Is O2a-M95 (now O1b1a1a-M95) oldest lineage in the region (SEA) associated with Hoabinhian hunter-

gatherers? and not Neolithic farmers spreading from Southern China to ISEA and SA around 4000 BP?

There are some problems when we equating uniparental markers (haplogroups) with populations or
cultures. Uniparental markers do not experience recombinations, but they are good tools to trace
genealogical ancestry and its origins. Genetic ancestry, OTOH, based on nuclear genome which
experiencing recombinations. It is difficult to distinguish present-day ethnolinguistic groups based on
their genetic ancestry (i.e. Austroasiatic-speaking populations with paternal markers M95, but
autosomally a mixture between Hoabinhian-like hunter-gatherers and Yangtze River rice farmers with
proportions ~30:70; Hugh McColl et al 2018), because they are admixed populations. Before 4000 years
ago, M95 marker could belong to SEA hunter-gatherers. But when we look into Man Bac site (~4000 BP),
admixture between these hunters and incoming farmers from Yangtze River, resulting distinct genetic
ancestry (widely known as Austroasiatic component) which now dominating Western Indonesian
populations.

How do we know if M95 marker in Western Indonesia (WI) already widespread before Neolithic
expansion from MSEA? The better way to answer this matter is by comparing M95 STR haplotype
diversity among ethnolinguistic groups in MSEA, East India, Peninsular Malaysia and Western Indonesia.

Based on Y-STR data the coalescent time of Indian M95 haplogroup was estimated to be >10 Kya
(Chaubey et al 2011; Zhang et al 2015). Recently, the reconstructed phylogeny of 8.8Mb region of Y
chromosome data showed that Indian M95 lineages coalesce within a clade nested within
East/Southeast Asian within the last ~5–7 Kya (Karmin et al 2015). This date estimate sets the upper
boundary for the main episode of gene fow of Y chromosomes from Southeast Asia to India. This is proof
that M95 marker existed in SEA before Neolithic expansion 4000 years ago. A-4400 years old individual
from Tanshishan (coastal Fujian) and 3445 years old Man Bac individual belong to subclade of M95
haplogroup. A-6000 years old Tam Hang (Laos) also belongs to subclade of M95. A-5850 years old Daxi in
China belongs to M95 haplogroup.

Unfortunately, we only have ancient sample belongs to subclade of M95 in Western Indonesia (Loyang
Ujung Karang dated to 2152 years BP; although, the presence of humans with Hoabinhian culture in
Loyang Ujung Karang and Loyang Mendale could be traced back to 5000 years ago). And then, we have
M95 arrived in Gua Cha, Malay Peninsula, around 2500 years ago. Gua Cha man's genetic ancestry looks
like present-day Austroasiatic-speaking groups (McColl 2018). While we can predict demographic
movements of M95 based on STR haplotype diversity and ancient DNA data, we still lack of older
samples from Western Indonesia predate Neolithic expansions. So, I'm not sure if M95 haplotype
existed in older populations of western ISEA.

Another issue regarding olders M95 among hunter-gatherers in western ISEA is dating the migration
events. Based on distributions of STR alleles, there's possibility that there are two different migrations of
M95 into SE Asian islands. Lower alleles size in Banjarmasin, Palu,
Mataram, Pekanbaru, and Toraja populations; and higher alleles size in Java, Bali, Malay, and Flores.
ISEA M95 age estimates based on the STR variance, the time taken for the population to accumulate
variance that is observed today (not the time of origin of the haplogroup), is about 7200 years old. This
contrasts with overall M95 expansion time of 6.4-5.6 Kya based on STR variance.

The geographic origin of a paternal lineage has a higher probability of originating in a region with many
populations showing high frequency and high STR variance of the lineage than a region with a single
population with similar attributes. This could make ISEA as a candidate of M95 deep antiquity, but not
place of origin because lack of ancestral haplotype and its subclades. Unfortunately, ISEA often excluded
in M95 studies because of high frequency of M95 in Bali. Laos is still the best candidate for present-day
M95 haplotype origins

From genetic ancestry perspective, populations with higher M95 markers tend to have genetic
component that already admixed (Hoabinhian-like HG and Yangtze River farmers). Their genetic
components are different from Hoabinhian-like hunters or Basal Asian in Melinda Yang et al 2020. With
this in mind, IMO, it looks like that M95 in present-day WI populations derived from Neolithic expansion
postdated Neolithic expansion.

The most important thing to consider is understanding the mosaic of admixture events with adjacent
population groups which could be explained by ancient DNA data. These aDNA data help us
understanding Austroasiatic ancestry in M95 individuals and its relationship with Hoabinhian-like
hunter-gatherers or basal Asians. If M95 have a deep antiquity in ISEA, it would be detected as basal
Asians. Many ancient SEA structure show that Western Indonesia populations lack Hoabinhian-like
hunter-gatherers or basal Asians ancestry. So, it's safe to conclude that present-day M95 most likely
derived from Neolithic expansion, and not the oldest layer. Australo-Papuans are still the oldest layer
albeit at lower frequency among WI populations.

Note: in search of population movements, avoid linguistic and cultural inferences. It'll only lead to
confusion. Languages and cultures evolve faster than genes.