137 Works

Data from: Old World and New World Phasmatodea: phylogenomics resolve the evolutionary history of stick and leaf insects

Sabrina Simon, Harald Letsch, Sarah Bank, Thomas R. Buckley, Alexander Donath, Shanlin Liu, Ryuichiro Machida, Karen Meusemann, Bernhard Misof, Lars Podsiadlowski, Xin Zhou, Benjamin Wipfler & Sven Bradler
Phasmatodea comprises over 3,000 extant species and stands out as one of the last remaining insect orders for which a robust, higher-level phylogenetic hypothesis is lacking. New research suggests that the extant diversity is the result of a surprisingly recent and rapid radiation that has been difficult to resolve with standard Sanger sequence data. In order to resolve the early branching events of stick and leaf insects, we analyzed transcriptomes from 61 species, including 38...

Data from: The origin of the central dogma through conflicting multilevel selection

Nobuto Takeuchi & Kunihiko Kaneko
The central dogma of molecular biology rests on two kinds of asymmetry between genomes and enzymes: informatic asymmetry, where information flows from genomes to enzymes but not from enzymes to genomes; and catalytic asymmetry, where enzymes provide chemical catalysis but genomes do not. How did these asymmetries originate? Here, we show that these asymmetries can spontaneously arise from conflict between selection at the molecular level and selection at the cellular level. We developed a model...

Data from: The roles of non-production vegetation in agroecosystems: a research framework for filling process knowledge gaps in a social-ecological context

Bradley Case, Jennifer Pannell, Margaret Stanley, David Norton, Anoek Brugman, Matt Funaki, Chloé Mathieu, Cao Songling, Febyana Suryaningrum & Hannah Buckley
1. An ever-expanding human population, climatic changes, and the spread of intensive farming practices is putting increasing pressure on agroecosystems and their inherent biodiversity. Non-production vegetation elements, such as woody patches, riparian margins, and restoration plantings, are vital for conserving agroecosystem biodiversity. Further, such elements are key building blocks that are manipulated via land management, thereby influencing the biotic and abiotic processes that underpin functioning agroecosystems. 2. Despite this critical role, there has been a...

Towards establishing extracellular vesicle-associated RNAs as biomarkers for HER2+ breast cancer

Colin L. Hisey, Petr Tomek, Yohanes N. S. Nursalim, Lawrence W. Chamley & Eupehmia Leung
Extracellular vesicles (EVs) are emerging as key players in breast cancer progression and hold immense promise as cancer biomarkers. However, difficulties in obtaining sufficient quantities of EVs for the identification of potential biomarkers hampers progress in this area. To circumvent this obstacle, we cultured BT-474 breast cancer cells in a two-chambered bioreactor with CDM-HD serum replacement to significantly improve the yield of cancer cell-associated EVs and eliminate bovine EV contamination. Cancer-relevant mRNAs BIRC5 (Survivin) and...

Data from: Species delimitation using genome-wide SNP data

Adam D. Leaché, Vladimir N. Minin, Remco R. Bouckaert & Matthew K. Fujita
The multispecies coalescent has provided important progress for evolutionary inferences, including increasing the statistical rigor and objectivity of comparisons among competing species delimitation models. However, Bayesian species delimitation methods typically require brute force integration over gene trees via Markov chain Monte Carlo (MCMC), which introduces a large computation burden and precludes their application to genomic-scale data. Here we combine a recently introduced dynamic programming algorithm for estimating species trees that bypasses MCMC integration over gene...

Data from: Dwarf brooder versus giant broadcaster: combining genetic and reproductive data to unravel cryptic diversity in an Antarctic brittle star

Quentin Jossart, Chester Sands & Mary A. Sewell
Poecilogony, or multiple developmental modes in a single species, is exceedingly rare. Several species described as poecilogenous were later demonstrated to be multiple (cryptic) species with a single developmental mode. The Southern Ocean is known to harbor a high proportion of brooders (Thorson's Rule) but with an increasing number of counter examples over recent years. Here we evaluated poecilogony versus crypticism in the brittle star Astrotoma agassizii across the Southern Ocean. This species was initially...

Data from: PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.

Robert Lanfear, Brett Calcott, Simon Y. W. Ho & Stephane Guindon
In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing an appropriate partitioning scheme is an important step in most analyses because it can affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit statistical justification. Here, we describe two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models....

DNA metabarcoding of prey reveals spatial, temporal, and diet partitioning of an island ecosystem by four invasive wasps

Julia Schmack, Gavin Lear, Carmen Astudillo-Garcia, Stéphane Boyer, Darren Ward & Jacqueline Beggs
1. Invasive alien species can cause detrimental changes in native ecosystems, but our understanding of the interactions between multiple exotic species is limited. To evaluate the joint effect of multiple sympatric invaders on an ecosystem, we must first understand how they interact with each other. 2. Here, we quantified the spatial distribution, dietary composition and overlap of four invasive generalist vespid species (two Vespula and two Polistes) that co-occur on Ahuahu off the north-east coast...

pgHMA: Application of the Heteroduplex mobility assay analysis in phylogenetics and population genetics

Teng Li, Thomas Wong, Louis Ranjard & Allen Rodrigo
The Heteroduplex mobility assay (HMA) has proven to be a robust tool for the detection of genetic variation. Here, we describe a simple and rapid application of the HMA by microfluidic capillary electrophoresis, for phylogenetics and population genetic analyses (pgHMA). We show how commonly applied techniques in phylogenetics and population genetics have equivalents with pgHMA: phylogenetic reconstruction with bootstrapping, skyline plots, and mismatch distribution analysis. We assess the performance and accuracy of pgHMA by comparing...

Data from: Novel interactions between non-native mammals and fungi facilitate establishment of invasive pines

Jamie R. Wood, Ian A. Dickie, Holly V. Moeller, Duane A. Peltzer, Karen I. Bonner, Gaye Rattray & Janet M. Wilmshurst
1. The role of novel ecological interactions between mammals, fungi and plants in invaded ecosystems remains unresolved, but may play a key role in the widespread successful invasion of pines and their ectomycorrhizal fungal associates, even where mammal faunas originate from different continents to trees and fungi as in New Zealand. 2. We examine the role of novel mammal associations in dispersal of ectomycorrhizal fungal inoculum of North American pines (Pinus contorta, Pseudotsuga menziesii), and...

Data from: Moa diet fits the bill: virtual reconstruction incorporating mummified remains and prediction of biomechanical performance in avian giants

Marie R. G. Attard, Laura A. B. Wilson, Trevor H. Worthy, Paul Scofield, Peter Johnston, William C. H. Parr & Stephen Wroe
The moa (Dinornithiformes) are large to gigantic extinct terrestrial birds of New Zealand. Knowledge about niche partitioning, feeding mode and preference among moa species is limited, hampering palaeoecological reconstruction and evaluation of the impacts of their extinction on remnant native biota, or the viability of exotic species as proposed ecological ‘surrogates'. Here we apply three-dimensional finite-element analysis to compare the biomechanical performance of skulls from five of the six moa genera, and two extant ratites,...

Data from: Bayesian total-evidence dating reveals the recent crown radiation of penguins

Alexandra Gavryushkina, Tracy A. Heath, Daniel T. Ksepka, Tanja Stadler, David Welch & Alexei J. Drummond
The total-evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This...

Data from: Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays

John E McCormack, Joseph Heled, Kathleen S Delaney, A Townsend Peterson & L Lacey Knowles
Estimates of the timing of divergence are central to testing the underlying causes of speciation. Relaxed molecular clocks and fossil calibration have improved these estimates; however, these advances are implemented in the context of gene trees, which can overestimate divergence times. Here we couple recent innovations for dating speciation events with the analytical power of species trees, where multilocus data are considered in a coalescent context. Divergence times are estimated in the bird genus Aphelocoma...

Data from: Genetic structure of an introduced paper wasp, Polistes chinensis antennalis (Hymenoptera, Vespidae) in New Zealand

Koji Tsuchida, Kazuyuki Kudo & Norio Ishiguro
Several eusocial wasps are prominent invaders to remote islands. The paper wasp Polistes chinensis antennalis is native to East Asia, was introduced to New Zealand in 1979, and has expanded its distribution there. This provides an excellent opportunity to examine the impacts of an initial bottleneck and subsequent expansion on genetic structure. We analysed and compared the genetic population structures of the native (Japan and South Korea) and invasive New Zealand populations. Although 94% of...

Data from: Multiple QTL underlie milk phenotypes at the CSF2RB locus

Thomas J. Lopdell, Kathryn Tiplady, Christine Couldrey, Thomas J. J. Johnson, Michael Keehan, Stephen R. Davis, Bevin L. Harris, Richard J. Spelman, Russell G. Snell & Mathew D. Littlejohn
Background: Over many years, artificial selection has substantially improved milk production by cows. However, the genes that underlie milk production quantitative trait loci (QTL) remain relatively poorly characterised. Here, we investigate a previously reported QTL located at the CSF2RB locus on chromosome 5, for several milk production phenotypes, to better understand its underlying genetic and molecular causes. Results: Using a population of 29,350 taurine dairy cows, we conducted association analyses for milk yield and composition...

Data from: De novo transcriptome analysis of the common New Zealand stick insect Clitarchus hookeri (Phasmatodea) reveals genes involved in olfaction, digestion and sexual reproduction

Chen Wu, Ross N Crowhurst, Alice B. Dennis, Victoria G. Twort, Shanlin Liu, Richard D. Newcomb, Howard A. Ross & Thomas R. Buckley
Phasmatodea, more commonly known as stick insects, have been poorly studied at the molecular level for several key traits, such as components of the sensory system and regulators of reproduction and development, impeding a deeper understanding of their functional biology. Here, we employ de novo transcriptome analysis to identify genes with primary functions related to female odour reception, digestion, and male sexual traits in the New Zealand common stick insect Clitarchus hookeri (White). The female...

Data from: Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances

Stephanie J. Galla, Thomas R. Buckley, Rob Elshire, Marie L. Hale, Michael Knapp, John McCallum, Roger Moraga, Anna W. Santure, Phillip Wilcox & Tammy E. Steeves
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here,...

Data from: Preschool children’s vision screening in New Zealand: a retrospective evaluation of referral accuracy

Miriam A. Langeslag-Smith, Alain C. Vandal, Vincent Briane, Benjamin Thompson & Nicola S. Anstice
Objectives: To assess the accuracy of preschool vision screening in a large, ethnically diverse, urban population in South Auckland, New Zealand. Design: Retrospective longitudinal study. Methods: B4 School Check vision screening records (n=5572) were compared with hospital eye department data for children referred from screening due to impaired acuity in one or both eyes who attended a referral appointment (n=556). False positive screens were identified by comparing screening data from the eyes that failed screening...

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: Frequent misdirected courtship in a natural community of colorful Habronattus jumping spiders

Lisa A. Taylor, Erin C. Powell & Kevin J. McGraw
Male courtship display is common in many animals; in some cases, males engage in courtship indiscriminately, spending significant time and energy courting heterospecifics with whom they have no chance of mating or producing viable offspring. Due to high costs and few if any benefits, we might expect mechanisms to evolve to reduce such misdirected courtship (or ‘reproductive interference’). In Habronattus jumping spiders, males frequently court heterospecifics with whom they do not mate or hybridize; females...

Data from: Influences of fire–vegetation feedbacks and post-fire recovery rates on forest landscape vulnerability to altered fire regimes

Alan J. Tepley, Enrique Thomann, Thomas T. Veblen, George L.W. Perry, Andrés Holz, Juan Paritsis, Thomas Kitzberger, Kristina J. Anderson-Teixeira & George L. W. Perry
1. In the context of on-going climatic warming, forest landscapes face increasing risk of conversion to non-forest vegetation through alteration of their fire regimes and their post-fire recovery dynamics. However, this pressure could be amplified or dampened, depending on how fire-driven changes to vegetation feed back to alter the extent or behavior of subsequent fires. 2. Here we develop a mathematical model to formalize understanding of how fire–vegetation feedbacks and the time to forest recovery...

Data from: The influence of selection on MHC DQA and DQB haplotypes in the endemic New Zealand Hector’s and Māui dolphins

Dorothea Heimeier, Alana Alexander, Rebecca M. Hamner, Franz Pichler & C Scott Baker
Strong balancing selection on the Major Histocompatibility Complex (MHC) can lead to different patterns in gene frequencies and neutral genomic variation within species. We investigated diversity and geographic structure of MHC genes DQA and DQB, as well as their inferred functional haplotypes, from two regional populations (East and West Coast) of the endangered Hector’s dolphin (Cephalorhynchus hectori hectori) and the critically endangered Māui dolphin (Cephalorhynchus hectori maui) (West Coast, North Island), and contrasted these results...

Deep-diving beaked whales dive together but forage apart

Jesús Alcázar Treviño, Mark Johnson, Patricia Arranz, Victoria Warren, Carlos Pérez-González, Tiago Marques, Peter Madsen & Natacha Aguilar De Soto
Echolocating animals that forage in social groups can potentially benefit from eavesdropping on other group members, cooperative foraging or social defence, but may also face problems of acoustic interference and intra-group competition for prey. Here, we investigated these potential trade-offs of sociality for extreme deep-diving Blainville´s and Cuvier’s beaked whales. These species perform highly synchronous group dives as a presumed predator-avoidance behaviour but the benefits and costs of this on foraging have not been investigated....

Data for: Male coercion and female injury in a sexually cannibalistic mantis

Nathan Burke & Gregory Holwell
Sexual conflict can generate male traits that enhance mating success but lead to injury in females. Pre-copulatory sexual cannibalism—where females eat males without mating—has the potential to select for harmful coercive traits as well, but few examples are known. Here, we show that males of the highly cannibalistic Springbok mantis, Miomantis caffra, wrestle females during pre-mating interactions. We find that most initial contacts between males and females involve a violent struggle whereby each sex tries...

Recent warming reduces the reproductive advantage of large size and contributes to evolutionary downsizing in nature

David C Fryxell, Alexander N. Hoover, Daniel A. Alvarez, Finn J. Arnesen, Javiera N. Benavente, Emma R. Moffett, Michael T. Kinnison, Kevin S. Simon & Eric P. Palkovacs
Body size is a key functional trait that is predicted to decline under warming. Warming is known to cause size declines via phenotypic plasticity, but evolutionary responses of body size to warming are poorly understood. To test for warming-induced evolutionary responses of body size and growth rates, we used populations of mosquitofish ( Gambusia affinis ) recently established (less than 100 years) from a common source across a strong thermal gradient (19–33°C) created by geothermal...

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