43 Works

Data from: Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing

Ya Yang, Michael J. Moore, Samuel F. Brockington, Douglas E. Soltis, Gane Ka-Shu Wong, Eric J. Carpenter, Yong Zhang, Li Chen, Zhixiang Yan, Yinlong Xie, Rowan F. Sage, Sarah Covshoff, Julian M. Hibberd, Matthew N. Nelson & Stephen A. Smith
Many phylogenomic studies based on transcriptomes have been limited to “single-copy” genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup...

Data from: Experimental evidence for phonemic contrasts in a nonhuman vocal system

Sabrina Engesser, Jodie M. S. Crane, James L. Savage, Andrew F. Russell & Simon W. Townsend
The ability to generate new meaning by rearranging combinations of meaningless sounds is a fundamental component of language. Although animal vocalizations often comprise combinations of meaningless acoustic elements, evidence that rearranging such combinations generates functionally distinct meaning is lacking. Here, we provide evidence for this basic ability in calls of the chestnut-crowned babbler (Pomatostomus ruficeps), a highly cooperative bird of the Australian arid zone. Using acoustic analyses, natural observations, and a series of controlled playback...

Data from: Colour polymorphism torn apart by opposing positive frequency-dependent selection, yet maintained in space

Swanne P. Gordon, Hanna Kokko, Bibiana Rojas, Ossi Nokelainen & Johanna Mappes
1. Polymorphic warning signals in aposematic species are enigmatic because predator learning and discrimination should select for the most common coloration, resulting in positive frequency-dependent survival selection. 2. Here, we investigated whether differential mating success could create sufficiently strong negative frequency-dependent selection for rare morphs to explain polymorphic (white and yellow) warning coloration in male wood tiger moths (Parasemia plantaginis). 3. We conducted an experiment in semi-natural conditions where we estimated mating success for both...

Data from: Amyloid precursor protein translation is regulated by a 3'UTR guanine quadruplex

Ezekiel Crenshaw, Brian P. Leung, Chun Kit Kwok, Michal Sharoni, Kalee Olson, Neeraj P. Sebastian, Sara Ansaloni, Reinhard Schweitzer-Stenner, Michael R. Akins, Philip C. Bevilacqua & Aleister J. Saunders
A central event in Alzheimer’s disease is the accumulation of amyloid β (Aβ) peptides generated by the proteolytic cleavage of the amyloid precursor protein (APP). APP overexpression leads to increased Aβ generation and Alzheimer’s disease in humans and altered neuronal migration and increased long term depression in mice. Conversely, reduction of APP expression results in decreased Aβ levels in mice as well as impaired learning and memory and decreased numbers of dendritic spines. Together these...

Data from: Disruptive viability selection on a black plumage trait associated with dominance

Paul Acker, Arnaud Grégoire, Margaux Rat, Claire N. Spottiswoode, René E. Van Dijk, Matthieu Paquet, Jennifer C. Kaden, Roger Pradel, Ben J. Hatchwell, Rita Covas & Claire Doutrelant
Traits used in communication, such as colour signals, are expected to have positive consequences for reproductive success, but their associations with survival are little understood. Previous studies have mainly investigated linear relationships between signals and survival, but both hump-shaped and U-shaped relationships can also be predicted, depending on the main costs involved in trait expression. Furthermore, few studies have taken the plasticity of signals into account in viability selection analyses. The relationship between signal expression...

Data from: Inbreeding ratio and genetic relationships among strains of the Western clawed frog, Xenopus tropicalis

Takeshi Igawa, Ai Watanabe, Atsushi Suzuki, Akihiko Kashiwagi, Keiko Kashiwagi, Anna Noble, Matt Guille, David E. Simpson, Marko E. Horb, Tamotsu Fujii & Masayuki Sumida
The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains...

Small rodent dynamics at Lathkill Dale SSSI, Derbys, 1971- 2005

J.R. Flowerdew, T. Amano & W.J. Sutherland
This dataset describes 35 years of 6-monthly population sampling of adult and juvenile bank voles Myodes glareolus and wood mice Apodemus sylvaticus in a Derbyshire Ash Fraxinus excelsior woodland, together with annual and seasonal ash fruit-fall and a measure of winter severity. Additional data describe a 4 year experiment on a nearby study area where in two winters supplementary ash fruit were supplied and population data collected in parallel to the main study area. Woodland...

Data from: Multilocus species trees show the recent adaptive radiation of the mimetic Heliconius butterflies

Krzysztof M. Kozak, Niklas Wahlberg, Andrew Neild, Kanchon K. Dasmahapatra, James Mallet, Chris D. Jiggins & Andrew F. E. Neild
Müllerian mimicry among Neotropical Heliconiini butterflies is an excellent example of natural selection, associated with the diversification of a large continental-scale radiation. Some of the processes driving the evolution of mimicry rings are likely to generate incongruent phylogenetic signals across the assemblage, and thus pose a challenge for systematics. We use a dataset of 22 mitochondrial and nuclear markers from 92% of species in the tribe, obtained by Sanger sequencing and de novo assembly of...

Data from: Parental care masks a density-dependent shift from cooperation to competition among burying beetle larvae

Matthew Schrader, Benjamin J. M. Jarrett & Rebecca M. Kilner
Studies of siblings have focused mainly on their competitive interactions and to a lesser extent on their cooperation. However, competition and cooperation are at opposite ends on a continuum of possible interactions and the nature of these interactions may be flexible with ecological factors tipping the balance towards competition in some environments and cooperation in others. Here we show that the presence of parental care and the density of larvae on the breeding carcass change...

Data from: Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation

Elisa G. Dierickx, Allison J. Shultz, Fumio Sato, Takashi Hiraoka & Scott V. Edwards
Evaluating the genetic and demographic independence of populations of threatened species is important for determining appropriate conservation measures, but different technologies can yield different conclusions. Despite multiple studies, the taxonomic status and extent of gene flow between the main breeding populations of Black-footed Albatross (Phoebastria nigripes), a Near-Threatened philopatric seabird, are still controversial. Here, we employ double digest RADseq to quantify the extent of genomewide divergence and gene flow in this species. Our genomewide data...

Data from: Spermatozoa scattering by a microchannel feature: an elastohydrodynamic model

Thomas D. Montenegro-Johnson, Hermes Gadêlha, David J. Smith & H. Gadelha
Sperm traverse their microenvironment through viscous fluid by propagating flagellar waves; the waveform emerges as a consequence of elastic structure, internal active moments and low Reynolds number fluid dynamics. Engineered microchannels have recently been proposed as a method of sorting and manipulating motile cells; the interaction of cells with these artificial environments therefore warrants investigation. A numerical method is presented for large-amplitude elastohydrodynamic interaction of active swimmers with domain features. This method is employed to...

Data from: The ecology and economics of shorebird conservation in a tropical human-modified landscape

Jonathan M. H. Green, Siriya Sripanomyom, Xingli Giam & David S. Wilcove
1. Rapid and extensive land-use change in intertidal foraging habitat and coastal roosting habitat is thought to be driving major population declines of shorebirds migrating through the East Asian-Australasian Flyway. Along the Inner Gulf of Thailand, a critical stopover and wintering ground for these birds, artificial wetlands (saltpans and aquaculture ponds) have replaced much of the natural coastal ecosystem. 2. We conducted a two-part study to: (i) assess the importance of saltpans and semi-traditional aquaculture...

Data from: Computed tomography, anatomical description and three-dimensional reconstruction of the lower jaw of Eusthenopteron foordi Whiteaves, 1881 from the Upper Devonian of Canada

Laura B. Porro, Emily J. Rayfield & Jennifer A. Clack
The cranial anatomy of the iconic early tetrapod Eusthenopteron foordi is probably the best understood of all fossil fishes. In contrast, the anatomy of the lower jaw – crucial for both phylogenetics and biomechanical analyses – has been only superficially described. Computed tomography data of three Eusthenopteron skulls were segmented using visualization software to digitally separate bone from matrix and individual bones from each other. Here, we present a new description of the lower jaw...

Data from: Parental effects alter the adaptive value of an adult behavioural trait

Rebecca M. Kilner, Giuseppe Boncoraglio, Jono M. Henshaw, Benjamin J. M. Jarrett, Ornela De Gasperin, Hanna Kokko, Benjamin JM Jarrett, Alfredo Attisano & Jonathan M Henshaw
The parents' phenotype, or the environment they create for their young, can have long-lasting effects on their offspring, with profound evolutionary consequences. Yet virtually no work has considered how such parental effects might change the adaptive value of behavioural traits expressed by offspring upon reaching adulthood. To address this problem, we combined experiments on burying beetles (Nicrophorus vespilloides) with theoretical modelling, and focussed on one adult behavioural trait in particular: the supply of parental care....

Data from: TAPBPR alters MHC class I peptide presentation by functioning as a peptide exchange catalyst

Clemens Hermann, Andy Van Hateren, Nico Trautwein, Andreas Neerincx, Patrick J. Duriez, Stefan Stevanović, John Trowsdale, Janet E. Deane, Tim Elliott & Louise H. Boyle
Our understanding of the antigen presentation pathway has recently been enhanced with the identification that the tapasin-related protein TAPBPR is a second MHC I-specific chaperone. We sought to determine whether, like tapasin, TAPBPR can also influence MHC I peptide selection by functioning as a peptide exchange catalyst. We show that TAPBPR can catalyse the dissociation of peptides from peptide-MHC I complexes, enhance the loading of peptide-receptive MHC I molecules, and discriminate between peptides based on...

Data from: Evolutionary novelty in a butterfly wing pattern through enhancer shuffling

Richard W. R. Wallbank, Simon W. Baxter, Carolina Pardo-Diaz, Joseph J. Hanly, Simon H. Martin, James Mallet, Kanchon K. Dasmahapatra, Camilo Salazar, Mathieu Joron, Nicola Nadeau, W. Owen McMillan & Chris D. Jiggins
An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in...

Data from: Synthesis, characterization and modelling of zinc and silicate co-substituted hydroxyapatite

Robert J. Friederichs, Helen F. Chappell, David V. Shepherd & Serena M. Best
Experimental chemistry and atomic modelling studies were performed here to investigate a novel ionic co-substitution in hydroxyapatite (HA). Zinc, silicate co-substituted HA (ZnSiHA) remained phase pure after heating to 1100°C with Zn and Si amounts of 0.6 wt% and 1.2 wt%, respectively. Unique lattice expansions in ZnSiHA, silicate Fourier transform infrared peaks and changes to the hydroxyl IR stretching region suggested Zn and silicate co-substitution in ZnSiHA. Zn and silicate insertion into HA was modelled...

Data from: On heels and toes: how ants climb with adhesive pads and tarsal friction hair arrays

Thomas Endlein & Walter Federle
Ants are able to climb effortlessly on vertical and inverted smooth surfaces. When climbing, their feet touch the substrate not only with their pretarsal adhesive pads but also with dense arrays of fine hairs on the ventral side of the 3rd and 4th tarsal segments. To understand what role these different attachment structures play during locomotion, we analysed leg kinematics and recorded single-leg ground reaction forces in Weaver ants (Oecophylla smaragdina) climbing vertically on a...

Data from: Establishing a community-wide DNA barcode library as a new tool for arctic research

H. Wirta, G. Várkonyi, C. Rasmussen, R. Kaartinen, N. M. Schmidt, P. D. N. Hebert, M. Barták, G. Blagoev, H. Disney, S. Ertl, P. Gjelstrup, D. J. Gwiazdowicz, L. Huldén, J. Ilmonen, J. Jakovlev, M. Jaschhof, J. Kahanpää, T. Kankaanpää, P. H. Krogh, R. Labbee, C. Lettner, V. Michelsen, S. A. Nielsen, T. R. Nielsen, L. Paasivirta … & T. Roslin
DNA sequences offer powerful tools for describing the members and interactions of natural communities. In this study, we establish the to-date most comprehensive library of DNA barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively studied area of the High Arctic, the Zackenberg Valley in Northeast Greenland. To demonstrate its utility, we apply the library to identify nearly 20 000 arthropod individuals from two Malaise traps, each operated...

Data from: Measuring asymmetry in time-stamped phylogenies

Bethany L. Dearlove & Simon D. W. Frost
Previous work has shown that asymmetry in viral phylogenies may be indicative of heterogeneity in transmission, for example due to acute HIV infection or the presence of ‘core groups’ with higher contact rates. Hence, evidence of asymmetry may provide clues to underlying population structure, even when direct information on, for example, stage of infection or contact rates, are missing. However, current tests of phylogenetic asymmetry (a) suffer from false positives when the tips of the...

Data from: Fine-scale genetic structure reflects sex-specific dispersal strategies in a population of sociable weavers (Philetairus socius)

René E. Van Dijk, Rita Covas, Claire Doutrelant, Claire N. Spottiswoode & Ben J. Hatchwell
Dispersal is a critical driver of gene flow, with important consequences for population genetic structure, social interactions and other biological processes. Limited dispersal may result in kin-structured populations in which kin selection may operate, but it may also increase the risk of kin competition and inbreeding. Here, we use a combination of long-term field data and molecular genetics to examine dispersal patterns and their consequences for the population genetics of a highly social bird, the...

Data from: Cell cycle-dependent differentiation dynamics balances growth and endocrine differentiation in the pancreas

Yung Hae Kim, Hjalte List Larsen, Pau Rué, Laurence A. Lemaire, Jorge Ferrer & Anne Grapin-Botton
Organogenesis relies on the spatiotemporal balancing of differentiation and proliferation driven by an expanding pool of progenitor cells. In the mouse pancreas, lineage tracing at the population level has shown that the expanding pancreas progenitors can initially give rise to all endocrine, ductal, and acinar cells but become bipotent by embryonic day 13.5, giving rise to endocrine cells and ductal cells. However, the dynamics of individual progenitors balancing self-renewal and lineage-specific differentiation has never been...

Data from: Antagonistic effect of helpers on breeding male and female survival in a cooperatively breeding bird

Matthieu Paquet, Claire Doutrelant, Ben J. Hatchwell, Claire N. Spottiswoode & Rita Covas
1. Cooperatively breeding species are typically long lived and hence, according to theory, are expected to maximize their lifetime reproductive success through maximizing survival. Under these circumstances, the presence of helpers could be used to lighten the effort of current reproduction for parents to achieve higher survival. 2. In addition, individuals of different sexes and ages may follow different strategies, but whether male and female breeders and individuals of different ages benefit differently from the...

Data from: Adaptive responses to cool climate promotes persistence of a non-native lizard

Geoffrey M. While, Joseph Williamson, Graham Prescott, Terézia Horváthová, Belén Fresnillo, Nicholas J. Beeton, Ben Halliwell, Sozos Michaelides, Tobias Uller & T. Horvathova
Successful establishment and range expansion of non-native species often require rapid accommodation of novel environments. Here, we use common-garden experiments to demonstrate parallel adaptive evolutionary response to a cool climate in populations of wall lizards (Podarcis muralis) introduced from southern Europe into England. Low soil temperatures in the introduced range delay hatching, which generates directional selection for a shorter incubation period. Non-native lizards from two separate lineages have responded to this selection by retaining their...

Data from: Selection on male sex pheromone composition contributes to butterfly reproductive isolation

Paul M. B. Bacquet, Oskar Brattström, Hong-Lei Wang, Cerisse E. Allen, Christer Löfstedt, Paul M. Brakefield, Caroline M. Nieberding, C. Lofstedt, H.- L. Wang & O. Brattstrom
Selection can facilitate diversification by inducing character displacement in mate choice traits that reduce the probability of maladaptive mating between lineages. Although reproductive character displacement (RCD) has been demonstrated in two-taxa case studies, the frequency of this process in nature is still debated. Moreover, studies have focused primarily on visual and acoustic traits, despite the fact that chemical communication is probably the most common means of species recognition. Here, we showed in a large, mostly...

Registration Year

  • 2015
    43

Resource Types

  • Dataset
    43

Affiliations

  • University of Cambridge
    43
  • University of Sheffield
    6
  • French National Centre for Scientific Research
    4
  • University of Exeter
    4
  • Australian National University
    3
  • University of Zurich
    3
  • University of Cape Town
    3
  • University of Porto
    3
  • University of Copenhagen
    2
  • Harvard University
    2