Hill, Catherine E. (2005) Mitochondrial DNA Variation in Island Southeast Asia. Doctoral thesis, University of Huddersfield.

It is known that Island Southeast Asia was colonised relatively early in the history of
modem humans; however, it is still a matter of some debate as to whether the modem
inhabitants of Island Southeast Asia are descended from these original inhabitants or are
the result of some later migration. Currently, the prevailing theory in both archaeology
and linguistics is that the modem inhabitants of Island Southeast Asia are largely
descended from an agricultural people who originated in China and Taiwan around
6,000 years ago. From there they are thought to have migrated through the Philippines
and into Eastern Island Southeast Asia around 2,500-1,500 B.C. assimilating or
replacing the indigenous peoples. However, other researchers have suggested that a
model of regional continuity is more suitable for Island Southeast Asia and that the
modem inhabitants are the direct descendents of the original Pleistocene inhabitants.
Still others have suggested that intermediate models would be more appropriate.
This study aimed to use mitochondrial DNA to test the validity of these models. A
secondary aim was to look at the mitochondrial DNA of the indigenous Orang AsH
groups of the Malay Peninsula in an attempt to reconstruct a picture of the early
Pleistocene variation of Southeast Asia. To this end, mitochondrial DNA was obtained
and sequenced from 885 individuals from various locations in Island Southeast Asia and
also 259 Orang AsHindividuals.
This study has demonstrated that the populations of Island Southeast Asia contain a
high level of genetic diversity, including a number of novel haplogroups. Significant
differences have also been found between Eastern and Western populations suggesting
that they have been established long enough to become regionally specific. Most Island
Southeast Asian haplogroups date to the Pleistocene or early Holocene which suggests
that they are mostly indigenous to the area. Those which could have a connection to
Taiwan seem too old to have been part of an 'out of Taiwan' event as it has been
traditionally visualised. Only -13% ofmtDNA types (belonging to haplogroups M7clc,
D5 and Y2) could be linked to such an event suggesting that if a migration did occur it
was demographically minor.
A number of novel haplogroups were also found in the Orang Asli which form strong
support for the theory that that at least the Semang, if not all Orang Asli groups in part,
are descended from the original Pleistocene inhabitants of the Malay Peninsula. These
novel haplogroups diverge from the same set of founder types as the haplogroups found
across the rest of Eurasia; that they diverge from close to the roots of these founder
types suggests they are of considerable antiquity. This, along with expansion dates of
-60,000 obtained in this study, suggests that only a single, early 'out of Africa' event
took place which led to the peopling of the rest of the world by modem humans.

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