20 Works

Data from: Early bursts of body size and shape evolution are rare in comparative data

Luke J. Harmon, Jonathan B. Losos, T. Jonathan Davies, Rosemary G. Gillespie, John L. Gittleman, W. Bryan Jennings, Kenneth H. Kozak, Mark A. McPeek, Franck Moreno-Roark, Thomas J. Near, Andy Purvis, Robert E. Ricklefs, Dolph Schluter, , Ole Seehausen, Brian L. Sidlauskas, Omar Torres-Carvajal, Jason T. Weir & Arne Ø. Mooers
George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations—more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed...

Data from: The early diversification history of didelphid marsupials: a window into South America’s “Splendid Isolation”

Sharon A. Jansa, F. Keith Barker & Robert S. Voss
The geological record of South American mammals is spatially biased because productive fossil sites are concentrated at high latitudes. As a result, the history of mammalian diversification in Amazonia and other tropical biomes is largely unknown. Here we report diversification analyses based on a time-calibrated molecular phylogeny of opossums (Didelphidae), a species-rich clade of mostly tropical marsupials descended from a Late Oligocene common ancestor. Optimizations of habitat and geography on this phylogeny suggest that (1)...

Data from: Effects of gene flow on phenotype matching between two varieties of Joshua tree (Yucca brevifolia; Agavaceae) and their pollinators

Jeremy B. Yoder, Christopher I. Smith, Daniel J. Rowley, Ramona Flatz, William Godsoe, Christopher Drummond, Olle Pellmyr, W. Godsoe, D. J. Rowley, C. Drummond, O. Pellmyr, C. I. Smith, R. Flatz & J. B. Yoder
In animal-pollinated plants, local adaptation to pollinator behaviour or morphology can restrict gene flow among plant populations; but gene flow may also prevent divergent adaptation. Here, we examine possible effects of gene flow on plant-pollinator trait matching in two varieties of Joshua tree (Agavaceae: Yucca brevifolia). The two varieties differ in strikingly in floral morphology, which matches differences in the morphology of their pollinators. However, this co-divergence is not present at a smaller scale: within...

Data from: Range dynamics, rather than convergent selection, explain the mosaic distribution of red-winged blackbird phenotypes

Matthew J. Dufort, F. Keith Barker & F. Keith Barker
Geographic distributions of genetic and phenotypic characters can illuminate historical evolutionary processes. In particular, mosaic distributions of phenotypically similar populations can arise from parallel evolution or from irregular patterns of dispersal and colonization by divergent forms. Two phenotypically divergent forms of the red-winged blackbird (Agelaius phoeniceus) show a mosaic phenotypic distribution, with a “bicolored” form occurring disjunctly in California and Mexico. We analyzed the relationships among these bicolored populations and neighboring typical populations, using ~600...

Data from: Three keys to the radiation of angiosperms into freezing environments

Amy E. Zanne, David C. Tank, William K. Cornwell, Jonathan M. Eastman, Stephen A. Smith, Richard G. FitzJohn, Daniel J. McGlinn, Brian C. O'Meara, Angela T. Moles, Peter B. Reich, Dana L. Royer, Douglas E. Soltis, Peter F. Stevens, Mark Westoby, Ian J. Wright, Lonnie Aarssen, Robert I. Bertin, Andre Calaminus, Rafaël Govaerts, Frank Hemmings, Michelle R. Leishman, Jacek Oleksyn, Pamela S. Soltis, Nathan G. Swenson, Laura Warman … & Alejandro Ordonez
Early flowering plants are thought to have been woody species restricted to warm habitats1, 2, 3. This lineage has since radiated into almost every climate, with manifold growth forms4. As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf...

Data from: Physiological adaptation along environmental gradients and replicated hybrid zone structure in swordtails (Teleostei: Xiphophorus)

Z. W. Culumber, D. B. Shepard, S. W. Coleman, G. G. Rosenthal & M. Tobler
Local adaptation is often invoked to explain hybrid zone structure, but empirical evidence of this is generally rare. Hybrid zones between two poeciliid fishes, Xiphophorus birchmanni and X. malinche, occur in multiple tributaries with independent replication of upstream-to-downstream gradients in morphology and allele frequencies. Ecological niche modelling revealed that temperature is a central predictive factor in the spatial distribution of pure parental species and their hybrids and explains spatial and temporal variation in the frequency...

Data from: Oral bisphosphonates are associated with increased risk of atypical femoral fractures in elderly women

Juan Erviti, Alvaro Alonso, Belén Oliva, Javier Gorricho, Antonio López, Julia Timoner, Consuelo Huerta, Miguel Gil & Francisco De Abajo
Objectives: To evaluate the association between bisphosphonate use and the risk of atypical femoral fractures among women aged 65 or older. Design: Nested case–control study. Setting: General practice research database in Spain. Exposures Use of oral bisphosphonates before the occurrence of atypical fractures among cases or the corresponding index date among controls. Bisphosphonate use was categorised as ever versus never users. Ever users were divided according to the total time since first prescription. Main outcome...

Data from: Lincoln estimates of mallard (Anas platyrhynchos) abundance in North America

Ray T. Alisauskas, Todd W. Arnold, James O. Leafloor, David L. Otis & James S. Sedinger
Estimates of range-wide abundance, harvest, and harvest rate are fundamental for sound inferences about the role of exploitation in the dynamics of free-ranging wildlife populations, but reliability of existing survey methods for abundance estimation is rarely assessed using alternative approaches. North American mallard populations have been surveyed each spring since 1955 using internationally coordinated aerial surveys, but population size can also be estimated with Lincoln's method using banding and harvest data. We estimated late summer...

Data from: An empirical comparison of a character-based and a coalescent-based approach to species delimitation in a young avian complex

Bailey D. McKay, , Yuchun Wu, Hui Li, Cheng-Te Yao, Isao Nishiumi, Fasheng Zou & Herman L. Mays
The process of discovering species is a fundamental responsibility of systematics. Recently, there has been a growing interest in coalescent-based methods of species delimitation aimed at objectively identifying species early in the divergence process. However, few empirical studies have compared these new methods with character-based approaches for discovering species. In this study, we applied both a character-based and a coalescent-based approaches to delimit species in a closely related avian complex, the light-vented/Taiwan bulbul (Pycnonotus sinensis/Pycnonotus...

Data from: Going to extremes: contrasting rates of diversification in a recent radiation of New World passerine birds

Frederick Keith Barker, Kevin J. Burns, John Klicka, Scott M. Lanyon, Irby J. Lovette, Frederick Keith Barker, Kevin J. Burns, John Klicka, Scott M. Lanyon, Irby J. Lovette & F. Keith Barker
Recent analyses suggest that a few major shifts in diversification rate may be enough to explain most of the disparity in diversity among vertebrate lineages. At least one significant increase in diversification rate appears to have occurred within the birds; however, several nested lineages within birds have been identified as hyperdiverse by different studies. A clade containing the finches and relatives (within the avian order Passeriformes), including a large radiation endemic to the New World...

Data from: Genome-wide discovery and characterization of maize long non-coding RNAs

Lin Li, Steven R. Eichten, Rena Shimizu, Katherine Petsch, Cheng-Ting Yeh, Wei Wu, Michael J. Scanlon, Jianming Yu, Patrick S. Schnable, Marja C. P. Timmermans, Nathan M. Springer & Gary J. Muehlbauer
Background: Long noncoding RNAs (lncRNAs) are transcripts that are 200 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation. However, the number, characteristics and expression inheritance pattern of lncRNAs in maize are still largely unknown. Results: By exploiting available public ESTs, maize whole genome sequence annotation and RNA-seq datasets from 30 different experiments, we identified 20,163 putative lncRNA. Of these lncRNAs, more than 90% are predicted to be...

Data from: Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula

Timothy Paape, Thomas Bataillon, Peng Zhou, Tom J. Y. Kono, Roman Briskine, Nevin D. Young, Peter Tiffin & Tom J. Y. Kono
Sequence data for >20 000 annotated genes from 56 accessions of Medicago truncatula were used to identify potential targets of positive selection, the determinants of evolutionary rate variation and the relative importance of positive and purifying selection in shaping nucleotide diversity. Based upon patterns of intraspecific diversity and interspecific divergence, c. 50–75% of nonsynonymous polymorphisms are subject to strong purifying selection and 1% of the sampled genes harbour a signature of positive selection. Combining polymorphism...

Data from: Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula

John Stanton-Geddes, Timothy Paape, Brendan Epstein, Roman Briskine, Jeremy Yoder, Joann Mudge, Arvind K. Bharti, Andrew D. Farmer, Peng Zhou, Roxanne Denny, Gregory D. May, Stephanie Erlandson, Mohammed Yakub, Masayuki Sugawara, Michael J. Sadowsky, Nevin D. Young & Peter Tiffin
Genome-wide association study (GWAS) has revolutionized the search for the genetic basis of complex traits. To date, GWAS have generally relied on relatively sparse sampling of nucleotide diversity, which is likely to bias results by preferentially sampling high-frequency SNPs not in complete linkage disequilibrium (LD) with causative SNPs. To avoid these limitations we conducted GWAS with >6 million SNPs identified by sequencing the genomes of 226 accessions of the model legume Medicago truncatula. We used...

Data from: Cryptic speciation reversal in the Etheostoma zonale (Teleostei: Percidae) species group, with an examination of the effect of recombination and introgression on species tree inference

Dominik Halas & Andrew M. Simons
Mitochondrial and nuclear introgression among closely related taxa can greatly complicate the process of determining their phylogenetic relationships. In the Central Highlands of North America, many fish taxa have undergone introgression; in this study, we demonstrate the existence of an unusual introgression event in the Etheostoma zonale species group. We used one mitochondrial and seven nuclear loci to determine the relationships of the taxa within the E. zonale group, and their degree of differentiation. We...

Data from: The distribution of fruit and seed toxicity during development for eleven Neotropical trees and vines in Central Panama

Noelle G. Beckman
Secondary compounds in fruit mediate interactions with natural enemies and seed dispersers, influencing plant survival and species distributions. The functions of secondary metabolites in plant defenses have been well-studied in green tissues, but not in reproductive structures of plants. In this study, the distribution of toxicity within plants was quantified and its influence on seed survival was determined in Central Panama. To investigate patterns of allocation to chemical defenses and shifts in allocation with fruit...

Data from: Phylogenetic signal variation in the genomes of Medicago (Fabaceae)

Jeremy B. Yoder, Roman Briskine, Joann Mudge, Andrew Farmer, Timothy Paape, Kelly Steele, George D. Weiblen, Arvind K. Bharti, Peng Zhou, Gregory D. May, Nevin D. Young & Peter Tiffin
Genome-scale data offer the opportunity to clarify phylogenetic relationships that are difficult to resolve with few loci, but they can also identify genomic regions with evolutionary history distinct from that of the species history. We collected whole-genome sequence data from 29 taxa in the legume genus Medicago, then aligned these sequences to the M. truncatula reference genome to confidently identify 87,596 variable homologous sites. We used this data set to estimate phylogenetic relationships among Medicago...

Data from: Anthropogenic environments exert variable selection on cranial capacity in mammals

Emilie C. Snell-Rood, Naomi Wick, E. C. Snell-Rood & N. Wick
It is thought that behaviourally flexible species will be able to cope with novel and rapidly changing environments associated with human activity. However, it is unclear whether such environments are selecting for increases in behavioural plasticity, and whether some species show more pronounced evolutionary changes in plasticity. To test whether anthropogenic environments are selecting for increased behavioural plasticity within species, we measured variation in relative cranial capacity over time and space in 10 species of...

Data from: Anolis sex chromosomes are derived from a single ancestral pair

Tony Gamble, Anthony J. Geneva, Richard E. Glor & David Zarkower
To explain the frequency and distribution of heteromorphic sex chromosomes in the lizard genus Anolis we compared the relative roles of sex chromosome conservation vs. turnover of sex determining mechanisms. We used model based comparative methods to reconstruct karyotype evolution and the presence of heteromorphic sex chromosomes onto a newly generated Anolis phylogeny. We found that heteromorphic sex chromosomes evolved multiple times in the genus. Fluorescent in situ hybridization (FISH) of repetitive DNA showed variable...

Data from: Tempo and mode of multicellular adaptation in experimentally evolved Saccharomyces cerevisiae

William C. Ratcliff, Jennifer T. Pentz & Michael Travisano
Multicellular complexity is a central topic in biology, but the evolutionary processes underlying its origin are difficult to study and remain poorly understood. Here we use experimental evolution to investigate the tempo and mode of multicellular adaptation during a de novo evolutionary transition to multicellularity. Multicelled “snowflake” yeast evolved from a unicellular ancestor after 7 days of selection for faster settling through liquid media. Over the next 220 days, snowflake yeast evolved to settle 44%...

Data from: Diffuse symbioses: roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiome

Matthew G. Bakker, Daniel C. Schlatter, Lindsey Otto-Hanson & Linda L. Kinkel
A conceptual model emphasizing direct host–microbe interactions has dominated work on host-associated microbiomes. To understand plant–microbiome associations, however, broader influences on microbiome composition and functioning must be incorporated, such as those arising from plant–plant and microbe–microbe interactions. We sampled soil microbiomes associated with target plant species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, Lupinus perennis) grown in communities varying in plant richness (1-, 4-, 8- or 16-species). We assessed Streptomyces antagonistic activity and analysed bacterial and...

Registration Year

  • 2013

Resource Types

  • Dataset


  • University of Minnesota
  • Department of Plant Biology
  • University of Idaho
  • University of Missouri–St. Louis
  • Colorado State University
  • University of British Columbia
  • University of Kansas
  • National Evolutionary Synthesis Center
  • National Museum
  • University of Washington