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 τ = μT and θ = 4μgN using the Markov chain Monte Carlo method, where μ is the mutation rate and g is the generation time. Although the estimated τHC differed across chromosomes, τHC and τHCG were strongly correlated across chromosomes, indicating that variation in τ is subject to variation in μ, 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 μ 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.

Tempo and mode of genomic mutations unveil human evolutionary history

“…These observations are likely to provide a lower mutation rate even with the phylogenetic approach. Indeed, assuming k of 0.012 after excluding indels, N ranging from 59,300 to 122,000 (Hara et al, 2012;, T at 6 million years ago, and a generation time of 20-25 years, I calculated μ as 1.10-1.67 × 10 -8 , which is comparable with the estimates based on high-throughput sequencing (Table 1).…”

“…While the averages of estimated τ HC (= μT HC ) and τ HCG (= μT HCG ), where T HC and T HCG represent speciation times between human and chimpanzee and between the ancestor of human/chimpanzee and gorilla, respectively, varied among the human chromosomes, the averages of τ HC and τ HCG of the human chromosomes were highly correlated (Fig. 1A) (Hara et al, 2012). One simple explanation for this observation is that mutation rates differ across chromosomes through mechanisms that have not yet been clarified (Hara et al, 2012).…”

Composition and evolutionary importance of transposable elements in humans and primates

“…Many studies have proved and identified the genome and information of gorilla (Gibbs and Rogers 2012;Hara et al 2012;Scally and Durbin 2012;Ventura et al 2011;Vigilant and Bradley 2004). Gorilla is in the family of hominidae along with human, orangutan and chimpanzee.…”

“…In the similar manner to gorillas, chimpanzee is another primate that has analogous DNA to human (Han et al 2007b;Hara et al 2012;Li and Saunders 2005;Liu et al 2009;Olson and Varki 2002;Prüfer et al 2012; The chimpanzee sequencing and analysis consortium 2005; Ventura et al 2011). Chimpanzees are included in the This data are modified from Smit et al 2010.…”

“…Orangutans are native to Malaysia and Indonesia, and there are many studies about orangutans (Hara et al 2012;Locke et al 2011;Walker et al 2012, Yohn et al 2005. Orangutans are also included in the family of hominidae.…”