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66 results for “Parentage”
Genetic parentage reveals the (un)natural history of Central Valley Hatchery steelhead
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Assessment of parentage relationships in Cottus bairdi at the Coweeta Hydrologic Laboratory in 1999
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Data from: Validating dispersal distances inferred from autoregressive occupancy models with genetic parentage assignments
1.Dispersal distances are commonly inferred from occupancy data but have rarely been validated. Estimating dispersal from occupancy data is further complicated by imperfect detection and the presence of unsurveyed patches. 2.We compared dispersal distances inferred from seven years of occupancy data for 212 wetlands in a metapopulation of the secretive and threatened California black rail (Laterallus jamaicensis coturniculus) to distances between parent-offspring dyads identified with 16 microsatellites. 3.We used a novel autoregressive multi-season occupancy model that accounted for both unsurveyed patches and imperfect detection to quantify patch isolation using buffer radius (BRM) and incidence function (IFM) connectivity measures at 15 scales (1–10, 15, 20, 25, and 30 km). Connectivity measures were then fit as colonization covariates in occupancy models to estimate a model-averaged dispersal distance. 4.As predicted, colonization was more strongly related to connectivity at small spatial scales (< 10 km). AIC weights were greatest at 7 km for BRM and at 4 km for IFM. 5.Model-averaged dispersal distances (BRM = 7.46 km; IFM = 5.48 km) showed good agreement with the mean (± SE) dispersal distance from 23 parent-offspring dyads (5.58 ± 1.92 km), indicating reasonably accurate mean dispersal distances can be inferred from occupancy data when isolation strongly affects colonization.
Data from: Parentage of 920 gray-sided voles (Myodes rufocanus) born in a 3-ha outdoor enclosure between September 1992 and May 1994
<p class="MsoNormal"><span>This dataset provides the estimated birth location, sex, assigned parents, and estimated birth and death dates of 920 gray-sided voles (<em>Myodes rufocanus</em>) born in a 3-ha outdoor enclosure in Sapporo, Japan between September 1992 and May 1994, as well as capture–recapture data for 30 trapping sessions.</span><span> We introduced 22 males and 25 females from several natural populations into the enclosure in late September 1992. Individuals in the enclosure were captured using live traps every two weeks until late April 1994, except for periods with deep snow cover. The location, body weight, and reproductive status of each vole were monitored throughout the study period. Complementary trapping was performed within the home ranges of breeding females to mark juveniles as early as possible. Upon first capture, each individual was marked by toe clipping for subsequent identification, and the cut toes were used as DNA samples. For each individual, candidate parents were selected based on female reproduction history and capture points, and then parentage was determined using genotypes at 3–5 microsatellite loci with the CERVUS program. The results show that individuals born in the enclosure (<em>N</em> = 920) were derived from 215 litters, among which multiple males sired 51 litters. We used this database to elucidate the promiscuous mating system and inbreeding-avoidance mechanism of the gray-sided vole and to develop a ne</span><span>w method for estimating the frequency of multiple-male mating. This dataset will contribute to future behavioral ecological research on this and other small mammal species.</span></p>
Diverse parentage relationships in paternal mouth-brooders
<p>While mouthbrooding is not an uncommon parental care strategy in fishes, paternal mouthbrooding only occurs in eight fish families and little studied. The high cost of paternal mouthbrooding to the male implies a low risk of investment in another male's offspring but genetic parentage patterns are poorly known for paternal mouthbrooders. Here we used single nucleotide polymorphism (SNP) genetic data to investigate parentage relationships of broods of two mouthbrooders of northern Australian rivers, mouth almighty <em>Glossamia aprion</em> and blue catfish <em>Neoarius graeffei</em>. For <em>N. graeffei</em>, we found that the parentage pattern was largely monogamous with the brooder male as the sire. For <em>G. aprion</em>, the parentage pattern was more heterogeneous including observations of monogamous broods with the brooder male as the sire (73%), polygyny (13%), cuckoldry (6%) and a brood genetically unrelated to the brooder male (6%). Findings demonstrate the potential for complex interrelationships of male care, paternity confidence, and mating behaviour in mouthbrooding fishes.</p>
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>
Genetic parentage reconstruction as a practical tool applied to aquaculture and restoration programs for the European flat oyster, Ostrea edulis
<p>Preserving and maximizing genetic diversity in conservation programs, including for restocking, are of high importance. The threatened European flat oyster (<em>Ostrea edulis</em>) is currently the subject of several applied conservation and restocking programs, but concerns have been raised over potential negative side effects of these programs, for example due to our limited knowledge about the genetic effects in natural populations of releasing offspring of hatchery origin. Here, we developed a cost-effective, easily applicable and highly reliable method to assess the genetic diversity and parental contributions in flat oyster hatchery production based on analyses of 17 microsatellite loci. We analyzed broodstock and hatchery-produced spat (total n = 289) and compared diversity to that in wild samples of adults and spat from the broodstock source in the Limfjorden (total n = 190). Based on four hatchery tank experiments, we found that five swarming events (larval releases) were characterized by a single maternal and multiple paternal contributions, and that the number of contributing parents varied greatly both among individual tanks, and between swarming events within tank. On average, the effective number of breeders was only one third of the actual broodstock size. Although the broodstock exhibited high genetic variation, the high reproductive skew resulted in produced seed representing only a relatively small subset of this variation. The work demonstrates potential impact of hatchery reared offspring on decreasing genetic diversity in wild populations, but also that genetic monitoring can be integrated in conservation programs to minimize negative effects on restoration and supplementary restocking programs that utilize hatchery reared spats to support natural populations.</p>
Single parentage dataset for Chinook salmon
<p>Objective<br>Parentage analysis is a routine methodology in fisheries research, but study systems exist where it is impractical to sample both parents. The ability to reliably assign offspring to a single parent is beneficial in these situations. We apply single-parentage assignments to a naturally spawning population of Chinook Salmon <em>Oncorhynchus tshawytscha</em> to quantify production of anadromous returns by unsampled precocial males.</p> <p>Methods</p> <p>We use an approach that addresses two important aspects of parentage analyses: 1.) addressing the presence of family structure within the sampled parents and 2.) controlling for false-positive and false-negative assignments.</p> <p>Result</p> <p>Results indicate that 30% of reproductively successful males were precocials which produced 20% of the returning anadromous offspring.</p> <p>Conclusion</p> <p>This study provides a framework for applying single-parent assignments in a salmonid study system while explicitly addressing sources of assignment errors.</p>
Supporting information for: The correct name for an Aquilegia (Ranunculaceae) hybrid of the parentage Aquilegia flavescens × A. formosa
<p><span><em>Aquilegia</em> </span><span>x</span><span> <em>miniana</em></span><span> (J.F.Macbr. & Payson) Cronk, hybr. & stat. nov. is the correct name for the hybrid <em>Aquilegia</em> <em>flavescens</em> S.Watson x <em>A</em>. <em>formosa</em> Fisch. ex DC. var. <em>formosa</em>. In 1916, Payson and Macbride, while exploring the mountains of Idaho, found populations of <em>Aquilegia</em> that were pink in flower colour and appeared intermediate between the yellow-flowered <em>A</em>. <em>flavescens</em> and red-flowered <em>A. formosa</em>. They named these plants <em>A. flavescens</em> var. <em>miniana</em> J.F.Macbr. & Payson. There has been uncertainty over whether their type collections (in GH, RM, MO, US, E, CM, CAS, NY) do indeed represent hybrids or pink-flowered morphs of <em>A. flavescens</em>. Using a Wells diagram, the holotype (in the Gray Herbarium of Harvard University) is shown to be intermediate, allowing its identification as a clear hybrid. However, some of the isotype material is indistinguishable from <em>A. flavescens</em>. The holotype matches material from British Columbia that has been determined as being of hybrid origin using molecular and morphological data. <em>A. flavescens</em> var. <em>miniana</em> J.F.Macbr. & Payson is, therefore, an available name for the hybrid, which is here raised to the status of hybrid binomial.</span></p>
Single parentage dataset for Chinook salmon
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Data from: Validating dispersal distances inferred from autoregressive occupancy models with genetic parentage assignments
Open the record for dataset details and reuse information.
Supporting information for: The correct name for an Aquilegia (Ranunculaceae) hybrid of the parentage Aquilegia flavescens × A. formosa
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Diverse parentage relationships in paternal mouth-brooders
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Relative influences of microhabitat incubation conditions and genetic parentage effects on lake sturgeon (Acipenser fulvescens) offspring traits during early ontogeny (DATA)
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Data from: Parentage of 920 gray-sided voles (Myodes rufocanus) born in a 3-ha outdoor enclosure between September 1992 and May 1994
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Data From: Parentage‐based tagging combined with genetic stock identification is a cost‐effective and viable replacement for coded‐wire tagging in large‐scale assessments of marine Chinook salmon fisheries in British Columbia, Canada
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Microsatellite genotypes of A. chlorotica parentage analysis
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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
<p><span><span><span><span><span><span><span><span><span><span><span>Dispersal is a critical process for the persistence and productivity of marine populations. For many reef species, there is increasing evidence that local demography and self-recruitment have major consequences on their genetic diversity and adaptation to environmental change. Yet empirical data of dispersal patterns in reef-building species remain scarce. Here, we document the first genetic estimates of self-recruitment and dispersal distances in a free-spawning marine invertebrate, the hydrocoral <i>Millepora platyphylla</i>. Using twelve microsatellite markers, we gathered genotypic information from 3,160 georeferenced colonies collected over 9,000 m<sup>2</sup> of a single reef in three adjacent habitats in Moorea, French Polynesia; the mid slope, upper slope, and back reef. Although the adult population was predominantly clonal (85% were clones), our parentage analysis revealed a moderate self-recruitment rate with 8 to 37% of sexual propagules produced locally. Assigned offspring often settled at less than 10 meters from their parents and dispersal events decrease with increasing geographic distance. There were no discrepancies between the dispersal distances of offspring assigned to parents belonging to clonal <i>versus</i> non-clonal genotypes. Inter-habitat dispersal events via cross-reef transport were also detected for sexual and asexual propagules. Sibship analysis showed that full siblings recruit together on the reef (more than 40% settled at < 30 m), resulting in sibling aggregations. Our findings highlight the importance of self-recruitment together with clonality in stabilizing population dynamics, which may ultimately enhance local sustainability and resilience to disturbance.</span></span></span></span></span></span></span></span></span></span></span></p>
SNP array for parentage assignment of the Manila clam, Ruditapes philippinarum
<p>The Manila clam <i>Ruditapes philippinarum</i>, a major cultured shellfish species, is threatened by infection with the microparasite <i>Perkinsus olseni</i>, whose prevalence increases with high water temperatures. Under the current trend of climate change, the already severe effects of this parasitic infection might rapidly increase the frequency of mass mortality events. Treating infectious diseases in bivalves is notoriously problematic, therefore selective breeding for resistance represents a key strategy for mitigating the negative impact of pathogens. A crucial step in initiating selective breeding is the estimation of genetic parameters for traits of interest, which relies on the ability to record parentage and accurate phenotypes in a large number of individuals. Here, to estimate the heritability of resistance against <i>P. olseni</i>, a field experiment mirroring conditions in industrial clam production was set up, a genomic tool was developed for parentage assignment, and parasite load was determined through quantitative PCR.</p> <p>A mixed-family cohort of potentially 1479 clam families was produced in a hatchery by mass spawning of 53 dams and 57 sires. The progenies were seeded in a commercial clam production area in the Venice lagoon, Italy, where high prevalence of <i>P. olseni</i> had previously been reported. Growth and parasite load were monitored every month and, after one year, more than 1000 individuals were collected and DNA and phenotype records.</p> <p>A 245-SNP panel was developed using candidate markers obtained from a pooled sequencing approach on two DNA samples from all the potential parents and from a Venice lagoon clam population. For 246 individuals of the mixed-family F1, sire and dam representation were high (75 and 85%, respectively), indicating a very limited risk of inbreeding. Moderate heritability (0.20 – 0.30) was estimated for growth traits, while parasite load showed high heritability, estimated at 0.52. No significant genetic correlations were found between growth-associated traits and parasite load.</p> <p>Overall, the study shows high potential for selecting clams resistant to parasite<i> </i>load<i>.</i> Breeding for resistance may help limit the negative effects of climate change on clam production, as the prevalence of the parasite is predicted to increase under a future scenario of higher temperatures. Finally, the limited genetic correlation between resistance and growth suggests that breeding programs could incorporate dual selection without negative interactions.</p>
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Allen Brain Atlas
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OpenNeuro
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