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25 results for “parentage analysis”
Isolation-by-distance and genetic parentage analysis provide similar larval dispersal estimates
<p>An R studio project that includes original SNP data files used to quantify dispersal in <em>Elacatinus lori</em> via the isolation-by-distance (IBD) method. Associated R-code used to generate IBD regression slopes, calculate sigma, and construct dispersal kernels. Includes output from NeEstimator, estimating effective population size. </p> <p>Folders 1-3 contain the code/data needed to obtain the slope of the IBD relationship, effective population size, and the standard deviation (sigma) of the dispersal distribution, respectively. Folder 4 contains the R code needed to construct Laplacian dispersal kernels. </p>
Microsatellite genotypes of A. chlorotica parentage analysis
<p><span>Historical events of population fragmentation, expansion and admixture over geological time may result in complex patterns of reproductive isolation and may explain why, for some taxa, the study of mitochondrial (mt) and nuclear (nu) genetic data results in discordant evolutionary patterns. Complex patterns of taxonomic diversity were recently revealed in earthworms for which distribution is largely the result of paleogeographical events</span><span>. Here, we investigated reproductive isolation patterns in a complex of cryptic species of earthworms in which discordant patterns between mt and nu genetic lineages were previously revealed, the <em>Allolobophora chlorotica</em> aggregate. Using four nu microsatellite markers and a fragment of the <em>cytochrome c oxidase</em> <em>subunit I</em> mt gene we carried out a parentage analysis to investigate </span><span>the mating patterns </span><span>(i) </span><span>between individuals belonging to two divergent mt lineages that cannot be distinguished with nu markers and (ii) between individuals belonging to lineages that are differentiated both at the mt and nu levels. Among the 157 field collected individuals, 66 adults were used in cross-breeding experiments to form 22 trios based on their assignment to a mt lineage, and 453 obtained juveniles were genotyped. We showed that adults that mated with both their potential mates in the trio produced significantly more juveniles. In crosses between lineages that diverged exclusively at the mt level, a sex-specific pattern of reproduction characteristic to each lineage was observed, suggesting a possible conflict of interest concerning the use of male/female function between mating partners. In crosses between lineages that diverged both at the mt and nu level, a high production of cocoons was counterbalanced by a low hatching rate, suggesting a post-zygotic reproductive isolation. Different degrees of reproductive isolation, from differential sex allocation to post-zygotic isolation, were thus revealed. Lineages appear to be at different stages in the speciation process, which likely explain the observed opposite patterns of mito-nuclear congruence.</span></p>
Microsatellite genotypes of A. chlorotica parentage analysis
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Data from: Large-scale parentage analysis reveals reproductive patterns and heritability of spawn timing in a hatchery population of steelhead (Oncorhynchus mykiss)
Understanding life history traits is an important first step in formulating effective conservation and management strategies. The use of artificial propagation and supplementation as such a strategy can have numerous effects on the supplemented natural populations and minimizing life history divergence is crucial in minimizing these effects. Here, we use single nucleotide polymorphism (SNP) genotypes for large-scale parentage analysis and pedigree reconstruction in a hatchery population of steelhead, the anadromous form of rainbow trout. Nearly complete sampling of the broodstock for several consecutive years in two hatchery programmes allowed inference about multiple aspects of life history. Reconstruction of cohort age distribution revealed a strong component of fish that spawn at 2 years of age, in contrast to programme goals and distinct from naturally spawning steelhead in the region, which raises a significant conservation concern. The first estimates of variance in family size for steelhead in this region can be used to calculate effective population size and probabilities of inbreeding, and estimation of iteroparity rate indicates that it is reduced by hatchery production. Finally, correlations between family members in the day of spawning revealed for the first time a strongly heritable component to this important life history trait in steelhead and demonstrated the potential for selection to alter life history traits rapidly in response to changes in environmental conditions. Taken together, these results demonstrate the extraordinary promise of SNP-based pedigree reconstruction for providing biological inference in high-fecundity organisms that is not easily achievable with traditional physical tags.
Data from: A comparison of single nucleotide polymorphism and microsatellite markers for analysis of parentage and kinship in a cooperatively breeding bird
The development of genetic markers has revolutionized molecular studies within and among populations. Although poly-allelic microsatellites are the most commonly used genetic marker for within-population studies of free-living animals, biallelic single nucleotide polymorphisms, or SNPs, have also emerged as a viable option for use in nonmodel systems. We describe a robust method of SNP discovery from the transcriptome of a nonmodel organism that resulted in more than 99% of the markers working successfully during genotyping. We then compare the use of 102 novel SNPs with 15 previously developed microsatellites for studies of parentage and kinship in cooperatively breeding superb starlings (Lamprotornis superbus) that live in highly kin-structured groups. For 95% of the offspring surveyed, SNPs and microsatellites identified the same genetic father, but only when behavioural information about the likely parents at a nest was included to aid in assignment. Moreover, when such behavioural information was available, the number of SNPs necessary for successful parentage assignment was reduced by half. However, in a few cases where candidate fathers were highly related, SNPs did a better job at assigning fathers than microsatellites. Despite high variation between individual pairwise relatedness values, microsatellites and SNPs performed equally well in kinship analyses. This study is the first to compare SNPs and microsatellites for analyses of parentage and relatedness in a species that lives in groups with a complex social and kin structure. It should also prove informative for those interested in developing SNP loci from transcriptome data when published genomes are unavailable.
Data from: Genetic parentage analysis confirms a polygynandrous breeding system in the European grayling (Thymallus thymallus)
Knowing the breeding system of a species is important in order to understand individual variation in reproductive success. Large variation in reproductive success and thus reproductive skew strongly impacts on the effective number of breeders and thus the long-term effective population size (Ne). Fishes, in particular species belonging to the salmonid family, exhibit a wide diversity of breeding systems. In general, however, breeding systems are rarely studied in detail in the wild. Here we examine the breeding system of the spring-spawning European grayling Thymallus thymallus from a small Norwegian stream using parentage assignment based on the genotyping of 19 polymorphic microsatellite loci. In total 895 individual grayling fry and 154 mature grayling (57 females and 97 males) were genotyped. A total of 466 offspring were assigned a father, a mother, or a parent pair with a confidence of 90% or higher. Successfully reproducing males had on average 11.9 ± 13.3 (SD) offspring with on average 2.1 ± 1.2 partners, whereas successful females had on average 9.5 ± 12.8 offspring and 2.3 ± 1.5 partners. Parents with more partners also produced more offspring. Thus the grayling breeding system within this small stream revealed a polygynandrous breeding system, similar to what has been observed for many other salmonid fish species. The present study thus unambiguously corroborates a polygynadrous breeding system in the European grayling. This knowledge is critical for managing populations of this species, which has suffered significant local population declines throughout its range over the last several decades.
Single-parentage analysis of Sockeye Salmon
<p>Understanding reproductive patterns in endangered species is critical for supporting their recovery efforts. In this study we use a combination of paired-parent and single-parent assignments to examine the reproductive patterns in an endangered population of sockeye salmon (<em>Oncorhynchus nerka</em>) that uses Redfish Lake in central Idaho as a spawning and nursery lake. Recovery efforts include the release of maturing adults into the lake for volitional spawning. The lake is also inhabited by a population of resident <em>O. nerka</em> that is genetically indistinguishable, but phenotypically smaller, to the maturing adults released into the lake. The resident population is difficult to sample and the reproductive patterns between the two groups are unknown. We used results of paired- and single-parentage assignments to specifically examine the reproductive patterns of male fish released into the lake under an equal sex ratio and a male-biased sex ratio. Assignment results of offspring leaving the lake indicated a reproductive shift by males under the two scenarios. Males displayed an assortative mating pattern under an equal sex ratio and spawned almost exclusively with the released females. Under a male-biased sex ratio most males shifted to a negative-assortative mating pattern and spawned with smaller females from the resident population. These males were younger and smaller than males that spawned with released females suggesting they were unable to compete with larger males for spawning opportunities with the larger, released females. The results provided insights into the reproductive behavior of this endangered population and has implications for recovery efforts.</p>
Data from: Parentage analysis of Ansell's mole-rat family groups indicates a high reproductive skew despite relatively relaxed ecological constraints on dispersal
To better understand evolutionary pathways leading to eusociality, interspecific comparisons are needed, which would use a common axis, such as that of reproductive skew, to array species. African mole-rats (Bathyergidae, Rodentia) provide an outstanding model of social evolution because of a wide range of social organizations within a single family; however, their reproductive skew is difficult to estimate, due to their cryptic lifestyle. A maximum skew could theoretically be reached in groups where reproduction is monopolized by a stable breeding pair, but the value could be decreased by breeding-male and breeding-female turnover, shared reproduction and extra-group mating. The frequency of such events should be higher in species or populations inhabiting mesic environments with relaxed ecological constraints on dispersal. To test this prediction, we studied patterns of parentage and relatedness within 16 groups of Ansell's mole-rat (Fukomys anselli) in mesic miombo woodland. Contrary to expectation, there was no shared reproduction (more than one breeder of a particular sex) within the studied groups, and proportion of immigrants and offspring not assigned to current breeding males was low. The within-group parentage and relatedness patterns observed resemble arid populations of 'eusocial' Fukomys damarensis, rather than a mesic population of 'social' Cryptomys hottentotus. As a possible explanation, we propose that the extent ecological conditions affect reproductive skew may be markedly affected by life history and natural history traits of the particular species and genera.
Data from: Genetic parentage analysis confirms a polygynandrous breeding system in the European grayling (Thymallus thymallus)
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Data from: Mating patterns and determinants of individual reproductive success in brown trout (Salmo trutta) revealed by parentage analysis of an entire stream living population
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Data from: Parentage analysis of Ansell's mole-rat family groups indicates a high reproductive skew despite relatively relaxed ecological constraints on dispersal
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Data from: Sperm dispersal distances estimated by parentage analysis in a brooding scleractinian coral
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Single-parentage analysis of Sockeye Salmon
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Data from: Large-scale parentage analysis reveals reproductive patterns and heritability of spawn timing in a hatchery population of steelhead (Oncorhynchus mykiss)
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Data from: Using parentage analysis to estimate rates of straying and homing in Chinook salmon (Oncorhynchus tshawytscha)
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Data from: A comparison of single nucleotide polymorphism and microsatellite markers for analysis of parentage and kinship in a cooperatively breeding bird
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Data from: Genetic evidence for polygynandry in the black-striped pipefish Syngnathus abaster: a microsatellite-based parentage analysis
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Data from: Estimation of migration rates from marker based parentage analysis
Coupled with rapid developments of efficient genetic markers, powerful population genetics methods were proposed to estimate migration rates (m) in natural populations in much broader spatial and temporal scales than the traditional mark-release-recapture (MRR) methods. Highly polymorphic (e.g. microsatellites) and genomic wide (e.g. SNPs) markers provide sufficient information to assign individuals to their populations or parents of origin, and thereby to estimate directly m in a way similar to MRR. Such direct estimates of current migration rates are particularly useful in understanding the ecology and microevolution of wild populations and in managing the populations in the future. In this study I proposed and implemented, in the software MigEst, a likelihood method to use marker based parentage assignments in jointly estimating m and candidate parent sampling proportions (x) in a subset of populations, investigated its power and accuracy using data simulated in various scenarios of population properties (e.g. the actual m, number, size and differentiation of populations) and sampling properties (e.g. the numbers of sampled parent candidates, offspring, and markers), compared it with the population assignment approach implemented in the software BayesAss, and demonstrated its usefulness by analysing a microsatellite dataset from three natural populations of Brazilian bats. Simulations showed that MigEst provides unbiased and accurate estimates of m, and performs better than BayesAss except when populations are highly differentiated with very small and ecologically insignificant migration rates. A valuable property of MigEst is that in the presence of unsampled populations, it gives good estimates of the rate of migration among sampled populations as well as of the rate of migration into each sampled population from the pooled unsampled populations.
Data from: Relative accuracy of three common methods of parentage analysis in natural populations
Parentage studies and family reconstructions have become increasingly popular for investigating a range of evolutionary, ecological and behavioral processes in natural populations. However, a number of different assignment methods have emerged in common use, and the accuracy of each may differ in relation to the number of loci examined, allelic diversity, incomplete sampling of all candidate parents, and the presence of genotyping errors. Here we examine how these factors affect the accuracy of three popular parentage inference methods (COLONY, FaMoz and an exclusion-Bayes' theorem approach by Christie et al. (2010a)) to resolve true parent-offspring pairs using simulated data. Our findings demonstrate that accuracy increases with the number and diversity of loci. These were clearly the most important factors in obtaining accurate assignments explaining 75-90% of variance in overall accuracy across 60 simulated scenarios. Furthermore, the proportion of candidate parents sampled had a small but significant impact on the susceptibility of each method to either false positive or false negative assignments. Within the range of values simulated, COLONY outperformed FaMoz, which outperformed the exclusion-Bayes' theorem method. However, with 20 or more highly polymorphic loci, all methods could be applied with confidence. Our results show that for parentage inference in natural populations, careful consideration of the number and quality of markers will increase the accuracy of assignments and mitigate the effects of incomplete sampling of parental populations.
Investigating population dynamics from parentage analysis in the highly endangered fan mussel Pinna nobilis
<p>Understanding dispersal patterns is a major focus for conservation biology as it influences local survival and resilience in case of local disturbance, particularly for sessile species. Dispersal can be assessed through parentage analyses by estimating family structure and self-recruitment. This study documents the family structure of a pelagic spawner, <i>Pinna nobilis</i>, which is facing a major crisis that threatens its survival as most of its populations have been decimated by a parasite, <i>Haplosporidium pinnae</i>. In this context, we focused on a single population (Peyrefite, Banyuls-sur-mer, France) where 640 individuals were sampled in 2011, 2015 and 2018 and genotyped for 22 microsatellite markers. Genetic diversity was high and homogeneous among years, with mean allele numbers ranging between 13.6 and 14.8 and observed heterozygosities (<i>Ho</i>) between 0.7121 and 0.7331. Low, but significant, genetic differentiations were found between 2011 - 2015 and 2015 - 2018. A parentage analysis described 11 clusters, including one prevailing, and revealed that 46.9 % of individuals were involved in half-sib relationships, even between years, suggesting that source populations were recurrent year after year. There were few individuals resampled between years (30 in 2015 and 14 in 2018), indicating a rapid turnover. Considering the large number of half-sib relationships but the low number of relations per individual, we conclude that <i>P. nobilis</i> exhibit homogeneous reproductive success. Self-recruitment was not detected, making this population highly vulnerable as replenishment only relies on connectivity from neighboring populations. In the context of the pandemic caused by <i>H. pinnae</i>, these results will have to be considered when choosing a location to reintroduce individuals in potential future rescue plans.</p>
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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