ArticleMolecular biology and evolution2018
Loter: A Software Package to Infer Local Ancestry for a Wide Range of Species.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers, 1 of them a synthesis that pooled it.
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Who cites it
74 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Population genetic considerations for using biobanks as international resources in the pandemic era and beyond.BMC genomics · 2021Pooled it
- Whole-Genome Resequencing Reveals Genetic Diversity and Selective Sweep Signatures in Wuling Cattle.Genes · 2026Article
- Scalable high resolution ancestry deconvolution for genomic data.Nature communications · 2026Article
- Genome-Wide Diversity of Goats From Indonesia and the Philippines Reveals Local Ancestry With Different Levels of Cosmopolitan Admixture.Genome biology and evolution · 2026Article
- Distinct adaptation and ancestral retention signals in African and European indigenous cattle genomes.Communications biology · 2026Article
- Strategies in Global Ancestry and Local Ancestry Inference.Current protocols · 2026Article
- Divergent Eurasian ancestry and local adaptation shape the genetic landscapes of the Yugur and Uyghur.Briefings in bioinformatics · 2026Article
- Genetic admixture and adaptive signatures of Guanling cattle revealed by whole-genome sequence.BMC genomics · 2026Article
- The hybridization analysis of pedigree: whole-genome re-sequencing reveals genomics characterization and genetic basis of growth trait of Qinchuan black pigs.BMC genomics · 2026Article
- Climate and hybridization shape stomatal trait evolution in Populus.The New phytologist · 2026Article
- Whole-Genome Resequencing Analysis Reveals the Local Ancestry and Selection of Kongshan Cattle.Biology · 2025Article
- Genomic ancestry and adaptive signatures in the indigenous Hetian cattle from Xinjiang Province of China revealed by whole-genome sequencing.BMC genomics · 2025Article
- Estimation of genome-wide coupling in rattlesnake hybrids provides insight into the process of speciation and its progress.Nature communications · 2025Article
- The role of cytonuclear interactions to plant adaptation across aProceedings. Biological sciences · 2025Article
- The genetic diversity of Indonesian cattle has been shaped by multiple introductions and adaptive introgression.Nature communications · 2025Article
- Old vs. new local ancestry inference in HCHS/SOL: a comparative study.Human molecular genetics · 2025Article
- Phase-free local ancestry inference mitigates the impact of switch errors on phase-based methods.G3 (Bethesda, Md.) · 2025Article
- Recomb-Mix: fast and accurate local ancestry inference.Bioinformatics (Oxford, England) · 2025Article
- Potential Adaptive Introgression From Dogs in Iberian Grey Wolves (Canis lupus).Molecular ecology · 2025Article
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14 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Admixture between populations provides opportunity to study biological adaptation and phenotypic variation. Admixture studies rely on local ancestry inference for admixed individuals, which consists of computing at each locus the number of copies that originate from ancestral source populations. Existing software packages for local ancestry inference are tuned to provide accurate results on human data and recent admixture events. Here, we introduce Loter, an open-source software package that does not require any biological parameter besides haplotype data in order to make local ancestry inference available for a wide range of species. Using simulations, we compare the performance of Loter to HAPMIX, LAMP-LD, and RFMix. HAPMIX is the only software severely impacted by imperfect haplotype reconstruction. Loter is the less impacted software by increasing admixture time when considering simulated and admixed human genotypes. For simulations of admixed Populus genotypes, Loter and LAMP-LD are robust to increasing admixture times by contrast to RFMix. When comparing length of reconstructed and true ancestry tracts, Loter and LAMP-LD provide results whose accuracy is again more robust than RFMix to increasing admixture times. We apply Loter to individuals resulting from admixture between Populus trichocarpa and Populus balsamifera and lengths of ancestry tracts indicate that admixture took place ∼100 generations ago. We expect that providing a rapid and parameter-free software for local ancestry inference will make more accessible genomic studies about admixture processes.
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