Alexander Baynes

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.

Short overlap of humans and megafauna in Pleistocene Australia

Reappraisal of the reliability of numerical dating results for Australian extinct megafauna and archaeology reveals that many still-quoted ages are incorrect and should be eliminated from databases and discussions. We estimate that the megafauna-human overlap period on mainland Australia was about 3900 years (95% confidence interval 3158 to 4642 years) centred ~44,000 calendar years ago. Our results rule out climatic and environmental changes associated with the Last Glacial Maximum as contributing factors in Australian late Pleistocene megafauna extinctions, whereas the short overlap suggests instead that anthropogenic factors are likely to be dominant.

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.

Morphological and molecular evidence supports specific recognition of the recently extinct Bettongia anhydra (Marsupialia: Macropodidae)

In 1933, geologist and explorer Michael Terry collected the skull of a small macropodid captured by members of his party near Lake Mackay, western Northern Territory. In 1957, this skull was described as the sole exemplar of a distinct subspecies, Bettongia penicillata anhydra, but was later synonymized with B. lesueur and thereafter all but forgotten. We use a combination of craniodental morphology and ancient mitochondrial DNA to confirm that the Lake Mackay specimen is taxonomically distinct from all other species of Bettongia and recognize an additional specimen from a Western Australian Holocene fossil accumulation. B. anhydra is morphologically and genetically most similar to B. lesueur but differs in premolar shape, rostrum length, dentary proportions, and molar size gradient. In addition, it has a substantial mitochondrial cytochrome b pairwise distance of 9.6–12% relative to all other bettongs. The elevation of this recently extinct bettong to species status indicates that Australias mammal extinction record over the past 2 centuries is even worse than currently accepted. Like other bettongs, B. anhydra probably excavated much of its food and may have performed valuable ecological services that improved soil structure and water infiltration and retention, as well as playing an important role in the dispersal of seeds and mycorrhizal fungal spores. All extant species of Bettongia have experienced extensive range contractions since European colonization and some now persist only on island refugia. The near total loss of these ecosystem engineers from the Australian landscape has far-reaching ecological implications.

Pleistocene occupation of Yellabidde Cave in the northern Swan Coastal Plain, southwestern Australia

Abstract Evidence for human occupation of Western Australia’s northern Swan Coastal Plain derives mainly from Holocene coastal midden sites. Here, we present preliminary results from archaeological investigations at Yellabidde Cave, located 9 km inland from the present coast. Excavations in the limestone cave’s sandy floor deposit revealed cultural and palaeontological materials dating from c. 25,500 cal. BP to the 19th C. These provide the first evidence for Pleistocene occupation in the region, indicating that Yellabidde Cave was intermittently occupied throughout the late Pleistocene and Holocene, and reflecting dynamic human-environment relationships in present near-coastal to littoral environments.