1
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Zhang Y, Stern AJ, Nielsen R. The evolutionary dynamics of local adaptations under genetic rescue is determined by mutational load and polygenicity. J Hered 2024; 115:373-384. [PMID: 38146994 PMCID: PMC11235128 DOI: 10.1093/jhered/esad079] [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: 06/27/2023] [Revised: 11/27/2023] [Accepted: 12/22/2023] [Indexed: 12/27/2023] Open
Abstract
Inbred populations often suffer from increased mutational load and reduced fitness due to lower efficacy of purifying selection in groups with small effective population sizes. Genetic rescue (GR) is a conservation tool that is studied and deployed with the aim of increasing the fitness of such inbred populations by assisted migration of individuals from closely related outbred populations. The success of GR depends on several factors-such as their demographic history and distribution of dominance effects of mutations-that may vary across populations. While we understand the impact of these factors on the dynamics of GR, their impact on local adaptations remains unclear. To this end, we conduct a population genetics simulation study to evaluate the impact of trait complexity (Mendelian vs. polygenic), dominance effects, and demographic history on the efficacy of GR. We find that the impact on local adaptations depends highly on the mutational load at the time of GR, which is in turn shaped dynamically by interactions between demographic history and dominance effects of deleterious variation. Over time local adaptations are generally restored post-GR, though in the short term they are often compromised in the process of purging deleterious variation. We also show that while local adaptations are almost always fully restored, the degree to which ancestral genetic variation affecting the trait is replaced by donor variation can vary drastically and is especially high for complex traits. Our results provide insights on the impact of GR on trait evolution and considerations for the practical implementation of GR.
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Affiliation(s)
- Yulin Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Center for Computational Biology, UC Berkeley, Berkeley, CA, United States
| | - Aaron J Stern
- Center for Computational Biology, UC Berkeley, Berkeley, CA, United States
| | - Rasmus Nielsen
- Department of Integrative Biology, UC Berkeley, Berkeley, CA, United States
- Department of Statistics, UC Berkeley, Berkeley, CA, United States
- Center for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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2
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Lewis R, Pointer MD, Friend L, Gage MJG, Spurgin LG. Tests of evolutionary and genetic rescue using flour beetles, Tribolium castaneum, experimentally evolved to thermal conditions. Ecol Evol 2024; 14:e11313. [PMID: 38694756 PMCID: PMC11056960 DOI: 10.1002/ece3.11313] [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: 08/29/2023] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 05/04/2024] Open
Abstract
Small, isolated populations are often characterised by low levels of genetic diversity. This can result in inbreeding depression and reduced capacity to adapt to changes in the environment, and therefore higher risk of extinction. However, sometimes these populations can be rescued if allowed to increase in size or if migrants enter, bringing in new allelic variation and thus increasing genetic diversity. This study uses experimental manipulation of population size and migration to quantify their effects on fitness in a challenging environment to better understand genetic rescue. Using small, replicated populations of Tribolium castaneum experimentally evolved to different temperature regimes we tested genetic and demographic rescue, by performing large-scale manipulations of population size and migration and examining fitness consequences over multiple generations. We measured fitness in high temperature (38°C) thermal lines maintained at their usual 'small' population size of N = 100 individuals, and with 'large' scaled up duplicates containing N≈10,000 individuals. We compared these large lines with and without migration (m = 0.1) for 10 generations. Additionally, we assessed the effects of outcrossing at an individual level, by comparing fitness of hybrid (thermal line × stock) offspring with within-line crosses. We found that, at the population level, a rapid increase in the number of individuals in the population resulted in reduced fitness (represented by reproductive output and survival through heatwave conditions), regardless of migration. However, at an individual level, the hybrid offspring of migrants with native individuals generally demonstrated increased longevity in high temperature conditions compared with individuals from thermal selection lines. Overall, these populations showed no evidence that demographic manipulations led to genetic or evolutionary rescue. Following the effects of migration in individuals over several generations may be the next step in unravelling these conflicting results. We discuss these findings in the context of conservation intervention.
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Affiliation(s)
- Rebecca Lewis
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | | | - Lucy Friend
- School of Biological SciencesUniversity of East AngliaNorwichUK
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3
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Smeds L, Huson LSA, Ellegren H. Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration. Evol Appl 2024; 17:e13652. [PMID: 38333557 PMCID: PMC10848878 DOI: 10.1111/eva.13652] [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: 11/09/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
When populations decrease in size and may become isolated, genomic erosion by loss of diversity from genetic drift and accumulation of deleterious mutations is likely an inevitable consequence. In such cases, immigration (genetic rescue) is necessary to restore levels of genetic diversity and counteract inbreeding depression. Recent work in conservation genomics has studied these processes focusing on the genetic diversity of single nucleotide polymorphisms. In contrast, our knowledge about structural genomic variation (insertions, deletions, duplications and inversions) in endangered species is limited. We analysed whole-genome, short-read sequences from 212 wolves from the inbred Scandinavian population and from neighbouring populations in Finland and Russia, and detected >35,000 structural variants (SVs) after stringent quality and genotype frequency filtering; >26,000 high-confidence variants remained after manual curation. The majority of variants were shorter than 1 kb, with a distinct peak in the length distribution of deletions at 190 bp, corresponding to insertion events of SINE/tRNA-Lys elements. The site frequency spectrum of SVs in protein-coding regions was significantly shifted towards rare alleles compared to putatively neutral variants, consistent with purifying selection. The realized genetic load of SVs in protein-coding regions increased with inbreeding levels in the Scandinavian population, but immigration provided a genetic rescue effect by lowering the load and reintroducing ancestral alleles at loci fixed for derived SVs. Our study shows that structural variation comprises a common type of in part deleterious mutations in endangered species and that establishing gene flow is necessary to mitigate the negative consequences of loss of diversity.
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Affiliation(s)
- Linnéa Smeds
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Lars S. A. Huson
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Hans Ellegren
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
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4
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Reid JM, Dickel L, Keller LF, Nietlisbach P, Arcese P. Multi-generation genetic contributions of immigrants reveal cryptic elevated and sex-biased effective gene flow within a natural meta-population. Ecol Lett 2024; 27:e14377. [PMID: 38361472 DOI: 10.1111/ele.14377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 02/17/2024]
Abstract
Impacts of immigration on micro-evolution and population dynamics fundamentally depend on net rates and forms of resulting gene flow into recipient populations. Yet, the degrees to which observed rates and sex ratios of physical immigration translate into multi-generational genetic legacies have not been explicitly quantified in natural meta-populations, precluding inference on how movements translate into effective gene flow and eco-evolutionary outcomes. Our analyses of three decades of complete song sparrow (Melospiza melodia) pedigree data show that multi-generational genetic contributions from regular natural immigrants substantially exceeded those from contemporary natives, consistent with heterosis-enhanced introgression. However, while contributions from female immigrants exceeded those from female natives by up to three-fold, male immigrants' lineages typically went locally extinct soon after arriving. Both the overall magnitude, and the degree of female bias, of effective gene flow therefore greatly exceeded those which would be inferred from observed physical arrivals, altering multiple eco-evolutionary implications of immigration.
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Affiliation(s)
- Jane M Reid
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Lisa Dickel
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Natural History Museum, University of Zurich, Zurich, Switzerland
| | - Pirmin Nietlisbach
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Peter Arcese
- Department of Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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5
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Maroso F, Padovani G, Muñoz Mora VH, Giannelli F, Trucchi E, Bertorelle G. Fitness consequences and ancestry loss in the Apennine brown bear after a simulated genetic rescue intervention. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14133. [PMID: 37259604 DOI: 10.1111/cobi.14133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 06/02/2023]
Abstract
Reduction in population size, with its predicted effects on population fitness, is the most alarming anthropogenic impact on endangered species. By introducing compatible individuals, genetic rescue (GR) is a promising but debated approach for reducing the genetic load unmasked by inbreeding and for restoring the fitness of declining populations. Although GR can improve genetic diversity and fitness, it can also produce loss of ancestry, hampering local adaptation, or replace with introduced variants the unique genetic pools evolved in endemic groups. We used forward genetic simulations based on empirical genomic data to assess fitness benefits and loss of ancestry risks of GR in the Apennine brown bear (Ursus arctos marsicanus). There are approximately 50 individuals of this isolated subspecies, and they have lower genetic diversity and higher inbreeding than other European brown bears, and GR has been suggested to reduce extinction risks. We compared 10 GR scenarios in which the number and genetic characteristics of migrants varied with a non-GR scenario of simple demographic increase due to nongenetic factors. The introduction of 5 individuals of higher fitness or lower levels of deleterious mutations than the target Apennine brown bear from a larger European brown bear population produced a rapid 10-20% increase in fitness in the subspecies and up to 22.4% loss of ancestry over 30 generations. Without a contemporary demographic increase, fitness started to decline again after a few generations. Doubling the population size without GR gradually increased fitness to a comparable level, but without losing ancestry, thus resulting in the best strategy for the Apennine brown bear conservation. Our results highlight the importance for management of endangered species of realistic forward simulations grounded in empirical whole-genome data.
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Affiliation(s)
- Francesco Maroso
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
- Department of Biology, University of Padova, Padova, Italy
| | - Giada Padovani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | - Francesco Giannelli
- Department of Life and Environmental Science, Marche Polytechnic University, Ancona, Italy
| | - Emiliano Trucchi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
- Department of Life and Environmental Science, Marche Polytechnic University, Ancona, Italy
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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6
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Bossu CM, Rodriguez M, Rayne C, Chromczak DA, Higgins PG, Trulio LA, Ruegg KC. Genomic approaches to mitigating genetic diversity loss in declining populations. Mol Ecol 2023; 32:5228-5240. [PMID: 37610278 DOI: 10.1111/mec.17109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/17/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023]
Abstract
The accelerating pace of global biodiversity loss is exacerbated by habitat fragmentation and subsequent inbreeding in small populations. To address this problem, conservation practitioners often turn to assisted breeding programmes with the aim of enhancing genetic diversity in declining populations. Although genomic information is infrequently included in these efforts, it has the potential to significantly enhance the success of such programmes. In this study, we showcase the value of genomic approaches for increasing genetic diversity in assisted breeding efforts, specifically focusing on a highly inbred population of Western burrowing owls. To maximize genetic diversity in the resulting offspring, we begin by creating an optimal pairing decision tree based on sex, kinship and patterns of homozygosity across the genome. To evaluate the effectiveness of our strategy, we compare genetic diversity, brood size and nestling success rates between optimized and non-optimized pairs. Additionally, we leverage recently discovered correlations between telomere length and fitness across species to investigate whether genomic optimization could have long-term fitness benefits. Our results indicate that pairing individuals with contrasting patterns of homozygosity across the genome is an effective way to increase genetic diversity in offspring. Although short-term field-based metrics of success did not differ significantly between optimized and non-optimized pairs, offspring from optimized pairs had significantly longer telomeres, suggesting that genetic optimization can help reduce the risk of inbreeding depression. These findings underscore the importance of genomic tools for informing efforts to preserve the adaptive potential of small, inbred populations at risk of further decline.
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Affiliation(s)
- Christen M Bossu
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
| | - Marina Rodriguez
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
| | - Christine Rayne
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
| | - Debra A Chromczak
- Burrowing Owl Researcher & Consultant, Riegelsville, Pennsylvania, USA
| | | | - Lynne A Trulio
- Department of Environmental Studies, San José State University, San Jose, California, USA
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
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7
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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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8
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Kyriazis CC, Beichman AC, Brzeski KE, Hoy SR, Peterson RO, Vucetich JA, Vucetich LM, Lohmueller KE, Wayne RK. Genomic Underpinnings of Population Persistence in Isle Royale Moose. Mol Biol Evol 2023; 40:msad021. [PMID: 36729989 PMCID: PMC9927576 DOI: 10.1093/molbev/msad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Island ecosystems provide natural laboratories to assess the impacts of isolation on population persistence. However, most studies of persistence have focused on a single species, without comparisons to other organisms they interact with in the ecosystem. The case study of moose and gray wolves on Isle Royale allows for a direct contrast of genetic variation in isolated populations that have experienced dramatically differing population trajectories over the past decade. Whereas the Isle Royale wolf population recently declined nearly to extinction due to severe inbreeding depression, the moose population has thrived and continues to persist, despite having low genetic diversity and being isolated for ∼120 years. Here, we examine the patterns of genomic variation underlying the continued persistence of the Isle Royale moose population. We document high levels of inbreeding in the population, roughly as high as the wolf population at the time of its decline. However, inbreeding in the moose population manifests in the form of intermediate-length runs of homozygosity suggestive of historical inbreeding and purging, contrasting with the long runs of homozygosity observed in the smaller wolf population. Using simulations, we confirm that substantial purging has likely occurred in the moose population. However, we also document notable increases in genetic load, which could eventually threaten population viability over the long term. Overall, our results demonstrate a complex relationship between inbreeding, genetic diversity, and population viability that highlights the use of genomic datasets and computational simulation tools for understanding the factors enabling persistence in isolated populations.
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Affiliation(s)
- Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
| | | | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Sarah R Hoy
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Rolf O Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Leah M Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
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9
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Escoda L, Hawlitschek O, González-Esteban J, Castresana J. Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity. Sci Rep 2022; 12:21390. [PMID: 36496459 PMCID: PMC9741620 DOI: 10.1038/s41598-022-25619-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
Recently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (Galemys pyrenaicus). For this, we used the ddRADseq technique, which generated 1421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research.
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Affiliation(s)
- Lídia Escoda
- grid.507636.10000 0004 0424 5398Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003 Barcelona, Spain
| | - Oliver Hawlitschek
- grid.507636.10000 0004 0424 5398Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003 Barcelona, Spain ,grid.517093.90000 0005 0294 9006Leibniz Institute for the Analysis of Biodiversity Change, Centre for Molecular Biodiversity Research, Zoological Museum, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | | | - Jose Castresana
- grid.507636.10000 0004 0424 5398Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003 Barcelona, Spain
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10
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Smeds L, Ellegren H. From high masked to high realized genetic load in inbred Scandinavian wolves. Mol Ecol 2022; 32:1567-1580. [PMID: 36458895 DOI: 10.1111/mec.16802] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
When new mutations arise at functional sites they are more likely to impair than improve fitness. If not removed by purifying selection, such deleterious mutations will generate a genetic load that can have negative fitness effects in small populations and increase the risk of extinction. This is relevant for the highly inbred Scandinavian wolf (Canis lupus) population, founded by only three wolves in the 1980s and suffering from inbreeding depression. We used functional annotation and evolutionary conservation scores to study deleterious variation in a total of 209 genomes from both the Scandinavian and neighbouring wolf populations in northern Europe. The masked load (deleterious mutations in heterozygote state) was highest in Russia and Finland with deleterious alleles segregating at lower frequency than neutral variation. Genetic drift in the Scandinavian population led to the loss of ancestral alleles, fixation of deleterious variants and a significant increase in the per-individual realized load (deleterious mutations in homozygote state; an increase by 45% in protein-coding genes) over five generations of inbreeding. Arrival of immigrants gave a temporary genetic rescue effect with ancestral alleles re-entering the population and thereby shifting deleterious alleles from homozygous into heterozygote genotypes. However, in the absence of permanent connectivity to Finnish and Russian populations, inbreeding has then again led to the exposure of deleterious mutations. These observations provide genome-wide insight into the magnitude of genetic load and genetic rescue at the molecular level, and in relation to population history. They emphasize the importance of securing gene flow in the management of endangered populations.
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Affiliation(s)
- Linnéa Smeds
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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11
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Undin M, Castro I. Predicting breeding systems to guide conservation strategies: A kiwi example. Ethology 2022. [DOI: 10.1111/eth.13286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Malin Undin
- Department of Natural Sciences Mid Sweden University Sundsvall Sweden
- Wildlife and Ecology Group, School of Agriculture and Environment Massey University Palmerston North New Zealand
| | - Isabel Castro
- Wildlife and Ecology Group, School of Agriculture and Environment Massey University Palmerston North New Zealand
- Wildbase Research Massey University Palmerston North New Zealand
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12
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Pichler TR, Mallinger EC, Farmer MJ, Morrison MJ, Khadka B, Matzinger PJ, Kirschbaum A, Goodwin KR, Route WT, Van Stappen J, Van Deelen TR, Olson ER. Comparative biogeography of volant and nonvolant mammals in a temperate island archipelago. Ecosphere 2022. [DOI: 10.1002/ecs2.3911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Taylor R. Pichler
- Department of Natural Resources Northland College Ashland Wisconsin USA
| | | | - Morgan J. Farmer
- Department of Forest and Wildlife Ecology University of Wisconsin Madison Wisconsin USA
| | - Megan J. Morrison
- Department of Forest and Wildlife Ecology University of Wisconsin Madison Wisconsin USA
| | - Bijit Khadka
- Department of Natural Resources Northland College Ashland Wisconsin USA
- Department of Forest and Wildlife Ecology University of Wisconsin Madison Wisconsin USA
| | | | - Alan Kirschbaum
- National Park Service Great Lakes Inventory and Monitoring Network Ashland Wisconsin USA
| | - Katy R. Goodwin
- National Park Service Great Lakes Inventory and Monitoring Network Ashland Wisconsin USA
- Department of Biological Sciences North Dakota State University Fargo North Dakota USA
| | - William T. Route
- National Park Service Great Lakes Inventory and Monitoring Network Ashland Wisconsin USA
| | - Julie Van Stappen
- Planning and Resource Management Apostle Islands National Lakeshore Bayfield Wisconsin USA
| | - Timothy R. Van Deelen
- Department of Forest and Wildlife Ecology University of Wisconsin Madison Wisconsin USA
| | - Erik R. Olson
- Department of Natural Resources Northland College Ashland Wisconsin USA
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13
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Khan A, Patel K, Shukla H, Viswanathan A, van der Valk T, Borthakur U, Nigam P, Zachariah A, Jhala YV, Kardos M, Ramakrishnan U. Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. Proc Natl Acad Sci U S A 2021; 118:e2023018118. [PMID: 34848534 PMCID: PMC8670471 DOI: 10.1073/pnas.2023018118] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 01/03/2023] Open
Abstract
Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small-isolated and two large-connected populations in India. As expected, the small-isolated population had substantially higher average genomic inbreeding (FROH = 0.57) than the large-connected (FROH = 0.35 and FROH = 0.46) populations. The small-isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small-isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small-isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small-isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.
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Affiliation(s)
- Anubhab Khan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
| | - Kaushalkumar Patel
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Harsh Shukla
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Ashwin Viswanathan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- Nature Conservation Foundation, Mysore 570017, India
| | | | | | - Parag Nigam
- Wildlife Institute of India, Dehradun 248001, India
| | | | | | - Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112;
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
- Department of Biotechnology-Wellcome Trust India Alliance, Hyderabad 500034, India
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14
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Abstract
AbstractGenetic rescue is increasingly considered a promising and underused conservation strategy to reduce inbreeding depression and restore genetic diversity in endangered populations, but the empirical evidence supporting its application is limited to a few generations. Here we discuss on the light of theory the role of inbreeding depression arising from partially recessive deleterious mutations and of genetic purging as main determinants of the medium to long-term success of rescue programs. This role depends on two main predictions: (1) The inbreeding load hidden in populations with a long stable demography increases with the effective population size; and (2) After a population shrinks, purging tends to remove its (partially) recessive deleterious alleles, a process that is slower but more efficient for large populations than for small ones. We also carry out computer simulations to investigate the impact of genetic purging on the medium to long term success of genetic rescue programs. For some scenarios, it is found that hybrid vigor followed by purging will lead to sustained successful rescue. However, there may be specific situations where the recipient population is so small that it cannot purge the inbreeding load introduced by migrants, which would lead to increased fitness inbreeding depression and extinction risk in the medium to long term. In such cases, the risk is expected to be higher if migrants came from a large non-purged population with high inbreeding load, particularly after the accumulation of the stochastic effects ascribed to repeated occasional migration events. Therefore, under the specific deleterious recessive mutation model considered, we conclude that additional caution should be taken in rescue programs. Unless the endangered population harbors some distinctive genetic singularity whose conservation is a main concern, restoration by continuous stable gene flow should be considered, whenever feasible, as it reduces the extinction risk compared to repeated occasional migration and can also allow recolonization events.
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15
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Mech LD, Janssens LAA. An assessment of current wolf
Canis lupus
domestication hypotheses based on wolf ecology and behaviour. Mamm Rev 2021. [DOI: 10.1111/mam.12273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- L. David Mech
- Northern Prairie Wildlife Research Center U. S. Geological Survey Jamestown North Dakota58401USA
| | - Luc A. A. Janssens
- Department of Archaeology Leiden University Einsteinweg 2 2333 CCLeidenThe Netherlands
- Department of Archaeology Ghent University Sint‐Pietersnieuwstraat 35 9000GhentBelgium
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16
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Undin M, Lockhart PJ, Hills SFK, Armstrong DP, Castro I. Mixed Mating in a Multi-Origin Population Suggests High Potential for Genetic Rescue in North Island Brown Kiwi, Apteryx mantelli. FRONTIERS IN CONSERVATION SCIENCE 2021. [DOI: 10.3389/fcosc.2021.702128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Reinforcement translocations are increasingly utilised in conservation with the goal of achieving genetic rescue. However, concerns regarding undesirable results, such as genetic homogenisation or replacement, are widespread. One factor influencing translocation outcomes is the rate at which the resident and the introduced individuals interbreed. Consequently, post-release mate choice is a key behaviour to consider in conservation planning. Here we studied mating, and its consequences for genomic admixture, in the North Island brown kiwi Apteryx mantelli population on Ponui Island which was founded by two translocation events over 50 years ago. The two source populations used are now recognised as belonging to two separate management units between which birds differ in size and are genetically differentiated. We examined the correlation between male and female morphometrics for 17 known pairs and quantified the relatedness of 20 pairs from this admixed population. In addition, we compared the genetic similarity and makeup of 106 Ponui Island birds, including 23 known pairs, to birds representing the source populations for the original translocations. We found no evidence for size-assortative mating. On the contrary, genomic SNP data suggested that kiwi of one feather did not flock together, meaning that mate choice resulted in pairing between individuals that were less related than expected by random chance. Furthermore, the birds in the current Ponui Island population were found to fall along a gradient of genomic composition consistent with non-clustered representation of the two parental genomes. These findings indicate potential for successful genetic rescue in future Apteryx reinforcement translocations, a potential that is currently under utilised due to restrictive translocation policies. In light of our findings, we suggest that reconsideration of these policies could render great benefits for the future diversity of this iconic genus in New Zealand.
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17
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Camak DT, Osborne MJ, Turner TF. Population genomics and conservation of Gila Trout (Oncorhynchus gilae). CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01355-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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18
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Farmer M, Allen M, Olson E, Van Stappen J, Van Deelen T. Agonistic interactions and island biogeography as drivers of carnivore spatial and temporal activity at multiple scales. CAN J ZOOL 2021. [DOI: 10.1139/cjz-2020-0195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Carnivore communities can be diverse and complex, and lack of knowledge regarding intraguild interactions and alternative drivers of carnivore distributions can preclude effective conservation of co-occurring species. As such, our objectives were to evaluate the relative importance of intraguild interactions and island biogeography to carnivore community spatiotemporal activity at multiple spatial scales. We monitored the carnivore community of the Apostle Islands National Lakeshore (Wisconsin, USA) using a grid of camera traps from 2014 to 2018. We used generalized linear mixed-effects models and information-theoretic model selection to evaluate whether subordinate carnivore presence was related to dominant carnivore relative abundance (interactions) or to island biogeography at the island level and camera site level, and we calculated temporal overlap between each pair of species to determine whether subordinate carnivores were using temporal segregation. At the island level, the relative importance of interactions and island biogeography was species dependent. At the site level, relative abundance of dominant carnivores was not a significant predictor of subordinate carnivore presence, and all pairs exhibited high or neutral temporal overlap. At the island level, island biogeography and interactions may both impact species distributions; however, at finer spatial scales, the carnivore community may be using alternative segregation strategies, or the island system may preclude segregation.
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Affiliation(s)
- M.J. Farmer
- Department of Forest and Wildlife Ecology, University of Wisconsin, 1630 Linden Drive, Madison, WI 53706, USA
| | - M.L. Allen
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
| | - E.R. Olson
- Natural Resources, Northland College, 1411 Ellis Avenue South, Ashland, WI 54806, USA
| | - J. Van Stappen
- Resource Management, Apostle Islands National Lakeshore, 415 Washington Avenue, Bayfield, WI 54814, USA
| | - T.R. Van Deelen
- Department of Forest and Wildlife Ecology, University of Wisconsin, 1630 Linden Drive, Madison, WI 53706, USA
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19
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Lotsander A, Hasselgren M, Larm M, Wallén J, Angerbjörn A, Norén K. Low Persistence of Genetic Rescue Across Generations in the Arctic Fox (Vulpes lagopus). J Hered 2021; 112:276-285. [PMID: 33738472 PMCID: PMC8141685 DOI: 10.1093/jhered/esab011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/17/2021] [Indexed: 12/11/2022] Open
Abstract
Genetic rescue can facilitate the recovery of small and isolated populations suffering from inbreeding depression. Long-term effects are however complex, and examples spanning over multiple generations under natural conditions are scarce. The aim of this study was to test for long-term effects of natural genetic rescue in a small population of Scandinavian Arctic foxes (Vulpes lagopus). By combining a genetically verified pedigree covering almost 20 years with a long-term dataset on individual fitness (n = 837 individuals), we found no evidence for elevated fitness in immigrant F2 and F3 compared to native inbred foxes. Population inbreeding levels showed a fluctuating increasing trend and emergence of inbreeding within immigrant lineages shortly after immigration. Between 0–5 and 6–9 years post immigration, the average number of breeding adults decreased by almost 22% and the average proportion of immigrant ancestry rose from 14% to 27%. Y chromosome analysis revealed that 2 out of 3 native male lineages were lost from the gene pool, but all founders represented at the time of immigration were still contributing to the population at the end of the study period through female descendants. The results highlight the complexity of genetic rescue and suggest that beneficial effects can be brief. Continuous gene flow may be needed for small and threatened populations to recover and persist in a longer time perspective.
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Affiliation(s)
- Anna Lotsander
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Malin Larm
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Johan Wallén
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, Sweden
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20
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Kyriazis CC, Wayne RK, Lohmueller KE. Strongly deleterious mutations are a primary determinant of extinction risk due to inbreeding depression. Evol Lett 2021; 5:33-47. [PMID: 33552534 PMCID: PMC7857301 DOI: 10.1002/evl3.209] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 11/10/2020] [Accepted: 11/21/2020] [Indexed: 11/08/2022] Open
Abstract
Human-driven habitat fragmentation and loss have led to a proliferation of small and isolated plant and animal populations with high risk of extinction. One of the main threats to extinction in these populations is inbreeding depression, which is primarily caused by recessive deleterious mutations becoming homozygous due to inbreeding. The typical approach for managing these populations is to maintain high genetic diversity, increasingly by translocating individuals from large populations to initiate a "genetic rescue." However, the limitations of this approach have recently been highlighted by the demise of the gray wolf population on Isle Royale, which declined to the brink of extinction soon after the arrival of a migrant from the large mainland wolf population. Here, we use a novel population genetic simulation framework to investigate the role of genetic diversity, deleterious variation, and demographic history in mediating extinction risk due to inbreeding depression in small populations. We show that, under realistic models of dominance, large populations harbor high levels of recessive strongly deleterious variation due to these mutations being hidden from selection in the heterozygous state. As a result, when large populations contract, they experience a substantially elevated risk of extinction after these strongly deleterious mutations are exposed by inbreeding. Moreover, we demonstrate that, although genetic rescue is broadly effective as a means to reduce extinction risk, its effectiveness can be greatly increased by drawing migrants from small or moderate-sized source populations rather than large source populations due to smaller populations harboring lower levels of recessive strongly deleterious variation. Our findings challenge the traditional conservation paradigm that focuses on maximizing genetic diversity in small populations in favor of a view that emphasizes minimizing strongly deleterious variation. These insights have important implications for managing small and isolated populations in the increasingly fragmented landscape of the Anthropocene.
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Affiliation(s)
- Christopher C. Kyriazis
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCalifornia90095
| | - Robert K. Wayne
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCalifornia90095
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCalifornia90095
- Interdepartmental Program in BioinformaticsUniversity of CaliforniaLos AngelesCalifornia90095
- Department of Human Genetics, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCalifornia90095
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21
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Flesch EP, Graves TA, Thomson JM, Proffitt KM, White PJ, Stephenson TR, Garrott RA. Evaluating wildlife translocations using genomics: A bighorn sheep case study. Ecol Evol 2020; 10:13687-13704. [PMID: 33391673 PMCID: PMC7771163 DOI: 10.1002/ece3.6942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 08/12/2020] [Accepted: 09/25/2020] [Indexed: 01/10/2023] Open
Abstract
Wildlife restoration often involves translocation efforts to reintroduce species and supplement small, fragmented populations. We examined the genomic consequences of bighorn sheep (Ovis canadensis) translocations and population isolation to enhance understanding of evolutionary processes that affect population genetics and inform future restoration strategies. We conducted a population genomic analysis of 511 bighorn sheep from 17 areas, including native and reintroduced populations that received 0-10 translocations. Using the Illumina High Density Ovine array, we generated datasets of 6,155 to 33,289 single nucleotide polymorphisms and completed clustering, population tree, and kinship analyses. Our analyses determined that natural gene flow did not occur between most populations, including two pairs of native herds that had past connectivity. We synthesized genomic evidence across analyses to evaluate 24 different translocation events and detected eight successful reintroductions (i.e., lack of signal for recolonization from nearby populations) and five successful augmentations (i.e., reproductive success of translocated individuals) based on genetic similarity with the source populations. A single native population founded six of the reintroduced herds, suggesting that environmental conditions did not need to match for populations to persist following reintroduction. Augmentations consisting of 18-57 animals including males and females succeeded, whereas augmentations of two males did not result in a detectable genetic signature. Our results provide insight on genomic distinctiveness of native and reintroduced herds, information on the relative success of reintroduction and augmentation efforts and their associated attributes, and guidance to enhance genetic contribution of augmentations and reintroductions to aid in bighorn sheep restoration.
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Affiliation(s)
- Elizabeth P. Flesch
- Fish and Wildlife Ecology and Management ProgramEcology DepartmentMontana State UniversityBozemanMTUSA
| | - Tabitha A. Graves
- Northern Rocky Mountain Science CenterU.S. Geological SurveyWest GlacierMTUSA
| | | | | | - P. J. White
- Yellowstone Center for ResourcesNational Park ServiceMammothWYUSA
| | - Thomas R. Stephenson
- Sierra Nevada Bighorn Sheep Recovery ProgramCalifornia Department of Fish and WildlifeBishopCAUSA
| | - Robert A. Garrott
- Fish and Wildlife Ecology and Management ProgramEcology DepartmentMontana State UniversityBozemanMTUSA
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22
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Orning EK, Romanski MC, Moore S, Chenaux-Ibrahim Y, Hart J, Belant JL. Emigration and First-Year Movements of Initial Wolf Translocations to Isle Royale. Northeast Nat (Steuben) 2020. [DOI: 10.1656/045.027.0410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Elizabeth K. Orning
- SUNY College of Environmental Science and Forestry, Global Wildlife Conservation Center, 1 Forestry Drive, Syracuse, NY 13210
| | - Mark C. Romanski
- National Park Service, 800 E Lakeshore Drive, Isle Royale National Park, Houghton, MI 49931
| | - Seth Moore
- Grand Portage Band of Lake Superior Chippewa, 27 Store Rd, Grand Portage, MN 55605
| | | | - John Hart
- US Department of Agriculture-Animal Plant Health Inspection Service-Wildlife Services, 34912 US Hwy 2, Grand Rapids, MN 55744
| | - Jerrold L. Belant
- SUNY College of Environmental Science and Forestry, Global Wildlife Conservation Center, 1 Forestry Drive, Syracuse, NY 13210
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23
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Quinn CB, Alden PB, Sacks BN. Noninvasive Sampling Reveals Short-Term Genetic Rescue in an Insular Red Fox Population. J Hered 2020; 110:559-576. [PMID: 31002340 DOI: 10.1093/jhered/esz024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 04/15/2019] [Indexed: 11/12/2022] Open
Abstract
Genetic factors in the decline of small populations are extremely difficult to study in nature. We leveraged a natural experiment to investigate evidence of inbreeding depression and genetic rescue in a remnant population of subalpine-specialized Sierra Nevada red foxes (Vulpes vulpes necator) using noninvasive genetic monitoring during 2010-2017. Only 7 individuals were detected in the first 2 years. These individuals assigned genetically to the historical population and exhibited genetic hallmarks of inbreeding and no evidence of reproduction. Two years into the study, we detected 2 first-generation immigrant males from a recently expanding population of red foxes in the Great Basin Desert. Through annual resampling of individuals (634 red fox DNA samples, 41 individuals) and molecular reconstruction of pedigrees, we documented 1-3 litters/year for 5 years, all descended directly or indirectly from matings involving immigrant foxes. The observed heterozygosity and allelic richness of the population nearly doubled in 2 years. Abundance increased, indicative of a rapidly expanding population. Throughout the study, adult survival was high. Restoration of gene flow apparently improved the demographic trajectory of this population in the short term. Whether these benefits continue in the longer term could depend on numerous factors, such as maintenance of any locally adapted alleles. This study highlights the value of noninvasive genetic monitoring to assess rapidly shifting conditions in small populations. Uncertainties about the longer-term trajectory of this population underscore the need to continue monitoring and to research potential for both negative and positive aspects of continued genetic infusion.
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Affiliation(s)
- Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Preston B Alden
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA
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24
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Vucetich JA, Nelson MP, Bruskotter JT. What Drives Declining Support for Long-Term Ecological Research? Bioscience 2020. [DOI: 10.1093/biosci/biz151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AbstractSeveral recent papers have reinvigorated a chronic concern about the need for ecological science to focus more on long-term research. For a few decades, significant voices among ecologists have been assembling elements of a case in favor of long-term ecological research. In this article and for the first time, we synthesize the elements of this case and present it in succinct form. We also argue that this case is unlikely to result in more long-term research. Finally, we present ideas that, if implemented, are more likely to result in appropriate levels of investment in long-term research in ecological science. The article comes at an important time, because the US National Science Foundation is currently undertaking a 40-year review of its Long-Term Ecological Research Network.
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Affiliation(s)
- John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University Houghton
| | - Michael Paul Nelson
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis
| | - Jeremy T Bruskotter
- School Environment and Natural Resources, The Ohio State University, Columbus
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25
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Miller ML, Kronenberger JA, Fitzpatrick SW. Recent evolutionary history predicts population but not ecosystem-level patterns. Ecol Evol 2019; 9:14442-14452. [PMID: 31938531 PMCID: PMC6953670 DOI: 10.1002/ece3.5879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/14/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022] Open
Abstract
In the face of rapid anthropogenic environmental change, it is increasingly important to understand how ecological and evolutionary interactions affect the persistence of natural populations. Augmented gene flow has emerged as a potentially effective management strategy to counteract negative consequences of genetic drift and inbreeding depression in small and isolated populations. However, questions remain about the long-term impacts of augmented gene flow and whether changes in individual and population fitness are reflected in ecosystem structure, potentiating eco-evolutionary feedbacks. In this study, we used Trinidadian guppies (Poecilia reticulata) in experimental outdoor mesocosms to assess how populations with different recent evolutionary histories responded to a scenario of severe population size reduction followed by expansion in a high-quality environment. We also investigated how variation in evolutionary history of the focal species affected ecosystem dynamics. We found that evolutionary history (i.e., gene flow vs. no gene flow) consistently predicted variation in individual growth. In addition, gene flow led to faster population growth in populations from one of the two drainages, but did not have measurable impacts on the ecosystem variables we measured: zooplankton density, algal growth, and decomposition rates. Our results suggest that benefits of gene flow may be long-term and environment-dependent. Although small in replication and duration, our study highlights the importance of eco-evolutionary interactions in determining population persistence and sets the stage for future work in this area.
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Affiliation(s)
- Madison L. Miller
- W. K. Kellogg Biological StationMichigan State UniversityHickory CornersMIUSA
| | - John A. Kronenberger
- National Genomics Center for Wildlife and Fish ConservationUSDA Forest ServiceMissoulaMTUSA
| | - Sarah W. Fitzpatrick
- W. K. Kellogg Biological StationMichigan State UniversityHickory CornersMIUSA
- Department of Integrative BiologyMichigan State UniversityHickory CornersMIUSA
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26
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Thavornkanlapachai R, Mills HR, Ottewell K, Dunlop J, Sims C, Morris K, Donaldson F, Kennington WJ. Mixing Genetically and Morphologically Distinct Populations in Translocations: Asymmetrical Introgression in A Newly Established Population of the Boodie ( Bettongia lesueur). Genes (Basel) 2019; 10:E729. [PMID: 31546973 PMCID: PMC6770996 DOI: 10.3390/genes10090729] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 11/22/2022] Open
Abstract
The use of multiple source populations provides a way to maximise genetic variation and reduce the impacts of inbreeding depression in newly established translocated populations. However, there is a risk that individuals from different source populations will not interbreed, leading to population structure and smaller effective population sizes than expected. Here, we investigate the genetic consequences of mixing two isolated, morphologically distinct island populations of boodies (Bettongia lesueur) in a translocation to mainland Australia over three generations. Using 18 microsatellite loci and the mitochondrial D-loop region, we monitored the released animals and their offspring between 2010 and 2013. Despite high levels of divergence between the two source populations (FST = 0.42 and ϕST = 0.72), there was clear evidence of interbreeding between animals from different populations. However, interbreeding was non-random, with a significant bias towards crosses between the genetically smaller-sized Barrow Island males and the larger-sized Dorre Island females. This pattern of introgression was opposite to the expectation that male-male competition or female mate choice would favour larger males. This study shows how mixing diverged populations can bolster genetic variation in newly established mammal populations, but the ultimate outcome can be difficult to predict, highlighting the need for continued genetic monitoring to assess the long-term impacts of admixture.
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Affiliation(s)
- Rujiporn Thavornkanlapachai
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.
| | - Harriet R Mills
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, Western Australia 6027, Australia.
| | - Kym Ottewell
- Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Western Australia 6152, Australia.
| | - Judy Dunlop
- School of Veterinary and Biomedical Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia.
- Department of Biodiversity, Conservation and Attractions, PO Box 51, Wanneroo, Western Australia 6946, Australia.
| | - Colleen Sims
- Department of Biodiversity, Conservation and Attractions, PO Box 51, Wanneroo, Western Australia 6946, Australia.
| | - Keith Morris
- Department of Biodiversity, Conservation and Attractions, PO Box 51, Wanneroo, Western Australia 6946, Australia.
| | - Felicity Donaldson
- 360 Environmental, 10 Bermondsey Street, West Leederville, Western Australia 6007, Australia.
| | - W Jason Kennington
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.
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27
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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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28
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Trask AE, Fenn SR, Bignal EM, McCracken DI, Monaghan P, Reid JM. Evaluating the efficacy of independent versus simultaneous management strategies to address ecological and genetic threats to population viability. J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13464] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amanda E. Trask
- School of Biological Sciences, Zoology Building University of Aberdeen Aberdeen UK
| | - Sarah R. Fenn
- School of Biological Sciences, Zoology Building University of Aberdeen Aberdeen UK
| | | | - Davy I. McCracken
- Department of Integrated Land Management Scotland's Rural College Auchincruive Ayr UK
| | - Pat Monaghan
- Institute of Biodiversity, Animal Health & Comparative Medicine University of Glasgow Glasgow UK
| | - Jane M. Reid
- School of Biological Sciences, Zoology Building University of Aberdeen Aberdeen UK
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29
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Gallego‐García N, Forero‐Medina G, Vargas‐Ramírez M, Caballero S, Shaffer HB. Landscape genomic signatures indicate reduced gene flow and forest‐associated adaptive divergence in an endangered neotropical turtle. Mol Ecol 2019; 28:2757-2771. [DOI: 10.1111/mec.15112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 03/20/2019] [Accepted: 04/15/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Natalia Gallego‐García
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos LEMVA, Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
- Department of Ecology and Evolutionary Biology, California Conservation Science, Institute of the Environment and Sustainability University of California Los Angeles California USA
- Wildlife Conservation Society Turtle Survival Alliance Cali Colombia
| | | | - Mario Vargas‐Ramírez
- Biodiversidad y Conservación Genética, Instituto de Genética Universidad Nacional de Colombia Bogotá Colombia
| | - Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos LEMVA, Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
| | - Howard Bradley Shaffer
- Department of Ecology and Evolutionary Biology, California Conservation Science, Institute of the Environment and Sustainability University of California Los Angeles California USA
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30
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Hasselgren M, Angerbjörn A, Eide NE, Erlandsson R, Flagstad Ø, Landa A, Wallén J, Norén K. Genetic rescue in an inbred Arctic fox ( Vulpes lagopus) population. Proc Biol Sci 2019; 285:rspb.2017.2814. [PMID: 29593110 DOI: 10.1098/rspb.2017.2814] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/02/2018] [Indexed: 12/22/2022] Open
Abstract
Isolation of small populations can reduce fitness through inbreeding depression and impede population growth. Outcrossing with only a few unrelated individuals can increase demographic and genetic viability substantially, but few studies have documented such genetic rescue in natural mammal populations. We investigate the effects of immigration in a subpopulation of the endangered Scandinavian arctic fox (Vulpes lagopus), founded by six individuals and isolated for 9 years at an extremely small population size. Based on a long-term pedigree (105 litters, 543 individuals) combined with individual fitness traits, we found evidence for genetic rescue. Natural immigration and gene flow of three outbred males in 2010 resulted in a reduction in population average inbreeding coefficient (f), from 0.14 to 0.08 within 5 years. Genetic rescue was further supported by 1.9 times higher juvenile survival and 1.3 times higher breeding success in immigrant first-generation offspring compared with inbred offspring. Five years after immigration, the population had more than doubled in size and allelic richness increased by 41%. This is one of few studies that has documented genetic rescue in a natural mammal population suffering from inbreeding depression and contributes to a growing body of data demonstrating the vital connection between genetics and individual fitness.
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Affiliation(s)
- Malin Hasselgren
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Anders Angerbjörn
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Nina E Eide
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | - Rasmus Erlandsson
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | | | - Arild Landa
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | - Johan Wallén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Karin Norén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
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31
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Robinson JA, Räikkönen J, Vucetich LM, Vucetich JA, Peterson RO, Lohmueller KE, Wayne RK. Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction. SCIENCE ADVANCES 2019; 5:eaau0757. [PMID: 31149628 PMCID: PMC6541468 DOI: 10.1126/sciadv.aau0757] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 04/23/2019] [Indexed: 05/08/2023]
Abstract
The observation that small isolated populations often suffer reduced fitness from inbreeding depression has guided conservation theory and practice for decades. However, investigating the genome-wide dynamics associated with inbreeding depression in natural populations is only now feasible with relatively inexpensive sequencing technology and annotated reference genomes. To characterize the genome-wide effects of intense inbreeding and isolation, we performed whole-genome sequencing and morphological analysis of an iconic inbred population, the gray wolves (Canis lupus) of Isle Royale. Through population genetic simulations and comparison with wolf genomes from a variety of demographic histories, we find evidence that severe inbreeding depression in this population is due to increased homozygosity of strongly deleterious recessive mutations. Our results have particular relevance in light of the recent translocation of wolves from the mainland to Isle Royale, as well as broader implications for management of genetic variation in the fragmented landscape of the modern world.
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Affiliation(s)
- Jacqueline A. Robinson
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Corresponding author.
| | - Jannikke Räikkönen
- Department of Environmental Research and Monitoring, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden
| | - Leah M. Vucetich
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - John A. Vucetich
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Rolf O. Peterson
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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32
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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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33
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Grauer JA, Gilbert JH, Woodford JE, Eklund D, Anderson S, Pauli JN. Modest immigration can rescue a reintroduced carnivore population. J Wildl Manage 2019. [DOI: 10.1002/jwmg.21634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jennifer A. Grauer
- Department of Forest and Wildlife EcologyUniversity of Wisconsin‐Madison1630 Linden DriveMadisonWI53706USA
| | - Jonathan H. Gilbert
- Biological ServicesGreat Lakes Indian Fish and Wildlife CommissionP.O. Box 9 − 72682 Maple StreetOdanahWI54861USA
| | - James E. Woodford
- Bureau of Natural Heritage ConservationWisconsin Department of Natural Resources107 Sutliff AvenueRhinelanderWI54501USA
| | - Daniel Eklund
- U.S. Forest ServiceChequamegon Nicolet National Forest1170 4th Avenue SPark FallsWI54552USA
| | - Scott Anderson
- U.S. Forest ServiceChequamegon Nicolet National Forest1247 E Wall StreetEagle RiverWI54521USA
| | - Jonathan N. Pauli
- Department of Forest and Wildlife EcologyUniversity of Wisconsin‐Madison1630 Linden DriveMadisonWI53706USA
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34
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35
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Hedrick PW, Robinson JA, Peterson RO, Vucetich JA. Genetics and extinction and the example of Isle Royale wolves. Anim Conserv 2019. [DOI: 10.1111/acv.12479] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- P. W. Hedrick
- School of Life Sciences Arizona State University Tempe AZ USA
| | - J. A. Robinson
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | - R. O. Peterson
- School of Forest Resources and Environmental Science Michigan Technological University Houghton MI USA
| | - J. A. Vucetich
- School of Forest Resources and Environmental Science Michigan Technological University Houghton MI USA
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36
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Allen ML, Farmer MJ, Clare JDJ, Olson ER, Van Stappen J, Van Deelen TR. Is there anybody out there? Occupancy of the carnivore guild in a temperate archipelago. COMMUNITY ECOL 2018. [DOI: 10.1556/168.2018.19.3.8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- M. L. Allen
- Illinois Natural History Survey, University of Illinois, 1816 S. Oak Street, Champaign, IL 61820, USA
| | - M. J. Farmer
- Department of Forest and Wildlife Ecology, University of Wisconsin, 1630 Linden Drive, Madison, WI 53706, USA
| | - J. D. J Clare
- Department of Forest and Wildlife Ecology, University of Wisconsin, 1630 Linden Drive, Madison, WI 53706, USA
| | - E. R. Olson
- Natural Resources, Northland College, 1411 Ellis Ave S, Ashland, WI 54806, USA
| | - J. Van Stappen
- Planning and Resource Management, Apostle Islands National Lakeshore, 415 Washington Ave, Bayfield, WI 54814, USA
| | - T. R. Van Deelen
- Department of Forest and Wildlife Ecology, University of Wisconsin, 1630 Linden Drive, Madison, WI 53706, USA
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37
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Gable TD, Windels SK, Bump JK. Finding wolf homesites: improving the efficacy of howl surveys to study wolves. PeerJ 2018; 6:e5629. [PMID: 30280021 PMCID: PMC6166618 DOI: 10.7717/peerj.5629] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/23/2018] [Indexed: 12/03/2022] Open
Abstract
Locating wolf (Canis lupus) homesites is valuable for understanding the foraging behavior, population dynamics, and reproductive ecology of wolves during summer. During this period wolf pack members (adults and pups) readily respond to simulated wolf howls (i.e., howl surveys), which allows researchers to estimate the location of the homesite via triangulation. Confirming the actual locations of homesites via ground truthing is labor intensive because of the error surrounding estimated locations. Our objectives were (1) to quantify observer error during howl surveys and compare amongst experience levels, (2) provide a simple method for locating homesites in the field by incorporating observer error, and (3) further document the value of this method for monitoring wolf packs throughout the summer. We located 17 homesites by howl surveys during 2015–2017 in the Greater Voyageurs Ecosystem, Minnesota, USA. Of 62 bearings taken by observers during howl surveys, bearings erred by an average of 7.6° ± 6.3° (SD). There was no difference in observer error between novice and experienced observers. A simple way to increase efficiency when searching for homesites is to search concentric areas (bands) based on estimated observer error, specifically by: (1) adding ±10° error bands around howl survey bearings when ≥3 bearings can be obtained, (2) ±10° and ±20° error bands when 2 bearings are obtained, and (3) ±10° and ±26° error bands when 1 bearing is obtained. By incorporating observer error and understanding how frequently and how far wolves move homesites, it is possible to monitor wolf packs and confirm most, if not all, homesites used by a pack from at least June until August without having a collared individual in a pack.
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Affiliation(s)
- Thomas D Gable
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, St. Paul, MN, United States of America
| | - Steve K Windels
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, St. Paul, MN, United States of America.,Voyageurs National Park, International Falls, MN, United States of America
| | - Joseph K Bump
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, St. Paul, MN, United States of America
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38
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Mekonnen A, Rueness EK, Stenseth NC, Fashing PJ, Bekele A, Hernandez-Aguilar RA, Missbach R, Haus T, Zinner D, Roos C. Population genetic structure and evolutionary history of Bale monkeys (Chlorocebus djamdjamensis) in the southern Ethiopian Highlands. BMC Evol Biol 2018; 18:106. [PMID: 29986642 PMCID: PMC6038355 DOI: 10.1186/s12862-018-1217-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 06/13/2018] [Indexed: 12/31/2022] Open
Abstract
Background Species with a restricted geographic distribution, and highly specialized habitat and dietary requirements, are particularly vulnerable to extinction. The Bale monkey (Chlorocebus djamdjamensis) is a little-known arboreal, bamboo-specialist primate endemic to the southern Ethiopian Highlands. While most Bale monkeys inhabit montane forests dominated by bamboo, some occupy forest fragments where bamboo is much less abundant. We used mitochondrial DNA (mtDNA) sequences to analyse the genetic structure and evolutionary history of Bale monkeys covering the majority of their remaining distribution range. We analysed 119 faecal samples from their two main habitats, continuous forest (CF) and fragmented forests (FF), and sequenced 735 bp of the hypervariable region I (HVI) of the control region. We added 12 orthologous sequences from congeneric vervets (C. pygerythrus) and grivets (C. aethiops) as well as animals identified as hybrids, previously collected in southern Ethiopia. Results We found strong genetic differentiation (with no shared mtDNA haplotypes) between Bale monkey populations from CF and FF. Phylogenetic analyses revealed two distinct and highly diverged clades: a Bale monkey clade containing only Bale monkeys from CF and a green monkey clade where Bale monkeys from FF cluster with grivets and vervets. Analyses of demographic history revealed that Bale monkey populations (CF and FF) have had stable population sizes over an extended period, but have all recently experienced population declines. Conclusions The pronounced genetic structure and deep mtDNA divergence between Bale monkey populations inhabiting CF and FF are likely to be the results of hybridization and introgression of the FF population with parapatric Chlorocebus species, in contrast to the CF population, which was most likely not impacted by hybridization. Hybridization in the FF population was probably enhanced by an alteration of the bamboo forest habitat towards a more open woodland habitat, which enabled the parapatric Chlorocebus species to invade the Bale monkey's range and introgress the FF population. We therefore propose that the CF and FF Bale monkey populations should be managed as separate units when developing conservation strategies for this threatened species. Electronic supplementary material The online version of this article (10.1186/s12862-018-1217-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Addisu Mekonnen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway. .,Department of Zoological Sciences, Addis Ababa University, P.O. Box: 1176, Addis Ababa, Ethiopia.
| | - Eli K Rueness
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway.,Department of Zoological Sciences, Addis Ababa University, P.O. Box: 1176, Addis Ababa, Ethiopia
| | - Peter J Fashing
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway.,Department of Anthropology and Environmental Studies Program, California State University Fullerton, Fullerton, CA, 92834, USA
| | - Afework Bekele
- Department of Zoological Sciences, Addis Ababa University, P.O. Box: 1176, Addis Ababa, Ethiopia
| | - R Adriana Hernandez-Aguilar
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway
| | - Rose Missbach
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Tanja Haus
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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39
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Keepers K, Kane N, Martin AP. Following the Fate of Facilitated Migration In A Small Desert Spring. SOUTHWEST NAT 2018. [DOI: 10.1894/0038-4909-63.1.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Kyle Keepers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309
| | - Nolan Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309
| | - Andrew P. Martin
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309
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40
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Pfennig KS, Kelly AL, Pierce AA. Hybridization as a facilitator of species range expansion. Proc Biol Sci 2018; 283:rspb.2016.1329. [PMID: 27683368 DOI: 10.1098/rspb.2016.1329] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/01/2016] [Indexed: 01/02/2023] Open
Abstract
Explaining the evolution of species geographical ranges is fundamental to understanding how biodiversity is distributed and maintained. The solution to this classic problem in ecology and evolution remains elusive: we still do not fully know how species geographical ranges evolve and what factors fuel range expansions. Resolving this problem is now more crucial than ever with increasing biodiversity loss, global change and movement of species by humans. Here, we describe and evaluate the hypothesis that hybridization between species can contribute to species range expansion. We discuss how such a process can occur and the empirical data that are needed to test this hypothesis. We also examine how species can expand into new environments via hybridization with a resident species, and yet remain distinct species. Generally, hybridization may play an underappreciated role in influencing the evolution of species ranges. Whether-and to what extent-hybridization has such an effect requires further study across more diverse taxa.
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Affiliation(s)
- Karin S Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Audrey L Kelly
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Amanda A Pierce
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
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41
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Pierce AA, Gutierrez R, Rice AM, Pfennig KS. Genetic variation during range expansion: effects of habitat novelty and hybridization. Proc Biol Sci 2018; 284:rspb.2017.0007. [PMID: 28381622 DOI: 10.1098/rspb.2017.0007] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/08/2017] [Indexed: 12/31/2022] Open
Abstract
How species' ranges evolve remains an enduring problem in ecology and evolutionary biology. Species' range limits are potentially set by the inability of peripheral populations to adapt to range-edge habitat. Indeed, peripheral populations are often assumed to have reduced genetic diversity and population sizes, which limit evolvability. However, support for this assumption is mixed, possibly because the genetic effects of range expansion depend on two factors: the extent that habitat into which expansion occurs is novel and sources of gene flow. Here, we used spadefoot toads, Spea bombifrons, to contrast the population genetic effects of expansion into novel versus non-novel habitat. We further evaluated gene flow from conspecifics and from heterospecifics via hybridization with a resident species. We found that range expansion into novel habitat, relative to non-novel habitat, resulted in higher genetic differentiation, lower conspecific gene flow and bottlenecks. Moreover, we found that hybridizing with a resident species introduced genetic diversity in the novel habitat. Our results suggest the evolution of species' ranges can depend on the extent of differences in habitat between ancestral and newly occupied ranges. Furthermore, our results highlight the potential for hybridization with a resident species to enhance genetic diversity during expansions into novel habitat.
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Affiliation(s)
- Amanda A Pierce
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rafael Gutierrez
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Amber M Rice
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Karin S Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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42
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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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43
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Grogan KE, Sauther ML, Cuozzo FP, Drea CM. Genetic wealth, population health: Major histocompatibility complex variation in captive and wild ring-tailed lemurs ( Lemur catta). Ecol Evol 2017; 7:7638-7649. [PMID: 29043021 PMCID: PMC5632616 DOI: 10.1002/ece3.3317] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 07/13/2017] [Accepted: 07/18/2017] [Indexed: 12/24/2022] Open
Abstract
Across species, diversity at the major histocompatibility complex (MHC) is critical to individual disease resistance and, hence, to population health; however, MHC diversity can be reduced in small, fragmented, or isolated populations. Given the need for comparative studies of functional genetic diversity, we investigated whether MHC diversity differs between populations which are open, that is experiencing gene flow, versus populations which are closed, that is isolated from other populations. Using the endangered ring-tailed lemur (Lemur catta) as a model, we compared two populations under long-term study: a relatively "open," wild population (n = 180) derived from Bezà Mahafaly Special Reserve, Madagascar (2003-2013) and a "closed," captive population (n = 121) derived from the Duke Lemur Center (DLC, 1980-2013) and from the Indianapolis and Cincinnati Zoos (2012). For all animals, we assessed MHC-DRB diversity and, across populations, we compared the number of unique MHC-DRB alleles and their distributions. Wild individuals possessed more MHC-DRB alleles than did captive individuals, and overall, the wild population had more unique MHC-DRB alleles that were more evenly distributed than did the captive population. Despite management efforts to maintain or increase genetic diversity in the DLC population, MHC diversity remained static from 1980 to 2010. Since 2010, however, captive-breeding efforts resulted in the MHC diversity of offspring increasing to a level commensurate with that found in wild individuals. Therefore, loss of genetic diversity in lemurs, owing to small founder populations or reduced gene flow, can be mitigated by managed breeding efforts. Quantifying MHC diversity within individuals and between populations is the necessary first step to identifying potential improvements to captive management and conservation plans.
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Affiliation(s)
- Kathleen E. Grogan
- University Program in EcologyDuke UniversityDurhamNCUSA
- Department of Evolutionary AnthropologyDuke UniversityDurhamNCUSA
| | | | - Frank P. Cuozzo
- Lajuma Research CentreLouis Trichardt (Makhado)0920South Africa
| | - Christine M. Drea
- University Program in EcologyDuke UniversityDurhamNCUSA
- Department of Evolutionary AnthropologyDuke UniversityDurhamNCUSA
- Department of BiologyDuke UniversityDurhamNCUSA
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44
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Hedrick PW, Kardos M, Peterson RO, Vucetich JA. Genomic Variation of Inbreeding and Ancestry in the Remaining Two Isle Royale Wolves. J Hered 2017; 108:120-126. [PMID: 27940471 DOI: 10.1093/jhered/esw083] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/02/2016] [Indexed: 11/13/2022] Open
Abstract
Inbreeding, relatedness, and ancestry have traditionally been estimated with pedigree information, however, molecular genomic data can provide more detailed examination of these properties. For example, pedigree information provides estimation of the expected value of these measures but molecular genomic data can estimate the realized values of these measures in individuals. Here, we generate the theoretical distribution of inbreeding, relatedness, and ancestry for the individuals in the pedigree of the Isle Royale wolves, the first examination of such variation in a wild population with a known pedigree. We use the 38 autosomes of the dog genome and their estimated map lengths in our genomic analysis. Although it is known that the remaining wolves are highly inbred, closely related, and descend from only 3 ancestors, our analyses suggest that there is significant variation in the realized inbreeding and relatedness around pedigree expectations. For example, the expected inbreeding in a hypothetical offspring from the 2 remaining wolves is 0.438 but the realized 95% genomic confidence interval is from 0.311 to 0.565. For individual chromosomes, a substantial proportion of the whole chromosomes are completely identical by descent. This examination provides a background to use when analyzing molecular genomic data for individual levels of inbreeding, relatedness, and ancestry. The level of variation in these measures is a function of the time to the common ancestor(s), the number of chromosomes, and the rate of recombination. In the Isle Royale wolf population, the few generations to a common ancestor results in the high variance in genomic inbreeding.
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Affiliation(s)
- Philip W Hedrick
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Marty Kardos
- Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Flathead Lake Biological Station, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Rolf O Peterson
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
| | - John A Vucetich
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
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Smith JE, Lehmann KDS, Montgomery TM, Strauss ED, Holekamp KE. Insights from long‐term field studies of mammalian carnivores. J Mammal 2017. [DOI: 10.1093/jmammal/gyw194] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Wang P, Liu Y, Liu Y, Chang Y, Wang N, Zhang Z. The role of niche divergence and geographic arrangement in the speciation of Eared Pheasants (Crossoptilon, Hodgson 1938). Mol Phylogenet Evol 2017; 113:1-8. [PMID: 28487259 DOI: 10.1016/j.ympev.2017.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 04/28/2017] [Accepted: 05/04/2017] [Indexed: 10/19/2022]
Abstract
One of the most contentious theories in current ecology is the ecological niche conservatism, which is defined as conservatism among closely related species; however, the ecological niche can also be shifted, as documented in several cases. Genetic drift and ecological divergent selection may cause ecological niche divergence. The current study aims to test whether the ecological niche is conserved or divergent and to determine the main factor that drives ecological niche divergence or conservation. We analyzed the phylogenetic relationship, ecological niche model (ENM) and demographic history of Eared Pheasants in the genus Crossoptilon (Galliformes: Phasianidae) to test niche conservatism with respect to different geographically distributed patterns. The phylogenetic relationship was reconstructed using ∗BEAST with mitochondrial cytochrome b (cyt b) and 44 unlinked autosomal exonic loci, and ENMs were reconstructed in MAXENT using an average of 41 occurrence sites in each species and 22 bioclimatic variables. A background similarity test was used to detect whether the ecological niche is conserved. Demographic history was estimated using the isolation with migration (IM) model. We found that there was asymmetric gene flow between the allopatric sister species Crossoptilon mantchuricum and C. auritum and the parapatric sister species C. harmani and C. crossoptilon. We found that ecological niches were divergent, not conserved, between C. mantchuricum and C. auritum, which began to diverge at approximately 0.3 million years ago. However, the ecological niches were conserved between C. crossoptilon and C. harmani, which gradually diverged approximately half a million years ago. Ecological niches can be either conserved or divergent, and ecological divergent selection for local adaptation is probably an important factor that promotes and maintains niche divergence in the face of gene flow. This study provides a better understanding of the role that divergent selection has in the initial speciation process. The platform combined demographic processes and ecological niches to offer new insights into the mechanism of biogeography patterns.
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Affiliation(s)
- Pengcheng Wang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Yang Liu
- State Key Laboratory of Biocontrol, College of Ecology and Evolution/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Yinong Liu
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China; Beijing National Day School, Beijing 100039, PR China
| | - Yajing Chang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Nan Wang
- School of Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China.
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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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Grueber CE, Sutton JT, Heber S, Briskie JV, Jamieson IG, Robertson BC. Reciprocal translocation of small numbers of inbred individuals rescues immunogenetic diversity. Mol Ecol 2017; 26:2660-2673. [PMID: 28214377 DOI: 10.1111/mec.14063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/12/2016] [Accepted: 12/19/2016] [Indexed: 11/27/2022]
Abstract
Genetic rescue can reduce inbreeding depression and increase fitness of small populations, even when the donor populations are highly inbred. In a recent experiment involving two inbred island populations of the New Zealand South Island robin, Petroica australis, reciprocal translocations improved microsatellite diversity and individual fitness. While microsatellite loci may reflect patterns of genome-wide diversity, they generally do not indicate the specific genetic regions responsible for increased fitness. We tested the effectiveness of this reciprocal translocation for rescuing diversity of two immunogenetic regions: Toll-like receptor (TLR) and major histocompatibility complex (MHC) genes. We found that the relatively small number of migrants (seven and ten per island) effectively brought the characteristic TLR gene diversity of each source population into the recipient population. However, when migrants transmitted TLR alleles that were already present at high frequency in the recipient population, it was possible for offspring of mixed heritage to have decreased gene diversity compared to recipient population diversity prior to translocation. In contrast to TLRs, we did not observe substantial changes in MHC allelic diversity following translocation, with limited evidence of a decrease in differentiation, perhaps because most MHC alleles were observed at both sites prior to the translocation. Overall, we conclude that small numbers of migrants may successfully restore the diversity of immunogenetic loci with few alleles, but that translocating larger numbers of animals would provide additional opportunity for the genetic rescue of highly polymorphic immunity regions, such as the MHC, even when the source population is inbred.
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Affiliation(s)
- Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, RMC Gunn Building (B19), NSW 2006, Australia.,San Diego Zoo Global, PO Box 120551, San Diego, CA 92112, USA
| | - Jolene T Sutton
- Department of Biology, University of Hawai'i at Hilo, 200 West Kāwili Street, Hilo, HI 96720, USA
| | - Sol Heber
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - James V Briskie
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Ian G Jamieson
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Bruce C Robertson
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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Mussmann SM, Douglas MR, Anthonysamy WJB, Davis MA, Simpson SA, Louis W, Douglas ME. Genetic rescue, the greater prairie chicken and the problem of conservation reliance in the Anthropocene. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160736. [PMID: 28386428 PMCID: PMC5367285 DOI: 10.1098/rsos.160736] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/25/2017] [Indexed: 06/07/2023]
Abstract
A central question in conservation is how best to manage biodiversity, despite human domination of global processes (= Anthropocene). Common responses (i.e. translocations, genetic rescue) forestall potential extirpations, yet have an uncertain duration. A textbook example is the greater prairie chicken (GRPC: Tympanuchus cupido pinnatus), where translocations (1992-1998) seemingly rescued genetically depauperate Illinois populations. We re-evaluated this situation after two decades by genotyping 21 microsatellite loci from 1831 shed feathers across six leks in two counties over 4 years (2010-2013). Low migration rates (less than 1%) established each county as demographically independent, but with declining-population estimates (4 year average N = 79). Leks were genetically similar and significantly bottlenecked, with low effective population sizes (average Ne = 13.1; 4 year Ne/N = 0.166). Genetic structure was defined by 12 significantly different family groups, with relatedness r = 0.31 > half-sib r = 0.25. Average heterozygosity, indicating short-term survival, did not differ among contemporary, pre- and post-translocated populations, whereas allelic diversity did. Our results, the natural history of GRPC (i.e. few leks, male dominance hierarchies) and its controlled immigration suggest demographic expansion rather than genetic rescue. Legal protection under the endangered species act (ESA) may enhance recovery, but could exacerbate political-economic concerns on how best to manage 'conservation-reliant' species, for which GRPC is now an exemplar.
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Affiliation(s)
- S. M. Mussmann
- Biological Sciences, University of Arkansas, Fayetteville, AR, USA
- Illinois Natural History Survey, University of Illinois, Champaign, IL, USA
| | - M. R. Douglas
- Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | | | - M. A. Davis
- Illinois Natural History Survey, University of Illinois, Champaign, IL, USA
| | - S. A. Simpson
- Illinois Department of Natural Resources, Prairie Ridge State Natural Area, Newton, IL, USA
| | - W. Louis
- Illinois Department of Natural Resources, Gibson City, IL, USA
| | - M. E. Douglas
- Biological Sciences, University of Arkansas, Fayetteville, AR, USA
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