Dataset Information

Reconstructing the demographic history of the human lineage using whole-genome sequences from human and three great apes.

ABSTRACT: The demographic history of human would provide helpful information for identifying the evolutionary events that shaped the humanity but remains controversial even in the genomic era. To settle the controversies, we inferred the speciation times (T) and ancestral population sizes (N) in the lineage leading to human and great apes based on whole-genome alignment. A coalescence simulation determined the sizes of alignment blocks and intervals between them required to obtain recombination-free blocks with a high frequency. This simulation revealed that the size of the block strongly affects the parameter inference, indicating that recombination is an important factor for achieving optimum parameter inference. From the whole genome alignments (1.9 giga-bases) of human (H), chimpanzee (C), gorilla (G), and orangutan, 100-bp alignment blocks separated by ?5-kb intervals were sampled and subjected to estimate ? = ?T and ? = 4?gN using the Markov chain Monte Carlo method, where ? is the mutation rate and g is the generation time. Although the estimated ?(HC) differed across chromosomes, ?(HC) and ?(HCG) were strongly correlated across chromosomes, indicating that variation in ? is subject to variation in ?, rather than T, and thus, all chromosomes share a single speciation time. Subsequently, we estimated Ts of the human lineage from chimpanzee, gorilla, and orangutan to be 6.0-7.6, 7.6-9.7, and 15-19 Ma, respectively, assuming variable ? across lineages and chromosomes. These speciation times were consistent with the fossil records. We conclude that the speciation times in our recombination-free analysis would be conclusive and the speciation between human and chimpanzee was a single event.

SUBMITTER: Hara Y

PROVIDER: S-EPMC3752010 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Reconstructing the demographic history of the human lineage using whole-genome sequences from human and three great apes.

Hara Yuichiro Y Imanishi Tadashi T Satta Yoko Y

Genome biology and evolution 20120101 11

The demographic history of human would provide helpful information for identifying the evolutionary events that shaped the humanity but remains controversial even in the genomic era. To settle the controversies, we inferred the speciation times (T) and ancestral population sizes (N) in the lineage leading to human and great apes based on whole-genome alignment. A coalescence simulation determined the sizes of alignment blocks and intervals between them required to obtain recombination-free block ...[more]

PMID: 22975719

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Project description:Primate fingers are typically in direct contact with the environment during both locomotion and manipulation, and aspects of external phalangeal morphology are known to reflect differences in hand use. Since bone is a living tissue that can adapt in response to loading through life, the internal bone architecture of the manual phalanges should also reflect differences in manual behaviours. Here, we use the R package Morphomap to analyse high-resolution microCT scans of hominid proximal phalanges of digits 2-5 to determine whether cortical bone structure reflects variation in manual behaviours between bipedal (Homo), knuckle-walking (Gorilla, Pan) and suspensory (Pongo) taxa. We test the hypothesis that relative cortical bone distribution patterns and cross-sectional geometric properties will differ both among extant great apes and across the four digits due to locomotor and postural differences. Results indicate that cortical bone structure reflects the varied hand postures employed by each taxon. The phalangeal cortices of Pongo are significantly thinner and have weaker cross-sectional properties relative to the African apes, yet thick cortical bone under their flexor sheath ridges corresponds with predicted loading during flexed finger grips. Knuckle-walking African apes have even thicker cortical bone under the flexor sheath ridges, as well as in the region proximal to the trochlea, but Pan also has thicker diaphyseal cortices than Gorilla. Humans display a distinct pattern of distodorsal thickening, as well as relatively thin cortices, which may reflect the lack of phalangeal curvature combined with frequent use of flexed fingered hand grips during manipulation. Within each taxon, digits 2-5 have a similar cortical distribution in Pongo, Gorilla and, unexpectedly, Homo, which suggest similar loading of all fingers during habitual locomotion or hand use. In Pan, however, cortical thickness differs between the fingers, potentially reflecting differential loading during knuckle-walking. Inter- and intra-generic variation in phalangeal cortical bone structure reflects differences in manual behaviours, offering a comparative framework for reconstructing hand use in fossil hominins.

Dataset Information

Reconstructing the demographic history of the human lineage using whole-genome sequences from human and three great apes.

Publications

Reconstructing the demographic history of the human lineage using whole-genome sequences from human and three great apes.

Similar Datasets

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