24 Works

Data from: Genetic footprints of Iberian cattle in America 500 years after the arrival of Columbus

Amparo M. Martínez, Luis T. Gama, Javier Cañón, Catarina Ginja, Juan V. Delgado, Susana Dunner, Vincenzo Landi, Inmaculada Martín-Burriel, M. Cecilia T. Penedo, Clementina Rodellar, Jose Luis Vega-Pla, Atzel Acosta, Luz Ángela Álvarez, Esperanza Camacho, Óscar Cortés, José Ribamar Marques, Óscar Roberto Martínez, Rubén Darío Martínez, Lilia Melucci, Guillermo Martínez-Velázquez, Jose Ernesto Muñoz, Alicia Postiglioni, Jorge Quiroz, Philip Sponenberg, Odalys Uffo … & Ruben D. Martínez
BACKGROUND: American Creole cattle presumably descend from animals imported from the Iberian Peninsula during the period of colonization and settlement, through different migration routes, and may have also suffered the influence of cattle directly imported from Africa. The introduction of European cattle, which began in the 18th century, and later of Zebu from India, has threatened the survival of Creole populations, some of which have nearly disappeared or were admixed with exotic breeds. Assessment of...

Data from: Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux

Erin A. Lynch, Morgan G. I. Langille, Aaron Darling, Elizabeth G. Wilbanks, Caitlin Haltiner, Katie S. Y. Shao, Michael O. Starr, Clotilde Teiling, Timothy T. Harkins, Robert A. Edwards, Jonathan A. Eisen & Marc T. Facciotti
We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula. Ease of cultivation and the existence of well-developed genetic and biochemical tools for several diverse haloarchaeal species make haloarchaea a model group for the study of archaeal biology. The unique physiological properties of these organisms also make them good candidates for novel enzyme discovery for biotechnological applications. Seven genomes were sequenced to ~20×coverage and assembled to an average of 50 contigs...

Data from: Spontaneous hybrids between native and exotic Rubus in the Western United States produce offspring both by apomixis and by sexual recombination

Lindsay V. Clark & Marie Jasieniuk
Facultative asexual reproduction is a trait commonly found in invasive species. With a combination of sexual and asexual reproductive modes, such species may adapt to new environments via sexual recombination during range expansion, while at the same time having the benefits of asexuality such as the maintenance of fitness effects that depend upon heterozygosity. In the Western United States, native species of Rubus (Rosaceae) reproduce sexually whereas exotic naturalized Rubus species reproduce by pseudogamous apomixis....

Data from: Table scraps: inter-trophic food provisioning by pumas

L. Mark Elbroch & Heiko U. Wittmer
Large carnivores perform keystone ecological functions through direct predation, or indirectly, through food subsidies to scavengers or trophic cascades driven by their influence on the distributions of their prey. Pumas (Puma concolor) are an elusive, cryptic species difficult to study, and little is known about their inter-trophic level interactions in natural communities. Using new GPS technology, we discovered that pumas in Patagonia provided 232 ± 31 kg of edible meat/month/100 km2 to near-threatened Andean condors...

Data from: Characterizing genomic variation of Arabidopsis thaliana: the roles of geography and climate

Jesse R. Lasky, David L. Des Marais, John K. McKay, James H. Richards, Thomas E. Juenger & Timothy H. Keitt
Arabidopsis thaliana inhabits diverse climates and exhibits varied phenology across its range. Although A. thaliana is an extremely-well studied model species, the relationship between geography, growing season climate and its genetic variation is poorly characterized. We used redundancy analysis (RDA) to quantify the association of genomic variation [214,051 single nucleotide polymorphisms (SNPs)] with geography and climate among 1,003 accessions collected from 447 locations in Eurasia. We identified climate variables most correlated with genomic variation, which...

Data from: Is your phylogeny informative? Measuring the power of comparative methods

Carl Boettiger, Graham Coop & Peter L. Ralph
Phylogenetic comparative methods may fail to produce meaningful results when either the underlying model is inappropriate or the data contain insufficient information to inform the inference. The ability to measure the statistical power of these methods has become crucial to ensure that data quantity keeps pace with growing model complexity. Through simulations, we show that commonly applied model choice methods based on information criteria can have remarkably high error rates; this can be a problem...

Data from: The phylogenetics of Anguillicolidae (Nematoda: Anguillicolidea), swimbladder parasites of eels

Dominik R. Laetsch, Emanuel G. Heitlinger, Horst Taraschewski, Steven A. Nadler & Mark L. Blaxter
BACKGROUND: Anguillicolidae Yamaguti, 1935 is a family of nematode parasites infecting fresh-water eels of the genus Anguilla, with five species in the genera Anguillicola and Anguillicoloides. Anguillicolidae is part of Spirurina, a diverse clade made up of only animal parasites. Anguillicoloides crassus is of particular importance, as it has recently spread from its endemic range in the Eastern Pacific to Europe and North America, where it poses a significant threat to new, naïve hosts such...

Data from: Complex consequences of herbivory and interplant cues in three annual plants

Ian S. Pearse, Lauren M. Porensky, Louie H. Yang, Maureen L. Stanton, Richard Karban, Lisa Bhattacharyya, Rosa Cox, Karin Dove, August Higgins, Corrina Kamoroff, Travis Kirk, Christopher Knight, Rebecca Koch, Corwin Parker, Hilary Rollins & Kelsey Tanner
Information exchange (or signaling) between plants following herbivore damage has recently been shown to affect plant responses to herbivory in relatively simple natural systems. In a large, manipulative field study using three annual plant species (Achyrachaena mollis, Lupinus nanus, and Sinapis arvensis), we tested whether experimental damage to a neighboring conspecific affected a plant's lifetime fitness and interactions with herbivores. By manipulating relatedness between plants, we assessed whether genetic relatedness of neighboring individuals influenced the...

Data from: Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux

Erin A. Lynch, Morgan G. I. Langille, Aaron Darling, Elizabeth G. Wilbanks, Caitlin Haltiner, Katie S. Y. Shao, Michael O. Starr, Clotilde Teiling, Timothy T. Harkins, Robert A. Edwards, Jonathan A. Eisen, Marc T. Facciotti & Lennart Randau
We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula. Ease of cultivation and the existence of well-developed genetic and biochemical tools for several diverse haloarchaeal species make haloarchaea a model group for the study of archaeal biology. The unique physiological properties of these organisms also make them good candidates for novel enzyme discovery for biotechnological applications. Seven genomes were sequenced to ~20×coverage and assembled to an average of 50 contigs...

Data from: A jungle in there: bacteria in belly buttons are highly diverse, but predictable

Jiri Hulcr, Andrew M. Latimer, Jessica B. Henley, Nina R. Rountree, Noah Fierer, Andrea Lucky, Margaret D. Lowman & Robert R. Dunn
The belly button is one of the habitats closest to us, and yet it remains relatively unexplored. We analyzed bacteria and arachaea from the belly buttons of humans from two different populations sampled within a nation-wide citizen science project. We examined bacterial and archaeal phylotypes present and their diversity using multiplex pyrosequencing of 16S rDNA libraries. We then tested the oligarchy hypothesis borrowed from tropical macroecology, namely that the frequency of phylotypes in one sample...

Data from: The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps

Elena Mosca, Andrew J. Eckert, Erica A. Di Pierro, Duccio Rocchini, Nicola La Porta, Piero Belletti & David B. Neale
Climate is one of the most important drivers of local adaptation in forest tree species. Standing levels of genetic diversity and structure within and among natural populations of forest trees are determined by the interplay between climatic heterogeneity and the balance between selection and gene flow. To investigate this interplay single nucleotide polymorphisms (SNPs) were genotyped in 24 to 37 populations from four subalpine conifers, Abies alba Mill., Larix decidua L., Pinus cembra L. and...

Data from: Detailed food web networks of three Greater Antillean coral reef systems: the Cayman Islands, Cuba, and Jamaica

Peter D. Roopnarine & Rachel Hertog
Food webs represent one of the most complex aspects of community biotic interactions. Complex food webs are represented as networks of interspecific interactions, where nodes represent species or groups of species, and links are predator-prey interactions. This paper presents reconstructions of coral reef food webs in three Greater Antillean regions of the Caribbean: the Cayman Islands, Cuba, and Jamaica. Though not taxonomically comprehensive, each food web nevertheless comprises producers and consumers, single-celled and multicellular organisms,...

Data from: The new bioinformatics: integrating ecological data from the gene to the biosphere

Matthew B. Jones, Mark P. Schildahuer, O. J. Reichman, Shawn Bowers, Mark P. Schildhauer & O.J. Reichman
Bioinformatics, the application of computational tools to the management and analysis of biological data, has stimulated rapid research advances in genomics through the development of data archives such as GenBank, and similar progress is just beginning within ecology. One reason for the belated adoption of informatics approaches in ecology is the breadth of ecologically pertinent data (from genes to the biosphere) and its highly heterogeneous nature. The variety of formats, logical structures, and sampling methods...

Data from: Convergent evolution as a generator of phenotypic diversity in threespine stickleback

Matthew David McGee & Peter C. Wainwright
Convergent evolution, in which populations produce similar phenotypes in response to similar selection pressure, is strong evidence for the role of natural selection in shaping biological diversity. In some cases, closely related populations can produce functionally similar but phenotypically divergence forms in response to selection. Functional convergence with morphological divergence has been observed in laboratory selection experiments and computer simulations, but while potentially common, is rarely recognized in nature. Here, we present data from the...

Data from: Migration strategy affects avian influenza dynamics in mallards (Anas platyrhynchos)

Nichola J. Hill, John Y. Takekawa, Joshua T. Ackerman, Keith A. Hobson, Garth Herring, Carol J. Cardona, Jonathan A. Runstadler & Walter M. Boyce
Studies of pathogen transmission typically overlook that wildlife hosts can include both migrant and resident populations when attempting to model circulation. Through the application of stable isotopes in flight feathers, we estimated the migration strategy of mallards (Anas platyrhynchos) - resident, intermediate-distance migrant or long-distance migrant, occurring on California wintering grounds. Our study demonstrates that mallards, a principal host of avian influenza virus (AIV) in nature, contribute differently to virus gene flow depending on migration...

Data from: Evolution of root plasticity responses to variation in soil nutrient distribution and concentration

Judah D. Grossman & Kevin J. Rice
Root plasticity, a trait that can respond to selective pressure, may help plants forage for nutrients in heterogeneous soils. Agricultural breeding programs have artificially selected for increased yield under comparatively homogeneous soil conditions, potentially decreasing the capacity for plasticity in crop plants like barley (Hordeum vulgare). However, the effects of domestication on the evolution of root plasticity are essentially unknown. Using a split container approach, we examined differences in root plasticity among three domestication levels...

Data from: Nonadditive indirect effects of group genetic diversity on larval viability in Drosophila melanogaster imply key role of maternal decision-making

Julia B. Saltz, Evan T. Alicuben, Jessica Grubman, Matthew Harkenrider, Nichelle Megowan & Sergey V. Nuzhdin
Genetic variation can have important consequences for populations: high population genetic diversity is typically associated with ecological success. Some mechanisms that account for these benefits assume that local social groups with high genetic diversity are more successful than low-diversity groups. At the same time, active decision-making by individuals can influence group genetic diversity, a behavioral process not generally incorporated into discussions of population-level diversity effects. Here, we examine how maternal decisions that determine group genetic...

Data from: Elevated rates of morphological and functional diversification in reef-dwelling haemulid fishes.

Samantha Ann Price, Jose J. Tavera, Thomas J. Near & Peter C. Wainwright
The relationship between habitat complexity and species richness is well established but comparatively little is known about the evolution of morphological diversity in complex habitats. Reefs are structurally complex, highly productive shallow-water marine ecosystems found in tropical (coral reefs) and temperate zones (rocky reefs) which harbor exceptional levels of biodiversity. We investigated whether reef habitats promote the evolution of morphological diversity in the feeding and locomotion systems of grunts (Haemulidae), a group of predominantly nocturnal...

Data from: Late Paleozoic fusulinoidean gigantism driven by atmospheric hyperoxia

Jonathan L. Payne, John R. Groves, Adam B. Jost, Thienan Nguyen, Sarah E. Moffitt, Tessa M. Hill & Jan M. Skotheim
Atmospheric hyperoxia, with pO2 in excess of 30%, has long been hypothesized to account for late Paleozoic (360-250 million years ago) gigantism in numerous higher taxa. However, this hypothesis has not been evaluated statistically because comprehensive size data have not been compiled previously at sufficient temporal resolution to permit quantitative analysis. In this study, we test the hyperoxia-gigantism hypothesis by examining the fossil record of fusulinoidean foraminifers, a dramatic example of protistan gigantism with some...

Data from: Disentangling the roles of history and local selection in shaping clinal variation of allele frequencies and gene expression in Norway spruce (Picea abies)

Jun Chen, Thomas Källman, Xiaofei Ma, Niclas Gyllenstrand, Giusi Zaina, Michele Morgante, Jean Bousquet, Andrew Eckert, Jill Wegrzyn, David B. Neale, Ulf Lagercrantz, Martin Lascoux & David Neale
Understanding the genetic basis of local adaptation is challenging due to the subtle balance among conflicting evolutionary forces that are involved in its establishment and maintenance. One system with which to tease apart these difficulties are clines in adaptive characters. Here we analyzed genetic and phenotypic variation in bud set, a highly heritable and adaptive trait, among 18 populations of Norway spruce (Picea abies), arrayed along a latitudinal gradient ranging from 47°N to 68°N. We...

Data from: Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient.

Carl Vangestel, Joachim Mergeay, Deborah A. Dawson, Tom Callens, Viki Vandomme & Luc Lens
House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way...

Data from: Scale-dependent shifts in the species composition of flower visitors with changing floral density

Carla J. Essenberg
Responses of flower-visiting animals to floral density can alter interactions between plants, influencing a variety of biological processes, including plant population dynamics and the evolution of flowering phenology. Many studies have found effects of floral or plant density on pollinator visitation rates at patch scales, but little is known about responses of flower visitors to floral densities at larger scales. Here, I present data from an observational field study in which I measured the effects...

Data from: Love the one you're with: proximity determines paternity success in the barnacle Tetraclita rubescens

Morgan W. Kelly, Richard K. Grosberg & Eric Sanford
A species’ mating system sets limits on the strength of sexual selection. Sexual selection is widespread in dioecious species, but is less well documented in hermaphrodites, and may be less important. We used four highly polymorphic microsatellite markers to assign paternity to broods of the hermaphroditic eastern Pacific volcano barnacle Tetraclita rubescens. These data were used to describe the species’ mating system and to examine factors affecting male reproductive success. Tetraclita can sire broods over...

Data from: Global patterns of leaf defenses in oak species

Ian S. Pearse & Andrew L. Hipp
Plant defensive traits drive patterns of herbivory and herbivore diversity among plant species. Over the past 30 years, several prominent hypotheses have predicted the association of plant defenses with particular abiotic environments or geographic regions. We used a strongly supported phylogeny of oaks to test whether defensive traits of 56 oak species are associated with particular components of their climatic niche. Climate predicted both the chemical leaf defenses and the physical leaf defenses of oaks,...

Registration Year

  • 2012

Resource Types

  • Dataset


  • University of California, Davis
  • Dalhousie University
  • San Diego State University
  • Virginia Commonwealth University
  • Victoria University of Wellington
  • Ghent University
  • Stanford University
  • The University of Texas at Austin
  • Research Institute for Nature and Forest
  • Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias