30 Works

Shedding light: a phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves

Jingchun Li, Sarah Lemer, Lisa Kirkendale, Rudiger Bieler, Colleen Cavanaugh & Gonzalo Giribet
Background: Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive efforts have been devoted to study the short-term ecological interactions between coral hosts and their symbionts, long-term evolutionary dynamics of photosymbiosis in many marine animals are not well understood. Within Bivalvia, the second largest class of mollusks, obligate photosymbiosis is found in two marine lineages: the giant clams (subfamily...

Data from: Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda

Felipe Zapata, Nerida G. Wilson, Mark Howison, Sónia C. S. Andrade, Katharina M. Jörger, Michael Schrödl, Freya E. Goetz, Gonzalo Giribet & Casey W. Dunn
Gastropods are a highly diverse clade of molluscs that includes many familiar animals, such as limpets, snails, slugs and sea slugs. It is one of the most abundant groups of animals in the sea and the only molluscan lineage that has successfully colonized land. Yet the relationships among and within its constituent clades have remained in flux for over a century of morphological, anatomical and molecular study. Here, we re-evaluate gastropod phylogenetic relationships by collecting...

Data from: Stabilizing selection on individual pattern elements of aposematic signals

Anne E. Winters, Naomi F. Green, Nerida G. Wilson, Martin J. How, Mary J. Garson, Justin Marshall, Karen L. Cheney & N. Justin Marshall
Warning signal variation is ubiquitous but paradoxical: low variability should aid recognition and learning by predators. However, spatial variability in the direction and strength of selection for individual elements of the warning signal may allow phenotypic variation for some components, but not others. Variation in selection may occur if predators only learn particular colour pattern components rather than the entire signal. Here, we used a nudibranch mollusc, Goniobranchus splendidus, which exhibits a conspicuous red spot/white...

Etadunna bandicoot tip dated matrices

Kenny Travouillon
The oldest fossils referrable to the marsupial order Peramelemorphia (which includes modern bandicoots and bilbies) dates to the late Oligocene of Australia. The earliest geologically speaking of these are from the Etadunna Formation in central Australia. Here we describe additional peramelemorphian material from the Etadunna Formation, as well as specimens from the Namba and Wipajiri Formations. The new material fills gaps in the evolutionary history of the order showing that peramelemorphians were present in every...

From Gondwana to GAARlandia: Evolutionary history and biogeography of ogre‐faced spiders (Deinopis)

Lisa Chamberland, Anne McHugh, Sarah Kechejian, Greta Binford, Jason Bond, Jonathan Coddington, Gaynor Dolman, Chris Hamilton, Mark Harvey, Matjaz Kuntner & Ingi Agnarsson
Aim We explore the evolutionary history of the ogre‐faced spiders (Deinopis) from their Early Cretaceous origins to present day. Specifically, we investigate how vicariance and dispersal have shaped distribution patterns of this lineage. Within the Caribbean, we test the role of GAARlandia, a hypothesized land bridge that connected South America to the Greater Antilles during the Eocene–Oligocene transition (~35–33 Ma), in the biogeography of Deinopis. Taxon Araneae: Deinopidae: Deinopis. Location Caribbean islands, with additional global...

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: Species selection favors dispersive life histories in sea slugs, but higher per-offspring investment drives shifts to short-lived larvae

Patrick J. Krug, Jann E. Vendetti, Ryan A. Ellingson, Cynthia D. Trowbridge, Yayoi M. Hirano, Danielle Y. Trathen, Albert K. Rodriguez, Cornelis Swennen, Nerida G. Wilson & Ángel A. Valdés
For 40 years, paleontological studies of marine gastropods have suggested that species selection favors lineages with short-lived (lecithotrophic) larvae, which are less dispersive than long-lived (planktotrophic) larvae. Although lecithotrophs appeared to speciate more often and accumulate over time in some groups, lecithotrophy also increased extinction rates, and tests for state-dependent diversification were never performed. Molecular phylogenies of diverse groups instead suggested lecithotrophs accumulate without diversifying due to frequent, unidirectional character change. Although lecithotrophy has repeatedly...

Home range use in the West Australian seahorse Hippocampus subelongatus is influenced by sex and partner’s home range but not by body size or paired status

Charlotta Kvarnemo, Susanne E. Andersson, Jonas Elisson, Glenn I. Moore & Adam G. Jones
These data and scripts form the basis for Kvarnemo C, Andersson SE, Elisson J, Moore GI and Jones AG (2021). Home range use in the West Australian seahorse Hippocampus subelongatus is influenced by sex and partner's home range but not by body size or paired status. Journal of Ethology 39: 235–248. https://doi.org/10.1007/s10164-021-00698-y. The abstract below is from this paper: Genetic monogamy is the rule for many species of seahorse, including the West Australian seahorse Hippocampus...

Data from: Population genetics of a broadcast-spawning coral across a tropical-temperate transition zone reveals regional differentiation and isolation of high-latitude reefs

Richard Evans, Luke Thomas, W. Jason Kennington, Nicole Ryan, Nerida Wilson, Zoe Richards, Ryan Lowe & Chenae Tuckett
Aim: Genetic connectivity is a key component of species resilience to climate change in terms of recovery capacity following disturbance and capacity to disperse to novel locations as the climate warms and isotherms shift poleward. We aimed to strengthen our understanding of resilience in this context by characterizing patterns of connectivity and genetic diversity in a broadcast spawning coral across a tropical-temperate transition zone. We hypothesize genetic differentiation between tropical and temperate populations and decreasing...

Data from: Metabarcoding under Brine: Microbial ecology of five hyper-saline lakes at Rottnest Island (WA, Australia)

Mattia Saccò, Nicole E. White, Matthew Campbell, Sebastian Allard, William F. Humphreys, Paul Pringle, Farid Sepanta, Alex Laini & Morten E. Allentoft
Hypersaline ecosystems - aquatic environments where concentration of salt exceeds 35 g/L - host microbial communities which are highly specialized to cope with these extreme conditions. However, our knowledge on the taxonomic diversity and functional metabolisms characterising microbial communities in the water columns of hypersaline ecosystems is still limited, and this lack of knowledge may compromise the future preservation of these unique environments. DNA metabarcoding provides a reliable and affordable tool to investigate environmental dynamics...

Population genomics and sexual signals identify reproductive interference in Uperoleia

Renee Catullo, Frederick Jaya, Jessie Tanner, Michael Whitehead, Paul Doughty, Scott Keogh & Craig Moritz
When closely related species come into contact via range expansion, both may experience reduced fitness as a result of the interaction. Selection is expected to favor traits that minimize costly interspecies reproductive interactions (such as mismating) via a phenomenon called reproductive character displacement (RCD). Research on RCD frequently assumes secondary contact between species, but the geographic history of species interactions is often unknown. Landscape genomic data allows tests of geographic hypotheses about species origins and...

Data from: First circumglobal assessment of Southern Hemisphere humpback whale mitochondrial genetic variation and implications for management

Howard C. Rosenbaum, Francine Kershaw, Martin Mendez, Cristina Pomilla, Matthew S. Leslie, Ken P. Findlay, Peter B. Best, Timothy Collins, Michel Vely, Marcia H. Engel, Robert Baldwin, Gianna Minton, Michael Meyer, Lillian Florez-Gonzalez, M. Michael Poole, Nan Hauser, Claire Garrigue, Muriel Brasseur, John Bannister, Megan Anderson, Carlos Olavarria & C. Scott Baker
The description of genetic population structure over a species’ geographic range can provide insights into its evolutionary history and also support effective management efforts. Assessments for globally distributed species are rare, however, requiring significant international coordination and collaboration. The global distribution of demographically discrete populations for the humpback whale Megaptera novaeangliae is not fully known, hampering the definition of appropriate management units. Here, we present the first circumglobal assessment of mitochondrial genetic population structure across...

Data from: Phylogeny and biogeography of rainbowfishes (Melanotaeniidae) from Australia and New Guinea

Peter J. Unmack, Gerald R. Allen & Jerald B. Johnson
The family Melanotaeniidae (rainbowfishes) represents the largest monophyletic group of freshwater fishes found in Australia and New Guinea. The family consists of seven genera and a total of 81 species, which are broadly distributed throughout the region. We conducted a phylogenetic analysis of Melanotaeniidae based on nearly complete taxonomic sampling of all species. We sequenced seven protein coding mitochondrial genes and the first two introns of the nuclear S7 gene, for a total of 6827...

Data from: Cultural traditions across a migratory network shape the genetic structure of southern right whales around Australia and New Zealand

E. L. Carroll, C. S. Baker, M. Watson, R. Alderman, J. Bannister, O. E. Gaggiotti, D. R. Gröcke, N. Patenaude & R. Harcourt
Fidelity to migratory destinations is an important driver of connectivity in marine and avian species. Here we assess the role of maternally directed learning of migratory habitats, or migratory culture, on the population structure of the endangered Australian and New Zealand southern right whale. Using DNA profiles, comprising mitochondrial DNA (mtDNA) haplotypes (500 bp), microsatellite genotypes (17 loci) and sex from 128 individually-identified whales, we find significant differentiation among winter calving grounds based on both...

Evidence for speciation underground in diving beetles (Dytiscidae) from a subterranean archipelago

Barbara Langille, Josephine Hyde, Kathleen Saint, Tessa Bradford, Danielle Stringer, Simon Tierney, William Humphreys, Andrew Austin & Steven Cooper
Most subterranean animals are assumed to have evolved from surface ancestors following colonisation of a cave system, however very few studies have raised the possibility of ‘subterranean speciation’ in underground habitats (i.e. obligate cave-dwelling organisms (troglobionts) descended from troglobiotic ancestors). Numerous endemic subterranean diving beetle species from spatially-discrete calcrete aquifers in Western Australia (stygobionts) have evolved independently from surface ancestors; however, several cases of sympatric sister species raises the possibility of subterranean speciation. We tested...

Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions

Andrew Ontano, Guilherme Gainett, Shlomi Aharon, Jesús Balesteros, Ligia Benavides, Kevin Corbett, Efrat Gavish-Regev, Mark Harvey, Scott Monsma, Carlos Santibáñez-López, Emily Setton, Jakob Zehms, Jeanne Zeh, David Zeh & Prashant Sharma
Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch...

Phylogenomics of scorpions reveal a co-diversification of scorpion mammalian predators and mammal-specific sodium channel toxins

Carlos Santibanez, Shlomi Aharon, Jesús Ballesteros, Guilherme Gainett, Caitlin Baker, Edmundo González-Santillán, Mark Harvey, Mohamed Hassans, Ali Abu-Almaaty, Shorouk Aldeyarbi, Lionel Monod, Andrés Ojanguren-Affilastro, Robert Raven, Ricardo Pinto Da Rocha, Yoram Zvik, Efrat Gavish-Regev & Prashant Sharma
Scorpions constitute a charismatic lineage of arthropods and comprise more than 2,500 described species. Found throughout various tropical and temperate habitats, these predatory arachnids have a long evolutionary history, with a fossil record that began in the Silurian. While all scorpions are venomous, the asymmetrically diverse family Buthidae harbors nearly half the diversity of extant scorpions, and all but one of the 58 species that are medically significant to humans. Many aspects of scorpion evolutionary...

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: The linking of plate tectonics and evolutionary divergences

Matthew J. Phillips, Timothy J. Page, Mark De Bruyn, Joel A. Huey, William F. Humphreys, Jane M. Hughes, Scott R. Santos, Daniel J. Schmidt & Jonathan M. Waters
It is exciting to be living at a time when the big questions in biology can be investigated using modern genetics and computing. Bauzà-Ribot et al. take on one of the fundamental drivers of biodiversity, the effect of continental drift in the formation of the world’s biota, employing next-generation sequencing of whole mitochondrial genomes and modern Bayesian relaxed molecular clock analysis. Bauzà-Ribot et al. conclude that vicariance via plate tectonics best explains the genetic divergence...

Data from: Incorporating non-equilibrium dynamics into demographic history inferences of a migratory marine species

Emma L. Carroll, Rachael Alderman, John L. Bannister, Martine Bérubé, Peter B. Best, Laura Boren, C. Scott Baker, Rochelle Constantine, Ken Findlay, Robert Harcourt, Louisiane Lemaire, Per J. Palsbøll, Nathalie J. Patenaude, Victoria J. Rowntree, Jon Seger, Debbie Steel, Luciano O. Valenzuela, Mandy Watson & Oscar E. Gaggiotti
Understanding how dispersal and gene flow link geographically separated populations over evolutionary history is challenging, particularly in migratory marine species. In southern right whales (SRWs, Eubalaena australis), patterns of genetic diversity are likely influenced by the glacial climate cycle and recent history of whaling. Here we use a dataset of mitochondrial DNA (mtDNA) sequences (n=1,327) and nuclear markers (17 microsatellite loci, n=222) from major wintering grounds to investigate circumpolar population structure, historical demography, and effective...

Data from: Integrated evidence reveals a new species in the ancient blue coral genus Heliopora (Octocorallia)

Zoe T. Richards, Nina Yasuda, Taisei Kikuchi, Taryn Foster, Chika Mitsuyuki, Michael Stat, Yoshihisa Suyama & Nerida G. Wilson
Maintaining the accretion potential and three dimensional structure of coral reefs is a priority but reef-building scleractinian corals are highly threatened and retreating. Hence future reefs are predicted to be dominated by non-constructional taxa. Since the Late Triassic however, other non-scleractinian anthozoans such as Heliopora have contributed to tropical and subtropical reef-building. Heliopora is an ancient and highly conserved reef building octocoral genus within the monospecific Family Helioporidae, represented by a single extant species –...

Data from: Limited influence of landscape on the genetic structure of three small mammals in a heterogeneous arid environment

Esther Levy, Margaret Byrne, Joel A. Huey, Mia J. Hillyer, Renee C. Firman & Kym M. Ottewell
Aim: The complexity and biologically challenging nature of arid landscapes can generate high inter- and intra-species diversity, although these biomes remain poorly studied. We investigated whether prominent geomorphic features in an Australian arid landscape had similar influences on patterns of intra-specific genetic diversity of three small mammals with different distribution and life history traits. Specifically, we tested (1) whether mountain ranges harbour high diversity and act as refugia, (2) the extent to which ephemeral river...

Data from: Multi-locus sequence data illuminate demographic drivers of Pleistocene speciation in semi-arid southern Australian birds (Cinclosoma spp.)

Gaynor Dolman & Leo Joseph
Background: During the Pleistocene, shifts of species distributions and their isolation in disjunct refugia led to varied outcomes in how taxa diversified. Some species diverged, others did not. Here, we begin to address another facet of the role of the Pleistocene in generating today’s diversity. We ask which processes contributed to divergence in semi-arid southern Australian birds. We isolated 11 autosomal nuclear loci and one mitochondrial locus from a total of 29 specimens of the...

Data from: The global diversity and distribution of lizard clutch sizes

Shai Meiri, Luciano Avila, Aaron Bauer, David Chapple, Indraneil Das, Tiffany Doan, Paul Doughty, Ryan Ellis, Lee Grismer, Fred Kraus, Mariana Morando, Paul Oliver, Daniel Pincheira-Donoso, Marco-Antonio Ribeiro-Junior, Glenn Shea, Omar Torres-Carvajal, Alex Slavenko & Uri Roll
Aim. Clutch size is a key life-history trait. In lizards, it ranges over two orders of magnitude. The global drivers of spatial and phylogenetic variation in clutch have been extensively studied in birds, but such tests in other organisms are lacking. To test the generality of latitudinal gradients in clutch size, and their putative drivers, we present the first global-scale analysis of clutch sizes across of lizard taxa. Location, Global Time period. Recent Major taxa...

Mimicry and mitonuclear discordance in nudibranchs: new insights from exon capture phylogenomics

Kara K.S. Layton, Jose I. Carvajal & Nerida G. Wilson
Phylogenetic inference and species delimitation can be challenging in taxonomic groups that have recently radiated and where introgression produces conflicting gene trees, especially when species delimitation has traditionally relied on mitochondrial data and colour pattern. Chromodoris, a genus of colourful and toxic nudibranch in the Indo-Pacific, has been shown to have extraordinary cryptic diversity and mimicry, and has recently radiated, ultimately complicating species delimitation. In these cases, additional genome-wide data can help improve phylogenetic resolution...

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