Joe Dortch

An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia

Whole-genome data indicate that early modern humans expanded into Australia 62,000 to 75,000 years ago. We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.

A genomic history of Aboriginal Australia

The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama–Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.

Fossil avian eggshell preserves ancient DNA

Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has approximately 125 times lower bacterial load than bone, making it a highly suitable substrate for high-throughput sequencing approaches. Importantly, the preservation of DNA in Pleistocene eggshell from Australia and Holocene deposits from Madagascar indicates that eggshell is an excellent substrate for the long-term preservation of DNA in warmer climates. The successful recovery of DNA from this substrate has implications in a number of scientific disciplines; most notably archaeology and palaeontology, where genotypes and/or DNA-based species identifications can add significantly to our understanding of diets, environments, past biodiversity and evolutionary processes.

The size of the largest marsupial and why it matters

We show that at 2786 kg, the largest known marsupial, Diprotodon optatum, was much larger than has previously been suggested. Our results contradict the conclusion that the maximum attainable body mass of an Australian marsupial has been constrained by low productivity.

Scrapheap Challenge: A novel bulk-bone metabarcoding method to investigate ancient DNA in faunal assemblages

Highly fragmented and morphologically indistinct fossil bone is common in archaeological and paleontological deposits but unfortunately it is of little use in compiling faunal assemblages. The development of a cost-effective methodology to taxonomically identify bulk bone is therefore a key challenge. Here, an ancient DNA methodology using high-throughput sequencing is developed to survey and analyse thousands of archaeological bones from southwest Australia. Fossils were collectively ground together depending on which of fifteen stratigraphical layers they were excavated from. By generating fifteen synthetic blends of bulk bone powder, each corresponding to a chronologically distinct layer, samples could be collectively analysed in an efficient manner. A diverse range of taxa, including endemic, extirpated and hitherto unrecorded taxa, dating back to c.46,000 years BP was characterized. The method is a novel, cost-effective use for unidentifiable bone fragments and a powerful molecular tool for surveying fossils that otherwise end up on the taxonomic “scrapheap”.

Genetic diversity loss in a biodiversity hotspot: Ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial

The extent of genetic diversity loss and former connectivity between fragmented populations are often unknown factors when studying endangered species. While genetic techniques are commonly applied in extant populations to assess temporal and spatial demographic changes, it is no substitute for directly measuring past diversity using ancient DNA (aDNA). We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci from 64 historical fossil and skin samples of the critically endangered Western Australian woylie (Bettongia penicillata ogilbyi), and compared them with 231 (n = 152 for mtDNA) modern samples. In modern woylie populations 15 mitochondrial control region (CR) haplotypes were identified. Interestingly, mtDNA CR data from only 29 historical samples demonstrated 15 previously unknown haplotypes and detected an extinct divergent clade. Through modelling, we estimated the loss of CR mtDNA diversity to be between 46% and 91% and estimated this to have occurred in the past 2000–4000 years in association with a dramatic population decline. In addition, we obtained near‐complete 11‐loci microsatellite profiles from 21 historical samples. In agreement with the mtDNA data, a number of ‘new’ microsatellite alleles was only detected in the historical populations despite extensive modern sampling, indicating a nuclear genetic diversity loss >20%. Calculations of genetic diversity (heterozygosity and allelic rarefaction) showed that these were significantly higher in the past and that there was a high degree of gene flow across the woylies historical range. These findings have an immediate impact on how the extant populations are managed and we recommend the implementation of an assisted migration programme to prevent further loss of genetic diversity. Our study demonstrates the value of integrating aDNA data into current‐day conservation strategies.

Test excavation at the Oyster Harbour stone fish traps, King George Sound, Western Australia: An investigation aimed at determining the construction method and maximum age of the structures

Abstract Several stone structures on the northern foreshore of Oyster Harbour, King George Sound, Western Australia, are documented in ethnohistorical accounts and traditionally regarded as ‘fish traps’ maintained and used by resident Aboriginal groups, around the late eighteenth-early nineteenth century. Test excavation at one structure (‘Trap 7’), undertaken at the request of the local Aboriginal community, did show the structure’s mode of construction, though failed to uncover datable materials in incontestable primary position whose radiocarbon age would show when the structure was built. The age of this structure’s original construction and fi rst use remains unknown, though it and other structures at this site presumably post-date mid-Holocene sea-level rise to present height, as is the case with other stone weir or trap complexes on the Southern Ocean coast.

Intergenerational archaeology: Exploring niche construction in southwest Australian zooarchaeology

Abstract Niche construction theory concerns the modification of environments by all organisms, and gives a new perspective on zooarchaeological records in southwest Australia. Aboriginal people in this region historically used fire to improve habitat and hunt animals, suggesting pre-European traditions of environmental management. Analysis of a new faunal record from the Leeuwin-Naturaliste Region, at the Wonitji Janga rockshelter, suggests post-European changes in Aboriginal hunting are the result of changed firing regimes or restrictions on traditional management techniques. These preliminary findings suggest that similar research planned for the Swan Coastal Plain, coupled with advances in ancient DNA analysis, will demonstrate past landscape modification.

Genetic diversity and drivers of dwarfism in extinct island emu populations

Australias iconic emu (Dromaius novaehollandiae novaehollandiae) is the only living representative of its genus, but fossil evidence and reports from early European explorers suggest that three island forms (at least two of which were dwarfs) became extinct during the nineteenth century. While one of these—the King Island emu—has been found to be conspecific with Australian mainland emus, little is known about how the other two forms—Kangaroo Island and Tasmanian emus—relate to the others, or even the size of Tasmanian emus. We present a comprehensive genetic and morphological analysis of Dromaius diversity, including data from one of the few definitively genuine Tasmanian emu specimens known. Our genetic analyses suggest that all the island populations represent sub-populations of mainland D. novaehollandiae. Further, the size of island emus and those on the mainland appears to scale linearly with island size but not time since isolation, suggesting that island size—and presumably concomitant limitations on resource availability—may be a more important driver of dwarfism in island emus, though its precise contribution to emu dwarfism remains to be confirmed.

Dingo scat-bone ‘signature patterns’: an actualistic study and comparison of wild and captive scat-bone assemblages and interpretation of bone fragments from Witchcliffe Rock Shelter, south western Australia

Abstract Dingoes are a likely contributor to late Holocene Australian archaeological sites and distinguishing bone refuse resulting from either human meals or dingo scavenging is a well-recognised problem. To date, little research has been undertaken to differentiate bone modifications caused by different Australian carnivores in archaeological assemblages. In addition, inconsistencies have been found between observations recorded from captive and wild contexts, confounding attempts to use the bone refuse of captive dingos as reference material for the interpretation of archaeological assemblages. It has been suggested that the best results in identifying predators are achieved by combining an analysis of tooth marks with fragmentation patterns. In order to identify dingo ‘signature patterns’ of modification and whether results vary between captive and wild populations, 31 wild and 25 captive scats were disaggregated and analysed. Consistent lengths and breadths of dingo tooth pits on bone from the scats suggest that pits are a good indicator of dingo bone modification, particularly when used in conjunction with fragmentation patterns. Bone deposits from the late Holocene site Witchcliffe Rock Shelter in southwestern Australia, were used as a case study to test the tooth mark and fragmentation patterns identified in the actualistic studies. High levels of fragmentation alongside the presence of tooth pits consistent with those of dingoes suggest that they contributed to the multi-patterned faunal assemblage. Further research to identify signature modification patterns of other Australian carnivores is required.