1
|
Armstrong EE, Bissell KL, Fatima HS, Heikkinen MA, Jessup A, Junaid MO, Lee DH, Lieb EC, Liem JT, Martin EM, Moreno M, Otgonbayar K, Romans BW, Royar K, Adler MB, Needle DB, Harkess A, Kelley JL, Mooney JA, Mychajliw AM. Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae. G3 (BETHESDA, MD.) 2024; 14:jkae034. [PMID: 38366575 PMCID: PMC10989890 DOI: 10.1093/g3journal/jkae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/18/2024]
Abstract
Reference genome assemblies have been created from multiple lineages within the Canidae family; however, despite its phylogenetic relevance as a basal genus within the clade, there is currently no reference genome for the gray fox (Urocyon cinereoargenteus). Here, we present a chromosome-level assembly for the gray fox (U. cinereoargenteus), which represents the most contiguous, non-domestic canid reference genome available to date, with 90% of the genome contained in just 34 scaffolds and a contig N50 and scaffold N50 of 59.4 and 72.9 Megabases, respectively. Repeat analyses identified an increased number of simple repeats relative to other canids. Based on mitochondrial DNA, our Vermont sample clusters with other gray fox samples from the northeastern United States and contains slightly lower levels of heterozygosity than gray foxes on the west coast of California. This new assembly lays the groundwork for future studies to describe past and present population dynamics, including the delineation of evolutionarily significant units of management relevance. Importantly, the phylogenetic position of Urocyon allows us to verify the loss of PRDM9 functionality in the basal canid lineage, confirming that pseudogenization occurred at least 10 million years ago.
Collapse
Affiliation(s)
- Ellie E Armstrong
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Ky L Bissell
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - H Sophia Fatima
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Maya A Heikkinen
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Anika Jessup
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Maryam O Junaid
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Dong H Lee
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Emily C Lieb
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Josef T Liem
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Estelle M Martin
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Mauricio Moreno
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | | | - Betsy W Romans
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Kim Royar
- Vermont Department of Fish and Wildlife, Montpelier, VT 05620, USA
| | - Mary Beth Adler
- Vermont Department of Fish and Wildlife, Montpelier, VT 05620, USA
| | - David B Needle
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jazlyn A Mooney
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90007, USA
| | - Alexis M Mychajliw
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
- Program in Environmental Studies, Middlebury College, Middlebury, VT 05753, USA
| |
Collapse
|
2
|
Preckler-Quisquater S, Kierepka EM, Reding DM, Piaggio AJ, Sacks BN. Can demographic histories explain long-term isolation and recent pulses of asymmetric gene flow between highly divergent grey fox lineages? Mol Ecol 2023; 32:5323-5337. [PMID: 37632719 DOI: 10.1111/mec.17105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/28/2023]
Abstract
Secondary contact zones between deeply divergent, yet interfertile, lineages provide windows into the speciation process. North American grey foxes (Urocyon cinereoargenteus) are divided into western and eastern lineages that diverged approximately 1 million years ago. These ancient lineages currently hybridize in a relatively narrow zone of contact in the southern Great Plains, a pattern more commonly observed in smaller-bodied taxa, which suggests relatively recent contact after a long period of allopatry. Based on local ancestry inference with whole-genome sequencing (n = 43), we identified two distinct Holocene pulses of admixture. The older pulse (500-3500 YBP) reflected unidirectional gene flow from east to west, whereas the more recent pulse (70-200 YBP) of admixture was bi-directional. Augmented with genotyping-by-sequencing data from 216 additional foxes, demographic analyses indicated that the eastern lineage declined precipitously after divergence, remaining small throughout most of the late Pleistocene, and expanding only during the Holocene. Genetic diversity in the eastern lineage was highest in the southeast and lowest near the contact zone, consistent with a westward expansion. Concordantly, distribution modelling indicated that during their isolation, the most suitable habitat occurred far east of today's contact zone or west of the Great Plains. Thus, long-term isolation was likely caused by the small, distant location of the eastern refugium, with recent contact reflecting a large increase in suitable habitat and corresponding demographic expansion from the eastern refugium. Ultimately, long-term isolation in grey foxes may reflect their specialized bio-climatic niche. This system presents an opportunity for future investigation of potential pre- and post-zygotic isolating mechanisms.
Collapse
Affiliation(s)
- Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Elizabeth M Kierepka
- North Carolina Museum of Natural Sciences, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | - Dawn M Reding
- Department of Biology, Luther College, Decorah, Iowa, USA
| | - Antoinette J Piaggio
- USDA, Wildlife Services, National Wildlife Research Center, Wildlife Genetics Lab, Fort Collins, Colorado, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
| |
Collapse
|
3
|
da Silva Coelho FA, Gill S, Tomlin CM, Papavassiliou M, Farley SD, Cook JA, Sonsthagen SA, Sage GK, Heaton TH, Talbot SL, Lindqvist C. Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska. Mol Ecol 2023. [PMID: 37096383 DOI: 10.1111/mec.16960] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023]
Abstract
During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U. arctos) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged >100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre- and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak.
Collapse
Affiliation(s)
| | - Stephanie Gill
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | | | - Sean D Farley
- Alaska Department of Fish and Game, Anchorage, Alaska, USA
| | - Joseph A Cook
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Sarah A Sonsthagen
- U.S. Geological Survey, Nebraska Cooperative Fish and Wildlife Research Unit, University of Nebraska-Lincoln, School of Natural Resources, Lincoln, Nebraska, USA
| | - George K Sage
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Timothy H Heaton
- Department of Earth Sciences, University of South Dakota, Vermillion, South Dakota, USA
| | - Sandra L Talbot
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| |
Collapse
|
4
|
Puckett EE, Davis IS, Harper DC, Wakamatsu K, Battu G, Belant JL, Beyer DE, Carpenter C, Crupi AP, Davidson M, DePerno CS, Forman N, Fowler NL, Garshelis DL, Gould N, Gunther K, Haroldson M, Ito S, Kocka D, Lackey C, Leahy R, Lee-Roney C, Lewis T, Lutto A, McGowan K, Olfenbuttel C, Orlando M, Platt A, Pollard MD, Ramaker M, Reich H, Sajecki JL, Sell SK, Strules J, Thompson S, van Manen F, Whitman C, Williamson R, Winslow F, Kaelin CB, Marks MS, Barsh GS. Genetic architecture and evolution of color variation in American black bears. Curr Biol 2023; 33:86-97.e10. [PMID: 36528024 PMCID: PMC10039708 DOI: 10.1016/j.cub.2022.11.042] [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: 09/14/2022] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
Color variation is a frequent evolutionary substrate for camouflage in small mammals, but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The American black bear, Ursus americanus (U. americanus), exhibits a range of colors including the cinnamon morph, which has a similar color to the brown bear, U. arctos, and is found at high frequency in the American southwest. Reflectance and chemical melanin measurements showed little distinction between U. arctos and cinnamon U. americanus individuals. We used a genome-wide association for hair color as a quantitative trait in 151 U. americanus individuals and identified a single major locus (p < 10-13). Additional genomic and functional studies identified a missense alteration (R153C) in Tyrosinase-related protein 1 (TYRP1) that likely affects binding of the zinc cofactor, impairs protein localization, and results in decreased pigment production. Population genetic analyses and demographic modeling indicated that the R153C variant arose 9.36 kya in a southwestern population where it likely provided a selective advantage, spreading both northwards and eastwards by gene flow. A different TYRP1 allele, R114C, contributes to the characteristic brown color of U. arctos but is not fixed across the range.
Collapse
Affiliation(s)
- Emily E Puckett
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA.
| | - Isis S Davis
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Dawn C Harper
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kazumasa Wakamatsu
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Japan
| | - Gopal Battu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jerrold L Belant
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Dean E Beyer
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Colin Carpenter
- West Virginia Division of Natural Resources, Beckley, WV 25801, USA
| | - Anthony P Crupi
- Division of Wildlife Conservation, Alaska Department of Fish and Game, Douglas, Juneau, AK 99824, USA
| | - Maria Davidson
- The Louisiana Department of Wildlife and Fisheries, Baton Rouge, LA 70898, USA
| | - Christopher S DePerno
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695-7646, USA
| | - Nicholas Forman
- New Mexico Department of Game and Fish, Santa Fe, NM 87507, USA
| | - Nicholas L Fowler
- Division of Wildlife Conservation, Alaska Department of Fish and Game, Douglas, Juneau, AK 99824, USA
| | - David L Garshelis
- Minnesota Department of Natural Resources, Grand Rapids, MN 55744, USA; IUCN SSC Bear Specialist Group
| | - Nicholas Gould
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695-7646, USA
| | - Kerry Gunther
- National Park Service, Yellowstone National Park, WY 82190-0168, USA
| | - Mark Haroldson
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Interagency Grizzly Bear Study Team, Bozeman, MT 59715, USA
| | - Shosuke Ito
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Japan
| | - David Kocka
- Virginia Department of Wildlife Resources, Verona, VA 24482, USA
| | - Carl Lackey
- Nevada Department of Wildlife, Reno, NV 89512, USA
| | - Ryan Leahy
- National Park Service, Yosemite National Park Wildlife Management, Yosemite, CA 95389, USA
| | - Caitlin Lee-Roney
- National Park Service, Yosemite National Park Wildlife Management, Yosemite, CA 95389, USA
| | - Tania Lewis
- National Park Service, Glacier Bay National Park, Gustavus, AK 99826, USA
| | - Ashley Lutto
- U.S. Fish and Wildlife Service, Kenai National Wildlife Refuge, Soldotna, AK 99669, USA
| | - Kelly McGowan
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Mike Orlando
- Florida Fish and Wildlife Conservation Commission, Tallahassee, FL 32399, USA
| | - Alexander Platt
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew D Pollard
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Megan Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Jaime L Sajecki
- Virginia Department of Wildlife Resources, Verona, VA 24482, USA
| | - Stephanie K Sell
- Division of Wildlife Conservation, Alaska Department of Fish and Game, Douglas, Juneau, AK 99824, USA
| | - Jennifer Strules
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695-7646, USA
| | - Seth Thompson
- Virginia Department of Wildlife Resources, Verona, VA 24482, USA
| | - Frank van Manen
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Interagency Grizzly Bear Study Team, Bozeman, MT 59715, USA
| | - Craig Whitman
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Interagency Grizzly Bear Study Team, Bozeman, MT 59715, USA
| | - Ryan Williamson
- National Park Service, Great Smoky Mountains National Park, Gatlinburg, TN 37738, USA
| | | | - Christopher B Kaelin
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Departments of Pathology and Laboratory Medicine and of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
5
|
Gould MJ, Cain JW, Atwood TC, Harding LE, Johnson HE, Onorato DP, Winslow FS, Roemer GW. Pleistocene-Holocene vicariance, not Anthropocene landscape change, explains the genetic structure of American black bear ( Ursus americanus) populations in the American Southwest and northern Mexico. Ecol Evol 2022; 12:e9406. [PMID: 36248671 PMCID: PMC9551525 DOI: 10.1002/ece3.9406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
The phylogeography of the American black bear (Ursus americanus) is characterized by isolation into glacial refugia, followed by population expansion and genetic admixture. Anthropogenic activities, including overharvest, habitat loss, and transportation infrastructure, have also influenced their landscape genetic structure. We describe the genetic structure of the American black bear in the American Southwest and northern Mexico and investigate how prehistoric and contemporary forces shaped genetic structure and influenced gene flow. Using a suite of microsatellites and a sample of 550 bears, we identified 14 subpopulations organized hierarchically following the distribution of ecoregions and mountain ranges containing black bear habitat. The pattern of subdivision we observed is more likely a product of postglacial habitat fragmentation during the Pleistocene and Holocene, rather than a consequence of contemporary anthropogenic barriers to movement during the Anthropocene. We used linear mixed‐effects models to quantify the relationship between landscape resistance and genetic distance among individuals, which indicated that both isolation by resistance and geographic distance govern gene flow. Gene flow was highest among subpopulations occupying large tracts of contiguous habitat, was reduced among subpopulations in the Madrean Sky Island Archipelago, where montane habitat exists within a lowland matrix of arid lands, and was essentially nonexistent between two isolated subpopulations. We found significant asymmetric gene flow supporting the hypothesis that bears expanded northward from a Pleistocene refugium located in the American Southwest and northern Mexico and that major highways were not yet affecting gene flow. The potential vulnerability of the species to climate change, transportation infrastructure, and the US–Mexico border wall highlights conservation challenges and opportunities for binational collaboration.
Collapse
Affiliation(s)
- Matthew J. Gould
- Department of Fish, Wildlife and Conservation EcologyNew Mexico State UniversityLas CrucesNew MexicoUSA,Department of BiologyNew Mexico State UniversityLas CrucesNew MexicoUSA,U.S. Geological Survey, Northern Rocky Mountain Science CenterBozemanMontanaUSA
| | - James W. Cain
- Department of Fish, Wildlife and Conservation EcologyNew Mexico State UniversityLas CrucesNew MexicoUSA,Department of BiologyNew Mexico State UniversityLas CrucesNew MexicoUSA,U.S. Geological Survey New Mexico Cooperative Fish and Wildlife Research UnitNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Todd C. Atwood
- U.S. Geological SurveyAlaska Science CenterAnchorageAlaskaUSA
| | | | | | - Dave P. Onorato
- Fish and Wildlife Research InstituteFlorida Fish and Wildlife Conservation CommissionNaplesFloridaUSA
| | | | - Gary W. Roemer
- Department of Fish, Wildlife and Conservation EcologyNew Mexico State UniversityLas CrucesNew MexicoUSA,Department of BiologyNew Mexico State UniversityLas CrucesNew MexicoUSA
| |
Collapse
|
6
|
Gunn JC, Berkman LK, Koppelman J, Taylor AT, Brewer SK, Long JM, Eggert LS. Genomic divergence, local adaptation, and complex demographic history may inform management of a popular sportfish species complex. Ecol Evol 2022; 12:e9370. [PMID: 36225830 PMCID: PMC9534746 DOI: 10.1002/ece3.9370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/05/2022] Open
Abstract
The Neosho Bass (Micropterus velox), a former subspecies of the keystone top-predator and globally popular Smallmouth Bass (M. dolomieu), is endemic and narrowly restricted to small, clear streams of the Arkansas River Basin in the Central Interior Highlands (CIH) ecoregion, USA. Previous studies have detected some morphological, genetic, and genomic differentiation between the Neosho and Smallmouth Basses; however, the extent of neutral and adaptive divergence and patterns of intraspecific diversity are poorly understood. Furthermore, lineage diversification has likely been impacted by gene flow in some Neosho populations, which may be due to a combination of natural biogeographic processes and anthropogenic introductions. We assessed: (1) lineage divergence, (2) local directional selection (adaptive divergence), and (3) demographic history among Smallmouth Bass populations in the CIH using population genomic analyses of 50,828 single-nucleotide polymorphisms (SNPs) obtained through ddRAD-seq. Neosho and Smallmouth Bass formed monophyletic clades with 100% bootstrap support. We identified two major lineages within each species. We discovered six Neosho Bass populations (two nonadmixed and four admixed) and three nonadmixed Smallmouth Bass populations. We detected 29 SNPs putatively under directional selection in the Neosho range, suggesting populations may be locally adapted. Two populations were admixed via recent asymmetric secondary contact, perhaps after anthropogenic introduction. Two other populations were likely admixed via combinations of ancient and recent processes. These species comprise independently evolving lineages, some having experienced historical and natural admixture. These results may be critical for management of Neosho Bass as a distinct species and may aid in the conservation of other species with complex biogeographic histories.
Collapse
Affiliation(s)
- Joe C. Gunn
- Division of Biological SciencesUniversity of MissouriColumbiaMissouriUSA
| | | | | | - Andrew T. Taylor
- Department of BiologyUniversity of Central OklahomaEdmondOklahomaUSA
- Department of BiologyUniversity of North GeorgiaDahlonegaGeorgiaUSA
| | - Shannon K. Brewer
- U.S. Geological Survey, Alabama Cooperative Fish and Wildlife Research Unit, School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
| | - James M. Long
- U.S. Geological Survey, Oklahoma Cooperative Fish and Wildlife Research Unit, Department of Natural Resource Ecology and ManagementOklahoma State UniversityStillwaterOklahomaUSA
| | - Lori S. Eggert
- Division of Biological SciencesUniversity of MissouriColumbiaMissouriUSA
| |
Collapse
|
7
|
Pacheco C, Stronen AV, Jędrzejewska B, Plis K, Okhlopkov IM, Mamaev NV, Drovetski SV, Godinho R. Demography and evolutionary history of grey wolf populations around the Bering Strait. Mol Ecol 2022; 31:4851-4865. [PMID: 35822863 PMCID: PMC9545117 DOI: 10.1111/mec.16613] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 06/16/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
Glacial and interglacial periods throughout the Pleistocene have been substantial drivers of change in species distributions. Earlier analyses suggested that modern grey wolves (Canis lupus) trace their origin to a single Late Pleistocene Beringian population that expanded east and westwards, starting c. 25,000 years ago (ya). Here, we examined the demographic and phylogeographic histories of extant populations around the Bering Strait with wolves from two inland regions of the Russian Far East (RFE) and one coastal and two inland regions of North‐western North America (NNA), genotyped for 91,327 single nucleotide polymorphisms. Our results indicated that RFE and NNA wolves had a common ancestry until c. 34,400 ya, suggesting that these populations started to diverge before the previously proposed expansion out of Beringia. Coastal and inland NNA populations diverged c. 16,000 ya, concordant with the minimum proposed date for the ecological viability of the migration route along the Pacific Northwest coast. Demographic reconstructions for inland RFE and NNA populations reveal spatial and temporal synchrony, with large historical effective population sizes that declined throughout the Pleistocene, possibly reflecting the influence of broadscale climatic changes across continents. In contrast, coastal NNA wolves displayed a consistently lower effective population size than the inland populations. Differences between the demographic history of inland and coastal wolves may have been driven by multiple ecological factors, including historical gene flow patterns, natural landscape fragmentation, and more recent anthropogenic disturbance.
Collapse
Affiliation(s)
- Carolina Pacheco
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Astrid Vik Stronen
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Department of Biotechnology and Life Sciences, Insubria University, Varese, Italy.,Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Kamila Plis
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Innokentiy M Okhlopkov
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Nikolay V Mamaev
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Sergei V Drovetski
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| |
Collapse
|
8
|
Laczkó L, Jordán S, Sramkó G. The
RadOrgMiner
pipeline: Automated genotyping of organellar loci from
RADseq
data. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Levente Laczkó
- MTA‐DE “Lendület” Evolutionary Phylogenomics Research Group, Egyetem tér 1 H‐4032 Debrecen Hungary
- Department of Botany University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
- ELKH‐ DE Conservation Biology Research Group, Egyetem tér 1, Debrecen, H‐4032 Hungary
- Department of Metagenomics University of Debrecen Nagyerdei körút 98., Debrecen, H‐4032 Hungary
| | - Sándor Jordán
- Department of Botany University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
- Juhász‐Nagy Pál Doctoral School University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
| | - Gábor Sramkó
- MTA‐DE “Lendület” Evolutionary Phylogenomics Research Group, Egyetem tér 1 H‐4032 Debrecen Hungary
- Department of Botany University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
- ELKH‐ DE Conservation Biology Research Group, Egyetem tér 1, Debrecen, H‐4032 Hungary
| |
Collapse
|
9
|
Pease BS, Pacifici K, Kays R, Reich B. What drives spatially varying ecological relationships in a wide‐ranging species? DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Brent S. Pease
- Foresty Program Southern Illinois University Carbondale Illinois USA
| | - Krishna Pacifici
- Department of Forestry and Environmental Resources North Carolina State University Raleigh North Carolina USA
| | - Roland Kays
- Department of Forestry and Environmental Resources North Carolina State University Raleigh North Carolina USA
- North Carolina Museum of Natural Sciences Raleigh North Carolina USA
| | - Brian Reich
- Department of Statistics North Carolina State University Raleigh North Carolina USA
| |
Collapse
|
10
|
Kishida T, Ohashi M, Komatsu Y. Genetic diversity and population history of the Japanese black bear (
Ursus thibetanus japonicus
) based on the genome‐wide analyses. Ecol Res 2022. [DOI: 10.1111/1440-1703.12335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Takushi Kishida
- Museum of Natural and Environmental History, Shizuoka Shizuoka Japan
| | - Masataka Ohashi
- Wildlife Conservation Division Shizuoka Prefecture Shizuoka Japan
| | - Yosuke Komatsu
- Wildlife Conservation Division Shizuoka Prefecture Shizuoka Japan
| |
Collapse
|
11
|
Puckett EE, Davis IS. Spatial patterns of genetic diversity in eight bear (Ursidae) species. URSUS 2021. [DOI: 10.2192/ursus-d-20-00029.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Emily E. Puckett
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Isis S. Davis
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| |
Collapse
|
12
|
Light JE, Keane AS, Evans JW. Updating the Distribution of American Black Bears (Ursus americanus) in Texas Using Community Science, State Agencies, and Natural History Collections. WEST N AM NATURALIST 2021. [DOI: 10.3398/064.081.0308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Jessica E. Light
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX 77843
| | - Alaya S. Keane
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX 77843
| | | |
Collapse
|
13
|
Puckett EE, Murphy SM, Bradburd G. Phylogeographic analysis delimits three evolutionary significant units of least chipmunks in North America and identifies unique genetic diversity within the imperiled Peñasco population. Ecol Evol 2021; 11:12114-12128. [PMID: 34522364 PMCID: PMC8427584 DOI: 10.1002/ece3.7975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 11/10/2022] Open
Abstract
Although least chipmunks (Neotamias minimus) are a widely distributed North American species of least concern, the southernmost population, N. m. atristriatus (Peñasco least chipmunk), is imperiled and a candidate for federal listing as a subspecies. We conducted a phylogeographic analysis across the N. minimus range to assess genomic differentiation and distinctiveness of the N. m. atristriatus population. Additionally, we leveraged the historical component of sampling to conduct a temporal analysis of N. minimus genetic diversity and also considered climate change effects on range persistence probability by projecting a species distribution model into the IPCC5 RCP 2.6 and 8.5 scenarios. We identified three geographically structured groups (West, North, and South) that were supported by both mitochondrial and nuclear data. N. m. atristriatus grouped within a unique South subclade but were not reciprocally monophyletic from N. m. operarius, and nuclear genome analyses did not separate N. m. atristriatus, N. m. caryi, and N. m. operarius. Thus, while least chipmunks in the Southwest represent an evolutionary significant unit, subspecies distinctions were not supported and listing of the Peñasco population as a Distinct Population Segment of N. m. operarius may be warranted. Our results also support consideration of populations with North and West mitogenomes as two additional evolutionary significant units. We found that N. minimus genetic diversity declined by ~87% over the last century, and our models predicted substantial future habitat contraction, including the loss of the full contemporary ranges of N. m. atristriatus, N. m. arizonensis, and N. m. chuskaensis.
Collapse
Affiliation(s)
- Emily E. Puckett
- Department of Biological SciencesUniversity of MemphisMemphisTennesseeUSA
| | - Sean M. Murphy
- Wildlife Management DivisionNew Mexico Department of Game & FishSanta FeNew MexicoUSA
- Present address:
Department of Forestry and Natural ResourcesUniversity of KentuckyLexingtonKentuckyUSA
| | - Gideon Bradburd
- Department of Integrative BiologyEcology, Evolution, and Behavior GroupMichigan State UniversityEast LansingMichiganUSA
| |
Collapse
|
14
|
Pedersen MW, De Sanctis B, Saremi NF, Sikora M, Puckett EE, Gu Z, Moon KL, Kapp JD, Vinner L, Vardanyan Z, Ardelean CF, Arroyo-Cabrales J, Cahill JA, Heintzman PD, Zazula G, MacPhee RDE, Shapiro B, Durbin R, Willerslev E. Environmental genomics of Late Pleistocene black bears and giant short-faced bears. Curr Biol 2021; 31:2728-2736.e8. [PMID: 33878301 DOI: 10.1016/j.cub.2021.04.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/31/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1-3 by allowing for parallel sequencing of DNA from all trophic levels.4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.
Collapse
Affiliation(s)
- Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Nedda F Saremi
- Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emily E Puckett
- Department of Biological Sciences, University of Memphis, 3770 Walker Avenue, Ellington Hall, Memphis, TN 38152, USA
| | - Zhenquan Gu
- State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Beijing 100101, China
| | - Katherine L Moon
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Zaruhi Vardanyan
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ciprian F Ardelean
- Unidad Académica de Antropología, Universidad Autónoma de Zacatecas, Campus II, Col. Progreso, 98066 Zacatecas, Mexico; The Archaeology Centre, Department of Anthropology, University of Toronto, 19 Ursula Franklin Street, Toronto, ON M5S 2S2, Canada
| | - Joaquin Arroyo-Cabrales
- Laboratorio de Arqueozoologia, Subdireccion de Laboratorios y Apoyo Academico, Instituto Nacional de Antropologia e Historia, Moneda 16, Col. Centro, 06060 Mexico, CdMx, Mexico
| | - James A Cahill
- Laboratory of the Neurogenetics of Language, Rockefeller University, New York, NY, USA
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, PO Box 6050, Langnes, N-9037 Tromsø, Norway
| | - Grant Zazula
- Yukon Palaeontology Program, Department of Tourism & Culture, Government of Yukon, Whitehorse, YT Y1A 2C6, Canada
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY 12484, USA; American Museum of Natural History, New York, NY, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK; MARUM, University of Bremen, Bremen, Germany.
| |
Collapse
|
15
|
Reding DM, Castañeda-Rico S, Shirazi S, Hofman CA, Cancellare IA, Lance SL, Beringer J, Clark WR, Maldonado JE. Mitochondrial Genomes of the United States Distribution of Gray Fox (Urocyon cinereoargenteus) Reveal a Major Phylogeographic Break at the Great Plains Suture Zone. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.666800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We examined phylogeographic structure in gray fox (Urocyon cinereoargenteus) across the United States to identify the location of secondary contact zone(s) between eastern and western lineages and investigate the possibility of additional cryptic intraspecific divergences. We generated and analyzed complete mitochondrial genome sequence data from 75 samples and partial control region mitochondrial DNA sequences from 378 samples to investigate levels of genetic diversity and structure through population- and individual-based analyses including estimates of divergence (FST and SAMOVA), median joining networks, and phylogenies. We used complete mitochondrial genomes to infer phylogenetic relationships and date divergence times of major lineages of Urocyon in the United States. Despite broad-scale sampling, we did not recover additional major lineages of Urocyon within the United States, but identified a deep east-west split (∼0.8 million years) with secondary contact at the Great Plains Suture Zone and confirmed the Channel Island fox (Urocyon littoralis) is nested within U. cinereoargenteus. Genetic diversity declined at northern latitudes in the eastern United States, a pattern concordant with post-glacial recolonization and range expansion. Beyond the east-west divergence, morphologically-based subspecies did not form monophyletic groups, though unique haplotypes were often geographically limited. Gray foxes in the United States displayed a deep, cryptic divergence suggesting taxonomic revision is needed. Secondary contact at a common phylogeographic break, the Great Plains Suture Zone, where environmental variables show a sharp cline, suggests ongoing evolutionary processes may reinforce this divergence. Follow-up study with nuclear markers should investigate whether hybridization is occurring along the suture zone and characterize contemporary population structure to help identify conservation units. Comparative work on other wide-ranging carnivores in the region should test whether similar evolutionary patterns and processes are occurring.
Collapse
|
16
|
Fowler NL, Spady TJ, Wang G, Leopold BD, Belant JL. Denning, metabolic suppression, and the realisation of ecological opportunities in Ursidae. Mamm Rev 2021. [DOI: 10.1111/mam.12246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Nicholas L. Fowler
- Global Wildlife Conservation Center State University of New York College of Environmental Science and Forestry 1 Forestry Drive Syracuse NY13210USA
| | - Thomas J. Spady
- Department of Biological Sciences California State University San Marcos San Marcos CA92096USA
| | - Guiming Wang
- Department of Wildlife, Fisheries, and Aquaculture Mississippi State UniversityMississippi State Box 9690MS39762USA
| | - Bruce D. Leopold
- Department of Wildlife, Fisheries, and Aquaculture Mississippi State UniversityMississippi State Box 9690MS39762USA
| | - Jerrold L. Belant
- Global Wildlife Conservation Center State University of New York College of Environmental Science and Forestry 1 Forestry Drive Syracuse NY13210USA
| |
Collapse
|
17
|
Eriksson CE, Ruprecht J, Levi T. More affordable and effective noninvasive single nucleotide polymorphism genotyping using high‐throughput amplicon sequencing. Mol Ecol Resour 2020; 20:1505-1516. [DOI: 10.1111/1755-0998.13208] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/26/2022]
Affiliation(s)
| | - Joel Ruprecht
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| |
Collapse
|
18
|
Lewis T, Roffler G, Crupi A, Maraj R, Barten N. Unraveling the mystery of the glacier bear: Genetic population structure of black bears ( Ursus americanus) within the range of a rare pelage type. Ecol Evol 2020; 10:7654-7668. [PMID: 32760555 PMCID: PMC7391538 DOI: 10.1002/ece3.6490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/15/2020] [Accepted: 05/20/2020] [Indexed: 11/10/2022] Open
Abstract
Glacier bears are a rare grey color morph of American black bear (Ursus americanus) found only in northern Southeast Alaska and a small portion of western Canada. We examine contemporary genetic population structure of black bears within the geographic extent of glacier bears and explore how this structure relates to pelage color and landscape features of a recently glaciated and highly fragmented landscape. We used existing radiocollar data to quantify black bear home-range size within the geographic range of glacier bears. The mean home-range size of female black bears in the study area was 13 km2 (n = 11), whereas the home range of a single male was 86.9 km2. We genotyped 284 bears using 21 microsatellites extracted from noninvasively collected hair as well as tissue samples from harvested bears. We found ten populations of black bears in the study area, including several new populations not previously identified, divided largely by geographic features such as glaciers and marine fjords. Glacier bears were assigned to four populations found on the north and east side of Lynn Canal and the north and west side of Glacier Bay with a curious absence in the nonglaciated peninsula between. Lack of genetic relatedness and geographic continuity between black bear populations containing glacier bears suggest a possible unsampled population or an association with ice fields. Further investigation is needed to determine the genetic basis and the adaptive and evolutionary significance of the glacier bear color morph to help focus black bear conservation management to maximize and preserve genetic diversity.
Collapse
Affiliation(s)
- Tania Lewis
- Glacier Bay National Park and PreserveGustavusAKUSA
| | - Gretchen Roffler
- Division of Wildlife ConservationAlaska Department of Fish and GameDouglasAKUSA
| | - Anthony Crupi
- Division of Wildlife ConservationAlaska Department of Fish and GameDouglasAKUSA
| | - Ramona Maraj
- Faculty of Environmental DesignUniversity of CalgaryCalgaryABCanada
| | - Neil Barten
- Division of Wildlife ConservationAlaska Department of Fish and GameDillinghamAKUSA
| |
Collapse
|
19
|
Non-Pessimistic Predictions of the Distributions and Suitability of Metasequoia glyptostroboides under Climate Change Using a Random Forest Model. FORESTS 2020. [DOI: 10.3390/f11010062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Metasequoia glyptostroboides Hu & W. C. Cheng, which is a remarkable rare relict plant, has gradually been reduced to its current narrow range due to climate change. Understanding the comprehensive distribution of M. glyptostroboides under climate change on a large spatio-temporal scale is of great significance for determining its forest adaptation. In this study, based on 394 occurrence data and 10 bioclimatic variables, the global potential distribution of M. glyptostroboides under eight different climate scenarios (i.e., the past three, the current one, and the next four) from the Quaternary glacial to the future was simulated by a random forest model built with the biomod2 package. The key bioclimatic variables affecting the distribution of M. glyptostroboides are BIO2 (mean diurnal range), BIO1 (annual mean temperature), BIO9 (mean temperature of driest quarter), BIO6 (min temperature of coldest month), and BIO18 (precipitation of warmest quarter). The result indicates that the temperature affects the potential distribution of M. glyptostroboides more than the precipitation. A visualization of the results revealed that the current relatively suitable habitats of M. glyptostroboides are mainly distributed in East Asia and Western Europe, with a total area of approximately 6.857 × 106 km2. With the intensification of global warming in the future, the potential distribution and the suitability of M. glyptostroboides have a relatively non-pessimistic trend. Whether under the mild (RCP4.5) and higher (RCP8.5) emission scenarios, the total area of suitable habitats will be wider than it is now by the 2070s, and the habitat suitability will increase to varying degrees within a wide spatial range. After speculating on the potential distribution of M. glyptostroboides in the past, the glacial refugia of M. glyptostroboides were inferred, and projections regarding the future conditions of these places are expected to be optimistic. In order to better protect the species, the locations of its priority protected areas and key protected areas, mainly in Western Europe and East Asia, were further identified. Our results will provide theoretical reference for the long-term management of M. glyptostroboides, and can be used as background information for the restoration of other endangered species in the future.
Collapse
|
20
|
Jackson DJ, Cook JA. A precarious future for distinctive peripheral populations of meadow voles (Microtus pennsylvanicus). J Mammal 2019. [DOI: 10.1093/jmammal/gyz196] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Conservation efforts rely on robust taxonomic assessments that should be based on critical assessment of interspecific boundaries, infraspecific variation, and potentially distinctive peripheral populations. The meadow vole (Microtus pennsylvanicus) is widely distributed across North America, including 28 morphologically defined subspecies and numerous isolated populations. Because some subspecies are of high conservation concern, we examined geographic variation across the range of the species to test existing infraspecific taxonomy in terms of local and regional diversification. We sequenced mitochondrial DNA (mtDNA) from 20 subspecies of M. pennsylvanicus and contextualized infraspecific variation through comparison of pairwise genetic distances derived from an extended data set of 63 species of Microtus. We found strong support for at least three divergent clades within M. pennsylvanicus, with observed intraspecific clade divergence exceeding that between several pairwise comparisons of sister species within Microtus. Six nuclear genes were then sequenced to test the validity of mtDNA structure and to further evaluate the possibility of cryptic, species-level diversity using Bayes factor species delimitation (BFD) analyses. BFD consistently and decisively supported multiple species based on the multilocus approach. We propose that taxonomic revision of the meadow vole is required, with the eastern clade now identified as M. pennsylvanicus (Ord 1815), the western clade as M. drummondii (Audubon and Bachman 1853), and the coastal Florida clade as M. dukecampbelli (Woods, Post, and Kilpatrick 1982). We suggest that such an arrangement would more closely reflect evolutionary history and provide critical context for further examination of distinctive southern peripheral populations that harbor novel evolutionary legacies and adaptive potential.
Collapse
Affiliation(s)
- Donavan J Jackson
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| |
Collapse
|
21
|
DeCesare NJ, Weckworth BV, Pilgrim KL, Walker ABD, Bergman EJ, Colson KE, Corrigan R, Harris RB, Hebblewhite M, Jesmer BR, Newby JR, Smith JR, Tether RB, Thomas TP, Schwartz MK. Phylogeography of moose in western North America. J Mammal 2019. [DOI: 10.1093/jmammal/gyz163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AbstractSubspecies designations within temperate species’ ranges often reflect populations that were isolated by past continental glaciation, and glacial vicariance is believed to be a primary mechanism behind the diversification of several subspecies of North American cervids. We used genetics and the fossil record to study the phylogeography of three moose subspecies (Alces alces andersoni, A. a. gigas, and A. a. shirasi) in western North America. We sequenced the complete mitochondrial genome (16,341 base pairs; n = 60 moose) and genotyped 13 nuclear microsatellites (n = 253) to evaluate genetic variation among moose samples. We also reviewed the fossil record for detections of all North American cervids to comparatively assess the evidence for the existence of a southern refugial population of moose corresponding to A. a. shirasi during the last glacial maximum of the Pleistocene. Analysis of mtDNA molecular variance did not support distinct clades of moose corresponding to currently recognized subspecies, and mitogenomic haplotype phylogenies did not consistently distinguish individuals according to subspecies groupings. Analysis of population structure using microsatellite loci showed support for two to five clusters of moose, including the consistent distinction of a southern group of moose within the range of A. a. shirasi. We hypothesize that these microsatellite results reflect recent, not deep, divergence and may be confounded by a significant effect of geographic distance on gene flow across the region. Review of the fossil record showed no evidence of moose south of the Wisconsin ice age glaciers ≥ 15,000 years ago. We encourage the integration of our results with complementary analyses of phenotype data, such as morphometrics, originally used to delineate moose subspecies, for further evaluation of subspecies designations for North American moose.
Collapse
Affiliation(s)
| | | | - Kristine L Pilgrim
- Rocky Mountain Research Station, United States Forest Service, Missoula, MT, USA
| | - Andrew B D Walker
- British Columbia Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Penticton, British Columbia, Canada
| | | | | | - Rob Corrigan
- Alberta Environment and Parks, Edmonton, Alberta, Canada
| | | | | | | | - Jesse R Newby
- Montana Fish, Wildlife and Parks, Kalispell, MT, USA
| | - Jason R Smith
- North Dakota Game and Fish Department, Jamestown, ND, USA
| | - Rob B Tether
- Saskatchewan Ministry of Environment, Meadow Lake, Saskatchewan, Canada
| | | | - Michael K Schwartz
- Rocky Mountain Research Station, United States Forest Service, Missoula, MT, USA
| |
Collapse
|
22
|
Burkhart JJ, Puckett EE, Beringer CJ, Sholy CN, Semlitsch RD, Eggert LS. Post-Pleistocene differentiation in a Central Interior Highlands endemic salamander. Ecol Evol 2019; 9:11171-11184. [PMID: 31641463 PMCID: PMC6802018 DOI: 10.1002/ece3.5619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 11/07/2022] Open
Abstract
AIM For many endemic species with limited dispersal capacities, the relationship between landscape changes and species distributions is still unclear. We characterized the population structure of the endemic ringed salamander (Ambystoma annulatum) across its distribution in the Central Interior Highlands (CIH) of North America, an area of high species endemism, to infer the ecological and evolutionary history of the species. METHODS We sampled 498 individuals across the species distribution and characterized the population genetic structure using nuclear microsatellite and mitochondrial DNA (mtDNA) markers. RESULTS Ambystoma annulatum exist in two strongly supported nuclear genetic clusters across the CIH that correspond to a northern cluster that includes the Missouri Ozark populations and a southern cluster that includes the Arkansas and Oklahoma Ozarks and the Ouachita Mountains. Our demographic models estimated that these populations diverged approximately 2,700 years ago. Pairwise estimates of genetic differentiation at microsatellite and mtDNA markers indicated limited contemporary gene flow and suggest that genetic differentiation was primarily influenced by changes in the post-Pleistocene landscape of the CIH. MAIN CONCLUSIONS Both the geologic history and post-European settlement history of the CIH have influenced the population genetic structure of A. annulatum. The low mtDNA diversity suggests a retraction into and expansion out of refugial areas in the south-central Ozarks, during temperature fluctuations of the Pleistocene and Holocene epochs. Similarly, the estimated divergence time for the two nuclear clusters corresponds to changes in the post-Pleistocene landscape. More recently, decreased A. annulatum gene flow may be a result of increased habitat fragmentation and alteration post-European settlement.
Collapse
Affiliation(s)
| | - Emily E. Puckett
- Department of Biological SciencesUniversity of MemphisMemphisTNUSA
| | | | | | | | - Lori S. Eggert
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| |
Collapse
|
23
|
McGrath K, Rowsell K, Gates St-Pierre C, Tedder A, Foody G, Roberts C, Speller C, Collins M. Identifying Archaeological Bone via Non-Destructive ZooMS and the Materiality of Symbolic Expression: Examples from Iroquoian Bone Points. Sci Rep 2019; 9:11027. [PMID: 31363122 PMCID: PMC6667708 DOI: 10.1038/s41598-019-47299-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/26/2019] [Indexed: 12/01/2022] Open
Abstract
Today, practical, functional and symbolic choices inform the selection of raw materials for worked objects. In cases where we can discern the origin of worked bone, tooth, ivory and antler objects in the past, we assume that similar choices are being made. However, morphological species identification of worked objects is often impossible due to the loss of identifying characteristics during manufacture. Here, we describe a novel non-destructive ZooMS (Zooarchaeology by Mass Spectrometry) method which was applied to bone points from Pre-Contact St. Lawrence Iroquoian village sites in southern Quebec, Canada. The traditional ZooMS technique requires destructive analysis of a sample, which can be problematic when dealing with artefacts. Here we instead extracted proteins from the plastic bags in which the points had been stored. ZooMS analysis revealed hitherto unexpected species, notably black bear (Ursus americanus) and human (Homo sapiens sapiens), used in point manufacture. These surprising results (confirmed through genomic sequencing) highlight the importance of advancing biomolecular research in artefact studies. Furthermore, they unexpectedly and exceptionally allow us to identify and explore the tangible, material traces of the symbolic relationship between bears and humans, central to past and present Iroquoian cosmology and mythology.
Collapse
Affiliation(s)
- Krista McGrath
- BioArCh, Department of Archaeology, University of York, York, UK.
| | - Keri Rowsell
- BioArCh, Department of Archaeology, University of York, York, UK.,London School of Economics and Political Science, London, UK
| | | | - Andrew Tedder
- School of Chemistry & Bioscience, University of Bradford, Bradford, UK
| | - George Foody
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | | | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, York, UK.,Department of Anthropology, University of British Columbia, Vancouver, Canada
| | - Matthew Collins
- BioArCh, Department of Archaeology, University of York, York, UK.,EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| |
Collapse
|
24
|
Waraniak JM, Fisher JDL, Purcell K, Mushet DM, Stockwell CA. Landscape genetics reveal broad and fine-scale population structure due to landscape features and climate history in the northern leopard frog ( Rana pipiens) in North Dakota. Ecol Evol 2019; 9:1041-1060. [PMID: 30805139 PMCID: PMC6374656 DOI: 10.1002/ece3.4745] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/10/2018] [Accepted: 10/30/2018] [Indexed: 01/06/2023] Open
Abstract
Prehistoric climate and landscape features play large roles structuring wildlife populations. The amphibians of the northern Great Plains of North America present an opportunity to investigate how these factors affect colonization, migration, and current population genetic structure. This study used 11 microsatellite loci to genotype 1,230 northern leopard frogs (Rana pipiens) from 41 wetlands (30 samples/wetland) across North Dakota. Genetic structure of the sampled frogs was evaluated using Bayesian and multivariate clustering methods. All analyses produced concordant results, identifying a major east-west split between two R. pipiens population clusters separated by the Missouri River. Substructuring within the two major identified population clusters was also found. Spatial principal component analysis (sPCA) and variance partitioning analysis identified distance, river basins, and the Missouri River as the most important landscape factors differentiating R. pipiens populations across the state. Bayesian reconstruction of coalescence times suggested the major east-west split occurred ~13-18 kya during a period of glacial retreat in the northern Great Plains and substructuring largely occurred ~5-11 kya during a period of extreme drought cycles. A range-wide species distribution model (SDM) for R. pipiens was developed and applied to prehistoric climate conditions during the Last Glacial Maximum (21 kya) and the mid-Holocene (6 kya) from the CCSM4 climate model to identify potential refugia. The SDM indicated potential refugia existed in South Dakota or further south in Nebraska. The ancestral populations of R. pipiens in North Dakota may have inhabited these refugia, but more sampling outside the state is needed to reconstruct the route of colonization. Using microsatellite genotype data, this study determined that colonization from glacial refugia, drought dynamics in the northern Great Plains, and major rivers acting as barriers to gene flow were the defining forces shaping the regional population structure of R. pipiens in North Dakota.
Collapse
Affiliation(s)
- Justin M. Waraniak
- Department of Biological Sciences, Environmental and Conservation Sciences Graduate ProgramNorth Dakota State UniversityFargoNorth Dakota
| | - Justin D. L. Fisher
- Department of Biological Sciences, Environmental and Conservation Sciences Graduate ProgramNorth Dakota State UniversityFargoNorth Dakota
- Present address:
Natural Resource Conservation ServiceFergus FallsMinnesota
| | - Kevin Purcell
- Department of Biological Sciences, Environmental and Conservation Sciences Graduate ProgramNorth Dakota State UniversityFargoNorth Dakota
- Present address:
Data Science and Analytics ProgramHarrisburg UniversityHarrisburgPennsylvania
| | - David M. Mushet
- U.S. Geological SurveyNorthern Prairie Wildlife Research CenterJamestownNorth Dakota
| | - Craig A. Stockwell
- Department of Biological Sciences, Environmental and Conservation Sciences Graduate ProgramNorth Dakota State UniversityFargoNorth Dakota
| |
Collapse
|
25
|
Stobie CS, Cunningham MJ, Oosthuizen CJ, Bloomer P. Finding stories in noise: Mitochondrial portraits from RAD data. Mol Ecol Resour 2018; 19:191-205. [DOI: 10.1111/1755-0998.12953] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Cora Sabriel Stobie
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology University of Pretoria Hatfield, Pretoria South Africa
| | - Michael J. Cunningham
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology University of Pretoria Hatfield, Pretoria South Africa
| | - Carel J. Oosthuizen
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology University of Pretoria Hatfield, Pretoria South Africa
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology University of Pretoria Hatfield, Pretoria South Africa
| |
Collapse
|
26
|
Bradburd GS, Coop GM, Ralph PL. Inferring Continuous and Discrete Population Genetic Structure Across Space. Genetics 2018; 210:33-52. [PMID: 30026187 PMCID: PMC6116973 DOI: 10.1534/genetics.118.301333] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/16/2018] [Indexed: 11/23/2022] Open
Abstract
A classic problem in population genetics is the characterization of discrete population structure in the presence of continuous patterns of genetic differentiation. Especially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to genetic data deriving from geographically distributed populations. Here, we present a statistical framework for the simultaneous inference of continuous and discrete patterns of population structure. The method estimates ancestry proportions for each sample from a set of two-dimensional population layers, and, within each layer, estimates a rate at which relatedness decays with distance. This thereby explicitly addresses the "clines versus clusters" problem in modeling population genetic variation, and remedies some of the overfitting to which nonspatial models are prone. The method produces useful descriptions of structure in genetic relatedness in situations where separated, geographically distributed populations interact, as after a range expansion or secondary contact. We demonstrate the utility of this approach using simulations and by applying it to empirical datasets of poplars and black bears in North America.
Collapse
Affiliation(s)
- Gideon S Bradburd
- Ecology, Evolutionary Biology, and Behavior Graduate Group, Department of Integrative Biology, Michigan State University, East Lansing, Michigan 48824
| | - Graham M Coop
- Center for Population Biology, Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Peter L Ralph
- Institute of Ecology and Evolution, Departments of Mathematics and Biology, University of Oregon, Eugene, Oregon 97403
| |
Collapse
|
27
|
Whole-genome analysis of Mustela erminea finds that pulsed hybridization impacts evolution at high latitudes. Commun Biol 2018; 1:51. [PMID: 30271934 PMCID: PMC6123727 DOI: 10.1038/s42003-018-0058-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/20/2018] [Indexed: 01/19/2023] Open
Abstract
At high latitudes, climatic shifts hypothetically initiate recurrent episodes of divergence by isolating populations in glacial refugia—ice-free regions that enable terrestrial species persistence. Upon glacial recession, populations subsequently expand and often come into contact with other independently diverging populations, resulting in gene flow. To understand how recurrent periods of isolation and contact may have impacted evolution at high latitudes, we investigated introgression dynamics in the stoat (Mustela erminea), a Holarctic mammalian carnivore, using whole-genome sequences. We identify two spatio-temporally distinct episodes of introgression coincident with large-scale climatic shifts: contemporary introgression in a mainland contact zone and ancient contact ~200 km south of the contemporary zone, in the archipelagos along North America’s North Pacific Coast. Repeated episodes of gene flow highlight the central role of cyclic climates in structuring high-latitude diversity, through refugial divergence and introgressive hybridization. When introgression is followed by allopatric isolation (e.g., insularization) it may ultimately expedite divergence. Jocelyn Colella et al. report whole-genome sequences of 10 stoats (Mustela erminea) from four regions of glacial refugia. They find evidence for two past introgressive events between lineages that coincide with interglacial periods, a pattern that may extend to other high–latitude species.
Collapse
|
28
|
Genetic diversity, effective population size, and structure among black bear populations in the Lower Mississippi Alluvial Valley, USA. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1075-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
29
|
Kristensen TV, Puckett EE, Landguth EL, Belant JL, Hast JT, Carpenter C, Sajecki JL, Beringer J, Means M, Cox JJ, Eggert LS, White D, Smith KG. Spatial genetic structure in American black bears (Ursus americanus): female philopatry is variable and related to population history. Heredity (Edinb) 2018; 120:329-341. [PMID: 29234157 PMCID: PMC5842220 DOI: 10.1038/s41437-017-0019-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 09/29/2017] [Indexed: 11/08/2022] Open
Abstract
Previously, American black bears (Ursus americanus) were thought to follow the pattern of female philopatry and male-biased dispersal. However, recent studies have identified deviations from this pattern. Such flexibility in dispersal patterns can allow individuals greater ability to acclimate to changing environments. We explored dispersal and spatial genetic relatedness patterns across ten black bear populations-including long established (historic), with known reproduction >50 years ago, and newly established (recent) populations, with reproduction recorded <50 years ago-in the Interior Highlands and Southern Appalachian Mountains, United States. We used spatially explicit, individual-based genetic simulations to model gene flow under scenarios with varying levels of population density, genetic diversity, and female philopatry. Using measures of genetic distance and spatial autocorrelation, we compared metrics between sexes, between population types (historic and recent), and among simulated scenarios which varied in density, genetic diversity, and sex-biased philopatry. In empirical populations, females in recent populations exhibited stronger patterns of isolation-by-distance (IBD) than females and males in historic populations. In simulated populations, low-density populations had a stronger indication of IBD than medium- to high-density populations; however, this effect varied in empirical populations. Condition-dependent dispersal strategies may permit species to cope with novel conditions and rapidly expand populations. Pattern-process modeling can provide qualitative and quantitative means to explore variable dispersal patterns, and could be employed in other species, particularly to anticipate range shifts in response to changing climate and habitat conditions.
Collapse
Affiliation(s)
- Thea V Kristensen
- Department of Biological Sciences, Science and Engineering, University of Arkansas, Fayetteville, AR, USA.
- Biology Department, Amherst College, P.O. Box 5000, Amherst, MA, 01002, USA.
| | - Emily E Puckett
- Division of Biological Sciences, Tucker Hall, University of Missouri, Columbia, MO, USA
- Department of Biological Sciences and the Louis Calder Center-Biological Field Station, Fordham University, Armonk, NY, 10504, USA
| | - Erin L Landguth
- Computational Ecology Laboratory, School of Public and Community Health Sciences, University of Montana, Missoula, MT, USA
| | - Jerrold L Belant
- Carnivore Ecology Laboratory, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, Starkville, MS, USA
| | - John T Hast
- Department of Forestry, University of Kentucky, Lexington, KY, USA
| | - Colin Carpenter
- West Virginia Division of Natural Resources, Beckley, WV, USA
| | - Jaime L Sajecki
- Virginia Department of Game and Inland Fisheries, Forest, VA, USA
| | - Jeff Beringer
- Missouri Department of Conservation, Resource Science Center, Columbia, MO, USA
| | - Myron Means
- Arkansas Game and Fish Commission, Fort Smith, AR, USA
| | - John J Cox
- Carnivore Ecology Laboratory, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, Starkville, MS, USA
| | - Lori S Eggert
- Division of Biological Sciences, Tucker Hall, University of Missouri, Columbia, MO, USA
| | - Don White
- University of Arkansas Agricultural Experiment Station, Arkansas Forest Resources Center, University of Arkansas-Monticello, Monticello, AR, USA
| | - Kimberly G Smith
- Department of Biological Sciences, Science and Engineering, University of Arkansas, Fayetteville, AR, USA
| |
Collapse
|
30
|
Pedersen CET, Albrechtsen A, Etter PD, Johnson EA, Orlando L, Chikhi L, Siegismund HR, Heller R. A southern African origin and cryptic structure in the highly mobile plains zebra. Nat Ecol Evol 2018; 2:491-498. [PMID: 29358610 DOI: 10.1038/s41559-017-0453-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 12/14/2017] [Indexed: 12/30/2022]
Abstract
The plains zebra (Equus quagga) is an ecologically important species of the African savannah. It is also one of the most numerous and widely distributed ungulates, and six subspecies have been described based on morphological variation. However, the within-species evolutionary processes have been difficult to resolve due to its high mobility and a lack of consensus regarding the population structure. We obtained genome-wide DNA polymorphism data from more than 167,000 loci for 59 plains zebras from across the species range, encompassing all recognized extant subspecies, as well as three mountain zebras (Equus zebra) and three Grevy's zebras (Equus grevyi). Surprisingly, the population genetic structure does not mirror the morphology-based subspecies delineation, underlining the dangers of basing management units exclusively on morphological variation. We use demographic modelling to provide insights into the past phylogeography of the species. The results identify a southern African location as the most likely source region from which all extant populations expanded around 370,000 years ago. We show evidence for inclusion of the extinct and phenotypically divergent quagga (Equus quagga quagga) in the plains zebra variation and reveal that it was less divergent from the other subspecies than the northernmost (Ugandan) extant population.
Collapse
Affiliation(s)
- Casper-Emil T Pedersen
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Anders Albrechtsen
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark
| | - Paul D Etter
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Eric A Johnson
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lounes Chikhi
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Centre National de la Recherche Scientifique, Université Paul Sabatier, École Nationale de Formation Agronomique, UMR 5174 Laboratoire Évolution et Diversité Biologique, Toulouse, France
| | - Hans R Siegismund
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Heller
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
31
|
Draper JP, Waits LP, Adams JR, Seals CL, Steury TD. Genetic health and population monitoring of two small black bear (Ursus americanus) populations in Alabama, with a regional perspective of genetic diversity and exchange. PLoS One 2017; 12:e0186701. [PMID: 29117263 PMCID: PMC5695604 DOI: 10.1371/journal.pone.0186701] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/05/2017] [Indexed: 11/18/2022] Open
Abstract
One of the major concerns in conservation today is the loss of genetic diversity which is a frequent consequence of population isolation and small population sizes. Fragmentation of populations and persecution of carnivores has posed a substantial threat to the persistence of free ranging carnivores in North America since the arrival of European settlers. Black bears have seen significant reductions in range size from their historic extent, which is most pronounced in the southeastern United States and even more starkly in Alabama where until recently bears were reduced to a single geographically isolated population in the Mobile River Basin. Recently a second population has naturally re-established itself in northeastern Alabama. We sought to determine size, genetic diversity and genetic connectivity for these two populations in relation to other regional populations. Both populations of black bears in Alabama had small population sizes and had moderate to low genetic diversity, but showed different levels of connectivity to surrounding populations of bears. The Mobile River Basin population had a small population size at only 86 individuals (76–124, 95% C.I.), the lowest genetic diversity of compared populations (richness = 2.33, Ho and He = 0.33), and showed near complete genetic isolation from surrounding populations across multiple tests. The newly recolonizing population in northeastern Alabama had a small but growing population doubling in 3 years (34 individuals 26–43, 95% C.I.), relatively moderate genetic diversity compared to surrounding populations (richness = 3.32, Ho = 0.53, He = 0.65), and showed a high level of genetic connectivity with surrounding populations.
Collapse
Affiliation(s)
- John P Draper
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Jennifer R Adams
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Christopher L Seals
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Todd D Steury
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, Alabama, United States of America
| |
Collapse
|
32
|
Murphy SM, Augustine BC, Ulrey WA, Guthrie JM, Scheick BK, McCown JW, Cox JJ. Consequences of severe habitat fragmentation on density, genetics, and spatial capture-recapture analysis of a small bear population. PLoS One 2017; 12:e0181849. [PMID: 28738077 PMCID: PMC5524351 DOI: 10.1371/journal.pone.0181849] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 07/07/2017] [Indexed: 11/19/2022] Open
Abstract
Loss and fragmentation of natural habitats caused by human land uses have subdivided several formerly contiguous large carnivore populations into multiple small and often isolated subpopulations, which can reduce genetic variation and lead to precipitous population declines. Substantial habitat loss and fragmentation from urban development and agriculture expansion relegated the Highlands-Glades subpopulation (HGS) of Florida, USA, black bears (Ursus americanus floridanus) to prolonged isolation; increasing human land development is projected to cause ≥ 50% loss of remaining natural habitats occupied by the HGS in coming decades. We conducted a noninvasive genetic spatial capture-recapture study to quantitatively describe the degree of contemporary habitat fragmentation and investigate the consequences of habitat fragmentation on population density and genetics of the HGS. Remaining natural habitats sustaining the HGS were significantly more fragmented and patchier than those supporting Florida’s largest black bear subpopulation. Genetic diversity was low (AR = 3.57; HE = 0.49) and effective population size was small (NE = 25 bears), both of which remained unchanged over a period spanning one bear generation despite evidence of some immigration. Subpopulation density (0.054 bear/km2) was among the lowest reported for black bears, was significantly female-biased, and corresponded to a subpopulation size of 98 bears in available habitat. Conserving remaining natural habitats in the area occupied by the small, genetically depauperate HGS, possibly through conservation easements and government land acquisition, is likely the most important immediate step to ensuring continued persistence of bears in this area. Our study also provides evidence that preferentially placing detectors (e.g., hair traps or cameras) primarily in quality habitat across fragmented landscapes poses a challenge to estimating density-habitat covariate relationships using spatial capture-recapture models. Because habitat fragmentation and loss are likely to increase in severity globally, further investigation of the influence of habitat fragmentation and detector placement on estimation of this relationship is warranted.
Collapse
Affiliation(s)
- Sean M. Murphy
- Department of Forestry, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
| | - Ben C. Augustine
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Wade A. Ulrey
- Department of Forestry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Joseph M. Guthrie
- Department of Forestry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Brian K. Scheick
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, Florida, United States of America
| | - J. Walter McCown
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, Florida, United States of America
| | - John J. Cox
- Department of Forestry, University of Kentucky, Lexington, Kentucky, United States of America
| |
Collapse
|
33
|
Ferguson AW, McDonough MM, Guerra GI, Rheude M, Dragoo JW, Ammerman LK, Dowler RC. Phylogeography of a widespread small carnivore, the western spotted skunk ( Spilogale gracilis) reveals temporally variable signatures of isolation across western North America. Ecol Evol 2017; 7:4229-4240. [PMID: 28649336 PMCID: PMC5478080 DOI: 10.1002/ece3.2931] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 12/26/2016] [Accepted: 02/21/2017] [Indexed: 02/06/2023] Open
Abstract
We analyzed phylogeographic patterns in the western spotted skunk, Spilogale gracilis Merriam, 1890 (Carnivora: Mephitidae) in relation to historical events associated with Pre-Pleistocene Divergence (PPD) and Quaternary climate change (QCC) using mitochondrial DNA from 97 individuals distributed across Western North America. Divergence times were generated using BEAST to estimate when isolation in putative refugia occurred. Patterns and timing of demographic expansion was performed using Bayesian skyline plot. Putative climatic refugia resulting from Quaternary climate change were identified using paleoecological niche modeling and divergence dates compared to major vicariant events associated with Pre-Pleistocene conditions. We recovered three major mitochondrial clades corresponding to western North America (California, Baja, and across the Great Basin), east-central North America (Texas, central Mexico, New Mexico), and southwestern Arizona/northwestern Mexico. Time to most recent common ancestor for S. gracilis occurred ~1.36 Ma. Divergence times for each major clade occurred between 0.25 and 0.12 Ma, with signature of population expansion occurring 0.15 and 0.10 Ma. Ecological niche models identified three potential climatic refugia during the Last Interglacial, (1) west coast of California and Oregon, (2) northwestern Mexico, and (3) southern Texas/northeastern Mexico as well as two refugia during the Last Glacial Maximum, (1) western USA and (2) southern Texas/northeastern Mexico. This study supports PPD in shaping species-level diversity compared to QCC-driven changes at the intraspecific level for Spilogale, similar to the patterns reported for other small mammals (e.g., rodents and bats). Phylogeographic patterns also appear to have been shaped by both habitat and river vicariance, especially across the desert southwest. Further, continuing climate change during the Holocene coupled with anthropogenic modifications during the Anthropocene appears to be removing both of these barriers to current dispersal of western spotted skunks.
Collapse
Affiliation(s)
| | - Molly M. McDonough
- Division of MammalsNational Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Gema I. Guerra
- Department of BiologyAngelo State UniversitySan AngeloTXUSA
| | - Margaret Rheude
- United States Fish and Wildlife ServiceTwin Cities Ecological Services OfficeBloomingtonMNUSA
| | - Jerry W. Dragoo
- Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNMUSA
| | | | | |
Collapse
|
34
|
Kumar V, Lammers F, Bidon T, Pfenninger M, Kolter L, Nilsson MA, Janke A. The evolutionary history of bears is characterized by gene flow across species. Sci Rep 2017; 7:46487. [PMID: 28422140 PMCID: PMC5395953 DOI: 10.1038/srep46487] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/17/2017] [Indexed: 01/03/2023] Open
Abstract
Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to large amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. Evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow.
Collapse
Affiliation(s)
- Vikas Kumar
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University Frankfurt, Institute for Ecology, Evolution &Diversity, Biologicum, Max-von-Laue-Str. 13, D-60439 Frankfurt am Main, Germany
| | - Fritjof Lammers
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University Frankfurt, Institute for Ecology, Evolution &Diversity, Biologicum, Max-von-Laue-Str. 13, D-60439 Frankfurt am Main, Germany
| | - Tobias Bidon
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University Frankfurt, Institute for Ecology, Evolution &Diversity, Biologicum, Max-von-Laue-Str. 13, D-60439 Frankfurt am Main, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University Frankfurt, Institute for Ecology, Evolution &Diversity, Biologicum, Max-von-Laue-Str. 13, D-60439 Frankfurt am Main, Germany
| | - Lydia Kolter
- AG Zoologischer Garten Cologne, Riehler Straße 173, 50735 Cologne, Germany
| | - Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University Frankfurt, Institute for Ecology, Evolution &Diversity, Biologicum, Max-von-Laue-Str. 13, D-60439 Frankfurt am Main, Germany
| |
Collapse
|
35
|
Sun CC, Fuller AK, Hare MP, Hurst JE. Evaluating population expansion of black bears using spatial capture-recapture. J Wildl Manage 2017. [DOI: 10.1002/jwmg.21248] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Catherine C. Sun
- New York Cooperative Fish and Wildlife Research Unit; Department of Natural Resources; Cornell University; Ithaca NY 14853 USA
| | - Angela K. Fuller
- U.S. Geological Survey; New York Cooperative Fish and Wildlife Research Unit; Department of Natural Resources; Cornell University; Ithaca NY 14853 USA
| | - Matthew P. Hare
- Department of Natural Resources; Cornell University; Ithaca NY 14853 USA
| | - Jeremy E. Hurst
- New York State Department of Environmental Conservation; Albany NY 12233 USA
| |
Collapse
|
36
|
Caro T, Walker H, Rossman Z, Hendrix M, Stankowich T. Why is the giant panda black and white? Behav Ecol 2017. [DOI: 10.1093/beheco/arx008] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
37
|
Caspermeyer J. Genomics of American Black Bears Reveal Surprising Ancient Migration Patterns to Aid Conservation Efforts. Mol Biol Evol 2015; 32:2498-9. [DOI: 10.1093/molbev/msv132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|