The colossal size and body plan of sauropod dinosaurs are unparalleled in terrestrial vertebrates. However, to date, there have been only limited attempts to examine temporal and phylogenetic patterns in the sauropod bauplan. Here, we combine three-dimensional computational models with phylogenetic reconstructions to quantify the evolution of whole-body shape and body segment properties across the sauropod radiation. Limitations associated with the absence of soft tissue preservation in fossils result in large error bars about mean...
Data from: Population genomics of divergence within an obligate pollination mutualism: selection maintains differences between Joshua tree speciesAnne M. Royer, Matthew A. Streisfeld & Christopher Irwin Smith
PREMISE OF THE STUDY: Speciation is a complex process that can be shaped by many factors, from geographic isolation to interspecific interactions. In Joshua trees, selection from pollinators on style length has been hypothesized to contribute to the maintenance of differentiation between two hybridizing sister species. We used population genomics approaches to measure the extent of genetic differentiation between these species, test whether selection maintains differences between them, and determine whether genetic variants associated with...
Data from: Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflowerSean Stankowski, James M. Sobel & Matthew A. Streisfeld
A major goal of speciation research is to reveal the genomic signatures that accompany the speciation process. Genome scans are routinely used to explore genome-wide variation and identify highly differentiated loci that may contribute to ecological divergence, but they do not incorporate spatial, phenotypic or environmental data that might enhance outlier detection. Geographic cline analysis provides a potential framework for integrating diverse forms of data in a spatially explicit framework, but has not been used...
Data from: Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus AcroporaNatalie L. Rosser, Luke Thomas, Sean Stankowski, Zoe T. Richards, W. Jason Kennington & Michael S. Johnson
Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly diverged lineages of the phylogenetic marker PaxC. Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it...
Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi...
Data from: Rapid identification of major histocompatibility complex class I haplotypes using deep sequencing in an endangered Old World monkeyNoah D. Simons, Maria Jose Ruiz-Lopez, Colin A. Chapman, Tony L. Goldberg, Julie A. Karl, Roger W. Wiseman, Patrick S. Bohn, David H. O'Connor & Nelson Ting
Immunogenetic data from wild primate populations have been difficult to obtain, due to logistic and methodological constraints. We applied a well-characterized deep sequencing method for MHC I typing, developed for macaques, to a population of wild red colobus to assess the feasibility of identifying MHC I-A/B haplotypes. Ten individuals produced sufficient data from blood and tissue samples to assign haplotypes. Eighty-two sequences were classified as red colobus MHC I alleles distributed across six MHC I...
Data from: Coevolutionary interactions with parasites constrain the spread of self-fertilization into outcrossing host populationsSamuel Preston Slowinski, Levi T. Morran, , Eric R. Cui, Amrita Bhattacharya, Curtis M. Lively, Patrick C. Phillips & Raymond C. Parrish
Given the cost of sex, outcrossing populations should be susceptible to invasion and replacement by self-fertilization or parthenogenesis. However, biparental sex is common in nature, suggesting that cross-fertilization has substantial short-term benefits. The Red Queen hypothesis (RQH) suggests that coevolution with parasites can generate persistent selection favoring both recombination and outcrossing in host populations. We tested the prediction that coevolving parasites can constrain the spread of self-fertilization relative to outcrossing. We introduced wild-type Caenorhabditis elegans...
Data from: Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reactionMatthew J. Shurtleff, Morayma M. Temoche-Diaz, Kate V. Karfilis, Sayaka Ri & Randy Schekman
Exosomes are small vesicles that are secreted from metazoan cells and may convey selected membrane proteins and small RNAs to target cells for the control of cell migration, development and metastasis. To study the mechanisms of RNA packaging into exosomes, we devised a purification scheme based on the membrane marker CD63 to isolate a single exosome species secreted from HEK293T cells. Using immunoisolated CD63-containing exosomes we identified a set of miRNAs that are highly enriched...
Data from: Intrinsic differences between males and females determine sex-specific consequences of inbreedingEmily R. Ebel & Patrick C. Phillips
Background Inbreeding increases homozygosity and exposes deleterious recessive alleles, generally decreasing the fitness of inbred individuals. Interestingly, males and females are usually affected differently by inbreeding, though the more vulnerable sex depends on the species and trait measured. Results We used the soil-dwelling nematode Caenorhabditis remanei to examine sex-specific inbreeding depression across nine lineages, five levels of inbreeding, and hundreds of thousands of progeny. Female nematodes consistently suffered greater fitness losses than their male counterparts,...
Data from: A stochastic neuronal model predicts random search behaviors at multiple spatial scales in C. elegansWilliam M. Roberts, Steven B. Augustine, Kristy J. Lawton, Theodore H. Lindsay, Tod R. Thiele, Eduardo J. Izquierdo, Serge Faumont, Rebecca A. Lindsay, Matthew Cale Britton, Navin Pokala, Cornelia I. Bargmann & Shawn R. Lockery
Random search is a behavioral strategy used by organisms from bacteria to humans to locate food that is randomly distributed and undetectable at a distance. We investigated this behavior in the nematode Caenorhabditis elegans, an organism with a small, well-described nervous system. Here we formulate a mathematical model of random search abstracted from the C. elegans connectome and fit to a large-scale kinematic analysis of C. elegans behavior at submicron resolution. The model predicts behavioral...
Data from: Climate structures genetic variation across a species' elevation range: a test of range limits hypothesesJason P. Sexton, Matthew B. Hufford, Ashley Bateman, David B. Lowry, Harald Meimberg, Sharon Y. Strauss, Kevin J. Rice & Ashley C.Bateman
Gene flow may influence the formation of species range limits, yet little is known about the patterns of gene flow with respect to environmental gradients or proximity to range limits. With rapid environmental change it is especially important to understand patterns of gene flow to inform conservation efforts. Here we investigate the species range of the selfing, annual plant, Mimulus laciniatus, in the California Sierra Nevada. We assessed genetic variation, gene flow, and population abundance...
University of Oregon11
Indiana University Bloomington3
Institute of Vertebrate Paleontology and Paleoanthropology1
University of Kansas1
Michigan Technological University1
King Mongkut's University of Technology Thonburi1
California State University, Northridge1
University of Pennsylvania1