120 m during previous glacial maxima. An exponential population increase was also observed around 8000 years ago consistent with a post-glacial expansion, which was likely facilitated by increased ocean temperatures and rising sea levels. This study demonstrates that glacial cycles likely played an important role in the demographic history of C. auratus and adds to our growing understanding of how dynamic climatic changes have influenced the evolution of coastal marine species.
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17
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Aubry KB, Raley CM, Shirk AJ, McKelvey KS, Copeland JP. Climatic conditions limit wolverine distribution in the Cascade Range of southwestern North America. CAN J ZOOL 2022. [DOI: 10.1139/cjz-2022-0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recolonization of the Cascade Range in southern British Columbia, Canada, and Washington, USA, by wolverines ( Gulo gulo (L., 1758)) is an ongoing process whose ultimate outcome is unknown. A reliable species distribution model for the wolverine in the Cascades (i.e., their first-order habitat selection) is urgently needed to help inform management and conservation strategies. Using Argos location data obtained on 10 resident adult wolverines (six females, four males) from 2008 to 2016, we generated a multi-covariate species distribution model for the wolverine in the Cascades. Our final model included three climatic covariates and their quadratic terms: Proximity to the Transitional Zone Near Alpine Tree Line, Number of Frost-free Days per Year, and Annual Precipitation as Snow. Model validations indicated that our model was robust and could identify areas of potential wolverine distribution in the Cascades reliably. Our model provides evidence that wolverine distribution in the Cascades is constrained by climatic conditions and that snowy and cold environments define the geographic areas that are overwhelmingly associated with resident wolverines. In addition, our model provides a reliable basis for monitoring the direct effects of climate change on wolverines in the Cascade Range and for predicting the extent to which climate change may impact their populations under various scenarios.
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Affiliation(s)
- Keith B. Aubry
- US Forest Service, Pacific Northwest Research Station, 3625 93rd Avenue SW, Olympia, WA 98512, USA
| | - Catherine M. Raley
- US Forest Service, Pacific Northwest Research Station, 3625 93rd Avenue SW, Olympia, WA 98512, USA
| | - Andrew J. Shirk
- School of the Environment, University of Washington, Climate Impacts Group, P.O. Box 355674, Seattle, WA 98195, USA
| | - Kevin S. McKelvey
- US Forest Service, Rocky Mountain Research Station, 800 East Beckwith, Missoula, MT 59801, USA
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18
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Population structure of threatened caribou in western Canada inferred from genome-wide SNP data. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01475-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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19
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Provost K, Shue SY, Forcellati M, Smith BT. The Genomic Landscapes of Desert Birds Form over Multiple Time Scales. Mol Biol Evol 2022; 39:6711078. [PMID: 36134537 PMCID: PMC9577548 DOI: 10.1093/molbev/msac200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Spatial models show that genetic differentiation between populations can be explained by factors ranging from geographic distance to environmental resistance across the landscape. However, genomes exhibit a landscape of differentiation, indicating that multiple processes may mediate divergence in different portions of the genome. We tested this idea by comparing alternative geographic predctors of differentiation in ten bird species that co-occur in Sonoran and Chihuahuan Deserts of North America. Using population-level genomic data, we described the genomic landscapes across species and modeled conditions that represented historical and contemporary mechanisms. The characteristics of genomic landscapes differed across species, influenced by varying levels of population structuring and admixture between deserts, and the best-fit models contrasted between the whole genome and partitions along the genome. Both historical and contemporary mechanisms were important in explaining genetic distance, but particularly past and current environments, suggesting that genomic evolution was modulated by climate and habitat There were also different best-ftit models across genomic partitions of the data, indicating that these regions capture different evolutionary histories. These results show that the genomic landscape of differentiation can be associated with alternative geographic factors operating on different portions of the genome, which reflect how heterogeneous patterns of genetic differentiation can evolve across species and genomes.
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Affiliation(s)
| | - Stephanie Yun Shue
- Bergen County Academies, Hackensack, NJ, USA,Biological Sciences, University of California Berkeley, Berkeley, CA, USA
| | - Meghan Forcellati
- Bergen County Academies, Hackensack, NJ, USA,Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
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20
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Alvarado AH, Bossu CM, Harrigan RJ, Bay RA, Nelson ARP, Smith TB, Ruegg KC. Genotype‐environment associations across spatial scales reveal the importance of putative adaptive genetic variation in divergence. Evol Appl 2022; 15:1390-1407. [PMID: 36187181 PMCID: PMC9488676 DOI: 10.1111/eva.13444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/04/2022] [Indexed: 12/01/2022] Open
Abstract
Identifying areas of high evolutionary potential is a judicious strategy for developing conservation priorities in the face of environmental change. For wide‐ranging species occupying heterogeneous environments, the evolutionary forces that shape distinct populations can vary spatially. Here, we investigate patterns of genomic variation and genotype–environment associations in the hermit thrush (Catharus guttatus), a North American songbird, at broad (across the breeding range) and narrow spatial scales (at a hybrid zone). We begin by building a genoscape or map of genetic variation across the breeding range and find five distinct genetic clusters within the species, with the greatest variation occurring in the western portion of the range. Genotype–environment association analyses indicate higher allelic turnover in the west than in the east, with measures of temperature surfacing as key predictors of putative adaptive genomic variation rangewide. Since broad patterns detected across a species' range represent the aggregate of many locally adapted populations, we investigate whether our broadscale analysis is consistent with a finer scale analysis. We find that top rangewide temperature‐associated loci vary in their clinal patterns (e.g., steep clines vs. fixed allele frequencies) across a hybrid zone in British Columbia, suggesting that the environmental predictors and the associated candidate loci identified in the rangewide analysis are of variable importance in this particular region. However, two candidate loci exhibit strong concordance with the temperature gradient in British Columbia, suggesting a potential role for temperature‐related barriers to gene flow and/or temperature‐driven ecological selection in maintaining putative local adaptation. This study demonstrates how patterns identified at the broad (macrogeographic) scale can be validated by investigating genotype–environment correlations at the local (microgeographic) scale. Furthermore, our results highlight the importance of considering the spatial distribution of putative adaptive variation when assessing population‐level sensitivity to climate change and other stressors.
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Affiliation(s)
- Allison H. Alvarado
- Biology Department California State University Channel Islands Camarillo CA USA
| | - Christen M. Bossu
- Center for Tropical Research, Institute of Environment and Sustainability University of California Los Angeles CA USA
- Department of Biology Colorado State University Fort Collins CO USA
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of Environment and Sustainability University of California Los Angeles CA USA
| | - Rachael A. Bay
- Department of Evolution and Ecology University of California Davis CA USA
| | | | - Thomas B. Smith
- Center for Tropical Research, Institute of Environment and Sustainability University of California Los Angeles CA USA
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | - Kristen C. Ruegg
- Department of Biology Colorado State University Fort Collins CO USA
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21
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Young MK, Smith R, Pilgrim KL, Isaak DJ, McKelvey KS, Parkes S, Egge J, Schwartz MK. A Molecular Taxonomy of Cottus in western North America. WEST N AM NATURALIST 2022. [DOI: 10.3398/064.082.0208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Michael K. Young
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Rebecca Smith
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Kristine L. Pilgrim
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Daniel J. Isaak
- USDA Forest Service, Rocky Mountain Research Station, 322 East Front Street Suite 401, Boise, ID 83702
| | - Kevin S. McKelvey
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Sharon Parkes
- USDA Forest Service, Rocky Mountain Research Station, 322 East Front Street Suite 401, Boise, ID 83702
| | - Jacob Egge
- Department of Biology, Pacific Lutheran University, Tacoma, WA 98447
| | - Michael K. Schwartz
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
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22
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Wang L, Li Y, Noshiro S, Suzuki M, Arai T, Kobayashi K, Xie L, Zhang M, He N, Fang Y, Zhang F. Stepped Geomorphology Shaped the Phylogeographic Structure of a Widespread Tree Species ( Toxicodendron vernicifluum, Anacardiaceae) in East Asia. FRONTIERS IN PLANT SCIENCE 2022; 13:920054. [PMID: 35720535 PMCID: PMC9201781 DOI: 10.3389/fpls.2022.920054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Species' phylogeographic patterns reflect the interplay between landscape features, climatic forces, and evolutionary processes. Here, we used two chloroplast DNA (cpDNA) markers (trnL and trnL-F) to explore the role of stepped geomorphology in shaping the phylogeographic structure of Toxicodendron vernicifluum, an economically important tree species widely distributed in East Asia. The range-wide pattern of sequence variation was analyzed based on a dataset including 357 individuals from China, together with published sequences of 92 individuals mainly from Japan and South Korea. We identified five chloroplast haplotypes based on seven substitutions across the 717-bp alignment. A clear east-west phylogeographic break was recovered according to the stepped landforms of mainland China. The wild trees of the western clade were found to be geographically restricted to the "middle step", which is characterized by high mountains and plateaus, while those of the eastern clade were confined to the "low step", which is mainly made up of hills and plains. The two major clades were estimated to have diverged during the Early Pleistocene, suggesting that the cool glacial climate may have caused the ancestral population to retreat to at least two glacial refugia, leading to allopatric divergence in response to long-term geographic isolation. Migration vector analyses based on the outputs of ecological niche models (ENMs) supported a gradual range expansion since the Last Interglacial. Mountain ranges in western China and the East China Sea land bridge were inferred to be dispersal corridors in the western and eastern distributions of T. vernicifluum, respectively. Overall, our study provides solid evidence for the role of stepped geomorphology in shaping the phylogeographic patterns of T. vernicifluum. The resulting east-west genetic discontinuities could persist for a long time, and could occur at a much larger scale than previously reported, extending from subtropical (e.g., the Xuefeng Mountain) to warm-temperate China (e.g., the Taihang Mountain).
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Affiliation(s)
- Lu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Shuichi Noshiro
- Center for Obsidian and Lithic Studies, Meiji University, Tokyo, Japan
| | | | | | | | - Lei Xie
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Mingyue Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Na He
- Xi’an Research Institute of Chinese Lacquer, All China Federation of Supply and Marketing Cooperatives, Xi’an, China
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Feilong Zhang
- Xi’an Research Institute of Chinese Lacquer, All China Federation of Supply and Marketing Cooperatives, Xi’an, China
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Kadej M, Zając K, Gutowski JM, Jaworski T, Plewa R, Ruta R, Sikora K, Smolis A, Magoga G, Montagna M, Eckelt A, Birkemoe T, Bonacci T, Brandmayr P, Heibl C, Cizek L, Algis Davenis S, Fuchs L, Horak J, Kapla A, Kulijer D, Merkl O, Müller J, Noordijk J, Saluk S, Sverdrup-Thygeson A, Vrezec A, Kajtoch Ł. Disentangling phylogenetic relations and biogeographic history within the Cucujus haematodes species group (Coleoptera: Cucujidae). Mol Phylogenet Evol 2022; 173:107527. [DOI: 10.1016/j.ympev.2022.107527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022]
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24
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Mosher CM, Johnson CJ, Murray BW. Reduced genetic diversity associated with the northern expansion of an amphibian species with high habitat specialization,
Ascaphus truei
, resolved using two types of genetic markers. Ecol Evol 2022; 12:e8716. [PMID: 35342604 PMCID: PMC8931771 DOI: 10.1002/ece3.8716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Reconstruction of historical relationships between geographic regions within a species’ range can indicate dispersal patterns and help predict future responses to shifts in climate. Ascaphus truei (coastal tailed frog) is an indicator species of the health of forests and perennial streams in the Coastal and Cascade Mountains of the Pacific Northwest of North America. We used two genetic techniques—microsatellite and genotype‐by‐sequencing (GBS)—to compare the within‐region genetic diversity of populations near the northern extent of the species’ range (British Columbia, Canada) to two geographic regions in British Columbia and two in Washington, USA, moving toward the core of the range. Allelic richness and heterozygosity declined substantially as latitude increased. The northernmost region had the lowest mean expected heterozygosities for both techniques (microsatellite, M = 0.20, SE = 0.080; GBS, M = 0.025, SE = 0.0010) and the southernmost region had the highest (microsatellite, M = 0.88, SE = 0.054; GBS, M = 0.20, SE = 0.0029). The northernmost regions (NC and MC) clustered together in population structure models for both genetic techniques. Our discovery of reduced diversity may have important conservation and management implications for population connectivity and the response of A. truei to climate change.
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Affiliation(s)
- Cherie M. Mosher
- University of Northern British Columbia Prince George British Columbia Canada
| | - Chris J. Johnson
- University of Northern British Columbia Prince George British Columbia Canada
| | - Brent W. Murray
- University of Northern British Columbia Prince George British Columbia Canada
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25
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Manthey JD, Bourgeois Y, Meheretu Y, Boissinot S. Varied diversification patterns and distinct demographic trajectories in Ethiopian montane forest bird (Aves: Passeriformes) populations separated by the Great Rift Valley. Mol Ecol 2022; 31:2664-2678. [PMID: 35239243 DOI: 10.1111/mec.16417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 11/30/2022]
Abstract
Taxon-specific characteristics and extrinsic climatic and geological forces may both shape population differentiation and speciation. In geographically and taxonomically focused investigations, differentiation may occur synchronously as species respond to the same external conditions. Conversely, when evolution is investigated in taxa with largely varying traits, population differentiation and speciation is complex and shaped by interactions of Earth's template and species-specific traits. As such, it is important to characterize evolutionary histories broadly across the tree of life, especially in geographic regions that are exceptionally diverse and under pressures from human activities such as in biodiversity hotspots. Here, using whole-genome sequencing data, we characterize genomic variation in populations of six Ethiopian Highlands forest bird species separated by a lowland biogeographic barrier, the Great Rift Valley (GRV). In all six species, populations on either side of the GRV exhibited significant but varying levels of genetic differentiation. Species' dispersal ability was negatively correlated with levels of population differentiation. Isolation with migration models indicated varied patterns of population differentiation and connectivity among populations of the focal species. We found that demographic histories-estimated for each individual-varied by both species and population but were consistent between individuals of the same species and sampling region. We found that genomic diversity varied by half an order of magnitude across species, and that this variation could largely be explained by the harmonic mean of effective population size over the past 200,000 years. Overall, we found that even in highly dispersive species like birds, the GRV acts as a substantial biogeographic barrier.
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26
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Ikeda H. Decades-long phylogeographic issues: complex historical processes and ecological factors on genetic structure of alpine plants in the Japanese Archipelago. JOURNAL OF PLANT RESEARCH 2022; 135:191-201. [PMID: 35166981 PMCID: PMC8894158 DOI: 10.1007/s10265-022-01377-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Mountain regions are important places for biodiversity, where organisms could persist throughout prolonged periods and accumulate genetic divergence as well as promote speciation. Roles of mountains for biodiversity have been exclusively discussed in regions that have specifically diverse species or covered with ice-sheets during the Pleistocene glacial periods, whereas the importance of mountainous regions in East Asia has been less disputed. High mountains in the Japanese Archipelago, located at the eastern edge of the Eurasia continent, have one of southernmost populations of alpine and arctic-alpine plants that are also distributed in the northern Pacific and/or the circumarctic regions. Phylogeographic studies on the Japanese alpine plants have excluded their possible ephemeral occurrence during the current warm period, and rather, suggest persistence of alpine plants throughout several cycles of climate changes in the Pleistocene on high mountains in central Honshu, the main island of the Japanese Archipelago. In this review, I look through decade long phylogeographic studies and show complicated patterns of range dynamics of Japanese alpine plants. In addition, I note recent findings of genetic relationships of Japanese populations of alpine and/or arctic-alpine plants with those in northern regions and their possible ecological divergence in the Japanese Archipelago. Taken together, I provide several issues for understanding historical processes that established distribution of alpine plants following climate changes as well as their diversification and propose importance of Japanese populations of alpine plants on biodiversity in alpine communities across broader range, especially in the northern Pacific region.
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Affiliation(s)
- Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
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27
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Prado JR, Rubi TL, Baumgartner J, Hoffman SMG, Dantzer B, Lacey Knowles L. Postglacial colonization in the Great Lakes Region by the white-footed mouse (Peromyscus leucopus): conflicts between genomic and field data. J Mammal 2022. [DOI: 10.1093/jmammal/gyab158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
For regions that were covered by ice during the Pleistocene glaciations, species must have emigrated from unglaciated regions. However, it can be difficult to discern when and from what ancestral source populations such expansions took place, especially since warming climates introduce the possibility of very recent expansions. For example, in the Great Lakes region, pronounced climatic change includes past glaciations as well as recent, rapid warming. Here we evaluate different expansion hypotheses with a genomic study of the white-footed mouse (Peromyscus leucopus noveboracensis), which is one of the most common mammals throughout the Great Lakes region. Ecological surveys coupled with historical museum records suggest a recent range expansion of P. leucopus associated with the warming climate over the last decades. These detailed records have yet to be complemented by genomic data that provide the requisite resolution for detecting recent expansion, although some mitochondrial DNA (mtDNA) sequences have suggested possible hypotheses about the geography of expansion. With more than 7,000 loci generated using RADseq, we evaluate support for multiple hypotheses of a geographic expansion in the Upper Peninsula of Michigan (UP). Analysis of a single random single-nucleotide polymorphism per locus revealed a fine-scale population structure separating the Lower Peninsula (LP) population from all other populations in the UP. We also detected a genetic structure that reflects an evolutionary history of postglacial colonization from two different origins into the UP, one coming from the LP and one coming from the west. Instead of supporting a climate-driven range expansion, as suggested by field surveys, our results support more ancient postglacial colonization of the UP from two different ancestral sources. With these results, we offer new insights about P. leucopus geographic expansion history, as well as a more general phylogeographic framework for testing range shifts in the Great Lakes region.
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Affiliation(s)
- Joyce R Prado
- Departamento de Ciências Biológicas, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Tricia L Rubi
- Department of Psychology, The University of Michigan, Ann Arbor, MI, USA
| | | | | | - Ben Dantzer
- Department of Psychology, The University of Michigan, Ann Arbor, MI, USA
- Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, MI, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, MI, USA
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28
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Liang YY, Shi Y, Yuan S, Zhou BF, Chen XY, An QQ, Ingvarsson PK, Plomion C, Wang B. Linked selection shapes the landscape of genomic variation in three oak species. THE NEW PHYTOLOGIST 2022; 233:555-568. [PMID: 34637540 DOI: 10.1111/nph.17793] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Natural selection shapes genome-wide patterns of diversity within species and divergence between species. However, quantifying the efficacy of selection and elucidating the relative importance of different types of selection in shaping genomic variation remain challenging. We sequenced whole genomes of 101 individuals of three closely related oak species to track the divergence history, and to dissect the impacts of selective sweeps and background selection on patterns of genomic variation. We estimated that the three species diverged around the late Neogene and experienced a bottleneck during the Pleistocene. We detected genomic regions with elevated relative differentiation ('FST -islands'). Population genetic inferences from the site frequency spectrum and ancestral recombination graph indicated that FST -islands were formed by selective sweeps. We also found extensive positive selection; the fixation of adaptive mutations and reduction neutral diversity around substitutions generated a signature of selective sweeps. Prevalent negative selection and background selection have reduced genetic diversity in both genic and intergenic regions, and contributed substantially to the baseline variation in genetic diversity. Our results demonstrate the importance of linked selection in shaping genomic variation, and illustrate how the extent and strength of different selection models vary across the genome.
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Affiliation(s)
- Yi-Ye Liang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Shuai Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Biao-Feng Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xue-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Qing-Qing An
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | | | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
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30
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Wu ETY, Liu Y, Jennings L, Dong S, Davies TJ. Detecting the phylogenetic signal of glacial refugia in a bryodiversity hotspot outside the tropics. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ernest T. Y. Wu
- Department of Forest and Conservation Sciences Faculty of Forestry University of British Columbia Vancouver British Columbia Canada
- Department of Plant Sciences University of Oxford Oxford UK
| | - Yang Liu
- Fairy Lake Botanical Garden Chinese Academy of Sciences Shenzhen Guangdong China
| | - Linda Jennings
- Department of Botany Faculty of Sciences University of British Columbia Vancouver British Columbia Canada
- Herbarium, Beaty Biodiversity Museum University of British Columbia Vancouver British Columbia Canada
| | - Shanshan Dong
- Fairy Lake Botanical Garden Chinese Academy of Sciences Shenzhen Guangdong China
| | - T. Jonathan Davies
- Department of Forest and Conservation Sciences Faculty of Forestry University of British Columbia Vancouver British Columbia Canada
- Department of Botany Faculty of Sciences University of British Columbia Vancouver British Columbia Canada
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31
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Allen JL, McMullin RT, Wiersma YF, Scheidegger C. Population genetics and biogeography of the lungwort lichen in North America support distinct Eastern and Western gene pools. AMERICAN JOURNAL OF BOTANY 2021; 108:2416-2424. [PMID: 34634140 DOI: 10.1002/ajb2.1774] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Populations of species with large spatial distributions are shaped by complex forces that differ throughout their ranges. To maintain the genetic diversity of species, genepool-based subsets of widespread species must be considered in conservation assessments. METHODS The population genetics of the lichenized fungus Lobaria pulmonaria and its algal partner, Symbiochloris reticulata, were investigated using microsatellite markers to determine population structure, genetic diversity, and degree of congruency in eastern and western North America. Data loggers measuring temperature and humidity were deployed at selected populations in eastern North America to test for climatic adaptation. To better understand the role Pleistocene glaciations played in shaping population patterns, a North American, range-wide species distribution model was constructed and hindcast to 22,000 years before present and at 500-year time slices from then to the present. RESULTS The presence of two gene pools with minimal admixture was supported, one in the U.S. Pacific Northwest and one in eastern North America. Western populations were significantly more genetically diverse than eastern populations. There was no evidence for climatic adaptation among eastern populations, though there was evidence for range-wide adaptation to evapotranspiration rates. Hindcast distribution models suggest that observed genetic diversity may be due to a drastic Pleistocene range restriction in eastern North America, whereas a substantial coastal refugial area is inferred in the west. CONCLUSIONS Taken together the results show different, complex population histories of L. pulmonaria in eastern and western North America, and suggest that conservation planning for each gene pool should be considered separately.
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Affiliation(s)
- Jessica L Allen
- Eastern Washington University, Biology Department, Cheney, Washington, 99004, USA
- Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Department of Biodiversity and Conservation Biology, Birmensdorf, 8903, Switzerland
| | - R Troy McMullin
- Canadian Museum of Nature, Research and Collections, Ottawa, Ontario, K1P 6P4, Canada
| | - Yolanda F Wiersma
- Memorial University of Newfoundland and Labrador, Department of Biology, St. John's, Newfoundland and Labrador, A1C 5S7, Canada
| | - Christoph Scheidegger
- Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Department of Biodiversity and Conservation Biology, Birmensdorf, 8903, Switzerland
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32
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Oleinik AG, Bondar EI, Kukhlevsky AD, Skurikhina LA, Kovpak NE. Introgressive hybridization between two phylogenetic lineages of charrs (
Salvelinus
: Salmonidae) in northeastern Asia. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alla G. Oleinik
- A.V. Zhirmunsky National Scientific Center of Marine Biology Far Eastern Branch Russian Academy of Sciences Vladivostok Russia
| | - Evgeniia I. Bondar
- A.V. Zhirmunsky National Scientific Center of Marine Biology Far Eastern Branch Russian Academy of Sciences Vladivostok Russia
| | - Andrey D. Kukhlevsky
- A.V. Zhirmunsky National Scientific Center of Marine Biology Far Eastern Branch Russian Academy of Sciences Vladivostok Russia
| | - Lubov A. Skurikhina
- A.V. Zhirmunsky National Scientific Center of Marine Biology Far Eastern Branch Russian Academy of Sciences Vladivostok Russia
| | - Natalia E. Kovpak
- A.V. Zhirmunsky National Scientific Center of Marine Biology Far Eastern Branch Russian Academy of Sciences Vladivostok Russia
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33
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Taylor RS, Manseau M, Klütsch CFC, Polfus JL, Steedman A, Hervieux D, Kelly A, Larter NC, Gamberg M, Schwantje H, Wilson PJ. Population dynamics of caribou shaped by glacial cycles before the last glacial maximum. Mol Ecol 2021; 30:6121-6143. [PMID: 34482596 PMCID: PMC9293238 DOI: 10.1111/mec.16166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/04/2022]
Abstract
Pleistocene glacial cycles influenced the diversification of high‐latitude wildlife species through recurrent periods of range contraction, isolation, divergence, and expansion from refugia and subsequent admixture of refugial populations. We investigate population size changes and the introgressive history of caribou (Rangifer tarandus) in western Canada using 33 whole genome sequences coupled with larger‐scale mitochondrial data. We found that a major population expansion of caribou occurred starting around 110,000 years ago (kya), the start of the last glacial period. Additionally, we found effective population sizes of some caribou reaching ~700,000 to 1,000,000 individuals, one of the highest recorded historical effective population sizes for any mammal species thus far. Mitochondrial analyses dated introgression events prior to the LGM dating to 20–30 kya and even more ancient at 60 kya, coinciding with colder periods with extensive ice coverage, further demonstrating the importance of glacial cycles and events prior to the LGM in shaping demographic history. Reconstructing the origins and differential introgressive history has implications for predictions on species responses under climate change. Our results have implications for other whole genome analyses using pairwise sequentially Markovian coalescent (PSMC) analyses, as well as highlighting the need to investigate pre‐LGM demographic patterns to fully reconstruct the origin of species diversity, especially for high‐latitude species.
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Affiliation(s)
- Rebecca S Taylor
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Micheline Manseau
- Biology Department, Trent University, Peterborough, Ontario, Canada.,Landscape Science and Technology, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | | | - Jean L Polfus
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Audrey Steedman
- Parks Canada, Government of Canada, Winnipeg, Manitoba, Canada
| | - Dave Hervieux
- Department of Environment and Parks, Government of Alberta, Grande Prairie, Alberta, Canada
| | - Allicia Kelly
- Department of Environment and Natural Resources, Government of the Northwest Territories, Fort Smith, Northwest Territories, Canada
| | - Nicholas C Larter
- Department of Environment and Natural Resources, Government of the Northwest Territories, Fort Simpson, Northwest Territories, Canada
| | | | - Helen Schwantje
- BC Ministry of Forest, Lands, Natural Resource Operations, and Rural Development, Nanaimo, British Columbia, Canada
| | - Paul J Wilson
- Biology Department, Trent University, Peterborough, Ontario, Canada
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34
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McDonough MM, Ferguson AW, Dowler RC, Gompper ME, Maldonado JE. Phylogenomic systematics of the spotted skunks (Carnivora, Mephitidae, Spilogale): Additional species diversity and Pleistocene climate change as a major driver of diversification. Mol Phylogenet Evol 2021; 167:107266. [PMID: 34302947 DOI: 10.1016/j.ympev.2021.107266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 05/28/2021] [Accepted: 07/15/2021] [Indexed: 10/20/2022]
Abstract
Four species of spotted skunks (Carnivora, Mephitidae, Spilogale) are currently recognized: Spilogale angustifrons, S. gracilis, S. putorius, and S. pygmaea. Understanding species boundaries within this group is critical for effective conservation given that regional populations or subspecies (e.g., S. p. interrupta) have experienced significant population declines. Further, there may be currently unrecognized diversity within this genus as some taxa (e.g., S. angustifrons) and geographic regions (e.g., Central America) never have been assessed using DNA sequence data. We analyzed species limits and diversification patterns in spotted skunks using multilocus nuclear (ultraconserved elements) and mitochondrial (whole mitogenomes and single gene analysis) data sets from broad geographic sampling representing all currently recognized species and subspecies. We found a high degree of genetic divergence among Spilogale that reflects seven distinct species and eight unique mitochondrial lineages. Initial divergence between S. pygmaea and all other Spilogale occurred in the Early Pliocene (∼ 5.0 million years ago). Subsequent diversification of the remaining Spilogale into an "eastern" and a "western" lineage occurred during the Early Pleistocene (∼1.5 million years ago). These two lineages experienced temporally coincident patterns of diversification at ∼0.66 and ∼0.35 million years ago into two and ultimately three distinct evolutionary units, respectively. Diversification was confined almost entirely within the Pleistocene during a timeframe characterized by alternating glacial-interglacial cycles, with the origin of this diversity occurring in northeastern Mexico and the southwestern United States of America. Mitochondrial-nuclear discordance was recovered across three lineages in geographic regions consistent with secondary contact, including a distinct mitochondrial lineage confined to the Sonoran Desert. Our results have direct consequences for conservation of threatened populations, or species, as well as for our understanding of the evolution of delayed implantation in this enigmatic group of small carnivores.
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Affiliation(s)
- Molly M McDonough
- Chicago State University Department of Biological Sciences 9501 S. King Drive, WSC 290 Chicago, IL 60628-1598.
| | - Adam W Ferguson
- Gantz Family Collection Center Field Museum 1400 South Lake Shore Drive Chicago, IL 60605
| | - Robert C Dowler
- Department of Biology Angelo State University ASU Station 10890 San Angelo, TX 76909
| | - Matthew E Gompper
- Department of Fish, Wildlife, and Conservation Ecology New Mexico State University Las Cruces, NM 88003
| | - Jesús E Maldonado
- Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park PO Box 37012 MRC 5503 Washington, DC 20013
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35
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Wang S, Ore MJ, Mikkelsen EK, Lee-Yaw J, Toews DPL, Rohwer S, Irwin D. Signatures of mitonuclear coevolution in a warbler species complex. Nat Commun 2021; 12:4279. [PMID: 34257313 PMCID: PMC8277850 DOI: 10.1038/s41467-021-24586-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
Divergent mitonuclear coadaptation could facilitate speciation. We investigate this possibility in two hybridizing species of warblers, Setophaga occidentalis and S. townsendi, in western North America. Inland S. townsendi harbor distinct mitochondrial DNA haplotypes from those of S. occidentalis. These populations also differ in several nuclear DNA regions. Coastal S. townsendi demonstrate mixed mitonuclear ancestry from S. occidentalis and inland S. townsendi. Of the few highly-differentiated chromosomal regions between inland S. townsendi and S. occidentalis, a 1.2 Mb gene block on chromosome 5 is also differentiated between coastal and inland S. townsendi. Genes in this block are associated with fatty acid oxidation and energy-related signaling transduction, thus linked to mitochondrial functions. Genetic variation within this candidate gene block covaries with mitochondrial DNA and shows signatures of divergent selection. Spatial variation in mitonuclear ancestries is correlated with climatic conditions. Together, these observations suggest divergent mitonuclear coadaptation underpins cryptic differentiation in this species complex.
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Affiliation(s)
- Silu Wang
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd, University of British Columbia, Vancouver, BC, Canada.
- Department of Integrative Biology, University of California, Berkeley, CA, USA.
| | - Madelyn J Ore
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd, University of British Columbia, Vancouver, BC, Canada
- Cornell Lab of Ornithology, Ithaca, NY, USA
| | - Else K Mikkelsen
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd, University of British Columbia, Vancouver, BC, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Julie Lee-Yaw
- Department of Botany, 3200-6270 University Blvd, University of British Columbia, Vancouver, BC, Canada
- Biological Sciences, 4401 University Drive, University of Lethbridge, Lethbridge, AB, Canada
| | - David P L Toews
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sievert Rohwer
- Department of Biology and Burke Museum, Box 353010, University of Washington, Seattle, WA, USA
| | - Darren Irwin
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd, University of British Columbia, Vancouver, BC, Canada
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36
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Stone BW, Wolfe AD. Phylogeographic analysis of shrubby beardtongues reveals range expansions during the Last Glacial Maximum and implicates the Klamath Mountains as a hotspot for hybridization. Mol Ecol 2021; 30:3826-3839. [PMID: 34013537 DOI: 10.1111/mec.15992] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 12/26/2022]
Abstract
Quaternary glacial cycles often altered species' geographic distributions, which in turn altered the geographic structure of species' genetic diversity. In many cases, glacial expansion forced species in temperate climates to contract their ranges and reside in small pockets of suitable habitat (refugia), where they were likely to interact closely with other species, setting the stage for potential gene exchange. These introgression events, in turn, would have degraded species boundaries, making the inference of phylogenetic relationships challenging. Using high-throughput sequence data, we employed a combination of species distribution models and hybridization tests to assess the effect of glaciation on the geographic distributions, phylogenetic relationships, and patterns of gene flow of five species of Penstemon subgenus Dasanthera, long-lived shrubby angiosperms distributed throughout the Pacific Northwest of North America. Surprisingly, we found that rather than reducing their ranges to small refugia, most Penstemon subgenus Dasanthera species experienced increased suitable habitat during the Last Glacial Maximum relative to the present day. We also found substantial evidence for gene exchange between species, with the bulk of introgression events occurring in or near the Klamath Mountains of southwestern Oregon and northwestern California. Subsequently, our phylogenetic inference reveals blurred taxonomic boundaries in the Klamath Mountains, where introgression is most prevalent. Our results question the classical paradigm of temperate species' responses to glaciation and highlight the importance of contextualizing phylogenetic inference with species' histories of introgression.
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Affiliation(s)
- Benjamin W Stone
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Andrea D Wolfe
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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37
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Schwartz MK, Walters AD, Pilgrim KL, Moriarty KM, Slauson KM, Zielinski WJ, Aubry KB, Sacks BN, Zarn KE, Quinn CB, Young MK. Pliocene-Early Pleistocene Geological Events Structure Pacific Martens (Martes caurina). J Hered 2021; 111:169-181. [PMID: 32161974 DOI: 10.1093/jhered/esaa005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 02/10/2020] [Indexed: 11/15/2022] Open
Abstract
The complex topography, climate, and geological history of Western North America have shaped contemporary patterns of biodiversity and species distributions in the region. Pacific martens (Martes caurina) are distributed along the northern Pacific Coast of North America with disjunct populations found throughout the Northwestern Forested Mountains and Marine West Coast Forest ecoregions of the West Coast. Martes in this region have been classified into subspecies; however, the subspecific designation has been extensively debated. In this study, we use genomic data to delineate conservation units of Pacific marten in the Sierra-Cascade-Coastal montane belt in the western United States. We analyzed the mitochondrial genome for 94 individuals to evaluate the spatial distribution and divergence times of major lineages. We further genotyped 401 individuals at 13 microsatellite loci to investigate major patterns of population structure. Both nuclear and mitochondrial DNA suggest substantial genetic substructure concordant with historical subspecies designations. Our results revealed that the region contains 2 distinct mitochondrial lineages: a Cascades/Sierra lineage that diverged from the Cascades/coastal lineage 2.23 (1.48-3.14 mya), consistent with orogeny of the Cascade Mountain chain. Interestingly, Pacific Martes share phylogeographic patterns similar with other sympatric taxa, suggesting that the complex geological history has shaped the biota of this region. The information is critical for conservation and management efforts, and further investigation of adaptive diversity is warranted following appropriate revision of conservation management designations.
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Affiliation(s)
- Michael K Schwartz
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Ashley D Walters
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Kristine L Pilgrim
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Katie M Moriarty
- National Council for Air and Stream Improvement, Inc., Corvallis, OR
| | - Keith M Slauson
- USDA Forest Service, Pacific Southwest Research Station, Arcata, CA
| | - William J Zielinski
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT.,USDA Forest Service, Pacific Southwest Research Station, Arcata, CA
| | - Keith B Aubry
- USDA Forest Service, Pacific Northwest Research Station, Olympia, WA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Katherine E Zarn
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Michael K Young
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
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38
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Krejsa DM, Talbot SL, Sage GK, Sonsthagen SA, Jung TS, Magoun AJ, Cook JA. Dynamic landscapes in northwestern North America structured populations of wolverines (Gulo gulo). J Mammal 2021. [DOI: 10.1093/jmammal/gyab045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Cyclic climatic and glacial fluctuations of the Late Quaternary produced a dynamic biogeographic history for high latitudes. To refine our understanding of this history in northwestern North America, we explored geographic structure in a wide-ranging carnivore, the wolverine (Gulo gulo). We examined genetic variation in populations across mainland Alaska, coastal Southeast Alaska, and mainland western Canada using nuclear microsatellite genotypes and sequence data from the mitochondrial DNA (mtDNA) control region and Cytochrome b (Cytb) gene. Data from maternally inherited mtDNA reflect stable populations in Northwest Alaska, suggesting the region harbored wolverine populations since at least the Last Glacial Maximum (LGM; 21 Kya), consistent with their persistence in the fossil record of Beringia. Populations in Southeast Alaska are characterized by minimal divergence, with no genetic signature of long-term refugial persistence (consistent with the lack of pre-Holocene fossil records there). The Kenai Peninsula population exhibits mixed signatures depending on marker type: mtDNA data indicate stability (i.e., historical persistence) and include a private haplotype, whereas biparentally inherited microsatellites exhibit relatively low variation and a lack of private alleles consistent with a more recent Holocene colonization of the peninsula. Our genetic work is largely consistent with the early 20th century taxonomic hypothesis that wolverines on the Kenai Peninsula belong to a distinct subspecies. Our finding of significant genetic differentiation of wolverines inhabiting the Kenai Peninsula, coupled with the peninsula’s burgeoning human population and the wolverine’s known sensitivity to anthropogenic impacts, provides valuable foundational data that can be used to inform conservation and management prescriptions for wolverines inhabiting these landscapes.
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Affiliation(s)
- Dianna M Krejsa
- Department of Biology and Angelo State Natural History Collections, Angelo State University, ASU Station 10890, San Angelo, TX 76909-0890, USA
| | - Sandra L Talbot
- U.S. Geological Survey, Alaska Science Center, Anchorage, AK 99508, USA
| | - George K Sage
- U.S. Geological Survey, Alaska Science Center, Anchorage, AK 99508, USA
| | | | - Thomas S Jung
- Department of Environment, Government of Yukon, Whitehorse, YT, Y1A 2C6, Canada
| | - Audrey J Magoun
- Wildlife Research and Management, 3680 Non Road, Fairbanks, AK 99709, USA
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
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39
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Bontrager M, Usui T, Lee-Yaw JA, Anstett DN, Branch HA, Hargreaves AL, Muir CD, Angert AL. Adaptation across geographic ranges is consistent with strong selection in marginal climates and legacies of range expansion. Evolution 2021; 75:1316-1333. [PMID: 33885152 DOI: 10.1111/evo.14231] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/14/2021] [Indexed: 12/27/2022]
Abstract
Every species experiences limits to its geographic distribution. Some evolutionary models predict that populations at range edges are less well adapted to their local environments due to drift, expansion load, or swamping gene flow from the range interior. Alternatively, populations near range edges might be uniquely adapted to marginal environments. In this study, we use a database of transplant studies that quantify performance at broad geographic scales to test how local adaptation, site quality, and population quality change from spatial and climatic range centers toward edges. We find that populations from poleward edges perform relatively poorly, both on average across all sites (15% lower population quality) and when compared to other populations at home (31% relative fitness disadvantage), consistent with these populations harboring high genetic load. Populations from equatorial edges also perform poorly on average (18% lower population quality) but, in contrast, outperform foreign populations (16% relative fitness advantage), suggesting that populations from equatorial edges have strongly adapted to unique environments. Finally, we find that populations from sites that are thermally extreme relative to the species' niche demonstrate strong local adaptation, regardless of their geographic position. Our findings indicate that both nonadaptive processes and adaptive evolution contribute to variation in adaptation across species' ranges.
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Affiliation(s)
- Megan Bontrager
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Current Address: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada
| | - Takuji Usui
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Julie A Lee-Yaw
- Department of Biological Sciences, University of Lethbridge, Lethbridge, T1K 3M4, Canada
| | - Daniel N Anstett
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Haley A Branch
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | | | - Christopher D Muir
- School of Life Sciences, University of Hawaii, Honolulu, Hawaii, 96822, United States
| | - Amy L Angert
- Departments of Botany and Zoology and the Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
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40
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Jeon JY, Jung JH, Suk HY, Lee H, Min MS. The Asian plethodontid salamander preserves historical genetic imprints of recent northern expansion. Sci Rep 2021; 11:9193. [PMID: 33911092 PMCID: PMC8080585 DOI: 10.1038/s41598-021-88238-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/30/2021] [Indexed: 02/02/2023] Open
Abstract
The Korean Peninsula, located at the southern tip of Northeast Asia, has never been covered by ice sheets and was a temperate refugium during the Pleistocene. Karsenia koreana, the sole Asian plethodontid salamander species, occurs only on the southern half of the Korean Peninsula and is thought to have found various climatic refugia. Despite its phylogenetic and biogeographic importance, no population-level genetic analysis has been performed on this species. Here we study the population genetic structure of K. koreana using mitochondrial and microsatellite loci to understand the recent historical dispersion process that shaped its current distribution. Overall, the genetic distance between populations correlated well with the spatial distance, and the genetic structure among populations showed signs of a unilateral northward expansion from a southernmost refugium population. Given the distinct genetic structure formed among the populations, the level of historical gene flow among populations appears to have been very low. As the estimated effective population size of K. koreana was also small, these results suggest that the small, restricted populations of K. koreana are extremely vulnerable to environmental changes that may require high levels of genetic diversity to cope with. Thus, special management strategies are needed to preserve these remnant populations.
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Affiliation(s)
- Jong Yoon Jeon
- grid.31501.360000 0004 0470 5905Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, 08826 South Korea
| | - Ji-hwa Jung
- grid.31501.360000 0004 0470 5905Department of Forest Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 South Korea
| | - Ho Young Suk
- grid.413028.c0000 0001 0674 4447Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do 38541 South Korea
| | - Hang Lee
- grid.31501.360000 0004 0470 5905Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, 08826 South Korea
| | - Mi-Sook Min
- grid.31501.360000 0004 0470 5905Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, 08826 South Korea
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41
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Rankin AM, Anderson FE, Clutts SA, Espíndola A, Carstens BC, Lucid M, Sullivan J. Comparative phylogeography of two Northern Rocky Mountain endemics: the widespread Anguispira kochi occidentalis and the narrow-range Anguispira nimapuna (Gastropoda: Discidae). Biol J Linn Soc Lond 2021; 133:817-834. [PMID: 34220190 DOI: 10.1093/biolinnean/blab030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/08/2021] [Accepted: 02/12/2021] [Indexed: 11/14/2022]
Abstract
The Northern Rocky Mountain ecosystem supports rich biological diversity with many endemic and rare species. Extant endemics display two biogeographic patterns: widespread species with fragmented populations, and narrow-range endemics. These distributions are shown by the congeneric snails Anguispira kochi occidentalis and Anguispira nimapuna. These two taxa are disjunct from the remaining species of the genus, which achieves its greatest diversity in eastern North America. Given the disjunct nature of A. k. occidentalis and A. nimapuna, we here present a mtDNA phylogeny of the genus that includes both eastern and western species to assess the phylogenetic position of A. k. occidentalis and A. nimapuna. We then reconstruct the demographic history of A. k. occidentalis and A. nimapuna by analysing current patterns of genetic variation and interpreting the results considering the historical biogeography of the region. Both A. k. occidentalis and A. nimapuna represent unique taxa that are genetically and geographically distinct from their congeners. The current distribution and genetic structure of A. k. occidentalis has been shaped by both historical isolation in refugia and more recent northward shifts, whereas A. nimapuna is represented by two populations with shallow divergence in an area of long-term habitat stability.
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Affiliation(s)
- Andrew M Rankin
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Frank E Anderson
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA
| | - Stephanie A Clutts
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA
| | - Anahí Espíndola
- Department of Entomology, University of Maryland, College Park, 4291 Fieldhouse Drive, 3138 Plant Sciences Building, College Park, MD 20742-4454, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | | | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
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42
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Péros JP, Cousins P, Launay A, Cubry P, Walker A, Prado E, Peressotti E, Wiedemann-Merdinoglu S, Laucou V, Merdinoglu D, This P, Boursiquot JM, Doligez A. Genetic diversity and population structure in Vitis species illustrate phylogeographic patterns in eastern North America. Mol Ecol 2021; 30:2333-2348. [PMID: 33710711 DOI: 10.1111/mec.15881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 02/22/2021] [Accepted: 03/02/2021] [Indexed: 12/21/2022]
Abstract
Geographical distribution and diversity of current plant species have been strongly shaped by climatic oscillations during the Quaternary. Analysing the resulting divergence among species and differentiation within species is crucial to understand the evolution of taxa like the Vitis genus, which provides very useful genetic resources for grapevine improvement and might reveal original recolonization patterns due to growth habit and dispersal mode. Here, we studied the genetic structure in natural populations of three species from eastern North America: Vitis aestivalis, V. cinerea and V. riparia using different marker types. Vitis aestivalis and V. cinerea showed higher diversity than V. riparia. The two former species are less differentiated, confirming an earlier divergence of V. riparia. V. aestivalis and V. riparia exhibited different genetic groups on both sides of the Appalachian Mountains that could mirror different recolonization routes from southern refugia. Genetic structure was stronger in V. cinerea, for which two varieties (var. berlandieri and var. cinerea) are morphologically recognized. Our results confirm this distinction and suggest the existence of three other lineages within var. cinerea. These discontinuities appear linked to adaptation of var. berlandieri to dry and limy areas of Texas and partially to the Mississippi River Valley. Rapid range expansions from refugia upon climate warming are also suggested by the low linkage disequilibrium values observed. Furthermore, large variation for downy mildew resistance was observed in the three species. Our findings appeared consistent with the vegetation history of eastern North America.
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Affiliation(s)
- Jean-Pierre Péros
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | | | - Amandine Launay
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Philippe Cubry
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
| | - Andy Walker
- Department of Viticulture and Enology, University of Davis, Davis, CA, USA
| | | | | | | | - Valérie Laucou
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | | | - Patrice This
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Jean-Michel Boursiquot
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Agnès Doligez
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
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43
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Colella JP, Frederick LM, Talbot SL, Cook JA. Extrinsically reinforced hybrid speciation within Holarctic ermine (
Mustela
spp.) produces an insular endemic. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Jocelyn P. Colella
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
- Biodiversity Institute University of Kansas Lawrence KS USA
| | - Lindsey M. Frederick
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
- New Mexico Museum of Natural History and Science Albuquerque NM USA
| | | | - Joseph A. Cook
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
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44
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Bougie TC, Brelsford A, Hedin M. Evolutionary impacts of introgressive hybridization in a rapidly evolving group of jumping spiders (F. Salticidae, Habronattus americanus group). Mol Phylogenet Evol 2021; 161:107165. [PMID: 33798670 DOI: 10.1016/j.ympev.2021.107165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/11/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Introgressive hybridization can be a powerful force impacting patterns of evolution at multiple taxonomic levels. We aimed to understand how introgression has affected speciation and diversification within a species complex of jumping spiders. The Habronattus americanus subgroup is a recently radiating group of jumping spiders, with species now in contact after hypothesized periods of isolation during glaciation cycles of the Pleistocene. Effects of introgression on genomes and morphology were investigated using phylogenomic and clustering methods using RADseq, ultraconserved elements (UCEs), and morphological data. We characterized 14 unique species/morphs using non-metric multidimensional scaling of morphological data, a majority of which were not recovered as monophyletic in our phylogenomic analyses. Morphological clusters and genetic lineages are highly incongruent, such that geographic region was a greater predictor of phylogenetic relatedness and genomic similarity than species or morph identity. STRUCTURE analyses support this pattern, revealing clusters corresponding to larger geographic regions. A history of rapid radiation in combination with frequent introgression seems to have mostly homogenized the genomes of species in this system, while selective forces maintain distinct male morphologies. GEMMA analyses support this idea by identifying SNPs correlated with distinct male morphologies. Overall, we have uncovered a system at odds with a typical bifurcating evolutionary model, instead supporting one where closely related species evolve together connected through multiple introgression events, creating a reticulate evolutionary history.
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Affiliation(s)
- T C Bougie
- Dept. of Biology, San Diego State University, San Diego, CA 92182, United States; Evolution, Ecology, and Organismal Biology Department, University of California Riverside, Riverside, CA 92521, United States.
| | - A Brelsford
- Evolution, Ecology, and Organismal Biology Department, University of California Riverside, Riverside, CA 92521, United States
| | - M Hedin
- Dept. of Biology, San Diego State University, San Diego, CA 92182, United States
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45
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Landscape Genetic Connectivity and Evidence for Recombination in the North American Population of the White-Nose Syndrome Pathogen, Pseudogymnoascus destructans. J Fungi (Basel) 2021; 7:jof7030182. [PMID: 33802538 PMCID: PMC8001231 DOI: 10.3390/jof7030182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 11/28/2022] Open
Abstract
White-Nose Syndrome is an ongoing fungal epizootic caused by epidermal infections of the fungus, Pseudogymnoascus destructans (P. destructans), affecting hibernating bat species in North America. Emerging early in 2006 in New York State, infections of P. destructans have spread to 38 US States and seven Canadian Provinces. Since then, clonal isolates of P. destructans have accumulated genotypic and phenotypic variations in North America. Using microsatellite and single nucleotide polymorphism markers, we investigated the population structure and genetic relationships among P. destructans isolates from diverse regions in North America to understand its pattern of spread, and to test hypotheses about factors that contribute to transmission. We found limited support for genetic isolation of P. destructans populations by geographic distance, and instead identified evidence for gene flow among geographic regions. Interestingly, allelic association tests revealed evidence for recombination in the North American P. destructans population. Our landscape genetic analyses revealed that the population structure of P. destructans in North America was significantly influenced by anthropogenic impacts on the landscape. Our results have important implications for understanding the mechanism(s) of P. destructans spread.
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46
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Waves Out of the Korean Peninsula and Inter- and Intra-Species Replacements in Freshwater Fishes in Japan. Genes (Basel) 2021; 12:genes12020303. [PMID: 33669929 PMCID: PMC7924830 DOI: 10.3390/genes12020303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 11/24/2022] Open
Abstract
The Japanese archipelago is located at the periphery of the continent of Asia. Rivers in the Japanese archipelago, separated from the continent of Asia by about 17 Ma, have experienced an intermittent exchange of freshwater fish taxa through a narrow land bridge generated by lowered sea level. As the Korean Peninsula and Japanese archipelago were not covered by an ice sheet during glacial periods, phylogeographical analyses in this region can trace the history of biota that were, for a long time, beyond the last glacial maximum. In this study, we analyzed the phylogeography of four freshwater fish taxa, Hemibarbus longirostris, dark chub Nipponocypris temminckii, Tanakia ssp. and Carassius ssp., whose distributions include both the Korean Peninsula and Western Japan. We found for each taxon that a small component of diverse Korean clades of freshwater fishes migrated in waves into the Japanese archipelago to form the current phylogeographic structure of biota. The replacements of indigenous populations by succeeding migrants may have also influenced the phylogeography.
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47
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Fleming KJ, Schaefer JA, Abraham KF, Smith MA, Beresford DV. Evidence for passive dispersal of ground beetles (Coleoptera: Carabidae) in the Nearctic boreal forest. ECOSCIENCE 2021. [DOI: 10.1080/11956860.2021.1872265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Kaitlyn J. Fleming
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Canada
| | | | - Kenneth F. Abraham
- Wildlife Research and Development Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Canada
| | - M. Alex Smith
- Department of Integrative Biology, University of Guelph, Guelph, Canada
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48
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Bouzid NM, Archie JW, Anderson RA, Grummer JA, Leaché AD. Evidence for ephemeral ring species formation during the diversification history of western fence lizards (Sceloporus occidentalis). Mol Ecol 2021; 31:620-631. [PMID: 33565164 DOI: 10.1111/mec.15836] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/18/2021] [Accepted: 02/02/2021] [Indexed: 12/31/2022]
Abstract
Divergence is often ephemeral, and populations that diverge in response to regional topographic and climatic factors may not remain reproductively isolated when they come into secondary contact. We investigated the geographical structure and evolutionary history of population divergence within Sceloporus occidentalis (western fence lizard), a habitat generalist with a broad distribution that spans the major biogeographical regions of Western North America. We used double digest RAD sequencing to infer population structure, phylogeny and demography. Population genetic structure is hierarchical and geographically structured with evidence for gene flow between biogeographical regions. Consistent with the isolation-expansion model of divergence during Quaternary glacial-interglacial cycles, gene flow and secondary contact are supported as important processes explaining the demographic histories of populations. Although populations may have diverged as they spread northward in a ring-like manner around the Sierra Nevada and southern Cascade Ranges, there is strong evidence for gene flow among populations at the northern terminus of the ring. We propose the concept of an "ephemeral ring species" and contrast S. occidentalis with the classic North American ring species, Ensatina eschscholtzii. Contrary to expectations of lower genetic diversity at northern latitudes following post-Quaternary-glaciation expansion, the ephemeral nature of divergence in S. occidentalis has produced centres of high genetic diversity for different reasons in the south (long-term stability) vs. the north (secondary contact).
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Affiliation(s)
- Nassima M Bouzid
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
| | - James W Archie
- Biological Sciences, California State University, Long Beach, CA, USA
| | - Roger A Anderson
- Biology Department, Western Washington University, Bellingham, WA, USA
| | - Jared A Grummer
- Department of Zoology, University of British Columbia, Beaty Biodiversity Museum, Vancouver, BC, Canada
| | - Adam D Leaché
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
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49
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Watt C, Kierepka E, Ferreira C, Koen E, Row J, Bowman J, Wilson P, Murray D. Canada lynx ( Lynx canadensis) gene flow across a mountain transition zone in western North America. CAN J ZOOL 2021. [DOI: 10.1139/cjz-2019-0247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Mountain ecotones have the potential to cause multiple patterns in divergence, from simple barrier effects to more fundamental ecological divergence. Most work in mountain ecotones in North America has focused on reinforcement between refugial populations, making prediction of how mountains impact species that are not restricted to separate glacial refugia remains difficult. This study focused on the Canada lynx (Lynx canadensis Kerr, 1792), a highly mobile felid considered to be a habitat and dietary specialist. Specifically, we used 14 microsatellite loci and landscape genetic tools to investigate if the Rocky Mountains and associated climatic transitions influence lynx genetic differentiation in western North America. Although lynx exhibited high gene flow across the region, analyses detected structuring of neutral genetic variation across our study area. Gene flow for lynx most strongly related to temperature and elevation compared with other landscape variables (terrain roughness, percent forest cover, and habitat suitability index) and geographic distance alone. Overall, genetic structure in lynx is most consistent with barrier effects created by the Rocky Mountains rather than ecological divergence. Furthermore, warmer temperatures had a measurable impact on gene flow, which suggests connectivity may further decrease in peripheral or fragmented populations as climate warms.
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Affiliation(s)
- C.M. Watt
- Biology Department, Trent University, Trent University DNA Building, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - E.M. Kierepka
- North Carolina Museum of Natural Sciences, North Carolina State University, Department of Forestry and Environmental Resources, Raleigh, NC 27601, USA
| | - C.C. Ferreira
- Biology Department, Trent University, Trent University DNA Building, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
- UFZ-Helmholtz Centre for Environmental Research, Department of Conservation Biology, Permoserstr, 15, 04318 Leipzig, Germany
| | - E.L. Koen
- Ontario Ministry of Natural Resources, Trent University DNA Building, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - J.R. Row
- Minnow Environmental Inc., Queen’s University, Georgetown, ON L7G 3M9, Canada
| | - J. Bowman
- Ontario Ministry of Natural Resources, Trent University DNA Building, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - P.J. Wilson
- Biology Department, Trent University, Trent University DNA Building, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - D.L. Murray
- Biology Department, Trent University, Trent University DNA Building, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
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50
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Hessels EW, Lofroth EC, Weir RD, Gorrell JC. Characterizing the elusive Vancouver Island wolverine, Gulo gulo vancouverensis, using historical DNA. J Mammal 2021. [DOI: 10.1093/jmammal/gyaa175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The wolverine (Gulo gulo) is a Holarctic species found in North America primarily across the boreal forest, the subarctic, and along the Pacific coast, including Vancouver Island (VI), British Columbia. While wolverines on VI are rare and possibly extirpated, they have been previously described as a unique subspecies, G. g. vancouverensis, distinct from G. g. luscus from the mainland of North America. However, the validity of the VI subspecies is contentious, with conflicting results from studies of skull morphology. Here, we used molecular analyses to characterize the genetic diversity of the VI population and resolve this taxonomic debate to assist with conservation priorities. Historical DNA of VI wolverines was obtained from museum specimens, amplified at 16 nuclear microsatellite loci, and sequenced at the mitochondrial D-loop control region to compare with wolverines from mainland British Columbia. The VI population had lower allelic richness and was fixed for a single common mtDNA haplotype. Bayesian and non-Bayesian assignments using microsatellites generally revealed admixture across populations, implying allele frequencies between the VI and mainland populations were not significantly different. Hence, both types of genetic markers showed little evolutionary divergence between VI and the mainland population. Combined, these results do not provide evidence of significant genetic distinction for VI wolverines, nor support the subspecific classification. Immediate conservation efforts should focus on estimating population size, while future conservation planning can assume VI wolverines likely are not a unique genetic population and there remains the potential for natural recolonization of wolverines to VI.
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Affiliation(s)
- Evan W Hessels
- Biology Department, Vancouver Island University, Nanaimo, BC, Canada
| | | | - Richard D Weir
- Ministry of Environment, Government of British Columbia, Victoria, BC, Canada
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