Phylogenetic relationships and divergence dates of the whole mitochondrial genome sequences among three gibbon genera

Matsudaira, Kazunari; Ishida, Takafumi

doi:10.1016/j.ympev.2010.01.032

Cited by 59 publications

(69 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In agreement with this scenario we hypothesized that the HyA was heterozygous for variant forms of chromosomes 6, 8, 9, and 18, as reported in Figure 3. Our results are in agreement with the pattern found by Matsudaira and Ishida (2010) who sequenced the full mtDNA of the genera Hylobates, Nomascus, and Syndactylus and with Kim et al (2011), who based their conclusions on 60 kb of sequence data from a panel of 19 gibbons representing nine species from all four genera.…”

Section: Discussionsupporting

confidence: 92%

See 1 more Smart Citation

A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

Capozzi

Carbone²,

Stanyon

et al. 2012

Genome Res.

View full text Add to dashboard Cite

Chromosome rearrangements in small apes are up to 20 times more frequent than in most mammals. Because of their complexity, the full extent of chromosome evolution in these hominoids is not yet fully documented. However, previous work with array painting, BAC-FISH, and selective sequencing in two of the four karyomorphs has shown that highresolution methods can precisely define chromosome breakpoints and map the complex flow of evolutionary chromosome rearrangements. Here we use these tools to precisely define the rearrangements that have occurred in the remaining two karyomorphs, genera Symphalangus (2n = 50) and Hoolock (2n = 38). This research provides the most comprehensive insight into the evolutionary origins of chromosome rearrangements involved in transforming small apes genome. Bioinformatics analyses of the human-gibbon synteny breakpoints revealed association with transposable elements and segmental duplications, providing some insight into the mechanisms that might have promoted rearrangements in small apes. In the near future, the comparison of gibbon genome sequences will provide novel insights to test hypotheses concerning the mechanisms of chromosome evolution. The precise definition of synteny block boundaries and orientation, chromosomal fusions, and centromere repositioning events presented here will facilitate genome sequence assembly for these close relatives of humans.

show abstract

Section: Discussionsupporting

confidence: 92%

“…The importance of understanding their rapid genome evolution is also provided by their phylogenetic affinity to humans. Gibbons and humans diverged about 17-23 million years ago (Matsudaira and Ishida 2010) and are classified in the same superfamily Hominoidea.…”

mentioning

confidence: 99%

A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

Capozzi

Carbone²,

Stanyon

et al. 2012

Genome Res.

View full text Add to dashboard Cite

show abstract

“…Evidence for this comes from evolutionary comparisons of Great Apes to Old World monkeys (e.g., humans have a 30% slower evolutionary rate as compared to baboons) (Kim et al 2006). While generally bigger Decreasing the mutation rate would lead to a Late Miocene speciation time of up to 10 MYA, thus encompassing previous estimates of divergence at 6-8 MYA based on mtDNA (Chan et al 2010;Matsudaira and Ishida 2010;Van Ngoc et al 2010). However, fossil calibration-based estimates such as used in these studies are subject to their own biases (Lukoschek et al 2012), while estimates of demography from a single locus (especially a nonrecombining region of the genome, no matter how well resolved the gene tree) are subject to large evolutionary stochasticity (Rosenberg and Nordborg 2002).…”

mentioning

confidence: 87%

“…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 sequence Wall et al 2013), the phylogenetic relationships among the four gibbon genera remain unresolved, with at least seven different topologies being supported by different data. A recent study examined 1.5 Mb of orthologous autosomal sequence generated by second-generation sequencing from one individual representing each of the four genera .…”

mentioning

confidence: 99%

“…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 sequence Wall et al 2013), the phylogenetic relationships among the four gibbon genera remain unresolved, with at least seven different topologies being supported by different data.…”

mentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2015

View full text Add to dashboard Cite

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...

show abstract

Genetic Perspectives on Ape and Human Evolution

Disotell¹

2013

A Companion to Paleoanthropology

View full text Add to dashboard Cite

Phylogenetic relationships and divergence dates of the whole mitochondrial genome sequences among three gibbon genera

Cited by 59 publications

References 27 publications

A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

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

Genetic Perspectives on Ape and Human Evolution

Contact Info

Product

Resources

About