Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
Data from: Purifying selection and molecular adaptation in the genome of Verminephrobacter, the heritable symbiotic bacteria of earthwormsThomas Bataillon, Kasper U. Kjeldsen, Nicolás Pinel, Stéphane De Mita, Marie B. Lund, Frank Panitz, Christian Bendixen, David A. Stahl & Andreas Schramm
While genomic erosion is common among intracellular symbionts, patterns of genome evolution in heritable extracellular endosymbionts remain elusive. We study vertically transmitted extracellular endosymbionts (Verminephrobacter, Betaproteobacteria) that form a beneficial, species-specific, and evolutionarily old (60-130 MYA) association with earthworms. We assembled a draft genome of Verminephrobacter aporrectodeae and compared it to the genomes of Verminephrobacter eiseniae and two non-symbiotic close relatives (Acidovorax). Similar to V. eiseniae, the V. aporrectodeae genome was not markedly reduced in...
Skull measurements_AMNH_CynomysMeasurements are from specimens of Cynomys gunnisoni housed at the AMNH. Measurements were collected from digital images using Image J and recorded into an Excel spreadsheet. The column headings include: Specimen ID, Location, Year, Occipital condyle, zygomatic width, total skull length, whether skull sutures were fused, length of the upper right tooth row, and basicranial length. All measurements are reported in mm.
Data from: Analysis of inbreeding depression in mixed-mating plants provides evidence for selective interference and stable mixed matingAlice A Winn, Elizabeth Elle, Susan Kalisz, Pierre-Olivier Cheptou, Christopher G Eckert, Carol Goodwillie, Mark O. Johnston, David A Moeller, Richard H Ree, Risa D Sargent & Mario Vallejo-Marín
Hermaphroditic individuals can produce both selfed and outcrossed progeny, termed mixed mating. General theory predicts that mixed-mating populations should evolve quickly toward high rates of selfing, driven by rapid purging of genetic load and loss of inbreeding depression (ID), but the substantial number of mixed-mating species observed in nature calls this prediction into question. Greater average ID reported for selfing than for outcrossing populations is consistent with purging and suggests that mixed-mating taxa in evolutionary...
Data from: Comparison of population-genetic structuring in congeneric kelp- versus rock-associated snails: a test of a dispersal-by-rafting hypothesisRaisa Nikula, Hamish G. Spencer & Jonathan M. Waters
Phylogeographic studies indicate that many marine invertebrates lacking autonomous dispersal ability are able to achieve trans-oceanic colonization by rafting on buoyant macroalgae. However, less is known about the impact of rafting on on-going population-genetic connectivity of intertidal species associated with buoyant macroalgae. We hypothesize that such species will have higher levels of population-genetic connectivity than those exploiting nonbuoyant substrates such as rock. We tested this hypothesis by comparing nuclear multilocus population-genetic structuring in two sister...
Data from: Assessing adaptive phenotypic plasticity by means of conditional strategies from empirical data: the Latent Environmental Threshold ModelMathieu Buoro, Olivier Gimenez & Etienne Prévost
Conditional strategies are the most common form of discrete phenotypic plasticity. In a conditional strategy, the phenotype expressed by an organism is determined by the difference between an environmental cue and a threshold, both of which may vary among individuals. The Environmental Threshold model (ETM) has been proposed as a mean to understand the evolution of conditional strategies, but has been surprisingly seldom applied to empirical studies. A hindrance for the application of the ETM...
Data from: Species interactions mediate phylogenetic community structure in a hyper-diverse lizard assemblage from arid AustraliaDaniel L. Rabosky, Mark A. Cowan, Amanda L. Talaba & Irby J. Lovette
Evolutionary history can exert a profound influence on ecological communities, but few generalities have emerged concerning the relationships among phylogeny, community membership, and niche evolution. We compared phylogenetic community structure and niche evolution in three lizard clades (Ctenotus skinks, agamids, diplodactyline geckos) from arid Australia. We surveyed lizard communities at 32 sites in the northwestern Great Victoria Desert and generated complete species-level molecular phylogenies for regional representatives of the three clades. We document a striking...
Data from: How depressed? Estimates of inbreeding effects during seed development depend on reproductive conditionsLawrence D. Harder, Nina Hobbhahn & Shane A. Richards
Inbreeding depression can reduce the performance of offspring produced by mating between relatives, with consequences for population dynamics and sexual-system evolution. In flowering plants, inbreeding depression commonly acts most intensely during seed development. This predispersal component is typically estimated by comparing seed production following exclusive self- and cross-pollination, but such estimates are unbiased only if seed production is limited by ovule availability, rather than by pollen receipt or seed-development resources. To overcome this problem, we...
Data from: The evolution of males: support for predictions from sex allocation theory using mating arrays of Sagittaria latifolia (Alismataceae)Laura E. Perry & Marcel E. Dorken
Investment in male function should often yield diminishing fitness returns, subjecting the evolution of male phenotypes to substantial constraints. In plants, the subdivision of male function via the gradual presentation of pollen might minimize these constraints by preventing the saturation of receptive stigmas. Here we report on an investigation of (a) patterns of investment in male function by plants in hermaphroditic (monoecious) and dioecious populations of Sagittaria latifolia, and (b) patterns of siring success by...
Data from: Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus)Clare D. Marsden, Rosie Woodroffe, Michael G. L. Mills, J. Weldon McNutt, Scott Creel, Rosemary Groom, Masenga Emmanuel, Sarah Cleaveland, Pieter Kat, Gregory S. A. Rasmussen, Joshua Ginsberg, Robin Lines, Jean-Marc André, Colleen Begg, Robert K. Wayne & Barbara K. Mable
Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the Major Histocompatibility Complex (MHC), are increasingly being incorporated...
Data from: Rapid light-induced shifts in opsin expression: finding new opsins, discerning mechanisms of change, and implications for visual sensitivityRebecca C Fuller & Kristin M Claricoates
Light induced shifts in cone frequency and opsin expression occur in many aquatic species. Yet little is known about how quickly animals can alter opsin expression and, thereby, track their visual environments. Similarly, little is known about whether adult animals can alter opsin expression or whether shifts in opsin expression are limited to critical developmental windows. We took adult wild caught bluefin killifish (Lucania goodei) from three different lighting environments (spring, swamp, variable), placed them...
Data from: Persistence in peripheral refugia promotes phenotypic divergence and speciation in a rainforest frogConrad J. Hoskin, Maria Tonione, Megan Higgie, Jason B MacKenzie, Stephen E Williams, Jeremy VanDerWal & Craig Moritz
It is well established from the fossil record and phylogeographic analyses that late Quaternary climate fluctuations led to substantial changes in species' distribution, but whether and how these fluctuations resulted in phenotypic divergence and speciation is less clear. This question can be addressed through detailed analysis of traits relevant to ecology and mating within and among intraspecific lineages that persisted in separate refugia. In a biogeographic system (the Australian Wet Tropics, AWT) with a well-established...
Data from: Integration of molecular, ecological, morphological and endosymbiont data for species delimitation within the Pnigalio soemius complex (Hymenoptera: Eulophidae)Marco Gebiola, Jesús Gómez-Zurita, Maurilia M. Monti, Paolo Navone & Umberto Bernardo
Integrative taxonomy is a recently developed approach that uses multiple lines of evidence such as molecular, morphological, ecological and geographical data to test species limits, and it stands as one of the most promising approaches to species delimitation in taxonomically difficult groups. The Pnigalio soemius complex (Hymenoptera: Eulophidae) represents an interesting taxonomical and ecological study case, as it is characterized by a lack of informative morphological characters, deep mitochondrial divergence, and is susceptible to infection...
Data from: A genetic discontinuity in root-nodulating bacteria of cultivated pea in the Indian trans-HimalayasPraveen Rahi, Riti Kapoor, J. Peter W. Young & Arvind Gulati
Evolutionary relationships of 120 root-nodulating bacteria isolated from the nodules of Pisum sativum cultivated at 22 different locations of the trans-Himalayan valleys of Lahaul and Spiti in the state of Himachal Pradesh of India were studied using 16S rRNA gene PCR-RFLP, ERIC-PCR, sequencing of 16S rRNA, atpD, recA, nodC and nifH genes, carbon-source utilization pattern (BIOLOG™), and whole-cell fatty acid profiling. The results demonstrated that all isolates belonged to Rhizobium leguminosarum symbiovar viciae (Rlv). Isolates...
Data from: The role of physical barriers in the location of avian suture zones in the Guiana Shield, northern AmazoniaLuciano Nicholas Naka, Catherine L. Bechtoldt, L. Magalli Pinto Henriques, Robb T. Brumfield, Luciano Nicolas Naka & L. Magalli Pinto Henriques
Suture zones represent natural forums to examine the role of geography and ecology in the speciation process. Here, we conduct a comparative analysis designed to investigate the location of avian phylogeographic breaks and contact zones in the Guiana Shield, northern Amazonia. We use distributional and genetic data from 78 pairs of avian taxa to address whether phylogeographic breaks and contact zones are associated with contemporary landscape features. Using spatially explicit statistical models, we found that...
Data from: Jack of all nectars, master of most: DNA methylation and the epigenetic basis of niche width in a flower-living yeastCarlos M. Herrera, María I. Pozo & Pilar Bazaga
In addition to genetic differences between individuals due to nucleotide sequence variation, epigenetic changes experienced by genotypes due to DNA methylation may also contribute to population niche width, an intriguing possibility that remains essentially untested. Using the nectar-living yeast Metschnikowia reukaufii as study subject, we examine the hypothesis that changes in genome-wide DNA methylation patterns underly the ability of this fugitive species to exploit a broad resource range in its heterogeneous patchy environment. Data on...
Data from: Historical introgression and the role of selective vs. neutral processes in structuring nuclear genetic variation (AFLP) in a circumpolar marine fish, the capelin (Mallotus villosus)Gabriel J Colbeck, Julie Turgeon, Pascal Sirois & Julian J Dodson
The capelin (Mallotus villosus) is a widespread marine fish species for which previous work has identified geographically distinct mtDNA clades, the frontiers of which are well within adult and larval dispersal capabilities. Here, we use AFLPs to test for the presence of nuclear gene flow among clades. In addition, we evaluate genetic structuring within one clade, the Northwest Atlantic (NWA). We found that each of the mtDNA clades corresponds with a unique nuclear DNA genetic...
Data from: Genomic signature of natural and anthropogenic stress in wild populations of the waterflea Daphnia magna: validation in space, time and experimental evolutionLuisa Orsini, Katina I. Spanier & Luc De Meester
Natural populations are confronted with multiple selection pressures resulting in a mosaic of environmental stressors at landscape level. Identifying the genetic underpinning of adaptation to these complex selection environments and assigning causes of natural selection within multidimensional selection regimes in the wild is challenging. The water flea Daphnia is a renown ecological model system with its well-documented ecology, the possibility to analyze subfossil dormant egg banks, and the short generation time allowing an experimental evolution...
Data from: Parallel allochronic divergence in a winter moth due to disruption of reproductive period by winter harshnessSatoshi Yamamoto & Teiji Sota
The disruption of reproductive timing by climatic harshness may result in the temporal isolation of conspecific populations and, ultimately, in speciation. However, whether temporal isolation alone can act as the force initiating speciation and how often the same type of climatic disruption results in the divergence of allochronic populations in a lineage is largely unknown. The reproductive period of the winter geometrid moth Inurois punctigera is separated into early and late winter in habitats with...
Data from: Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatomsAndrew J Alverson, Robert K Jansen, Edward C Theriot, Andrew J. Alverson, Robert K. Jansen & Edward C. Theriot
Salinity imposes a significant barrier to he distribution of many organisms, including diatoms. Diatoms are ancestrally marine, and the number of times they have independently colonized fresh waters and the physiological adaptations that facilitated these transitions remain outstanding questions in diatom evolution. The colonization of fresh waters by diatoms has been compared to ‘‘crossing the Rubicon,’’ implying that successful colonization events are rare, irreversible, and lead to substantial species diversification. To test these hypotheses, we...
Data from: New fossil penguins (Aves, Sphenisciformes) from the Oligocene of New Zealand reveal the skeletal plan of stem penguinsDaniel T. Ksepka, R. Ewan Fordyce, Tatsuro Ando & Craig M. Jones
Three skeletons collected from the late Oligocene Kokoamu Greensand of New Zealand are among the most complete Paleogene penguins known. These specimens, described here as Kairuku waitaki gen. et sp. nov. and Kairuku grebneffi sp. nov., reveal for the first time the unique proportions of a giant fossil penguin and the morphology of many key elements of the stem penguin skeleton associated with underwater flight, including the first reasonably complete sternum, one of only two...
Data from: Using striated tooth marks on bone to predict body size in theropod dinosaurs: a model based on feeding observations of Varanus komodoensis, the Komodo monitorDomenic C. D'Amore & Robert J. Blumenschine
Mesozoic tooth marks on bone surfaces directly link consumers to fossil assemblage formation. Striated tooth marks are believed to form by theropod denticle contact, and attempts have been made to identify theropod consumers by comparing these striations with denticle widths of contemporaneous taxa. The purpose of this study is to test whether ziphodont theropod consumer characteristics may be accurately identified from striated tooth marks on fossil surfaces. There are three major objectives; 1) experimentally produce...
Data from: A suite of genetic markers useful in assessing wildcat (Felis silvestris ssp.) - domestic cat (Felis silvestris catus) admixtureCarlos Driscoll, Nobuyuki Yamaguchi, Stephen J O’Brien & David W Macdonald
The wildcat (Felis silvestris ssp.) is a conservation concern largely due to introgressive hybridization with its congener F. s. catus, the common domestic cat. Because of a recent divergence and entirely overlapping ranges, hybridization is common and pervasive between these taxa threatening the genetic integrity of remaining wildcat populations. Identifying pure wildcats for inclusion in conservation programs using current morphological discriminants is difficult because of gross similarity between them and the domestic, critically hampering conservation...
Data from: Identifying insecticide resistance genes in mosquito by combining AFLP genome scan and 454 pyrosequencingMargot Paris & Laurence Despres
AFLP-based genome scans are widely used to study the genetics of adaptation and to identify genomic regions potentially under selection. However, this approach usually fails to detect the actual genes or mutations targeted by selection due to the difficulty to obtain the sequences from AFLP fragments. Here we combine classical AFLP outlier detection to 454 sequencing of AFLP fragments obtained from chosen individuals to obtain the sequence of outliers. We applied this approach to the...
Imprinting describes the differential expression of alleles based upon their parent of origin. Deep sequencing of RNAs from maize endosperm and embryo tissue 14 days after pollination was used to identify imprinted genes among a set of ~12,000 genes that were expressed and contained sequence polymorphisms between the B73 and Mo17 genotypes. The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm including 54 maternally expressed...
The University of Texas at Austin9
University of Georgia7
University of Cambridge5
University of Montpellier5
University of Alberta4
Australian National University4
University of Otago4
University of Edinburgh4
University of Chicago4
North Carolina State University4
University of California, Davis4
University of Crete3
University of California System3