When did humans first arrive in greater Australia and why is it important to know?

42,000-year-old worked and pigment-stained Nautilus shell from Jerimalai (Timor-Leste): Evidence for an early coastal adaptation in ISEA

In this paper, we describe worked and pigment-stained Nautilus shell artefacts recovered from Jerimalai, Timor-Leste. Two of these artefacts come from contexts dating to between 38,000 and 42,000 cal. BP (calibrated years before present), and exhibit manufacturing traces (drilling, pressure flaking, grinding), as well as red colourant staining. Through describing more complete Nautilus shell ornaments from younger levels from this same site (>15,900, 9500, and 5000 cal. BP), we demonstrate that those dating to the initial occupation period of Jerimalai are of anthropogenic origin. The identification of such early shell working examples of pelagic shell in Island Southeast Asia not only adds to our growing understanding of the importance of marine resources to the earliest modern human communities in this region, but also indicates that a remarkably enduring shell working tradition was enacted in this area of the globe. Additionally, these artefacts provide the first material culture evidence that the inhabitants of Jerimalai were not only exploiting coastal resources for their nutritional requirements, but also incorporating these materials into their social technologies, and by extension, their social systems. In other words, we argue that the people of Jerimalai were already practicing a developed coastal adaptation by at least 42,000 cal. BP.

Investigating sex-specific dynamics using uniparental markers: West New Guinea as a case study

Mitochondrial DNA (mtDNA) and Y chromosome (NRY) genetic markers have been often contrasted to investigate sex-specific dynamics. Traditionally, isolation by distance, intrapopulation genetic diversity and population differentiation are estimated from both markers and compared. Two possible sources of bias are often neglected. First, kilometric distances are frequently used as predictor of the connectivity between groups, hiding the role played by environmental features at a microgeographic scale. Second, the comparison of intrapopulation diversity and population differentiation between mtDNA and NRY is hampered by their different mutational mechanisms and rates. Here, we show how to account for these biases by analyzing from a different perspective a published dataset of eight West New Guinea (WNG) populations for which mtDNA control region sequences and seven linked NRY microsatellites had been typed. First, we modeled the connectivity among sampled populations by computing the number of days required to travel between groups. Then, we investigated the differences between the two sexes accounting for the molecular characteristics of the markers examined to obtain estimates on the product of the effective population size and the migration rate among demes (Nm). We achieved this goal by studying the shape of the gene genealogy at several sampling levels and using spatial explicit simulations. Both the direction and the rate of migration differ between male and females, with an Nm estimated to be >6 times higher in the latter under many evolutionary scenarios. We finally highlight the importance of applying metapopulation models when analyzing the genetic diversity of a species. We have applied the prediction of the sampling theory in a meta-population and we have corroborated our finding using spatial explicit simulations. Both approaches are fundamentally meant to deal with structured populations: we strongly believe in the importance of tacking structure into account when inferring the demographic history of a species.

Autosomal microsatellite variability of the Arrernte people of Australia

The genomic diversity of the Arrernte people of Australia or caterpillar people was investigated utilizing 13 autosomal short tandem repeat (STR) markers. Significant departures from Hardy-Weinberg equilibrium were detected at the D18S51, TPOX and CSF1PO loci, which persisted after applying the Bonferroni correction. Gene diversity values oscillate between 0.6302 (CSF1PO) and 0.8731 (D21S11). Observed heterozygosity (Ho) ranges from 0.2632 (D18S51) to 0.8333 (vWA) and is lower than the expected heterozygosity (He) for 12 of the 13 loci analyzed. The genetic relationships of the Arrernte with Middle Eastern, East Asian, South Asian and Indian populations were analyzed by distance-based methods, including Neighbor-Joining trees and nonmetric multidimensional scaling. In addition, the genetic contribution of the populations included in the analysis to the Arrernte gene pool was estimated utilizing weighted least square coefficients. Although the Arrernte population exhibits a remarkable level of genetic differentiation, results of the phylogeographic analyses based on autosomal microsatellite data suggest a certain degree of genetic relatedness between the Arrernte tribe of Australia and populations from the Indian subcontinent. In contrast, the STR diversity analyses failed to detect substantial East Asian contribution to the genetic background of the Arrernte group.

Expanding Southwest Pacific Mitochondrial Haplogroups P and Q

Modern humans have occupied New Guinea and the nearby Bismarck and Solomon archipelagos of Island Melanesia for at least 40,000 years. Previous mitochondrial DNA (mtDNA) studies indicated that two common lineages in this region, haplogroups P and Q, were particularly diverse, with the coalescence for P considered significantly older than that for Q. In this study, we expand the definition of haplogroup Q so that it includes three major branches, each separated by multiple mutational distinctions (Q1, equivalent to the earlier definition of Q, plus Q2 and Q3). We report three whole-mtDNA genomes that establish Q2 as a major Q branch. In addition, we describe 314 control region sequences that belong to the expanded haplogroups P and Q from our Southwest Pacific collection. The coalescence dates for the largest P and Q branches (P1 and Q1) are similar to each other (approximately 50,000 years old) and considerably older than prior estimates. Newly identified Q2, which was found in Island Melanesian samples just to the east, is somewhat younger by more than 10,000 years. Our coalescence estimates should be more reliable than prior ones because they were based on significantly larger samples as well as complete mtDNA-coding region sequencing. Our estimates are roughly in accord with the current suggested dates for the first settlement of New Guinea-Sahul. The phylogeography of P and Q indicates almost total (female) isolation of ancient New Guinea-Island Melanesia from Australia that may have existed from the time of the first settlement. While Q subsequently diversified extensively in New Guinea-Island Melanesia, it has not been found in Australia. The only shared mtDNA haplogroup between Australia and New Guinea identified to date remains one minor branch of P.

Demographic estimates from Y chromosome microsatellite polymorphisms: analysis of a worldwide sample

Polymorphisms in microsatellites on the human Y chromosome have been used to estimate important demographic parameters of human history. We compare two coalescent-based statistical methods that give estimates for a number of demographic parameters using the seven Y chromosome polymorphisms in the HGDP-CEPH Cell Line Panel, a collection of samples from 52 worldwide populations. The estimates for the time to the most recent common ancestor vary according to the method used and the assumptions about the prior distributions of model parameters, but are generally consistent with other global Y chromosome studies. We explore the sensitivity of these results to assumptions about the prior distributions and the evolutionary models themselves.

Explaining the Pleistocene megafaunal extinctions: models, chronologies, and assumptions

Understanding of the Pleistocene megafaunal extinctions has been advanced recently by the application of simulation models and new developments in geochronological dating. Together these have been used to posit a rapid demise of megafauna due to over-hunting by invading humans. However, we demonstrate that the results of these extinction models are highly sensitive to implicit assumptions concerning the degree of prey naivety to human hunters. In addition, we show that in Greater Australia, where the extinctions occurred well before the end of the last Ice Age (unlike the North American situation), estimates of the duration of coexistence between humans and megafauna remain imprecise. Contrary to recent claims, the existing data do not prove the "blitzkrieg" model of overkill.

Mitochondrial DNA variability of West New Guinea populations

This paper reports human mitochondrial DNA variability in West New Guinea (the least known, western side of the island of New Guinea), not yet described from a molecular perspective. The study was carried out on 202 subjects from 12 ethnic groups, belonging to six different Papuan language families, representative of both mountain and coastal plain areas. Mitochondrial DNA hypervariable region 1 (HVS 1) and the presence of the 9-bp deletion (intergenic region COII-tRNA(Lys)) were investigated. HVS 1 sequencing identified 73 polymorphic sites defining 89 haplotypes; the 9-bp deletion, which is considered a marker of Austronesian migration in the Pacific, was found to be absent in the whole West New Guinea study sample. Statistical analysis applied to the resulting haplotypes reveal high heterogeneity and an intersecting distribution of genetic variability in these populations, despite their cultural and geographic diversity. The results of subsequent phylogenetic approaches subdivide mtDNA diversity in West New Guinea into three main clusters (groups I-III), defined by sets of polymorphisms which are also shared by some individuals from Papua New Guinea. Comparisons with worldwide HVS 1 sequences stored in the MitBASE database show the absence of these patterns outside Oceania and a few Indonesian subjects, who also lack the 9-bp deletion. This finding, which is consistent with the effects of genetic drift and prolonged isolation of West New Guinea populations, lead us to regard these patterns as New Guinea population markers, which may harbor the genetic memory of the earliest human migrations to the island.

Mitochondrial DNA variation in an aboriginal Australian population: evidence for genetic isolation and regional differentiation

The mitochondrial DNA (mt-DNA) variation of in the Walbiri tribe of the Northern Territories, Australia, was characterized by high resolution restriction fragment length polymorphism (HR-RFLP) analysis and control region sequencing. Surveying each mt-DNA for RFLPs with 14 different restriction enzymes detected 24 distinct haplotypes, whereas direct sequencing of the control region hypervariable segment I (HVS-I) of these mt-DNAs revealed 34 distinct sequences. Phylogenetic analysis of the RFLP haplotype and HVS-I sequence data depicted that the Walbiri have ten distinct haplotype groups (haplogroups), or mt-DNA lineages. The majority of the Walbiri RFLP haplotypes lacked polymorphisms common to Asian populations. In fact, most of the Walbiri haplogroups were unique to this population, although a few appeared to be subbranches of larger clusters of mt-DNAs that included other Aboriginal Australian and/or Papua New Guinea haplotypes. The similarity of these haplotypes suggested that Aboriginal Australian and Papua New Guinea populations may have once shared an ancient ancestral population(s), and then rapidly diverged from each other once geographically separated. Overall, the mt-DNA data corroborate the genetic uniqueness of Aboriginal Australian populations.

Sea level change through the last glacial cycle

Sea level change during the Quaternary is primarily a consequence of the cyclic growth and decay of ice sheets, resulting in a complex spatial and temporal pattern. Observations of this variability provide constraints on the timing, rates, and magnitudes of the changes in ice mass during a glacial cycle, as well as more limited information on the distribution of ice between the major ice sheets at any time. Observations of glacially induced sea level changes also provide information on the response of the mantle to surface loading on time scales of 10(3) to 10(5) years. Regional analyses indicate that the earth-response function is depth dependent as well as spatially variable. Comprehensive models of sea level change enable the migration of coastlines to be predicted during glacial cycles, including the anthropologically important period from about 60,000 to 20,000 years ago.

The revolution that wasn't: a new interpretation of the origin of modern human behavior

Proponents of the model known as the "human revolution" claim that modern human behaviors arose suddenly, and nearly simultaneously, throughout the Old World ca. 40-50 ka. This fundamental behavioral shift is purported to signal a cognitive advance, a possible reorganization of the brain, and the origin of language. Because the earliest modern human fossils, Homo sapiens sensu stricto, are found in Africa and the adjacent region of the Levant at >100 ka, the "human revolution" model creates a time lag between the appearance of anatomical modernity and perceived behavioral modernity, and creates the impression that the earliest modern Africans were behaviorally primitive. This view of events stems from a profound Eurocentric bias and a failure to appreciate the depth and breadth of the African archaeological record. In fact, many of the components of the "human revolution" claimed to appear at 40-50 ka are found in the African Middle Stone Age tens of thousands of years earlier. These features include blade and microlithic technology, bone tools, increased geographic range, specialized hunting, the use of aquatic resources, long distance trade, systematic processing and use of pigment, and art and decoration. These items do not occur suddenly together as predicted by the "human revolution" model, but at sites that are widely separated in space and time. This suggests a gradual assembling of the package of modern human behaviors in Africa, and its later export to other regions of the Old World. The African Middle and early Late Pleistocene hominid fossil record is fairly continuous and in it can be recognized a number of probably distinct species that provide plausible ancestors for H. sapiens. The appearance of Middle Stone Age technology and the first signs of modern behavior coincide with the appearance of fossils that have been attributed to H. helmei, suggesting the behavior of H. helmei is distinct from that of earlier hominid species and quite similar to that of modern people. If on anatomical and behavioral grounds H. helmei is sunk into H. sapiens, the origin of our species is linked with the appearance of Middle Stone Age technology at 250-300 ka.

Short tandem-repeat polymorphism/alu haplotype variation at the PLAT locus: implications for modern human origins

Two dinucleotide short tandem-repeat polymorphisms (STRPs) and a polymorphic Alu element spanning a 22-kb region of the PLAT locus on chromosome 8p12-q11.2 were typed in 1,287-1,420 individuals originating from 30 geographically diverse human populations, as well as in 29 great apes. These data were analyzed as haplotypes consisting of each of the dinucleotide repeats and the flanking Alu insertion/deletion polymorphism. The global pattern of STRP/Alu haplotype variation and linkage disequilibrium (LD) is informative for the reconstruction of human evolutionary history. Sub-Saharan African populations have high levels of haplotype diversity within and between populations, relative to non-Africans, and have highly divergent patterns of LD. Non-African populations have both a subset of the haplotype diversity present in Africa and a distinct pattern of LD. The pattern of haplotype variation and LD observed at the PLAT locus suggests a recent common ancestry of non-African populations, from a small population originating in eastern Africa. These data indicate that, throughout much of modern human history, sub-Saharan Africa has maintained both a large effective population size and a high level of population substructure. Additionally, Papua New Guinean and Micronesian populations have rare haplotypes observed otherwise only in African populations, suggesting ancient gene flow from Africa into Papua New Guinea, as well as gene flow between Melanesian and Micronesian populations.

Lapa vermelha IV Hominid 1: morphological affinities of the earliest known American

Several studies concerning the extra-continental morphological affinities of Paleo-Indian skeletons, carried out independently in South and North America, have indicated that the Americas were first occupied by non-Mongoloids that made their way to the New World through the Bering Strait in ancient times. The first South Americans show a clear resemblance to modern South Pacific and African populations, while the first North Americans seem to be at an unresolved morphological position between modern South Pacific and Europeans. In none of these analyses the first Americans show any resemblance to either northeast Asians or modern native Americans. So far, these studies have included affirmed and putative early skeletons thought to date between 8,000 and 10,000 years B.P. In this work the extra-continental morphological affinities of a Paleo-Indian skeleton well dated between 11,000 and 11,500 years B.P. (Lapa Vermelha IV Hominid 1, or "Luzia") is investigated, using as comparative samples Howells' (1989) world-wide modern series and Habgood's (1985) Old World Late Pleistocene fossil hominids. The comparison between Lapa Vermelha IV Hominid 1 and Howells' series was based on canonical variate analysis, including 45 size-corrected craniometric variables, while the comparison with fossil hominids was based on principal component analysis, including 16 size-corrected variables. In the first case, Lapa Vermelha IV Hominid 1 exhibited an undisputed morphological affinity firstly with Africans and secondly with South Pacific populations. In the second comparison, the earliest known American skeleton had its closest similarities with early Australians, Zhoukoudian Upper Cave 103, and Taforalt 18. The results obtained clearly confirm the idea that the Americas were first colonized by a generalized Homo sapiens population which inhabited East Asia in the Late Pleistocene, before the definition of the classic Mongoloid morphology.

Peopling of Sahul: mtDNA variation in aboriginal Australian and Papua New Guinean populations

We examined genetic affinities of Aboriginal Australian and New Guinean populations by using nucleotide variation in the two hypervariable segments of the mtDNA control region (CR). A total of 318 individuals from highland Papua New Guinea (PNG), coastal PNG, and Aboriginal Australian populations were typed with a panel of 29 sequence-specific oligonucleotide (SSO) probes. The SSO-probe panel included five new probes that were used to type an additional 1,037 individuals from several Asian populations. The SSO-type data guided the selection of 78 individuals from Australia and east Indonesia for CR sequencing. A gene tree of these CR sequences, combined with published sequences from worldwide populations, contains two previously identified highland PNG clusters that do not include any Aboriginal Australians; the highland PNG clusters have coalescent time estimates of approximately 80,000 and 122,000 years ago, suggesting ancient isolation and genetic drift. SSO-type data indicate that 84% of the sample of PNG highlander mtDNA belong to these two clusters. In contrast, the Aboriginal Australian sequences are intermingled throughout the tree and cluster with sequences from multiple populations. Phylogenetic and multidimensional-scaling analyses of CR sequences and SSO types split PNG highland and Aboriginal Australian populations and link Aboriginal Australian populations with populations from the subcontinent of India. These mtDNA results do not support a close relationship between Aboriginal Australian and PNG populations but instead suggest multiple migrations in the peopling of Sahul.

Distribution of haplotypes from a chromosome 21 region distinguishes multiple prehistoric human migrations

Despite mounting genetic evidence implicating a recent origin of modern humans, the elucidation of early migratory gene-flow episodes remains incomplete. Geographic distribution of haplotypes may show traces of ancestral migrations. However, such evolutionary signatures can be erased easily by recombination and mutational perturbations. A 565-bp chromosome 21 region near the MX1 gene, which contains nine sites frequently polymorphic in human populations, has been found. It is unaffected by recombination and recurrent mutation and thus reflects only migratory history, genetic drift, and possibly selection. Geographic distribution of contemporary haplotypes implies distinctive prehistoric human migrations: one to Oceania, one to Asia and subsequently to America, and a third one predominantly to Europe. The findings with chromosome 21 are confirmed by independent evidence from a Y chromosome phylogeny. Loci of this type will help to decipher the evolutionary history of modern humans.