Australian Centre for Ancient DNA (ACAD)
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The Australian Centre for Ancient DNA (ACAD) is one of the leading ancient DNA centres in the world. Established in 2005, it has an international reputation for highly-innovative research and a trans-disciplinary focus. Growing programs include research into Forensics, Genomics, 3rd Generation Sequencing, Human Evolution and Megafaunal Extinctions. ACAD’s key interests include molecular studies of population genetics, paleoenvironments, phylogeny, phylogeopraphy, molecular clocks, and the application of DNA sequences deposited through time.
Interested PhD students should visit the website for possible projects and full contact information http://www.adelaide.edu.au/acad/
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Item Metadata only Diverse plant and animal genetic records from Holocene and Pleistocene sediments(Amer Assoc Advancement Science, 2003) Willerslev, E.; Hansen, A.; Binladen, J.; Brand, T.; Gilbert, M.; Shapiro, B.; Bunce, M.; Wiuf, C.; Gilichinsky, D.; Cooper, A.Genetic analyses of permafrost and temperate sediments reveal that plant and animal DNA may be preserved for considerable time periods, even in the absence of obvious macrofossils. In Siberia, five permafrost cores ranging from 400-10 thousand years (kyr) contained at least 19 different plant taxa, including the oldest authenticated ancient DNA sequences known, and megafaunal sequences including mammoth, bison, and horse. The genetic data record a number of dramatic changes in the taxonomic diversity and composition of Beringian vegetation and fauna. Temperate cave sediments in New Zealand also yielded DNA sequences of extinct biota, including two species of ratite moa, and 29 plant taxa characteristic of the prehuman environment. Therefore, many sedimentary deposits may contain unique, and widespread, genetic records of paleoenvironments.Item Metadata only Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis(Nature Publishing Group, 2003) Bunce, M.; Worthy, T.; Ford, T.; Hoppitt, W.; Willerslev, E.; Drummond, A.; Cooper, A.The ratite moa (Aves; Dinornithiformes) were massive graviportal browsers weighing up to 250 kg (ref. 1) that dominated the New Zealand biota until their extinction approximately 500 yr ago. Despite an extensive Quaternary fossil record, moa taxonomy remains problematic and currently 11 species are recognized. Three Dinornis species were found throughout New Zealand and differed markedly in size (1-2 m height at back) and mass (from approximately 34 to 242 kg). Surprisingly, ancient mitochondrial DNA sequences show that the three species were genetically indistinguishable within each island, but formed separate North and South Island clades. Here we show, using the first sex-linked nuclear sequences from an extinct species, that on each island the three morphological forms actually represent just one species, whose size varied markedly according to sex and habitat. The largest females in this example of extreme reversed sexual size dimorphism were about 280% the weight and 150% the height of the largest males, which is unprecedented among birds and terrestrial mammals. The combination of molecular and palaeontological data highlights the difficulties of analysing extinct groups, even those with detailed fossil records.Item Metadata only Was there a second adaptive radiation of giant tortoises in the Indian Ocean? Using mitochondrial DNA to investigate speciation and biogeography of Aldabrachelys (Reptilia Testudinidae)(Blackwell Publishing Ltd, 2003) Austin, J.; Arnold, E.; Bour, R.A radiation of five species of giant tortoises (Cylindraspis) existed in the southwest Indian Ocean, on the Mascarene islands, and another (of Aldabrachelys) has been postulated on small islands north of Madagascar, from where at least eight nominal species have been named and up to five have been recently recognized. Of 37 specimens of Madagascan and small-island Aldabrachelys investigated by us, 23 yielded significant portions of a 428-base-pair (bp) fragment of mitochondrial (cytochrome b and tRNA-Glu), including type material of seven nominal species (A. arnoldi, A. dussumieri, A. hololissa, A. daudinii, A. sumierei, A. ponderosa and A. gouffei). These and nearly all the remaining specimens, including 15 additional captive individuals sequenced previously, show little variation. Thirty-three exhibit no differences and the remainder diverge by only 1–4 bp (0.23–0.93%). This contrasts with more widely accepted tortoise species which show much greater inter- and intraspecific differences. The non-Madagascan material examined may therefore only represent a single species and all specimens may come from Aldabra where the common haplotype is known to occur. The present study provides no evidence against the Madagascan origin for Aldabra tortoises suggested by a previous molecular phylogenetic analysis, the direction of marine currents and phylogeography of other reptiles in the area. Ancient mitochondrial DNA from the extinct subfossil A. grandidieri of Madagascar differs at 25 sites (5.8%) from all other Aldabrachelys samples examined here.Item Metadata only Early allelic selection in maize as revealed by ancient DNA(Amer Assoc Advancement Science, 2003) Jaenicke-Despres, V.; Buckler, E.; Smith, B.; Gilbert, M.; Cooper, A.; Doebley, J.; Paabo, S.Maize was domesticated from teosinte, a wild grass, by approximately 6300 years ago in Mexico. After initial domestication, early farmers continued to select for advantageous morphological and biochemical traits in this important crop. However, the timing and sequence of character selection are, thus far, known only for morphological features discernible in corn cobs. We have analyzed three genes involved in the control of plant architecture, storage protein synthesis, and starch production from archaeological maize samples from Mexico and the southwestern United States. The results reveal that the alleles typical of contemporary maize were present in Mexican maize by 4400 years ago. However, as recently as 2000 years ago, allelic selection at one of the genes may not yet have been complete.Item Metadata only Characterization of genetic miscoding lesions caused by postmortem damage(Univ Chicago Press, 2003) Gilbert, M.; Hansen, A.; Willerslev, E.; Rudbeck, E.; Barnes, I.; Lynnerup, N.; Cooper, A.The spectrum of postmortem damage in mitochondrial DNA was analyzed in a large data set of cloned sequences from ancient human specimens. The most common forms of damage observed are two complementary groups of transitions, termed "type 1" (adenine-->guanine/thymine-->cytosine) and "type 2" (cytosine-->thymine/guanine-->adenine). Single-primer extension PCR and enzymatic digestion with uracil-N-glycosylase confirm that each of these groups of transitions result from a single event, the deamination of adenine to hypoxanthine, and cytosine to uracil, respectively. The predominant form of transition-manifested damage varies by sample, though a marked bias toward type 2 is observed with increasing amounts of damage. The two transition types can be used to identify the original strand, light (L) or heavy (H), on which the initial damage event occurred, and this can increase the number of detected jumping-PCR artifacts by up to 80%. No bias toward H-strand-specific damage events is noted within the hypervariable 1 region of human mitochondria, suggesting the rapid postmortem degradation of the secondary displacement (D-loop) H strand. The data also indicate that, as damage increases within a sample, fewer H strands retain the ability to act as templates for enzymatic amplification. Last, a significant correlation between archaeological site and sample-specific level of DNA damage was detected.Item Metadata only Distribution patterns of postmortem damage in human mitochondrial DNA(Univ Chicago Press, 2003) Gilbert, M.; Willerslev, E.; Hansen, A.; Barnes, I.; Rudbeck, L.; Lynnerup, N.; Cooper, A.The distribution of postmortem damage in mitochondrial DNA retrieved from 37 ancient human DNA samples was analyzed by cloning and was compared with a selection of published animal data. A relative rate of damage (rho(v)) was calculated for nucleotide positions within the human hypervariable region 1 (HVR1) and cytochrome oxidase subunit III genes. A comparison of damaged sites within and between the regions reveals that damage hotspots exist and that, in the HVR1, these correlate with sites known to have high in vivo mutation rates. Conversely, HVR1 subregions with known structural function, such as MT5, have lower in vivo mutation rates and lower postmortem-damage rates. The postmortem data also identify a possible functional subregion of the HVR1, termed "low-diversity 1," through the lack of sequence damage. The amount of postmortem damage observed in mitochondrial coding regions was significantly lower than in the HVR1, and, although hotspots were noted, these did not correlate with codon position. Finally, a simple method for the identification of incorrect archaeological haplogroup designations is introduced, on the basis of the observed spectrum of postmortem damage.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 Metadata only Ancient DNA: would the real Neandertal please stand up?(Dell Press, 2004) Cooper, A.; Drummond, A.; Willerslev, E.Mitochondrial DNA sequences recovered from eight Neandertal specimens cannot be detected in either early fossil Europeans or in modern populations. This indicates that, if Neandertals made any genetic contribution at all to modern humans, it must have been limited, though the extent of the contribution cannot be resolved at present.Item Metadata only Long-term persistence of bacterial DNA(Dell Press, 2004) Willerslev, E.; Hansen, A.; Ronn, R.; Brand, T.; Barnes, I.; Wiuf, C.; Gilichinsky, D.; Mitchell, D.; Cooper, A.Item Metadata only Ancient mitochondrial DNA from hair(Dell Press, 2004) Gilbert, T.; Wilson, A.; Bunce, M.; Hansen, A.; Willerslev, E.; Shapiro, B.; Higham, T.; Richards, M.; O'Connell, T.; Tobin, D.; Janaway, R.; Cooper, A.Item Metadata only Neotenous origins for pelagic octopuses(Dell Press, 2004) Strugnell, J.; Norman, M.; Drummond, A.; Cooper, A.Item Metadata only Rise and fall of the Beringian steppe bison(Amer Assoc Advancement Science, 2004) Shapiro, B.; Drummond, A.; Rambaut, A.; Wilson, M.; Matheus, P.; Sher, A.; Pybus, O.; Gilbert, M.; Barnes, I.; Binladen, J.; Willerslev, E.; Hansen, A.; Baryshnikov, G.; Burns, J.; Davydov, S.; Driver, J.; Froese, D.; Harington, C.; Keddie, G.; Kosintsev, P.; et al.The widespread extinctions of large mammals at the end of the Pleistocene epoch have often been attributed to the depredations of humans; here we present genetic evidence that questions this assumption. We used ancient DNA and Bayesian techniques to reconstruct a detailed genetic history of bison throughout the late Pleistocene and Holocene epochs. Our analyses depict a large diverse population living throughout Beringia until around 37,000 years before the present, when the population's genetic diversity began to decline dramatically. The timing of this decline correlates with environmental changes associated with the onset of the last glacial cycle, whereas archaeological evidence does not support the presence of large populations of humans in Eastern Beringia until more than 15,000 years later.Item Metadata only Reconstructing an island radiation using ancient and recent DNA: the extinct and living day geckos (Phelsuma) of the Mascarene islands(Academic Press Inc Elsevier Science, 2004) Austin, J.; Arnold, E.; Jones, C.Mitochondrial (12SrRNA and cyt b, 1086 bp) and nuclear (c-mos, 374 bp) DNA sequences were used to investigate relationships and biogeography of 24 living and extinct taxa of Phelsuma geckos. Monophyly of Phelsuma and sister relationship to the SW African Rhoptropella is corroborated. Phelsuma originated on Madagascar and made multiple long-distance invasions of oceanic islands including the Mascarenes, Aldabra, Comores, Seychelles, Andamans, and perhaps Pemba. The Mascarenes were probably colonised once, about 4.2-5.1Ma, and here Phelsuma rosagularis and Phelsuma inexpectata are newly recognised as species, as are three lineages of Phelsuma cepediana. Mascarene relationships are: Phelsuma edwardnewtoni, Phelsuma gigas (Phelsuma guentheri ((((P. cepediana A (P. cepediana B, C)) P. rosagularis) Phelsuma borbonica) ((Phelsuma ornata, P. inexpectata) Phelsuma guimbeaui))). The two recently extinct species, P. edwardnewtoni and the giant secondarily nocturnal Phelsuma gigas, differentiated on Rodrigues while on Mauritius the large nocturnal P. guentheri separated from a small diurnal form that radiated into six species, a likely result of volcanic activity. Two small-bodied lineages from Mauritius invaded the more recent island of Réunion producing two more species. Outside the Mascarenes, two mainly Madagascan assemblages are substantiated: Phelsuma serraticauda (Phelsuma lineata, Phelsuma laticauda, Phelsuma quadriocellata); (Phelsuma m. kochi (Phelsuma m. grandis, Phelsuma abboti)) (Phelsuma astriata, Phelsuma sundbergi). Their relationships to the Mascarene clade, and to Phelsuma mutabilis, Phelsuma standingi and Phelsuma andamanensis are unresolved.Item Metadata only Prevalence and differential host-specificity of two avian blood parasite genera in the Australo-Papuan region(Blackwell Publishing Ltd, 2004) Gering, E.; Austin, J.; Beadell, J.; Dumbacher, J.; Peirce, M.; Pratt, T.; Atkinson, C.; Fleischer, R.The degree to which widespread avian blood parasites in the genera Plasmodium and Haemoproteus pose a threat to novel hosts depends in part on the degree to which they are constrained to a particular host or host family. We examined the host distribution and host-specificity of these parasites in birds from two relatively understudied and isolated locations: Australia and Papua New Guinea. Using polymerase chain reaction (PCR), we detected infection in 69 of 105 species, representing 44% of individuals surveyed (n = 428). Across host families, prevalence of Haemoproteus ranged from 13% (Acanthizidae) to 56% (Petroicidae) while prevalence of Plasmodium ranged from 3% (Petroicidae) to 47% (Ptilonorhynchidae). We recovered 78 unique mitochondrial lineages from 155 sequences. Related lineages of Haemoproteus were more likely to derive from the same host family than predicted by chance at shallow (average LogDet genetic distance = 0, n = 12, P = 0.001) and greater depths (average distance = 0.014, n = 11, P < 0.001) within the parasite phylogeny. Within two major Haemoproteus subclades identified in a maximum likelihood phylogeny, host-specificity was evident up to parasite genetic distances of 0.029 and 0.007 based on logistic regression. We found no significant host relationship among lineages of Plasmodium by any method of analysis. These results support previous evidence of strong host-family specificity in Haemoproteus and suggest that lineages of Plasmodium are more likely to form evolutionarily–stable associations with novel hosts.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 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 Worldwide phylogeography of wild boar reveals multiple centers of pig domestication(Amer Assoc Advancement Science, 2005) Larson, G.; Dobney, K.; Albarella, U.; Fang, M.; Matisoo-Smith, E.; Robins, J.; Lowden, S.; Finlayson, H.; Brand, T.; Willerslev, E.; Rowley-Conwy, P.; Andersson, L.; Cooper, A.Mitochondrial DNA (mtDNA) sequences from 686 wild and domestic pig specimens place the origin of wild boar in island Southeast Asia (ISEA), where they dispersed across Eurasia. Previous morphological and genetic evidence suggested pig domestication took place in a limited number of locations (principally the Near East and Far East). In contrast, new genetic data reveal multiple centers of domestication across Eurasia and that European, rather than Near Eastern, wild boar are the principal source of modern European domestic pigs.Item Metadata only Evolution of the extinct Sabretooths and the American cheetah-like cat(Dell Press, 2005) Barnett, R.; Barnes, I.; Phillips, M.; Martin, L.; Harington, C.; Leonard, J.; Cooper, A.Item Metadata only Phylogeography of an east Australian wet-forest bird, the satin bowerbird (Ptilonorhynchus violaceus), derived from mtDNA, and its relationship to morphology(Blackwell Publishing Ltd, 2005) Nicholls, J.; Austin, J.Australian wet forests have undergone a contraction in range since the mid-Tertiary, resulting in a fragmented distribution along the east Australian coast incorporating several biogeographical barriers. Variation in mitochondrial DNA and morphology within the satin bowerbird was used to examine biogeographical structure throughout almost the entire geographical extent of these wet forest fragments. We used several genetic analysis techniques, nested clade and barrier analyses, that use patterns inherent in the data to describe the spatial structuring. We also examined the validity of the two previously described satin bowerbird subspecies that are separated by well-defined biogeographical barriers and tested existing hypotheses that propose divergence occurs within each subspecies across two other barriers, the Black Mountain corridor and the Hunter Valley. Our data showed that the two subspecies were genetically and morphologically divergent. The northern subspecies, found in the Wet Tropics region of Queensland, showed little divergence across the Black Mountain corridor, a barrier found to be significant in other Wet Tropics species. Biogeographical structure was found through southeastern Australia; three geographically isolated populations showed genetic differentiation, although minimal divergence was found across the proposed Hunter Valley barrier. A novel barrier was found separating inland and coastal populations in southern New South Wales. Little morphological divergence was observed within subspecies, bar a trend for birds to be larger in the more southerly parts of the species' range. The results from both novel and well-established genetic analyses were similar, providing greater confidence in the conclusions about spatial divergence and supporting the validity of these new techniques.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.