Inferring the evolutionary histories of divergences in Hylobates and Nomascus gibbons through multilocus sequence data
Yi-Chiao Chan, Christian Roos, Miho Inoue-Murayama, Eiji Inoue, Chih-Chin Shih, Kurtis Jai-Chyi Pei & Linda Vigilant 2013
BMC Evol.Biol.13, 82 open access

Gibbons (Hylobatidae) are the most diverse group of living apes.
They exist as geographically-contiguous spp, which diverged more rapidly than did their close relatives, the great apes (Hominidae).
Of the 4 extant gibbon genera, the evol.histories of 2 poly-specific genera (Hylobates & Nomascus) have been the particular focus of research,
but the DNA sequence data used was largely derived from the maternally inherited mitochondrial DNA locus (mtDNA).
Results:
To investigate the evol.relationships & divergence processes of gibbon spp (esp. the Hylobates genus), we produced & analyzed 11.5 kb DNA of sequence at 14 bi-parentally inherited autosomal loci:
on average, gibbon genera have a high average sequence diversity, but a lower degree of genetic differentiation vs gr.ape genera.
Our multi-locus spp-tree features H.pileatus in a basal position & a grouping of the 4 Sundaic island spp (H.agilis, klossii, moloch & muelleri).
We conducted pair-wise comparisons, based on an isolation-with-migration (IM) model, and detect signals of asymmetric gene-flow between
- H.lar & moloch,
- H.agilis & muelleri,
- N.leucogenys & siki.
Concl.:
Our multi-locus analyses provide inferences of gibbon evol.histories complementary to those based on single gene data.
IM analyses suggest: the divergence processes of gibbons may be accompanied by gene-flow.
Future studies using analyses of multi-population model with samples of known provenance for Hylobates & Nomascus spp would expand the understanding of histories of gene-flow during divergences for these 2 gibbon genera.

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As you know, my hypothesis (cf my book p.299):

Early-Miocene Hominoidea lived on the island archipels between Arabafrica & Eurasia in coastal forests, where they became vertical waders-climbers ("bipedal"):
-larger body (later secondarily reduced in hylobatids),
-very wide sternum-thorax-pelvis (+ lateral leg movements, lateral & upward arm movements),
-shorter, less (7->5) & centrally-placed lumbar vertebrae (vertical posture), -complete tail loss (disadvantegous in water: wading).
From these island archipels,
1) hylobatids (early?mid-Miocene?) followed S-Asian coastal forests -> SE.Asia, 2) the Mesopotamian Seaway Closure 15-14 Ma split
- pongids-sivapiths E: S-Asia, N-Ind.Ocean,
- hominids-dryopiths W: peri-Medit.Sea: late-Miocene Gorilla-Homo-Pan in (the incipient) Red Sea forests.

What I still don't know:
did hylobatids in 1 gulf follow the N-Ind.Ocean coastal forests East-ward? or in different gulfs?
are some lesser apes closer relatives of the gr.apes than of other lesser apes??

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