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Item Metadata only A cryptic and critically endangered species revealed by mitochondrial DNA analyses: the Western Ground Parrot(Springer-Verlag Dordrecht, 2011) Murphy, S.; Joseph, L.; Burbidge, A.; Austin, J.We examined cytochrome b sequence data to resolve the intraspecific taxonomy of ground parrots Pezoporus wallicus. The species occurs in fragmented coastal heaths in south-eastern and south-western Australia. Net nucleotide divergences among all eastern populations were very low (0.0â 0.6%) and genetic diversity unstructured, suggesting relatively recent common ancestry. Gene flow among them was probably maintained via land bridges and the persistence of suitable habitat during the Pleistocene. In contrast, net nucleotide divergence was high (4.4â 5.1%) between western and eastern populations, suggesting more ancient divergence about 2Â million years ago. The magnitude of divergence between eastern and western lineages is similar to a wide range of avian congeners. Our data support the need to reconsider the intraspecific taxonomy of ground parrots, and we cautiously suggest the recognition of Western Ground Parrots as a species, P. flaviventris, for conservation prioritization, planning and management purposes. Given their recent precipitous decline to approximately 110 individuals, most of which occur at one location, this makes Western Ground Parrots one of the worldâ s most threatened bird species.Item Metadata only A deposition mechanism for Holocene miring bone deposits, South Island, New Zealand(Palaeontological Network Foundation, 2008) Wood, J.; Worthy, T.; Rawlence, N.; Jones, S.; Read, S.; Australian Centre for Ancient DNALocalised deposits of Late Pleistocene and Holocene bird bones occur in wetlands throughout New Zealand. These are characterised by dense accumulations of mostly disarticulated bones, with assemblages dominated by large, flightless bird taxa; in particular the extinct ratite moa (Aves: Dinornithiformes). A wide range of deposition mechanisms were historically proposed for these sites, including large floods and stampedes during wildfires. We outline a simple method for analysing the orientation and spatial distribution of bones within these deposits using GIS software, and apply this method to the interpretation of three such deposits from South Island, New Zealand. The results are consistent with non-catastrophic, periodic miring of individual moa. Long bones within these sites were preferentially orientated and subhorizontally inclined, indicating post-deposition disarticulation and movement of the bones within the sediment by sediment liquefaction and raking from the legs of mired birds, with a possible influence from water flow. Small, light skeletal elements were significantly under represented in the deposits. This may be due to post-mortem scavenging or weathering of vertebra and crania, 'pumping' to the surface of light, buoyant elements during liquefaction events, or crushing of these elements by subsequently mired birds.Item Metadata only A global molecular phylogeny of the small Puffinus shearwaters and implications for systematics of the the little-Audubon's shearwater complex(Amer Ornithologists Union, 2004) Austin, J.; Bretagnolle, V.; Pasquet, E.A molecular phylogeny based on 917 base pairs (bp) of the mitochondrial (mt) DNA cytochrome-b gene was used to test and reassess the systematics and conflicting taxonomic treatments of the small, black-and-white Puffinus shearwaters, including the P. assimilis-lherminieri species complex. Three geographically discrete clades were identified in the North Atlantic, Southern (Australasia) and tropical Pacific and Indian oceans that contain most of the P. assimilis-lherminieri taxa. Together with four other lineages (P. puffinus, P. opisthomelas, P. mauretanicus-P. yelkouan, P. newelli-P. myrtae), they form an unresolved polytomy. Puffinus hultoni-P. gavia, P. nativitatis, and P. subalaris are basal to this. The phylogenetic positions of P. myrtae and P. subalaris are unexpected and warrant further investigation. None of the competing taxonomic treatments of the P. assimilis-lherminieri complex art, supported. Instead, our phylogeny suggests that 14 taxa should be recognized, whereas five others (loyemilleri, colstoni, nicolae, polynesiae, and atrodorsalis) are phylogenetically undifferentiated from more widespread species (lherminieri, dichrous, and bailloni) and are probably not valid. Similarities in plumage and external morphological characters between unrelated species and differences between closely related species suggest that those traditional taxonomic characters are poor indicators of phylogenetic relatedness.Item Metadata only A lost link between a flightless parrot and a parasitic plant and the potential role of coprolites in conservation paleobiology(Blackwell Publishing Inc, 2012) Wood, J.; Wilmshurst, J.; Worthy, T.; Holzapfel, A.; Cooper, A.Late Quaternary extinctions and population fragmentations have severely disrupted animal-plant interactions globally. Detection of disrupted interactions often relies on anachronistic plant characteristics, such as spines in the absence of large herbivores or large fruit without dispersers. However, obvious anachronisms are relatively uncommon, and it can be difficult to prove a direct link between the anachronism and a particular faunal taxon. Analysis of coprolites (fossil feces) provides a novel way of exposing lost interactions between animals (depositors) and consumed organisms. We analyzed ancient DNA to show that a coprolite from the South Island of New Zealand was deposited by the rare and threatened kakapo (Strigops habroptilus), a large, nocturnal, flightless parrot. When we analyzed the pollen and spore content of the coprolite, we found pollen from the cryptic root-parasite Dactylanthus taylorii. The relatively high abundance (8.9% of total pollen and spores) of this zoophilous pollen type in the coprolite supports the hypothesis of a former direct feeding interaction between kakapo and D. taylorii. The ranges of both species have contracted substantially since human settlement, and their present distributions no longer overlap. Currently, the lesser short-tailed bat (Mystacina tuberculata) is the only known native pollinator of D. taylorii, but our finding raises the possibility that birds, and other small fauna, could have once fed on and pollinated the plant. If confirmed, through experimental work and observations, this finding may inform conservation of the plant. For example, it may be possible to translocate D. taylorii to predator-free offshore islands that lack bats but have thriving populations of endemic nectar-feeding birds. The study of coprolites of rare or extinct taxonomic groups provides a unique way forward to expand existing knowledge of lost plant and animal interactions and to identify pollination and dispersal syndromes. This approach of linking paleobiology with neoecology offers significant untapped potential to help inform conservation and restoration plans.Item Metadata only A mini-multiplex SNaPshot assay for the triage of degraded human DNA(Elsevier BV, 2018) Bardan, F.; Higgins, D.; Austin, J.Short Tandem Repeat (STR) genotyping is currently the primary DNA-based method for human identification, however it can have limited success when applied to degraded human remains. Massively parallel sequencing (MPS) provides new opportunities to obtain genetic data for hundreds of loci in a single assay with higher success from degraded samples. However, due to the extra requirement for specialised equipment, expertise and resources, routine use of MPS may not be feasible or necessary for many forensic cases. Here we describe the development of a mini-multiplex SNaPshot screening tool (Miniplex) for human samples which allows the qualitative comparison of short mitochondrial and nuclear DNA targets, as well as the interrogation of biogeographic ancestry, lineage, and phenotype single nucleotide polymorphisms (SNPs). This tool is useful to triage samples based on sample quality prior to downstream identification workflows and provides broad biological profile data for intelligence purposes.Item Metadata only A mitochondrial 12S and 16S rRNA phylogeny of critical genera of Phoridae (Diptera) and related families of Aschiza(Magnolia Press, 2004) Cook, C.; Austin, J.; Disney, H.Phylogenetic analysis of mitochondrial 12S and 16S rRNA gene sequences supports the monophyly of the Phoridae. Within this family the Phorinae clade includes two aberrant termitophilous subfamilies, the Thaumatoxeninae and the Termitoxeniinae, which cluster with Dohrniphora and Diplonevra. These two genera include termitophiles and parasitoids of termites, so we hypothesize that these termitophilous phorids are a monophyletic group. While the data neither refute nor support the assumed monophyly of the Metopininae, the genera of this subfamily were not monophyletic in our analysis, but fell into two subclades that correspond with the tribes Metopinini and Gymnophorini.Item Open Access A new dolphin species, the Burrunan dolphin Tursiops australis sp. nov., endemic to southern Australian coastal waters(Public Library of Science, 2011) Charlton-Robb, K.; Gershwin, L.; Thompson, R.; Austin, J.; Owen, K.; McKechnie, S.; Fleischer, R.C.Small coastal dolphins endemic to south-eastern Australia have variously been assigned to described species Tursiops truncatus, T. aduncus or T. maugeanus; however the specific affinities of these animals is controversial and have recently been questioned. Historically ‘the southern Australian Tursiops’ was identified as unique and was formally named Tursiops maugeanus but was later synonymised with T. truncatus. Morphologically, these coastal dolphins share some characters with both aforementioned recognised Tursiops species, but they also possess unique characters not found in either. Recent mtDNA and microsatellite genetic evidence indicates deep evolutionary divergence between this dolphin and the two currently recognised Tursiops species. However, in accordance with the recommendations of the Workshop on Cetacean Systematics, and the Unified Species Concept the use of molecular evidence alone is inadequate for describing new species. Here we describe the macro-morphological, colouration and cranial characters of these animals, assess the available and new genetic data, and conclude that multiple lines of evidence clearly indicate a new species of dolphin. We demonstrate that the syntype material of T. maugeanus comprises two different species, one of which is the historical ‘southern form of Tursiops’ most similar to T. truncatus, and the other is representative of the new species and requires formal classification. These dolphins are here described as Tursiops australis sp. nov., with the common name of ‘Burrunan Dolphin’ following Australian aboriginal narrative. The recognition of T. australis sp. nov. is particularly significant given the endemism of this new species to a small geographic region of southern and south-eastern Australia, where only two small resident populations in close proximity to a major urban and agricultural centre are known, giving them a high conservation value and making them susceptible to numerous anthropogenic threats.Item Metadata only A new species of Ctenophorus (Lacertilia: Agamidae) from Lake Disappointment Western Australia(Herpetologists League, 2007) Doughty, P.; Maryan, B.; Melville, J.; Austin, J.Ctenophorus is the largest genus of Australian agamid lizards, with an extensive radiation in the arid zone. Here we describe a distinctive new dragon species—Ctenophorus nguyarna—from the isolated Lake Disappointment in Western Australia. The new species is characterised by heterogeneous dorsal scales tending to form vertical rows on the flanks, a reticulated orange and black background color, and black bars on the dorsum and black vertical bars on the tail. To provide a molecular context as to the distinctiveness and placement of the new species we analysed five sequences of Ctenophorus sp. nov., two new sequences of C. salinarum and 11 previously published sequences of Ctenophorus species, representing 1573 bases of the mitochondrial genome. Our phylogeny strongly supports at least two independent origins of salt lake specialization in both the western and eastern arid zone. Based on molecular data the sister taxon is C. salinarum, which is also associated with salt lakes in Western Australia. The other specialist is the Lake Eyre Dragon (C. maculosus) from South Australia that lives on and under the salt crust itself, and has a number of unique derived characters for Ctenophorus. There are likely to be other new species of agamid lizards in Australia's vast and little-explored arid zone.Item Metadata only A novel 154-bp deletion in the human mitochondrial DNA control region in healthy individuals(Wiley-Liss, 2008) Behar, D.; Blue-Smith, J.; Soria-Hernanz, D.; Tzur, S.; Hadid, Y.; Bormans, C.; Moen, A.; Tyler-Smith, C.; Quintana-Murci, L.; Wells, R.; Schurr, T.; Santos, F.; Bertranpetit, J.; Comas, D.; Balanovska, E.; Balanovsky, O.; Mitchell, R.; Jin, L.; Soodyall, H.; Pitchappan, R.; et al.; Cooper, AlanThe biological role of the mitochondrial DNA (mtDNA) control region in mtDNA replication remains unclear. In a worldwide survey of mtDNA variation in the general population, we have identified a novel large control region deletion spanning positions 16154 to 16307 (m.16154_16307del154). The population prevalence of this deletion is low, since it was only observed in 1 out of over 120,000 mtDNA genomes studied. The deletion is present in a nonheteroplasmic state, and was transmitted by a mother to her two sons with no apparent past or present disease conditions. The identification of this large deletion in healthy individuals challenges the current view of the control region as playing a crucial role in the regulation of mtDNA replication, and supports the existence of a more complex system of multiple or epigenetically-determined replication origins.Item Metadata only A perspective for resolving the systematics of Rattus, the vertebrates with the most influence on human welfare(Magnolia Press, 2018) Thomson, V.A.; Wiewel, A.S.; Chinen, A.; Maryanto, I.; Sinaga, M.H.; How, R.; Aplin, K.; Suzuki, H.The murid rodent genus Rattus Fischer 1803 contains several species that are responsible for massive loss of crops and food, extinction of other species and the spread of zoonotic diseases to humans, as well as a laboratory species used to answer important questions in physiology, immunology, pharmacology, toxicology, nutrition, behaviour and learning. Despite the well-known significant impacts of Rattus, a definitive evolutionary based systematic framework for the genus is not yet available. The past 75 years have seen more dramatic changes in membership of Rattus than in almost any other genus of mammals. In fact, the Rattus genus has been a receptacle for any generalised Old World murine that lacked morphological specialisation and at one point, has included more than 560 species and/or subspecies, spread across Eurasia, Africa and the Australo-Papuan region. The dissolution of Rattus is ongoing as many of its constituent species and many genera of Rattini remain unsampled in any molecular study. To address this sampling limitation, we sequenced the mitochondrial cytochrome b (cytb) gene and examined phylogenetic relationships using both Bayesian and Maximum Likelihood algorithms for an expanded set of taxa within Rattus and among closely related genera. Here we place previously unsampled taxa in a phylogenetic context for the first time, including R. burrus, R. hoogerwerfi, R. lugens, and R. mindorensis within the Asian Rattus group, R. facetus within the Australo-Papuan Rattus radiation, and the undescribed ‘Bisa Rat’ described by Flannery as sister to the recently described genus Halmaheramys. We also present an exploratory foray into the wider topic of Rattus phylogenetics and propose that a reorganisation of the Rattus genus should require that it be a monophyletic group, include at least the type species R. norvegicus and R. rattus (plus their close allies); and exclude the Bandicota/Nesokia clade and other such specialised genera.Item Metadata only A primer to metabarcoding surveys of Antarctic terrestrial biodiversity(Cambridge University Press, 2017) Czechowski, P.; Clarke, L.J.; Cooper, A.; Stevens, M.I.Ice-free regions of Antarctica are concentrated along the coastal margins but are scarce throughout the continental interior. Environmental changes, including the introduction of non-indigenous species, increasingly threaten these unique habitats. At the same time, the unique biotic communities subsisting in isolation across the continent are difficult to survey due to logistical constraints, sampling challenges and problems related to the identification of small and cryptic taxa. Baseline biodiversity data from remote Antarctic habitats are still missing for many parts of the continent but are critical to the detection of community changes over time, including newly introduced species. Here we review the potential of standardized (non-specialist) sampling in the field (e.g. from soil, vegetation or water) combined with high-throughput sequencing (HTS) of bulk DNA as a possible solution to overcome some of these problems. In particular, HTS metabarcoding approaches benefit from being able to process many samples in parallel, while workflow and data structure can stay highly uniform. Such approaches have quickly gained recognition and we show that HTS metabarcoding surveys are likely to play an important role in continent-wide biomonitoring of all Antarctic terrestrial habitats.Item Metadata only Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims(Soc General Microbiology, 2004) Gilbert, T.; Cuccui, J.; White, W.; Lynnerup, N.; Titball, R.; Cooper, A.; Prentice, M.This study reports the results of a collaborative study undertaken by two independent research groups to (a) confirm recent PCR-based detection of Yersinia pestis DNA in human teeth from medieval plague victims in France, and (b) to extend these observations over five different European burial sites believed to contain plague victims dating from the late 13th to 17th centuries. Several different sets of primers were used, including those previously documented to yield positive results on ancient DNA extracts. No Y. pestis DNA could be amplified from DNA extracted from 108 teeth belonging to 61 individuals, despite the amplification of numerous other bacterial DNA sequences. Several methods of extracting dentine prior to the DNA extraction were also compared. PCR for bacterial 16S rDNA indicated the presence of multiple bacterial species in 23 out of 27 teeth DNA extracts where dentine was extracted using previously described methods. In comparison, positive results were obtained from only five out of 44 teeth DNA extracts for which a novel contamination-minimizing embedding technique was used. Therefore, high levels of environmental bacterial DNA are present in DNA extracts where previously described methods of tooth manipulation are used. To conclude, the absence of Y. pestis-specific DNA in an exhaustive search using specimens from multiple putative European plague burial sites does not allow us to confirm the identification of Y. pestis as the aetiological agent of the Black Death and subsequent plagues. In addition, the utility of the published tooth-based ancient DNA technique used to diagnose fatal bacteraemias in historical epidemics still awaits independent corroboration.Item Metadata only Accuracy of rate estimation using relaxed-clock models with a critical focus on the early Metazoan radiation(Oxford Univ Press, 2005) Ho, S.; Phillips, M.; Drummond, A.; Cooper, A.In recent years, a number of phylogenetic methods have been developed for estimating molecular rates and divergence dates under models that relax the molecular clock constraint by allowing rate change throughout the tree. These methods are being used with increasing frequency, but there have been few studies into their accuracy. We tested the accuracy of several relaxed-clock methods (penalized likelihood and Bayesian inference using various models of rate change) using nucleotide sequences simulated on a nine-taxon tree. When the sequences evolved with a constant rate, the methods were able to infer rates accurately, but estimates were more precise when a molecular clock was assumed. When the sequences evolved under a model of auto-correlated rate change, rates were accurately estimated using penalized likelihood and by Bayesian inference using lognormal and exponential models of rate change, while other models did not perform as well. When the sequences evolved under a model of uncorrelated rate change, only Bayesian inference using an exponential rate model performed well. Collectively, the results provide a strong recommendation for using the exponential model of rate change if a conservative approach to divergence time estimation is required. A case study is presented in which we use a simulation-based approach to examine the hypothesis of elevated rates in the Cambrian period, and it is found that these high rate estimates might be an artifact of the rate estimation method. If this bias is present, then the ages of metazoan divergences would be systematically underestimated. The results of this study have implications for studies of molecular rates and divergence dates.Item Metadata only Accurate hydrogen sorption measurements via differential pressure analyses(American Institute of Chemical Engineers, 2005) Zielinski, J.; Coe, C.; Cooper, A.; Pez, G.; 2005 AIChE Annual Meeting (30 Oct 2005 - 4 Nov 2005 : Cincinnati, Ohio)A differential pressure adsorption unit (DPAU) has been constructed which is capable of accurately measuring isotherm data up to 2400 psia with as little as 50 mg of sample. This non-traditional adsorption/desorption method has been benchmarked by comparing hydrogen and methane isotherms measured with standard volumetric and gravimetric instruments on a NaA (4A) zeolite and an activated carbon at near ambient temperatures. The results from stability tests and a discussion of the mathematical analysis will be provided as well as a discussion of the unit's recent application in measuring credible hydrogen sorption isotherms on a series of well-defined single walled carbon nanotubes.Item Metadata only Affinities of Miocene Waterfowl (Anatidae: Manuherikia, Dunstanetta and Miotadorna) from the St Bathans Fauna, New Zealand(Blackwell Publ Ltd, 2008) Worthy, T.; Lee, M.Abstract: The recently described St Bathans Fauna, from the Manuherikia Group, Early–Middle Miocene, 19–16 Ma, New Zealand, includes six anatid taxa. Here we present detailed morphological descriptions of all available skeletal elements of the three best represented anatids: Manuherikia lacustrina (551 specimens), Dunstanetta johnstoneorum (7 specimens), and Miotadorna sanctibathansi (115 specimens). The affinities of these taxa, and of the similar‐aged European taxon Mionetta blanchardi, are evaluated with phylogenetic analyses using a dataset of 133 characters (128 osteological, 5 integumental) and 57 terminal taxa. Representatives of all main anatid groups were included, with dense sampling of Australasian taxa including the recently extinct New Zealand forms (Cnemiornis, Chenonetta finschi), and relatively primitive taxa (anserines, Dendrocygna, oxyurines, tadornines). Analyses were conducted with no constraints, and with certain taxa constrained to conform to arrangements supported by multiple independent genetic studies. In the preferred (constrained) analyses: (1) anserines were the most basal anatids; (2) the four Tertiary fossil taxa were more derived than anserines and Dendrocygna; and (3) the European Mionetta blanchardi was basal to an oxyurine clade. The New Zealand fossils Manuherikia and Dunstanetta either associated with this oxyurine clade or formed separate lineages of an approximately oxyurine evolutionary grade, depending on whether diving characters were included or excluded. Similarly, Biziura, Thalassornis, and a Stictonetta–Malacorhynchus clade either associated with oxyurines or formed independent lineages of approximately oxyurine grade. Above oxyurines, a well‐supported clade groups Miotadorna with Tadorna species exclusive of T. radjah. These results cast doubt on the distinctiveness of Dendrocheninae , and instead suggest oxyurine affinities for the Miocene fossils Mionetta, Dendrochen, Manuherikia and Dunstanetta, and the modern Biziura, Thalassornis, Oxyura, Nomonyx, Stictonetta and Malacorhynchus. The association of Mionetta with oxyurines indicates that the divergence between oxyurines and higher anatids occurred around 25 Ma, while the position of Miotadorna within Tadorna indicates that the basal divergence between living Tadorna occurred by the Early–Middle Miocene; together, these two dates indicate that many basal splits within anatids occurred within a short interval during the Miocene.Item Open Access Allelic bias when performing in-solution enrichment of ancient human DNA(Wiley, 2023) Davidson, R.; Williams, M.P.; Roca-Rada, X.; Kassadjikova, K.; Tobler, R.; Fehren-Schmitz, L.; Llamas, B.In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent-which enriches 1,237,207 genome-wide SNPs-since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240 k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g. Principal Components Analysis, ƒ-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In ƒ-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.Item Metadata only An optimized method for the extraction of ancient eukaryote DNA from marine sediments(Wiley, 2020) Armbrecht, L.; Herrando-Pérez, S.; Eisenhofer, R.; Hallegraeff, G.M.; Bolch, C.J.S.; Cooper, A.Marine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo-communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead-beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica-solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size-selection of low molecular-weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead-beating, DNA binding in silica-solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post-library LMW size-selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data-processing protocol should improve quantitative paleo-monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments.Item Open Access An Outlook for the Acquisition of Marine Sedimentary Ancient DNA (sedaDNA) From North Atlantic Ocean Archive Material(American Geophysical Union (AGU), 2022) Selway, C.A.; Armbrecht, L.; Thornalley, D.Studies incorporating sedimentary ancient DNA (sedaDNA) analyses to investigate paleo-environments have increased considerably over the last few years, and the possibility of utilizing archived sediment cores from previous field campaigns could unlock an immense resource of sampling material for such paleo-investigations. However, sedaDNA research is at a high risk of contamination by modern environmental DNA, as sub-optimal sediment storage conditions may allow for contaminants (e.g., fungi) to grow and become dominant over preserved sedaDNA in the sample. Here, we test the feasibility of sedaDNA analysis applied to archive sediment material from five sites in the North Atlantic, collected between 1994 and 2013. We analyzed two samples (one younger and one older) per site using a metagenomic shotgun approach and were able to recover eukaryotic sedaDNA from all samples. We characterized the authenticity of each sample through sedaDNA fragment size and damage analyses, which allowed us to disentangle sedaDNA and contaminant DNA. Although we determined that contaminant sequences originated mainly from Ascomycota (fungi), most samples were dominated by Emiliania huxleyi, a haptophyte species that commonly blooms in the study region. We attribute the presence of contaminants to non-ideal sampling and sample storage conditions of the investigated samples. Therefore, while we demonstrate that sedaDNA analysis of archival North Atlantic seafloor sediment samples are generally achievable, we stress the importance of best-practice ship-board sampling techniques and storage conditions to minimize contamination. We highly recommend the application of robust bioinformatic tools that help distinguish ancient genetic signals from modern contaminants, especially when working with archive material.Item Metadata only Ancient DNA(Royal Soc London, 2005) Willerslev, E.; Cooper, A.In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.Item Metadata only Ancient DNA analysis of dental calculus(Elsevier, 2015) Weyrich, L.; Dobney, K.; Cooper, A.Abstract not available