21 Works

Data from: The sampling and estimation of marine paleodiversity patterns: implications of a Pliocene model

James W. Valentine, David Jablonski, Andrew Z. Krug & Sarah K. Berke
Data that accurately capture the spatial structure of biodiversity are required for many paleobiological questions, from assessments of changing provinciality and the role of geographic ranges in extinction and originations, to estimates of global taxonomic or morphological diversity through time. Studies of temporal changes in diversity and global biogeographic patterns have attempted to overcome fossil sampling biases through sampling standardization protocols, but such approaches must ultimately be limited by available literature and museum collections. One...

Data from: Measuring ectomycorrhizal fungal dispersal: macroecological patterns driven by microscopic propagules

Kabir G. Peay, Max G. Schubert, Nhu H. Nguyen & Thomas D. Bruns
Dispersal plays a prominent role in most conceptual models of community assembly. However, direct measurement of dispersal across a whole community is difficult at ecologically relevant spatial scales. For cryptic organisms, such as fungi and bacteria, the scale and importance of dispersal limitation has become a major point of debate. We use an experimental island biogeographic approach to measure the effects of dispersal limitation on the ecological dynamics of an important group of plant symbionts,...

Data from: Diversification and phylogeographic structure in widespread Azteca plant-ants from the northern Neotropics

Elizabeth G. Pringle, Timothy C. Bonebrake, Santiago R. Ramírez, Deborah M. Gordon & Rodolfo Dirzo
The Neotropical myrmecophytic tree Cordia alliodora hosts symbiotic Azteca ants in most of its widespread range. The taxonomy of the genus Azteca is notoriously difficult, which has frequently obscured species identity in ecological studies. We used sequence data from one mitochondrial and four nuclear loci to infer phylogenetic relationships, patterns of geographic distribution, and timing of diversification for 181 colonies of Azteca from Mexico to Colombia. We identified at least eight lineages of C. alliodora-dwelling...

Data from: Montane refugia predict population genetic structure in the Large-blotched Ensatina salamander

Thomas J. Devitt, Susan E. Cameron Devitt, Bradford D. Hollingsworth, Jimmy A. McGuire & Craig Moritz
Understanding the biotic consequences of Pleistocene range shifts and fragmentation remains a fundamental goal in historical biogeography and evolutionary biology. Here, we combine species distribution models (SDM) from the present and two late Quaternary time periods with multilocus genetic data (mitochondrial DNA and microsatellites) to evaluate the effect of climate-induced habitat shifts on population genetic structure in the Large-blotched Ensatina (Ensatina eschscholtzii klauberi), a plethodontid salamander endemic to middle and high-elevation conifer forest in the...

Data from: A modular framework characterizes micro- and macroevolution of Old World monkey dentitions

Theresa M. Grieco, Oliver T. Rizk & Leslea J. Hlusko
The study of modularity can provide a foundation for integrating development into studies of phenotypic evolution. The dentition is an ideal phenotype for this as it is developmentally relatively simple, adaptively highly significant, and evolutionarily tractable through the fossil record. Here, we use phenotypic variation in the dentition to test a hypothesis about genetic modularity. Quantitative genetic analysis of size variation in the baboon dentition indicates a genetic modular framework corresponding to tooth type categories....

Data from: Polyploidy and microsatellite variation in the relict tree Prunus lusitanica L.: how effective are refugia in preserving genotypic diversity of clonal taxa?

Carlos García-Verdugo, Juan Antonio Calleja, Pablo Vargas, Luis Silva, Orlanda Moreira & Fernando Pulido
Refugia are expected to preserve genetic variation of relict taxa, especially in polyploids, because high gene dosages could prevent genetic erosion in small isolated populations. However, other attributes linked to polyploidy, such as asexual reproduction, may strongly limit the levels of genetic variability in relict populations. Here, ploidy levels and patterns of genetic variation at nuclear microsatellite loci were analysed in Prunus lusitanica, a polyploid species with clonal reproduction that is considered a paradigmatic example...

Data from: Genetic divergence is decoupled from ecological diversification in the Hawaiian Nesosydne planthoppers

Kari Roesch Goodman, Stephen C. Welter & George K. Roderick
Adaptive radiation involves ecological shifts coupled with isolation of gene pools. However, we know little about what drives the initial stages of divergence. We study a system in which ecological diversification is found within a chronologically well-defined geological matrix to provide insight into this enigmatic phase of radiation. We tested the hypothesis that a period of geographic isolation precedes ecological specialization in an adaptive radiation of host-specialized Hawaiian planthoppers. We examined population structure and history...

Data from: Invasion facilitates hybridization with introgression in the Rattus rattus species complex

Justin B. Lack, Daniel U. Greene, Chris John Conroy, Meredith J. Hamilton, Janet K. Braun, Michael A. Mares & Ronald A. Van Den Bussche
Biological invasions result in novel species interactions, which can have significant evolutionary impacts on both native and invading taxa. One evolutionary concern with invasions is hybridization among lineages that were previously isolated, but make secondary contact in their invaded range(s). Black rats, consisting of several morphologically very similar but genetically distinct taxa that collectively have invaded six continents, are arguably the most successful mammalian invaders on the planet. We used mitochondrial cytochrome b sequences, two...

Data from: Colonization history and population genetics of the color-polymorphic Hawaiian happy-face spider Theridion grallator (Araneae, Theridiidae)

Peter J. P. Croucher, Geoffrey Stuart Oxford, Athena Lam, Neesha Mody & Rosemary G. Gillespie
Past geological and climatological processes shape extant biodiversity. In the Hawaiian Islands these processes have provided the physical environment for a number of extensive adaptive radiations. Yet single species that occur throughout the islands provide some of the best cases for understanding how species respond to the shifting dynamics of the islands in the context of colonization history and associated demographic and adaptive shifts. Here we focus on the Hawaiian happy-face spider, a single color-polymorphic...

Data from: Natural selection in utero induced by mass layoffs: the hCG evidence

Ralph Catalano, Claire Margerison-Zilko, Sidra Goldman-Mellor, Michelle Pearl, Elizabeth Anderson, Katherine Saxton, Tim Bruckner, Meenakshi Subbaraman, Julia Goodman, Mollie Epstein, Robert Currier & Martin Kharrazi
Evolutionary theory, when coupled with research from epidemiology, demography, and population endocrinology, suggests that contracting economies affect the fitness and health of human populations via natural selection in utero. We know, for example, that fetal death increases more among males than females when the economy unexpectedly contracts; that unexpected economic contraction predicts low secondary sex ratios; and that males from low sex ratio birth cohorts live, on average, longer than those from high sex ratio...

Data from: A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia

Jonathan J. Fong, Jeremy M. Brown, Matthew K. Fujita & Bastien Boussau
In resolving the vertebrate tree of life, two fundamental questions remain: 1) what is the phylogenetic position of turtles within amniotes, and 2) what are the relationships between the three major lissamphibian (extant amphibian) groups? These relationships have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, and four proposed branching patterns within Lissamphibia. We compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa) to address these outstanding...

Data from: Quantifying past and present connectivity illuminates a rapidly changing landscape for the African elephant

Clinton W. Epps, Samuel K. Wasser, Jonah L. Keim, Benezeth M. Mutayoba & Justin S. Brashares
There is widespread concern about impacts of land-use change on connectivity among animal and plant populations, but those impacts are difficult to quantify. Moreover, lack of knowledge regarding ecosystems before fragmentation may obscure appropriate conservation targets. We use occurrence and population genetic data to contrast connectivity for a long-lived mega-herbivore over historical and contemporary time frames. We test whether (i) historical gene flow is predicted by persistent landscape features rather than human settlement, (ii) contemporary...

Data from: The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Angelique D'Hont, France Denoeud, Jean-Marc Aury, Franc-Christophe Baurens, Françoise Carreel, Olivier Garsmeur, Benjamin Noel, Stéphanie Bocs, Gaëtan Droc, Mathieu Rouard, Corinne Da Silva, Jabbari Kamel, Céline Cardi, Julie Poulain, Marlène Souquet, Karine Labadie, Cyril Jourda, Juliette Lengellé, Marguerite Rodier-Goud, Adriana Alberti, Maria Bernard, Margot Correa, Saravanaraj Ayyampalayam, Michael R. McKain, Jim Leebens-Mack … & Patrick Wincker
Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries1. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations2, and selection of diploid...

Data from: Forward chemical genetic screens in Arabidopsis identify genes that influence sensitivity to the phytotoxic compound sulfamethoxazole

Darrell Desveaux, Karl J. Schreiber, Ryan S. Austin, Yunchen Gong, Jianfeng Zhang, Pauline Fung, Pauline W. Wang & David S. Guttman
BACKGROUND: The sulfanilamide family comprises a clinically important group of antimicrobial compounds which also display bioactivity in plants. While there is evidence that sulfanilamides inhibit folate biosynthesis in both bacteria and plants, the complete network of plant responses to these compounds remains to be characterized. As such, we initiated two forward genetic screens in Arabidopsis in order to identify mutants that exhibit altered sensitivity to sulfanilamide compounds. These screens were based on the growth phenotype...

Data from: An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences

Molly Schumer, Rongfeng Cui, Bastien Boussau, Ronald Brice Walter, Gil G. Rosenthal & Peter Andolfatto
Once thought rare in animal taxa, hybridization has been increasingly recognized as an important and common force in animal evolution. In the past decade, a number of studies have suggested that hybridization has driven speciation in some animal groups. We investigate the signature of hybridization in the genome of a putative hybrid species, Xiphophorus clemenciae, through whole genome sequencing of this species and its hypothesized progenitors. Based on analysis of this data, we find that...

Data from: Forecasting changes in population genetic structure of alpine plants in response to global warming

Flora Jay, Stéphanie Manel, Nadir Alvarez, Eric Y. Durand, Wilfried Thuiller, Rolf Holderegger, Pierre Taberlet & Olivier François
Species range shifts in response to climate and land use change are commonly forecasted with species distribution models based on species occurrence or abundance data. Although appealing, these models ignore the genetic structure of species, and the fact that different populations might respond in different ways due to adaptation to their environment. Here, we introduced ancestry distribution models, i.e., statistical models of the spatial distribution of ancestry proportions, for forecasting intra-specific changes based on genetic...

Data from: Global gradients in vertebrate diversity predicted by historical area-productivity dynamics and contemporary environment

Walter Jetz & Paul V. A. Fine
Broad-scale geographic gradients in species richness have now been extensively documented, but their historical underpinning is still not well understood. While the importance of productivity, temperature, and a scale-dependence of the determinants of diversity is broadly acknowledged, we here argue that limitation to a single analysis scale and data pseudoreplication have impeded an integrated evolutionary and ecological understanding of diversity gradients. We develop and apply a hierarchical analysis framework for global diversity gradients that incorporates...

Data from: Modelling dynamics in protein crystal structures by ensemble refinement

B. Tom Burnley, Pavel V. Afonine, Paul D. Adams & Piet Gros
Single-structure models derived from X-ray data do not adequately account for the inherent, functionally important dynamics of protein molecules. We generated ensembles of structures by time-averaged refinement, where local molecular vibrations were sampled by molecular-dynamics (MD) simulation whilst global disorder was partitioned into an underlying overall translation–libration–screw (TLS) model. Modeling of 20 protein datasets at 1.1–3.1 Å resolution reduced cross-validated R_free values by 0.3–4.9%, indicating that ensemble models fit the X-ray data better than single...

Data from: Floral paedomorphy leads to secondary specialization in pollination of Malagasy Dalechampia (Euphorbiaceae)

W. Scott Armbruster, Joongku Lee, Mary E. Edwards & Bruce G. Baldwin
The traditional evolutionary interpretation of Von Baer’s “laws” of embryology is that retention of early developmental forms into adulthood (paedomorphosis) leads to the evolution of simpler or more generalized morphology and ecology. Here we show that paedomorphosis can also be involved in an increase in ecological specialization, in this case of plant-pollinator relationships. A paedomorphic transition from generalized pollination (by several functional types of pollinators) to specialized pollination (by one or a few species in...

Data from: Dynamic antagonism between phytochromes and PIF-family bHLHs induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis

Pablo Leivar, James M. Tepperman, Megan M. Cohn, Elena Monte, Bassem Al-Sady, Erika Erickson & Peter H. Quail
Plants respond to shade-modulated light-signals, via the phytochrome (phy) system, by adaptive changes, collectively termed the shade avoidance syndrome (SAS). To examine the roles of the Phy-Interacting bHLH Factors, PIF1, 3, 4 and 5, in relaying this information to the transcriptional network, we compared the genome-wide expression profiles of wild-type and quadruple pif (pifq) mutants in response to shade. The data identify a subset of genes, enriched in transcription-factor-encoding loci, that respond rapidly (within 1...

Data from: Phylogenetic analysis using Lévy processes: finding jumps in the evolution of continuous traits

Michael J. Landis, Joshua G. Schraiber & Mason Liang
Gaussian processes, a class of stochastic processes including Brownian motion and the Ornstein–Uhlenbeck process, are widely used to model continuous trait evolution in statistical phylogenetics. Under such processes, observations at the tips of a phylogenetic tree have a multivariate Gaussian distribution, which may lead to suboptimal model specification under certain evolutionary conditions, as supposed in models of punctuated equilibrium or adaptive radiation. To consider non-normally distributed continuous trait evolution, we introduce a method to compute...

Registration Year

  • 2012
    21

Resource Types

  • Dataset
    21

Affiliations

  • University of California, Berkeley
    21
  • French National Centre for Scientific Research
    2
  • University of Washington
    1
  • University of Évry Val d'Essonne
    1
  • Stanford University
    1
  • Princeton University
    1
  • Sokoine University of Agriculture
    1
  • University of Georgia
    1
  • Oregon State University
    1
  • California Department of Public Health
    1