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66 results for “Parentage”
Data from: An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population
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Single-parentage analysis of Sockeye Salmon
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Parentage analyses identify local dispersal events and sibling aggregations in a natural population of Millepora hydrocorals, a free-spawning marine invertebrate
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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: Parentage and relatedness reconstruction in Pinus sylvestris using genotyping by sequencing
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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: Insights on the concept of indicator populations derived from parentage-based tagging in a large-scale coho salmon application in British Columbia, Canada
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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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SNP array for parentage assignment of the Manila clam, Ruditapes philippinarum
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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.
Correcting parentage relationships in the endangered California condor: Improving mean kinship estimates for conservation management
<p><span>Maintaining the existing biodiversity of endangered species is a goal of conservation management programs, and a major component of many collaborative efforts undertaken by zoos, field biologists, and conservation scientists. Over the past three decades, the San Diego Zoo has performed long-term genetic studies in support of the recovery program for the critically endangered California condor (<em>Gymnogyps californianus</em>). This work has included sex determination of hatchlings and parentage confirmation using microsatellite genotyping. This paper describes the genetic work associated with the California condor recovery program, which aims to provide a highly accurate pedigree for making informed captive pairing and release recommendations. Initial genotyping began after reintroduced California condors started reproducing, and the focus was on birds hatched from their wild-laid eggs. However, genetic analysis showed discrepancies relative to behavioral observations of wild birds, and led to the species-wide testing of all available samples. This genetic study has resolved instances of individual misidentifications and parental misassignments, verified the first cases of extra-pair paternity in this species, identified parentage where chicks were observed being raised by trios, and found two apparent de novo mutations in the captive condor population. Correcting the California condor pedigree according to genetic parental analysis has produced more accurate estimates of mean kinship values among living birds, ranking potential breeders according to their actual breeding value and helping managers to make informed decisions about captive pairing and release of condors in the wild.</span></p>
Molecular parentage data: a study on competitive fertilizations in spiders
<p><span>Sperm competition drives traits that enhance fertilization success. The amount of sperm transferred relative to competitors </span><span>is key for attaining paternity. Female reproductive morphology and male mating order may also influence fertilization, however the outcome for sperm precedence under intense sperm competition remains poorly understood. In the polyandrous spider <em>Pisaura mirabilis</em>, males offer nuptial gifts which prolong copulation and increase sperm transfer, factors proposed to alter sperm precedence patterns under strong sperm competition. First, we assessed the degree of female polyandry by genotyping wild broods. A conservative analysis identified up to 4 sires, with a mean of 2 sires per brood, consistent with an optimal mating female rate. Then we asked whether intense sperm competition shifts sperm precedence patterns from first male priority, as expected from female morphology, to last male advantage. We varied sexual selection intensity experimentally and determined competitive fertilization outcome by genotyping broods. In double matings, one male monopolised paternity regardless of mating order. A mating order effect with first male priority was revealed when females were mated to 4 males, however this effect disappeared when females were mated to 6 males, likely due to increased sperm mixing. The proportion of males that successfully sired offspring drastically decreased with the number of competitors. Longer copulations translated into higher paternity shares independently of mating order, reinforcing the advantage of traits that prolong copulation duration under intense competition, such as the nuptial gift. Sperm competition intensity enhances the impact of competitive sexual traits and imposes </span><span>multiple effects on paternity.</span></p>
Data from: Using probability modelling and genetic parentage assignment to test the role of local mate availability in mating system variation.
The formal testing of mating system theories with empirical data is important for evaluating the relative importance of different processes in shaping mating systems in wild populations. Here we present a generally applicable probability modelling framework to test the role of local mate availability in determining a population's level of genetic monogamy. We provide a significance test for detecting departures in observed mating patterns from model expectations based on mate availability alone, allowing the presence and direction of behavioural effects to be inferred. The assessment of mate availability can be flexible and in this study it was based on population density, sex ratio and spatial arrangement. This approach provides a useful tool for (1) isolating the effect of mate availability in variable mating systems and (2) in combination with genetic parentage analyses, gaining insights into the nature of mating behaviours in elusive species. To illustrate this modelling approach, we have applied it to investigate the variable mating system of the mountain brushtail possum (Trichosurus cunninghami) and compared the model expectations with the outcomes of genetic parentage analysis over an 18 year study. The observed level of monogamy was higher than predicted under the model. Thus, behavioural traits, such as mate guarding or selective mate choice, may increase the population level of monogamy. We show that combining genetic parentage data with probability modelling can facilitate an improved understanding of the complex interactions between behavioural adaptations and demographic dynamics in driving mating system variation.
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>
Supplementary material 1 from: Giangregorio P, Mucci N, Norman AJ, Pedrotti L, Filacorda S, Molinari P, Spong G, Davoli F (2023) Performance of SNP markers for parentage analysis in the Italian Alpine brown bear using non-invasive samples. Nature Conservation 53: 105-123. https://doi.org/10.3897/natureconservation.53.86739
Genetic and field data
Data from: Relative accuracy of three common methods of parentage analysis in natural populations
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Data from: Using probability modelling and genetic parentage assignment to test the role of local mate availability in mating system variation.
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Data from: Parentage and sibship inference from markers in polyploids
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.