Abstractthe vertebrate fossil deposits of the naracoorte Caves in south eastern South Australia preserve a long-term record of local faunas. We provide here an updated list of small mammal faunas of late Quaternary (c. <50 ka) aged fossil assemblages from Wet, Robertson and blanche Caves as a basis for understanding past and future patterns in species occurrence. the updated list includes seven species previously unrecorded from the <50 ka period from this region. Of these, two species (Dasycercus sp. indet. and Pseudomys novaehollandiae) are new to the naracoorte fossil record and have no known regional historical (european colonisation to 1950) or contemporary (post 1950) distribution. Review of fossil collections such as these is crucial for providing up-to-date species occurrence data which can be used to establish baselines of past species diversity and information about the past geographic ranges of individual taxa through time.

We examined mammal occurrence and variability through the Late Pleistocene vertebrate fossil deposit of Grant Hall in Victoria Fossil Cave, Naracoorte, South Australia. To determine long‐term patterns of change, we compared the composition and relative abundance trends of the assemblage with a nearby Middle Pleistocene deposit in Cathedral Cave. Total species richness did not change through the Grant Hall sequence, dated from 93 ± 8 to 70 ± 5 ka. However, species relative abundances varied between ecologically divergent species, and in some cases between species that demonstrate similar environmental preferences. For some species this variation is comparable to that recorded in Cathedral Cave. Of those showing similar trends between the two deposits, the forest inhabitant, Pseudomys fumeus, recorded an 8.6% decline through Grant Hall, coincident with a 9.7% increase in the dry heath/mallee dweller Pseudomys apodemoides. These patterns indicate that climatic transition from relatively warm, moist to cooler, drier conditions impacted some species in similar ways through climatic cycles of the past. However, the majority of the fauna demonstrated complex responses that are individual and variable through time. Statistical tests of species trends from the Grant Hall assemblage caution that large fossil samples are required to validate patterns observed. Copyright © 2012 John Wiley & Sons, Ltd.

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Natural variation describes the normal fluctuations that occur in ecosystems over time in the absence of significant human‐driven disturbance, providing a buffer that facilitates ecological resilience. Long‐term data on ecosystems are useful in developing baselines of natural variation and identifying the limits to resilience within different ecosystems. Here, we examined two contemporaneous vertebrate fossil assemblages of the Naracoorte Caves in southern Australia to determine the magnitude and extent of natural variation and resilience exhibited by a small‐mammal paleocommunity through the last glacial cycle (c. 50–10 kyr BP). We also investigated the effect of sampling the assemblages at different timescales on observed patterns of variability and quantified sampling effects to test the robustness of the temporal trends. Our results show that the paleocommunity was structurally and compositionally stable through the early glacial period and last glacial maximum (LGM), with variability exhibited only in species abundances. Significant variability in species abundances, abundance ranks, and species richness during the post‐LGM deglaciation reveals paleocommunity reorganization and a loss of resilience to climatic change at this time. A nearby marine‐core record suggests that the paleocommunity reorganization was associated with sea‐surface temperatures warming past 16°C, postdating the onset of warming following the LGM by c. 1–3 kyr. This suggests that the paleocommunity was sensitive to specific temperature thresholds rather than shifts between warming or cooling trends per se. Our results also show that patterns of natural variability are sensitive to time‐averaging, which can smooth out rapid and short‐term changes and limit our capacity to temporally correlate faunal changes to their environmental or climatic drivers. The responses of the small‐mammal paleocommunity conform to models derived from other paleontological and modern assemblages in which changes in species abundances may not always lead to community restructuring.

Although there is a long history of research into the fossil deposits of the Naracoorte Caves (South Australia), ancient DNA (aDNA) has not been integrated into any palaeontological study from this World Heritage site. Here, we provide the first evidence of aDNA preservation in Holocene‐ and Pleistocene‐aged fossil bone from a deposit inside Robertson Cave. Using a combination of metabarcoding and shotgun next‐generation sequencing approaches, we demonstrate that aDNA from diverse taxa can be retrieved from bulk bone as old as 18 600 cal a BP. However, the DNA is highly degraded and contains a lower relative proportion of endogenous sequences in bone older than 8400 cal a BP. Furthermore, modelling of DNA degradation suggests that the decay rate is rapid, and predicts a very low probability of obtaining informative aDNA sequences from extinct megafaunal bones from Naracoorte (ca. 50 000 cal a BP). We also provide new information regarding the past faunal biodiversity of Robertson Cave, including families that have not been formerly described in the fossil record from here before. Collectively, these data demonstrate the potential for future aDNA studies to be conducted on material from Naracoorte, which will aid in the understanding of faunal turnover in southern Australia.