2,848 Works

Data from: Tracking earthworm communities from soil DNA

Friederike Bienert, Sébastien De Danieli, Christian Miquel, Eric Coissac, Carole Poillot, Jean-Jacques Brun & Pierre Taberlet
Earthworms are known for their important role within the functioning of an ecosystem, and their diversity can be used as an indicator of ecosystem health. To date, earthworm diversity has been investigated through conventional extraction methods such as handsorting, soil washing or the application of a mustard solution. Such techniques are time-consuming and often difficult to apply. We showed that combining DNA metabarcoding and next generation sequencing facilitates the identification of earthworm species from soil...

Data from: Genetic diversity of wild grapevine populations in Spain and their genetic relationships with cultivated grapevines

Maria T. De Andrés, Alejandro Benito, Gemma Pérez-Rivera, Rafael Ocete, María A. Lopez, Laura Gaforio, Gregorio Muñoz, Felix Cabello, José M. Martínez-Zapater, Rosa Arroyo-Garcia, Maria T. De Andrés, Alejandro Benito, Gemma Pérez-Rivera, Rafael Ocete, María A. Lopez, Laura Gaforio, Gregorio Muñoz, Felix Cabello, José M. Martínez-Zapater & Rosa Arroyo-Garcia
The wild grapevine, Vitis vinifera L. ssp sylvestris (Gmelin) Hegi, considered as the ancestor of the cultivated grapevine, is native from Eurasia. In Spain natural populations of Vitis vinifera ssp sylvestris can still be found along river banks. In this work we have performed a wide search of wild grapevine populations in Spain and characterized the amount and distribution of their genetic diversity using 25 nuclear SSR loci. We have also analyzed the possible coexistence...

Data from: Phylogeny and taxonomy of an enigmatic sterile lichen

Brendan P. Hodkinson & James C. Lendemer
Crustose, asexually reproducing taxa represent a large component of lichen biodiversity that is often overlooked and underestimated; as a result, remarkable potential remains for discovery of new species in this neglected, polyphyletic group. For this study, ITS and mtSSU rDNA sequences were analyzed in conjunction with chemical and anatomical data to understand the systematic placement of an enigmatic, sterile lichen. This species, despite references in the literature, and being known for over half a decade,...

Data from: Does hybridization drive the transition to asexuality in diploid Boechera?

James Benjamin Beck, Patrick J. Alexander, Loreen Allphin, Ihsan A. Al-Shehbaz, Catherine Rushworth, C. Donovan Bailey & Michael D. Windham
Gametophytic apomixis is a common form of asexual reproduction in plants. Virtually all gametophytic apomicts are polyploids, and some view polyploidy as a prerequisite for the transition to apomixis. However, any causal link between apomixis and polyploidy is complicated by the fact that most apomictic polyploids are allopolyploids, leading some to speculate that hybridization, rather than polyploidy, enables apomixis. Diploid apomixis presents a rare opportunity to isolate the role of hybridization, and a number of...

Data from: The evolution of cranial form and function in theropod dinosaurs: insights from geometric morphometrics

Stephen L. Brusatte, Manabu Sakamoto, Shaena Montanari & William E. H. Harcourt Smith
Theropod dinosaurs, an iconic clade of fossil species including Tyrannosaurus and Velociraptor, developed a great diversity of body size, skull form, and feeding habits over their 160+ million year evolutionary history. Here we utilise geometric morphometrics to study broad patterns in theropod skull shape variation, and compare the distribution of taxa in cranial morphospace (form) to both phylogeny and quantitative metrics of biting behaviour (function). We find that theropod skulls primarily differ in relative anteroposterior...

Data from: Wing patterning gene redefines the mimetic history of Heliconius butterflies

Heather M. Hines, Brian A. Counterman, Riccardo Papa, Priscila Albuquerque De Moura, Marcio Z. Cardoso, Mauricio Linares, James Mallet, Robert D. Reed, Chris D. Jiggins, Marcus R. Kronforst, W. Owen McMillan, R. D. Reed, J. Mallet, W. O. McMillan, M. R. Kronforst, H. M. Hines, B. A. Counterman, M. Linares, M. Z. Cardoso & C. D. Jiggins
The mimetic butterflies Heliconius erato and H. melpomene have undergone parallel radiations to form a near-identical patchwork of over 20 different wing pattern races across the Neotropics. Previous molecular phylogenetic work on these radiations has suggested that similar but geographically disjunct color patterns arose multiple times independently in each species. The neutral markers used in these studies, however, can move freely across color pattern boundaries and therefore might not represent the history of the adaptive...

Data from: Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with E. coli

Mickaël Le Gac, Jessica Plucain, Thomas Hindré, Richard E. Lenski & Dominique Schneider
Closely related organisms usually occupy similar ecological niches, leading to intense competition and even extinction. Such competition also can promote rapid phenotypic evolution and ecological divergence. This process may end with the stable occupation of distinct niches or, alternatively, may entail repeated bouts of evolution. Here we examine two Escherichia coli lineages, called L and S, that coexisted for more than 30,000 generations after diverging from a common ancestor. Both lineages underwent sustained phenotypic evolution...

Data from: Ecological effects on metabolic scaling amphipod responses to fish predators in freshwater springs

Douglas S. Glazier, Eric M. Butler, Sara A. Lombardi, Travis J. Deptola, Andrew J. Reese & Erin V. Satterthwaite
Metabolic rate is commonly thought to scale with body mass to the 3/4-power as a result of universal body-design constraints. However, recent comparative work has shown that the metabolic scaling slope may vary significantly among species and higher taxa, apparently in response to different lifestyles and ecological conditions, though the precise mechanisms involved are not well understood. To better understand these under-appreciated ecological effects and their causes, it is important to control for extraneous phylogenetic...

Data from: Genotype-dependent responses to levels of sibling competition over maternal resources in mice

Reinmar Hager, James M. Cheverud, Jason B. Wolf, J B Wolf, R Hager & J M Cheverud
Research on phenotypic plasticity has often focused on how a given genotype responds to changing physical environments. However, for many species the social environment plays an equally important role due to competition for resources. During early development, the level of competition for limited resources will often depend critically on the number of siblings. Therefore, competition among siblings should drive the evolution of genes that allow flexible responses to realized levels of competition and maternal resource...

Data from: Spatial genetic structure of the mountain pine beetle (Dendroctonus ponderosae) outbreak in western Canada: historical patterns and contemporary dispersal

G. D. N. Gayathri Samarasekera, Nicholas V. Bartell, B. Staffan Lindgren, Janice E. K. Cooke, Corey S. Davis, Patrick M. A. James, David W. Coltman, Karen E. Mock, Brent W. Murray, G. D. N. Gayathri Samarasekera, Nicholas V. Bartell, B. Staffan Lindgren, Janice E. K. Cooke, Corey S. Davis, Patrick M. A. James, David W. Coltman, Karen E. Mock & Brent W. Murray
Environmental change has a wide range of ecological consequences, including species extinction and range expansion. Many studies have shown that insect species respond rapidly to climatic change. A mountain pine beetle epidemic of record size in North America has led to unprecedented mortality of lodgepole pine, and a significant range expansion to the northeast of its historic range. Our goal was to determine the spatial genetic variation found among outbreak population from which genetic structure,...

Data from: Noise pollution filters bird communities based on vocal frequency

Clinton D. Francis, Catherine P. Ortega & Alexander Cruz
BACKGROUND: Human-generated noise pollution now permeates natural habitats worldwide, presenting evolutionarily novel acoustic conditions unprecedented to most landscapes. These acoustics are not only harmful to humans, but threaten wildlife, and especially birds, via changes to species densities, foraging behavior, reproductive success, and predator-prey interactions. Explanations for the negative effects of noise on birds include the disruption of acoustic communication through energetic masking, potentially forcing species that rely upon acoustic communication to abandon otherwise suitable areas....

Data from: Reconstructing the origins of high-alpine niches and cushion life form in the genus Androsace s.l. (Primulaceae)

Florian Boucher, Wilfried Thuiller, Cristina Roquet, Rolland Douzet, Serge Aubert, Nadir Alvarez & Sébastien Lavergne
Relatively few species have been able to colonize extremely cold alpine environments. We investigate the role played by the cushion life form in the evolution of climatic niches in the plant genus Androsace s.l., which spreads across the mountain ranges of the Northern Hemisphere. Using robust methods that account for phylogenetic uncertainty, intraspecific variability of climatic requirements and different life history evolution scenarios, we show that climatic niches of Androsace s.l. exhibit low phylogenetic signal...

Data from: Male-mediated effects on female meiotic recombination

Laurie S Stevison
Recombination rates vary owing to an individual’s genetic composition and/or its environmental condition. Yet, the effects of mating partner on recombination rates have not been considered. Here, I document a previously undescribed male-mediated effect on female recombination rates. After crossing females to males from different genetic backgrounds, I observed a significant difference in proportion of recombinant offspring based on the genetic background of the father (p=0.0292; 3 df; F=3.07). Genetic variation in male ability to...

Data from: Multiple Quaternary refugia in the eastern Guiana Shield revealed by comparative phylogeography of 12 frog species

Antoine Fouquet, Brice P. Noonan, Miguel T. Rodrigues, Nicolas Pech, André Gilles & Neil J. Gemmell
The Guiana Shield is one of the most pristine regions of Amazonia and biologically one of the richest areas on Earth. How and when the massive diversity of life that exists in Amazonia arose remains the subject of considerable debate. The prevailing hypothesis of Quaternary glacial refugia suggests that a part of the eastern Guiana Shield, among other areas in Amazonia, served as stable, forested refugia during periods of aridity. However, the recently proposed Disturbance-Vicariance...

Data from: Functional constraints on coiling geometry and aperture inclination in gastropods

Koji Noshita, Takahiro Asami & Takao Ubukata
We studied the morphological diversity of gastropod shell forms from the viewpoint of theoretical morphology, emphasizing the relationships of shell form to postural stability and the available space for soft body, which we assessed in terms of the moment of force and soft-tissue ratio calculations, respectively. The results of computer simulations suggest a functional trade-off between postural stability and available space for soft body: a compact shell possessing a low spire and small umbilicus exhibits...

Data from: Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood

Yufeng Wu
Incomplete lineage sorting can cause incongruence between the phylogenetic history of genes (the gene tree) and that of the species (the species tree), which can complicate the inference of phylogenies. In this paper, I present a new coalescent-based algorithm for species tree inference with maximum likelihood. I first describe an improved method for computing the probability of a gene tree topology given a species tree, which is much faster than an existing algorithm by Degnan...

Data from: Eutrophication and predation risk interact to affect sexual trait expression and mating success

Rickey Duane Cothran, Andy R Stiff, Punidan D Jeyasingh & Rick A Relyea
Sexual traits are especially sensitive to low food resources. Other environmental parameters (e.g., predation) should also affect sexual trait expression by favoring investment in viability traits rather than sexual traits. We know surprisingly little about how predators alter investment in sexual traits, or how predator and resource environments interact to affect sexual trait investment. We explored how increasing phosphorous (P) availability, at a level mimicking cultural eutrophication, affects the development of sexual, non-sexual, and viability...

Data from: Increasing temperature, not mean temperature, is a cue for avian timing of reproduction

Sonja Verena Schaper, Alistair S. Dawson, Peter J. Sharp, Phillip Gienapp, Samuel P. Caro, Marcel E. Visser, Sonja V. Schaper & Alistair Dawson
Timing of reproduction in temperate zone birds is strongly correlated with spring temperature, with an earlier onset of breeding in warmer years. Females adjust their laying between years to be synchronized with local food sources and thereby optimize reproductive output. However, climate change currently disrupts the link between predictive environmental cues and spring phenology. To investigate direct effects of temperature on the decision to lay, and its genetic basis, we used pairs of Great Tits...

Data from: Pleistocene speciation in the genus Populus (Salicaceae)

Nicholas D. Levsen, Peter Tiffin & Matthew S. Olson
The macro-evolutionary consequences of recent climate change remain controversial and there is little paleobotanical or morphological evidence that Pleistocene (1.8-0.12 Ma) glacial cycles acted as drivers of speciation, especially among lineages with long generation times, such as trees. We combined genetic and ecogeographic data from two closely related North American tree species, Populus balsamifera and P. trichocarpa (Salicacaeae) to determine if their divergence coincided with and was possibly caused by Pleistocene climatic events. We analyzed...

Data from: Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales

Brant C. Faircloth, John E. McCormack, Nicholas G. Crawford, Michael G. Harvey, Robb T. Brumfield & Travis C. Glenn
Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated...

Data from: Intrachromosomal rearrangements in avian genome evolution: evidence for regions prone to breakpoints

Darren K. Griffin, Benjamin M. Skinner, Darren K. Griffin, Benjamin M. Skinner, B M Skinner & D K Griffin
It is generally believed that the organization of avian genomes remains highly conserved in evolution as chromosome number is constant and comparative chromosome painting demonstrated there to be very few interchromosomal rearrangements. The recent sequencing of the zebra finch (Taeniopygia guttata) genome allowed an assessment of the number of intra-chromosomal rearrangements between it and the chicken (Gallus gallus) genome, revealing a surprisingly high number of intra-chromosomal rearrangements. With the publication of the turkey (Meleagris gallopavo)...

Data from: Citizen science reveals unexpected continental-scale evolutionary change in a model organism

Jonathan Silvertown, Laurence Cook, Robert Cameron, Mike Dodd, Kevin McConway, Jenny Worthington, Peter Skelton, Christian Anton, Oliver Bossdorf, Bruno Baur, Menno Schilthuizen, Benoît Fontaine, Helmut Sattmann, Giorgio Bertorelle, Maria Correia, Cristina Oliveira, Beata Pokryszko, Małgorzata Ożgo, Arturs Stalažs, Eoin Gill, Üllar Rammul, Péter Sólymos, Zoltan Féher & Xavier Juan
Organisms provide some of the most sensitive indicators of climate change and evolutionary responses are becoming apparent in species with short generation times. Large datasets on genetic polymorphism that can provide an historical benchmark against which to test for recent evolutionary responses are very rare, but an exception is found in the brown-lipped banded snail (Cepaea nemoralis). This species is sensitive to its thermal environment and exhibits several polymorphisms of shell colour and banding pattern...

Data from: Molecular cytogenetic and genomic insights to chromosomal evolution

Aurora Ruiz-Herrera, Marta Farré, Terence J. Robinson & T J Robinson
This review summarizes aspects of the extensive literature on the patterns and processes underpinning chromosomal evolution in vertebrates and especially placental mammals. It highlights the growing synergy between molecular cytogenetics and comparative genomics, particularly with respect to fully or partially sequenced genomes, and provides novel insights into changes in chromosome number and structure across deep division of the vertebrate tree of life. The examination of basal numbers in the deeper branches of the vertebrate tree...

Data from: Antagonistic responses to natural and sexual selection and the sex-specific evolution of cuticular hydrocarbons in Drosophila simulans

Manmohan D. Sharma, John Hunt & David J. Hosken
Natural and sexual selection are classically thought to oppose one another, and while there is evidence for this, direct experimental demonstrations of this antagonism are largely lacking. Here we assessed the effects of sexual and natural selection on the evolution of cuticular hydrocarbons (CHCs), a character subject to both modes of selection, in Drosophila simulans. Natural selection and sexual selection were manipulated in a fully factorial design, and after 27 generations of experimental evolution the...

Data from: Evaluation of two approaches to genotyping MHC class I in a passerine – CE-SSCP and 454 pyrosequencing

Marta Promerová, Wiesław Babik, Josef Bryja, Tomáš Albrecht, Michał Stuglik & Jacek Radwan
Genes of the highly dynamic major histocompatibility complex (MHC) are directly linked to individual fitness and are of high interest in evolutionary ecology and conservation genetics. Gene duplication and positive selection usually lead to high levels of polymorphism in the MHC region, making genotyping of MHC a challenging task. Here, we compare the performance of two methods for MHC class I genotyping in a passerine with highly duplicated MHC class I genes: capillary electrophoresis single...

Registration Year

  • 2011

Resource Types

  • Dataset


  • The University of Texas at Austin
  • University of Georgia
  • University of Montpellier
  • University of Cambridge
  • University of Otago
  • Duke University
  • University of Alberta
  • University of Pittsburgh
  • Smithsonian Institution
  • University of Oslo
  • UNSW Sydney
  • James Cook University
  • North Carolina State University
  • University of Tokyo
  • University of California, Davis