20 Works

Data from: Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments

Bonnie Laverock, Karen Tait, Jack A. Gilbert, A. Mark Osborn & Steve Widdicombe
In marine environments, macrofauna living in or on the sediment surface may alter the structure, diversity and function of benthic microbial communities. In particular, microbial nitrogen (N)-cycling processes may be enhanced by the activity of large bioturbating organisms. Here, we study the effect of the burrowing mud shrimp Upogebia deltaura upon temporal variation in the abundance of genes representing key N-cycling functional guilds. The abundance of bacterial genes representing different N-cycling guilds displayed different temporal...

Data from: Genome-level homology and phylogeny of Vibrionaceae (Gammaproteobacteria: Vibrionales) with three new complete genome sequences

Rebecca B. Dikow & William Leo Smith
Background: Phylogenetic hypotheses based on complete genome data are presented for the Gammaproteobacteria family Vibrionaceae. Two taxon samplings are presented: one including all those taxa for which the genome sequences are complete in terms of arrangement (chromosomal location of fragments; 19 taxa) and one for which the genome sequences contain multiple contigs (44 taxa). Analyses are presented under the Maximum Parsimony and Maximum Likelihood optimality criteria for total evidence datasets, the two chromosomes separately, and...

Data from: Molecular phylogeny and symbiotic selectivity of the green algal genus Dictyochloropsis sensu lato (Trebouxiophyceae): a polyphyletic and widespread group forming photobiont-mediated guilds in the lichen family Lobariaceae

Francesco Dal Grande, Andreas Beck, Carolina Cornejo, Garima Singh, Saran Cheenacharoen, Matthew P. Nelsen & Christoph Scheidegger
Dictyochloropsis s.l. is an ecologically important, common but little-studied genus of green algae. Here, we examined the diversity and host selectivity of algae attributed to this genus at both species-to-species and species-to-community levels. We conducted a molecular investigation of 15 cultured strains and several lichen photobionts, using 18S rRNA, rbcL and ITS sequence data. We further used seven alga-specific microsatellite markers to study algal sharing among fungi of the family Lobariaceae in two populations in...

Data from: Bioturbation determines the response of benthic ammonia oxidising microorganisms to ocean acidification

Bonnie Laverock, Vassilis Kitidis, Karen Tait, Jack A. Gilbert, A. Mark Osborn & Steve Widdicombe
Ocean acidification (OA), caused by the dissolution of increasing concentrations of atmospheric carbon dioxide (CO2) in seawater, is projected to cause significant changes to marine ecology and biogeochemistry. Potential impacts on the microbially driven cycling of nitrogen are of particular concern. Specifically, under seawater pH levels approximating future OA scenarios, rates of ammonia oxidation (the rate-limiting first step of the nitrification pathway) have been shown to dramatically decrease in seawater, but not in underlying sediments....

Data from: Transformation of stimulus correlations by the retina

Kristina D. Simmons, Jason S. Prentice, Gašper Tkačik, Jan Homann, Heather K. Yee, Stephanie E. Palmer, Philip C. Nelson & Vijay Balasubramanian
Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online....

Data from: Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis: Orobanchaceae)

Deren A. R. Eaton & Richard H. Ree
Phylogenetic relationships among recently diverged species are often difficult to resolve due to insufficient phylogenetic signal in available markers and/or conflict among gene trees. Here we explore the use of reduced-representation genome sequencing, specifically in the form of restriction-site associated DNA (RAD), for phylogenetic inference and the detection of ancestral hybridization in non-model organisms. As a case study, we investigate Pedicularis section Cyathophora, a systematically recalcitrant clade of flowering plants in the broomrape family (Orobanchaceae)....

Data from: 'Escaping' the X chromosome leads to increased gene expression in the male germline of Drosophila melanogaster

Claus Kemkemer, Ana Catalán & John Parsch
Genomic analyses of Drosophila species suggest that the X chromosome presents an unfavourable environment for the expression of genes in the male germline. A previous study in D. melanogaster used a reporter gene driven by a testis-specific promoter to show that expression was greatly reduced when the gene was inserted onto the X chromosome as compared with the autosomes. However, a limitation of this study was that only the expression regulated by a single, autosomal-derived...

Data from: A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa

David W. Bapst
1.) Applying phylogeny-based analyses of trait evolution and diversification in the fossil record generally involves transforming an unscaled cladogram into a phylogeny scaled to geologic time. Current methods produce single time-scaled phylogenies with artificial zero-length branches and no indication of the uncertainty in the temporal relationships. 2.) Here I present a stochastic algorithm for time-scaling phylogenies of fossil taxa by randomly sampling node ages from a constrained distribution, with the ultimate goal of producing large...

Data from: The role of founder effects on the evolution of reproductive isolation

Daniel R. Matute
Several theories argue that large changes in allele frequencies through genetic drift after a small founding population becomes allopatrically isolated can lead to significant changes in reproductive isolation and thus trigger the origin of new species. For this reason, founder speciation has been proposed as a potent force in the generation of new species. Nonetheless, the relative importance of such “founder effects” remains largely untested. In this report, I used experimental evolution to create one...

Data from: Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing

Xue Qin Wang, Lei Zhao, Deren A. R. Eaton, De Zhu Li & Zhen Hua Guo
Phylogenetic relationships among temperate species of bamboo are difficult to resolve, owing to both the challenge of detecting sufficiently variable markers and their polyploid history. Here, we use restriction site–associated DNA sequencing to identify candidate loci with fixed allelic differences segregating between and within two temperate species of bamboos: Arundinaria faberi and Yushania brevipaniculata. Approximately 27 million paired-end sequencing reads were generated across four samples. From pooled data, we assembled 67 685 and 70 668...

Data from: Evolution of displays within the pair bond

Maria R. Servedio, Trevor D. Price & Russell Lande
Although sexual selection is an important cause of display evolution, in socially monogamous species (e.g. many birds), displays continue after formation of the pair bond. Here, we consider that these displays evolve because they stimulate the partner to increase investment in offspring. Our study is motivated by elaborate mutual displays in species that are largely monomorphic and have long-term pair bonds (e.g. the great crested grebe, Podiceps cristatus) and by many empirical results evidencing that...

Data from: Diversification in a biodiversity hotspot: landscape correlates of phylogeographic patterns in the African spotted reed frog

Lucinda P. Lawson
The Eastern Afromontane Biodiversity Hotspot is known for microendemism and exceptional population genetic structure. The region's landscape heterogeneity is thought to limit gene flow between fragmented populations and create opportunities for regional adaptation, but the processes involved are poorly understood. Using a combination of phylogeographic analyses and circuit theory, I investigate how characteristics of landscape heterogeneity including regional distributions of slope, rivers and streams, habitat and hydrological basins (drainages) impact genetic distance among populations of...

Data from: The role of glucosinolates and the jasmonic acid pathway in resistance of Arabidopsis thaliana against molluskan herbivores

Kimberly L. Falk, Julia Kästner, Natacha Bodenhausen, Katharina Schramm, Christian Paetz, Daniel Vassao, Michael Reichelt, Dietrich Von Knorre, Joy Bergelson, Matthias Erb, Jonathan Gershenzon & Stefan Meldau
Although slugs and snails play important roles in terrestrial ecosystems and cause considerable damage on a variety of crop plants, knowledge about the mechanisms of plant immunity to mollusks is limited. We found slugs to be natural herbivores of Arabidopsis thaliana and therefore investigated possible resistance mechanisms of this species against several molluskan herbivores. Treating wounded leaves with the mucus residue (“slime trail”) of the Spanish slug Arion lusitanicus increased wound-induced jasmonate levels, suggesting the...

Data from: Parallel evolution of local adaptation and reproductive isolation in the face of gene flow

Roger K. Butlin, Maria Saura, Grégory Charrier, Benjamin Jackson, Carl André, Armando Caballero, Jerry A. Coyne, Juan Galindo, John W. Grahame, Johann Hollander, Petri Kemppainen, Mónica Martínez-Fernández, Marina Panova, Humberto Quesada, Kerstin Johannesson, Emilio Rolán-Alvarez & Johan Hollander
Parallel evolution of similar phenotypes provides strong evidence for the operation of natural selection. Where these phenotypes contribute to reproductive isolation, they further support a role for divergent, habitat-associated selection in speciation. However, the observation of pairs of divergent ecotypes currently occupying contrasting habitats in distinct geographical regions is not sufficient to infer parallel origins. Here we show striking parallel phenotypic divergence between populations of the rocky-shore gastropod, Littorina saxatilis, occupying contrasting habitats exposed to...

Data from: Complete genome sequences provide a case study for the evaluation of gene-tree thinking

Rebecca B. Dikow & William Leo Smith
Complete genome sequences from a genus of Gammaproteobacteria, Shewanella, are used to generate a genome-wide exploration of the gene-tree species-tree dichotomy. A number of datasets were constructed and analyses were attempted. Single genes were chosen from 243 regions of collinear gene homology (128 of these 243 chosen genes are from the core Shewanella genome and 162 of 243 have the complete taxon sampling) from a previous study (Dikow, 2011) and subjected to phylogenetic analysis both...

Data from: When can clades be potentially resolved with morphology?

David W. Bapst
Morphology-based phylogenetic analyses are the only option for reconstructing relationships among extinct lineages, but often find support for conflicting hypotheses of relationships. The resulting lack of phylogenetic resolution is generally explained in terms of data quality and methodological issues, such as character selection. A previous suggestion is that sampling ancestral morphotaxa or sampling multiple taxa descended from a long-lived, unchanging lineage can also yield clades which have no opportunity to share synapomorphies. This lack of...

Data from: Constraints on mammalian forelimb development: insights from developmental disparity

Darcy L. Ross, Jonathan D. Marcot, Keith J. Betteridge, Nanette Nasone-Yoder, C. Scott Bailey, Karen E. Sears, Darcy Ross & Nanette Nascone-Yoder
Tetrapod limb development has been studied extensively for decades, yet the strength and role of developmental constraints in this process remains unresolved. Mammals exhibit a particularly wide array of limb morphologies associated with various locomotion modes and behaviors, providing a useful system for identifying periods of developmental constraint and conserved developmental mechanisms or morphologies. In this study, landmark-based geometric morphometrics are used to investigate levels and patterns of morphological diversity (disparity) among the developing forelimbs...

Data from: The influence of abdominal pigmentation in desiccation and UV-resistance in two species of Drosophila

Daniel Ricardo Matute & Alexandra Harris
Drosophila yakuba and D. santomea are sister species that differ in their levels of abdominal pigmentation; D. yakuba shows heavily pigmented posterior abdominal segments in both sexes, whereas D. santomea lacks dark pigment anywhere on its body. Using naturally collected lines, we demonstrate the existence of altitudinal variation in abdominal pigmentation in D. yakuba but not in D. santomea. We use the variation in pigmentation within D. yakuba and two body-color mutants in D. yakuba...

Data from: A locus in Drosophila sechellia affecting tolerance of a host plant toxin

Eric A. Hungate, Eric J. Earley, Ian A. Boussy, David A. Turissini, Chau-Ti Ting, Jennifer R. Moran, Mao-Lien Wu, Chung-I Wu & Corbin D. Jones
Many insects feed on only one or a few types of host. These host specialists often evolve a preference for chemical cues emanting from their host and develop mechanisms for circumventing their host’s defenses. Adaptations like these are central to evolutionary biology, yet our understanding of their genetics remains incomplete. Drosophila sechellia, an emerging model for the genetics of host specialization, is an island endemic that has adapted to chemical toxins present in the fruit...

Data from: Investigation of the geographic scale of adaptive phenological variation and its underlying genetics in Arabidopsis thaliana

Benjamin Brachi, Romain Villoutreix, Nathalie Faure, Nina-Coralie Hautekèete, Yves Piquot, Maxime Pauwels, Dominique Roby, Joel Cuguen, Joy Bergelson & Fabrice Roux
Despite the increasing number of genomic tools, identifying the genetics underlying adaptive complex traits remains challenging in the model species Arabidopsis thaliana. This is due, at least in part, to the lack of data on the geographical scale of adaptive phenotypic variation. The aims of this study were (i) to tease apart the historical roles of adaptive and nonselective processes in shaping phenological variation in A. thaliana in France and (ii) to gain insights into...

Registration Year

  • 2013

Resource Types

  • Dataset


  • University of Chicago
  • University of Sheffield
  • Field Museum of Natural History
  • University of North Carolina
  • Plymouth Marine Laboratory
  • University of Pennsylvania
  • Princeton University
  • University of California System
  • Lund University
  • University of Western Brittany