24 Works

Data from: A genomic approach for distinguishing between recent and ancient admixture as applied to cattle

Emily Jane McTavish & David M. Hillis
Genomic data facilitate opportunities to track complex population histories of divergence and gene flow. We developed a metric, scaled block size (SBS), that uses the unrecombined block size of introgressed regions of chromosomes to differentiate between recent and ancient admixture, and applied it to reconstructing admixture in cattle. Cattle are descendants of two independently domesticated lineages, taurine and indicine, that diverged 200,000 or more years ago. Several breeds have hybrid ancestry between these divergent lineages....

Data from: Long-branch attraction and the phylogeny of true water bugs (Hemiptera: Nepomorpha) as estimated from mitochondrial genomes

Teng Li, Jimeng Hua, April M. Wright, Ying Cui, Qiang Xie, Wenjun Bu & David M. Hillis
Background: Most previous studies of morphological and molecular data have consistently supported the monophyly of the true water bugs (Hemiptera: Nepomorpha). An exception is a recent study by Hua et al. (2009; BMC Evol Biol 9: 134) based on nine nepomorphan mitochondrial genomes. In the analysis of Hua et al. (2009), the water bugs in the group Pleoidea formed the sister group to a clade that consisted of Nepomorpha (the remaining true water bugs) +...

Data from: Metatranscriptomics of the human oral microbiome during health and disease

Peter Jorth, Keith H. Turner, Pinar Gumus, Nejat Nizam, Nurcan Buduneli & Marvin Whiteley
The human microbiome plays important roles in health, but when disrupted these same indigenous microbes can cause disease. The composition of the microbiome changes during the transition from health to disease; however, these changes are often not conserved among patients. Since microbiome-associated diseases like periodontitis cause similar patient symptoms despite inter-patient variability in microbial community composition, we hypothesized that human-associated microbial communities undergo conserved changes in metabolism during disease. Here we used patient-matched healthy and...

Data from: Ontogenetic stage-specific quantitative trait loci contribute to divergence in developmental trajectories of sexually dimorphic fins between medaka populations

Maiko Kawajiri, Kohta Yoshida, Shingo Fujimoto, Daniel Frikli Mokodongan, Mark Ravinet, Mark Kirkpatrick, Kazunori Yamahira & Jun Kitano
Sexual dimorphism can evolve when males and females differ in phenotypic optima. Genetic constraints can, however, limit the evolution of sexual dimorphism. One possible constraint is derived from alleles expressed in both sexes. Because males and females share most of their genome, shared alleles with different fitness effects between sexes are faced with intralocus sexual conflict. Another potential constraint is derived from genetic correlations between developmental stages. Sexually dimorphic traits are often favoured at adult...

Data from: Frequent and seasonally variable sublethal anthrax infections are accompanied by short-lived immunity in an endemic system

Carrie A. Cizauskas, Steven E. Bellan, Wendy C. Turner, Russell E. Vance & Wayne M. Getz
1. Few studies have examined host-pathogen interactions in wildlife from an immunological perspective, particularly in the context of seasonal and longitudinal dynamics. In addition, though most ecological immunology studies employ serological antibody assays, endpoint titer determination is usually based on subjective criteria and needs to be made more objective. 2. Despite the fact that anthrax is an ancient and emerging zoonotic infectious disease found worldwide, its natural ecology is not well understood. In particular, little...

Data from: Evolutionary renovation of L/M opsin polymorphism confers a fruit discrimination advantage to ateline New World monkeys

Yoshifumi Matsumoto, Chihiro Hiramatsu, Yuka Matsushita, Norihiro Ozawa, Ryuichi Ashino, Makiko Nakata, Satoshi Kasagi, Anthony Di Fiore, Colleen Schaffner, Filippo Aureli, Amanda D. Melin, Shoji Kawamura & Colleen M. Schaffner
New World monkeys exhibit prominent color vision variation due to allelic polymorphism of the long-to-middle wavelength (L/M) opsin gene. The known spectral variation of L/M opsins in primates is broadly determined by amino acid composition at three sites: 180, 277 and 285 (the “three-sites” rule). However, two L/M opsin alleles found in the black-handed spider monkeys (Ateles geoffroyi) are known exceptions, presumably due to novel mutations. The spectral separation of the two L/M photopigments is...

Data from: The genetic architecture of constitutive and induced trichome density in two new RIL populations of Arabidopsis thaliana: phenotypic plasticity, epistasis, and bidirectional leaf damage response

Rebecca H. Bloomer, Alan M. Lloyd & V. Vaughan Symonds
Background: Herbivory imposes an important selective pressure on plants. In Arabidopsis thaliana leaf trichomes provide a key defense against insect herbivory; however, trichome production incurs a fitness cost in the absence of herbivory. Previous work on A. thaliana has shown an increase in trichome density in response to leaf damage, suggesting a mechanism by which the cost associated with constitutively high trichome density might be mitigated; however, the genetic basis of trichome density induction has...

Data from: Emergence timing and fitness consequences of variation in seed oil composition in Arabidopsis thaliana

Sandra E. Pelc & C. Randal Linder
Early seedling emergence can increase plant fitness under competition. Seed oil composition (the types and relative amounts of fatty acids in the oils) may play an important role in determining emergence timing and early growth rate in oilseeds. Saturated fatty acids provide more energy per carbon atom than unsaturated fatty acids but have substantially higher melting points (when chain length is held constant). This characteristic forms the basis of an adaptive hypothesis that lower melting...

Data from: Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity

Daniel Bolnick, Lisa Snowberg, William Stutz, Greg Caporaso, Christian Lauber, Rob Knight, Daniel I. Bolnick, Chris Lauber, J. Gregory Caporaso, William E. Stutz & Lisa K. Snowberg
Individuals harbor diverse communities of symbiotic bacteria, which differ dramatically among host individuals. This heterogeneity poses an immunological challenge of distinguishing between mutualistic and pathogenic members of diverse and host-specific microbial communities. We propose that Major Histocompatibility class II (MHC) genotypes contribute to recognition and regulation of gut microbes, and thus MHC polymorphism contributes to microbial variation among hosts. Here, we confirm that, within a single wild vertebrate population of threespine stickleback, different MHC II...

Data from: Multilocus phylogeny and a new classification for Southeast Asian and Melanesian forest frogs (family Ceratobatrachidae)

Rafe M. Brown, Cameron D. Siler, Stephen J. Richards, Arvin C. Diesmos & David C. Cannatella
We present a near comprehensive, densely sampled, multilocus phylogenetic estimate of species relationships within the anuran family Ceratobatrachidae, a morphologically and ecologically diverse group of frogs from the island archipelagos of Southeast Asia and the South-West Pacific. Ceratobatrachid frogs consist of three clades: a small clade of enigmatic, primarily high-elevation, semi-aquatic Sundaland species currently assigned to Ingerana (for which we erect a new genus), which is the sister taxon of two large, monophyletic radiations, each...

Data from: Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.)

Eli Meyer, Michael J. Aspinwall, David B. Lowry, Juan Diego Palacio-Mejía, Tierney L. Logan, Philip A. Fay & Thomas E. Juenger
Background: In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel...

Data from: Endocranial anatomy of a new fossil porpoise (Odontoceti: Phocoenidae) from the Pliocene San Diego Formation of California

Rachel A. Racicot & Timothy Rowe
The Pliocene fossil porpoise SDSNH 65276 has extremely elongate mandibular morphology, unlike that of any marine amniote, and is superficially most similar to the living bird species known as skimmers (Rynchops sp.). Endocasts of the pterygoid sinuses and endocranial cavity were digitally segmented from high-resolution X-ray CT scans of the specimen to explore internal anatomy of functionally and phylogenetically important anatomical features of this specimen and odontocetes in general. The sinuses are similar in volume...

Data from: Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs

Jeffrey W. Streicher, Thomas J. Devitt, Caren S. Goldberg, John H. Malone, Heath Blackmon & Matthew K. Fujita
Young species complexes that are widespread across ecologically disparate regions offer important insights into the process of speciation because of their relevance to how local adaptation and gene flow influence diversification. We used mitochondrial DNA and up to 28,152 genome-wide SNPs from polytypic barking frogs (Craugastor augusti complex) to infer phylogenetic relationships and test for the signature of introgressive hybridization among diverging lineages. Our phylogenetic reconstructions suggest (1) a rapid Pliocene-Pleistocene radiation that produced at...

Data from: Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli

Colin Raeside, Joël Gaffé, Daniel E. Deatherage, Olivier Tenaillon, Adam M. Briska, Ryan N. Ptashkin, Stéphane Cruveiller, Claudine Médigue, Richard E. Lenski, Jeffrey E. Barrick & Dominique Schneider
Large-scale rearrangements may be important in evolution because they can alter chromosome organization and gene expression in ways not possible through point mutations. In a long-term evolution experiment, twelve Escherichia coli populations have been propagated in a glucose-limited environment for over 25 years. We used whole-genome mapping (optical mapping) combined with genome sequencing and PCR analysis to identify the large-scale chromosomal rearrangements in clones from each population after 40,000 generations. A total of 110 rearrangement...

Data from: Stepwise Threshold Clustering: a new method for genotyping MHC loci using next-generation sequencing technology

William E. Stutz & Daniel I. Bolnick
Genes of the vertebrate major histocompatibility complex (MHC) are of great interest to biologists because of their important role in immunity and disease, and their extremely high levels of genetic diversity. Next generation sequencing (NGS) technologies are quickly becoming the method of choice for high-throughput genotyping of multi-locus templates like MHC in non-model organisms. Previous approaches to genotyping MHC genes using NGS technologies suffer from two problems: 1) a “gray zone” where low frequency alleles...

Data from: Exploring the role of Micronesian islands in the maintenance of coral genetic diversity in the Pacific Ocean

Sarah W. Davies, Eric A. Treml, Carly D. Kenkel & Mikhail V. Matz
Understanding how genetic diversity is maintained across patchy marine environments remains a fundamental problem in marine biology. The Coral Triangle, located in the Indo-West Pacific, is the center of marine biodiversity and has been proposed as an important source of genetic diversity for remote Pacific reefs. Several studies highlight Micronesia, a scattering of hundreds of small islands situated within the North Equatorial Counter Current, as a potentially important migration corridor. To test this hypothesis, we...

Data from: Chemical warfare among invaders: a detoxification interaction facilitates an ant invasion

Edward G. LeBrun, Nathan T. Jones & Lawrence E. Gilbert
As tawny crazy ants (Nylanderia fulva) invade the southern USA, they often displace imported fire ants (Solenopsis invicta). Following exposure to S. invicta venom, N. fulva applies abdominal exocrine gland secretions to its cuticle. Bioassays reveal that these secretions detoxify S. invicta venom. Further, formic acid, from N. fulva venom, is the detoxifying agent. N. fulva exhibits this detoxification behavior after conflict with a variety of ant species; however, it expresses it most intensely after...

Data from: Prevalence and beta diversity in avian malaria communities: host species is a better predictor than geography

Elizabeth S. C. Scordato & Melissa R. Kardish
1. Patterns of diversity and turnover in macroorganism communities can often be predicted from differences in habitat, phylogenetic relationships among species, and the geographic scale of comparisons. In this study, we asked if these factors also predict diversity and turnover in parasite communities. 2. We studied communities of avian malaria in two sympatric, ecologically similar, congeneric host species at three different sites. We asked if parasite prevalence and community structure varied with host population, host...

Data from: Evolutionary origins of a bioactive peptide buried within preproalbumin

Alysha G. Elliott, Christina Delay, Huanle Liu, Zaiyang Phua, K. Johan Rosengren, Aurélie H. Benfield, Jose L. Panero, Michelle L. Colgrave, Achala S. Jayasena, Kerry M. Dunse, Marilyn A. Anderson, Edward E. Schilling, Daniel Ortiz-Barrientos, David J. Craik & Joshua S. Mylne
The de novo evolution of proteins is now considered a frequented route for biological innovation, but the genetic and biochemical processes that lead to each newly created protein are often poorly documented. The common sunflower (Helianthus annuus) contains the unusual gene PawS1 (Preproalbumin with SFTI-1) that encodes a precursor for seed storage albumin; however, in a region usually discarded during albumin maturation, its sequence is matured into SFTI-1, a protease-inhibiting cyclic peptide with a motif...

Data from: Methods for the quantitative comparison of molecular estimates of clade age and the fossil record

Julia A. Clarke & Clint A. Boyd
Approaches quantifying relative congruence, or incongruence, of molecular divergence estimates and the fossil record have been limited. Previously proposed methods are largely node specific, assessing incongruence at particular nodes for which both fossil data and molecular divergence estimates are available. These existing metrics, and other methods that quantify incongruence across topologies including entirely extinct clades, have so far not taken into account uncertainty surrounding both the divergence estimates and the ages of fossils. They have...

Data from: Modular color evolution facilitated by a complex nanostructure in birds

Chad M. Eliason, Rafael Maia & Matthew D. Shawkey
The way in which a complex trait varies, and thus evolves, is critically affected by the independence, or modularity, of its subunits. How modular designs facilitate phenotypic diversification is well studied in non-ornamental (e.g., cichlid jaws), but not ornamental traits. Diverse feather colors in birds are produced by light absorption by pigments and/or light scattering by nanostructures. Such structural colors are deterministically related to the nanostructures that produce them and are therefore excellent systems to...

Data from: Stability of the gorilla microbiome despite simian immunodeficiency virus infection

Andrew H. Moeller, Martine Peeters, Ahidjo Ayouba, Eitel Mpoudi Ngole, Amadine Esteban, Beatrice H. Hahn & Howard Ochman
Simian immunodeficiency viruses (SIVs) have been discovered in over 45 primate species; however, the pathogenic potential of most SIV strains remains unknown due to difficulties inherent in observing wild populations. Because those SIV infections that are pathogenic have been shown to induce changes in the host's gut microbiome, monitoring the microbiota present in faecal samples can provide a noninvasive means for studying the effects of SIV infection on the health of wild-living primates. Here, we...

Data from: Estimating tempo and mode of Y chromosome turnover: explaining Y chromosome loss with the fragile Y hypothesis

Heath Blackmon & Jeffery P. Demuth
Chromosomal sex determination is phylogenetically widespread, having arisen independently in many lineages. Decades of theoretical work provide predictions about sex chromosome differentiation that are well supported by observations in both XY and ZW systems. However, the phylogenetic scope of previous work gives us a limited understanding of the pace of sex chromosome gain and loss and why Y or W chromosomes are more often lost in some lineages than others, creating XO or ZO systems....

Data from: Ecological fidelity of functional traits based on species presence-absence in a modern mammalian bone assemblage (Amboseli, Kenya)

Joshua H. Miller, Anna Kay Behrensmeyer, Andrew Du, S. Kathleen Lyons, David Patterson, Anikó Tóth, Amelia Villaseñor, Erustus Kanga & Denné Reed
Comparisons between modern death assemblages and their source communities have demonstrated fidelity to species diversity across a variety of environments and taxonomic groups. However, differential species preservation and collection (including body-size bias) in both modern and fossil death assemblages may still skew the representation of other important ecological characteristics. Here, we move beyond live-dead taxonomic fidelity and focus on the recovery of functional ecology (how species interact with their ecosystem) at the community level for...

Registration Year

  • 2014

Resource Types

  • Dataset


  • The University of Texas at Austin
  • University of Colorado Boulder
  • University of Kansas
  • United States Department of Agriculture
  • Yale University
  • National Museum
  • University of Pennsylvania
  • Cooperative Institute for Research in Environmental Sciences
  • Princeton University
  • Kyushu University