ArticleGenetics2017
Modeling Human Population Separation History Using Physically Phased Genomes.
Article in Genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
29 citing papers in PubMed.
- A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact.Genetics · 2025Article
- Linguistic capacity was present in theFrontiers in psychology · 2025Article
- Phased nanopore assembly with Shasta and modular graph phasing with GFAse.Genome research · 2024Article
- Phased nanopore assembly with Shasta and modular graph phasing with GFAse.bioRxiv : the preprint server for biology · 2023Article
- eSMC: a statistical model to infer admixture events from individual genomics data.BMC genomics · 2022Article
- Benchmarking phasing software with a whole-genome sequenced cattle pedigree.BMC genomics · 2022Article
- Elucidation of the speciation history of three sister species of crown-of-thorns starfish (Acanthaster spp.) based on genomic analysis.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Article
- The deep population history in Africa.Human molecular genetics · 2021Review
- Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Origins of modern human ancestry.Nature · 2021Review
- Fully Phased Sequence of a Diploid Human Genome DeterminedG3 (Bethesda, Md.) · 2020Article
- Insights into human genetic variation and population history from 929 diverse genomes.Science (New York, N.Y.) · 2020Article
- Tracking human population structure through time from whole genome sequences.PLoS genetics · 2020Article
- A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data.Ecology and evolution · 2020Review
- Article
- SNP-Density Crossover Maps of Polymorphic Transposable Elements and HLA Genes Within MHC Class I Haplotype Blocks and Junction.Frontiers in genetics · 2020Article
- Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps.PLoS computational biology · 2019Article
- Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa.Cell · 2019Article
- Towards population genomics in non-model species with large genomes: a case study of the marine zooplanktonRoyal Society open science · 2019Article
- Rapid evolution of a skin-lightening allele in southern African KhoeSan.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Phased haplotype sequences are a key component in many population genetic analyses since variation in haplotypes reflects the action of recombination, selection, and changes in population size. In humans, haplotypes are typically estimated from unphased sequence or genotyping data using statistical models applied to large reference panels. To assess the importance of correct haplotype phase on population history inference, we performed fosmid pool sequencing and resolved phased haplotypes of five individuals from diverse African populations (including Yoruba, Esan, Gambia, Maasai, and Mende). We physically phased 98% of heterozygous SNPs into haplotype-resolved blocks, obtaining a block N50 of 1 Mbp. We combined these data with additional phased genomes from San, Mbuti, Gujarati, and Centre de'Etude du Polymorphism Humain European populations and analyzed population size and separation history using the pairwise sequentially Markovian coalescent and multiple sequentially Markovian coalescent models. We find that statistically phased haplotypes yield a more recent split-time estimation compared with experimentally phased haplotypes. To better interpret patterns of cross-population coalescence, we implemented an approximate Bayesian computation approach to estimate population split times and migration rates by fitting the distribution of coalescent times inferred between two haplotypes, one from each population, to a standard isolation-with-migration model. We inferred that the separation between hunter-gatherer populations and other populations happened ∼120-140 KYA, with gene flow continuing until 30-40 KYA; separation between west-African and out-of-African populations happened ∼70-80 KYA; while the separation between Maasai and out-of-African populations happened ∼50 KYA.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.