ArticleMolecular ecology resources2017
Pedigree reconstruction from SNP data: parentage assignment, sibship clustering and beyond.
Article in Molecular ecology resources, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 109 papers.
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Who cites it
109 citing papers in PubMed.
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- The paradoxical extinction: Exploring signatures of assortative mating as a possible mechanism that maintains canonical Red Wolf genetic ancestry in the American Gulf Coast canids.The Journal of heredity · 2026Article
- Population genomics reveals multi-scale mechanisms sustaining schistosomiasis re-emergence in a near-elimination setting.PLoS neglected tropical diseases · 2026Article
- Single Nucleotide Polymorphisms in Distant Kinship Inference and Forensic Genetic Genealogy.International journal of molecular sciences · 2026Review
- MixedUpParents: A New and Improved Method for Genetic Parentage Assignment in Admixed Populations.Molecular ecology resources · 2026Article
- Extensive parasite transmission and variation in a functional receptor associated with drug resistance in endemicScience advances · 2026Article
- Genomic Data Describe Population Structure but Struggle to Estimate Directed Connectivity Networks.Molecular ecology resources · 2026Article
- Fault-tolerant pedigree reconstruction from pairwise kinship relations.Bioinformatics (Oxford, England) · 2026Article
- Mothers Matter Most: Maternal, but Not Paternal, Age and Inbreeding Affect Nestling Telomere Length in a Wild Passerine.Molecular ecology · 2026Article
- Development and Applications of a 1K SNP Panel for Whiteleg Shrimp: From Pedigree Reconstruction to Genomic Selection.International journal of molecular sciences · 2026Article
- Assessing kinship detection: single nucleotide polymorphism array density and estimator comparison in white-tailed deer.G3 (Bethesda, Md.) · 2026Article
- Social Structure and Interactions Differentially Shape Aerotolerant and Anaerobic Gut Microbiomes in a Cooperative Breeding Species.Molecular ecology · 2026Article
- An olive parentage atlas: founder cultivars, regional diversification, and implications for breeding programs.BMC plant biology · 2026Article
- A Dominant Founder Lineage Has Possible Fitness Costs for the Endangered Mexican Grey Wolf.Molecular ecology · 2026Article
- Genetic Diversity of Sexually Propagated Corals Is Maintained From the Aquarium to the Reef.Molecular ecology · 2026Article
- A validated amplicon panel for parentage reconstruction and selection monitoring in whitefish (Conservation genetics resources · 2026Article
- Unmeasured prior viability selection resolves the paradox of stasis for body size in wild Soay sheep.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Boost or Bust? The Impact of Supplementation on Functional Genetic Diversity and Selective Processes in Tasmanian Devils.Molecular ecology · 2025Article
- Genomic Insights Into the Origin, Decline and Recovery of the Once Critically Endangered Iberian Lynx.Molecular ecology · 2025Review
49 more citing papers are in PubMed but not listed here.
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1 author.
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Abstract
Data on hundreds or thousands of single nucleotide polymorphisms (SNPs) provide detailed information about the relationships between individuals, but currently few tools can turn this information into a multigenerational pedigree. I present the r package sequoia, which assigns parents, clusters half-siblings sharing an unsampled parent and assigns grandparents to half-sibships. Assignments are made after consideration of the likelihoods of all possible first-, second- and third-degree relationships between the focal individuals, as well as the traditional alternative of being unrelated. This careful exploration of the local likelihood surface is implemented in a fast, heuristic hill-climbing algorithm. Distinction between the various categories of second-degree relatives is possible when likelihoods are calculated conditional on at least one parent of each focal individual. Performance was tested on simulated data sets with realistic genotyping error rate and missingness, based on three different large pedigrees (N = 1000-2000). This included a complex pedigree with overlapping generations, occasional close inbreeding and some unknown birth years. Parentage assignment was highly accurate down to about 100 independent SNPs (error rate <0.1%) and fast (<1 min) as most pairs can be excluded from being parent-offspring based on opposite homozygosity. For full pedigree reconstruction, 40% of parents were assumed nongenotyped. Reconstruction resulted in low error rates (<0.3%), high assignment rates (>99%) in limited computation time (typically <1 h) when at least 200 independent SNPs were used. In three empirical data sets, relatedness estimated from the inferred pedigree was strongly correlated to genomic relatedness.
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