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Erwin JA, Logan KA, Trumbo DR, Funk WC, Culver M. Effects of hunting on mating, relatedness, and genetic diversity in a puma population. Mol Ecol 2024; 33:e17237. [PMID: 38084858 DOI: 10.1111/mec.17237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 10/18/2024]
Abstract
Hunting mortality can affect population abundance, demography, patterns of dispersal and philopatry, breeding, and genetic diversity. We investigated the effects of hunting on the reproduction and genetic diversity in a puma population in western Colorado, USA. We genotyped over 11,000 single nucleotide polymorphisms (SNPs), using double-digest, restriction site-associated DNA sequencing (ddRADseq) in 291 tissue samples collected as part of a study on the effects of hunting on puma population abundance and demography in Colorado from 2004 to 2014. The study was designed with a reference period (years 1-5), during which hunting was suspended, followed by a treatment period (years 6-10), in which hunting was reinstated. Our objectives were to examine the effects of hunting on: (1) paternity and male reproductive success; (2) the relatedness between pumas within the population, and (3) genetic diversity. We found that hunting reduced the average age of male breeders. The number of unique fathers siring litters increased each year without hunting and decreased each year during the hunting period. Mated pairs were generally unrelated during both time periods, and females were more closely related than males. Hunting was also associated with increased relatedness among males and decreased relatedness among females in the population. Finally, genetic diversity increased during the period without hunting and decreased each year when hunting was present. This study demonstrates the utility of merging demographic data with large-scale genomic datasets in order to better understand the consequences of management actions. Specifically, we believe that this study highlights the need for long-term experimental research in which hunting mortality is manipulated, including at least one non-harvested control population, as part of a broader adaptive, zone management scheme.
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Affiliation(s)
- John A Erwin
- Florida International University College of Law, Miami, Florida, USA
| | | | - Daryl R Trumbo
- Department of Biology, Colorado State University Pueblo, Pueblo, Colorado, USA
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | - Melanie Culver
- U.S. Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, University of Arizona, Tucson, Arizona, USA
- School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, USA
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2
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vonHoldt BM, DeCandia AL, Cassidy KA, Stahler EE, Sinsheimer JS, Smith DW, Stahler DR. Patterns of reproduction and autozygosity distinguish the breeding from nonbreeding gray wolves of Yellowstone National Park. J Hered 2024; 115:327-338. [PMID: 37793153 PMCID: PMC11235126 DOI: 10.1093/jhered/esad062] [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: 03/25/2023] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 10/06/2023] Open
Abstract
For species of management concern, accurate estimates of inbreeding and associated consequences on reproduction are crucial for predicting their future viability. However, few studies have partitioned this aspect of genetic viability with respect to reproduction in a group-living social mammal. We investigated the contributions of foundation stock lineages, putative fitness consequences of inbreeding, and genetic diversity of the breeding versus nonreproductive segment of the Yellowstone National Park gray wolf population. Our dataset spans 25 years and seven generations since reintroduction, encompassing 152 nuclear families and 329 litters. We found more than 87% of the pedigree foundation genomes persisted and report influxes of allelic diversity from two translocated wolves from a divergent source in Montana. As expected for group-living species, mean kinship significantly increased over time but with minimal loss of observed heterozygosity. Strikingly, the reproductive portion of the population carried a significantly lower genome-wide inbreeding coefficients, autozygosity, and more rapid decay for linkage disequilibrium relative to the nonbreeding population. Breeding wolves had significantly longer lifespans and lower inbreeding coefficients than nonbreeding wolves. Our model revealed that the number of litters was negatively significantly associated with heterozygosity (R = -0.11). Our findings highlight genetic contributions to fitness, and the importance of the reproductively active individuals in a population to counteract loss of genetic variation in a wild, free-ranging social carnivore. It is crucial for managers to mitigate factors that significantly reduce effective population size and genetic connectivity, which supports the dispersion of genetic variation that aids in rapid evolutionary responses to environmental challenges.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States
| | - Alexandra L DeCandia
- Department of Biology, Georgetown University, Washington, DC, United States
- Center for Conservation Genomics, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Kira A Cassidy
- Yellowstone Center for Resources, Yellowstone National Park, WY, United States
| | - Erin E Stahler
- Yellowstone Center for Resources, Yellowstone National Park, WY, United States
| | - Janet S Sinsheimer
- Department of Biostatistics, Fielding School of Public Health, UCLA, Los Angeles, CA, United States
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Douglas W Smith
- Yellowstone Center for Resources, Yellowstone National Park, WY, United States
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, WY, United States
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3
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Eriksson CE, Roffler GH, Allen JM, Lewis A, Levi T. The origin, connectivity, and individual specialization of island wolves after deer extirpation. Ecol Evol 2024; 14:e11266. [PMID: 38633525 PMCID: PMC11021858 DOI: 10.1002/ece3.11266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/28/2024] [Accepted: 03/30/2024] [Indexed: 04/19/2024] Open
Abstract
Wolves are assumed to be ungulate obligates, however, a recently described pack on Pleasant Island, Alaska USA, is persisting on sea otters and other marine resources without ungulate prey, violating this long-held assumption. We address questions about these wolves regarding their origin and fate, degree of isolation, risk of inbreeding depression, and diet specialization by individual and sex. We applied DNA metabarcoding and genotyping by amplicon sequencing using 957 scats collected from 2016 to 2022, and reduced representation sequencing of tissue samples to establish a detailed understanding of Pleasant Island wolf ecology and compare them with adjacent mainland wolves. Dietary overlap was higher among individual wolves on Pleasant Island (Pianka's index mean 0.95 ± 0.03) compared to mainland wolves (0.70 ± 0.21). The individual diets of island wolves were dominated by sea otter, ranging from 40.6% to 63.2% weighted percent of occurrence (wPOO) (mean 55.5 ± 8.7). In contrast, individual mainland wolves primarily fed on ungulates (42.2 ± 21.3) or voles during a population outbreak (31.2 ± 23.2). We traced the origin of the Pleasant Island pack to a mainland pair that colonized around 2013 and produced several litters. After this breeding pair was killed, their female offspring and an immigrant male became the new breeders in 2019. We detected 20 individuals of which 8 (40%) were trapped and killed while two died of natural causes during the 6-year study. Except for the new breeding male, the pedigree analysis and genotype results showed no additional movement to or from the island, indicating limited dispersal but no evidence of inbreeding. Our findings suggest wolves exhibit more flexible foraging behavior than previously believed, and hunting strategies can substantially differ between individuals within or between packs. Nevertheless, anthropogenic and natural mortality combined with limited connectivity to the mainland may inhibit the continued persistence of Pleasant Island wolves.
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Affiliation(s)
- Charlotte E. Eriksson
- Department of Fisheries, Wildlife, and Conservation SciencesOregon State UniversityCorvallisOregonUSA
| | - Gretchen H. Roffler
- Alaska Department of Fish and GameDivision of Wildlife ConservationDouglasAlaskaUSA
| | - Jennifer M. Allen
- Department of Fisheries, Wildlife, and Conservation SciencesOregon State UniversityCorvallisOregonUSA
| | - Alex Lewis
- Alaska Department of Fish and GameDivision of Wildlife ConservationDouglasAlaskaUSA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation SciencesOregon State UniversityCorvallisOregonUSA
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4
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Hoy SR, Hedrick PW, Peterson RO, Vucetich LM, Brzeski KE, Vucetich JA. The far-reaching effects of genetic process in a keystone predator species, grey wolves. SCIENCE ADVANCES 2023; 9:eadc8724. [PMID: 37611108 PMCID: PMC10446474 DOI: 10.1126/sciadv.adc8724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 07/24/2023] [Indexed: 08/25/2023]
Abstract
Although detrimental genetic processes are known to adversely affect the viability of populations, little is known about how detrimental genetic processes in a keystone species can affect the functioning of ecosystems. Here, we assessed how changes in the genetic characteristics of a keystone predator, grey wolves, affected the ecosystem of Isle Royale National Park over two decades. Changes in the genetic characteristic of the wolf population associated with a genetic rescue event, followed by high levels of inbreeding, led to a rise and then fall in predation rates on moose, the primary prey of wolves and dominant mammalian herbivore in this system. Those changes in predation rate led to large fluctuations in moose abundance, which in turn affected browse rates on balsam fir, the dominant forage for moose during winter and an important boreal forest species. Thus, forest dynamics can be traced back to changes in the genetic characteristics of a predator population.
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Affiliation(s)
- Sarah R. Hoy
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931
| | | | - Rolf O. Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931
| | - Leah M. Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931
| | - Kristin E. Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931
| | - John A. Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931
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5
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SunderRaj J, Rabe JW, Cassidy KA, McIntyre R, Stahler DR, Smith DW. Breeding displacement in gray wolves (Canis lupus): Three males usurp breeding position and pup rearing from a neighboring pack in Yellowstone National Park. PLoS One 2022; 17:e0256618. [PMID: 36449452 PMCID: PMC9710779 DOI: 10.1371/journal.pone.0256618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/02/2022] [Indexed: 12/02/2022] Open
Abstract
Gray Wolves (Canis lupus) are territorial, group living carnivores that live in packs typically consisting of a dominant breeding pair and their offspring. Breeding tenures are relatively short and competitive, with vacancies usually occurring following a breeder's death, and are often filled by unrelated immigrants or by relatives of the previous breeder. The frequency and conditions of active breeder displacements are poorly understood. Position changes in the dominance hierarchy are common yet rarely documented in detail. We describe a male breeding position turnover in a wolf pack by males from a neighboring pack in mid-summer 2016 in Yellowstone National Park. Over the course of two months, three males from the Mollie's pack displaced the breeding male of the neighboring Wapiti Lake pack, joined the pack's two adult females, and subsequently raised the previous male's four approximately three-month old pups. In the five years following the displacement (2017 to 2021), at least one of the intruding males has successfully bred with the dominant female and most years with a subordinate female (who was one of the pups at the time of displacement). The pack reared pups to adulthood each year. Male breeding displacements are likely influenced by male-male competition and female mate choice. These changes are the result of individuals competing to improve breeding position and may lead to increased pack stability and greater reproductive success. We report in detail on the behavior of a closely observed breeding displacement and we discuss the adaptive benefits of the change.
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Affiliation(s)
- Jeremy SunderRaj
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, United States of America
- * E-mail:
| | - Jack W. Rabe
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, United States of America
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Kira A. Cassidy
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, United States of America
| | - Rick McIntyre
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, United States of America
| | - Daniel R. Stahler
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, United States of America
| | - Douglas W. Smith
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, United States of America
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6
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Caragiulo A, Gaughran SJ, Duncan N, Nagy C, Weckel M, vonHoldt BM. Coyotes in New York City Carry Variable Genomic Dog Ancestry and Influence Their Interactions with Humans. Genes (Basel) 2022; 13:1661. [PMID: 36140828 PMCID: PMC9498729 DOI: 10.3390/genes13091661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/03/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Coyotes are ubiquitous on the North American landscape as a result of their recent expansion across the continent. They have been documented in the heart of some of the most urbanized cities, such as Chicago, Los Angeles, and New York City. Here, we explored the genomic composition of 16 coyotes in the New York metropolitan area to investigate genomic demography and admixture for urban-dwelling canids in Queens County, New York. We identified moderate-to-high estimates of relatedness among coyotes living in Queens (r = 0.0-0.5) and adjacent neighborhoods, suggestive of a relatively small population. Although we found low background levels of domestic-dog ancestry across most coyotes in our sample (5%), we identified a male suspected to be a first-generation coyote-dog hybrid with 46% dog ancestry, as well as his two putative backcrossed offspring that carried approximately 25% dog ancestry. The male coyote-dog hybrid and one backcrossed offspring each carried two transposable element insertions that are associated with human-directed hypersociability in dogs and gray wolves. An additional, unrelated coyote with little dog ancestry also carried two of these insertions. These genetic patterns suggest that gene flow from domestic dogs may become an increasingly important consideration as coyotes continue to inhabit metropolitan regions.
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Affiliation(s)
| | - Stephen J. Gaughran
- American Museum of Natural History, New York, NY 10024, USA
- Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Neil Duncan
- American Museum of Natural History, New York, NY 10024, USA
| | | | - Mark Weckel
- American Museum of Natural History, New York, NY 10024, USA
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Rubbi L, Zhang H, Feng J, He C, Kurnia P, Ratan P, Tammana A, House S, Thompson M, Farrell C, Snir S, Stahler D, Ostrander EA, vonHoldt BM, Pellegrini M. The effects of age, sex, weight, and breed on canid methylomes. Epigenetics 2022; 17:1497-1512. [PMID: 35502722 PMCID: PMC9586589 DOI: 10.1080/15592294.2022.2069385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Unlike genomes, which are static throughout the lifespan of an organism, DNA methylomes are dynamic. To study these dynamics, we developed quantitative models that measure the effect of multiple factors on DNA methylomes including, age, sex, weight, and genetics. We conducted our study in canids, which prove to be an ideal species to assess epigenetic moderators due to their extreme variability in size and well-characterized genetic structure. We collected buccal swabs from 217 canids (207 domestic dogs and 10 grey wolves) and used targeted bisulphite sequencing to measure methylomes. We also measured genotypes at over one thousand single nucleotide polymorphisms (SNPs). As expected, we found that DNA methylomes are strongly associated with age, enabling the construction of epigenetic clocks. However, we also identify novel associations between methylomes and sex, weight, and sterilization status, leading to accurate models that predict these factors. Methylomes are also affected by genetics, and we observe multiple associations between SNP loci and methylated CpGs. Finally, we show that several factors moderate the relationship between epigenetic ages and real ages, such as body weight, which increases epigenetic ageing. In conclusion, we demonstrate that the plasticity of DNA methylomes is impacted by myriad genetics and physiological factors, and that DNA methylation biomarkers are accurate predictors of age, sex and sterilization status.
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Affiliation(s)
- Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Haoxuan Zhang
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Junxi Feng
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Christopher He
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Patrick Kurnia
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Prashansa Ratan
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Aakash Tammana
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Sabina House
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael Thompson
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Colin Farrell
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Sagi Snir
- Department Evolutionary and Environmental Biology, University of Haifa, Israel
| | - Daniel Stahler
- Yellowstone Center for Resources, Yellowstone National Park, Wyo, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, CA, USA
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
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8
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Comparing wolves and dogs: current status and implications for human ‘self-domestication’. Trends Cogn Sci 2022; 26:337-349. [DOI: 10.1016/j.tics.2022.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 01/02/2023]
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9
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Galla SJ, Brown L, Couch-Lewis Ngāi Tahu Te Hapū O Ngāti Wheke Ngāti Waewae Y, Cubrinovska I, Eason D, Gooley RM, Hamilton JA, Heath JA, Hauser SS, Latch EK, Matocq MD, Richardson A, Wold JR, Hogg CJ, Santure AW, Steeves TE. The relevance of pedigrees in the conservation genomics era. Mol Ecol 2021; 31:41-54. [PMID: 34553796 PMCID: PMC9298073 DOI: 10.1111/mec.16192] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/12/2021] [Accepted: 09/17/2021] [Indexed: 01/21/2023]
Abstract
Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome‐wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.
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Affiliation(s)
- Stephanie J Galla
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA.,School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Liz Brown
- New Zealand Department of Conservation, Twizel, Canterbury, New Zealand
| | | | - Ilina Cubrinovska
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Daryl Eason
- New Zealand Department of Conservation, Invercargill, Southland, New Zealand
| | - Rebecca M Gooley
- Smithsonian-Mason School of Conservation, Front Royal, Maryland, USA.,Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Jill A Hamilton
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Julie A Heath
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - Samantha S Hauser
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Emily K Latch
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science, Program in Ecology, Evolution and Conservation Biology, University of Nevada Reno, Reno, Nevada, USA
| | - Anne Richardson
- The Isaac Conservation and Wildlife Trust, Christchurch, Canterbury, New Zealand
| | - Jana R Wold
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Auckland, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
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10
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Benítez-Burraco A, Pörtl D, Jung C. Did Dog Domestication Contribute to Language Evolution? Front Psychol 2021; 12:695116. [PMID: 34589022 PMCID: PMC8473740 DOI: 10.3389/fpsyg.2021.695116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/02/2021] [Indexed: 11/20/2022] Open
Abstract
Different factors seemingly account for the emergence of present-day languages in our species. Human self-domestication has been recently invoked as one important force favoring language complexity mostly via a cultural mechanism. Because our self-domestication ultimately resulted from selection for less aggressive behavior and increased prosocial behavior, any evolutionary or cultural change impacting on aggression levels is expected to have fostered this process. Here, we hypothesize about a parallel domestication of humans and dogs, and more specifically, about a positive effect of our interaction with dogs on human self-domestication, and ultimately, on aspects of language evolution, through the mechanisms involved in the control of aggression. We review evidence of diverse sort (ethological mostly, but also archeological, genetic, and physiological) supporting such an effect and propose some ways of testing our hypothesis.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain
| | - Daniela Pörtl
- Psychiatric Department, Saale-Unstrut Klinikum, Teaching Hospital Leipzig and Jena Universities, Naumburg, Germany
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11
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DeCandia AL, Cassidy KA, Stahler DR, Stahler EA, vonHoldt BM. Social environment and genetics underlie body site-specific microbiomes of Yellowstone National Park gray wolves ( Canis lupus). Ecol Evol 2021; 11:9472-9488. [PMID: 34306636 PMCID: PMC8293786 DOI: 10.1002/ece3.7767] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/20/2021] [Accepted: 05/24/2021] [Indexed: 12/17/2022] Open
Abstract
The host-associated microbiome is an important player in the ecology and evolution of species. Despite growing interest in the medical, veterinary, and conservation communities, there remain numerous questions about the primary factors underlying microbiota, particularly in wildlife. We bridged this knowledge gap by leveraging microbial, genetic, and observational data collected in a wild, pedigreed population of gray wolves (Canis lupus) inhabiting Yellowstone National Park. We characterized body site-specific microbes across six haired and mucosal body sites (and two fecal samples) using 16S rRNA amplicon sequencing. At the phylum level, we found that the microbiome of gray wolves primarily consists of Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria, consistent with previous studies within Mammalia and Canidae. At the genus level, we documented body site-specific microbiota with functions relevant to microenvironment and local physiological processes. We additionally employed observational and RAD sequencing data to examine genetic, demographic, and environmental correlates of skin and gut microbiota. We surveyed individuals across several levels of pedigree relationships, generations, and social groups, and found that social environment (i.e., pack) and genetic relatedness were two primary factors associated with microbial community composition to differing degrees between body sites. We additionally reported body condition and coat color as secondary factors underlying gut and skin microbiomes, respectively. We concluded that gray wolf microbiota resemble similar host species, differ between body sites, and are shaped by numerous endogenous and exogenous factors. These results provide baseline information for this long-term study population and yield important insights into the evolutionary history, ecology, and conservation of wild wolves and their associated microbes.
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Affiliation(s)
- Alexandra L. DeCandia
- Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
- Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Kira A. Cassidy
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
| | - Daniel R. Stahler
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
| | - Erin A. Stahler
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
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12
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DeCandia AL, Schrom EC, Brandell EE, Stahler DR, vonHoldt BM. Sarcoptic mange severity is associated with reduced genomic variation and evidence of selection in Yellowstone National Park wolves ( Canis lupus). Evol Appl 2021; 14:429-445. [PMID: 33664786 PMCID: PMC7896714 DOI: 10.1111/eva.13127] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/28/2020] [Accepted: 08/25/2020] [Indexed: 01/25/2023] Open
Abstract
Population genetic theory posits that molecular variation buffers against disease risk. Although this "monoculture effect" is well supported in agricultural settings, its applicability to wildlife populations remains in question. In the present study, we examined the genomics underlying individual-level disease severity and population-level consequences of sarcoptic mange infection in a wild population of canids. Using gray wolves (Canis lupus) reintroduced to Yellowstone National Park (YNP) as our focal system, we leveraged 25 years of observational data and biobanked blood and tissue to genotype 76,859 loci in over 400 wolves. At the individual level, we reported an inverse relationship between host genomic variation and infection severity. We additionally identified 410 loci significantly associated with mange severity, with annotations related to inflammation, immunity, and skin barrier integrity and disorders. We contextualized results within environmental, demographic, and behavioral variables, and confirmed that genetic variation was predictive of infection severity. At the population level, we reported decreased genome-wide variation since the initial gray wolf reintroduction event and identified evidence of selection acting against alleles associated with mange infection severity. We concluded that genomic variation plays an important role in disease severity in YNP wolves. This role scales from individual to population levels, and includes patterns of genome-wide variation in support of the monoculture effect and specific loci associated with the complex mange phenotype. Results yielded system-specific insights, while also highlighting the relevance of genomic analyses to wildlife disease ecology, evolution, and conservation.
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Affiliation(s)
| | - Edward C. Schrom
- Ecology & Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
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Rieseberg L, Warschefsky E, O’Boyle B, Taberlet P, Ortiz‐Barrientos D, Kane NC, Sibbett B. Editorial 2021. Mol Ecol 2020. [DOI: 10.1111/mec.15759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Schell CJ. Investigating the genetic and environmental architecture of interpack aggression in North American grey wolves. Mol Ecol 2020; 29:1757-1760. [PMID: 32323884 DOI: 10.1111/mec.15453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/01/2020] [Accepted: 04/09/2020] [Indexed: 11/30/2022]
Abstract
Aggression confers several fitness benefits including increased breeding opportunities and resource acquisition. Determining the relative contributions of genetic and environmental components to shaping aggression is essential for advancing our understanding of how selection affects the distribution of aggressive phenotypes in a population. In a From the Cover article in this issue of Molecular Ecology, vonHoldt et al. (2020) used RAD-seq methods to obtain genome-wide single nucleotide polymorphism (SNP) data to estimate heritability of interpack aggression of 141 North American grey wolves (Canis lupus) surveyed from 1995-2018. The authors inferred heritability using both a SNP-based genetic relationship matrix (GRM) and a consensus pedigree informed by: (a) previously obtained microsatellite data; (b) past observations of parentage; and (c) statistical reconstruction of parent-offspring pairs. SNP-based (i.e., GRM) and pedigree-based (i.e., consensus pedigree) heritability estimates were 37% and 14%, respectively, with an additional 14%-16% explained by natal pack effects. The study confirmed the previously discovered strong effects of relative pack size and breeding status on interpack aggression, illustrating how social dynamics and density-dependent factors induce variance in aggressive behaviours. Finally, the authors found associations between average individual aggression scores (IAS) and specific candidate genes (MY09A and TRAK1). In sum, vonHoldt et al. (2020) provides an unprecedented and nuanced synthesis that not only suggests gene-aggression associations, but also emphasizes how additive genetic variance and density-dependent factors interact to maintain phenotypic variance in aggression over time.
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Affiliation(s)
- Christopher J Schell
- School of Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, WA, USA
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