Patterns of Genetic Variation Within and Between Gibbon Species

Abstract

Gibbons are small, arboreal, highly endangered apes that are understudied compared with other hominoids. At present, there are four recognized genera and approximately 17 species, all likely to have diverged from each other within the last 5–6 My. Although the gibbon phylogeny has been investigated using various approaches (i.e., vocalization, morphology, mitochondrial DNA, karyotype, etc.), the precise taxonomic relationships are still highly debated. Here, we present the first survey of nuclear sequence variation within and between gibbon species with the goal of estimating basic population genetic parameters. We gathered ∼60 kb of sequence data from a panel of 19 gibbons representing nine species and all four genera. We observe high levels of nucleotide diversity within species, indicative of large historical population sizes. In addition, we find low levels of genetic differentiation between species within a genus comparable to what has been estimated for human populations. This is likely due to ongoing or episodic gene flow between species, and we estimate a migration rate between Nomascus leucogenys and N. gabriellae of roughly one migrant every two generations. Together, our findings suggest that gibbons have had a complex demographic history involving hybridization or mixing between diverged populations.

A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

“…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.…”

A Phylogeny Based on the Concatenated 9 Protein-coding Gene Sequences of Mt Genomes among Three Gibbon Genera

“…The family Hylobatidae is monophyletic with predominantly strongly supported (100% bootstrap support) and each of the three genera with multiple species also show monophyly with high support (98-100% bootstrap support). At this point, our result is consistent with all previous result, including numerous morphological and molecular studies on the phylogenetic relationships among Hylobatidae members (Hayashi et al, 1995;Müller et al, 2003;Brandon-Jones et al, 2004;Takacs et al, 2005;Monda et al, 2007;Whittaker et al, 2007;Matsudaira and Ishida, 2010;Kim et al, 2011;Chan et al, 2012;Meyer et al, 2012;Wall et al, 2013).…”

“…The mitochondrial phylogeny of the three gibbon genera, Nomascus, Symphalangus, and Hylobates, based on the 9 concatenated protein coding genes was identical to that based on the whole mitochondrial genome (Hayashi et al, 1995;Müller et al, 2003;Brandon-Jones et al, 2004;Takacs et al, 2005;Monda et al, 2007;Whittaker et al, 2007;Chan et al, 2010;Matsudaira and Ishida, 2010;Kim et al, 2011;Chan et al, 2012;Meyer et al, 2012;Finstermeier et al, 2013;Wall et al, 2013). However, previous phylogenetic studies using the whole mitochondrial genome, Matsudaira and Ishida (2010) and Finstermeier et al (2013) both included only one Nomascus species.…”

“…A number of molecular studies have been performed, including karyotypes (Müller et al, 2003), mitochondrial DNA (mtDNA) (Hayashi et al, 1995;Takacs et al, 2005;Monda et al, 2007;Whittaker et al, 2007;Chan et al, 2010;Matsudaira and Ishida, 2010), Y chromosomes (Chan et al, 2012), Arthrobacter luteus (ALU) repeats (Meyer et al, 2012), and short stretches of autosomal sequence (Kim et al, 2011;Wall et al, 2013), the phylogenetic relationships among the four gibbon genera are still confidently unresolved; phylogenetic relationships proposed in the studies using different data were inconsistent (reviewed in (Kim et al, 2011;Wall et al, 2013)). …”

Repetitive sequences originating from the centromere constitute large-scale heterochromatin in the telomere region in the siamang, a small ape

“…The phylogenetic relationship of these genera is still not clear probably because of the relatively short time span in which their lineages diverged, and some additional factors such as gene flow among species (Van Ngoc et al, 2010;Kim et al, 2011). In our discussion below, we consider three of them (Symphalangus, Hylobates and Nomascus) because the materials we used in the present study were from species of these three genera.…”