Y chromosomes and mtDNA from the Maldives

 

Of interest from the paper:

The haplogroup J(M304) Y chromosomes are all in subgroup J2(M172).

...

However, Eaaswarkhanth et al. (2010) report that Muslims and non-Muslims in India largely have the same Y-haplogroup frequency distribution, except that in Muslims low frequencies of Y-E1b1b1a(M78), Y-J(M304)(xJ2(M172)), and Y-G(M201) are found that are absent in non-Muslims (Eaaswarkhanth et al., 2010). In our Maldivian sample, none of those Y-haplogroups were found.

AJPA DOI: 10.1002/ajpa.22256
Indian ocean crossroads: Human genetic origin and population structure in the maldives
Jeroen Pijpe et al.
The Maldives are an 850 km-long string of atolls located centrally in the northern Indian Ocean basin. Because of this geographic situation, the present-day Maldivian population has potential for uncovering genetic signatures of historic migration events in the region. We therefore studied autosomal DNA-, mitochondrial DNA-, and Y-chromosomal DNA markers in a representative sample of 141 unrelated Maldivians, with 119 from six major settlements. We found a total of 63 different mtDNA haplotypes that could be allocated to 29 mtDNA haplogroups, mostly within the M, R, and U clades. We found 66 different Y-STR haplotypes in 10 Y-chromosome haplogroups, predominantly H1, J2, L, R1a1a, and R2. Parental admixture analysis for mtDNA- and Y-haplogroup data indicates a strong genetic link between the Maldive Islands and mainland South Asia, and excludes significant gene flow from Southeast Asia. Paternal admixture from West Asia is detected, but cannot be distinguished from admixture from South Asia. Maternal admixture from West Asia is excluded. Within the Maldives, we find a subtle genetic substructure in all marker systems that is not directly related to geographic distance or linguistic dialect. We found reduced Y-STR diversity and reduced male-mediated gene flow between atolls, suggesting independent male founder effects for each atoll. Detected reduced female-mediated gene flow between atolls confirms a Maldives-specific history of matrilocality. In conclusion, our new genetic data agree with the commonly reported Maldivian ancestry in South Asia, but furthermore suggest multiple, independent immigration events and asymmetrical migration of females and males across the archipelago. Am J Phys Anthropol 000:000–000, 2013. © 2013 Wiley Periodicals, Inc.

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Connections between Indus Valley and Mesopotamia

 

Of interest from the paper:

Based on this distribution of values, it would appear from our preliminary analysis that almost half of the individuals sampled from the Harappa cemetery have isotope values outside the local baseline (0.7158-0.7189). Most of these individuals have values below the Harappa range. In addition, there are at least three non-local individuals with higher values, including one with an extremely isotope ratio that cannot be from the Harappa region. A more detailed discussion of the Harappa samples will be presented in a future publication on the Harappa cemetery, but it is clear that many of what appear to be local individuals at Harappa are females and they are associated in burial with nearby males who are clearly not local. These preliminary patterns require further testing before major conclusions can be proposed, but it does suggest that they represent a unique population of people from multiple regions of the Indus valley or beyond.

Journal of Archaeological Science
Volume 40, Issue 5, May 2013, Pages 2286–2297
A new approach to tracking connections between the Indus Valley and Mesopotamia: initial results of strontium isotope analyses from Harappa and Ur
J. Mark Kenoyer et al.
Exchange and interaction between early state-level societies in Mesopotamia and the Indus Valley during the 3rd millennium BC has been documented for some time. The study of this interaction has been dominated by the analysis of artifacts such as carnelian beads and marine shell, along with limited textual evidence. With the aid of strontium, carbon, and oxygen isotopes, it is now possible to develop more direct means for determining the presence of non-local people in both regions. This preliminary study of tooth enamel from individuals buried at Harappa and at the Royal Cemetery of Ur, indicates that it should be feasible to identify Harappans in Mesopotamia. It is also possible to examine the mobility of individuals from communities within the greater Indus Valley region.
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The case for earlier Out-of-Africa (Boivin et al. 2013)

The case for earlier Out-of-Africa (Boivin et al. 2013)

An informative review critical of the ~60kya coastal-Out-of-Africa hypothesis. On the left, the authors' estimate of the distribution of hominin groups during MIS5.

From the paper:

Another under-appreciated issue is the anomalous nature of the genetic evidence for a rapid spread of modern humans from Africa to Asia. Echoing the fossil date anomaly, the mtDNA branch lengths for sampled populations are longest for those which are farthest east, in Near Oceania, and shortest in the Asian areas that would have been encountered first (Merriwether et al., 2005; Oppenheimer, 2009). The real problem, however, is that the variation in branch lengths suggests that a single genotype engaged in the expansion actually existed for 30 ka, which does not support a rapid expansion. The anomaly can be explained by what we call an an ‘M buffer’ effect (see Supplementary material A) which implies that the branch ages we observe are considerable underestimates of the time of arrival of the genotype to these areas. Such anomalously long-lived genotypes have been directly observed through ancient DNA in species such as the Iberian lynx (Dalen et al., 2011).

and:

We have focused here on the possibility that the modern human exit recorded by fossil evidence in the Levant in MIS 5 does not represent a failed dispersal, and that in fact our species was not only in the Levant but also the Arabian peninsula during this marine isotope stage, and spread to India before the Toba eruption at 74 ka (Petraglia et al., 2007). Another valid hypothesis we do not explore here is that H. sapiens was able to leave Africa in MIS 6 via a grassland corridor (Frumkin et al., 2011; see also Scally and Durbin, 2012). Yet another is that our species dispersed out of Africa shortly after its first appearance c. 195 ka, in MIS 7 (Dennell and Roebroeks, 2005: 1102). One other possibility is that there were several, separate dispersals of our species out of Africa (Dennell and Petraglia, 2012). At the same time, we acknowledge that major demographic changes occurred in MIS 4 and MIS 3, perhaps explaining the relatively young mtDNA coalescence age in living populations. The increasing evidence for complexity as well as the clear patterns of bias for all records, whether archaeological, fossil or genetic, suggests the need for an open mind to multiple scenarios for Out of Africa, as well as for more rather than less complex models of H. sapiens dispersal across Eurasia.

Quaternary International doi:10.1016/j.quaint.2013.01.008

Human Dispersal Across Diverse Environments of Asia during the Upper Pleistocene

Nicole Boivin et al.

The initial out of Africa dispersal of H. sapiens, which saw anatomically modern humans reach the Levant in Marine Isotope Stage 5, is generally regarded as a ‘failed dispersal’. Fossil, archaeological and genetic findings are seen to converge around a consensus view that a single population of H. sapiens exited Africa sometime around 60 thousand years ago (ka), and rapidly reached Australia by following a coastal dispersal corridor. We challenge the notion that current evidence supports this straightforward model. We argue that the fossil and archaeological records are too incomplete, the coastal route too problematic, and recent genomic evidence too incompatible for researchers not to remain fully open to other hypotheses. We specifically explore the possibility of a sustained exit by anatomically modern humans, drawing in particular upon palaeoenvironmental data across southern Asia to demonstrate its feasibility. Current archaeological, genetic and fossil data are not incompatible with the model presented, and appear to increasingly favour a more complex out of Africa scenario involving multiple exits, varying terrestrial routes, a sub-divided African source population, slower progress to Australia, and a degree of interbreeding with archaic varieties of Homo.

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Gene flow between Indian populations and Australasia ~4,000 years ago

Gene flow between Indian populations and Australasia ~4,000 years ago

Only the press release is available so far, I will add the paper abstract when I see it on the PNAS website:

Researcher Irina Pugach and colleagues now analysed genetic variation from across the genome from aboriginal Australians, New Guineans, island Southeast Asians, and Indians. Their findings suggest substantial gene flow from India to Australia 4,230 years ago. i.e. during the Holocene and well before European contact. “Interestingly,” says Pugach, “this date also coincides with many changes in the archaeological record of Australia, which include a sudden change in plant processing and stone tool technologies, with microliths appearing for the first time, and the first appearance of the dingo in the fossil record. Since we detect inflow of genes from India into Australia at around the same time, it is likely that these changes were related to this migration.” 

Their analyses also reveal a common origin for populations from Australia, New Guinea and the Mamanwa – a Negrito group from the Philippines – and they estimated that these groups split from each other about 36,000 years ago. Mark Stoneking says: “This finding supports the view that these populations represent the descendants of an early ‘southern route’ migration out of Africa, while other populations in the region arrived later by a separate dispersal.“ This also indicates that Australians and New Guineans diverged early in the history of Sahul, and not when the lands were separated by rising sea waters around 8,000 years ago.

A relationship between Indian and Australasian populations has long been suspected on various grounds (e.g., HGDP Papuans often show membership in a "South Asian" ancestral component at low levels of resolution). It will be interesting to see the model proposed in the new paper about the admixture event leading to modern Australasians.

UPDATE: Ed Yong covers the story in Nature News:

Some aboriginal Australians can trace as much as 11% of their genomes to migrants who reached the island around 4,000 years ago from India, a study suggests. Along with their genes, the migrants brought different tool-making techniques and the ancestors of the dingo, researchers say1.

From World News Australia:

The study suggests that in addition to an earlier northern route of migration out of Africa, into Asia, and then South East Asia about 60,000 to 70,000 years ago, the second wave occurred much later, arriving during the Holocene period about 4,230 years ago.
...
“About that point in the archaeological record, there were significant changes in the use of stone tools, in hunting techniques and significantly, the introduction of the dingo,” Professor Cooper said.
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There are other theories that may support the evidence of a more recent influx of migrants from India, including that they brought with them a disease of epidemic proportions that wiped out earlier Aboriginal populations.

UPDATE II: I added the abstract.

PNAS doi: 10.1073/pnas.1211927110

Genome-wide data substantiate Holocene gene flow from India to Australia 

Irina Pugach et al.

The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early “southern route” migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.

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