40 Works

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: 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: 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...

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: 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: 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...

Phylogenomics, biogeography and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade

Damien Esquerre, Daniel J. D. Natusch, Jessica A. Lyons, Amir Hamidy, Alan R. Lemmon, Emily M. Lemmon, Awal Riyanto, J. Scott Keogh & Stephen Donnellan
The large and enigmatic New Guinean pythons in the genus Leiopython are harvested from the wild to supply the international trade in pets. Six species are currently recognized (albertisii, biakensis, fredparkeri, huonensis, meridionalis, montanus) but the taxonomy of this group has been controversial. We combined analysis of 421 nuclear loci and complete mitochondrial genomes with morphological data to construct a detailed phylogeny of this group, understand their biogeographic patterns and establish the systematic diversity of...

Data from: Evaluating evolutionary history in the face of high gene tree discordance in Australian Gehyra (Reptilia: Gekkonidae)

Mark J. Sistrom, Terry Bertozzi, Mark N. Hutchinson & Steve C. Donnellan
Species tree methods have provided improvements for estimating species relationships and the timing of diversification in recent radiations by allowing for gene tree discordance. Although gene tree discordance is often observed, most discordance is attributed to incomplete lineage sorting rather than other biological phenomena, and the causes of discordance are rarely investigated. We use species trees from multi-locus data to estimate the species relationships, evolutionary history and timing of diversification among Australian Gehyra—a group renowned...

Data from: An early Cambrian chelicerate from the Emu Bay Shale, South Australia

James B. Jago, Diego C. García-Bellido & James G. Gehling
The Emu Bay Shale Lagerstätte (Cambrian Series 2, Stage 4) occurs on the north coast of Kangaroo Island, South Australia. Over 50 species are known from here, including trilobites and non-biomineralized arthropods, palaeoscolecids, a lobopodian, a polychaete, vetulicolians, nectocaridids, hyoliths, brachiopods, sponges and chancelloriids. A new chelicerate, Wisangocaris barbarahardyae gen. et sp. nov., is described herein, based on a collection of some 270 specimens. It is up to 60 mm long, with the length of...

Data from: Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards

Sonal Singhal, Huateng Huang, Pascal O. Title, Stephen C. Donnellan, Iris Holmes & Daniel L. Rabosky
Genetic diversity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic diversity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 individuals spanning 76 nominal species of Australian scincid lizards in the genus Ctenotus. To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based...

Data from: Across the Indian Ocean: a remarkable example of trans-oceanic dispersal in an austral mygalomorph spider

Sophie E. Harrison, Mark S. Harvey, Steven J.B. Cooper, Andrew D. Austin, Michael G. Rix & Steve J. B. Cooper
The Migidae are a family of austral trapdoor spiders known to show a highly restricted and disjunct distribution pattern. Here, we aim to investigate the phylogeny and historical biogeography of the group, which was previously thought to be vicariant in origin, and examine the biogeographic origins of the genus Moggridgea using a dated multi-gene phylogeny. Moggridgea specimens were sampled from southern Australia and Africa, and Bertmainus was sampled from Western Australia. Sanger sequencing methods were...

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)...

Data from: Global biodiversity assessment and hyper-cryptic species complexes: more than one species of elephant in the room?

Mark Adams, Tarmo A. Raadik, Christopher P. Burridge & Arthur Georges
Several recent estimates of global biodiversity have concluded that the total number of species on Earth lies near the lower end of the wide range touted in previous decades. However, none of these recent estimates formally explore the real ‘elephant in the room’, namely, what proportion of species are taxonomically invisible to conventional assessments, and thus, as undiagnosed cryptic species, remain uncountable until revealed by multi-gene molecular assessments. Here we explore the significance and extent...

Data from: Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution

Chen Wu, Melissa D. Jordan, Richard D. Newcomb, Neil J. Gemmell, Sarah Bank, Karen Meusemann, Peter K. Dearden, Elizabeth J. Duncan, Sefanie Grosser, Kim Rutherford, Paul P. Gardner, Ross N. Crowhurst, Bernd Steinwender, Leah K. Tooman, Mark I. Stevens & Thomas R. Buckley
Background: The New Zealand collembolan genus Holacanthella contains the largest species of springtails (Collembola) in the world. Using Illumina technology we have sequenced and assembled a draft genome and transcriptome from Holacanthella duospinosa (Salmon). We have used this annotated assembly to investigate the genetic basis of a range of traits critical to the evolution of the Hexapoda, the phylogenetic position of H. duospinosa and potential horizontal gene transfer events. Results: Our genome assembly was ~375...

Data from: Selection outweighs drift at a fine scale: lack of MHC differentiation within a family living lizard across geographically close but disconnected rocky outcrops

Sarah K. Pearson, C. Michael Bull & Michael G. Gardner
The highly polymorphic genes of the major histocompatibility complex (MHC) are involved in disease resistance, mate choice, and kin recognition. Therefore, they are widely used markers for investigating adaptive variation. Although selection is the key driver, gene flow and genetic drift also influence adaptive genetic variation, sometimes in opposing ways and with consequences for adaptive potential. To further understand the processes that generate MHC variation, it is helpful to compare variation at the MHC with...

Data from: Rise of the machines – recommendations for ecologists when using next generation sequencing for microsatellite development.

Michael G Gardner, Alison J Fitch, Terry Bertozzi & Andrew J Lowe
Next generation sequencing (NGS) is revolutionizing molecular ecology by simplifying the development of molecular genetic markers, including microsatellites. Here we summarize the results of the large scale development of microsatellites for 54 non-model species using NGS and show there are clear differences amongst plants, invertebrates and vertebrates for the number and proportion of motif types recovered that are able to be utilised as markers. We highlight that the heterogeneity within each group is very large....

Data from: Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species

Emese Meglécz, Gabriel Nève, Ed Biffin & Michael G. Gardner
Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within...

Data from: Cytonuclear evidence for hybridogenetic reproduction in natural populations of the Australian carp gudgeon (Hypseleotris: Eleotridae).

Daniel J Schmidt, Nicholas R Bond, Mark Adams & Jane M Hughes
Although most vertebrates reproduce sexually, a small number of fishes, amphibians, and reptiles are known in which reproduction is asexual i.e. without meiotic recombination. In fishes, these so-called “unisexual” lineages usually comprise only females, and utilize co-occurring males of a related sexual species to reproduce via gynogenesis or hybridogenesis. Here we examine patterns of microsatellite and mitochondrial DNA (mtDNA) variation in a widespread group of freshwater fishes (carp gudgeons; Hypseleotris spp.) to investigate a long-standing...

Data from: Experimental manipulation suggests effect of polyandry but not mate familiarity on within-pair aggression in the social skink, Liopholis whitii

Thomas Botterill-James, Jacinta Silince, Tobias Uller, David G. Chapple, Michael G. Gardner, Erik Wapstra, Geoffrey M. While & Jacinta Sillince
Long-term monogamy is a key characteristic of family living across animals. The evolutionary maintenance of long-term monogamy has been suggested to be facilitated by increased reproductive coordination as a result of mate familiarity, leading to increased reproductive success. However, such effects can be compromised if females mate outside the pair bond (e.g. female polyandry), introducing conflicts of interest between the male and female. Here, we experimentally test the effects of both mate familiarity and female...

Radiation of tropical island bees and the role of phylogenetic niche conservatism as an important driver of biodiversity

James B Dorey, Scott SVC Groom, Elisha Freedman, Cale Matthews, Olivia K Davies, Ella Deans, Celina Rebola, Mark I Stevens, Michael SY Lee & Michael P Schwarz
Island biogeography explores how biodiversity in island ecosystems arises and is maintained. The topographical complexity of islands can drive speciation by providing a diversity of niches that promote adaptive radiation and speciation. However, recent studies have argued that phylogenetic niche conservatism, combined with topographical complexity and climate change, could also promote speciation if populations are episodically fragmented into climate refugia that enable allopatric speciation. Adaptive radiation and phylogenetic niche conservatism therefore both predict that topographical...

The evolution of broadly polylectic behaviour in Lasioglossum (Chilalictus) (Halictidae, Apoidea)

Trace Akankunda, Carlos Rodriguez Lopez, Remko Leijs & Ken Walker
Based on the number of pollen hosts utilised, bees have been categorised as generalists (polylectic) or specialists (oligolectic). Faced with a changing habitat, polylectic bees can diversify their pollen ‘portfolio’, while oligolectic bees cannot and therefore may go locally extinct. Research into the evolution and maintenance of broad polylecty is scant. Instead, research has mainly focussed on the factors that constrain oligolectic species to a narrow diet. Here, we developed a molecular phylogeny of a...

Data from: Phylogeography of the Australian freshwater turtle Chelodina expansa reveals complex relationships among inland and coastal bioregions

Kate Hodges, Arthur Georges, Steve Donnellan & Stephen Donnellan
We examined range-wide mitochondrial phylogeographic structure in the riverine freshwater turtle Chelodina expansa to determine if this species exhibits deep genetic divergence between coastal and inland hydrological provinces as seen in co-distributed freshwater taxa. We sequenced two mitochondrial loci, genealogical relationships were assessed using a network approach, and relationships among biogeographic regions were tested using analyses of molecular variance. Population history was evaluated using neutrality tests, indices of demographic expansion, and mismatch analyses. Twenty one...

Data from: Diversification rates and phenotypic evolution in venomous snakes (Elapidae)

Michael S. Y. Lee, Kate L. Sanders, Benedict King & Alessandro Palci
The relationship between rates of diversification and of body size change (a common proxy for phenotypic evolution) was investigated across Elapidae, the largest radiation of highly venomous snakes. Time-calibrated phylogenetic trees for 175 species of elapids (more than 50% of known taxa) were constructed using seven mitochondrial and nuclear genes. Analyses using these trees revealed no evidence for a link between speciation rates and changes in body size. Two clades (Hydrophis, Micrurus) show anomalously high...

Data from: The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

Alessandro Palci, Mark N. Hutchinson, Michael W. Caldwell & Michael S. Y. Lee
The inner ear morphology of 80 snake and lizard species, representative of a range of ecologies, is here analysed and compared to that of the fossil stem snake Dinilysia patagonica, using three-dimensional geometric morphometrics. Inner ear morphology is linked to phylogeny (we find here a strong phylogenetic signal in the data that can complicate ecological correlations), but also correlated with ecology, with Dinilysia resembling certain semi-fossorial forms (Xenopeltis and Cylindrophis), consistent with previous reports. We...

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,...

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