ArticlePLoS genetics2007
Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model.
Article in PLoS genetics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 153 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
153 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary.Frontiers in genetics · 2019Pooled it
- Generation Length: Often Ignored and Sometimes Misunderstood.Evolutionary applications · 2026Review
- Population Size Differences Can Lead to Biases in Phylogenetic Inference and Introgression Detection in the Presence of Purifying Selection.Systematic biology · 2026Article
- Predicting extinction risk of gibbons from genomes of extinct Yunnan lar gibbon.Genome biology · 2026Article
- Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments Using AIC.Systematic biology · 2026Article
- Not Just Ne Ne-More: New Applications for SMC from Ecology to Phylogenies.Genome biology and evolution · 2026Review
- Comprehensive Analysis of Rodent-SpecificBiology · 2025Article
- Cephalopod sex determination and its ancient evolutionary origin.Current biology : CB · 2025Article
- The Genomic Landscape, Causes, and Consequences of Extensive Phylogenomic Discordance in Murine Rodents.Genome biology and evolution · 2025Article
- A region of suppressed recombination misleads neoavian phylogenomics.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- TRAILS: Tree reconstruction of ancestry using incomplete lineage sorting.PLoS genetics · 2024Article
- Inference of Coalescence Times and Variant Ages Using Convolutional Neural Networks.Molecular biology and evolution · 2023Article
- Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae).Systematic biology · 2023Article
- Towards a great ape dictionary: Inexperienced humans understand common nonhuman ape gestures.PLoS biology · 2023Article
- Revised time estimation of the ancestral human chromosome 2 fusion.BMC genomics · 2022Article
- Annotation-free delineation of prokaryotic homology groups.PLoS computational biology · 2022Article
- Article
- Champagne: Automated Whole-Genome Phylogenomic Character Matrix Method Using Large Genomic Indels for Homoplasy-Free Inference.Genome biology and evolution · 2022Article
- Factors That Affect the Rates of Adaptive and Nonadaptive Evolution at the Gene Level in Humans and Chimpanzees.Genome biology and evolution · 2022Article
- Changing Population Size in McDonald-Kreitman Style Analyses: Artifactual Correlations and Adaptive Evolution between Humans and Chimpanzees.Genome biology and evolution · 2022Article
93 more citing papers are in PubMed but not listed here.
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
The genealogical relationship of human, chimpanzee, and gorilla varies along the genome. We develop a hidden Markov model (HMM) that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes. Our HMM is an analytically tractable approximation to the coalescent process with recombination, and in simulations we see no apparent bias in the HMM estimates. We apply the HMM to four autosomal contiguous human-chimp-gorilla-orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human-chimp (4.1 +/- 0.4 million years), and fairly large ancestral effective population sizes (65,000 +/- 30,000 for the human-chimp ancestor and 45,000 +/- 10,000 for the human-chimp-gorilla ancestor). Furthermore, around 50% of the human genome coalesces with chimpanzee after speciation with gorilla. We also consider 250,000 base pairs of X-chromosome alignments and find an effective population size much smaller than 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogies correlates well with the region-wide present-day human recombination rate, but does not correlate with the fine-scale recombination rates and recombination hot spots, suggesting that the latter are evolutionarily transient.
Indexed as
Identifiers
What OpenQuestion holds
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.