Mitochondrial DNA hypervariable region‐1 sequence variation and phylogeny of the concolor gibbons, Nomascus

Abstract

The still little known concolor gibbons are represented by 14 taxa (five species, nine subspecies) distributed parapatrically in China, Myanmar, Vietnam, Laos and Cambodia. To set the stage for a phylogeographic study of the genus we examined DNA sequences from the highly variable mitochondrial hypervariable region-1 (HVR-1 or control region) in 51 animals, mostly of unknown geographic provenance. We developed gibbon-specific primers to amplify mtDNA noninvasively and obtained >477 bp sequences from 38 gibbons in North American and European zoos and >159 bp sequences from ten Chinese museum skins. In hindsight, we believe these animals represent eight of the nine nominal subspecies and four of the five nominal species. Bayesian, maximum likelihood and maximum parsimony haplotype network analyses gave concordant results and show Nomascus to be monophyletic. Significant intraspecific variation within N. leucogenys (17 haplotypes) is comparable with that reported earlier in Hylobates lar and less than half the known interspecific pairwise distances in gibbons. Sequence data support the recognition of five species (concolor, leucogenys, nasutus, gabriellae and probably hainanus) and suggest that nasutus is the oldest and leucogenys, the youngest taxon. In contrast, the subspecies N. c. furvogaster, N. c. jingdongensis, and N. leucogenys siki, are not recognizable at this otherwise informative genetic locus. These results show that HVR-1 sequence is variable enough to define evolutionarily significant units in Nomascus and, if coupled with multilocus microsatellite or SNP genotyping, more than adequate to characterize their phylogeographic history. There is an urgent need to obtain DNA from gibbons of known geographic provenance before they are extirpated to facilitate the conservation genetic management of the surviving animals.

Molecular demographic history of the Hainan Peacock Pheasant (Polyplectron katsumatae) and its conservation implications

“…In this case, P. katsumatae currently retains lower mtDNA nucleotide diversity and smaller population size compared with other pheasant species [33] and its mainland relative P. bicalcaratum (unpublished data). The pattern of low mtDNA genetic diversity was consistent with other Hainan faunas [13,14,34] 12, P>0.05). In general, a negative value of D or Fs implied that a recent population expansion or the selection, while non-significant value of H could be recognized as the indicator of the population expansion event instead of the selection.…”

“…However, the understanding of how wildlife on Hainan Island responded to climate change remains poor. One major reason for this lack of understanding could be the severe anthropogenic contraction of endemic wildlife on the island [13,14].…”

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

“…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 .…”

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

“…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)). …”