1
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Lowe WH, Addis BR, Cochrane MM. Outbreeding reduces survival during metamorphosis in a headwater stream salamander. Mol Ecol 2024; 33:e17375. [PMID: 38699973 DOI: 10.1111/mec.17375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 05/05/2024]
Abstract
Assessing direct fitness effects of individual genetic diversity is challenging due to the intensive and long-term data needed to quantify survival and reproduction in the wild. But resolving these effects is necessary to determine how inbreeding and outbreeding influence eco-evolutionary processes. We used 8 years of capture-recapture data and single nucleotide polymorphism genotypes for 1906 individuals to test for effects of individual heterozygosity on stage-specific survival probabilities in the salamander Gyrinophilus porphyriticus. The life cycle of G. porphyriticus includes an aquatic larval stage followed by metamorphosis into a semi-aquatic adult stage. In our study populations, the larval stage lasts 6-10 years, metamorphosis takes several months, and lifespan can reach 20 years. Previous studies showed that metamorphosis is a sensitive life stage, leading us to predict that fitness effects of individual heterozygosity would occur during metamorphosis. Consistent with this prediction, monthly probability of survival during metamorphosis declined with multi-locus heterozygosity (MLH), from 0.38 at the lowest MLH (0.10) to 0.06 at the highest MLH (0.38), a reduction of 84%. Body condition of larvae also declined significantly with increasing MLH. These relationships were consistent in the three study streams. With evidence of localised inbreeding within streams, these results suggest that outbreeding disrupts adaptations in pre-metamorphic and metamorphic individuals to environmental gradients along streams, adding to evidence that headwater streams are hotspots of microgeographic adaptation. Our results also underscore the importance of incorporating life history in analyses of the fitness effects of individual genetic diversity and suggest that metamorphosis and similar discrete life stage transitions may be critical periods of viability selection.
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Affiliation(s)
- Winsor H Lowe
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Brett R Addis
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Madaline M Cochrane
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
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2
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Samartino S, Christie D, Penna A, Sicotte P, Ting N, Wikberg E. Social network dynamics, infant loss, and gut microbiota composition in female Colobus vellerosus during time periods with alpha male challenges. Primates 2024:10.1007/s10329-024-01132-w. [PMID: 38735025 DOI: 10.1007/s10329-024-01132-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 04/11/2024] [Indexed: 05/13/2024]
Abstract
The gut microbiota of group-living animals is strongly influenced by their social interactions, but it is unclear how it responds to social instability. We investigated whether social instability associated with the arrival of new males and challenges to the alpha male position could explain differences in the gut microbiota in adult female Colobus vellerosus at Boabeng-Fiema, Ghana. First, we used a data set collected during May-August 2007 and May 2008-2009 that consisted of (i) 50 fecal samples from adult females in eight social groups for V4 16S rRNA sequencing to determine gut microbiota composition, and (ii) demographic and behavioral data ad libitum to determine male immigration, challenges to the alpha male position, and infant births and deaths. Sørensen and Bray-Curtis beta diversity indices (i.e., between-sample microbiota variation) were predicted by year, alpha male stability, group identity, and age. Next, we used a more detailed behavioral data set collected during focal observations of adult females in one group with a prolonged alpha male takeover and three cases of infant loss, to create 12-month versus 3-month 1-m proximity networks that preceded and overlapped the gut microbiome sampling period in that group. The long versus short-term networks were not correlated, suggesting temporal variation in proximity networks. In this group, beta diversity among the five adult females was predicted by similarity in infant loss status and short-term (rather than yearly) 1-m proximity ties. Although the mechanism driving this association needs to be further investigated in future studies, our findings indicate that alpha male takeovers are associated with gut microbiota variation and highlight the importance of taking demographic and social network dynamics into account.
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Affiliation(s)
- Shelby Samartino
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA.
| | - Diana Christie
- Department of Anthropology and Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Anna Penna
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Pascale Sicotte
- Department of Biology, Concordia University, Montreal, QC, Canada
| | - Nelson Ting
- Department of Anthropology and Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Eva Wikberg
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA.
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3
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Patterson C, Pilakouta N. Effects of Parental Care on the Magnitude of Inbreeding Depression: A Meta-Analysis in Fishes. Am Nat 2024; 203:E50-E62. [PMID: 38306289 DOI: 10.1086/728001] [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] [Indexed: 02/04/2024]
Abstract
AbstractInbreeding results from matings between relatives and often leads to a reduction in the fitness of inbred offspring, known as inbreeding depression. There is substantial variation in the magnitude of inbreeding depression among and within species, driven by differences in the biotic and abiotic environment. Recent studies in three species found that parental care has the potential to buffer against inbreeding depression in the offspring, but the generality of this pattern is still unknown. Here, we performed a meta-analysis to test whether variation in the magnitude of inbreeding depression is related to among-species differences in parental care in fishes. We synthesized 536 effect sizes across 56 studies and 18 species, spanning 47 years of research. We found that inbred offspring suffer a smaller reduction in fitness in species that provide biparental care than in species with uniparental or no care. By using a comparative approach, this study provides novel insights into the capacity of parental care to moderate inbreeding depression and suggests that these effects may currently be underappreciated. Considering the potential effects of parental care on inbreeding depression can help us understand why some species avoid inbreeding, whereas others tolerate or even prefer inbreeding, which has important implications for the maintenance of genetic variation within populations.
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4
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Pérez-González J, Carranza J, Anaya G, Broggini C, Vedel G, de la Peña E, Membrillo A. Comparative Analysis of Microsatellite and SNP Markers for Genetic Management of Red Deer. Animals (Basel) 2023; 13:3374. [PMID: 37958129 PMCID: PMC10650148 DOI: 10.3390/ani13213374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The analysis of population genetic structure and individual multilocus heterozygosity are crucial for wildlife management and conservation. Microsatellite markers have traditionally been used to assess these genetic parameters. However, single-nucleotide polymorphisms (SNPs) are becoming increasingly popular. Our goal here was to determine to what extent SNPs can provide better insights than microsatellites into the overall genetic status and population genetic processes in the species. To this end, we genotyped 210 red deer (Cervus elaphus) in the Spanish wild population with both 11 microsatellites and 31,712 SNPs. We compared parameters related to population genetic structure and individual multilocus heterozygosity obtained with both types of markers. Our results showed correlations between parameters measured using both microsatellites and SNPs, particularly those related to the level of genetic diversity and genetic differentiation. However, we found notably lower precision of microsatellites in measuring the distribution of genetic diversity among individuals. We conclude that microsatellites can be used to monitor the overall genetic status and detect broad patterns in red deer populations. Nevertheless, the greater precision of SNPs in inferring genetic structure and multilocus heterozygosity leads us to encourage scientists and wildlife managers to prioritize their use whenever possible.
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Affiliation(s)
- Javier Pérez-González
- Biology and Ethology Unit, Veterinary Faculty, University of Extremadura, 10003 Caceres, Spain
| | - Juan Carranza
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
| | - Gabriel Anaya
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
- Department of Genetics, University of Cordoba, 14071 Cordoba, Spain
| | - Camilla Broggini
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
| | - Giovanni Vedel
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
| | - Eva de la Peña
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
- Institute for Game and Wildlife Research (IREC), 13005 Ciudad Real, Spain
| | - Alberto Membrillo
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
- Department of Specific Didactics, Faculty of Education Sciences, University of Cordoba, 14071 Cordoba, Spain
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5
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The tails of two invasive species: genetic responses to acute and chronic bottlenecks. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02844-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractGenetic diversity can affect population viability and can be reduced by both acute and chronic mechanisms. Using the history of the establishment and management of two invasive rat species on Tetiaroa atoll, French Polynesia, we investigated the intensity and longevity of contrasting population bottleneck mechanisms on genetic diversity and bottleneck signal. Using microsatellite loci we show how both a chronic reduction over approximately 50 years of a Rattus exulans population caused by the arrival of its competitor R. rattus, and an acute reduction in a R. rattus population caused by a failed eradication approximately 10 years ago, caused similar magnitudes of genetic diversity loss. Furthermore, these strong bottleneck signals were in addition to the lasting signal from initial colonisation by each species many decades to centuries earlier, characterising a genetic paradox of biological invasion. These findings have implications for the study of population genetics of invasive species, and underscore how important historical context of population dynamics is when interpreting snapshots of genetic diversity.
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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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How well do genetic markers inform about responses to intraspecific admixture? A comparative analysis of microsatellites and RADseq. BMC Genom Data 2021; 22:22. [PMID: 34182923 PMCID: PMC8237422 DOI: 10.1186/s12863-021-00974-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/20/2021] [Indexed: 11/21/2022] Open
Abstract
Background Fitness consequences of intraspecific genetic admixture can vary from positive to negative depending on the genetic composition of the populations and environmental conditions. Because admixture has potential to influence the success of management and conservation efforts, genetic similarity has been suggested to be used as a proxy to predict the outcome. Studies utilizing microsatellites (a neutral marker) to investigate associations between genetic distance and admixture effects show conflicting results. Marker types that yield information on genome-wide and/or adaptive variation might be more useful for predicting responses to inter-population hybridization. In this study we utilized published data for three populations of pike (Esox lucius) to investigate associations between offspring performance (hatching success) and parental genetic similarity in experimentally purebred and admixed families, based on neutral (microsatellites), genome-wide neutral (RADseq SNPs), and adaptive (SNPs under selection) markers. Results Estimated similarity varied among the markers, likely reflecting differences in their inherent properties, but was consistently higher in purebred than admixed families. A significant interaction between marker type and admixture treatment reflected that neutral SNPs yielded higher estimates than adaptive SNPs for admixed families whereas no difference was found for purebred families, which indicates that neutral similarity was not reflective of adaptive similarity. When all samples were pooled, no association between similarity and performance was found for any marker. For microsatellites, similarity was positively correlated with hatching success in purebred families, whereas no association was found in admixed families; however, the direction of the effect differed between the population combinations. Conclusions The results strengthen the notion that, as of today, there is no proxy that can reliably predicted the outcome of admixture. This emphasizes the need of further studies to advance knowledge that can shed light on how to safeguard against negative consequences of admixture, and thereby inform management and promote conservation of biological diversity. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00974-3.
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8
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Sin SYW, Hoover BA, Nevitt GA, Edwards SV. Demographic History, Not Mating System, Explains Signatures of Inbreeding and Inbreeding Depression in a Large Outbred Population. Am Nat 2021; 197:658-676. [PMID: 33989142 DOI: 10.1086/714079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractInbreeding depression is often found in small, inbred populations, but whether it can be detected in and have evolutionary consequences for large, wide-ranging populations is poorly known. Here, we investigate the possibility of inbreeding in a large population to determine whether mild levels of inbreeding can still have genetic and phenotypic consequences and how genomically widespread these effects can be. We apply genome-wide methods to investigate whether individual and parental heterozygosity is related to morphological, growth, or life-history traits in a pelagic seabird, Leach's storm-petrel (Oceanodroma leucorhoa). Examining 560 individuals as part of a multiyear study, we found a substantial effect of maternal heterozygosity on chick traits: chicks from less heterozygous (relatively inbred) mothers were significantly smaller than chicks from more heterozygous (noninbred) mothers. We show that these heterozygosity-fitness correlations were due to general genome-wide effects and demonstrate a correlation between heterozygosity and inbreeding, suggesting inbreeding depression. We used population genetic models to further show that the variance in inbreeding was probably due to past demographic events rather than the current mating system and ongoing mate choice. Our findings demonstrate that inbreeding depression can be observed in large populations and illustrate how the integration of genomic techniques and fieldwork can elucidate its underlying causes.
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9
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Knief U, Forstmeier W, Pei Y, Wolf J, Kempenaers B. A test for meiotic drive in hybrids between Australian and Timor zebra finches. Ecol Evol 2020; 10:13464-13475. [PMID: 33304552 PMCID: PMC7713956 DOI: 10.1002/ece3.6951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/14/2020] [Accepted: 09/28/2020] [Indexed: 12/16/2022] Open
Abstract
Meiotic drivers have been proposed as a potent evolutionary force underlying genetic and phenotypic variation, genome structure, and also speciation. Due to their strong selective advantage, they are expected to rapidly spread through a population despite potentially detrimental effects on organismal fitness. Once fixed, autosomal drivers are cryptic within populations and only become visible in between-population crosses lacking the driver or corresponding suppressor. However, the assumed ubiquity of meiotic drivers has rarely been assessed in crosses between populations or species. Here we test for meiotic drive in hybrid embryos and offspring of Timor and Australian zebra finches-subspecies that have evolved in isolation for about two million years-using 38,541 informative transmissions of 56 markers linked to either centromeres or distal chromosome ends. We did not find evidence for meiotic driver loci on specific chromosomes. However, we observed a weak overall transmission bias toward Timor alleles at centromeres in females (transmission probability of Australian alleles of 47%, nominal p = 6 × 10-5). While this is in line with the centromere drive theory, it goes against the expectation that the subspecies with the larger effective population size (i.e., the Australian zebra finch) should have evolved the more potent meiotic drivers. We thus caution against interpreting our finding as definite evidence for centromeric drive. Yet, weak centromeric meiotic drivers may be more common than generally anticipated and we encourage further studies that are designed to detect also small effect meiotic drivers.
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Affiliation(s)
- Ulrich Knief
- Department of Behavioural Ecology and Evolutionary GeneticsMax Planck Institute for OrnithologySeewiesenGermany
- Division of Evolutionary BiologyFaculty of BiologyLudwig Maximilian University of MunichPlanegg‐MartinsriedGermany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary GeneticsMax Planck Institute for OrnithologySeewiesenGermany
| | - Yifan Pei
- Department of Behavioural Ecology and Evolutionary GeneticsMax Planck Institute for OrnithologySeewiesenGermany
| | - Jochen Wolf
- Division of Evolutionary BiologyFaculty of BiologyLudwig Maximilian University of MunichPlanegg‐MartinsriedGermany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary GeneticsMax Planck Institute for OrnithologySeewiesenGermany
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10
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Pei 裴一凡 Y, Forstmeier W, Wang 王代平 D, Martin K, Rutkowska J, Kempenaers B. Proximate Causes of Infertility and Embryo Mortality in Captive Zebra Finches. Am Nat 2020; 196:577-596. [PMID: 33064590 DOI: 10.1086/710956] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractSome species show high rates of reproductive failure, which is puzzling because natural selection works against such failure in every generation. Hatching failure is common in both captive and wild zebra finches (Taeniopygia guttata), yet little is known about its proximate causes. Here we analyze data on reproductive performance (the fate of >23,000 eggs) based on up to 14 years of breeding of four captive zebra finch populations. We find that virtually all aspects of reproductive performance are negatively affected by inbreeding (mean r=-0.117); by an early-starting, age-related decline (mean r=-0.132); and by poor early-life nutrition (mean r=-0.058). However, these effects together explain only about 3% of the variance in infertility, offspring mortality, fecundity, and fitness. In contrast, individual repeatability of different fitness components varied between 15% and 50%. As expected, we found relatively low heritability in fitness components (median: 7% of phenotypic variation and 29% of individually repeatable variation). Yet some of the heritable variation in fitness appears to be maintained by antagonistic pleiotropy (negative genetic correlations) between male fitness traits and female and offspring fitness traits. The large amount of unexplained variation suggests a potentially important role of local dominance and epistasis, including the possibility of segregating genetic incompatibilities.
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11
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Botero-Delgadillo E, Gilsenan C, Mueller JC, Kempenaers B. Negative effects of individual heterozygosity on reproductive success in a wild bird population. Mol Ecol 2020; 29:3196-3216. [PMID: 32668071 DOI: 10.1111/mec.15553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/03/2020] [Indexed: 01/01/2023]
Abstract
The evolutionary consequences of individual genetic diversity are frequently studied by assessing heterozygosity-fitness correlations (HFCs). The prevalence of positive and negative HFCs and the predominance of general versus local effects in wild populations are far from understood, partly because comprehensive studies testing for both inbreeding and outbreeding depression are lacking. We studied a genetically diverse population of blue tits in southern Germany using a genome-wide set of 87 microsatellites to investigate the relationship between proxies of reproductive success and measures of multilocus and single-locus individual heterozygosity (MLH and SLH). We used complimentary measures of MLH and partitioned markers into functional categories according to their position in the blue tit genome. HFCs based on MLH were consistently negative for functional loci, whereas correlations were rather inconsistent for loci found in nonfunctional areas of the genome. Clutch size was the only reproductive variable showing a general effect. We found evidence for local effects for three measures of reproductive success: arrival date at the breeding site, the probability of breeding at the study site and male reproductive success. For these, we observed consistent, and relatively strong, negative effects at one functional locus. Remarkably, this marker had a similar effect in another blue tit population from Austria (~400 km to the east). We suggest that a genetic local effect on timing of arrival might be responsible for most negative HFCs detected, with carry-over effects on other reproductive traits. This effect could reflect individual differences in the distance between overwintering areas and breeding sites.
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Affiliation(s)
- Esteban Botero-Delgadillo
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Carol Gilsenan
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Jakob C Mueller
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
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12
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Galla SJ, Moraga R, Brown L, Cleland S, Hoeppner MP, Maloney RF, Richardson A, Slater L, Santure AW, Steeves TE. A comparison of pedigree, genetic and genomic estimates of relatedness for informing pairing decisions in two critically endangered birds: Implications for conservation breeding programmes worldwide. Evol Appl 2020; 13:991-1008. [PMID: 32431748 PMCID: PMC7232769 DOI: 10.1111/eva.12916] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/18/2022] Open
Abstract
Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimize relatedness between individuals in an effort to avoid inbreeding, maximize diversity and maintain evolutionary potential. However, conservation breeding programmes struggle to use this approach when pedigrees are shallow or incomplete. While genetic data (i.e., microsatellites) can be used to estimate relatedness to inform pairing decisions, emerging evidence indicates this approach may lack precision in genetically depauperate species, and more effective estimates will likely be obtained from genomic data (i.e., thousands of genome-wide single nucleotide polymorphisms, or SNPs). Here, we compare relatedness estimates and subsequent pairing decisions using pedigrees, microsatellites and SNPs from whole-genome resequencing approaches in two critically endangered birds endemic to New Zealand: kakī/black stilt (Himantopus novaezelandiae) and kākāriki karaka/orange-fronted parakeet (Cyanoramphus malherbi). Our findings indicate that SNPs provide more precise estimates of relatedness than microsatellites when assessing empirical parent-offspring and full sibling relationships. Further, our results show that relatedness estimates and subsequent pairing recommendations using PMx are most similar between pedigree- and SNP-based approaches. These combined results indicate that in lieu of robust pedigrees, SNPs are an effective tool for informing pairing decisions, which has important implications for many poorly pedigreed conservation breeding programmes worldwide.
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Affiliation(s)
- Stephanie J. Galla
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Roger Moraga
- Tea Break Bioinformatics, LtdPalmerston NorthNew Zealand
| | - Liz Brown
- New Zealand Department of ConservationTwizelNew Zealand
| | | | - Marc P. Hoeppner
- Institute for Clinical Molecular BiologyChristian‐Albrechts‐University KielKielGermany
| | | | - Anne Richardson
- The Isaac Conservation and Wildlife TrustChristchurchNew Zealand
| | - Lyndon Slater
- New Zealand Department of ConservationRangioraNew Zealand
| | - Anna W. Santure
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Tammy E. Steeves
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
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13
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Interactions between social groups of colobus monkeys (Colobus vellerosus) explain similarities in their gut microbiomes. Anim Behav 2020. [DOI: 10.1016/j.anbehav.2020.02.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Mitrus C, Mitrus J, Rutkowski R. Individual Heterozygosity Influences Arrival Times and Mating Success of Male Red-Breasted Flycatchers Ficedula parva. Zool Stud 2020; 59:e12. [PMID: 32760458 PMCID: PMC7396921 DOI: 10.6620/zs.2020.59-12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 02/22/2020] [Indexed: 11/18/2022]
Abstract
We examined the relationship between individual heterozygosity of male Red-breasted Flycatchers (Ficedula parva; a small long-distance migratory, socially monogamous bird species) and their mating success, arrival time and age. Using eight polymorphic microsatellite loci, we found that male heterozygosity is related to both mating success and arrival time, but not to age. Mated and earlier arriving males had higher heterozygosity than later arrivals and bachelors, but we did not find a relationship between age and individual heterozygosity of males. To our knowledge, this is the first study to provide evidence about the relationship between individual genetic diversity and arrival time, thus arrival time could be used as a signal of individual heterozygosity and quality.
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Affiliation(s)
- Cezary Mitrus
- Department of Vertebrate Ecology and Paleontology, Institute of Biology, Wrocław University of Environmental and Life Sciences, Chełmońskiego 38c, 51-631 Wrocław, Poland. E-mail: (C. Mitrus)
| | - Joanna Mitrus
- Department of Plant Physiology and Genetics, Siedlce University of Natural Sciences and Humanities, Prusa 12, 08-110 Siedlce, Poland. E-mail: (J. Mitrus)
| | - Robert Rutkowski
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679 Warsaw, Poland. E-mail: (Rutkowski)
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15
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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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16
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Lindsay WR, Andersson S, Bererhi B, Höglund J, Johnsen A, Kvarnemo C, Leder EH, Lifjeld JT, Ninnes CE, Olsson M, Parker GA, Pizzari T, Qvarnström A, Safran RJ, Svensson O, Edwards SV. Endless forms of sexual selection. PeerJ 2019; 7:e7988. [PMID: 31720113 PMCID: PMC6839514 DOI: 10.7717/peerj.7988] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 10/04/2019] [Indexed: 12/11/2022] Open
Abstract
In recent years, the field of sexual selection has exploded, with advances in theoretical and empirical research complementing each other in exciting ways. This perspective piece is the product of a “stock-taking” workshop on sexual selection and sexual conflict. Our aim is to identify and deliberate on outstanding questions and to stimulate discussion rather than provide a comprehensive overview of the entire field. These questions are organized into four thematic sections we deem essential to the field. First we focus on the evolution of mate choice and mating systems. Variation in mate quality can generate both competition and choice in the opposite sex, with implications for the evolution of mating systems. Limitations on mate choice may dictate the importance of direct vs. indirect benefits in mating decisions and consequently, mating systems, especially with regard to polyandry. Second, we focus on how sender and receiver mechanisms shape signal design. Mediation of honest signal content likely depends on integration of temporally variable social and physiological costs that are challenging to measure. We view the neuroethology of sensory and cognitive receiver biases as the main key to signal form and the ‘aesthetic sense’ proposed by Darwin. Since a receiver bias is sufficient to both initiate and drive ornament or armament exaggeration, without a genetically correlated or even coevolving receiver, this may be the appropriate ‘null model’ of sexual selection. Thirdly, we focus on the genetic architecture of sexually selected traits. Despite advances in modern molecular techniques, the number and identity of genes underlying performance, display and secondary sexual traits remains largely unknown. In-depth investigations into the genetic basis of sexual dimorphism in the context of long-term field studies will reveal constraints and trajectories of sexually selected trait evolution. Finally, we focus on sexual selection and conflict as drivers of speciation. Population divergence and speciation are often influenced by an interplay between sexual and natural selection. The extent to which sexual selection promotes or counteracts population divergence may vary depending on the genetic architecture of traits as well as the covariance between mating competition and local adaptation. Additionally, post-copulatory processes, such as selection against heterospecific sperm, may influence the importance of sexual selection in speciation. We propose that efforts to resolve these four themes can catalyze conceptual progress in the field of sexual selection, and we offer potential avenues of research to advance this progress.
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Affiliation(s)
- Willow R Lindsay
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Staffan Andersson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Badreddine Bererhi
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Arild Johnsen
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Charlotta Kvarnemo
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Erica H Leder
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Jan T Lifjeld
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Calum E Ninnes
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.,Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States of America
| | - Mats Olsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Geoff A Parker
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Tommaso Pizzari
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, United Kingdom
| | - Anna Qvarnström
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Rebecca J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States of America
| | - Ola Svensson
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America.,Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology, Göteborg, Sweden
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17
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Pérez-Tris J, Llanos-Garrido A, Bloor P, Carbonell R, Tellería JL, Santos T, Díaz JA. Increased individual homozygosity is correlated with low fitness in a fragmented lizard population. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
AbstractIsolation owing to anthropogenic habitat fragmentation is expected to increase the homozygosity of individuals, which might reduce their fitness as a result of inbreeding depression. Using samples from a fragmented population of the lizard Psammodromus algirus, for which we had data about two correlates of fitness, we genotyped individuals for six microsatellite loci that correctly capture genome-wide individual homozygosity of these lizards (as validated with an independent sample of lizards genotyped for both these microsatellites and > 70 000 single nucleotide polymorphisms). Our data revealed genetic structure at a very small geographical scale, which was compatible with restricted gene flow among populations disconnected in a matrix of inhospitable habitat. Lizards from the same fragment were genetically more related to one another than expected by chance, and individual homozygosity was greater in small than in large fragments. Within fragments, individual homozygosity was negatively associated with adult body size and clutch mass, revealing a link among reduced gene flow, increased homozygosity and lowered fitness that might reduce population viability deterministically. Our results contribute to mounting evidence of the impact of the loss of genetic diversity on fragmented wild populations.
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Affiliation(s)
- Javier Pérez-Tris
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain
| | - Alejandro Llanos-Garrido
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain
| | - Paul Bloor
- Instituto de Genética, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Roberto Carbonell
- Consejería de Medio Ambiente, Servicio Espacios Naturales, Valladolid, Spain
| | - José Luis Tellería
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain
| | - Tomás Santos
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain
| | - José A Díaz
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain
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18
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Ralston J, Lorenc L, Montes M, DeLuca WV, Kirchman JJ, Woodworth BK, Mackenzie SA, Newman A, Cooke HA, Freeman NE, Sutton AO, Tauzer L, Norris DR. Length polymorphisms at two candidate genes explain variation of migratory behaviors in blackpoll warblers ( Setophaga striata). Ecol Evol 2019; 9:8840-8855. [PMID: 31410284 PMCID: PMC6686290 DOI: 10.1002/ece3.5436] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/30/2019] [Accepted: 06/15/2019] [Indexed: 12/12/2022] Open
Abstract
Migratory behaviors such as the timing and duration of migration are genetically inherited and can be under strong natural selection, yet we still know very little about the specific genes or molecular pathways that control these behaviors. Studies in candidate genes Clock and Adcyap1 have revealed that both of these loci can be significantly correlated with migratory behaviors in birds, though observed relationships appear to vary across species. We investigated geographic genetic structure of Clock and Adcyap1 in four populations of blackpoll warblers (Setophaga striata), a Neotropical-Nearctic migrant that exhibits geographic variation in migratory timing and duration across its boreal breeding distribution. Further, we used data on migratory timing and duration, obtained from light-level geolocator trackers to investigate candidate genotype-phenotype relationships at the individual level. While we found no geographic structure in either candidate gene, we did find evidence that candidate gene lengths are correlated with five of the six migratory traits. Maximum Clock allele length was significantly and negatively associated with spring arrival date. Minimum Adcyap1 allele length was significantly and negatively associated with spring departure date and positively associated with fall arrival date at the wintering grounds. Additionally, we found a significant interaction between Clock and Adcyap1 allele lengths on both spring and fall migratory duration. Adcyap1 heterozygotes also had significantly shorter migration duration in both spring and fall compared to homozygotes. Our results support the growing body of evidence that Clock and Adcyap1 allele lengths are correlated with migratory behaviors in birds.
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Affiliation(s)
- Joel Ralston
- Department of BiologySaint Mary's CollegeNotre DameINUSA
| | - Lydia Lorenc
- Department of BiologySaint Mary's CollegeNotre DameINUSA
| | - Melissa Montes
- Department of BiologySaint Mary's CollegeNotre DameINUSA
| | - William V. DeLuca
- Department of Environmental ConservationUniversity of MassachusettsAmherstMAUSA
| | | | - Bradley K. Woodworth
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
- School of Biological SciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | | | - Amy Newman
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | | | | | - Alex O. Sutton
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Lila Tauzer
- Wildlife Conservation Society CanadaWhitehorseYTCanada
| | - D. Ryan Norris
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
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19
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Litzke V, Ottensmann M, Forcada J, Heitzmann L, Ivan Hoffman J. Heterozygosity at neutral and immune loci is not associated with neonatal mortality due to microbial infection in Antarctic fur seals. Ecol Evol 2019; 9:7985-7996. [PMID: 31380066 PMCID: PMC6662382 DOI: 10.1002/ece3.5317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/02/2019] [Accepted: 05/08/2019] [Indexed: 11/08/2022] Open
Abstract
Numerous studies have reported correlations between the heterozygosity of genetic markers and fitness. These heterozygosity-fitness correlations (HFCs) play a central role in evolutionary and conservation biology, yet their mechanistic basis remains open to debate. For example, fitness associations have been widely reported at both neutral and functional loci, yet few studies have directly compared the two, making it difficult to gauge the relative contributions of genome-wide inbreeding and specific functional genes to fitness. Here, we compared the effects of neutral and immune gene heterozygosity on death from bacterial infection in Antarctic fur seal (Arctocephalus gazella) pups. We specifically developed a panel of 13 microsatellites from expressed immune genes and genotyped these together with 48 neutral loci in 234 individuals, comprising 39 pups that were classified at necropsy as having most likely died of bacterial infection together with a five times larger matched sample of healthy surviving pups. Identity disequilibrium quantified from the neutral markers was positive and significant, indicative of variance in inbreeding within the study population. However, multilocus heterozygosity did not differ significantly between healthy and infected pups at either class of marker, and little evidence was found for fitness associations at individual loci. These results support a previous study of Antarctic fur seals that found no effects of heterozygosity at nine neutral microsatellites on neonatal survival and thereby help to refine our understanding of how HFCs vary across the life cycle. Given that nonsignificant HFCs are underreported in the literature, we also hope that our study will contribute toward a more balanced understanding of the wider importance of this phenomenon.
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Affiliation(s)
- Vivienne Litzke
- Department of Animal BehaviourBielefeld UniversityBielefeldGermany
| | | | | | | | - Joseph Ivan Hoffman
- Department of Animal BehaviourBielefeld UniversityBielefeldGermany
- British Antarctic Survey, High CrossCambridgeUK
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20
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McLennan EA, Wright BR, Belov K, Hogg CJ, Grueber CE. Too much of a good thing? Finding the most informative genetic data set to answer conservation questions. Mol Ecol Resour 2019; 19:659-671. [DOI: 10.1111/1755-0998.12997] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Elspeth A. McLennan
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Belinda R. Wright
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Katherine Belov
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Carolyn J. Hogg
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Catherine E. Grueber
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
- San Diego Zoo Global San Diego California
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21
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Inbreeding load and inbreeding depression estimated from lifetime reproductive success in a small, dispersal-limited population. Heredity (Edinb) 2019; 123:192-201. [PMID: 30809076 DOI: 10.1038/s41437-019-0197-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 11/08/2022] Open
Abstract
The fitness consequences of inbreeding and the individual behaviors that prevent its detrimental effects can be challenging to document in wild populations. Here, we use field and molecular data from a 17-year study of banner-tailed kangaroo rats (Dipodomys spectabilis) to quantify the relationship between inbreeding, mate kinship, and lifetime reproductive success. Using a pedigree that was reconstructed using genetic and field data within a Bayesian framework (median probability of parental assignment = 0.92, mean pedigree depth = 6 generations), we estimated both inbreeding coefficients and kinship between individuals that produced offspring (mean inbreeding coefficient = 0.07, mean mate kinship = 0.08). We also used the pedigree, in combination with census data, to generate a series of fitness estimates, ranging from survival to reproductive maturity to lifetime reproductive success. We found that the population's inbreeding load was low to moderate (0.98-4.66 haploid lethal equivalents) and increased with the time frame over which fitness was estimated (lowest for survival to maturity, highest for adult-to-adult reproductive success). Fitness decreased with increasing inbreeding coefficients. For example, lifetime reproductive success was reduced by 24% for individuals with inbreeding coefficients greater than twice the population mean. Within full sibling pairs, the sibling with less-related mates produced an average of 30% more offspring over its lifetime. These data further illustrate that inbreeding can have a negative effect on lifetime reproductive success.
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22
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Bichet C, Vedder O, Sauer‐Gürth H, Becker PH, Wink M, Bouwhuis S. Contrasting heterozygosity‐fitness correlations across life in a long‐lived seabird. Mol Ecol 2019; 28:671-685. [DOI: 10.1111/mec.14979] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/09/2018] [Accepted: 12/10/2018] [Indexed: 01/14/2023]
Affiliation(s)
| | - Oscar Vedder
- Institute of Avian Research Wilhelmshaven Germany
- Groningen Institute for Evolutionary Life Sciences University of Groningen Groningen The Netherlands
| | - Hedwig Sauer‐Gürth
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Heidelberg Germany
| | | | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Heidelberg Germany
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23
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Martinez AS, Willoughby JR, Christie MR. Genetic diversity in fishes is influenced by habitat type and life-history variation. Ecol Evol 2018; 8:12022-12031. [PMID: 30598796 PMCID: PMC6303716 DOI: 10.1002/ece3.4661] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 01/14/2023] Open
Abstract
Populations of fishes are increasingly threatened by over-exploitation, pollution, habitat destruction, and climate change. In order to better understand the factors that can explain the amount of genetic diversity in wild populations of fishes, we collected estimates of genetic diversity (mean heterozygosity and mean rarefied number of alleles per locus) along with habitat associations, conservation status, and life-history information for 463 fish species. We ran a series of phylogenetic generalized least squares models to determine which factors influence genetic diversity in fishes after accounting for shared evolutionary history among related taxa. We found that marine fishes had significantly higher genetic diversity than freshwater fishes with marine fishes averaging 11.3 more alleles per locus than their freshwater counterparts. However, contrary to our expectations, genetic diversity was not found to be lower in threatened versus not-threatened fishes. Finally, we found that both age at maturity and fecundity were negatively related to genetic variation in both marine and freshwater fishes. Our results demonstrate that both life-history characteristics and habitat play a role in shaping patterns of genetic diversity in fishes and should be considered when prioritizing species for conservation.
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Affiliation(s)
| | - Janna R. Willoughby
- Department of Biological SciencesPurdue UniversityWest LafayetteIndiana
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteIndiana
| | - Mark R. Christie
- Department of Biological SciencesPurdue UniversityWest LafayetteIndiana
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteIndiana
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24
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Robinson CV, Garcia de Leaniz C, James J, Cable J, Orozco‐terWengel P, Consuegra S. Genetic diversity and parasite facilitated establishment of the invasive signal crayfish ( Pacifastacus leniusculus) in Great Britain. Ecol Evol 2018; 8:9181-9191. [PMID: 30377493 PMCID: PMC6194297 DOI: 10.1002/ece3.4235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/01/2018] [Accepted: 05/03/2018] [Indexed: 11/25/2022] Open
Abstract
Successful establishment of non-native species is strongly influenced, among other factors, by the genetic variation of founding populations, which can be enhanced by multiple introductions through admixture. Coexisting pathogens can also facilitate the establishment of non-native species by detrimentally impacting on the native fauna acting as novel weapons. The signal crayfish (Pacifastacus leniusculus) is a highly invasive species, which has caused mass declines of native crayfish in Europe through displacement and transmission of the oomycete Aphanomyces astaci (crayfish plague), which is typically lethal to native European crayfish. However, whether Aphanomyces astaci may have facilitated the invasion of the signal crayfish is not known. We estimated the genetic diversity at microsatellite DNA loci, effective population size, and potential origins of seven infected and noninfected signal crayfish populations in Europe and one founder population in North America. Approximate Bayesian computation analysis and population structuring suggested multiple host introductions from diverse source populations, as well as higher heterozygosity among infected than uninfected populations, which could reflect a fitness advantage. Low effective population size, moderate heterozygosity, and lack of isolation by distance suggest that some invasive signal crayfish populations may not be fully established or that their genetic diversity may have been reduced by eradication attempts.
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Affiliation(s)
| | | | - Joanna James
- Cardiff UniversityCardiffWalesUK
- Environment AgencyBramptonUK
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25
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Reid JM, Wolak ME. Is there indirect selection on female extra-pair reproduction through cross-sex genetic correlations with male reproductive fitness? Evol Lett 2018; 2:159-168. [PMID: 30283673 PMCID: PMC6121835 DOI: 10.1002/evl3.56] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/16/2018] [Accepted: 04/25/2018] [Indexed: 11/16/2022] Open
Abstract
One key hypothesis explaining the evolution and persistence of polyandry, and resulting female extra‐pair reproduction in socially monogamous systems, is that female propensity for extra‐pair reproduction is positively genetically correlated with male reproductive fitness and consequently experiences positive cross‐sex indirect selection. However, key genetic correlations have rarely been estimated, especially in free‐living populations experiencing natural (co)variation in reproductive strategies and fitness. We used long‐term life‐history and pedigree data from song sparrows (Melospiza melodia) to estimate the cross‐sex genetic correlation between female propensity for extra‐pair reproduction and adult male lifetime reproductive success, and thereby test a key hypothesis regarding mating system evolution. There was substantial additive genetic variance in both traits, providing substantial potential for indirect selection on female reproductive strategy. However, the cross‐sex genetic correlation was estimated to be close to zero. Such small correlations might arise because male reproductive success achieved through extra‐pair paternity was strongly positively genetically correlated with success achieved through within‐pair paternity, implying that the same successful males commonly sire offspring produced by polyandrous and monogamous females. Cross‐sex indirect selection may consequently have limited capacity to drive evolution of female extra‐pair reproduction, or hence underlying polyandry, in systems where multiple routes to paternity success exist.
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Affiliation(s)
- Jane M Reid
- School of Biological Sciences University of Aberdeen Aberdeen United Kingdom
| | - Matthew E Wolak
- School of Biological Sciences University of Aberdeen Aberdeen United Kingdom.,Department of Biological Sciences Auburn University Auburn Alabama 36849
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26
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Wells DA, Cant MA, Nichols HJ, Hoffman JI. A high-quality pedigree and genetic markers both reveal inbreeding depression for quality but not survival in a cooperative mammal. Mol Ecol 2018; 27:2271-2288. [PMID: 29603504 DOI: 10.1111/mec.14570] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 03/05/2018] [Accepted: 03/12/2018] [Indexed: 01/07/2023]
Abstract
Inbreeding depression, the reduced fitness of offspring of closely related parents, is commonplace in both captive and wild populations and has important consequences for conservation and mating system evolution. However, because of the difficulty of collecting pedigree and life-history data from wild populations, relatively few studies have been able to compare inbreeding depression for traits at different points in the life cycle. Moreover, pedigrees give the expected proportion of the genome that is identical by descent (IBDg ) whereas in theory with enough molecular markers realized IBDg can be quantified directly. We therefore investigated inbreeding depression for multiple life-history traits in a wild population of banded mongooses using pedigree-based inbreeding coefficients (fped ) and standardized multilocus heterozygosity (sMLH) measured at 35-43 microsatellites. Within an information theoretic framework, we evaluated support for either fped or sMLH as inbreeding terms and used sequential regression to determine whether the residuals of sMLH on fped explain fitness variation above and beyond fped . We found no evidence of inbreeding depression for survival, either before or after nutritional independence. By contrast, inbreeding was negatively associated with two quality-related traits, yearling body mass and annual male reproductive success. Yearling body mass was associated with fped but not sMLH, while male annual reproductive success was best explained by both fped and residual sMLH. Thus, our study not only uncovers variation in the extent to which different traits show inbreeding depression, but also reveals trait-specific differences in the ability of pedigrees and molecular markers to explain fitness variation and suggests that for certain traits, genetic markers may capture variation in realized IBDg above and beyond the pedigree expectation.
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Affiliation(s)
- David A Wells
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, Germany.,School of Natural Science and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Michael A Cant
- College of Life and Environmental Sciences, University of Exeter, Penryn, UK
| | - Hazel J Nichols
- School of Natural Science and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Joseph I Hoffman
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, Germany
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27
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Nietlisbach P, Keller LF, Camenisch G, Guillaume F, Arcese P, Reid JM, Postma E. Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population. Proc Biol Sci 2018; 284:rspb.2016.2763. [PMID: 28250184 DOI: 10.1098/rspb.2016.2763] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/06/2017] [Indexed: 01/14/2023] Open
Abstract
Although the pedigree-based inbreeding coefficient F predicts the expected proportion of an individual's genome that is identical-by-descent (IBD), heterozygosity at genetic markers captures Mendelian sampling variation and thereby provides an estimate of realized IBD. Realized IBD should hence explain more variation in fitness than their pedigree-based expectations, but how many markers are required to achieve this in practice remains poorly understood. We use extensive pedigree and life-history data from an island population of song sparrows (Melospiza melodia) to show that the number of genetic markers and pedigree depth affected the explanatory power of heterozygosity and F, respectively, but that heterozygosity measured at 160 microsatellites did not explain more variation in fitness than F This is in contrast with other studies that found heterozygosity based on far fewer markers to explain more variation in fitness than F Thus, the relative performance of marker- and pedigree-based estimates of IBD depends on the quality of the pedigree, the number, variability and location of the markers employed, and the species-specific recombination landscape, and expectations based on detailed and deep pedigrees remain valuable until we can routinely afford genotyping hundreds of phenotyped wild individuals of genetic non-model species for thousands of genetic markers.
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Affiliation(s)
- Pirmin Nietlisbach
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Jane M Reid
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK
| | - Erik Postma
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Penryn TR10 9EZ, UK
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28
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Luikart G, Kardos M, Hand BK, Rajora OP, Aitken SN, Hohenlohe PA. Population Genomics: Advancing Understanding of Nature. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_60] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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29
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Indykiewicz P, Podlaszczuk P, Surmacki A, Kudelska K, Kosicki J, Kamiński M, Minias P. Scale-of-choice effect in the assortative mating by multiple ornamental and non-ornamental characters in the black-headed gull. Behav Ecol Sociobiol 2017. [DOI: 10.1007/s00265-017-2411-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Pedersen NC, Shope B, Liu H. An autosomal recessive mutation in SCL24A4 causing enamel hypoplasia in Samoyed and its relationship to breed-wide genetic diversity. Canine Genet Epidemiol 2017; 4:11. [PMID: 29201383 PMCID: PMC5699110 DOI: 10.1186/s40575-017-0049-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/17/2017] [Indexed: 01/29/2023] Open
Abstract
Background Pure breeding of dogs has led to over 700 heritable disorders, of which almost 300 are Mendelian in nature. Seventy percent of the characterized mutations have an autosomal recessive mode of inheritance, indicative of positive selection during bouts of inbreeding primarily for new desired conformational traits. Samoyed suffer from several common complex genetic disorders, but up to this time only two X-linked and one autosomal dominant disorder have been identified. Previous studies based on pedigrees and SNP arrays have concluded that Samoyed breeders have done a good job in maintaining genetic diversity and avoiding excessive inbreeding. This may explain why autosomal recessive disorders have not occurred to the extent observed in many other breeds. However, an enamel hypoplasia analogous to a form of autosomal recessive amelogenesis imperfecta (ARAI) in humans has been recently characterized in Samoyed, although the causative mutation appears to have existed for three or more decades. The rise of such a mutation indicates that bouts of inbreeding for desired conformational traits are still occurring despite an old and well-defined breed standard. Therefore, the present study has two objectives: 1) measure genetic diversity in the breed using DNA and short tandem repeats (STR), and 2) identify the exact mutation responsible for enamel hypoplasia in the breed, possible explanations for its recent spread, and the effect of eliminating the mutation on existing genetic diversity. Results The recent discovery of an autosomal recessive amelogenesis imperfecta (ARAI) in Samoyed provides an opportunity to study the mutation as well as genetic factors that favored its occurrence and subsequent spread. The first step in the study was to use 33 short tandem repeat (STR) loci on 25/38 autosomes and seven STRs across the dog leukocyte antigen (DLA) class I and II regions on CFA12 to determine the DNA-based genetic profile of 182 individuals from North America, Europe and Australia. Samoyed from the three continents constituted a single breed with only slight genetic differences. Breed-wide genetic diversity was low, most likely from a small founder population and subsequent artificial genetic bottlenecks. Two alleles at each autosome locus occurred in 70–95% of the dogs and 54% of alleles were homozygous. The number of DLA class I and II haplotypes was also low and three class I and two class II haplotypes occurred in 80–90% of individuals. Therefore, most Samoyed belong to two lines, with most dogs possessing a minority of existing genetic diversity and a minority of dogs containing a majority of diversity. Although contemporary Samoyed lack genetic diversity, the bulk of parents are as unrelated as possible with smaller subpopulations either more inbred or outbred than the total population. A familial disorder manifested by hypocalcification of enamel has been recently identified. A genome wide association study (GWAS) on seven affected and five unrelated healthy dogs pointed to a region of extended homozygosity on Canis familiaris autosome 8 (CFA8). The region contained a gene in the solute carrier 24 family (SCL24A4) that encodes a protein involved in potassium dependent sodium/calcium exchange and transport. Mutations in this gene were recently found to cause a similar type of enamel hypoplasia in people. Sequencing of this candidate gene revealed a 21 bp duplication in exon 17. A test for the duplication was in concordance with the disease phenotype. The exact incidence of affected dogs is unknown, but 12% of the 168 healthy dogs tested were heterozygous for the mutation. This population was biased toward close relatives, so a liberal estimate of the incidence of affected dogs in the breed would be around 3.6/1000. Theoretical calculations based on the comparison of the whole population with a population devoid of carriers indicated that eliminating the trait would not affect existing genetic diversity at this time. Conclusions The contemporary Samoyed, like many other breeds, has retained only a small portion of the genetic diversity that exists among all dogs. This limited genetic diversity along with positive genetic selection for desirable traits has led to at least three simple non-recessive genetic disorders and a low incidence of complex genetic traits such as autoimmune disease and hip dysplasia. Unlike many other pure breeds, the Samoyed has been spared the spate of deleterious autosomal recessive traits that have plagued many other pure breeds. However, ARAI due to a mutation in the SCL24A4 gene has apparently existed in the breed for several decades but is being increasingly diagnosed. The increase in diseased dogs is most likely due to a period of intensified positive selection for some desired conformational trait. A genetic test has been developed for identifying the mutation carriers which will enable the breeders to eliminate enamel hypoplasia in Samoyed by selective breeding and it appears that this mutation can be eliminated now without loss of genetic diversity.
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Affiliation(s)
- Niels C Pedersen
- Center for Companion Animal Health, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - Bonnie Shope
- Veterinary Dental Services, LLC, 530 Massachusetts Ave, Boxborough, MA 01719 USA
| | - Hongwei Liu
- Department of Veterinary Pathology, Microbiology and Immunology, University of California, One Shields Avenue, Davis, CA 65616 USA
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31
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Kardos M, Åkesson M, Fountain T, Flagstad Ø, Liberg O, Olason P, Sand H, Wabakken P, Wikenros C, Ellegren H. Genomic consequences of intensive inbreeding in an isolated wolf population. Nat Ecol Evol 2017; 2:124-131. [PMID: 29158554 DOI: 10.1038/s41559-017-0375-4] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/19/2017] [Indexed: 12/26/2022]
Abstract
Inbreeding (mating between relatives) is a major concern for conservation as it decreases individual fitness and can increase the risk of population extinction. We used whole-genome resequencing of 97 grey wolves (Canis lupus) from the highly inbred Scandinavian wolf population to identify 'identical-by-descent' (IBD) chromosome segments as runs of homozygosity (ROH). This gave the high resolution required to precisely measure realized inbreeding as the IBD fraction of the genome in ROH (F ROH). We found a striking pattern of complete or near-complete homozygosity of entire chromosomes in many individuals. The majority of individual inbreeding was due to long IBD segments (>5 cM) originating from ancestors ≤10 generations ago, with 10 genomic regions showing very few ROH and forming candidate regions for containing loci contributing strongly to inbreeding depression. Inbreeding estimated with an extensive pedigree (F P) was strongly correlated with realized inbreeding measured with the entire genome (r 2 = 0.86). However, inbreeding measured with the whole genome was more strongly correlated with multi-locus heterozygosity estimated with as few as 500 single nucleotide polymorphisms, and with F ROH estimated with as few as 10,000 single nucleotide polymorphisms, than with F P. These results document in fine detail the genomic consequences of intensive inbreeding in a population of conservation concern.
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Affiliation(s)
- Marty Kardos
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.,Flathead Lake Biological Station, University of Montana, Polson, MA, 59860, USA
| | - Mikael Åkesson
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
| | - Toby Fountain
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Øystein Flagstad
- Norwegian Institute for Nature Research, PO Box 5685, Sluppen, NO-7485, Trondheim, Norway
| | - Olof Liberg
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
| | - Pall Olason
- Wallenberg Advanced Bioinformatics Infrastructure, Science for Life Laboratory, Uppsala University, 75123, Uppsala, Sweden
| | - Håkan Sand
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
| | - Petter Wabakken
- Faculty of Applied Ecology and Agricultural Sciences, Campus Evenstad, Inland Norway University of Applied Sciences, NO-2480, Elverum, Norway
| | - Camilla Wikenros
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.
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32
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Wang D, Forstmeier W, Kempenaers B. No mutual mate choice for quality in zebra finches: Time to question a widely held assumption. Evolution 2017; 71:2661-2676. [PMID: 28857165 DOI: 10.1111/evo.13341] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 07/26/2017] [Accepted: 08/23/2017] [Indexed: 11/30/2022]
Abstract
Studies of mate choice typically assume that individuals prefer high quality mates and select them based on condition-dependent indicator traits. In species with biparental care, mutual mate choice is expected to result in assortative mating for quality. When assortment is not perfect, the lower quality pair members are expected to compensate by increased parental investment to secure their partner (positive differential allocation). This framework has been assumed to hold for monogamous species like the zebra finch (Taeniopygia guttata), but progress has been hampered by the difficulty to define individual quality. By combining multiple measures of causes (inbreeding, early nutrition) and consequences (ornaments, displays, fitness components) of variation in quality into a single principal component, we here show that quality variation can be quantified successfully. We further show that variation in quality indeed predicts individual pairing success, presumably because it reflects an individual's vigor or ability to invest in reproduction. However, despite high statistical power, we found no evidence for either assortative mating or for positive differential allocation. We suggest that zebra finch ornaments and displays are not sufficiently reliable for the benefits of choosiness to exceed the costs of competition for the putative best partner. To assess the generality of these findings unbiased quantification of signal honesty and preference strength is required, rather than selective reporting of significant results.
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Affiliation(s)
- Daiping Wang
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
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33
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Eastwood JR, Ribot RFH, Rollins LA, Buchanan KL, Walder K, Bennett ATD, Berg ML. Host heterozygosity and genotype rarity affect viral dynamics in an avian subspecies complex. Sci Rep 2017; 7:13310. [PMID: 29042596 PMCID: PMC5645371 DOI: 10.1038/s41598-017-13476-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/25/2017] [Indexed: 11/09/2022] Open
Abstract
Genetic diversity at community, population and individual levels is thought to influence the spread of infectious disease. At the individual level, inbreeding and heterozygosity are associated with increased risk of infection and disease severity. Host genotype rarity may also reduce infection risk if pathogens are co-adapted to common or local hosts, but to date, no studies have investigated the relative importance of genotype rarity and heterozygosity for infection in a wild, sexually reproducing vertebrate. With beak and feather disease virus (BFDV) infection in a wild parrot (Platycercus elegans), we show that both heterozygosity and genotype rarity of individual hosts predicted infection, but in contrasting ways. Heterozygosity was negatively associated with probability of infection, but not with infection load. In contrast, increased host genotype rarity was associated with lower viral load in infected individuals, but did not predict infection probability. These effects were largely consistent across subspecies, but were not evident at the population level. Subspecies and age were also strongly associated with infection. Our study provides novel insights into infection dynamics by quantifying rarity and diversity simultaneously. We elucidate roles that host genetic diversity can play in infection dynamics, with implications for understanding population divergence, intraspecific diversity and conservation.
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Affiliation(s)
- Justin R Eastwood
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3216, Victoria, Australia. .,School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia.
| | - Raoul F H Ribot
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3216, Victoria, Australia
| | - Lee Ann Rollins
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3216, Victoria, Australia
| | - Katherine L Buchanan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3216, Victoria, Australia
| | - Ken Walder
- Metabolic Research Unit, School of Medicine, Deakin University, Geelong, 3216, Victoria, Australia
| | - Andrew T D Bennett
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3216, Victoria, Australia
| | - Mathew L Berg
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3216, Victoria, Australia
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34
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Head ML, Kahn AT, Henshaw JM, Keogh JS, Jennions MD. Sexual selection on male body size, genital length and heterozygosity: Consistency across habitats and social settings. J Anim Ecol 2017; 86:1458-1468. [PMID: 28815592 DOI: 10.1111/1365-2656.12742] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/30/2017] [Indexed: 12/22/2022]
Abstract
Spatial and temporal variation in environmental factors and the social setting can help to maintain genetic variation in sexually selected traits if it affects the strength of directional selection. A key social parameter which affects the intensity of, and sometimes predicts the response to, mating competition is the operational sex ratio (OSR; ratio of receptive males to females). How the OSR affects selection for specific male traits is poorly understood. It is also unclear how sexual selection is affected by interactions between the OSR and environmental factors, such as habitat complexity, that alter key male-female interactions such as mate encounter rates. Here, we experimentally manipulated the OSR and habitat complexity and quantified sexual selection on male mosquitofish (Gambusia holbrooki) by directly measuring male reproductive success (i.e. paternity). We show that despite a more equitable sharing of paternity (i.e. higher levels of multiple paternity) under a male-biased OSR, selection on focal male traits was unaffected by the OSR or habitat complexity. Instead, sexual selection consistently, and significantly, favoured smaller bodied males, males with higher genome wide heterozygosity (based on >3,000 SNP markers) and males with a relatively long gonopodium (intromittent organ). Our results show that sexual selection on male body size, relative genital size and heterozygosity in this system is consistent across environments that vary in ecological parameters that are expected to influence mate encounter rates.
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Affiliation(s)
- Megan L Head
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - Andrew T Kahn
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - Jonathan M Henshaw
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - Michael D Jennions
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australia
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35
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Grueber CE, Fitzpatrick JL, Devigili A, Gasparini C, Ramnarine IW, Evans JP. Population demography and heterozygosity-fitness correlations in natural guppy populations: An examination using sexually selected fitness traits. Mol Ecol 2017; 26:4631-4643. [PMID: 28734054 DOI: 10.1111/mec.14243] [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: 08/04/2016] [Accepted: 06/12/2017] [Indexed: 11/30/2022]
Abstract
Heterozygosity-fitness correlations (HFCs) have been examined in a wide diversity of contexts, and the results are often used to infer the role of inbreeding in natural populations. Although population demography, reflected in population-level genetic parameters such as allelic diversity or identity disequilibrium, is expected to play a role in the emergence and detectability of HFCs, direct comparisons of variation in HFCs across many populations of the same species, with different genetic histories, are rare. Here, we examined the relationship between individual microsatellite heterozygosity and a range of sexually selected traits in 660 male guppies from 22 natural populations in Trinidad. Similar to previous studies, observed HFCs were weak overall. However, variation in HFCs among populations was high for some traits (although these variances were not statistically different from zero). Population-level genetic parameters, specifically genetic diversity levels (number of alleles, observed/expected heterozygosity) and measures of identity disequilibrium (g2 and heterozygosity-heterozygosity correlations), were not associated with variation in population-level HFCs. This latter result indicates that these metrics do not necessarily provide a reliable predictor of HFC effect sizes across populations. Importantly, diversity and identity disequilibrium statistics were not correlated, providing empirical evidence that these metrics capture different essential characteristics of populations. A complex genetic architecture likely underpins multiple fitness traits, including those associated with male fitness, which may have reduced our ability to detect HFCs in guppy populations. Further advances in this field would benefit from additional research to determine the demographic contexts in which HFCs are most likely to occur.
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Affiliation(s)
- Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia.,San Diego Zoo Global, San Diego, CA, USA.,Department of Zoology, University of Otago, Dunedin, New Zealand
| | - John L Fitzpatrick
- Department of Zoology, Stockholm University, Stockholm, Sweden.,Centre for Evolutionary Biology, School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Alessandro Devigili
- Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Biology, University of Padova, Padua, Italy
| | - Clelia Gasparini
- Centre for Evolutionary Biology, School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Indar W Ramnarine
- Department of Life Sciences, University of the West Indies, St Augustine, Trinidad and Tobago
| | - Jonathan P Evans
- Centre for Evolutionary Biology, School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
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36
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Heterozygosity–fitness correlations in blue tit nestlings (Cyanistis caeruleus) under contrasting rearing conditions. Evol Ecol 2017. [DOI: 10.1007/s10682-017-9911-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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37
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Willoughby JR, Ivy JA, Lacy RC, Doyle JM, DeWoody JA. Inbreeding and selection shape genomic diversity in captive populations: Implications for the conservation of endangered species. PLoS One 2017; 12:e0175996. [PMID: 28423000 PMCID: PMC5396937 DOI: 10.1371/journal.pone.0175996] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/04/2017] [Indexed: 12/01/2022] Open
Abstract
Captive breeding programs are often initiated to prevent species extinction until reintroduction into the wild can occur. However, the evolution of captive populations via inbreeding, drift, and selection can impair fitness, compromising reintroduction programs. To better understand the evolutionary response of species bred in captivity, we used nearly 5500 single nucleotide polymorphisms (SNPs) in populations of white-footed mice (Peromyscus leucopus) to measure the impact of breeding regimes on genomic diversity. We bred mice in captivity for 20 generations using two replicates of three protocols: random mating (RAN), selection for docile behaviors (DOC), and minimizing mean kinship (MK). The MK protocol most effectively retained genomic diversity and reduced the effects of selection. Additionally, genomic diversity was significantly related to fitness, as assessed with pedigrees and SNPs supported with genomic sequence data. Because captive-born individuals are often less fit in wild settings compared to wild-born individuals, captive-estimated fitness correlations likely underestimate the effects in wild populations. Therefore, minimizing inbreeding and selection in captive populations is critical to increasing the probability of releasing fit individuals into the wild.
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Affiliation(s)
- Janna R. Willoughby
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
| | - Jamie A. Ivy
- San Diego Zoo Global Collections Department, San Diego, California, United States of America
| | - Robert C. Lacy
- Chicago Zoological Society, Brookfield, Illinois, United States of America
| | - Jacqueline M. Doyle
- Department of Biological Sciences, Towson University, Towson, Maryland, United States of America
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
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38
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Forstmeier W, Ihle M, Opatová P, Martin K, Knief U, Albrechtová J, Albrecht T, Kempenaers B. Testing the phenotype-linked fertility hypothesis in the presence and absence of inbreeding. J Evol Biol 2017; 30:968-976. [DOI: 10.1111/jeb.13062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 03/02/2017] [Indexed: 12/14/2022]
Affiliation(s)
- W. Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Seewiesen Germany
| | - M. Ihle
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Seewiesen Germany
| | - P. Opatová
- Department of Botany and Zoology; Faculty of Science; Masaryk University; Brno Czech Republic
- External Research Facility Studenec; Institute of Vertebrate Biology; Czech Academy of Sciences; Brno Czech Republic
| | - K. Martin
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Seewiesen Germany
| | - U. Knief
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Seewiesen Germany
| | - J. Albrechtová
- External Research Facility Studenec; Institute of Vertebrate Biology; Czech Academy of Sciences; Brno Czech Republic
- Department of Zoology; Faculty of Science; Charles University; Prague Czech Republic
| | - T. Albrecht
- External Research Facility Studenec; Institute of Vertebrate Biology; Czech Academy of Sciences; Brno Czech Republic
- Department of Zoology; Faculty of Science; Charles University; Prague Czech Republic
| | - B. Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Seewiesen Germany
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39
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Wang D, Kempenaers N, Kempenaers B, Forstmeier W. Male zebra finches have limited ability to identify high-fecundity females. Behav Ecol 2017. [DOI: 10.1093/beheco/arx037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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40
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Feiner ZS, DeWoody JA, Breck JE, Höök TO. Influences of multilocus heterozygosity on size during early life. Ecol Evol 2017. [DOI: 10.1002/ece3.2781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Zachary S. Feiner
- Department of Forestry and Natural Resources; Purdue University; West Lafayette IN USA
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources; Purdue University; West Lafayette IN USA
| | - James E. Breck
- Program in the Environment and School of Natural Resources and Environment; University of Michigan; Ann Arbor MI USA
| | - Tomas O. Höök
- Department of Forestry and Natural Resources; Purdue University; West Lafayette IN USA
- Illinois-Indiana Sea Grant; Purdue University; West Lafayette IN USA
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41
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Allendorf FW. Genetics and the conservation of natural populations: allozymes to genomes. Mol Ecol 2017; 26:420-430. [DOI: 10.1111/mec.13948] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/28/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Fred W. Allendorf
- Division of Biological Sciences University of Montana Missoula MT 59812 USA
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42
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Mitchell J, Vitikainen EIK, Wells DA, Cant MA, Nichols HJ. Heterozygosity but not inbreeding coefficient predicts parasite burdens in the banded mongoose. J Zool (1987) 2016. [DOI: 10.1111/jzo.12424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. Mitchell
- School of Natural Science and Psychology Liverpool John Moores University Liverpool UK
| | - E. I. K. Vitikainen
- Centre for Ecology and Conservation University of Exeter (Penryn campus) Penryn Cornwall UK
| | - D. A. Wells
- School of Natural Science and Psychology Liverpool John Moores University Liverpool UK
- Department of Animal Behaviour University of Bielefeld Bielefeld Germany
| | - M. A. Cant
- Centre for Ecology and Conservation University of Exeter (Penryn campus) Penryn Cornwall UK
| | - H. J. Nichols
- School of Natural Science and Psychology Liverpool John Moores University Liverpool UK
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43
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Bolton PE, West AJ, Cardilini APA, Clark JA, Maute KL, Legge S, Brazill-Boast J, Griffith SC, Rollins LA. Three Molecular Markers Show No Evidence of Population Genetic Structure in the Gouldian Finch (Erythrura gouldiae). PLoS One 2016; 11:e0167723. [PMID: 27936082 PMCID: PMC5147959 DOI: 10.1371/journal.pone.0167723] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/20/2016] [Indexed: 11/18/2022] Open
Abstract
Assessment of genetic diversity and connectivity between regions can inform conservation managers about risk of inbreeding, potential for adaptation and where population boundaries lie. The Gouldian finch (Erythrura gouldiae) is a threatened species in northern Australia, occupying the savannah woodlands of the biogeographically complex monsoon tropics. We present the most comprehensive population genetic analysis of diversity and structure the Gouldian finch using 16 microsatellite markers, mitochondrial control region and 3,389 SNPs from genotyping-by-sequencing. Mitochondrial diversity is compared across three related, co-distributed finches with different conservation threat-statuses. There was no evidence of genetic differentiation across the western part of the range in any of the molecular markers, and haplotype diversity but not richness was lower than a common co-distributed species. Individuals within the panmictic population in the west may be highly dispersive within this wide area, and we urge caution when interpreting anecdotal observations of changes to the distribution and/or flock sizes of Gouldian finch populations as evidence of overall changes to the population size of this species.
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Affiliation(s)
- Peri E Bolton
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Andrea J West
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Adam P A Cardilini
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Jennalee A Clark
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Kimberley L Maute
- Institute of Conservation Biology and Environmental Management, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Wildlife Conservancy, Perth, Western Australia, Australia
| | - Sarah Legge
- Australian Wildlife Conservancy, Perth, Western Australia, Australia
| | - James Brazill-Boast
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Lee A Rollins
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
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44
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Widdig A, Muniz L, Minkner M, Barth Y, Bley S, Ruiz-Lambides A, Junge O, Mundry R, Kulik L. Low incidence of inbreeding in a long-lived primate population isolated for 75 years. Behav Ecol Sociobiol 2016; 71:18. [PMID: 28018027 PMCID: PMC5145906 DOI: 10.1007/s00265-016-2236-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 11/13/2022]
Abstract
ABSTRACT When close relatives mate, offspring are expected to suffer fitness consequences due to inbreeding depression. Inbreeding has previously been quantified in two ways: using a sufficiently large panel of markers or deep and complete pedigrees over several generations. However, the application of both approaches is still limited by the challenge of compiling such data for species with long generation times, such as primates. Here, we assess inbreeding in rhesus macaques living on Cayo Santiago (Puerto Rico), a population genetically isolated since 1938, but descendant of a large set of presumably unrelated founders. Using comprehensive genetic data, we calculated inbreeding coefficients (F) for 2669 individuals with complete three generation pedigrees and 609 individuals with complete four generation pedigrees. We found that 0.79 and 7.39% of individuals had an F > 0 when using data from three and four generation pedigrees, respectively. No evidence of an increase in inbreeding over the study period (up to 23 years) was found. Furthermore, the observed mean relatedness of breeding pairs differed significantly from the distribution of parental relatedness expected as simulated based on previous reproductive data, suggesting that kin generally avoid breeding with each other. Finally, inbreeding was not a predictor of early mortality measured as survival until weaning and sexual maturation, respectively. Our results remain consistent with three estimators of inbreeding (standardized heterozygosity, internal relatedness, and homozygosity by loci) using up to 42 highly polymorphic microsatellites for the same set of individuals. Together, our results demonstrate that close inbreeding may not be prevalent even in populations isolated over long periods when mechanisms of inbreeding avoidance can operate. SIGNIFICANCE STATEMENT When close relatives mate, offspring may suffer from such inbreeding, e.g., via lower survival and/or fertility. Using (i) a large panel of genetic markers and (ii) complete three or four generation pedigrees, respectively, we show that incidences of inbreeding in a long-lived primate population are rare, even after genetic isolation for 75 years. Moreover, our simulations suggest that kin in our population generally avoid breeding with each other. Finally, the few inbred individuals detected in our large sample did not suffer from lower survival. Given that many animal species face dramatic habitat loss combined with critical population declines, our study provides important implications for conservation biology in general and for population management in particular.
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Affiliation(s)
- Anja Widdig
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
- German Center for Integrative Biodiversity Research (iDiv), Deutscher Platz 5E, 04103 Leipzig, Germany
| | - Laura Muniz
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Mirjam Minkner
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Yvonne Barth
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Stefanie Bley
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Angelina Ruiz-Lambides
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
- Caribbean Primate Research Center, University of Puerto Rico, Medical Sciences Campus, Punta Santiago, PO Box 906, San Juan, PR 00741 USA
| | - Olaf Junge
- Institute of Medical Informatics and Statistics, University Medical Center Schleswig-Holstein, Campus Kiel, Brunswiker Straße 10, 24105 Kiel, Germany
| | - Roger Mundry
- Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Lars Kulik
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
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45
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Pérez‐González J, Costa V, Santos P, Carranza J, Zsolnai A, Fernández‐Llario P, Monteiro NM, Anton I, Beja‐Pereira A. Heterozygosity decrease in wild boar mating system ‐ a case of outbreeding avoidance? J Zool (1987) 2016. [DOI: 10.1111/jzo.12426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. Pérez‐González
- Ungulate Research Unit Cátedra de Recursos Cinegéticos y Piscícolas (CRCP) University of Córdoba Córdoba Spain
| | - V. Costa
- Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto (CIBIO‐UP) Vairão Portugal
| | - P. Santos
- Departamento de Paisagem, Ambiente e Ordenamento Escola de Ciências e Tecnologia Instituto de Ciências Agrárias e Ambientais Mediterrânicas Instituto de Investigaçao e Formaçao Avançada Universidade de Évora Évora Portugal
| | - J. Carranza
- Ungulate Research Unit Cátedra de Recursos Cinegéticos y Piscícolas (CRCP) University of Córdoba Córdoba Spain
| | - A. Zsolnai
- NARIC ‐ Research Institute for Animal Breeding Nutrition and Food Science Herceghalom Hungary
- University of Kaposvár Kaposvár Hungary
| | - P. Fernández‐Llario
- Biology and Ethology Unit University of Extremadura Cáceres Spain
- Innovación en Gestión y Conservación de Ungulados S.L. Cáceres Spain
| | - N. M. Monteiro
- Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto (CIBIO‐UP) Vairão Portugal
- Centro de Investigação em Biomedicina (CEBIMED) Faculty of Health Sciences University Fernando Pessoa Porto Portugal
| | - I. Anton
- NARIC ‐ Research Institute for Animal Breeding Nutrition and Food Science Herceghalom Hungary
| | - A. Beja‐Pereira
- Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto (CIBIO‐UP) Vairão Portugal
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46
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Hedrick PW, Garcia-Dorado A. Understanding Inbreeding Depression, Purging, and Genetic Rescue. Trends Ecol Evol 2016; 31:940-952. [DOI: 10.1016/j.tree.2016.09.005] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 01/17/2023]
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47
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Kardos M, Taylor HR, Ellegren H, Luikart G, Allendorf FW. Genomics advances the study of inbreeding depression in the wild. Evol Appl 2016; 9:1205-1218. [PMID: 27877200 PMCID: PMC5108213 DOI: 10.1111/eva.12414] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/05/2016] [Indexed: 12/12/2022] Open
Abstract
Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus of ecology, evolution, and conservation biology. Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild. Studying inbreeding depression in natural populations has been hampered by the inability to precisely measure individual inbreeding. Fortunately, the rapidly increasing availability of high-throughput sequencing data means it is now feasible to measure the inbreeding of any individual with high precision. Here, we review how genomic data are advancing our understanding of inbreeding depression in the wild. Recent results show that individual inbreeding and inbreeding depression can be measured more precisely with genomic data than via traditional pedigree analysis. Additionally, the availability of genomic data has made it possible to pinpoint loci with large effects contributing to inbreeding depression in wild populations, although this will continue to be a challenging task in many study systems due to low statistical power. Now that reliably measuring individual inbreeding is no longer a limitation, a major focus of future studies should be to more accurately quantify effects of inbreeding depression on population growth and viability.
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Affiliation(s)
- Marty Kardos
- Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | | | - Hans Ellegren
- Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Gordon Luikart
- Division of Biological SciencesUniversity of MontanaMissoulaMTUSA
- Flathead Lake Biological StationDivision of Biological SciencesUniversity of MontanaPolsonMTUSA
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48
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Daïnou K, Blanc-Jolivet C, Degen B, Kimani P, Ndiade-Bourobou D, Donkpegan ASL, Tosso F, Kaymak E, Bourland N, Doucet JL, Hardy OJ. Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences - a case study in the tree genus Milicia. BMC Evol Biol 2016; 16:259. [PMID: 27903256 PMCID: PMC5131513 DOI: 10.1186/s12862-016-0831-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 11/17/2016] [Indexed: 12/22/2022] Open
Abstract
Background Species delimitation in closely related plant taxa can be challenging because (i) reproductive barriers are not always congruent with morphological differentiation, (ii) use of plastid sequences might lead to misinterpretation, (iii) rare species might not be sampled. We revisited molecular-based species delimitation in the African genus Milicia, currently divided into M. regia (West Africa) and M. excelsa (from West to East Africa). We used 435 samples collected in West, Central and East Africa. We genotyped SNP and SSR loci to identify genetic clusters, and sequenced two plastid regions (psbA-trnH, trnC-ycf6) and a nuclear gene (At103) to confirm species’ divergence and compare species delimitation methods. We also examined whether ecological niche differentiation was congruent with sampled genetic structure. Results West African M. regia, West African and East African M. excelsa samples constituted three well distinct genetic clusters according to SNPs and SSRs. In Central Africa, two genetic clusters were consistently inferred by both types of markers, while a few scattered samples, sympatric with the preceding clusters but exhibiting leaf traits of M. regia, were grouped with the West African M. regia cluster based on SNPs or formed a distinct cluster based on SSRs. SSR results were confirmed by sequence data from the nuclear region At103 which revealed three distinct ‘Fields For Recombination’ corresponding to (i) West African M. regia, (ii) Central African samples with leaf traits of M. regia, and (iii) all M. excelsa samples. None of the plastid sequences provide indication of distinct clades of the three species-like units. Niche modelling techniques yielded a significant correlation between niche overlap and genetic distance. Conclusions Our genetic data suggest that three species of Milicia could be recognized. It is surprising that the occurrence of two species in Central Africa was not reported for this well-known timber tree. Globally, our work highlights the importance of collecting samples in a systematic way and the need for combining different nuclear markers when dealing with species complexes. Recognizing cryptic species is particularly crucial for economically exploited species because some hidden taxa might actually be endangered as they are merged with more abundant species. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0831-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kasso Daïnou
- Nature + asbl / TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium. .,Université d'Agriculture de Kétou, BP 43, Kétou, Benin.
| | - Céline Blanc-Jolivet
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927, Grosshansdorf, Germany
| | - Bernd Degen
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927, Grosshansdorf, Germany
| | - Priscilla Kimani
- Kenya Forestry Research Institute, Biotechnology Section, P. O. Box 20412-00200, Nairobi, Kenya
| | | | - Armel S L Donkpegan
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Félicien Tosso
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Esra Kaymak
- Evolutionary Biology and Ecology - CP 160⁄12, Faculté des Sciences, Université Libre de Bruxelles, Av. F. Roosevelt 50, 1050, Brussels, Belgium
| | - Nils Bourland
- Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Jean-Louis Doucet
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Olivier J Hardy
- Evolutionary Biology and Ecology - CP 160⁄12, Faculté des Sciences, Université Libre de Bruxelles, Av. F. Roosevelt 50, 1050, Brussels, Belgium
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49
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Wikberg EC, Jack KM, Fedigan LM, Campos FA, Yashima AS, Bergstrom ML, Hiwatashi T, Kawamura S. Inbreeding avoidance and female mate choice shape reproductive skew in capuchin monkeys (Cebus capucinus imitator). Mol Ecol 2016; 26:653-667. [DOI: 10.1111/mec.13898] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 09/21/2016] [Accepted: 09/21/2016] [Indexed: 12/01/2022]
Affiliation(s)
- Eva C. Wikberg
- Department of Integrated Biosciences; University of Tokyo; Bioscience Building 502, 5-1-5 Kashiwanoha Kashiwa Chiba 277-8562 Japan
- Department of Anthropology and Archaeology; University of Calgary; 2500 University Drive NW Calgary AB T2N 1N4 Canada
| | - Katharine M. Jack
- Department of Anthropology; Tulane University; 6823 St. Charles Avenue, 101 Dinwiddie Hall New Orleans LA 70119 USA
| | - Linda M. Fedigan
- Department of Anthropology and Archaeology; University of Calgary; 2500 University Drive NW Calgary AB T2N 1N4 Canada
| | - Fernando A. Campos
- Department of Anthropology; Tulane University; 6823 St. Charles Avenue, 101 Dinwiddie Hall New Orleans LA 70119 USA
| | - Akiko S. Yashima
- Department of Integrated Biosciences; University of Tokyo; Bioscience Building 502, 5-1-5 Kashiwanoha Kashiwa Chiba 277-8562 Japan
| | - Mackenzie L. Bergstrom
- Department of Anthropology and Archaeology; University of Calgary; 2500 University Drive NW Calgary AB T2N 1N4 Canada
| | - Tomohide Hiwatashi
- Department of Integrated Biosciences; University of Tokyo; Bioscience Building 502, 5-1-5 Kashiwanoha Kashiwa Chiba 277-8562 Japan
| | - Shoji Kawamura
- Department of Integrated Biosciences; University of Tokyo; Bioscience Building 502, 5-1-5 Kashiwanoha Kashiwa Chiba 277-8562 Japan
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50
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Huchard E, Schliehe-Diecks S, Kappeler PM, Kraus C. The inbreeding strategy of a solitary primate,Microcebus murinus. J Evol Biol 2016; 30:128-140. [DOI: 10.1111/jeb.12992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/10/2016] [Accepted: 10/12/2016] [Indexed: 11/30/2022]
Affiliation(s)
- E. Huchard
- ISEM UMR 5554; CNRS; Université de Montpellier; Montpellier France
| | - S. Schliehe-Diecks
- Behavioral Ecology Sociobiology Unit; German Primate Center; Göttingen Germany
- Department of Sociobiology/Anthropology; Georg-August-University of Göttingen; Göttingen Germany
| | - P. M. Kappeler
- Behavioral Ecology Sociobiology Unit; German Primate Center; Göttingen Germany
- Department of Sociobiology/Anthropology; Georg-August-University of Göttingen; Göttingen Germany
| | - C. Kraus
- Behavioral Ecology Sociobiology Unit; German Primate Center; Göttingen Germany
- Department of Sociobiology/Anthropology; Georg-August-University of Göttingen; Göttingen Germany
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