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92 results for “pedigree”
Comparing genome-based estimates of relatedness for use in pedigree-based conservation management
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Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur
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Wild pedigrees inform mutation rates and historic abundance in baleen whales
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Results of quantitative genetic sensitivity analysis performed on reconstructed pedigrees based on large-scale genealogies
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Data for: Comparative evaluation of phenotypic, pedigree, and family-based selection in insect breeding using stochastic simulation
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Estimation of breeding population size using DNA-based pedigree reconstruction in brown bears
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IO Islamic 2124. Risâla-i-Afghânân, A Short Treatise on the Origin and Pedigree of the Afghâns
<p>IO Islamic 2124. Risâla-i-Afghânân, A Short Treatise on the Origin and Pedigree of the Afghâns</p>
IO Islamic 1214. Risâla-i-Afghânân, A Short Treatise on the Origin and Pedigree of the Afghâns
<p>IO Islamic 1214. Risâla-i-Afghânân, A Short Treatise on the Origin and Pedigree of the Afghâns</p>
An evaluation of inbreeding measures using a whole genome sequenced cattle pedigree
<p>The estimation of the inbreeding coefficient (F) is essential for the study of inbreeding depression (ID) or for the management of populations under conservation. Several methods have been proposed to estimate the realized F using genetic markers, but it remains unclear which one should be used. Here we used whole-genome sequence data for 245 individuals from a Holstein cattle pedigree to empirically evaluate which estimators best capture homozygosity at variants causing ID, such as rare deleterious alleles or loci presenting heterozygote advantage and segregating at intermediate frequency. Estimators relying on the correlation between uniting gametes (F<sub>UNI</sub>) or on the genomic relationships (F<sub>GRM</sub>) presented the highest correlations with these variants. However, homozygosity at rare alleles remained poorly captured. A second group of estimators relying on excess homozygosity (F<sub>HOM</sub>), homozygous-by-descent segments (F<sub>HBD</sub>), runs-of-homozygosity (F<sub>ROH</sub>) or on the known genealogy (F<sub>PED</sub>) was better at capturing whole genome homozygosity, reflecting the consequences of inbreeding on all variants, and for young alleles with low to moderate frequencies. The results indicate that F<sub>UNI</sub> and F<sub>GRM</sub> might present a stronger association with ID. However, the situation might be different when recessive deleterious alleles reach higher frequencies, such as in populations with a small effective population size. For locus specific inbreeding measures or at low marker density, the ranking of the methods can also change as F<sub>HBD </sub>makes better use of the information from neighbouring markers. Finally, we confirmed that genomic measures are in general superior to pedigree-based estimates. In particular, F<sub>PED</sub> was uncorrelated with locus specific homozygosity.</p>
Data from: Mechanisms of kin discrimination inferred from pedigrees and the spatial distribution of mates
Where animals avoid inbreeding, different mechanisms of kin discrimination can leave different "signatures" in the patterns of observed mate relationship. For example, consider a species with no paternal care. If females avoid mating with familiar individuals, one would expect a deficit of offspring whose parents are maternal half-siblings, but paternal half-siblings would be unfamiliar with each other and thus mate at the frequency expected by chance. If spatial cues are used to avoid inbreeding, females would be expected to produce few offspring with males (even unrelated males) living near the female's birth site. We searched for these and other signatures with data from a long-term study of bannertailed kangaroo rats Dipodomys spectabilis in Arizona, USA, using a combination of intensive censusing, mapping of available dens, microsatellite-based parentage determination, and a randomization routine that determines the numbers of offspring expected if females in the population mate indiscriminately among the males available to them. The data are consistent with the hypothesis that kangaroo rats discriminate kin by association, rather than by using spatial cues or self-referential phenotype matching. Our randomization routine also demonstrates that in this species, dispersal alone is not particularly effective at eliminating opportunities for inbreeding. Our approach can be applied wherever the spatial distribution of individual mates and their pedigree relationships are known, and should be widely applicable as a means of assessing the degree to which both kin recognition and dispersal influence inbreeding.
Data from: A comparison of pedigree- and genetic-based measures for identifying inbreeding depression in the critically endangered Attwater's Prairie-chicken
The primary goal of captive breeding programs for endangered species is to prevent extinction, a component of which includes the preservation of genetic diversity and avoidance of inbreeding. This is typically accomplished by minimizing mean kinship in the population, thereby maintaining equal representation of the genetic founders used to initiate the captive population. If errors in the pedigree do exist, such an approach becomes less effective for minimizing inbreeding depression. In this study both pedigree- and DNA-based methods were used to assess whether inbreeding depression existed in the captive population of the critically endangered Attwater's Prairie-chicken (Tympanuchus cupido attwateri), a subspecies of prairie grouse that has experienced a significant decline in abundance and concurrent reduction of neutral genetic diversity. When examining the captive population for signs of inbreeding, variation in pedigree-based inbreeding coefficients (f_pedigree) was less than that obtained from DNA-based methods (f_DNA). Mortality of chicks and adults in captivity were also positively correlated with parental relatedness (r_DNA) and f_DNA, respectively, while no correlation was observed with pedigree-based measures when controlling for additional variables such as age, breeding facility, gender, and captive/release status. Further, individual homozygosity by loci (HL) and parental r_DNA values were positively correlated with adult mortality in captivity and the occurrence of a lethal congenital defect in chicks, respectively, suggesting that inbreeding may be a contributing factor increasing the frequency of this condition among Attwater's Prairie-chickens. This study highlights the importance of using DNA-based methods to better inform management decisions when pedigrees are incomplete or errors may exist due to uncertainty in pairings.
Data from: Evaluating the reintroduction project of Przewalski's horse in China using genetic and pedigree data
Przewalski's horse went extinct in the wild in the mid 1960's. Starting in 1985, individuals were brought from western zoos to two centers in China and breeding programs were initiated. With the increasing size of captive populations, two reintroduction projects were launched in the northwestern China in 2001 and 2010. Knowledge on genetic diversity in China's horse populations is limited, but would help improve the genetic management and assess the success of the reintroduction. Accordingly, one reintroduced and two captive populations were examined with 10 microsatellite loci together with pedigree data. The results showed higher level of diversity within the captive populations than the reintroduced population, indicating some alleles may have been lost during reintroduction. Genetic differentiation was detected among populations (FST=0.09±0.05, RhoST=0.05±0.02) and Bayesian clustering supported the presence of three subpopulations. The highest genetic differentiation was observed between the captive and reintroduced populations, and inbreeding coefficients were generally higher in the reintroduced population. Temporal estimates of both pedigree and microsatellite data showed a high, but decreasing level inbreeding. Through simulations, we estimated that the reintroduced population needs more than 100 individuals to retain approximately 90% of its current, already depauperate, genetic diversity. We have provided recommendations for the management program concerning introgressed genes from domestic horse and the number and origin of individuals for future reintroductions.
Data from: Pedigree error due to extra-pair reproduction substantially biases estimates of inbreeding depression
Understanding the evolutionary dynamics of inbreeding and inbreeding depression requires unbiased estimation of inbreeding depression across diverse mating systems. However, studies estimating inbreeding depression often measure inbreeding with error, for example, based on pedigree data derived from observed parental behavior that ignore paternity error stemming from multiple mating. Such paternity error causes error in estimated coefficients of inbreeding (f) and reproductive success and could bias estimates of inbreeding depression. We used complete "apparent" pedigree data compiled from observed parental behavior and analogous "actual" pedigree data comprising genetic parentage to quantify effects of paternity error stemming from extra-pair reproduction on estimates of f, reproductive success, and inbreeding depression in free-living song sparrows (Melospiza melodia). Paternity error caused widespread error in estimates of f and male reproductive success, causing inbreeding depression in male and female annual and lifetime reproductive success and juvenile male survival to be substantially underestimated. Conversely, inbreeding depression in adult male survival tended to be overestimated when paternity error was ignored. Pedigree error stemming from extra-pair reproduction therefore caused substantial and divergent bias in estimates of inbreeding depression that could bias tests of evolutionary theories regarding inbreeding and inbreeding depression and their links to variation in mating system.
Data from: Genetic pedigree analysis of the pilot breeding program for the rediscovered Galapagos giant tortoise from Floreana island
An aim of many captive breeding programs is to increase population sizes for reintroduction and establishment of self-sustaining wild populations. Genetic analyses play a critical role in these programs: monitoring genetic variation, identifying the origin of individuals, and assigning parentage to track family sizes. Here we use genetic pedigree analyses to examine three seasons of a pilot breeding program for the Floreana island Galapagos giant tortoise, C. niger, that had been declared extinct for ~150 years until individuals with mixed ancestry were recently discovered. We determined that eight of nine founding individuals were assigned parentage to at least one of 130 offspring produced, though there was considerable reproductive skew. In addition, we observed that genetic diversity of the progeny was lower than that of the founders. Despite the observed reproductive skew, we did not see evidence for assortative mating based on relatedness, but there was a trend towards reduced fitness when more related individuals bred. Finally, we found that the majority of progeny had ancestry assigned to the Floreana species (mean±SE = 0.51±0.02), though individual estimates varied. The success of these pilot seasons bodes well for a larger breeding program to help restore the previously extinct tortoise from Floreana island. Future efforts should continue to monitor for reproductive skew and assortative mating in order to maintain allelic diversity. We would also recommend forming smaller breeding groups and rotating individuals among them to prevent long-term reproductive skew among pairs.
Data from: Relationship type affects the reliability of dispersal distance estimated using pedigree inferences in partially sampled populations: a case study involving invasive American mink in Scotland
Estimating dispersal—a key parameter for population ecology and management—is notoriously difficult. The use of pedigree assignments, aided by likelihood-based software, has become popular to estimate dispersal rate and distance. However, the partial sampling of populations may produce false assignments. Further, it is unknown how the accuracy of assignment is affected by the genealogical relationships of individuals and is reflected by software-derived assignment probabilities. Inspired by a project managing invasive American mink (Neovison vison), we estimated individual dispersal distances using inferred pairwise relationships of culled individuals. Additionally, we simulated scenarios to investigate the accuracy of pairwise inferences. Estimates of dispersal distance varied greatly when derived from different inferred pairwise relationships, with mother–offspring relationship being the shortest (average = 21 km) and the most accurate. Pairs assigned as maternal half-siblings were inaccurate, with 64%–97% falsely assigned, implying that estimates for these relationships in the wild population were unreliable. The false assignment rate was unrelated to the software-derived assignment probabilities at high dispersal rates. Assignments were more accurate when the inferred parents were older and immigrants and when dispersal rates between subpopulations were low (1% and 2%). Using 30 instead of 15 loci increased pairwise reliability, but half-sibling assignments were still inaccurate (>59% falsely assigned). The most reliable approach when using inferred pairwise relationships in polygamous species would be not to use half-sibling relationship types. Our simulation approach provides guidance for the application of pedigree inferences under partial sampling and is applicable to other systems where pedigree assignments are used for ecological inference.
Data from: Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population
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.
Data from: The influence of nonrandom extra-pair paternity on heritability estimates derived from wild pedigrees
Quantitative genetic analysis is often fundamental for understanding evolutionary processes in wild populations. Avian populations provide a model system due to the relative ease of inferring relatedness amongst individuals through observation. However, extra-pair paternity (EPP) creates erroneous links within the social pedigree. Previous work has suggested this causes minor underestimation of heritability if paternal misassignment is random and hence not influenced by the trait being studied. Nevertheless, much literature suggests numerous traits are associated with EPP and the accuracy of heritability estimates for such traits remains unexplored. We show analytically how non-random pedigree errors can influence heritability estimates. Then, combining empirical data from a large great tit (Parus major) pedigree with simulations, we assess how heritability estimates derived from social pedigrees change depending on the mode of the relationship between EPP and the focal trait. We show that the magnitude of the underestimation is typically small (<15%). Hence, our analyses suggest that quantitative genetic inference from pedigrees derived from observations of social relationships are relatively robust; our approach also provides a widely-applicable method for assessing the consequences of non-random EPP.
Data from: Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches
The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genome-wide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long-term study population of Soay sheep on St Kilda using three increasingly complete and accurate estimates of relatedness: (1) Pedigree 1, using observation-derived maternal links and microsatellite-derived paternal links; (2) Pedigree 2, using SNP-derived assignment of both maternity and paternity; and (3) whole-genome relatedness at 37,037 autosomal SNPs. In initial analyses, heritability estimates were strikingly similar for all three methods while standard errors were systematically lower in analyses based on Pedigree 2 and genomic relatedness. Genetic correlations were generally strong, differed little between the three estimates of relatedness and the standard errors declined only very slightly with improved relatedness information. When partitioning maternal effects into separate genetic and environmental components, maternal genetic effects found in juvenile traits increased substantially across the three relatedness estimates. Heritability declined compared to parallel models where only a maternal environment effect was fitted, suggesting that maternal genetic effects are confounded with direct genetic effects and that more accurate estimates of relatedness were better able to separate maternal genetic effects from direct genetic effects. We found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates. Finally, we present guidelines for the use of genomic relatedness in future quantitative genetics studies in natural populations.
Data from: Recovery of native genetic background in admixed Populations Using haplotypes, phenotypes, and pedigree information – using Cika cattle as a case breed
The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had direct or indirect historical contribution to the genetic makeup of the breed of interest.
Data from: Estimating relatedness and inbreeding using molecular markers and pedigrees: the effect of demographic history
Estimates of inbreeding and relatedness are commonly calculated using molecular markers, although the accuracy of such estimates has been questioned. As a further complication, in many situations, such estimates are required in populations with reduced genetic diversity, which is likely to affect their accuracy. We investigated the correlation between microsatellite- and pedigree-based coefficients of inbreeding and relatedness in laboratory populations of Drosophila melanogaster that had passed through bottlenecks to manipulate their genetic diversity. We also used simulations to predict expected correlations between marker- and pedigree-based estimates and to investigate the influence of linkage between loci and null alleles. Our empirical data showed lower correlations between marker- and pedigree-based estimates in our control (nonbottleneck) population than were predicted by our simulations or those found in similar studies. Correlations were weaker in bottleneck populations, confirming that extreme reductions in diversity can compromise the ability of molecular estimates to detect recent inbreeding events. However, this result was highly dependent on the strength of the bottleneck and we did not observe or predict any reduction in correlations in our population that went through a relatively severe bottleneck of N = 10 for one generation. Our results are therefore encouraging, as molecular estimates appeared robust to quite severe reductions in genetic diversity. It should also be remembered that pedigree-based estimates may not capture realized identity-by-decent and that marker-based estimates may actually be more useful in certain situations.
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