On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs

Santure, Anna W.; Stapley, Jessica; Ball, Alexander D.; Birkhead, Tim R.; Burke, Terry; Slate, Jon

doi:10.1111/j.1365-294x.2010.04554.x

Cited by 136 publications

(162 citation statements)

References 49 publications

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“…This and other recent findings (for example, Hoffman et al, 2014;Keller et al, 2011) are in stark contrast to previous studies that used few genetic markers and did not consider the effects of linkage and recombination on the relative performance of pedigree-versus marker-based measures of inbreeding (for example, Balloux et al, 2004;Slate et al, 2004;Santure et al, 2010). The current explosion of DNA sequence data from nonmodel organisms is providing the tools necessary to precisely measure IBD G with genetic markers in any organism.…”

Section: Discussioncontrasting

confidence: 50%

Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees

2015

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Inbreeding (mating between relatives) can dramatically reduce the fitness of offspring by causing parts of the genome to be identical by descent. Thus, measuring individual inbreeding is crucial for ecology, evolution and conservation biology. We used computer simulations to test whether the realized proportion of the genome that is identical by descent (IBD G ) is predicted better by the pedigree inbreeding coefficient (F P ) or by genomic (marker-based) measures of inbreeding. Genomic estimators of IBD G included the increase in individual homozygosity relative to mean Hardy-Weinberg expected homozygosity (F H ), and two measures (F ROH and F E ) that use mapped genetic markers to estimate IBD G . IBD G was more strongly correlated with F H , F E and F ROH than with F P across a broad range of simulated scenarios when thousands of SNPs were used. For example, IBD G was more strongly correlated with F ROH , F H and F E (estimated with ⩾ 10 000 SNPs) than with F P (estimated with 20 generations of complete pedigree) in populations with a recent reduction in the effective populations size (from N e = 500 to N e = 75). F ROH , F H and F E generally explained 490% of the variance in IBD G (among individuals) when 35 K or more SNPs were used. F P explained o80% of the variation in IBD G on average in all simulated scenarios, even when pedigrees included 20 generations. Our results demonstrate that IBD G can be more precisely estimated with large numbers of genetic markers than with pedigrees. We encourage researchers to adopt genomic marker-based measures of IBD G as thousands of loci can now be genotyped in any species.

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Section: Discussioncontrasting

confidence: 50%

Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees

2015

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“…Limited X-linked SNPs were evaluated in this study and, because of its transmission pattern, X-linked genes are good candidates for selection during domestication and deserve further investigation. SNPs have already demonstrated the potential to equal or even outperform microsatellites for specific questions such as individual ancestry (Lao et al, 2008), population assignment (for example, Seddon et al, 2005;Narum et al, 2008;Smith and Seeb, 2008;Coates et al, 2009) and pedigree studies (Santure et al, 2010;Hauser et al, 2011), and proved to have large allele frequency differences among populations (Freamo et al, 2011). The inclusion of SNPs associated with specific known domestic cat phenotypes, particularly recessive traits such as melanism, hair types and gloving (for review see Lyons, 2010;2012,) would likely increase the power for domestic cat introgression into wildcats.…”

Section: Detection Of Hybridization In Natural Populations Using Snpsmentioning

confidence: 99%

Toward a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris)

et al. 2015

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Endemic gene pools have been severely endangered by human-mediated hybridization, which is posing new challenges in the conservation of several vertebrate species. The endangered European wildcat is an example of this problem, as several natural populations are suffering introgression of genes from the domestic cat. The implementation of molecular methods for detecting hybridization is crucial for supporting appropriate conservation programs on the wildcat. In this study, genetic variation at 158 single-nucleotide polymorphisms (SNPs) was analyzed in 139 domestic cats, 130 putative European wildcats and 5 captive-bred hybrids (N = 274). These SNPs were variable both in wild (H E = 0.107) and domestic cats (H E = 0.340). Although we did not find any SNP that was private in any population, 22 SNPs were monomorphic in wildcats and pairwise F CT values revealed marked differences between domestic and wildcats, with the most divergent 35 loci providing an average F CT 40.74. The power of all the loci to accurately identify admixture events and discriminate the different hybrid categories was evaluated. Results from simulated and real genotypes show that the 158 SNPs provide successful estimates of admixture, with 100% hybrid individuals (two to three generations in the past) being correctly identified in STRUCTURE and over 92% using the NEWHYBRIDS' algorithm. None of the unclassified cats were wrongly allocated to another hybrid class. Thirty-five SNPs, showing the highest F CT values, provided the most parsimonious panel for robust inferences of parental and first generations of admixed ancestries. This approach may be used to further reconstruct the evolution of wildcat populations and, hopefully, to develop sound conservation guidelines for its legal protection in Europe.

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“…This will, for example, facilitate QTL mapping studies and will increase the quality of outlier-and structure analyses. Massively increasing the number of markers will enable researchers not only to get better precision in population genetic studies (Novembre et al, 2008), QTL and linkage disequilibrium (LD) mapping projects (Slate et al, 2009) and kinship assignments (Santure et al, 2010), but also to pursue topics such as historical demographic patterns, introgression and admixture (Jakobsson et al, 2008).…”

Section: Large-scale Identification and Development Of Molecular Markersmentioning

confidence: 99%

Applications of next generation sequencing in molecular ecology of non-model organisms

2010

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As most biologists are probably aware, technological advances in molecular biology during the last few years have opened up possibilities to rapidly generate large-scale sequencing data from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', it is worthwhile to review how this may impact molecular ecology. The first studies to put the next generation sequencing (NGS) to the test in ecologically well-characterized species without previous genome information were published in 2007 and the beginning of 2008. Since then several studies have followed in their footsteps, and a large number are undoubtedly under way. This review focuses on how NGS has been, and can be, applied to ecological, population genetic and conservation genetic studies of non-model species, in which there is no (or very limited) genomic resources. Our aim is to draw attention to the various possibilities that are opening up using the new technologies, but we also highlight some of the pitfalls and drawbacks with these methods. We will try to provide a snapshot of the current state of the art for this rapidly advancing and expanding field of research and give some likely directions for future developments.

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On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs

Cited by 136 publications

References 49 publications

Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees

Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees

Toward a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris)

Applications of next generation sequencing in molecular ecology of non-model organisms

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