Doubt cast on Tam Pa Ling age

For reference, see the post on the original article:

• Tam Pa Ling: modern humans in Southeast Asia at 63-46ka

From a criticism of the original paper:

Hence, contrary to the authors' assertion that TPL1 has a “minimum secured age of 46 ka and a maximum age of ∼63 ka”, the published stratigraphy, if correct, indicates that the TPL1 specimen is no older than 46 ka. TPL1’s status as “the earliest well-dated modern human fossil east of the Jordan Valley” also appears weak compared with the Liujiang specimen dated to ∼153 ka (3), the Callao Cave fossil in the Philippines dated to 67 ka (4), and, above all, the ∼100 ka modern fossil from Zhirendong (5), discovered only 484 km northeast of Tam Pa Ling in Southern China.

Irreconcilable differences between stratigraphy and direct dating cast doubts upon the status of Tam Pa Ling fossil

Alain Pierret et al.

Link

... and from a reply to the criticism by the authors:

They question the validity of the dating because of an apparent “reverse stratigraphy” (Fig. 1), whereby “older” dates are located higher in the section [i.e., 51.4 (14C) at 2.1 m] and “younger” dates are at the bottom of the section [i.e., 48 ka (optically stimulated luminescence [OSL]) and >49.2 ka (14C) at 4.3 m] (2). This criticism ignores the presented SEs (table 2 and table S1 in ref. 1), which make the results statistically equivalent (Table 1). More importantly, they ignore that the radiocarbon results are well beyond the accepted radiocarbon barrier of ∼40 ka (3), indicating that the charcoal has a minimum age of ∼40 ka. Bearing in mind these problems, we have conservatively estimated the burial age to be ∼46 ka according to the luminescence dating of the sediments. As the luminescence results are stratigraphically consistent, we perceive no irreconcilable differences between the stratigraphy and dating.

...

Finally, we interpret TPL1 as the earliest human fossil that is both well-dated and fully modern in morphology. Zhirendong demonstrates a mixture of archaic and modern traits, making it significant but not fully modern in appearance (4). Similarly, the metatarsal from Callao Cave is only diagnostic to the genus Homo given that it falls within “the morphological and size ranges of Homo habilis and H. floresiensis” (ref. 5, p. 123). Although the modernity of the Liujiang fossil is not questioned, it has no direct date and no secure stratigraphic provenance. It has been variably dated to ca. 20 ka, ca. 67 ka, 111 to 139 ka, and >153 ka (6), and this uncertain stratigraphic context has prevented many scholars from accepting any of the dates currently attributed to it (6).

Reply to Pierret et al.: Stratigraphic and dating consistency reinforces the status of Tam Pa Ling fossil

Fabrice Demeter et al.

Link

Southeast Asian Neolithic dogs

Southeast Asian Neolithic dogs

From the paper:

Nevertheless, the close phylogenetic clustering of haplotypes from Thailand, Brunei, Bali, and the Philippines suggests these populations originated from the same source, consistent with a single migration event, whereas the dingoes, NGSDs, and dogs from Taiwan appear sufficiently distinct from these to reflect a distinct migration event (Fig. 2b-c). The clustering of the three Island Southeast Asian populations with Thailand also was more consistent with origination from Mainland Southeast Asia than Taiwan (in agreement with mtDNA findings of Oskarsson et al. 2011).

and:

In light of findings from the present study, it seems clear that both post-Victorian and Neolithic exchanges link eastern and western Eurasian dogs. However, the cause of post-Victorian haplotype sharing between Western breed dogs and Southeast Asian village dogs apparently reflects very recent introduction of Western dogs to the East rather than extraction of Eastern dogs to create Western breeds during the Victorian Era.

and:

Specifically, our aging of this European haplogroup to 5,800 (±SE = 1750) or 8,400 (±SE = 2500) years (depending on the dingo calibration to 3,500 or 5,000 years, respectively) suggests that the connection between pre-Victorian European and Southeast Asian dogs traces only to the Neolithic period and is not of sufficient antiquity to support the hypothesis of a single origin of dogs from Southeast Asia. Thus, although future studies are needed to combine the Y SNPs and STR markers in a geographically broader sampling of dogs than was considered here, our findings support the hypothesis for a massive Neolithic expansion of dogs from Southeast Asia rather than a Paleolithic origin of dogs from this region.

This massive Neolithic expansion of Southeast Asian dogs is testable by looking at early European dogs; these ought not to belong to haplogroup H1. It would also be interesting to speculate about the trade routes and/or population movements that facilitated the spread of dogs from SE Asia to Europe during the Neolithic.

Mol Biol Evol (2013) doi: 10.1093/molbev/mst027

Y chromosome analysis of dingoes and Southeast Asian village dogs suggests a Neolithic continental expansion from Southeast Asia followed by multiple Austronesian dispersals

Benjamin N. Sacks et al.

Dogs originated >14,000 BP, but the location(s) where they first arose is uncertain. The earliest archaeological evidence of ancient dogs was discovered in Europe and the Middle East, some 5–7 millennia before that from Southeast Asia. However, mitochondrial DNA analyses suggest that most modern dogs derive from Southeast Asia, which has fueled the controversial hypothesis that dog domestication originated in this region despite the lack of supporting archaeological evidence. We propose and investigate with Y chromosomes an alternative hypothesis for the proximate origins of dogs from Southeast Asia--a massive Neolithic expansion of dogs from this region that largely replaced more primitive dogs to the west and north. Previous attempts to test matrilineal findings with independent patrilineal markers have lacked the necessary genealogical resolution and mutation rate estimates. Here, we used Y chromosome genotypes, composed of 29 SNPs and 5 STRs, from 338 Australian dingoes, New Guinea singing dogs, and village dogs from Island Southeast Asia, along with modern European breed dogs, to estimate the evolutionary mutation rates of Y chromosome STRs based on calibration to the independently known age of the dingo population. Dingoes exhibited a unique haplogroup characterized by a single distinguishing SNP mutation and 14 STR haplotypes. The age of the European haplogroup was estimated to be only 1.7 times older than that of the dingo population, suggesting an origin during the Neolithic rather than the Paleolithic (as predicted by the Southeast Asian origins hypothesis). We hypothesize that isolation of Neolithic dogs from wolves in Southeast Asia was a key step accelerating their phenotypic transformation, enhancing their value in trade and as cargo, and enabling them to rapidly expand and replace more primitive dogs to the West. Our findings also suggest that dingoes could have arrived in Australia directly from Taiwan, independently of later dispersals of dogs through Thailand to Island Southeast Asia.

Link

Deep whole-genome sequencing of 100 Malays

Deep whole-genome sequencing of 100 Malays

The 1000 Genomes Project is the largest collection of full human genomes currently available, but most of its 2.5k samples have been sequenced at low coverage. One downside of this is that infrequent variants are often missed. If an individual is polymorphic at some site, then the chance of detecting this polymorphism increases with the number of reads covering that site. If a number of individuals are sampled, then polymorphisms that are common in the population will probably be detected in a few individuals even if a low number of reads is used for each of them; but, if they are infrequent, then they are more likely to be missed. Hence, low-coverage sequencing of population samples will tend to find common variants and will tend to miss less common variants relative to high-coverage sequencing.

This idea is intuitively correct, but the question of the added power of high-coverage sequencing to detect variants can only be addressed by giving the same individuals both low- and high-coverage sequencing. This is the topic of a new paper in AJHG which creates a useful comparison benchmark for the performance of the two types of sequencing methods. High-coverage sequencing may be needed for things like disease studies (because deleterious alleles tend to be low-frequency), or the study of recent human demography (because recent population growth has resulted in an abundance of low-frequency SNPs that have not had enough time to reach a high population frequency yet).

AJHG dx.doi.org/10.1016/j.ajhg.2012.12.005

Deep Whole-Genome Sequencing of 100 Southeast Asian Malays

Lai-Ping Wong et al.


Whole-genome sequencing across multiple samples in a population provides an unprecedented opportunity for comprehensively characterizing the polymorphic variants in the population. Although the 1000 Genomes Project (1KGP) has offered brief insights into the value of population-level sequencing, the low coverage has compromised the ability to confidently detect rare and low-frequency variants. In addition, the composition of populations in the 1KGP is not complete, despite the fact that the study design has been extended to more than 2,500 samples from more than 20 population groups. The Malays are one of the Austronesian groups predominantly present in Southeast Asia and Oceania, and the Singapore Sequencing Malay Project (SSMP) aims to perform deep whole-genome sequencing of 100 healthy Malays. By sequencing at a minimum of 30? coverage, we have illustrated the higher sensitivity at detecting low-frequency and rare variants and the ability to investigate the presence of hotspots of functional mutations. Compared to the low-pass sequencing in the 1KGP, the deeper coverage allows more functional variants to be identified for each person. A comparison of the fidelity of genotype imputation of Malays indicated that a population-specific reference panel, such as the SSMP, outperforms a cosmopolitan panel with larger number of individuals for common SNPs. For lower-frequency (less than 5%) markers, a larger number of individuals might have to be whole-genome sequenced so that the accuracy currently afforded by the 1KGP can be achieved. The SSMP data are expected to be the benchmark for evaluating the value of deep population-level sequencing versus low-pass sequencing, especially in populations that are poorly represented in population-genetics studies.

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