Evolution of the primate lineage leading to modern humans: Phylogenetic and demographic inferences from DNA sequences

Takahata, Naoyuki; Satta, Yoko

doi:10.1073/pnas.94.9.4811

Cited by 174 publications

(154 citation statements)

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“…Second, comparative analyses indicate that these repeat elements have existed within the pericentromeric regions prior to the divergence of the Old World and hominoid primate lineages (Fig. 2b), generally estimated to have occurred 30-35 mya (Li 1997;Takahata and Satta 1997). In contrast, many of the duplications associated with these elements, such as the creatine transporter and neurofibromatosis loci, appear to have originated more recently (10-25 mya) with no evidence of duplicated loci found among Old World primates (Eichler et al 1996;Regnier et al 1997).…”

Section: Discussionmentioning

confidence: 99%

“…The comparative data indicate that both the sequence of the repeat and its nonrandom distribution within the pericentromeric region have been conserved properties of primate genome since the radiation of the catarrhine primates (∼30 mya). (Li 1997;Takahata and Satta 1997) Figure 2 Evolutionary conservation and distribution of the CAGGG repeat. (a) A 1.9-kb subclone (p196.3.12) was constructed within the CAGGG interspersed repeat sequences that flank the CTR-CDM (creatine-transporter/DXS1357E) duplicated locus on 16p11.2 (Fig.…”

Section: Evolution Of the Caggg Repeatmentioning

confidence: 99%

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CAGGG Repeats and the Pericentromeric Duplication of the Hominoid Genome

Eichler¹,

Archidiacono²,

Rocchi³

1999

Genome Res.

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Gene duplication is one of the primary forces of evolutionary change. We present data from three different pericentromeric regions of human chromosomes, which indicate that such regions of the genome have been sites of recent genomic duplication. This form of duplication has involved the evolutionary movement of segments of genomic material, including both intronic and exonic sequence, from diverse regions of the genome toward the pericentromeric regions. Sequence analyses of the target sites of duplication have identified a novel class of interspersed GC-rich repeats located precisely at the boundaries of duplication. Estimates of the evolutionary age of these duplications indicate that they have occurred between 10 and 25 mya. In contrast, comparative analyses confirm that the GC-rich pericentromeric repeats have existed within the pericentromeric regions of primate chromosomes before the divergence of the cercopithecoid and hominoid lineages (∼30 mya). These data provide molecular evidence for considerable interchromosomal duplication of genic segments during the evolution of the hominoid genome and strongly implicate GC-rich repeat elements as playing a direct role in the pericentromeric localization of these events Genome evolution is dependent on the processes of single-base-pair mutation and gene duplication. Duplication of a gene followed by mutation is responsible for the emergence of new genes with specialized functions in an evolving species. Two distinct molecular mechanisms of gene duplication are generally recognized. Tandem duplication of an ancestral gene, vis-à-vis processes of unequal crossover, produces a clustered family of related genes (Smith 1976). In contrast, whole-genome duplication (polyploidy) followed by chromosomal rearrangement and the re-establishment of the disomic state has been proposed as a mechanism for the interchromosomal duplication of large segments of a genome (Ohno 1970). The latter model, put forward originally by Susumu Ohno, explains observations of conserved genic synteny among nonhomologous chromosomes. Because of the genetic consequences of polyploidy, such events, although important in the early expansion of eukaryotic genomes, are rare and ancient (Ohno 1993;Wolfe and Shields 1997). Within the vertebrate lineage, for example, the last tetraploidization event leading to genome duplication is estimated to have occurred >400 mya (Lundin 1993). If polyploidy were the only model by which entire genes could be duplicated among nonhomologous chromosomes, it would then follow that interchromosomal paralogs of recent origin would be unexpected.Recent analyses of data from the Human Genome Project suggest a third form of genomic duplication, which is mechanistically distinct from polyploidy and tandem duplication models of genome evolution. Several independent reports indicate that genic segments, ranging in length from 5 kb to 30 kb, possess duplicate copies within the pericentromeric regions of human autosomes (Borden et

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Section: Discussionmentioning

confidence: 99%

Section: Evolution Of the Caggg Repeatmentioning

confidence: 99%

CAGGG Repeats and the Pericentromeric Duplication of the Hominoid Genome

Eichler¹,

Archidiacono²,

Rocchi³

1999

Genome Res.

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“…A phylogenetic estimate of m for great apes that is often used is 1 3 10 29 per site per year, an estimate based on calibrating sequence divergence with the fossil record (Takahata and Satta 1997;Nachman and Crowell 2000). This would place the radiation of gibbon genera within the early Pliocene 5 MYA.…”

Section: Uncertainty In Timing Of the Gibbon Radiationmentioning

confidence: 99%

Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach

et al. 2015

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Gibbons are believed to have diverged from the larger great apes 16.8 MYA and today reside in the rainforests of Southeast Asia. Based on their diploid chromosome number, the family Hylobatidae is divided into four genera, Nomascus, Symphalangus, Hoolock, and Hylobates. Genetic studies attempting to elucidate the phylogenetic relationships among gibbons using karyotypes, mitochondrial DNA (mtDNA), the Y chromosome, and short autosomal sequences have been inconclusive . To examine the relationships among gibbon genera in more depth, we performed second-generation whole genome sequencing (WGS) to a mean of 153 coverage in two individuals from each genus. We developed a coalescent-based approximate Bayesian computation (ABC) method incorporating a model of sequencing error generated by high coverage exome validation to infer the branching order, divergence times, and effective population sizes of gibbon taxa. Although Hoolock and Symphalangus are likely sister taxa, we could not confidently resolve a single bifurcating tree despite the large amount of data analyzed. Instead, our results support the hypothesis that all four gibbon genera diverged at approximately the same time. Assuming an autosomal mutation rate of 1 3 10 29 /site/year this speciation process occurred 5 MYA during a period in the Early Pliocene characterized by climatic shifts and fragmentation of the Sunda shelf forests. Whole genome sequencing of additional individuals will be vital for inferring the extent of gene flow among species after the separation of the gibbon genera.KEYWORDS approximate Bayesian computation; gibbon species; rapid radiation; whole genome sequences T HE family Hylobatidae, commonly known as gibbons, is believed to have diverged from the larger great apes 16.8 MYA . Sometimes known as small apes, gibbons demonstrate substantial morphological differentiation from the great apes; their much smaller bodies are highly adapted to an arboreal mode of locomotion in the rainforests of Southeast Asia. They also demonstrate very little sexual dimorphism that may, in part, be related to their generally monogamous mating patterns (Fuentes 2000) (although some gibbon species develop differences in coat color at sexual maturity).Each species demonstrates distinct "call" and "song" types (Geissmann 2002); however, attempts to classify gibbon species and genera based solely on morphological features have been problematic (Mootnick 2006). Primarily on the basis of their karyotypes, gibbons are now divided into four major genera, with Nomascus, Symphalangus, Hylobates, and Hoolock each possessing 52, 50, 44, and 38 diploid chromosomes, respectively. While many genetic studies have been performed, including a number based on karyotypes (Müller et al. 2003), mitochondrial DNA (mtDNA) (Hayashi et al. 1995;Takacs et al. 2005;Monda et al. 2007;Whittaker et al. 2007;Matsudaira and Ishida 2010;Van Ngoc et al. 2010), Y chromosomes (Chan et al. 2012), Arthrobacter luteus (ALU) repeats (Meyer et al. 2012), and short stretches of autosomal seq...

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“…The absence of fixed differences at multiple loci is itself informative about population demography during cichlid diversification, indicating that the effective population sizes of cichlid species remained large (ϳ 10 5 ) throughout the history of their adaptive radiation. There are many other examples of shared neutral polymorphisms documented between closely related species, but in only a few cases have genealogical patterns been inferred at multiple loci and used to infer historical demography (Takahata and Nei 1985;Hey and Kliman 1993;Takahata and Satta 1997;Wang et al 1997;Hilton and Gaut 1998;Li et al 1999;Kliman et al 2000).…”

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confidence: 99%

Genetic Evidence on the Demography of Speciation in Allopatric Dolphin Species

2002

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Abstract. Under a neutral model, the stochastic lineage sorting that leads to gene monophyly proceeds slowly in large populations. Therefore, in many recent species with large population size, the genome will have mixed support for monophyly unless historical bottlenecks have accelerated coalescence. We use genealogical patterns in mitochondrial DNA and in introns of four nuclear loci to test for historical bottlenecks during the speciation and divergence of two temperate Lagenorhynchus dolphin species isolated by tropical Pacific waters (an antitropical distribution). Despite distinct morphologies, foraging behaviors, and mitochondrial DNAs, these dolphin species are polyphyletic at all four nuclear loci. The abundance of shared polymorphisms between these sister taxa is most consistent with the maintenance of large effective population sizes (5.09 ϫ 10 4 to 10.9 ϫ 10 4 ) during 0.74-1.05 million years of divergence. A variety of population size histories are possible, however. We used gene tree coalescent probabilities to explore the rejection region for historical bottlenecks of different intensity given best estimates of effective population size under a strict isolation model of divergence. In L. obliquidens the data are incompatible with a colonization propagule of an effective size of 10 or fewer individuals. Although the ability to reject less extreme historical bottlenecks will require data from additional loci, the intermixed genealogical patterns observed between these dolphin sister species are highly probable only under an extended history of large population size. If similar demographic histories are inferred for other marine antitropical taxa, a parsimonious model for the Pleistocene origin of these distributions would not involve rare breaches of a constant dispersal barrier by small colonization propagules. Instead, a history of large population size in L. obliquidens and L. obscurus contributes to growing biological and environmental evidence that the equatorial barrier became permeable during glacial/interglacial cycles, leading to vicariant isolation of antitropical populations.

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Evolution of the primate lineage leading to modern humans: Phylogenetic and demographic inferences from DNA sequences

Cited by 174 publications

References 40 publications

CAGGG Repeats and the Pericentromeric Duplication of the Hominoid Genome

CAGGG Repeats and the Pericentromeric Duplication of the Hominoid Genome

Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach

Genetic Evidence on the Demography of Speciation in Allopatric Dolphin Species

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