54 Works

Data from: Inflation of molecular clock rates and dates: molecular phylogenetics, biogeography, and diversification of a global cicada radiation from Australasia (Hemiptera: Cicadidae: Cicadettini)

David C. Marshall, Kathy B. R. Hill, Max S. Moulds, Dan Vanderpool, John R. Cooley, Alma Mohagan & Chris Simon
Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate...

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: Insular biogeographic origins and high phylogenetic distinctiveness for a recently depleted lizard fauna from Christmas Island, Australia

Paul M. Oliver, Mozes P.K. Blom, Harold G. Cogger, Robert N. Fisher, Jonathan Q. Richmond, John C.Z. Woinarski & John C. Z. Woinarski
Striking faunal turnover across Asia and Australasia, most famously along the eastern edge of the Sunda Shelf or ‘Wallace’s Line’, has been a focus of biogeographic research for over 150 years. Here we investigate the origins of a highly threatened endemic lizard fauna (4 species) on Christmas Island. Despite occurring less 350 km south of the Sunda Shelf, this fauna mostly comprises species from clades centred on the more distant regions of Wallacea, the Pacific...

Prevalence of Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans in thre Hoang Lien Range, northwest Vietnam

Benjamin Tapley, Phillip Jervis, Luan Nguyen, Christopher Portway, Chung Nguyen, Hao Luong, Daniel Kane, Lola Brookes, Matthew Perkins, Pria Ghosh, Claudia Wierzbicki, Jennifer Shelton, Matthew Fisher & Jodi Rowley
This study aims to investigate the presence of the amphibian chytrid fungi Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) in the Hoang Lien Range, northwest Vietnam as well as any patterns in Bd infection in space, time and host species over a five-year sampling period. This study also aims to investigate the presence of Bsal in the Hoang Lien Range.

Data from: The biogeography of marine invertebrate life histories

Dustin J. Marshall, Patrick J. Krug, Elena K. Kupriyanova, Maria Byrne & Richard B. Emlet
Biologists have long sought to identify and explain patterns in the diverse array of marine life histories. The most famous speculation about such patterns is Gunnar Thorson’s suggestion that species producing planktonic larvae are rarer at higher latitudes (Thorson’s rule). Although some elements of Thorson’s rule have proven incorrect, other elements remain untested. With a wealth of new life-history data, statistical approaches, and remote-sensing technology, new insights into marine reproduction can be generated. We gathered...

Data from: Multilocus phylogeny and a new classification for Southeast Asian and Melanesian forest frogs (family Ceratobatrachidae)

Rafe M. Brown, Cameron D. Siler, Stephen J. Richards, Arvin C. Diesmos & David C. Cannatella
We present a near comprehensive, densely sampled, multilocus phylogenetic estimate of species relationships within the anuran family Ceratobatrachidae, a morphologically and ecologically diverse group of frogs from the island archipelagos of Southeast Asia and the South-West Pacific. Ceratobatrachid frogs consist of three clades: a small clade of enigmatic, primarily high-elevation, semi-aquatic Sundaland species currently assigned to Ingerana (for which we erect a new genus), which is the sister taxon of two large, monophyletic radiations, each...

Data from: Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture

Luisa C. Teasdale, Frank Köhler, Kevin D. Murray, Tim O'Hara & Adnan Moussalli
The qualification of orthology is a significant challenge when developing large, multiloci phylogenetic data sets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts and mis-indexing, which pose problems to automated methods of orthology assessment. Here, we identify a set of orthologous single-copy genes from transcriptome assemblies for the land snails and slugs (Eupulmonata) using a thorough approach to orthology determination involving manual alignment curation, gene tree assessment and sequencing from genomic...

Data from: Two speed invasion: assisted and intrinsic dispersal of common mynas over 150-years of colonization

Kyle M. Ewart, Andrea S. Griffin, Rebecca N. Johnson, Salit Kark, Tali Magory Cohen, Nathan Lo & Richard E. Major
Aim: Despite the common myna’s widespread distribution, and the significant impact it has caused in parts of its non-native range, there have been no comprehensive genomic studies of its invasion of any region. We aimed to characterize the common myna invasion of the Australian continent to understand its population genetic landscape, introduction history, dispersal characteristics, and the interconnectedness between different source populations and invasive fronts. Location: Common mynas from 26 geographical locations spanning the Australian...

Data from: Analysis of phylogenomic tree space resolves relationships among marsupial families

David A. Duchêne, Jason G. Bragg, Sebastian Duchêne, Linda E. Neaves, Sally Potter, Craig Moritz, Rebecca N. Johnson, Simon Y. W. Ho & Mark D. B. Eldridge
A fundamental challenge in resolving evolutionary relationships across the Tree of Life is to account for heterogeneity in the evolutionary signal across loci. Studies of marsupial mammals have demonstrated that this heterogeneity can be substantial, leaving considerable uncertainty in the evolutionary timescale and relationships within the group. Using simulations and a new phylogenomic data set comprising nucleotide sequences of 1550 loci from 18 of the 22 extant marsupial families, we demonstrate the power of a...

Data from: Mitochondrial rate variation among lineages of passerine birds

Jacqueline M. T. Nguyen & Simon Y. W. Ho
The order Passeriformes comprises the majority of extant avian species. Analyses of molecular data have provided important insights into the evolution of this diverse order. However, molecular estimates of the evolutionary and demographic timescales of passerine species have been hindered by a lack of reliable calibrations. This has led to a reliance on the application of standard substitution rates to mitochondrial DNA data, particularly rates estimated from analyses of the gene encoding cytochrome b (CYTB)....

Data from: Genetic signatures through space, time and multiple disturbances in a ubiquitous brooding coral

Jim N. Underwood, Zoe T. Richards, Karen J. Miller, Marji L. Puotinen & James P. Gilmour
The predominance of self-recruitment in many reef-building corals has fundamental and complex consequences for their genetic diversity, population persistence and responses to climate change. Knowledge of genetic structure over local scales needs to be placed within a broad spatial context, and also integrated with genetic monitoring through time to disentangle these consequences. Here, we examined patterns of genetic diversity over multiple spatio-temporal scales across tropical Australia in the ubiquitous brooding coral, Seriatopora hystrix. We also...

Data from: The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow-mouthed frogs (Anura, Microhylidae)

Pedro L. V. Peloso, Darrel R. Frost, Stephen J. Richards, Miguel T. Rodrigues, Stephen Donnellan, Masafumi Matsui, Cristopher J. Raxworthy, S. D. Biju, Emily Moriarty Lemmon, Ward C. Wheeler, Alan R. Lemmon, Pedro L.V. Peloso & S.D. Biju
Despite considerable progress in unravelling the phylogenetic relationships of microhylid frogs, relationships among subfamilies remain largely unstable and many genera are not demonstrably monophyletic. Here, we used five alternative combinations of DNA sequence data (ranging from seven loci for 48 taxa to up to 73 loci for as many as 142 taxa) generated using the anchored phylogenomics sequencing method (66 loci, derived from conserved genome regions, for 48 taxa) and Sanger sequencing (seven loci for...

Environmental DNA reveals a multi-taxa biogeographic break across the Arabian Sea and Sea of Oman

Joseph DiBattista, Michael Berumen, Mark Priest, Maarten De Brauwer, Darren Coker, Tane Sinclair-Taylor, Amanda Hay, Gerd Bruss, Shawky Mansour, Michael Bunce, Christopher Goatley, Matthew Power & Alyssa Marshell
Environmental DNA (eDNA) is increasingly being used to assess community composition in marine ecosystems. Applying eDNA approaches across broad spatial scales now provide the potential to inform biogeographic analyses. However, to date, few studies have employed this technique to assess broad biogeographic patterns across multiple taxonomic groups. Here, we compare eDNA-derived communities of bony fishes and invertebrates, including corals and sponges, from 15 locations spanning the entire length of the Omani coast. This survey includes...

Data from: Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity

Michael Stat, Jeffrey John, Joseph D. DiBattista, Stephen J. Newman, Michael Bunce & Euan S. Harvey
Monitoring communities of fish is important for the management and health of fisheries and marine ecosystems. Baited remote underwater video systems (BRUVs) are one of the most effective non‐destructive techniques for sampling bony fishes and elasmobranchs (sharks, rays, and skates). However, while BRUVs can sample visually conspicuous biota, some taxa are under‐sampled or not recorded at all. Here, we compared the diversity of fishes characterised using BRUVs with metabarcoding of environmental DNA (eDNA) extracted from...

Data from: Barcoding snakeheads (Teleostei, Channidae) revisited: discovering greater species diversity and resolving perpetuated taxonomic confusions

Cecilia Conte-Grand, Ralf Britz, Neelesh Dahanukar, Rajeev Raghavan, Rohan Pethiyagoda, Hoek Hui Tan, Renny Kurnia Hadiaty, Norsham S. Yaakob, Lukas Rüber & Heok Hui Tan
Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group...

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...

Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems

Joseph DiBattista, James Reimer, Michael Stat, Giovanni Masucci, Piera Biondi, Maarten De Brauwer, Shaun Wilkinson, Anthony Chariton & Michael Bunce
Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of ‘snapshots’ across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine...

Data from: Unusual but consistent latitudinal patterns in macroalgal habitats and their invertebrate communities across two countries

Hannah Lloyd, Juan Cruz-Motta, Tim Glasby, Pat Hutchings & Paul Gribben
Aim: The physical characteristics of biogenic habitats and environmental conditions are important determinants of biodiversity, yet their relative importance can change across spatial scales. We aimed to understand how relationships between the physical characteristics of macroalgal habitats and their invertebrate communities varied across spatial scales and whether general ecological patterns occurred across two countries. Location: 18 sites across the temperate east coasts of Australia (over 1,300 km) and New Zealand (over 1,000 km), with the...

Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia

Katrina West, Michael Travers, Michael Stat, Euan Harvey, Zoe Richards, Joseph DiBattista, Stephen Newman, Alastair Harry, Craig Skepper, Matthew Heydenrych, Michael Bunce, Michael J. Travers, Euan S. Harvey, Zoe T. Richards, Joseph D. DiBattista, Stephen J. Newman & Craig L. Skepper
Aim: Environmental DNA (eDNA) metabarcoding has demonstrated its applicability as a highly sensitive biomonitoring tool across small spatial and temporal scales in marine ecosystems. However, it has rarely been tested across large spatial scales, or biogeographical barriers. Here, we scale up marine eDNA metabarcoding, test its ability to detect a major marine biogeographic break, and evaluate its use as a regional biomonitoring tool in Australia. Location: North-western Australia (NWA) Methods: We applied metabarcoding assays targeting...

Climate-assisted persistence of tropical fish vagrants in temperate marine ecosystems

Joseph DiBattista, Laura Gajdzik, Thomas DeCarlo, Adam Koziol, Mahsa Mousavi-Derazmahalleh, Megan Coghlan, Matthew Power, Michael Bunce, David Fairclough, Michael Travers & Glenn Moore
Rising temperatures and extreme climatic events are propelling tropical species into temperate marine ecosystems, but not all species can persist. Here, we used the heatwave-driven expatriation of tropical black rabbitfish (Siganus fuscescens) to the temperate environments of Western Australia to assess the ecological and evolutionary mechanisms that may entail their persistence. Population genomic assays for this rabbitfish indicated little genetic differentiation between tropical residents and vagrants to temperate environments due to high migration rates, which...

Monitoring vertebrate biodiversity of a protected coastal wetland using eDNA metabarcoding

Pablo Saenz-Agudelo, Erwan Delrieu-Trottin, Joseph D. DiBattista, Diego Martinez, Sarai Morales-Gonzáles, Felipe Pontigo, Paula Ramirez, Andrea Silva, Mauricio Soto & Cristian Correa
Monitoring plans using environmental DNA have the potential to offer a standardized and cost-efficient method to survey biodiversity in aquatic ecosystems. Among these ecosystems, coastal wetlands are key elements that serve as transition zones between marine and freshwater ecosystems and are today the target of many conservation and restoration efforts. In this sense, eDNA monitoring could provide a rapid and efficient tool for studying and generating baseline biodiversity information to guide coastal wetland management programs....

Data from: Hyper-longirostry and kinematic disparity in extinct toothed whales

Matthew R. McCurry & Nicholas D. Pyenson
Toothed cetacean (Odontoceti) lineages in the Miocene and Pliocene evolved rostra that are proportionally more elongate than any other aquatic mammal or reptile, living or extinct. Their similarities in cranial proportions to billfish may suggest a convergent feeding style, where the rostrum is swept through the water to hit and stun prey. Here we calculated second moment of area from rostral cross-sections of these fossil odontocete taxa, as well as from extant ecological analogues, to...

Data from: Repeated evolution of amphibious behavior in fish and its implications for the colonization of novel environments

Terry J. Ord & Georgina M. Cooke
We know little about on how frequently transitions into new habitats occur, especially the colonization of novel environments that are the most likely to instigate adaptive evolution. One of the most extreme ecological transitions has been the shift in habitat associated with the move from water to land by amphibious fish. We provide the first phylogenetic investigation of these transitions for living fish. Thirty-three families have species reported to be amphibious and these are likely...

Data from: Lizards in pinstripes: morphological and genomic evidence for two new species of scincid lizards within Ctenotus piankai Storr and C. duricola Storr (Reptilia: Scincidae) in the Australian arid zone

Daniel L Rabosky, Paul Doughty & Huateng Huang
The scincid lizard genus Ctenotus is one of the most species-rich genera of squamate reptiles, but few molecular phylogenetic studies have been undertaken on the group. Here we assess molecular and morphological variation within C. piankai and C. duricola, an arid-adapted pair of nominate species characterized by a pattern of thin pale longitudinal lines on a dark background that occur primarily in the western deserts and Pilbara region of Australia. We sequenced mitochondrial DNA and...

Data from: Macronutrient selection of free-ranging urban Australian white ibis (Threskiornis moluccus)

Sean C. P. Coogan, Gabriel E. Machovsky-Capuska, Alistair M. Senior, John M. Martin, Richard E. Major & David Raubenheimer
Anthropogenic habitats often provide urban wildlife the opportunity to feed on a range of nutritionally diverse foods, which may ultimately lead to human-wildlife conflict. The Australian white ibis (Threskiornis moluccus) provides an exemplar model for examining the nutritional priorities and constraints of a native vertebrate that is successfully transitioning to an urban specialist. Here, we used field-based feeding trials to investigate the macronutrient preferences of free-ranging ibis in Sydney, Australia. Feeding trials (n = 61)...

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