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Menor-Flores M, Vega-Rodríguez MA, Molina F. Iterative Level-0: A new and fast algorithm to traverse mating networks calculating the inbreeding and relationship coefficients. Comput Biol Med 2023; 164:107296. [PMID: 37566933 DOI: 10.1016/j.compbiomed.2023.107296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/24/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
In population medical genetics, the study of autosomal recessive disorders in highly endogamous populations is a major topic where calculating the inbreeding and relationship coefficients on mating networks is crucial. However, a challenge arises when dealing with large and complex mating networks, making their traversal difficult during the calculation process. For this calculation, we propose using Iterative Level-0 (IL0) as a new and faster algorithm that traverses mating networks more efficiently. The purpose of this work is to explain in detail the IL0 algorithm and prove its superiority by comparing it with two algorithms based on the best-known algorithms in the area: Depth First Search (DFS) and Breadth First Search (BFS). A Cytoscape application has been developed to calculate the inbreeding and relationship coefficients of individuals composing any mating network. In this application, the IL0 proposal together with DFS-based and BFS-based algorithms have been implemented. Any user can access this freely available Cytoscape application (https://apps.cytoscape.org/apps/inbreeding) that allows the comparison between the IL0 proposal and the best-known algorithms (based on DFS and BFS). In addition, a diverse set of mating networks has been collected in terms of complexity (number of edges) and species (humans, primates, and dogs) for the experiments. The runtime obtained by the IL0, DFS-based, and BFS-based algorithms when calculating the inbreeding and relationship coefficients proved the improvement of IL0. In fact, a speedup study reflected that the IL0 algorithm is 7.60 to 127.50 times faster than DFS-based and BFS-based algorithms. Moreover, a scalability study found that the growth of the IL0 runtime has a linear dependence on the number of edges of the mating network, while the DFS-based and BFS-based runtimes have a quadratic dependence. Therefore, the IL0 algorithm can solve the problem of calculating the inbreeding and relationship coefficients many times faster (up to 127.50) than the two algorithms based on the famous DFS and BFS. Furthermore, our results demonstrate that IL0 scales much better as the complexity of mating networks increases.
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Affiliation(s)
- Manuel Menor-Flores
- Escuela Politécnica, Universidad de Extremadura(1), Campus Universitario s/n, 10003 Cáceres, Spain.
| | - Miguel A Vega-Rodríguez
- Escuela Politécnica, Universidad de Extremadura(1), Campus Universitario s/n, 10003 Cáceres, Spain.
| | - Felipe Molina
- Facultad de Ciencias, Universidad de Extremadura (1), Avda. de Elvas s/n, 06006 Badajoz, Spain.
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2
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Mendoza Cavazos C, Heredia MY, Owens LA, Knoll LJ. Using Entamoeba muris To Model Fecal-Oral Transmission of Entamoeba in Mice. mBio 2023; 14:e0300822. [PMID: 36744962 PMCID: PMC9973306 DOI: 10.1128/mbio.03008-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/09/2023] [Indexed: 02/07/2023] Open
Abstract
There are several Entamoeba species that colonize humans, but only Entamoeba histolytica causes severe disease. E. histolytica is transmitted through the fecal-oral route to colonize the intestinal tract of 50 million people worldwide. The current mouse model to study E. histolytica intestinal infection directly delivers the parasite into the surgically exposed cecum, which circumvents the natural route of infection. To develop a fecal-oral mouse model, we screened our vivarium for a natural murine Entamoeba colonizer via a pan-Entamoeba PCR targeting the 18S ribosomal gene. We determined that C57BL/6 mice were chronically colonized by Entamoeba muris. This amoeba is closely related to E. histolytica, as determined by 18S sequencing and cross-reactivity with an E. histolytica-specific antibody. In contrast, outbred Swiss Webster (SW) mice were not chronically colonized by E. muris. We orally challenged SW mice with 1 × 105 E. muris cysts and discovered they were susceptible to infection, with peak cyst shedding occurring between 5 and 7 days postinfection. Most infected SW mice did not lose weight significantly but trended toward decreased weight gain throughout the experiment compared to mock-infected controls. Infected mice treated with paromomycin, an antibiotic used against noninvasive intestinal disease, do not become colonized by E. muris. Within the intestinal tract, E. muris localizes exclusively to the cecum and colon. Purified E. muris cysts treated with bovine bile in vitro excyst into mobile, pretrophozoite stages. Overall, this work describes a novel fecal-oral mouse model for the important global pathogen E. histolytica. IMPORTANCE Infection with parasites from the Entamoeba genus are significantly underreported causes of diarrheal disease that disproportionally impact tropical regions. There are several species of Entamoeba that infect humans to cause a range of symptoms from asymptomatic colonization of the intestinal tract to invasive disease with dissemination. All Entamoeba species are spread via the fecal-oral route in contaminated food and water. Studying the life cycle of Entamoeba, from host colonization to infectious fecal cyst production, can provide targets for vaccine and drug development. Because there is not an oral challenge rodent model, we screened for a mouse Entamoeba species and identified Entamoeba muris as a natural colonizer. We determine the peak of infection after an oral challenge, the efficacy of paromomycin treatment, the intestinal tract localization, and the cues that trigger excystation. This oral infection mouse model will be valuable for the development of novel therapeutic options for Entamoeba infections.
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Affiliation(s)
- Carolina Mendoza Cavazos
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Marienela Y. Heredia
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Leah A. Owens
- Department of Pathobiological Sciences, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, Wisconsin, USA
| | - Laura J. Knoll
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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3
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Cristescu RH, Strickland K, Schultz AJ, Kruuk LEB, de Villiers D, Frère CH. Susceptibility to a sexually transmitted disease in a wild koala population shows heritable genetic variance but no inbreeding depression. Mol Ecol 2022; 31:5455-5467. [PMID: 36043238 PMCID: PMC9826501 DOI: 10.1111/mec.16676] [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: 01/13/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 01/11/2023]
Abstract
The koala, one of the most iconic Australian wildlife species, is facing several concomitant threats that are driving population declines. Some threats are well known and have clear methods of prevention (e.g., habitat loss can be reduced with stronger land-clearing control), whereas others are less easily addressed. One of the major current threats to koalas is chlamydial disease, which can have major impacts on individual survival and reproduction rates and can translate into population declines. Effective management strategies for the disease in the wild are currently lacking, and, to date, we know little about the determinants of individual susceptibility to disease. Here, we investigated the genetic basis of variation in susceptibility to chlamydia using one of the most intensively studied wild koala populations. We combined data from veterinary examinations, chlamydia testing, genetic sampling and movement monitoring. Out of our sample of 342 wild koalas, 60 were found to have chlamydia. Using genotype information on 5007 SNPs to investigate the role of genetic variation in determining disease status, we found no evidence of inbreeding depression, but a heritability of 0.11 (95% CI: 0.06-0.23) for the probability that koalas had chlamydia. Heritability of susceptibility to chlamydia could be relevant for future disease management, as it suggests adaptive potential for the population.
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Affiliation(s)
- Romane H. Cristescu
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQueenslandAustralia
| | - Kasha Strickland
- Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
| | - Anthony J. Schultz
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQueenslandAustralia,Icelandic Museum of Natural History (Náttúruminjasafn Íslands)ReykjavikIceland
| | - Loeske E. B. Kruuk
- Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK,Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | | | - Céline H. Frère
- School of Biological SciencesUniversity of QueenslandSt LuciaQueenslandAustralia
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4
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Recovery of an isolated badger (Meles meles) population in The Netherlands. EUR J WILDLIFE RES 2022. [DOI: 10.1007/s10344-022-01596-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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5
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Inbreeding is associated with shorter early-life telomere length in a wild passerine. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01441-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractInbreeding can have negative effects on survival and reproduction, which may be of conservation concern in small and isolated populations. However, the physiological mechanisms underlying inbreeding depression are not well-known. The length of telomeres, the DNA sequences protecting chromosome ends, has been associated with health or fitness in several species. We investigated effects of inbreeding on early-life telomere length in two small island populations of wild house sparrows (Passer domesticus) known to be affected by inbreeding depression. Using genomic measures of inbreeding we found that inbred nestling house sparrows (n = 371) have significantly shorter telomeres. Using pedigree-based estimates of inbreeding we found a tendency for inbred nestling house sparrows to have shorter telomeres (n = 1195). This negative effect of inbreeding on telomere length may have been complemented by a heterosis effect resulting in longer telomeres in individuals that were less inbred than the population average. Furthermore, we found some evidence of stronger effects of inbreeding on telomere length in males than females. Thus, telomere length may reveal subtle costs of inbreeding in the wild and demonstrate a route by which inbreeding negatively impacts the physiological state of an organism already at early life-history stages.
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6
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Larison B, Pinho GM, Haghani A, Zoller JA, Li CZ, Finno CJ, Farrell C, Kaelin CB, Barsh GS, Wooding B, Robeck TR, Maddox D, Pellegrini M, Horvath S. Epigenetic models developed for plains zebras predict age in domestic horses and endangered equids. Commun Biol 2021; 4:1412. [PMID: 34921240 PMCID: PMC8683477 DOI: 10.1038/s42003-021-02935-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/02/2021] [Indexed: 01/09/2023] Open
Abstract
Effective conservation and management of threatened wildlife populations require an accurate assessment of age structure to estimate demographic trends and population viability. Epigenetic aging models are promising developments because they estimate individual age with high accuracy, accurately predict age in related species, and do not require invasive sampling or intensive long-term studies. Using blood and biopsy samples from known age plains zebras (Equus quagga), we model epigenetic aging using two approaches: the epigenetic clock (EC) and the epigenetic pacemaker (EPM). The plains zebra EC has the potential for broad application within the genus Equus given that five of the seven extant wild species of the genus are threatened. We test the EC's ability to predict age in sister taxa, including two endangered species and the more distantly related domestic horse, demonstrating high accuracy in all cases. By comparing chronological and estimated age in plains zebras, we investigate age acceleration as a proxy of health status. An interaction between chronological age and inbreeding is associated with age acceleration estimated by the EPM, suggesting a cumulative effect of inbreeding on biological aging throughout life.
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Affiliation(s)
- Brenda Larison
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA.
| | - Gabriela M Pinho
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Amin Haghani
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Joseph A Zoller
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Caesar Z Li
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Colin Farrell
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Bernard Wooding
- Quagga Project, Elandsberg Farms, Hermon, 7308, South Africa
| | - Todd R Robeck
- Zoological Operations, SeaWorld Parks and Entertainment, 7007 SeaWorld Drive, Orlando, FL, USA
| | - Dewey Maddox
- White Oak Conservation, 581705 White Oak Road, Yulee, FL, 32097, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Steve Horvath
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego, CA, USA.
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A continent-wide high genetic load in African buffalo revealed by clines in the frequency of deleterious alleles, genetic hitchhiking and linkage disequilibrium. PLoS One 2021; 16:e0259685. [PMID: 34882683 PMCID: PMC8659316 DOI: 10.1371/journal.pone.0259685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/24/2021] [Indexed: 11/19/2022] Open
Abstract
A high genetic load can negatively affect population viability and increase susceptibility to diseases and other environmental stressors. Prior microsatellite studies of two African buffalo (Syncerus caffer) populations in South Africa indicated substantial genome-wide genetic load due to high-frequency occurrence of deleterious alleles. The occurrence of these alleles, which negatively affect male body condition and bovine tuberculosis resistance, throughout most of the buffalo's range were evaluated in this study. Using available microsatellite data (2-17 microsatellite loci) for 1676 animals from 34 localities (from 25°S to 5°N), we uncovered continent-wide frequency clines of microsatellite alleles associated with the aforementioned male traits. Frequencies decreased over a south-to-north latitude range (average per-locus Pearson r = -0.22). The frequency clines coincided with a multilocus-heterozygosity cline (adjusted R2 = 0.84), showing up to a 16% decrease in southern Africa compared to East Africa. Furthermore, continent-wide linkage disequilibrium (LD) at five linked locus pairs was detected, characterized by a high fraction of positive interlocus associations (0.66, 95% CI: 0.53, 0.77) between male-deleterious-trait-associated alleles. Our findings suggest continent-wide and genome-wide selection of male-deleterious alleles driven by an earlier observed sex-chromosomal meiotic drive system, resulting in frequency clines, reduced heterozygosity due to hitchhiking effects and extensive LD due to male-deleterious alleles co-occurring in haplotypes. The selection pressures involved must be high to prevent destruction of allele-frequency clines and haplotypes by LD decay. Since most buffalo populations are stable, these results indicate that natural mammal populations, depending on their genetic background, can withstand a high genetic load.
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8
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Foster Y, Dutoit L, Grosser S, Dussex N, Foster BJ, Dodds KG, Brauning R, Van Stijn T, Robertson F, McEwan JC, Jacobs JME, Robertson BC. Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō. G3 (BETHESDA, MD.) 2021; 11:jkab307. [PMID: 34542587 PMCID: PMC8527487 DOI: 10.1093/g3journal/jkab307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023]
Abstract
Events of inbreeding are inevitable in critically endangered species. Reduced population sizes and unique life-history traits can increase the severity of inbreeding, leading to declines in fitness and increased risk of extinction. Here, we investigate levels of inbreeding in a critically endangered flightless parrot, the kākāpō (Strigops habroptilus), wherein a highly inbred island population and one individual from the mainland of New Zealand founded the entire extant population. Genotyping-by-sequencing (GBS), and a genotype calling approach using a chromosome-level genome assembly, identified a filtered set of 12,241 single-nucleotide polymorphisms (SNPs) among 161 kākāpō, which together encompass the total genetic potential of the extant population. Multiple molecular-based estimates of inbreeding were compared, including genome-wide estimates of heterozygosity (FH), the diagonal elements of a genomic-relatedness matrix (FGRM), and runs of homozygosity (RoH, FRoH). In addition, we compared levels of inbreeding in chicks from a recent breeding season to examine if inbreeding is associated with offspring survival. The density of SNPs generated with GBS was sufficient to identify chromosomes that were largely homozygous with RoH distributed in similar patterns to other inbred species. Measures of inbreeding were largely correlated and differed significantly between descendants of the two founding populations. However, neither inbreeding nor ancestry was found to be associated with reduced survivorship in chicks, owing to unexpected mortality in chicks exhibiting low levels of inbreeding. Our study highlights important considerations for estimating inbreeding in critically endangered species, such as the impacts of small population sizes and admixture between diverse lineages.
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Affiliation(s)
- Yasmin Foster
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Stefanie Grosser
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Nicolas Dussex
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Brodie J Foster
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Ken G Dodds
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Rudiger Brauning
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Tracey Van Stijn
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Fiona Robertson
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - John C McEwan
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | | | - Bruce C Robertson
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
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9
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Flanagan AM, Masuda B, Grueber CE, Sutton JT. Moving from trends to benchmarks by using regression tree analysis to find inbreeding thresholds in a critically endangered bird. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:1278-1287. [PMID: 33025666 DOI: 10.1111/cobi.13650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/03/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Understanding how inbreeding affects endangered species in conservation breeding programs is essential for their recovery. The Hawaiian Crow ('Alalā) (Corvus hawaiiensis) is one of the world's most endangered birds. It went extinct in the wild in 2002, and, until recent release efforts starting in 2016, nearly all of the population remained under human care for conservation breeding. Using pedigree inbreeding coefficients (F), we evaluated the effects of inbreeding on Hawaiian Crow offspring survival and reproductive success. We used regression tree analysis to identify the level of inbreeding (i.e., inbreeding threshold) that explains a substantial decrease in 'Alalā offspring survival to recruitment. Similar to a previous study of inbreeding in 'Alalā, we found that inbreeding had a negative impact on offspring survival but that parental (vs. artificial) egg incubation improved offspring survival to recruitment. Furthermore, we found that inbreeding did not substantially affect offspring reproductive success, based on the assumption that offspring that survive to adulthood breed with distantly related mates. Our novel application of regression tree analysis showed that offspring with inbreeding levels exceeding F = 0.098 were 69% less likely to survive to recruitment than more outbred offspring, providing a specific threshold value for ongoing population management. Our results emphasize the importance of assessing inbreeding depression across all life history stages, confirm the importance of prioritizing parental over artificial egg incubation in avian conservation breeding programs, and demonstrate the utility of regression tree analysis as a tool for identifying inbreeding thresholds, if present, in any pedigree-managed population.
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Affiliation(s)
- Alison M Flanagan
- Hawaii Endangered Bird Conservation Program, Institute for Conservation Research, San Diego Zoo Global, P.O. Box 39, Volcano, HI, 96785, U.S.A
| | - Bryce Masuda
- Hawaii Endangered Bird Conservation Program, Institute for Conservation Research, San Diego Zoo Global, P.O. Box 39, Volcano, HI, 96785, U.S.A
| | - Catherine E Grueber
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jolene T Sutton
- Department of Biology, University of Hawaii at Hilo, Hilo, HI, 96720, U.S.A
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10
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Rabier R, Lesobre L, Robert A. Reproductive performance in houbara bustard is affected by the combined effects of age, inbreeding and number of generations in captivity. Sci Rep 2021; 11:7813. [PMID: 33837276 PMCID: PMC8035203 DOI: 10.1038/s41598-021-87436-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022] Open
Abstract
Although captive breeding programs are valuable for conservation, they have been shown to be associated with genetic changes, such as adaptation to captivity or inbreeding. In addition, reproductive performance is strongly age-dependent in most animal species. These mechanisms that potentially impact reproduction have often been studied separately, while their interactions have rarely been addressed. In this study, using a large dataset of nine male and female reproductive parameters measured for 12,295 captive houbara bustards (Chlamydotis undulata undulata) over 24 years, we investigated the relative and interactive effects of age, inbreeding and number of generations in captivity on reproduction. We clearly identified (1) senescence patterns in all parameters studied; (2) negative effects of inbreeding on sperm characteristics, display behavior, egg weight, egg volume and hatching probability; and (3) changes in phenotypic values for seven parameters according to number of generations in captivity. However, the effect sizes associated with age were substantially greater than those associated with inbreeding and number of generations in captivity. Beyond the independent effects of these three factors on reproductive parameters, the results highlighted their interactive effects and thus the importance of integrating them in the design of genetic management plans for conservation breeding programs.
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Affiliation(s)
- Robin Rabier
- Reneco International Wildlife Consultant LLC, Abu Dhabi, United Arab Emirates.
- Centre d'Ecologie et des Sciences de la Conservation (CESCO), Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, 57 rue Cuvier, CP 135, 75005, Paris, France.
- Emirates Center for Wildlife Propagation, Missour, Morocco.
| | - Loïc Lesobre
- Reneco International Wildlife Consultant LLC, Abu Dhabi, United Arab Emirates
- Emirates Center for Wildlife Propagation, Missour, Morocco
| | - Alexandre Robert
- Centre d'Ecologie et des Sciences de la Conservation (CESCO), Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, 57 rue Cuvier, CP 135, 75005, Paris, France
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11
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Marjamäki PH, Dugdale HL, Delahay R, McDonald RA, Wilson AJ. Genetic, social and maternal contributions to Mycobacterium bovis infection status in European badgers (Meles meles). J Evol Biol 2021; 34:695-709. [PMID: 33617698 DOI: 10.1111/jeb.13775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 11/30/2022]
Abstract
Within host populations, individuals can vary in their susceptibility to infections and in the severity and progression of disease once infected. Though mediated through differences in behaviour, resistance or tolerance, variation in disease outcomes ultimately stems from genetic and environmental (including social) factors. Despite obvious implications for the evolutionary, ecological and epidemiological dynamics of disease traits, the relative importance of these factors has rarely been quantified in naturally infected wild animal hosts. Here, we use a long-term capture-mark-recapture study of group-living European badgers (Meles meles) to characterize genetic and environmental sources of variation in host infection status by Mycobacterium bovis, the causative agent of bovine tuberculosis (bTB). We find that genetic factors contribute to M. bovis infection status, whether measured over a lifetime or across repeated captures. In the latter case, the heritability (h2 ) of infection status is close to zero in cubs and yearlings but increases in adulthood. Overall, environmental influences arising from a combination of social group membership (defined in time and space) and maternal effects appear to be more important than genetic factors. Thus, while genes do contribute to among-individual variation, they play a comparatively minor role, meaning that rapid evolution of host defences under parasite-mediated selection is unlikely (especially if selection is on young animals where h2 is lowest). Conversely, our results lend further support to the view that social and early-life environments are important drivers of the dynamics of bTB infection in badger populations specifically, and of disease traits in wild hosts more generally.
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Affiliation(s)
- Paula H Marjamäki
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Hannah L Dugdale
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh, The Netherlands
| | - Richard Delahay
- National Wildlife Management Centre, Animal and Plant Health Agency, Gloucestershire, UK
| | - Robbie A McDonald
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, UK
| | - Alastair J Wilson
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
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12
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Affiliation(s)
- Jean‐Michel Gaillard
- Laboratoire de Biométrie et Biologie Evolutive UMR5558 CNRS Université Lyon 1 University of Lyon Villeurbanne France
| | - Jean‐François Lemaître
- Laboratoire de Biométrie et Biologie Evolutive UMR5558 CNRS Université Lyon 1 University of Lyon Villeurbanne France
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13
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Moss JB, Gerber GP, Welch ME. Heterozygosity-Fitness Correlations Reveal Inbreeding Depression in Neonatal Body Size in a Critically Endangered Rock Iguana. J Hered 2019; 110:818-829. [PMID: 31617903 DOI: 10.1093/jhered/esz060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 10/09/2019] [Indexed: 01/16/2023] Open
Abstract
Inbreeding depression, though challenging to identify in nature, may play an important role in regulating the dynamics of small and isolated populations. Conversely, greater expression of genetic load can enhance opportunities for natural selection. Conditional expression concentrates these opportunities for selection and may lead to failure of detection. This study investigates the possibility for age-dependent expression of inbreeding depression in a critically endangered population of rock iguanas, Cyclura nubila caymanensis. We employ heterozygote-fitness correlations to examine the contributions of individual genetic factors to body size, a fitness-related trait. Nonsignificant reductions in homozygosity (up to 7%) were detected between neonates and individuals surviving past their first year, which may reflect natural absorption of inbreeding effects by this small, fecund population. The majority of variation in neonate body size was attributed to maternal or environmental effects (i.e., clutch identity and incubation length); however, heterozygosity across 22 microsatellite loci also contributed significantly and positively to model predictions. Conversely, effects of heterozygosity on fitness were not detectable when adults were examined, suggesting that inbreeding depression in body size may be age dependent in this taxon. Overall, these findings emphasize the importance of taking holistic, cross-generational approaches to genetic monitoring of endangered populations.
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Affiliation(s)
- Jeanette B Moss
- Biological Sciences Department, Mississippi State University, Mississippi State, MS
| | - Glenn P Gerber
- Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | - Mark E Welch
- Biological Sciences Department, Mississippi State University, Mississippi State, MS
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Gaughran A, MacWhite T, Mullen E, Maher P, Kelly DJ, Good M, Marples NM. Dispersal patterns in a medium-density Irish badger population: Implications for understanding the dynamics of tuberculosis transmission. Ecol Evol 2019; 9:13142-13152. [PMID: 31871635 PMCID: PMC6912907 DOI: 10.1002/ece3.5753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/26/2019] [Accepted: 09/15/2019] [Indexed: 11/12/2022] Open
Abstract
European badgers (Meles meles) are group-living mustelids implicated in the spread of bovine tuberculosis (TB) to cattle and act as a wildlife reservoir for the disease. In badgers, only a minority of individuals disperse from their natal social group. However, dispersal may be extremely important for the spread of TB, as dispersers could act as hubs for disease transmission. We monitored a population of 139 wild badgers over 7 years in a medium-density population (1.8 individuals/km2). GPS tracking collars were applied to 80 different individuals. Of these, we identified 25 dispersers, 14 of which were wearing collars as they dispersed. This allowed us to record the process of dispersal in much greater detail than ever before. We show that dispersal is an extremely complex process, and measurements of straight-line distance between old and new social groups can severely underestimate how far dispersers travel. Assumptions of straight-line travel can also underestimate direct and indirect interactions and the potential for disease transmission. For example, one female disperser which eventually settled 1.5 km from her natal territory traveled 308 km and passed through 22 different territories during dispersal. Knowledge of badgers' ranging behavior during dispersal is crucial to understanding the dynamics of TB transmission, and for designing appropriate interventions, such as vaccination.
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Affiliation(s)
- Aoibheann Gaughran
- Department of ZoologySchool of Natural SciencesTrinity College DublinDublinIreland
- Trinity Centre for Biodiversity ResearchTrinity College DublinDublinIreland
| | | | - Enda Mullen
- Department of Culture, Heritage and the GaeltachtNational Parks and Wildlife ServiceDublinIreland
| | - Peter Maher
- Department of Agriculture, Food and the MarineDublinIreland
| | - David J. Kelly
- Department of ZoologySchool of Natural SciencesTrinity College DublinDublinIreland
- Trinity Centre for Biodiversity ResearchTrinity College DublinDublinIreland
| | - Margaret Good
- Department of ZoologySchool of Natural SciencesTrinity College DublinDublinIreland
- Trinity Centre for Biodiversity ResearchTrinity College DublinDublinIreland
| | - Nicola M. Marples
- Department of ZoologySchool of Natural SciencesTrinity College DublinDublinIreland
- Trinity Centre for Biodiversity ResearchTrinity College DublinDublinIreland
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15
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Mysterud A, Madslien K, Viljugrein H, Vikøren T, Andersen R, Güere ME, Benestad SL, Hopp P, Strand O, Ytrehus B, Røed KH, Rolandsen CM, Våge J. The demographic pattern of infection with chronic wasting disease in reindeer at an early epidemic stage. Ecosphere 2019. [DOI: 10.1002/ecs2.2931] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Atle Mysterud
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo NO‐0316 P.O. Box 1066 Blindern Oslo Norway
| | - Knut Madslien
- Norwegian Veterinary Institute NO‐0106 P.O. Box 750 Sentrum Oslo Norway
| | | | - Turid Vikøren
- Norwegian Veterinary Institute NO‐0106 P.O. Box 750 Sentrum Oslo Norway
| | - Roy Andersen
- Norwegian Institute for Nature Research (NINA) NO‐7485 P. O. Box 5685 Torgarden Trondheim Norway
| | - Mariella Evelyn Güere
- Department of Basic Sciences and Aquatic Medicine Norwegian University of Life Sciences NO‐0102 P.O. Box 369 Sentrum Oslo Norway
| | | | - Petter Hopp
- Norwegian Veterinary Institute NO‐0106 P.O. Box 750 Sentrum Oslo Norway
| | - Olav Strand
- Norwegian Institute for Nature Research (NINA) NO‐7485 P. O. Box 5685 Torgarden Trondheim Norway
| | - Bjørnar Ytrehus
- Norwegian Institute for Nature Research (NINA) NO‐7485 P. O. Box 5685 Torgarden Trondheim Norway
| | - Knut H. Røed
- Department of Basic Sciences and Aquatic Medicine Norwegian University of Life Sciences NO‐0102 P.O. Box 369 Sentrum Oslo Norway
| | - Christer M. Rolandsen
- Norwegian Institute for Nature Research (NINA) NO‐7485 P. O. Box 5685 Torgarden Trondheim Norway
| | - Jørn Våge
- Norwegian Veterinary Institute NO‐0106 P.O. Box 750 Sentrum Oslo Norway
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Péron G, Lemaître JF, Ronget V, Tidière M, Gaillard JM. Variation in actuarial senescence does not reflect life span variation across mammals. PLoS Biol 2019; 17:e3000432. [PMID: 31518381 PMCID: PMC6760812 DOI: 10.1371/journal.pbio.3000432] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/25/2019] [Accepted: 08/29/2019] [Indexed: 12/22/2022] Open
Abstract
The concept of actuarial senescence (defined here as the increase in mortality hazards with age) is often confounded with life span duration, which obscures the relative role of age-dependent and age-independent processes in shaping the variation in life span. We use the opportunity afforded by the Species360 database, a collection of individual life span records in captivity, to analyze age-specific mortality patterns in relation to variation in life span. We report evidence of actuarial senescence across 96 mammal species. We identify the life stage (juvenile, prime-age, or senescent) that contributes the most to the observed variation in life span across species. Actuarial senescence only accounted for 35%-50% of the variance in life span across species, depending on the body mass category. We computed the sensitivity and elasticity of life span to five parameters that represent the three stages of the age-specific mortality curve-namely, the duration of the juvenile stage, the mean juvenile mortality, the prime-age (i.e., minimum) adult mortality, the age at the onset of actuarial senescence, and the rate of actuarial senescence. Next, we computed the between-species variance in these five parameters. Combining the two steps, we computed the relative contribution of each of the five parameters to the variance in life span across species. Variation in life span was increasingly driven by the intensity of actuarial senescence and decreasingly driven by prime-age adult mortality from small to large species because of changes in the elasticity of life span to these parameters, even if all the adult survival parameters consistently exhibited a canalization pattern of weaker variability among long-lived species than among short-lived ones. Our work unambiguously demonstrates that life span cannot be used to measure the strength of actuarial senescence, because a substantial and variable proportion of life span variation across mammals is not related to actuarial senescence metrics.
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Affiliation(s)
- Guillaume Péron
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, Villeurbanne, France
- * E-mail:
| | - Jean-François Lemaître
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, Villeurbanne, France
| | - Victor Ronget
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, Villeurbanne, France
| | - Morgane Tidière
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, Villeurbanne, France
| | - Jean-Michel Gaillard
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, Villeurbanne, France
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Queirós J, Vicente J. Inbreeding shapes tuberculosis progression in female adult badgers (Meles meles). J Anim Ecol 2018; 87:1497-1499. [PMID: 30298536 DOI: 10.1111/1365-2656.12901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 08/20/2018] [Indexed: 11/28/2022]
Abstract
In Focus: Beton, C. H., Delahay, R. J., Smith, F. A. P., Robertson, A., McDonald, R. A., Young, A. J., Burke T. A., & Hodgson, D. (2018). Inbreeding intensifies sex- and age-dependent disease in a wild mammal. Journal of Animal Ecology, 87, 1497-1499. https://doi.org/10.1111/1365-2656.12878 Increasing crossbreeding of relatives promotes inbreeding which, in turn, can cause a reduction in fitness and the emergence of a phenomenon known as inbreeding depression. Benton et al., used the badger (Meles meles)-Mycobacterium bovis model system to study the relationship between inbreeding, disease, ageing and sex. A link between multilocus homozygosity (general effect) and TB progression (measured as antibody response to infection) and between homozygosity at specific loci (local effect) and TB progression were established in this study, highlighting the importance of host genetic background in determining host disease outcomes, and thus on shaping disease dynamics in wild populations. Moreover, the authors demonstrated for the first time in a natural population that this positive association might be modulated by sex and age. In infected individuals, inbreeding only affects disease progression in adult females.
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Affiliation(s)
- João Queirós
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
| | - Joaquín Vicente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
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