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Bercovitch FB. Conservation and evolution: Inbreeding, small populations, and sex differences in life history. Primates 2023; 64:277-283. [PMID: 37145305 DOI: 10.1007/s10329-023-01069-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 04/13/2023] [Indexed: 05/06/2023]
Affiliation(s)
- Fred B Bercovitch
- Wildlife Research Center, Kyoto, Japan.
- Anne Innis Dagg Foundation, Toronto, Canada.
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2
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Gussone L, Hüllen A, Vitt S, Scherer U, Thünken T. Impact of genetic relatedness on reproductive behavior in Pelvicachromis pulcher, a biparental cichlid fish with mutual mate choice and ornamentation. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2023; 110:17. [PMID: 37140644 PMCID: PMC10160185 DOI: 10.1007/s00114-023-01842-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023]
Abstract
Inbreeding can result in inbreeding depression. Therefore, many species seek to avoid inbreeding. However, theory predicts that inbreeding can be beneficial. Accordingly, some species tolerate inbreeding or even prefer mating with close relatives. Evidence for active inbreeding, i.e., kin-mating preference was reported in the biparental African cichlid fish Pelvicachromis taeniatus. Related mating partners revealed better parental cooperation due to kin selection, a potential benefit of inbreeding. In this study, we investigated kin-mating preference in a genetically diverse, outbred F2-lab population of Pelvicachromis pulcher, a closely related species to P. taeniatus. Like P. taeniatus, this species shows mutual ornamentation and mate choice as well as intense biparental brood care. The F1 P. pulcher generation had revealed signs of inbreeding depression but no inbreeding avoidance. We studied mating behavior and aggression in trios consisting of a male P. pulcher, an unfamiliar sister, and an unfamiliar, unrelated female. Because the study focused on kin-mating patterns, female pairs were matched for body size and coloration. The results provide no evidence for inbreeding avoidance but rather suggest inbreeding preference. We also found no significant impact of inbreeding on offspring survival. The results suggest no inbreeding avoidance in P. pulcher; however, the strength of inbreeding preference and inbreeding depression seems to be variable. We discuss possible causes for this variation like context-dependent inbreeding depression. The number of eggs positively correlated with female body size and coloration. Furthermore, the female aggressiveness was positively correlated with female coloration indicating that coloration signal female dominance and quality.
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Affiliation(s)
- Leonie Gussone
- Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121, Bonn, Germany
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Anna Hüllen
- Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121, Bonn, Germany
| | - Simon Vitt
- Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121, Bonn, Germany
| | - Ulrike Scherer
- Institute of Zoology, University of Hamburg, Martin-Luther-King Platz 3, 20146, Hamburg, Germany
- Department of Biology and Ecology of Fishes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
- Faculty of Life Sciences, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115, Berlin, Germany
| | - Timo Thünken
- Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121, Bonn, Germany.
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3
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Pérez‐Pereira N, López‐Cortegano E, García‐Dorado A, Caballero A. Prediction of fitness under different breeding designs in conservation programs. Anim Conserv 2022. [DOI: 10.1111/acv.12804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- N. Pérez‐Pereira
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
| | - E. López‐Cortegano
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
| | - A. García‐Dorado
- Departamento de Genética, Facultad de Ciencias Biológicas Universidad Complutense Madrid Spain
| | - A. Caballero
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
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Kleemann S, Sandow D, Stevens M, Schultz DJ, Taggart DA, Croxford A. Non-invasive monitoring and reintroduction biology of the brush-tailed rock-wallaby (. AUST J ZOOL 2022. [DOI: 10.1071/zo21009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Thirty-nine endangered brush-tailed rock-wallabies (Petrogale penicillata) were reintroduced to Grampians National Park, western Victoria, between 2008 and 2012. Subsequent high mortality, low breeding, and no recruitment were linked to fox predation and physical disturbance during monitoring. From 2014 to 2017, the colony was left undisturbed and monitored only by remote camera. Five adult animals were identified across this period (1 ♂ and 3 ♀s – all tagged; and one untagged female), and an average of 0.7 pouch young were birthed per tagged female per year. In 2019, camera-monitoring and non-invasive genetic monitoring (faecal) were used to identify colony members, genetic diversity, and breeding. Camera monitoring in 2019 identified the same five individuals, whereas genetic monitoring using 12 microsatellites identified eight individuals (two male and six female genotypes). Genetic diversity within the colony was moderate (expected heterozygosity (He) = 0.655, observed heterozygosity (Ho) = 0.854). Leaving the colony undisturbed after 2013 correlated with improved adult survival, increased breeding, and successful recruitment of young to the population. Recommendations for the Grampians colony include continuation of regular camera- and scat monitoring to improve our understanding of the reintroduction biology of P. penicillata and other marsupials in open, unfenced landscapes.
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Harder AM, Walden KKO, Marra NJ, Willoughby JR. High-quality reference genome for an arid-adapted mammal, the banner-tailed kangaroo rat (Dipodomys spectabilis). Genome Biol Evol 2022; 14:6506520. [PMID: 35026029 PMCID: PMC8800484 DOI: 10.1093/gbe/evac005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2022] [Indexed: 11/29/2022] Open
Abstract
Kangaroo rats in the genus Dipodomys are found in a variety of habitat types in western North America, including deserts, arid and semiarid grasslands, and scrublands. Many Dipodomys species are experiencing strong population declines due to increasing habitat fragmentation, with two species listed as federally endangered in the United States. The precarious state of many Dipodomys populations, including those occupying extreme environments, make species of this genus valuable subjects for studying the impacts of habitat degradation and fragmentation on population genomic patterns and for characterizing the genomic bases of adaptation to harsh conditions. To facilitate exploration of such questions, we assembled and annotated a reference genome for the banner-tailed kangaroo rat (Dipodomys spectabilis) using PacBio HiFi sequencing reads, providing a more contiguous genomic resource than two previously assembled Dipodomys genomes. Using the HiFi data for D. spectabilis and publicly available sequencing data for two other Dipodomys species (Dipodomys ordii and Dipodomys stephensi), we demonstrate the utility of this new assembly for studies of congeners by conducting inference of historic effective population sizes (Ne) and linking these patterns to the species’ current extinction risk statuses. The genome assembly presented here will serve as a valuable resource for population and conservation genomic studies of Dipodomys species, comparative genomic research within mammals and rodents, and investigations into genomic adaptation to extreme environments and changing landscapes.
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Affiliation(s)
- Avril M Harder
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, Alabama, USA
| | - Kimberly K O Walden
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Nicholas J Marra
- Division of Science, Mathematics, and Technology, Governors State University,University Park, Illinois, USA
| | - Janna R Willoughby
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, Alabama, USA
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DeWoody JA, Harder AM, Mathur S, Willoughby JR. The long-standing significance of genetic diversity in conservation. Mol Ecol 2021; 30:4147-4154. [PMID: 34191374 DOI: 10.1111/mec.16051] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/20/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022]
Abstract
Since allozymes were first used to assess genetic diversity in the 1960s and 1970s, biologists have attempted to characterize gene pools and conserve the diversity observed in domestic crops, livestock, zoos and (more recently) natural populations. Recently, some authors have claimed that the importance of genetic diversity in conservation biology has been greatly overstated. Here, we argue that a voluminous literature indicates otherwise. We address four main points made by detractors of genetic diversity's role in conservation by using published literature to firmly establish that genetic diversity is intimately tied to evolutionary fitness, and that the associated demographic consequences are of paramount importance to many conservation efforts. We think that responsible management in the Anthropocene should, whenever possible, include the conservation of ecosystems, communities, populations and individuals, and their underlying genetic diversity.
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Affiliation(s)
- J Andrew DeWoody
- Department of Forestry and Natural Resources, Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Avril M Harder
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, Alabama, USA
| | - Samarth Mathur
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
| | - Janna R Willoughby
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, Alabama, USA
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Zilko JP, Harley D, Hansen B, Pavlova A, Sunnucks P. Accounting for cryptic population substructure enhances detection of inbreeding depression with genomic inbreeding coefficients: an example from a critically endangered marsupial. Mol Ecol 2020; 29:2978-2993. [PMID: 32627274 DOI: 10.1111/mec.15540] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 05/16/2020] [Accepted: 06/18/2020] [Indexed: 12/21/2022]
Abstract
Characterizing inbreeding depression in wildlife populations can be critical to their conservation. Coefficients of individual inbreeding can be estimated from genome-wide marker data. The degree to which sensitivity of inbreeding coefficients to population genetic substructure alters estimates of inbreeding depression in wild populations is not well understood. Using generalized linear models, we tested the power of two frequently used inbreeding coefficients that are calculated from genome-wide SNP markers, FH and F^III , to predict four fitness traits estimated over two decades in an isolated population of the critically endangered Leadbeater's possum. FH estimates inbreeding as excess observed homozygotes relative to equilibrium expectations, whereas F^III quantifies allelic similarity between the gametes that formed an individual, and upweights rare homozygotes. We estimated FH and F^III from 1,575 genome-wide SNP loci in individuals with fitness trait data (N = 179-237 per trait), and computed revised coefficients, FH by group and F^IIIby group , adjusted for population genetic substructure by calculating them separately within two different genetic groups of individuals identified in the population. Using FH or F^III in the models, inbreeding depression was detected for survival to sexual maturity, longevity and whether individuals bred during their lifetime. F^IIIby group (but not FH by group ) additionally revealed significant inbreeding depression for lifetime reproductive output (total offspring assigned to each individual). Estimates of numbers of lethal equivalents indicated substantial inbreeding load, but differing between inbreeding estimators. Inbreeding depression, declining population size, and low and declining genetic diversity suggest that genetic rescue may assist in preventing extinction of this unique Leadbeater's possum population.
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Affiliation(s)
- Joseph P Zilko
- School of Biological Sciences, Monash University, Clayton, Vic, Australia
| | - Dan Harley
- Zoos Victoria, Parkville, Vic, Australia
| | - Birgita Hansen
- Centre for eResearch and Digital Innovation, Federation University, Ballarat, Vic, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton, Vic, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton, Vic, Australia
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