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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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2
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Ochoa A, Onorato DP, Roelke-Parker ME, Culver M, Fitak RR. Give and Take: Effects of Genetic Admixture on Mutation Load in Endangered Florida Panthers. J Hered 2022; 113:491-499. [PMID: 35930593 DOI: 10.1093/jhered/esac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 08/02/2022] [Indexed: 11/14/2022] Open
Abstract
Genetic admixture is a biological event inherent to genetic rescue programs aimed at the long-term conservation of endangered wildlife. Although the success of such programs can be measured by the increase in genetic diversity and fitness of subsequent admixed individuals, predictions supporting admixture costs to fitness due to the introduction of novel deleterious alleles are necessary. Here, we analyzed nonsynonymous variation from conserved genes to quantify and compare levels of mutation load (i.e., proportion of deleterious alleles and genotypes carrying these alleles) among endangered Florida panthers and non-endangered Texas pumas. Specifically, we used canonical (i.e., non-admixed) Florida panthers, Texas pumas, and F1 (canonical Florida x Texas) panthers dating from a genetic rescue program and Everglades National Park panthers with Central American ancestry resulting from an earlier admixture event. We found neither genetic drift nor selection significantly reduced overall proportions of deleterious alleles in the severely bottlenecked canonical Florida panthers. Nevertheless, the deleterious alleles identified were distributed into a disproportionately high number of homozygous genotypes due to close inbreeding in this group. Conversely, admixed Florida panthers (either with Texas or Central American ancestry) presented reduced levels of homozygous genotypes carrying deleterious alleles but increased levels of heterozygous genotypes carrying these variants relative to canonical Florida panthers. Although admixture is likely to alleviate the load of standing deleterious variation present in homozygous genotypes, our results suggest introduced novel deleterious alleles (temporarily present in heterozygous state) in genetically rescued populations could potentially be expressed in subsequent generations if their effective sizes remain small.
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Affiliation(s)
- Alexander Ochoa
- Department of Biology and Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL
| | - David P Onorato
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL
| | - Melody E Roelke-Parker
- Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD
| | - Melanie Culver
- U.S. Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, and School of Natural Resources and the Environment, University of Arizona, Tucson, AZ
| | - Robert R Fitak
- Department of Biology and Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL
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3
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Anderson H, Davison S, Lytle KM, Honkanen L, Freyer J, Mathlin J, Kyöstilä K, Inman L, Louviere A, Chodroff Foran R, Forman OP, Lohi H, Donner J. Genetic epidemiology of blood type, disease and trait variants, and genome-wide genetic diversity in over 11,000 domestic cats. PLoS Genet 2022; 18:e1009804. [PMID: 35709088 PMCID: PMC9202916 DOI: 10.1371/journal.pgen.1009804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 05/06/2022] [Indexed: 11/30/2022] Open
Abstract
In the largest DNA-based study of domestic cats to date, 11,036 individuals (10,419 pedigreed cats and 617 non-pedigreed cats) were genotyped via commercial panel testing elucidating the distribution and frequency of known disease, blood type, and physical trait associated genetic variants across cat breeds. This study provides allele frequencies for many disease-associated variants for the first time and provides updates on previously reported information with evidence suggesting that DNA testing has been effectively used to reduce disease associated variants within certain pedigreed cat populations over time. We identified 13 disease-associated variants in 47 breeds or breed types in which the variant had not previously been documented, highlighting the relevance of comprehensive genetic screening across breeds. Three disease-associated variants were discovered in non-pedigreed cats only. To investigate the causality of nine disease-associated variants in cats of different breed backgrounds our veterinarians conducted owner interviews, reviewed clinical records, and invited cats to have follow-up clinical examinations. Additionally, genetic variants determining blood types A, B and AB, which are relevant clinically and in cat breeding, were genotyped. Appearance-associated genetic variation in all cats is also discussed. Lastly, genome-wide SNP heterozygosity levels were calculated to obtain a comparable measure of the genetic diversity in different cat breeds. This study represents the first comprehensive exploration of informative Mendelian variants in felines by screening over 10,000 pedigreed cats. The results qualitatively contribute to the understanding of feline variant heritage and genetic diversity and demonstrate the clinical utility and importance of such information in supporting breeding programs and the research community. The work also highlights the crucial commitment of pedigreed cat breeders and registries in supporting the establishment of large genomic databases, that when combined with phenotype information can advance scientific understanding and provide insights that can be applied to improve the health and welfare of cats. Domestic cats are one of the world’s most popular companion animals, of which pedigreed cats represent small unique subpopulations. Genetic research on pedigreed cats has facilitated discoveries of heritable conditions resulting in the availability of DNA testing for studying and managing inherited disorders and traits in specific cat breeds. We have explored an extensive study cohort of 11,036 domestic cat samples representing pedigreed cats of 90 breeds and breed types. This work provided insight into the heritage of feline disease and trait alleles. We gained knowledge on the most common and relevant genetic markers for inherited disorders and physical traits, and the genetic determinants of the clinically relevant AB blood group system. We also used a measure of genetic diversity to compare inbreeding levels within and between breeds. This information can help support sustainable breeding goals within the cat fancy. Direct-to-consumer genetic tests help to raise awareness of various inherited single gene conditions in cats and provide information that owners can share with their veterinarians. In due course, ventures of this type will enable the genetics of common complex feline disease to be deciphered, paving the way for precision healthcare with the potential to ultimately improve welfare for all cats.
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Affiliation(s)
- Heidi Anderson
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
- * E-mail:
| | - Stephen Davison
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Katherine M. Lytle
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Leena Honkanen
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Jamie Freyer
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Julia Mathlin
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Kaisa Kyöstilä
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Laura Inman
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Annette Louviere
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Rebecca Chodroff Foran
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Oliver P. Forman
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Jonas Donner
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
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Hyperthyroidism in the Domestic Cat ( Felis catus): Informed Treatment Choice Based on Survival Analysis. MACEDONIAN VETERINARY REVIEW 2022. [DOI: 10.2478/macvetrev-2022-0015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Hyperthyroidism is the most frequently diagnosed endocrine disorder in cats. Therapy may include pharmacological, surgical (thyroidectomy), radioactive (iodine), and dietary treatment. The choice of treatment is believed to be strongly influenced by the veterinarian’s experience, level of education, and knowledge of the current scientific literature. The history of survival rates can affect the decision for treatment by both the veterinarian and the owner. This study aimed to explore the longevity in cats diagnosed with hyperthyroidism and to identify significant variables which affect survival rates by using retrospective data from the practice. A multivariate Cox regression was applied with the following results: surgical thyroidectomy and methimazole medication produced similar longevity (median 23.5 months, P>0.05); Domestic Short Hair cats survived longer than pure breeds (median 27.2 vs 9.4 months, P<0.05); as do cats without chronic renal disease (median 28.1 vs 6.2 months, P<0.001); and those with low activities of alanine aminotransferase (median 27.1 vs 17.0 months, P<0.01). Hyperthyroidism is comorbid with renal diseases, but no cumulative effect was found on survivability. There was no difference in survival rates between surgical and pharmaceutical treatment, therefore the discussion of treatment options with owners can focus on other factors (e.g., cost, owners’ compliance, cats’ tolerance to medication, presence of comorbidities). We propose that surgery may be the preferred treatment when the survival rates are expected to be higher than one year. This would avoid high costs and potential side effects of medication.
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6
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Logan KA, Runge JP. Effects of Hunting on a Puma Population in Colorado. WILDLIFE MONOGRAPHS 2021. [DOI: 10.1002/wmon.1061] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Kenneth A. Logan
- Colorado Parks and Wildlife, 2300 S. Townsend Avenue Montrose CO 81401 USA
| | - Jonathan P. Runge
- Colorado Parks and Wildlife, 317 W. Prospect Road Fort Collins CO 80526 USA
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7
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Newhouse AE, Powell WA. Intentional introgression of a blight tolerance transgene to rescue the remnant population of American chestnut. CONSERVATION SCIENCE AND PRACTICE 2020. [DOI: 10.1111/csp2.348] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Andrew E. Newhouse
- Department of Environmental and Forest Biology SUNY College of Environmental Science and Forestry Syracuse New York USA
| | - William A. Powell
- Department of Environmental and Forest Biology SUNY College of Environmental Science and Forestry Syracuse New York USA
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8
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De Novo Assembly and Annotation from Parental and F 1 Puma Genomes of the Florida Panther Genetic Restoration Program. G3-GENES GENOMES GENETICS 2019; 9:3531-3536. [PMID: 31519748 PMCID: PMC6829145 DOI: 10.1534/g3.119.400629] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In the mid-1990s, the population size of Florida panthers became so small that many individuals manifested traits associated with inbreeding depression (e.g., heart defects, cryptorchidism, high pathogen-parasite load). To mitigate these effects, pumas from Texas were introduced into South Florida to augment genetic variation in Florida panthers. In this study, we report a de novo puma genome assembly and annotation after resequencing 10 individual genomes from partial Florida-Texas-F1 trios. The final genome assembly consisted of ∼2.6 Gb and 20,561 functionally annotated protein-coding genes. Foremost, expanded gene families were associated with neuronal and embryological development, whereas contracted gene families were associated with olfactory receptors. Despite the latter, we characterized 17 positively selected genes related to the refinement of multiple sensory perceptions, most notably to visual capabilities. Furthermore, genes under positive selection were enriched for the targeting of proteins to the endoplasmic reticulum, degradation of mRNAs, and transcription of viral genomes. Nearly half (48.5%) of ∼6.2 million SNPs analyzed in the total sample set contained putative unique Texas alleles. Most of these alleles were likely inherited to subsequent F1 Florida panthers, as these individuals manifested a threefold increase in observed heterozygosity with respect to their immediate, canonical Florida panther predecessors. Demographic simulations were consistent with a recent colonization event in North America by a small number of founders from South America during the last glacial period. In conclusion, we provide an extensive set of genomic resources for pumas and elucidate the genomic effects of genetic rescue on this iconic conservation success story.
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9
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Malmberg JL, Lee JS, Gagne RB, Kraberger S, Kechejian S, Roelke M, McBride R, Onorato D, Cunningham M, Crooks KR, VandeWoude S. Altered lentiviral infection dynamics follow genetic rescue of the Florida panther. Proc Biol Sci 2019; 286:20191689. [PMID: 31640509 DOI: 10.1098/rspb.2019.1689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Wildlife translocations are a commonly used strategy in endangered species recovery programmes. Although translocations require detailed assessment of risk, their impact on parasite distribution has not been thoroughly assessed. This is despite the observation that actions that alter host-parasite distributions can drive evolution or introduce new parasites to previously sequestered populations. Here, we use a contemporary approach to amplify viral sequences from archived biological samples to characterize a previously undocumented impact of the successful genetic rescue of the Florida panther (Puma concolor coryi). Our efforts reveal transmission of feline immunodeficiency virus (FIV) during translocation of pumas from Texas to Florida, resulting in extirpation of a historic Florida panther FIV subtype and expansion of a genetically stable subtype that is highly conserved in Texas and Florida. We used coalescent theory to estimate viral demography across time and show an exponential increase in the effective population size of FIV coincident with expansion of the panther population. Additionally, we show that FIV isolates from Texas are basal to isolates from Florida. Interestingly, FIV genomes recovered from Florida and Texas demonstrate exceptionally low interhost divergence. Low host genomic diversity and lack of additional introgressions may underlie the surprising lack of FIV evolution over 2 decades. We conclude that modern FIV in the Florida panther disseminated following genetic rescue and rapid population expansion, and that infectious disease risks should be carefully considered during conservation efforts involving translocations. Further, viral evolutionary dynamics may be significantly altered by ecological niche, host diversity and connectivity between host populations.
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Affiliation(s)
- Jennifer L Malmberg
- Department of Veterinary Sciences, University of Wyoming, Wyoming State Veterinary Laboratory, Laramie, WY, USA
| | - Justin S Lee
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Roderick B Gagne
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Simona Kraberger
- The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Sarah Kechejian
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | | | | | - Dave Onorato
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL, USA
| | - Mark Cunningham
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, FL, USA
| | - Kevin R Crooks
- Department of Fish, Wildlife, and Conservation Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
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Kerk M, Onorato DP, Hostetler JA, Bolker BM, Oli MK. Dynamics, Persistence, and Genetic Management of the Endangered Florida Panther Population. WILDLIFE MONOGRAPHS 2019. [DOI: 10.1002/wmon.1041] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Madelon Kerk
- Department of Wildlife Ecology and Conservation University of Florida 110 Newins‐Ziegler Hall Gainesville FL 32611‐0430 USA
| | - David P. Onorato
- Fish and Wildlife Research Institute Florida Fish and Wildlife Conservation Commission 298 Sabal Palm Road Naples FL 34114 USA
| | - Jeffrey A. Hostetler
- Fish and Wildlife Research Institute Florida Fish and Wildlife Conservation Commission 100 8th Avenue SE St. Petersburg FL 33701 USA
| | - Benjamin M. Bolker
- Departments of Mathematics and Statistics and Biology McMaster University 314 Hamilton Hall Hamilton ON L8S 4K1 Canada
| | - Madan K. Oli
- Department of Wildlife Ecology and Conservation University of Florida 110 Newins‐Ziegler Hall Gainesville FL 32611‐0430 USA
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11
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Benson JF, Mahoney PJ, Vickers TW, Sikich JA, Beier P, Riley SPD, Ernest HB, Boyce WM. Extinction vortex dynamics of top predators isolated by urbanization. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01868. [PMID: 30892753 DOI: 10.1002/eap.1868] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/30/2018] [Accepted: 01/03/2019] [Indexed: 05/18/2023]
Abstract
Extinction risk is elevated in small, isolated populations due to demographic and genetic interactions. Therefore, it is critical to model these processes realistically in population viability analyses (PVA) to inform local management and contribute to a greater understanding of mechanisms within the extinction vortex. We conducted PVA's for two small mountain lion populations isolated by urbanization in southern California to predict population growth, extinction probability, and loss of genetic diversity with empirical data. Specifically, we (1) provide the first PVA for isolated mountain lions in the Santa Ana Mountains (SAM) that considers both demographic and genetic risk factors and (2) test the hypothesis that variation in abundance and mortality between the SAM and Santa Monica Mountains (SMM) result in differences in population growth, loss of heterozygosity, and extinction probability. Our models predicted 16-21% probability of local extinction in the SAM due purely to demographic processes over 50 yr with current low levels or no immigration. Our models also predicted that genetic diversity will further erode in the SAM such that concern regarding inbreeding depression is warranted unless gene flow is increased, and that if inbreeding depression occurs, rapid local extinction will be highly likely. Dynamics of the two populations were broadly similar, but they also exhibited differences driven by larger population size and higher mortality in the SAM. Density-independent scenarios predicted a rapidly increasing population in the SMM, whereas growth potential did not differ from a stable trend in the SAM. Demographic extinction probability and loss of heterozygosity were greater in the SMM for density-dependent scenarios without immigration. However, higher levels of immigration had stronger, positive influences on both demographic viability and retention of genetic diversity in the SMM driven by lower abundance and higher adult survival. Our results elucidate demographic and genetic threats to small populations within the extinction vortex, and how these vary relative to demographic structure. Importantly, simulating seemingly attainable increases in connectivity was sufficient to greatly reduce extinction probability. Our work highlights that conservation of large carnivores is achievable within urbanized landscapes, but requires land protection, connectivity, and strategies to promote coexistence with humans.
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Affiliation(s)
- John F Benson
- School of Natural Resources, University of Nebraska, Lincoln, Nebraska, 68583, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, California, 90095, USA
| | - Peter J Mahoney
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - T Winston Vickers
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, California, 95616, USA
| | - Jeff A Sikich
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, California, 91360, USA
| | - Paul Beier
- School of Forestry, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Seth P D Riley
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, California, 90095, USA
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, California, 91360, USA
| | - Holly B Ernest
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, 82071, USA
| | - Walter M Boyce
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, California, 95616, USA
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12
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Genetic source–sink dynamics among naturally structured and anthropogenically fragmented puma populations. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1125-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Malukiewicz J. A Review of Experimental, Natural, and Anthropogenic Hybridization in Callithrix Marmosets. INT J PRIMATOL 2018. [DOI: 10.1007/s10764-018-0068-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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McDonald TK, Yeaman S. Effect of migration and environmental heterogeneity on the maintenance of quantitative genetic variation: a simulation study. J Evol Biol 2018; 31:1386-1399. [PMID: 29938863 DOI: 10.1111/jeb.13341] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 06/15/2018] [Accepted: 06/19/2018] [Indexed: 01/15/2023]
Abstract
The paradox of high genetic variation observed in traits under stabilizing selection is a long-standing problem in evolutionary theory, as mutation rates appear too low to explain observed levels of standing genetic variation under classic models of mutation-selection balance. Spatially or temporally heterogeneous environments can maintain more standing genetic variation within populations than homogeneous environments, but it is unclear whether such conditions can resolve the above discrepancy between theory and observation. Here, we use individual-based simulations to explore the effect of various types of environmental heterogeneity on the maintenance of genetic variation (VA ) for a quantitative trait under stabilizing selection. We find that VA is maximized at intermediate migration rates in spatially heterogeneous environments and that the observed patterns are robust to changes in population size. Spatial environmental heterogeneity increased variation by as much as 10-fold over mutation-selection balance alone, whereas pure temporal environmental heterogeneity increased variance by only 45% at max. Our results show that some combinations of spatial heterogeneity and migration can maintain considerably more variation than mutation-selection balance, potentially reconciling the discrepancy between theoretical predictions and empirical observations. However, given the narrow regions of parameter space required for this effect, this is unlikely to provide a general explanation for the maintenance of variation. Nonetheless, our results suggest that habitat fragmentation may affect the maintenance of VA and thereby reduce the adaptive capacity of populations.
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Affiliation(s)
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Canada
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15
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Cairns KM, Shannon LM, Koler-Matznick J, Ballard JWO, Boyko AR. Elucidating biogeographical patterns in Australian native canids using genome wide SNPs. PLoS One 2018; 13:e0198754. [PMID: 29889854 PMCID: PMC5995383 DOI: 10.1371/journal.pone.0198754] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 05/24/2018] [Indexed: 11/19/2022] Open
Abstract
Dingoes play a strong role in Australia's ecological framework as the apex predator but are under threat from hybridization and agricultural control programs. Government legislation lists the conservation of the dingo as an important aim, yet little is known about the biogeography of this enigmatic canine, making conservation difficult. Mitochondrial and Y chromosome DNA studies show evidence of population structure within the dingo. Here, we present the data from Illumina HD canine chip genotyping for 23 dingoes from five regional populations, and five New Guinea Singing Dogs to further explore patterns of biogeography using genome-wide data. Whole genome single nucleotide polymorphism (SNP) data supported the presence of three distinct dingo populations (or ESUs) subject to geographical subdivision: southeastern (SE), Fraser Island (FI) and northwestern (NW). These ESUs should be managed discretely. The FI dingoes are a known reservoir of pure, genetically distinct dingoes. Elevated inbreeding coefficients identified here suggest this population may be genetically compromised and in need of rescue; current lethal management strategies that do not consider genetic information should be suspended until further data can be gathered. D statistics identify evidence of historical admixture or ancestry sharing between southeastern dingoes and South East Asian village dogs. Conservation efforts on mainland Australia should focus on the SE dingo population that is under pressure from domestic dog hybridization and high levels of lethal control. Further data concerning the genetic health, demographics and prevalence of hybridization in the SE and FI dingo populations is urgently needed to develop evidence based conservation and management strategies.
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Affiliation(s)
- Kylie M. Cairns
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail: ,
| | - Laura M. Shannon
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Janice Koler-Matznick
- The New Guinea Singing Dog Conservation Society, Central Point, Oregon, United States of America
| | - J. William O. Ballard
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Adam R. Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
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16
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Levänen R, Kunnasranta M, Pohjoismäki J. Mitochondrial DNA Introgression at the Northern Edge of the Brown Hare (Lepus europaeus) Range. ANN ZOOL FENN 2018. [DOI: 10.5735/086.055.0103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Riikka Levänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
| | - Mervi Kunnasranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
- Natural Resources Institute Finland (Luke), Yliopistokatu 6, FI-80100, Joensuu, Finland
| | - Jaakko Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
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17
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Benson JF, Mahoney PJ, Sikich JA, Serieys LEK, Pollinger JP, Ernest HB, Riley SPD. Interactions between demography, genetics, and landscape connectivity increase extinction probability for a small population of large carnivores in a major metropolitan area. Proc Biol Sci 2017; 283:rspb.2016.0957. [PMID: 27581877 DOI: 10.1098/rspb.2016.0957] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/11/2016] [Indexed: 11/12/2022] Open
Abstract
The extinction vortex is a theoretical model describing the process by which extinction risk is elevated in small, isolated populations owing to interactions between environmental, demographic, and genetic factors. However, empirical demonstrations of these interactions have been elusive. We modelled the dynamics of a small mountain lion population isolated by anthropogenic barriers in greater Los Angeles, California, to evaluate the influence of demographic, genetic, and landscape factors on extinction probability. The population exhibited strong survival and reproduction, and the model predicted stable median population growth and a 15% probability of extinction over 50 years in the absence of inbreeding depression. However, our model also predicted the population will lose 40-57% of its heterozygosity in 50 years. When we reduced demographic parameters proportional to reductions documented in another wild population of mountain lions that experienced inbreeding depression, extinction probability rose to 99.7%. Simulating greater landscape connectivity by increasing immigration to greater than or equal to one migrant per generation appears sufficient to largely maintain genetic diversity and reduce extinction probability. We provide empirical support for the central tenet of the extinction vortex as interactions between genetics and demography greatly increased extinction probability relative to the risk from demographic and environmental stochasticity alone. Our modelling approach realistically integrates demographic and genetic data to provide a comprehensive assessment of factors threatening small populations.
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Affiliation(s)
- John F Benson
- La Kretz Center for California Conservation, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Peter J Mahoney
- Department of Wildland Resources, Utah State University, Logan, UT 84231, USA
| | - Jeff A Sikich
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, CA 91302, USA
| | - Laurel E K Serieys
- Department of Environmental Studies, University of California, Santa Cruz, CA 95064, USA University of Cape Town, Cape Town, South Africa
| | - John P Pollinger
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Holly B Ernest
- Department of Veterinary Science, University of Wyoming, Laramie, WY 82070, USA
| | - Seth P D Riley
- La Kretz Center for California Conservation, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, CA 91302, USA Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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Ochoa A, Onorato DP, Fitak RR, Roelke-Parker ME, Culver M. Evolutionary and Functional Mitogenomics Associated With the Genetic Restoration of the Florida Panther. J Hered 2017; 108:449-455. [PMID: 28204600 DOI: 10.1093/jhered/esx015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/14/2017] [Indexed: 01/02/2023] Open
Abstract
Florida panthers are endangered pumas that currently persist in reduced patches of habitat in South Florida, USA. We performed mitogenome reference-based assemblies for most parental lines of the admixed Florida panthers that resulted from the introduction of female Texas pumas into South Florida in 1995. With the addition of 2 puma mitogenomes, we characterized 174 single nucleotide polymorphisms (SNPs) across 12 individuals. We defined 5 haplotypes (Pco1-Pco5), one of which (Pco1) had a geographic origin exclusive to Costa Rica and Panama and was possibly introduced into the Everglades National Park, Florida, prior to 1995. Haplotype Pco2 was native to Florida. Haplotypes Pco3 and Pco4 were exclusive to Texas, whereas haplotype Pco5 had an undetermined geographic origin. Phylogenetic inference suggests that haplotypes Pco1-Pco4 diverged ~202000 (95% HPDI = 83000-345000) years ago and that haplotypes Pco2-Pco4 diverged ~61000 (95% HPDI = 9000-127000) years ago. These results are congruent with a south-to-north continental expansion and with a recent North American colonization by pumas. Furthermore, pumas may have migrated from Texas to Florida no earlier than ~44000 (95% HPDI = 2000-98000) years ago. Synonymous mutations presented a greater mean substitution rate than other mitochondrial functional regions: nonsynonymous mutations, tRNAs, rRNAs, and control region. Similarly, all protein-coding genes were under predominant negative selection constraints. We directly and indirectly assessed the presence of potential deleterious SNPs in the ND2 and ND5 genes in Florida panthers prior to and as a consequence of the introduction of Texas pumas. Screenings for such variants are recommended in extant Florida panthers.
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Affiliation(s)
- Alexander Ochoa
- From the School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85721 (Ochoa and Culver); Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL 34114 (Onorato); Department of Biology, Duke University, Durham, NC 27708 (Fitak); Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 20892 (Roelke-Parker); and US Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, Tucson, AZ 85721 (Culver)
| | - David P Onorato
- From the School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85721 (Ochoa and Culver); Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL 34114 (Onorato); Department of Biology, Duke University, Durham, NC 27708 (Fitak); Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 20892 (Roelke-Parker); and US Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, Tucson, AZ 85721 (Culver)
| | - Robert R Fitak
- From the School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85721 (Ochoa and Culver); Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL 34114 (Onorato); Department of Biology, Duke University, Durham, NC 27708 (Fitak); Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 20892 (Roelke-Parker); and US Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, Tucson, AZ 85721 (Culver)
| | - Melody E Roelke-Parker
- From the School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85721 (Ochoa and Culver); Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL 34114 (Onorato); Department of Biology, Duke University, Durham, NC 27708 (Fitak); Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 20892 (Roelke-Parker); and US Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, Tucson, AZ 85721 (Culver)
| | - Melanie Culver
- From the School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85721 (Ochoa and Culver); Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL 34114 (Onorato); Department of Biology, Duke University, Durham, NC 27708 (Fitak); Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 20892 (Roelke-Parker); and US Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, Tucson, AZ 85721 (Culver)
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19
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Karelus DL, McCown JW, Scheick BK, van de Kerk M, Bolker BM, Oli MK. Effects of environmental factors and landscape features on movement patterns of Florida black bears. J Mammal 2017. [DOI: 10.1093/jmammal/gyx066] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
A greater understanding of how environmental factors and anthropogenic landscape features influence animal movements can inform management and potentially aid in mitigating human–wildlife conflicts. We investigated the movement patterns of 16 Florida black bears (Ursus americanus floridanus; 6 females, 10 males) in north-central Florida at multiple temporal scales using GPS data collected from 2011 to 2014. We calculated bi-hourly step-lengths and directional persistence, as well as daily and weekly observed displacements and expected displacements. We used those movement metrics as response variables in linear mixed models and tested for effects of sex, season, and landscape features. We found that step-lengths of males were generally longer than step-lengths of females, and both sexes had the shortest step-lengths during the daytime. Bears moved more slowly (shorter step-lengths) and exhibited less directed movement when near creeks, in forested wetlands, and in marsh habitats, possibly indicating foraging behavior. In urban areas, bears moved more quickly (longer step-lengths) and along more directed paths. The results were similar across all temporal scales. Major roads tended to act as a semipermeable barrier to bear movement. Males crossed major roads more frequently than females but both sexes crossed major roads much less frequently than minor roads. Our findings regarding the influence of landscape and habitat features on movement patterns of Florida black bears could be useful for planning effective wildlife corridors and understanding how future residential or commercial development and road expansions may affect animal movement.
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Affiliation(s)
- Dana L Karelus
- Department of Wildlife Ecology and Conservation, and School of Natural Resources and Environment, Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL 32611, USA (DLK, MK, MKO)
| | - J Walter McCown
- Florida Fish and Wildlife Conservation Commission, 4005 S. Main St., Gainesville, FL 32601, USA (JWM, BKS)
| | - Brian K Scheick
- Florida Fish and Wildlife Conservation Commission, 4005 S. Main St., Gainesville, FL 32601, USA (JWM, BKS)
| | - Madelon van de Kerk
- Department of Wildlife Ecology and Conservation, and School of Natural Resources and Environment, Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL 32611, USA (DLK, MK, MKO)
| | - Benjamin M Bolker
- Departments of Mathematics & Statistics and Biology, McMaster University, 314 Hamilton Hall, Hamilton, Ontario L8S 4K1, Canada (BMB)
| | - Madan K Oli
- Department of Wildlife Ecology and Conservation, and School of Natural Resources and Environment, Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL 32611, USA (DLK, MK, MKO)
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Gustafson KD, Vickers TW, Boyce WM, Ernest HB. A single migrant enhances the genetic diversity of an inbred puma population. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170115. [PMID: 28573020 PMCID: PMC5451821 DOI: 10.1098/rsos.170115] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/25/2017] [Indexed: 05/11/2023]
Abstract
Migration is essential for maintaining genetic diversity among populations, and pumas (Puma concolor) provide an excellent model for studying the genetic impacts of migrants on populations isolated by increasing human development. In densely populated southern California, USA, puma populations on the east and west side of interstate highway 15 (I-15) have become fragmented into a small inbred population on the west side (Santa Ana Mountains) and a relatively larger, more diverse population on the east side (Eastern Peninsular Range). From 146 sampled pumas, genetic analyses indicate seven pumas crossed I-15 over the last 15 years, including four males from west to east, and three males from east to west. However, only a single migrant (named M86) was detected to have produced offspring and contribute to gene flow across the I-15 barrier. Prior to the M86 migration, the Santa Ana population exhibited inbreeding and had significantly lower genetic diversity than the Eastern Peninsular Range population. After M86 emigrated, he sired 11 offspring with Santa Ana females, decreasing inbreeding measures and raising heterozygosity to levels similar to pumas in the Eastern Peninsular Range. The emigration of M86 also introduced new alleles into the Santa Ana population, although allelic richness still remained significantly lower than the Eastern Peninsular population. Our results clearly show the benefit of a single migrant to the genetics of a small, isolated population. However, ongoing development and habitat loss on both sides of I-15 will increasingly strengthen the barrier to successful migration. Further monitoring, and potential human intervention, including minimizing development effects on connectivity, adding or improving freeway crossing structures, or animal translocation, may be needed to ensure adequate gene flow and long-term persistence of the Santa Ana puma population.
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Affiliation(s)
- Kyle D. Gustafson
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY 82070, USA
| | - T. Winston Vickers
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Walter M. Boyce
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Holly B. Ernest
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY 82070, USA
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21
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CHEN Y, AN B, LIU N. Asymmetrical introgression patterns between rusty-necklaced partridge (Alectoris magna) and chukar partridge (Alectoris chukar) in China. Integr Zool 2016; 11:403-12. [DOI: 10.1111/1749-4877.12195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yanke CHEN
- Experiment Center of Biomedical Research School of Medicine; Xi'an Jiaotong University; Xi'an China
| | - Bei AN
- School of Life Sciences; Lanzhou University; Lanzhou China
| | - Naifa LIU
- School of Life Sciences; Lanzhou University; Lanzhou China
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22
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Todesco M, Pascual MA, Owens GL, Ostevik KL, Moyers BT, Hübner S, Heredia SM, Hahn MA, Caseys C, Bock DG, Rieseberg LH. Hybridization and extinction. Evol Appl 2016; 9:892-908. [PMID: 27468307 PMCID: PMC4947151 DOI: 10.1111/eva.12367] [Citation(s) in RCA: 333] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/28/2016] [Indexed: 01/29/2023] Open
Abstract
Hybridization may drive rare taxa to extinction through genetic swamping, where the rare form is replaced by hybrids, or by demographic swamping, where population growth rates are reduced due to the wasteful production of maladaptive hybrids. Conversely, hybridization may rescue the viability of small, inbred populations. Understanding the factors that contribute to destructive versus constructive outcomes of hybridization is key to managing conservation concerns. Here, we survey the literature for studies of hybridization and extinction to identify the ecological, evolutionary, and genetic factors that critically affect extinction risk through hybridization. We find that while extinction risk is highly situation dependent, genetic swamping is much more frequent than demographic swamping. In addition, human involvement is associated with increased risk and high reproductive isolation with reduced risk. Although climate change is predicted to increase the risk of hybridization‐induced extinction, we find little empirical support for this prediction. Similarly, theoretical and experimental studies imply that genetic rescue through hybridization may be equally or more probable than demographic swamping, but our literature survey failed to support this claim. We conclude that halting the introduction of hybridization‐prone exotics and restoring mature and diverse habitats that are resistant to hybrid establishment should be management priorities.
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Affiliation(s)
- Marco Todesco
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Mariana A Pascual
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Gregory L Owens
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Katherine L Ostevik
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Brook T Moyers
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada; Department of Bioagricultural Sciences and Pest Management Colorado State University Ft Collins CO USA
| | - Sariel Hübner
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Sylvia M Heredia
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Min A Hahn
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Celine Caseys
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Dan G Bock
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada; Department of Biology Indiana University Bloomington IN USA
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23
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Hamilton JA, Miller JM. Adaptive introgression as a resource for management and genetic conservation in a changing climate. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2016; 30:33-41. [PMID: 26096581 DOI: 10.1111/cobi.12574] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 05/22/2023]
Abstract
Current rates of climate change require organisms to respond through migration, phenotypic plasticity, or genetic changes via adaptation. We focused on questions regarding species' and populations' ability to respond to climate change through adaptation. Specifically, the role adaptive introgression, movement of genetic material from the genome of 1 species into the genome of another through repeated interbreeding, may play in increasing species' ability to respond to a changing climate. Such interspecific gene flow may mediate extinction risk or consequences of limited adaptive potential that result from standing genetic variation and mutation alone, enabling a quicker demographic recovery in response to changing environments. Despite the near dismissal of the potential benefits of hybridization by conservation practitioners, we examined a number of case studies across different taxa that suggest gene flow between sympatric or parapatric sister species or within species that exhibit strong ecotypic differentiation may represent an underutilized management option to conserve evolutionary potential in a changing environment. This will be particularly true where advanced-generation hybrids exhibit adaptive traits outside the parental phenotypic range, a phenomenon known as transgressive segregation. The ideas presented in this essay are meant to provoke discussion regarding how we maintain evolutionary potential, the conservation value of natural hybrid zones, and consideration of their important role in adaptation to climate.
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Affiliation(s)
- Jill A Hamilton
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, U.S.A..
- Department of Biological Sciences, North Dakota State University, Fargo, ND, 58102, U.S.A..
| | - Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
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24
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McBride R, Sensor R. Efficacy of Trail Cameras to Identify Individual Florida Panthers. SOUTHEAST NAT 2015. [DOI: 10.1656/058.014.0215] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Whiteley AR, Fitzpatrick SW, Funk WC, Tallmon DA. Genetic rescue to the rescue. Trends Ecol Evol 2015; 30:42-9. [DOI: 10.1016/j.tree.2014.10.009] [Citation(s) in RCA: 355] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 10/30/2014] [Accepted: 10/31/2014] [Indexed: 01/26/2023]
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26
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Bay RA, Ramakrishnan U, Hadly EA. A call for tiger management using "reserves" of genetic diversity. J Hered 2013; 105:295-302. [PMID: 24336928 DOI: 10.1093/jhered/est086] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Tigers (Panthera tigris), like many large carnivores, are threatened by anthropogenic impacts, primarily habitat loss and poaching. Current conservation plans for tigers focus on population expansion, with the goal of doubling census size in the next 10 years. Previous studies have shown that because the demographic decline was recent, tiger populations still retain a large amount of genetic diversity. Although maintaining this diversity is extremely important to avoid deleterious effects of inbreeding, management plans have yet to consider predictive genetic models. We used coalescent simulations based on previously sequenced mitochondrial fragments (n = 125) from 5 of 6 extant subspecies to predict the population growth needed to maintain current genetic diversity over the next 150 years. We found that the level of gene flow between populations has a large effect on the local population growth necessary to maintain genetic diversity, without which tigers may face decreases in fitness. In the absence of gene flow, we demonstrate that maintaining genetic diversity is impossible based on known demographic parameters for the species. Thus, managing for the genetic diversity of the species should be prioritized over the riskier preservation of distinct subspecies. These predictive simulations provide unique management insights, hitherto not possible using existing analytical methods.
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Affiliation(s)
- Rachael A Bay
- the Department of Biology, Stanford University, Stanford, CA 94305
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27
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Casas-Marce M, Soriano L, López-Bao JV, Godoy JA. Genetics at the verge of extinction: insights from the Iberian lynx. Mol Ecol 2013; 22:5503-15. [PMID: 24128177 DOI: 10.1111/mec.12498] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 11/30/2022]
Abstract
Population viability might become compromised by the loss of genetic diversity and the accumulation of inbreeding resulting from population decline and fragmentation. The Iberian lynx (Lynx pardinus) provides a paradigmatic example of a species at the verge of extinction, and because of the well-documented and different demographic histories of the two remaining populations (Doñana and Andújar), it provides the opportunity to evaluate the performance of analytical methods commonly applied to recently declined populations. We used mitochondrial sequences and 36 microsatellite markers to evaluate the current genetic status of the species and to assess the genetic signatures of its past history. Mitochondrial diversity was extremely low with only two haplotypes, alternatively fixed in each population. Both remnant populations have low levels of genetic diversity at microsatellite markers, particularly the population from Doñana, and genetic differentiation between the two populations is high. Bayesian coalescent-based methods suggest an earlier decline starting hundreds of years ago, while heterozygosity excess and M-ratio tests did not provide conclusive and consistent evidence for recent bottlenecks. Also, a model of gene flow received overwhelming support over a model of pure drift. Results that are in conflict with the known recent demography of the species call for caution in the use of these methods, especially when no information on previous demographic history is available. Overall, our results suggest that current genetic patterns in the Iberian lynx are mainly the result of its recent decline and fragmentation and alerts on possible genetic risks for its persistence. Conservation strategies should explicitly consider this threat and incorporate an integrated genetic management of wild, captive and re-introduced populations, including genetic restoration through translocations.
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Affiliation(s)
- M Casas-Marce
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), C/ Américo Vespucio s/n, 41092, Sevilla, Spain
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Bartareau T, Onorato D, Jansen D. Growth in Body Length and Mass of the Florida Panther: An Evaluation of Different Models and Sexual Size Dimorphism. SOUTHEAST NAT 2013. [DOI: 10.1656/058.012.0103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Hostetler JA, Onorato DP, Jansen D, Oli MK. A cat's tale: the impact of genetic restoration on Florida panther population dynamics and persistence. J Anim Ecol 2012; 82:608-20. [DOI: 10.1111/1365-2656.12033] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/06/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Jeffrey A. Hostetler
- Department of Wildlife Ecology and Conservation; University of Florida; 110 Newins-Ziegler Hall; Gainesville; FL; 32611-0430; USA
| | - David P. Onorato
- Fish and Wildlife Research Institute; Florida Fish and Wildlife Conservation Commission; 298 Sabal Palm Road; Naples; FL; 34114; USA
| | - Deborah Jansen
- Big Cypress National Preserve; 33100 Tamiami Trail East; Ochopee; FL; 34141; USA
| | - Madan K. Oli
- Department of Wildlife Ecology and Conservation; University of Florida; 110 Newins-Ziegler Hall; Gainesville; FL; 32611-0430; USA
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30
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Does genetic introgression improve female reproductive performance? A test on the endangered Florida panther. Oecologia 2011; 168:289-300. [DOI: 10.1007/s00442-011-2083-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 07/06/2011] [Indexed: 10/17/2022]
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