53 Works

Data from: Blood transcriptomes and de novo identification of candidate loci for mating success in lekking great snipe (Gallinago media)

Jacob Höglund, Biao Wang, Stein Are Saether, Mozes Pil Kyu Blom, Peder Fiske, Peter Halvarsson, Gavin J. Horsburgh, Terry Burke, John Atle Kålås & Robert Ekblom
We assembled the great snipe blood transcriptome using data from fourteen lekking males, in order to de novo identify candidate genes related to sexual selection, and determined the expression profiles in relation to mating success. The three most highly transcribed genes were encoding different haemoglobin subunits. All tended to be overexpressed in males with high mating success. We also called Single Nucleotide Polymorphisms (SNPs) from the transcriptome data and found considerable genetic variation for many...

Data from: Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards

Matthew C. Brandley, Jason G. Bragg, Sonal Singhal, David G. Chapple, Charlotte K. Jennings, Alan R. Lemmon, Emily M. Lemmon, Michael B. Thompson & Craig Moritz
Background: High-throughput sequencing using targeted enrichment and transcriptomic methods enables rapid construction of phylogenomic data sets incorporating hundreds to thousands of loci. These advances have enabled access to an unprecedented amount of nucleotide sequence data, but they also pose new questions. Given that the loci targeted for enrichment are often highly conserved, how informative are they at different taxonomic scales, especially at the intraspecific / phylogeographic scale? We investigate this question using Australian scincid lizards...

Data from: Cryptic lineage diversity, body size divergence and sympatry in a species complex of Australian lizards (Gehyra)

Craig C. Moritz, Renae C. Pratt, Sarah Bank, Gayleen Bourke, Jason G. Bragg, Paul Doughty, J. Scott Keogh, Rebecca J. Laver, Sally Potter, Luisa C. Teasdale, Leonardo G. Tedeschi & Paul M. Oliver
Understanding the joint evolutionary and ecological underpinnings of sympatry among close relatives remains a key challenge in biology. This problem can be addressed through joint phylogenomic and phenotypic analysis of complexes of closely related lineages within, and across, species and hence representing the speciation continuum. For a complex of tropical geckos from northern Australia – Gehyra nana and close relatives – we combine mtDNA phylogeography, exon-capture sequencing and morphological data to resolve independently evolving lineages...

Data from: Generalist predator's niche shifts reveal ecosystem changes in an experimentally fragmented landscape

Julian Resasco, Kika T. Tuff, Saul A. Cunningham, Brett A. Melbourne, Andrew L. Hicks, Seth D. Newsome & Kendi F. Davies
Habitat fragmentation can alter the trophic structure of communities and environmental conditions, thus driving changes in biodiversity and ecosystem functions. Quantifying niches of generalist predators can reveal how fragmentation alters ecosystems. In a habitat fragmentation experiment, we used stable isotopes of a generalist predator skink to test predictions from spatial theory on trophic structure and to quantify abiotic changes associated with fragmentation among continuous forest, fragments, and matrix habitats. We predicted that in fragments and...

Data from: A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes

Timothée Bonnet, Raphaël Leblois, Francois Rousset & Pierre-André Crochet
Hybridization is increasingly recognized as a significant evolutionary process, in particular because it can lead to introgression of genes from one species to another. A striking pattern of discordance in the amount of introgression between mitochondrial and nuclear markers exists such that substantial mitochondrial introgression is often found in combination with no or little nuclear introgression. Multiple mechanisms have been proposed to explain this discordance, including positive selection for introgressing mitochondrial variants, several types of...

Data from: Phylogenetic evidence for mid-Cenozoic turnover of a diverse continental biota

Paul M. Oliver & Andrew F. Hugall
Rapid climatic change at the beginning of the Oligocene epoch is concordant with global biotic turnover in the fossil record. However, while Southern Hemisphere geological movement played a key role in shaping these global climatic shifts, given generally poor terrestrial fossil records, evidence for matching turnover in entire Austral biotas is lacking. Emerging comprehensive phylogenetic frameworks provide alternative avenues to explore for signals of mass turnover or restructuring. Here, we combine phylogenetic data with empirical...

Data from: Why does inbreeding reduce male paternity? Effects on sexually selected traits

Jason N. Marsh, Regina Vega-Trejo, Michael Dawson Jennions & Megan L. Head
Why does inbreeding reduce paternity? Effects on sexually selected traitsThis is the data associated with the manuscript "Why does inbreeding reduce paternity? Effects on sexually selected traits". The data file contains 5 worksheets. The first "association data" contains data from experiment 1 of the associated paper looking at female association time with inbred and outbred males. The second third and fourth contain data associated with the second experiment of the associated paper looking at the...

Data from: New findings in a 400 million-year-old Devonian placoderm shed light on jaw structure and function in basal gnathostomes

Yuzhi Hu, Jing Lu & Gavin C. Young
Arthodire placoderms have been proposed as the sister group of Chinese ‘maxillate’ placoderms plus all the more crownward gnathostomes. These basal groups provide key information for understanding the early evolution of jaws. Here, we test previous assumptions about placoderm jaw structure and function by using high-resolution computed tomography, digital dissection, and enlarged 3D printouts on a unique articulated 400 million-year-old buchanosteid arthrodire. The upper jaw has a double ethmoid and a palatobasal connection, but no...

Data from: Multimodal coordination enhances the responses to an avian duet

Paweł Ręk
Animals communicate with their whole bodies, so their signals can be complex and multimodal. The joint intelligibility of multimodal signal components depends on their temporal coordination, which, when only one signaler is involved, depends on the synchronization between the different modalities of signals involved. Coordination is a challenge, however, in cooperatively signaling species because it requires continuous monitoring of the partner’s behavior. Previous research showed that vocal coordination between cooperating individuals increases the perceived threat...

Data from: Pleistocene climatic changes drive diversification across a tropical savanna

Sally Potter, Alexander T. Xue, Jason G. Bragg, Dan F. Rosauer, Emily J. Roycroft & Craig Moritz
Spatial responses of species to past climate change depend on both intrinsic traits (climatic niche breadth, dispersal rates) and the scale of climatic fluctuations across the landscape. New capabilities in generating and analysing population genomic data, along with spatial modelling, have unleashed our capacity to infer how past climate changes have shaped populations, and by extension, complex communities. Combining these approaches, we uncover lineage diversity across four co-distributed lizards from the Australian Monsoonal Tropics and...

Data from: Modern pollen from small hollows reflects Athrotaxis cupressoides density across a wildfire gradient in subalpine forests of the Central Plateau, Tasmania, Australia

Philip E. Higuera, Jesse L. Morris, Simon Haberle & Cathy Whitlock
Pollen assemblages from 50 small hollows were used to resolve fire-caused vegetation patterns in a ~2-km2 subalpine landscape on the Central Plateau of Tasmania, Australia. Sites were characterized by varying abundance of the dominant tree species, Athrotaxis cupressoides, reflecting mortality from a wildfire that occurred 53 years prior to sampling. Sites were classified a priori based on fire-related Athrotaxis mortality as burned (100% standing dead), unburned (<5% standing dead), and mixed (intermediate proportions). Non-parametric analysis...

Data from: The importance of scattered trees for biodiversity conservation: a global meta-analysis

Jayme A. Prevedello, Mauricio Almeida-Gomes & David B. Lindenmayer
1. Scattered trees are thought to be keystone structures for biodiversity in landscapes worldwide. However, such trees have been largely neglected by researchers and their importance for biodiversity remains unclear. 2. We completed a global meta-analysis to quantify relationships between scattered trees and the species richness, abundance and composition of vertebrates, arthropods and plants. First, we tested whether areas near scattered trees support higher levels of species richness and abundance than nearby open areas. Second,...

Data from: Broad-scale variation in sexual dichromatism in songbirds is not explained by sex differences in exposure to predators during incubation

Beata Matysiokova, Vladimir Remes & Andrew Cockburn
The evolution of sexual dichromatism provoked one of the greatest disagreements between Charles Darwin and Alfred Russel Wallace. According to Darwin the main driving force is sexual selection, whereby choosy females prefer showy males, leading to the evolution of conspicuous male plumage. On the other hand, Wallace suggested that dichromatism may arise because nest predation favors more cryptic females. To test the role of natural selection in the evolution of dichromatism we combined quantitative data...

Data from: Measuring CO2 and HCO3- permeabilities of isolated chloroplasts using a MIMS-18O approach

Dimitri Tolleter, Vincent Chochois, Richard Poiré, G. Dean Price & Murray R. Badger
To support photosynthetic CO2 fixation by Rubisco, the chloroplast must be fed with inorganic carbon in the form of CO2 or bicarbonate. However, the mechanisms allowing the rapid passage of this gas and this charged molecule through the bounding membranes of the chloroplast envelope are not yet completely elucidated. We describe here a method allowing us to measure the permeability of these two molecules through the chloroplast envelope using a membrane inlet mass spectrometer and...

Data from: Phylogenetically informed spatial planning is required to conserve the mammalian tree of life

Dan F. Rosauer, Laura J. Pollock, Simon Linke & Walter Jetz
In the face of the current extinction crisis and severely limited conservation resources, safeguarding the tree of life is increasingly recognized as a high priority. We conducted a first systematic global assessment of the conservation of phylogenetic diversity (PD) that uses realistic area targets and highlights the key areas for conservation of the mammalian tree of life. Our approach offers a substantially more effective conservation solution than one focused on species. In many locations, priorities...

Data from: Mass turnover and recovery dynamics of a diverse Australian continental radiation

Ian G. Brennan & Paul M. Oliver
Trends in global and local climate history have been linked to observed macroevolutionary patterns across a variety of organisms. These climatic pressures may unilaterally or asymmetrically influence the evolutionary trajectory of clades. To test and compare signatures of changing global (Eocene-Oligocene boundary cooling) and continental (Miocene aridification) environments on a continental fauna, we investigated the macroevolutionary dynamics of one of Australia's most diverse endemic radiations, pygopodoid geckos. We generated a time-calibrated phylogeny (>90% taxon coverage)...

Data from: Intraspecific variation in climate-relevant traits in a tropical rainforest lizard

John Llewelyn, Stewart L. Macdonald, Amberlee Hatcher, Craig Moritz & Ben L. Phillips
Aim The exceptionally rich biodiversity found in tropical rainforest is under threat from anthropogenic climate change. We recognize the threat, yet we have little knowledge of the capacity of tropical species to adjust their climate sensitivity in response to it. One indicator of a species’ capacity to adjust to different climates is the amount of intraspecific variation observed in its climate-relevant traits; if a climate-relevant trait varies, and this variation is correlated with local climates,...

Data from: Territorial battles between fiddler crab species

Huon L. Clark & Patricia R. Y. Backwell
Many species worldwide are impacted by habitat loss. This may result in increased competition both within species and between species. Many studies have demonstrated that when two previously non-overlapping species are forced to compete over a resource, one species is likely to become dominant over the other. This study explores the impact a larger species of fiddler crab (Tabuca elegans—previously known as Uca elegans) has when invading an area previously used solely by a smaller...

Data from: Evaluating multilocus Bayesian species delimitation for discovery of cryptic mycorrhizal diversity

Michael R. Whitehead, Renee A. Catullo, Monica Ruibal, Kingsley W. Dixon, Rod Peakall & Celeste C. Linde
The increasing availability of DNA sequence data enables exciting new opportunities for fungal ecology. However, it amplifies the challenge of how to objectively classify the diversity of fungal sequences into meaningful units, often in the absence of morphological characters. Here, we test the utility of modern multilocus Bayesian coalescent-based methods for delimiting cryptic fungal diversity in the orchid mycorrhiza morphospecies Serendipita vermifera. We obtained 147 fungal isolates from Caladenia, a speciose clade of Australian orchids...

Data from: Chromosomal speciation in the genomics era: disentangling phylogenetic evolution of rock-wallabies

Sally Potter, Jason G. Bragg, Mozes P. Blom, Janine E. Deakin, Mark Kirkpatrick, Mark D. Eldridge, Craig Moritz, Mozes P. K. Blom & Mark D. B. Eldridge
The association of chromosome rearrangements with speciation is well established, and there is a long history of theory and evidence relating to “chromosomal speciation”. Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about...

Data from: Precipitation drives global variation in natural selection

Adam Siepielski, Michael B. Morrissey, Mathieu Buoro, Stephanie M. Carlson, Christina M. Caruso, Sonya M. Clegg, Tim Coulson, Joseph DiBattista, Kiyoko M. Gotanda, Clinton D. Francis, Joe Hereford, Joel G. Kingsolver, Kate E. Augustine, Loeske E. B. Kruuk, Ryan A. Martin, Ben C. Sheldon, Nina Sletvold, Erik I. Svensson, Michael J. Wade & Andrew D. C. MacColl
Climate change has the potential to affect the ecology and evolution of every species on Earth. Although the ecological consequences of climate change are increasingly well documented, the effects of climate on the key evolutionary process driving adaptation—natural selection—are largely unknown. We report that aspects of precipitation and potential evapotranspiration, along with the North Atlantic Oscillation, predicted variation in selection across plant and animal populations throughout many terrestrial biomes, whereas temperature explained little variation. By...

Data from: The phylogeny and biogeography of Hakea (Proteaceae) reveals the role of biome shifts in a continental plant radiation

Marcel Cardillo, Peter H. Weston, Zoe K.M. Reynolds, Peter M. Olde, Austin R. Mast, Emily Lemmon, Alan Richard Lemmon, Lindell Bromham, Emily M. Lemmon & Zoe K. M. Reynolds
The frequency of evolutionary biome shifts during diversification has important implications for our ability to explain geographic patterns of plant diversity. Recent studies present several examples of biome shifts, but whether frequencies of biome shifts closely reflect geographic proximity or environmental similarity of biomes remains poorly known. We explore this question by using phylogenomic methods to estimate the phylogeny of Hakea, a diverse Australian genus occupying a wide range of biomes. Model-based estimation of ancestral...

Data from: Range instability leads to cytonuclear discordance in a morphologically cryptic ground squirrel species complex

Mark A. Phuong, Ke Bi & Craig Moritz
The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture dataset and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O. beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central, and Southern lineages...

Data from: Egg shape mimicry in parasitic cuckoos

Marie R.G. Attard, Iliana Medina, Naomi E. Langmore, Emma Sherratt & M. R. G. Attard
Parasitic cuckoos lay their eggs in nests of host species. Rejection of cuckoo eggs by hosts has led to the evolution of egg mimicry by cuckoos, whereby their eggs mimic the colour and pattern of their host eggs to avoid egg recognition and rejection. There is also evidence of mimicry in egg size in some cuckoo-host systems, but currently it is unknown whether cuckoos can also mimic the egg shape of their hosts. In this...

Data from: A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

, Anne Bruneau, Nasim Azani, Marielle Babineau, Edeline Gagnon, Carole Sinou, Royce Steeves, Erin Zimmerman, C. Donovan Bailey, Lynsey Kovar, Madhugiri Nageswara-Rao, Hannah Banks, RuthP. Clark, Manuel De La Estrella, Peter Gasson, GeoffreyC. Kite, BenteB. Klitgaard, GwilymP. Lewis, Danilo Neves, Gerhard Prenner, María De Lourdes Rico-Arce, ArianeR. Barbosa, Maria Cristina López-Roberts, Luciano Paganucci De Queiroz, PétalaG. Ribeiro … & Tingshuang Yi
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most...

Registration Year

  • 2017

Resource Types

  • Dataset


  • Australian National University
  • University of Melbourne
  • Royal Botanic Gardens
  • University of Minnesota
  • University of California, Berkeley
  • University of Zurich
  • Lund University
  • University of Edinburgh
  • Museum of Vertebrate Zoology
  • French National Centre for Scientific Research