The South Australian Museum is a natural history museum and research institution in Adelaide, South Australia, founded in 1856. It occupies a complex of buildings on North Terrace in the cultural precinct of the Adelaide Parklands. Wikipedia.
King B.,Flinders University |
Lee M.S.Y.,University of Adelaide |
Lee M.S.Y.,South Australian Museum
Systematic Biology | Year: 2015
Virtually all models for reconstructing ancestral states for discrete characters make the crucial assumption that the trait of interest evolves at a uniform rate across the entire tree. However, this assumption is unlikely to hold in many situations, particularly as ancestral state reconstructions are being performed on increasingly large phylogenies. Here, we show how failure to account for such variable evolutionary rates can cause highly anomalous (and likely incorrect) results, while three methods that accommodate rate variability yield the opposite, more plausible, and more robust reconstructions. The random local clock method, implemented in BEAST, estimates the position and magnitude of rate changes on the tree; split BiSSE estimates separate rate parameters for pre-specified clades; and the hidden rates model partitions each character state into a number of rate categories. Simulations show the inadequacy of traditional models when characters evolve with both asymmetry (different rates of change between states within a character) and heterotachy (different rates of character evolution across different clades). The importance of accounting for rate heterogeneity in ancestral state reconstruction is highlighted empirically with a new analysis of the evolution of viviparity in squamate reptiles, which reveal a predominance of forward (oviparous-viviparous) transitions and very few reversals. © 2015 © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: firstname.lastname@example.org.
Lee M.S.Y.,South Australian Museum |
Lee M.S.Y.,University of Adelaide
Current Biology | Year: 2013
One of the major remaining gaps in the vertebrate fossil record concerns the origin of turtles. The enigmatic little reptile Eunotosaurus could represent an important transitional form, as it has a rudimentary shell that resembles the turtle carapace. © 2013 Elsevier Ltd. All rights reserved.
Skinner A.,University of Adelaide |
Skinner A.,South Australian Museum
Systematic Biology | Year: 2010
Rates of phenotypic evolution derive from numerous interrelated processes acting at varying spatial and temporal scales and frequently differ substantially among lineages. Although current models employed in reconstructing ancestral character states permit independent rates for distinct types of transition (forward and reverse transitions and transitions between different states), these rates are typically assumed to be identical for all branches in a phylogeny. In this paper, I present a general model of character evolution enabling rate heterogeneity among branches. This model is employed in assessing the extent to which the assumption of uniform transition rates affects reconstructions of ancestral limb morphology in the scincid lizard clade Lerista and, accordingly, the potential for rate variability to mislead inferences of evolutionary patterns. Permitting rate variation among branches significantly improves model fit for both the manus and the pes. A constrained model in which the rate of digit acquisition is assumed to be effectively zero is strongly supported in each case; when compared with a model assuming unconstrained transition rates, this model provides a substantially better fit for the manus and a nearly identical fit for the pes. Ancestral states reconstructed assuming the constrained model imply patterns of limb evolution differing significantly from those implied by reconstructions for uniform-rate models, particularly for the pes; whereas ancestral states for the uniform-rate models consistently entail the reacquisition of pedal digits, those for the model incorporating among-lineage rate heterogeneity imply repeated, unreversed digit loss. These results indicate that the assumption of identical transition rates for all branches in a phylogeny may be inappropriate in modeling the evolution of phenotypic traits and emphasize the need for careful evaluation of phylogenetic tests of Dollo's law. © The Author(s) 2010.
News Article | December 9, 2016
Recent surveys by Australian scientists have identified an apparent significant decline in the numbers of trapdoor spiders across southern Australia. Famous for their carefully camouflaged burrows - some with lids or 'trapdoors' from which they launch themselves to catch their prey - trapdoor spiders are remarkable animals. The females of some species are known to live in the same burrow for more than 25 years. Led by the University of Adelaide, in collaboration with the Western Australian Museum, the Queensland Museum, the Department of Parks and Wildlife (WA) and The University of Western Australia, the scientists have compared numbers of trapdoors at various locations across Australia's southern agricultural and arid zones with survey data from the 1950s to the present. The findings have been published in the journal Austral Entomology. "We have good historical records of trapdoor spiders going back 60 years which showed population numbers were reasonably good, but recent surveys of the same areas show numbers are extremely low, and in some cases spiders are completely absent," says project leader Professor Andrew Austin, from the University of Adelaide's Australian Centre for Evolution Biology and Biodiversity. Trapdoor spiders are sometimes encountered in domestic gardens in towns and cities around Australia when they emerge from their burrows to feed or look for a mate. However, these represent just a few common species, when in fact there are several hundred species found in particular habitats, most of which haven't even received a formal scientific name. Now there is concern that this major and unique component of Australia's fauna may be threatened. "The problem in some areas looks to be that the few spiders surviving are old females, and an absence of males means there is no capacity to reproduce, and they eventually die and the population disappears," says team member Dr Mark Harvey, a national expert on spiders based at the Western Australian Museum. "The reasons for this decline are probably complex but are undoubtedly linked to a century of intensive land clearing and the fact that trapdoor spiders are susceptible to soil disturbance around their burrows." Lead author Dr Mike Rix, who did his research at the University of Adelaide and is now at the Queensland Museum, says the results of this research are concerning on their own, but may also be representative of a decline in populations of other invertebrate animals. "To get a better handle on the extent of the problem, there is a real need for more detailed follow up surveys, including to assess where remnant populations still exist," he says. This research was funded by the Australian Research Council, with additional support from BHP Billiton, Rio Tinto, Biota Environmental Sciences, the South Australian Museum, and the Western Australian Museum. Dr Mike Rix, former University of Adelaide, now at Queensland Museum. Mobile: +61 (0) 407 694 713, email@example.com
News Article | November 4, 2016
According to a new study, humans occupied Australia's arid lands and started to develop sophisticated tools approximately 10,000 years earlier than previously documented, placing them roughly 49,000 years in the past. The study, published in the journal Nature on Nov. 2, was conducted by researchers from the University of Adelaide and it analyzes the oldest evidence of Aboriginal occupation in South Australia. While people have reached the Australian territory roughly 50,000 years ago, it was unclear whether they actually remained there to occupy it or simply migrated toward another place. Led by Giles Hamm, research archaeologist and Honorary Fellow of the South Australian Museum, and his conjoined team, the study suggests that people settled down in the Australian region a few millennia since arriving on the continent. During that time, they developed key technologies, started important cultural practices and essentially built a cultural community long before previously believed. Among the instruments and possessions recovered from different layers of sediment at the Warratyi Rock Shelter in the desert region of northern South Australia were bone tools, stone tools as well as red ochre, found to be utilized as pigment. The discovery shifts the perception of how the civilization evolved massively because of the very early use of such materials. Gypsum was also found at the site. As part of the research procedure, the geochronology of the study was undertaken, which involved the identification of the time period when people habited the area. This was based on a series of factors from ground layers to the objects' characteristics. "One of the key strengths of this study is the chronology, which has typically proved to be a contentious issue at early archaeological sites in Australia. We have used a range of complementary dating techniques and targeted different types of materials to ensure that the age of the site is reliably known," explained geochronology specialist Lee Arnold, ARC Future Fellow with the University of Adelaide. In order to identify the dates of the objects they discovered as precisely as possible, the researchers used a single-grain optically stimulated luminescence procedure to establish the date when the sediments containing the fossils and artifacts were deposited. Along with complementary statistical techniques, the team managed to find out a precise occupation history of the archaeological site. According to the results of the research, the occupation of the arid zone took place long before the last ice age, being contemporaneous with the Australian megafauna. The study puts into perspective the development of the Australian culture and civilization, by comparison to Europe's development. © 2017 Tech Times, All rights reserved. Do not reproduce without permission.
Pyke G.H.,University of Technology, Sydney |
Pyke G.H.,Macquarie University |
Pyke G.H.,South Australian Museum
Methods in Ecology and Evolution | Year: 2015
Summary: Interest in Lévy walks within the context of movement of organisms has recently soared, with some now referring to this approach as the Lévy walk/flight paradigm. The principal assumptions, taken from the world of physics, have been that organisms searching for food or some other resource adopt random walks, whereby the direction of each successive step in the walk is chosen at random from the complete circle and the length of each step, unless terminated through resource encounter, is chosen from a Lévy probability distribution with a particular exponent μ. The additional assumption that organisms forage optimally, such that μ maximizes the rate of resource encounter, has led to the so-called Lévy foraging hypothesis, with many attempts to test it. However, the Lévy walk model is unrealistic, especially as it omits directionality between successive steps, a typical feature of movements of individual organisms at spatial scales relevant to their movement decisions. It also results in lower foraging efficiency than other more realistic models and the evidence that organisms actually 'do the Lévy walk' is weak to non-existent, despite claims to the contrary. Early optimal foraging studies of movements of organisms and a new generation of movement models avoid these problems. It is therefore time to divorce the Lévy walk model from optimal foraging theory, revisit some of the early optimal foraging studies of movements and pursue the new generation of movement models. However, the Lévy approach may still prove useful at relatively large spatial scales, in terms of both theory and observations, especially in relation to distribution, dispersal and other population-level phenomena, and in this way biology, physics and mathematics may yet work well together. © 2014 The Author.
Frankham R.,Macquarie University |
Frankham R.,South Australian Museum
Heredity | Year: 2012
Levels of genetic diversity in finite populations are crucial in conservation and evolutionary biology. Genetic diversity is required for populations to evolve and its loss is related to inbreeding in random mating populations, and thus to reduced population fitness and increased extinction risk. Neutral theory is widely used to predict levels of genetic diversity. I review levels of genetic diversity in finite populations in relation to predictions of neutral theory. Positive associations between genetic diversity and population size, as predicted by neutral theory, are observed for microsatellites, allozymes, quantitative genetic variation and usually for mitochondrial DNA (mtDNA). However, there are frequently significant deviations from neutral theory owing to indirect selection at linked loci caused by balancing selection, selective sweeps and background selection. Substantially lower genetic diversity than predicted under neutrality was found for chromosomes with low recombination rates and high linkage disequilibrium (compared with normally recombining chromosomes within species and adjusted for different copy numbers and mutation rates), including W (median 100% lower) and Y (89% lower) chromosomes, dot fourth chromosomes in Drosophila (94% lower) and mtDNA (67% lower). Further, microsatellite genetic and allelic diversity were lost at 12 and 33% faster rates than expected in populations adapting to captivity, owing to widespread selective sweeps. Overall, neither neutral theory nor most versions of the genetic draft hypothesis are compatible with all empirical results. © 2012 Macmillan Publishers Limited All rights reserved.
Smales L.R.,South Australian Museum
Journal of Parasitology | Year: 2013
Eight species of Neoechinorhynchus were reported from Australian waters. Neoechinorhynchus vittiformis n. Sp. is described from Eleutheronema tetradactylum (Shaw). It can be distinguished from all its congeners by the following combination of characters: long cylindrical trunk without cuticular plaques, globular proboscis, proboscis armature with the anterior circle of hooks larger with simple roots and the middle and posterior hooks the same size and smaller, short neck, lemnisci nearly equal, almost reaching the anterior testis which is more than half the length of the posterior testis. Neoechinorhynchus (Neoechinorhynchus) bryanti n. Sp., described from Liza subviridis (Valenciennes), also with an elongated trunk, can be distinguished from its congeners by the combination of a wider anterior trunk without cuticular plaques, a relatively long conical neck, a subglobular proboscis having anterior hooks with manubria, the hooks becoming gradually smaller posteriorly, the lemnisci not reaching level of testes and the anterior testis being longer than posterior testis. Neoechinorhynchus sp. resembled Neoechinorhynchus aldrichettae Edmonds, 1971 but had a rectangular-shaped proboscis with larger anterior hooks. New host and locality records were presented for N. aldrichettae, Neoechinorhynchus (Hebesoma) agilis (Rudolphi) and Neoechinorhynchus tylosuri Yamaguti, 1939. No additional specimens of either Neoechinorhynchus ningalooensis Pichelin and Cribb, 2001 or the species inquirenda, Neoechinorhynchus magnus Southwell and Macfie, 1925, were available for study. Of the 8 putative species listed here, 5 (N. [N.] bryanti, N. magnus, N. ningalooensis, N. vittiformis, and Neoechinorhynchus sp.) are endemic to Australian waters. By comparison with the North American fauna the Australian fauna was considered impoverished. The morphological and zoogeographical similarities within the group of 8 long, slender neoechinorhynchid species found in the African, Indo Malayan, and Western Pacific Regions, including the 3 found in Australia, may reflect a degree of evolutionary affinity. © 2013 American Society of Parasitologists.
Kohler F.,South Australian Museum |
Criscione F.,South Australian Museum
Journal of Biogeography | Year: 2013
Aim: Camaenidae are amongst the most diverse land snail groups in Southeast Asia and Australasia, but their phylogeny and biogeography are poorly understood. The monophyly and biogeographical origin of the Australian species has remained uncertain. Being reported from north-western Australia as well as from the Lesser Sunda Islands, the genus Rhagada is crucial to our understanding of camaenid biogeography. By resolving the phylogeny of Rhagada, we aim to uncover spatial and temporal patterns of its diversification at the interface between Oriental and Australian biogeographical regions. Location: North-western Australia, Lesser Sunda Islands. Methods: We implemented Bayesian and maximum likelihood methods to generate the most complete mitochondrial phylogeny of Rhagada land snails to date. Divergence times of clades were estimated by employing a relaxed molecular clock and two internal calibrations from fossil and tectonic data. Ancestral areas of clades were inferred using character history reconstruction based on parsimony, as implemented in Mesquite. Results: Rhagada clustered into eight well-supported clades that are restricted to certain geographical areas. Species from the Kimberley, Western Australia, formed the earliest branching clades. A single Lesser Sunda clade was sister to a radiation in the Western Australian Pilbara. Molecular age estimates placed the evolutionary origin of Rhagada between the late Miocene and early Pleistocene, and dispersal from Western Australia onto the Lesser Sunda Islands in a period between the mid-Pliocene and early Pleistocene. Main conclusions: The camaenid Rhagada originated in the Kimberley and subsequently expanded its range through the Pilbara and into the Shark Bay area, probably during the late Pliocene and mid-Pleistocene. From the Kimberley, Rhagada snails colonized the Lesser Sunda Islands probably not before 1.9 Ma following emergence of the youngest islands, which may have acted as 'stepping stones'. Over-sea dispersal might have occurred during the mid-Pleistocene when lowered sea levels facilitated faunal exchange across the region. © 2013 John Wiley & Sons Ltd.
Faith D.P.,South Australian Museum
Annals of the New York Academy of Sciences | Year: 2013
Evolutionary biology is a core discipline in biodiversity science. Evolutionary history or phylogeny provides one natural measure of biodiversity through the popular phylogenetic diversity (PD) measure. The evolutionary model underlying PD means that it can be interpreted as quantifying the relative feature diversity of sets of species. Quantifying feature diversity measures possible future uses and benefits or option values. Interpretation of PD as counting-up features is the basis for an emerging broad family of PD calculations, of use to both biodiversity researchers and decision makers. Many of these calculations extend conventional species-level indices to the features level. Useful PD calculations include PD complementarity and endemism, Hill and Valley numbers incorporating abundance, and PD dissimilarities. A flexible analysis framework is provided by expected PD calculations, applied to either probabilities of extinction or presence-absence. Practical extensions include phylogenetic risk analysis and measures of distinctiveness and endemism. These support the integration of phylogenetic diversity into biodiversity conservation and monitoring programs. © 2013 The Authors. Annals of the New York Academy of Sciences published by Wiley Periodicals Inc. on behalf of The New York Academy of Sciences.