44 Works

Data from: Molecular phylogeny and phylogeography of the Australian freshwater fish genus Galaxiella, with an emphasis on dwarf Galaxias (G. pusilla)

Peter J. Unmack, Justin C. Bagley, Mark Adams, Michael P. Hammer & Jerald B. Johnson
The freshwater fauna of Southern Australia is primarily restricted to the southwestern and southeastern corners of the continent, and is separated by a large, arid region that is inhospitable to this biota. This geographic phenomenon has attracted considerable interest from biogeographers looking to explain evolutionary diversification in this region. Here, we employed phylogenetic and phylogeographic approaches to evaluate the effect of this barrier on a group of four galaxiid fish species (Galaxiella) endemic to temperate...

Data from: Modular tagging of amplicons using a single PCR for high-throughput sequencing

Laurence J. Clarke, Paul Czechowski, Julien Soubrier, Mark I. Stevens & Alan Cooper
High-throughput sequencing (HTS) of PCR amplicons is becoming the method of choice to sequence one or several targeted loci for phylogenetic and DNA barcoding studies. Although the development of HTS has allowed rapid generation of massive amounts of DNA sequence data, preparing amplicons for HTS remains a rate-limiting step. For example, HTS platforms require platform-specific adapter sequences to be present at the 5′ and 3′ end of the DNA fragment to be sequenced. In addition,...

Data from: Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds

Andrea Cau, Gareth J. Dyke, Michael S. Y. Lee & Darren Naish
Recent discoveries have highlighted the dramatic evolutionary transformation of massive, ground-dwelling theropod dinosaurs into light, volant birds. Here, we apply Bayesian approaches (originally developed for inferring geographic spread and rates of molecular evolution in viruses) in a different context: to infer size changes and rates of anatomical innovation (across up to 1549 skeletal characters) in fossils. These approaches identify two drivers underlying the dinosaur-bird transition. The theropod lineage directly ancestral to birds undergoes sustained miniaturization...

Data from: Multiple morphological clocks and total-evidence tip-dating in mammals

Michael Lee & Michael S. Y. Lee
Morphological integration predicts that correlated characters will coevolve; thus, each distinct suite of correlated characters might be expected to evolve according to a separate clock or ‘pacemaker’. Characters in a large morphological dataset for mammals were found to be evolving according to seven separate clocks, each distinct from the molecular clock. Total-evidence tip-dating using these multiple clocks inflated divergence time estimates, but potentially improved topological inference. In particular, single-clock analyses placed several meridiungulates and condylarths...

Data from: Palaeoecological inferences for the fossil Australian snakes Yurlunggur and Wonambi (Serpentes, Madtsoiidae)

Alessandro Palci, Mark N. Hutchinson, Michael W. Caldwell, John D. Scanlon, Michael S.Y. Lee & Michael S. Y. Lee
Madtsoiids are among the most basal snakes, with a fossil record dating back to the Upper Cretaceous (Cenomanian). Most representatives went extinct by the end of the Eocene, but some survived in Australia until the late Cenozoic. Yurlunggur and Wonambi are two of these late forms, and also the best-known madtsoiids to date. A better understanding of the anatomy and palaeoecology of these taxa may shed light on the evolution and extinction of this poorly...

Data from: Specific MHC class I supertype associated with parasite infection and colour morph in a wild lizard population

Jessica D. Hacking, Devi Stuart-Fox, Stephanie S. Godfrey & Michael G. Gardner
The major histocompatibility complex (MHC) is a large gene family that plays a central role in the immune system of all jawed vertebrates. Non-avian reptiles are under-represented within the MHC literature and little is understood regarding the mechanisms maintaining MHC diversity in this vertebrate group. Here, we examined the relative roles of parasite-mediated selection and sexual selection in maintaining MHC class I diversity of a colour polymorphic lizard. We discovered evidence for parasite-mediated selection acting...

Run and output files from: Holocene population expansion of a tropical bee coincides with early human colonisation of Fiji rather than climate change

James B. Dorey, Scott V.C. Groom, Alejandro Velasco-Castrillón, Mark Stevens, Michael S.Y. Lee & Michael P. Schwarz
There is substantial debate about the relative roles of climate change and human activities on biodiversity and species demographies over the Holocene. In some cases, these two factors can be resolved using fossil data, but for many taxa such data are not available. Inferring historical demographies of taxa has become common, but the methodologies are mostly recent and their shortcomings often unexplored. The bee genus Homalictus is developing into a tractable model system for understanding...

Data from: Opsin transcripts of predatory diving beetles: a comparison of surface and subterranean photic niches

Simon M. Tierney, Steven J. B. Cooper, Kathleen M. Saint, Terry Bertozzi, Josephine Hyde, William F. Humphreys & Andrew D. Austin
The regressive evolution of eyes has long intrigued biologists yet the genetic underpinnings remain opaque. A system of discrete aquifers in arid Australia provides a powerful comparative means to explore trait regression at the genomic level. Multiple surface ancestors from two tribes of diving beetles (Dytiscidae) repeatedly invaded these calcrete aquifers and convergently evolved eye-less phenotypes. We use this system to assess transcription of opsin photoreceptor genes among the transcriptomes of two surface and three...

Data from: Panmixia supports divergence with gene flow in Darwin’s small ground finch, Geospiza fuliginosa, on Santa Cruz, Galápagos Islands

Toby H. Galligan, Stephen C. Donnellan, Frank J. Sulloway, Alison J. Fitch, Terry Bertozzi & Sonia Kleindorfer
The divergence-with-gene-flow model of speciation has a strong theoretical basis with a growing number of plausible examples in nature, but remains hotly debated. Darwin’s finches of the Galápagos Archipelago have played an important role in our understanding of speciation processes. Recent studies suggest that this group may also provide insights into speciation via divergence with gene flow. On the island of Santa Cruz, recent studies found evidence for adaptive divergence in Darwin’s small ground finch,...

Data from: Recent rapid speciation and ecomorph divergence in Indo-Australian sea snakes

Kate L. Sanders, Arne R. Rasmussen, , Johan Elmberg, Anslem De Silva, Michael L. Guinea, Michael S.Y. Lee & Michael S. Y. Lee
The viviparous sea snakes (Hydrophiinae) are a young radiation of at least 62 species that display spectacular morphological diversity and high levels of local sympatry. To shed light on the mechanisms underlying sea snake diversification, we investigated recent speciation and eco-morphological differentiation in a clade of four nominal species with overlapping ranges in Southeast Asia and Australia. Analyses of morphology and stomach contents identified the presence of two distinct ecomorphs: a ‘macrocephalic’ ecomorph that reaches...

Data from: Avian predation intensity as a driver of clinal variation in colour morph frequency

Genevieve Matthews, Celine T. Goulet, Kaspar Delhey, Zak S. Atkins, Geoffrey M. While, Michael G. Gardner & David G. Chapple
1) Phenotypic variation provides the framework for natural selection to work upon, enabling adaptive evolution. One of the most discernible manifestations of phenotypic variability is colour variation. When this variation is discrete, genetically-based colour pattern morphs occur simultaneously within a population. 2) Why and how colour polymorphisms are maintained is an evolutionary puzzle. Several evolutionary drivers have been hypothesized as influencing clinal patterns of morph frequency, with spatial variation in climate and predation being considered...

Data from: Landscape genetics informs mesohabitat preference and conservation priorities for a surrogate indicator species in a highly fragmented river system

James Lean, Michael P. Hammer, Peter J. Unmack, Mark Adams & Luciano B. Beheregaray
Poor dispersal species represent conservative benchmarks for biodiversity management because they provide insights into ecological processes influenced by habitat fragmentation that are less evident in more dispersive organisms. Here we used the poorly dispersive and threatened river blackfish (Gadopsis marmoratus) as a surrogate indicator system for assessing the effects of fragmentation in highly modified river basins and for prioritizing basin-wide management strategies. We combined individual, population and landscape-based approaches to analyze genetic variation in samples...

Data from: Resources for phylogenomic analyses of Australian terrestrial vertebrates

Jason G. Bragg, Sally Potter, Ke Bi, Renee Catullo, Stephen C. Donnellan, Mark D. B. Eldridge, Leo Joseph, J. Scott Keogh, Paul Oliver, Kevin C. Rowe & Craig Moritz
High-throughput sequencing methods promise to improve our ability to infer the evolutionary histories of lineages and to delimit species. These are exciting prospects for the study of Australian vertebrates, a group comprised of many globally unique lineages with a long history of isolation. The evolutionary relationships within many of these lineages have been difficult to resolve with small numbers of loci, and we now know that many lineages also exhibit substantial cryptic diversity. Here, we...

Phylogeography, historical demography and systematics of the world’s smallest pythons (Pythonidae, Antaresia)

Damien Esquerré, Stephen Donnellan, Carlos Pavón-Vázquez, Jéssica Fenker & Scott Keogh
Advances from empirical studies in phylogeography, systematics and species delimitation highlight the importance of integrative approaches for quantifying taxonomic diversity. Genomic data have greatly improved our ability to discern both systematic diversity and evolutionary history. Here we combine analyses of mitochondrial DNA sequences, thousands of genome-wide SNPs and linear and geometric morphometrics on Antaresia, a clade of four currently recognised dwarf pythons from Australia and New Guinea (Antaresia childreni, A. stimsoni, A. maculosa and A....

Comparative phylogeography reveals consistently shallow genetic diversity in a mitochondrial marker in Antarctic bdelloid rotifers

Diego Fontaneto, Zeyneb Vildan Cakil, Giuseppe Garlasché, Nataliia Iakovenko, Andrea Di Cesare, Ester M. Eckert, Roberto Guidetti, Lina Hamdan, Karel Janko, Dzmitry Lukashanets, Lorena Rebecchi, Stefano Schiaparelli, Tommaso Sforzi, Eva Štefková Kašparová, Alejandro Velasco-Castrillón & Elizabeth Walsh
Aim: The long history of isolation of the Antarctic continent, coupled with the harsh ecological conditions of freezing temperatures could affect the patterns of genetic diversity in the organisms living there. We aim (1) to test whether such pattern can be seen in a mitochondrial marker of bdelloid rotifers, a group of microscopic aquatic and limno-terrestrial animals, and (2) to speculate on the potential mechanisms driving the pattern. Location: focus on Antarctica. Taxon: Rotifera Bdelloidea....

Data from: Crossing the line: increasing body size in a trans-Wallacean lizard radiation (Cyrtodactylus, Gekkota)

Paul M. Oliver, Phillip Skipwith & Michael S. Y. Lee
The region between the Asian and Australian continental plates (Wallacea) demarcates the transition between two differentiated regional biotas. Despite this striking pattern, some terrestrial lineages have successfully traversed the marine barriers of Wallacea and subsequently diversified in newly colonized regions. The hypothesis that these dispersals between biogeographic realms are correlated with detectable shifts in evolutionary trajectory has however rarely been tested. Here, we analyse the evolution of body size in a widespread and exceptionally diverse...

Data from: Multilocus phylogeography reveals nested endemism in a gecko across the monsoonal tropics of Australia

Craig Moritz, Matthew Fujita, Dan F. Rosauer, Rosa Agudo, Gayleen Bourke, Russell Palmer, Mitzy Pepper, Sally Potter, Renae Pratt, Mitchell Scott, Maria Tonione, Stephen Donnellan, Paul Doughty, D. Rosauer & M. K. Fujita
Multilocus phylogeography can uncover taxonomically unrecognized lineage diversity across complex biomes. The Australian monsoonal tropics includes vast, ecologically intact savanna-woodland plains interspersed with ancient sandstone uplands. Though recognized in general for its high species richness and endemism, the biodiversity of the region remains underexplored due to its remoteness. This is despite a high rate of ongoing species discovery, especially in wetter regions and for rock-restricted taxa. To provide a baseline for ongoing comparative analyses, we...

Data from: A multigene molecular assessment of cryptic biodiversity in the iconic freshwater blackfishes (Teleostei: Percichthyidae: Gadopsis) of south-eastern Australia

Michael P. Hammer, Peter J. Unmack, Mark Adams, Tarmo A. Raadik & Jerald B. Johnson
Freshwater biodiversity is under ever increasing threat from human activities, and its conservation and management require a sound knowledge of species-level taxonomy. Cryptic biodiversity is a common feature for aquatic systems, particularly in Australia, where recent genetic assessments suggest that the actual number of freshwater fish species may be considerably higher than currently listed. The freshwater blackfishes (genus Gadopsis) are an iconic group in south-eastern Australia and, in combination with their broad, naturally divided distribution...

Data from: The role of continental shelf width in determining freshwater phylogeographic patterns in southeastern Australian pygmy perches (Teleostei: Percichthyidae)

Peter J. Unmack, Michael P. Hammer, Mark Adams, Jerald B. Johnson & Thomas E. Dowling
Biogeographic patterns displayed by obligate freshwater organisms are intimately related to the nature and extent of connectivity between suitable habitats. Two of the more significant barriers to freshwater connections are seawater and major drainage divides. South-eastern Australia provides a contrast between these barriers as it has discrete areas that are likely influenced to a greater or lesser extent by each barrier type. We use continental shelf width as a proxy for the potential degree of...

Data from: Deep phylogeographic structuring of populations of the trapdoor spider Moggridgea tingle (Migidae) from southwestern Australia: evidence for long-term refugia within refugia

Steven J.B. Cooper, Mark S. Harvey, Kathleen M. Saint & Barbara Y. Main
Southwestern Australia has been recognized as a biodiversity hotspot of global significance, and it is particularly well known for its considerable diversity of flowering plant species. Questions of interest are how this region became so diverse and whether its fauna show similarly diverse patterns of speciation. Here we have carried out a phylogeographic study of trapdoor spiders (Migidae: Moggridgea), a presumed Gondwanan lineage found in wet forest localities across southwestern Australia. Phylogenetic, molecular clock and...

Data from: Allegory of a cave crustacean: systematic and biogeographic reality of Halosbaena (Peracarida: Thermosbaenacea) sought with molecular data at multiple scales

Timothy J. Page, Jane M. Hughes, Kathryn M. Real, Mark I. Stevens, Rachael A. King & William F. Humphreys
Halosbaena Stock, 1976 are small crustaceans found in a number of distant, isolated subterranean locations in the Northern (Caribbean and Canary Islands) and Southern Hemispheres (Christmas Island and north-western Australia in Cape Range, Barrow Island and Pilbara regions). This distribution is surprising for an animal that produces few eggs, has no free-living larval stage, and succours their young in a dorsal brood pouch. It is usually explained by the passive movement of ancestral populations on...

Data from: High detectability with low impact: optimising large PIT tracking systems for cave-dwelling bats

Emmi Van Harten, Terry Reardon, Linda Lumsden, Noel Meyers, Thomas Prowse, John Weyland & Ruth Lawrence
Passive integrated transponder (PIT) tag technology permits the ‘resighting’ of animals tagged for ecological research without the need for physical re-trapping. While this is effective if animals pass within centimetres of tag readers, short-distance detection capabilities have prevented the use of this technology with many species. To address this problem, we optimised a large (15 m-long) flexible antenna system to provide a c. 8 m2 vertical detection plane for detecting animals in flight. We installed...

Character set and phylogenetic analyses of the living and fossil egerniine scincids of Australia

Kailah Thorn, Mark Hutchinson, Michael Lee, Aaron Camens & Trevor Worthy
The diverse living Australian lizard fauna contrasts greatly with their limited Oligo-Miocene fossil record. New Oligo-Miocene fossil vertebrates from the Namba Formation (south of Lake Frome, South Australia) were uncovered from multiple expeditions from 2007–2018. Abundant disarticulated material of small vertebrates was concentrated in shallow lenses along the palaeo-lake edges, now exposed on the western shore. The fossiliferous lens occurring within the Namba Formation, also known from Billeroo Creek 2 km northeast of Lake Pinpa,...

The roles of aridification and sea level changes in the diversification and persistence of freshwater fish lineages

Sean Buckley, Chris Brauer, Peter Unmack, Michael Hammer & Luciano Beheregaray
While the influence of Pleistocene climatic changes on divergence and speciation has been well-documented across the globe, complex spatial interactions between hydrology and eustatics over longer timeframes may also determine species evolutionary trajectories. Within the Australian continent, glacial cycles were not associated with changes in ice cover and instead largely resulted in fluctuations from moist to arid conditions across the landscape. Here, we investigate the role of hydrological and coastal topographic changes brought about by...

Data from: Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing

Carole P. Elliott, Neal J. Enright, Richard J. N. Allcock, Michael G. Gardner, Emese Meglécz, Janet Anthony & Siegfried L. Krauss
The development and screening of microsatellite markers have been accelerated by next-generation sequencing (NGS) technology and in particular GS-FLX pyro-sequencing (454). More recent platforms such as the PGM semiconductor sequencer (Ion Torrent) offer potential benefits such as dramatic reductions in cost, but to date have not been well utilized. Here, we critically compare the advantages and disadvantages of microsatellite development using PGM semiconductor sequencing and GS-FLX pyro-sequencing for two gymnosperm (a conifer and a cycad)...

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