Thorough assessment of DNA preservation from fossil bone and sediments excavated from a late Pleistocenee-Holocene cave deposit on Kangaroo Island, South Australia

Fossils and sediments preserved in caves are an excellent source of information for investigating impacts of past environmental changes on biodiversity. Until recently studies have relied on morphology-based palaeontological approaches, but recent advances in molecular analytical methods offer excellent potential for extracting a greater array of biological information from these sites. This study presents a thorough assessment of DNA preservation from late Pleistocene-Holocene vertebrate fossils and sediments from Kelly Hill Cave Kangaroo Island, South Australia. Using a combination of extraction techniques and sequencing technologies, ancient DNA was characterised from over 70 bones and 20 sediment samples from 15 stratigraphic layers ranging in age from >20 ka to ~6.8 ka. A combination of primers targeting marsupial and placental mammals, reptiles and two universal plant primers were used to reveal genetic biodiversity for comparison with the mainland and with the morphological fossil record for Kelly Hill Cave. We demonstrate that Kelly Hill Cave has excellent long-term DNA preservation, back to at least 20 ka. This contrasts with the majority of Australian cave sites thus far explored for ancient DNA preservation, and highlights the great promise Kangaroo Island caves hold for yielding the hitherto-elusive DNA of extinct Australian Pleistocene species

Experiment2

Fasta files of amplicon reads from Experiment 2 for both the MiSeq and Ion Torrent. All fasta files are non-dereplicated and have been separated into sample batches based on MID (index) tags and all primers have been removed. No further quality or abundance filtering has been performed on the fasta file

Experiment1

Fasta files of amplicon reads from Experiment 1 for both the GS Junior and Ion Torrent. All fasta files are non-dereplicated and have been separated into sample batches based on MID (index) tags and all primers have been removed. No further quality or abundance filtering has been performed on the fasta file

Experiment5

Fasta file of amplicon reads from Experiment 5 for the Ion Torrent. The file non-dereplicated and has only been separated based on MID (index) tag. Primers have not been removed and no quality or abundance filtering has been performed on the fasta file

Impact of analysis parameters on the numbers of taxonomic units obtained for a bulk-bone sample.

<p>A number of analysis parameters were used to analyse a complex mixture containing numerous taxa. Different quality and abundance filtering methods were used in addition to two taxonomy-independent measures of analysis, full definitions and explanations of which are in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0124671#pone.0124671.g001" target="_blank">Fig 1</a>. The spread in the numbers of taxonomic units obtained across the combinations of parameters chosen is seen. The radius of each semicircle represents the number of taxonomic units obtained given a set combination of the parameters used. The number of taxonomic units is also indicated above each semicircle. Each semicircle is proportional to all others. AFM—abundance filtering method; QFM—quality filtering method; TIM—taxonomy-independent method.</p

Average sequencing error rates across a single amplicon region.

<p>Average sequencing error rates are shown for multiple bird species across the whole of a short 12S rRNA gene region <b>(A)</b>. Additionally, the error profile across the gene region is shown for <i>Calyptorhynchus lathami</i> for both the Ion Torrent PGM <b>(B)</b> and MiSeq <b>(C)</b> with key. The error patterns observed were similar across all species sequenced. Error rates are shown across 5 bp segments and where error rates were above 1% for a single base this is indicated through the red circles.</p

Changes in ectomycorrhizal fungal community composition and declining diversity along a 2-million-year soil chronosequence

Ectomycorrhizal (ECM) fungal communities covary with host plant communities along soil fertility gradients, yet it is unclear whether this reflects changes in host composition, fungal edaphic specialization or priority effects during fungal community establishment. We grew two co-occurring ECM plant species (to control for host identity) in soils collected along a 2-million-year chronosequence representing a strong soil fertility gradient and used soil manipulations to disentangle the effects of edaphic properties from those due to fungal inoculum. Ectomycorrhizal fungal community composition changed and richness declined with increasing soil age; these changes were linked to pedogenesis-driven shifts in edaphic properties, particularly pH and resin-exchangeable and organic phosphorus. However, when differences in inoculum potential or soil abiotic properties among soil ages were removed while host identity was held constant, differences in ECM fungal communities and richness among chronosequence stages disappeared. Our results show that ECM fungal communities strongly vary during long-term ecosystem development, even within the same hosts. However, these changes could not be attributed to short-term fungal edaphic specialization or differences in fungal inoculum (i.e. density and composition) alone. Rather, they must reflect longer-term ecosystem-level feedback between soil, vegetation and ECM fungi during pedogenesis.Fil: Albornoz, Felipe E.. University of Western Australia; AustraliaFil: Teste, Francois. University of Western Australia; Australia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis ; ArgentinaFil: Lambers, Hans. University of Western Australia; AustraliaFil: Bunce, Michael. Curtin University; AustraliaFil: Murray, Dáithí C.. Curtin University; AustraliaFil: White, Nicole E.. Curtin University; AustraliaFil: Laliberté, Etienne. University of Western Australia; Australia. University of Montreal; Canad

TCM_006

Animal and Plant Sequences from Traditional Chinese Medicine Sample No.

DNA metabarcoding for diet analysis and biodiversity A case study using the endangered Australian sea lion

Results from a dietary study. The file contains mostly unique filtered fasta files of DNA sequences extracted and amplified from the scat of the Australian Sea Lion (Neophoca cinerea). The assays used focused mainly on fish, crustaceans, and cephalopods