40 Works

Data from: Multilocus coalescent analyses reveal the demographic history and speciation patterns of mouse lemur sister species

Christopher Blair, Kellie L. Heckman, Amy L. Russell & Anne D. Yoder
Background: Debate continues as to whether allopatric speciation or peripatric speciation through a founder effect is the predominant force driving evolution in vertebrates. The mouse lemurs of Madagascar are a system in which evolution has generated a large number of species over a relatively recent time frame. Here, we examine speciation patterns in a pair of sister species of mouse lemur, Microcebus murinus and M. griseorufus. These two species have ranges that are disparately proportioned...

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: Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Fay-Wei Li
Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor—neochrome—that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome...

Data from: Competition for hummingbird pollination shapes flower color variation in Andean Solanaceae

Nathan Muchhala, Sönke Johnsen & Stacey Dewitt Smith
One classic explanation for the remarkable diversity of flower colors across angiosperms involves evolutionary shifts among different types of pollinators with different color preferences. However, the pollinator shift model fails to account for the many examples of color variation within clades that share the same pollination system. An alternate explanation is the competition model, which suggests that color divergence evolves in response to interspecific competition for pollinators, as a means to decrease interspecific pollinator movements....

Data from: Divergent population structure and climate associations of a chromosomal inversion polymorphism across the Mimulus guttatus species complex

Elen Oneal, David B. Lowry, Kevin M. Wright, Zhirui Zhu & John H. Willis
Chromosomal rearrangement polymorphisms are common and increasingly found to be associated with adaptive ecological divergence and speciation. Rearrangements, such as inversions, reduce recombination in heterozygous individuals and thus can protect favorable allelic combinations at linked loci, facilitating their spread in the presence of gene flow. Recently, we identified a chromosomal inversion polymorphism that contributes to ecological adaptation and reproductive isolation between annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatus. Here we evaluate the...

Data from: The socio-genetics of a complex society: female gelada relatedness patterns mirror association patterns in a multi-level society.

Noah Snyder-Mackler, Susan C. Alberts & Thore J. Bergman
Multilevel societies with fission–fusion dynamics—arguably the most complex animal societies—are defined by two or more nested levels of organization. The core of these societies are modular social units that regularly fission and fuse with one another. Despite convergent evolution in disparate taxa, we know strikingly little about how such societies form and how fitness benefits operate. Understanding the kinship structure of complex societies could inform us about the origins of the social structure as well...

Data from: Levers and linkages: Mechanical trade-offs in a power-amplified system

Philip S. L. Anderson, Thomas Claverie & S. N. Patek
Mechanical redundancy within a biomechanical system (e.g., many-to-one mapping) allows morphologically divergent organisms to maintain equivalent mechanical outputs. However, most organisms depend on the integration of more than one biomechanical system. Here we test whether coupled mechanical systems follow a pattern of amplification (mechanical changes are congruent and evolve towards the same functional extreme) or independence (mechanisms evolve independently). We examined the correlated evolution and evolutionary pathways of the coupled 4-bar linkage and lever systems...

Data from: Genomic characterization of large heterochromatic gaps in the human genome assembly

Nicolas Altemose, Karen H. Miga, Mauro Maggioni & Huntington F. Willard
The largest gaps in the human genome assembly correspond to multi-megabase heterochromatic regions composed primarily of two related families of tandem repeats, Human Satellites 2 and 3 (HSat2,3). The abundance of repetitive DNA in these regions challenges standard mapping and assembly algorithms, and as a result, the sequence composition and potential biological functions of these regions remain largely unexplored. Furthermore, existing genomic tools designed to predict consensus-based descriptions of repeat families cannot be readily applied...

Data from: Joined at the hip: linked characters and the problem of missing data in studies of disparity

Andrew John Smith, Michael V. Rosario, Thomas P. Eiting & Elizabeth R. Dumont
Paleontological investigations into morphological diversity, or disparity, are often confronted with large amounts of missing data. We illustrate how missing discrete data effects disparity using a novel simulation for removing data based on parameters from published datasets that contain both extinct and extant taxa. We develop an algorithm that assesses the distribution of missing characters in extinct taxa, and simulates data loss by applying that distribution to extant taxa. We term this technique ‘linkage’. We...

Data from: Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species

Daniel J. Hasselman, Emily E. Argo, Meghan C. McBride, Paul Bentzen, Thomas F. Schultz, Anna A. Perez-Umphrey & Eric P. Palkovacs
Most evidence for hybrid swarm formation stemming from anthropogenic habitat disturbance comes from the breakdown of reproductive isolation between incipient species, or introgression between allopatric species following secondary contact. Human impacts on hybridization between divergent species that naturally occur in sympatry has received considerably less attention. Theory predicts that reinforcement should act to preserve reproductive isolation under such circumstances, potentially making reproductive barriers resistant to human habitat alteration. Using 15 microsatellites we examined hybridization between...

Data from: Effects of feral cats on the evolution of anti-predator behaviours in island reptiles: insights from an ancient introduction

Binbin Li, Anat Belasen, Panayiotis Pafilis, Peter Bednekoff & Johannes Foufopoulos
Exotic predators have been the driving force behind the extinction of many island endemic species. We examined impacts of feral cats (Felis catus) on the abundance and anti-predator behaviors of Aegean wall lizards (Podarcis erhardii) in the Cyclades (Greece), where cats were introduced thousands of years ago. We compared populations with high and low cat density on Naxos and populations on surrounding islets with no cats. Results show that cats have strong negative effects on...

Data from: Next-generation approaches to advancing eco-immunogenomic research in critically endangered primates

Peter A. Larsen, C. Ryan Campbell & Anne D. Yoder
High-throughput sequencing platforms are generating massive amounts of genomic data from nonmodel species, and these data sets are valuable resources that can be mined to advance a number of research areas. An example is the growing amount of transcriptome data that allow for examination of gene expression in nonmodel species. Here, we show how publicly available transcriptome data from nonmodel primates can be used to design novel research focused on immunogenomics. We mined transcriptome data...

Data from: Harmonic calls and indifferent females: no preference for human consonance in an anuran

Karin L. Akre, Ximena Bernal, A. Stanley Rand & Michael J. Ryan
The human music faculty might have evolved from rudimentary components that occur in non-human animals. The evolutionary history of these rudimentary perceptual features is not well understood and rarely extends beyond a consideration of vertebrates that possess a cochlea. One such antecedent is a preferential response to what humans perceive as consonant harmonic sounds, which are common in many animal vocal repertoires. We tested the phonotactic response of female túngara frogs (Physalaemus pustulosus) to variations...

Data from: Size, sex, and individual-level behavior drive intra-population variation in cross-ecosystem foraging of a top-predator

James C. Nifong, Craig A. Layman & Brian R. Silliman
1. Large-bodied, top-predators are often highly mobile, with the potential to provide important linkages between spatially distinct food webs. What biological factors contribute to variation in cross-ecosystem movements, however, have rarely been examined. 2. Here, we investigated how ontogeny (body size), sex, and individual-level behavior impacts intra-population variation in cross-ecosystem foraging (i.e., between freshwater and marine systems), by the top-predator Alligator mississippiensis. 3. Field surveys revealed A. mississippiensis uses marine ecosystems regularly and are abundant...

Data from: Social affiliation matters: both same-sex and opposite-sex relationships predict survival in wild female baboons

Elizabeth A. Archie, Jenny Tung, Michael Clark, Jeanne Altmann & Susan C. Alberts
Social integration and support can have profound effects on human survival. The extent of this phenomenon in non-human animals is largely unknown, but such knowledge is important to understanding the evolution of both lifespan and sociality. Here, we report evidence that levels of affiliative social behaviour (i.e. ‘social connectedness’) with both same-sex and opposite-sex conspecifics predict adult survival in wild female baboons. In the Amboseli ecosystem in Kenya, adult female baboons that were socially connected...

Data from: Investigating evolutionary lag using the species-pairs evolutionary lag test (SPELT)

Charles L. Nunn & Natalie Cooper
For traits showing correlated evolution, one trait may evolve more slowly than the other, producing evolutionary lag. The species-pairs evolutionary lag test (SPELT) uses an independent contrasts based approach to detect evolutionary lag on a phylogeny. We investigated the statistical performance of SPELT in relation to degree of lag, sample size (species pairs), and strength of association between traits. We simulated trait evolution under two models: one in which trait X changes during speciation and...

Data from: Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures

Taj Morton, Jalean Petricka, David L. Corcoran, Song Li, Cara M. Winter, Alexa Carda, Philip N. Benfey, Uwe Ohler & Molly Megraw
Understanding plant gene promoter architecture has long been a challenge due to the lack of relevant large-scale data sets and analysis methods. Here, we present a publicly available, large-scale transcription start site (TSS) data set in plants using a high-resolution method for analysis of 5′ ends of mRNA transcripts. Our data set is produced using the paired-end analysis of transcription start sites (PEAT) protocol, providing millions of TSS locations from wild-type Columbia-0 Arabidopsis thaliana whole...

Data from: Life history profiles for 27 strepsirrhine primate taxa generated using captive data from the Duke Lemur Center

Sarah M. Zehr, Richard G. Roach, David Haring, Julie Taylor, Freda H. Cameron & Anne D. Yoder
Since its establishment in 1966, the Duke Lemur Center (DLC) has accumulated detailed records for nearly 4200 individuals from over 40 strepsirrhine primate taxa – the lemurs, lorises, and galagos. Here we present verified data for 3627 individuals of 27 taxa in the form of a life history table containing summarized species values for variables relating to ancestry, reproduction, longevity, and body mass, as well as the two raw data files containing direct and calculated...

Data from: Longitudinal recordings of the vocalizations of immature Gombe chimpanzees for developmental studies

Frans X. Plooij, Hetty Van De Rijt-Plooij, Martha Fischer & Anne Pusey
Many researchers are interested in chimpanzee vocal communication, both as an important aspect of chimpanzee social behavior and as a source of insights into the evolution of human language. Nonetheless, very little is known about how chimpanzee vocal communication develops from infancy to adulthood. The largest dataset of audiorecordings from free-living immature chimpanzees was collected by the late Hetty van de Rijt-Plooij and Frans X. Plooij at Gombe National Park, Tanzania (1971–1973). These recordings have...

Data from: Abortion legislation, maternal healthcare, fertility, female literacy, sanitation, violence against women, and maternal deaths: a natural experiment in 32 Mexican states

Elard Koch, Monique Chireau, Fernando Pliego, Joseph Stanford, Sebastián Haddad, Byron Calhoun, Paula Aracena, Miguel Bravo, Sebastián Gatica & John Thorp
Objective: To test whether there is an association between abortion legislation and maternal mortality outcomes after controlling for other factors thought to influence maternal health. Design: Population-based natural experiment. Setting and data sources: Official maternal mortality data from 32 federal states of Mexico between 2002 and 2011. Main outcomes: Maternal mortality ratio (MMR), MMR with any abortive outcome (MMRAO) and induced abortion mortality ratio (iAMR). Independent variables: Abortion legislation grouped as less (n=18) or more...

Data from: Exposure to mitochondrial genotoxins and dopaminergic neurodegeneration in Caenorhabditis elegans

Claudia P. Gonzalez-Hunt, Maxwell C. K. Leung, Rakesh K. Bodhicharla, Madeline G. McKeever, Andrew E. Arrant, Kathleen M. Margillo, Ian T. Ryde, Derek D. Cyr, Sara G. Kosmaczewski, Marc Hammarlund & Joel N. Meyer

Data from: The extent and genetic basis of phenotypic divergence in life history traits in Mimulus guttatus

Jannice Friedman, Alex D. Twyford, John H. Willis & Benjamin K. Blackman
Differential natural selection acting on populations in contrasting environments often results in adaptive divergence in multivariate phenotypes. Multivariate trait divergence across populations could be caused by selection on pleiotropic alleles or through many independent loci with trait-specific effects. Here, we assess patterns of association between a suite of traits contributing to life history divergence in the common monkeyflower, Mimulus guttatus, and examine the genetic architecture underlying these correlations. A common garden survey of 74 populations...

Data from: Data-driven discovery of the spatial scales of habitat choice by elephants

Andrew F. Mashintonio, Stuart L. Pimm, Grant M. Harris, Rudi J. Van Aarde & Gareth J. Russell
Setting conservation goals and management objectives relies on understanding animal habitat preferences. Models that predict preferences combine location data from tracked animals with environmental information, usually at a spatial resolution determined by the available data. This resolution may be biologically irrelevant for the species in question. Individuals likely integrate environmental characteristics over varying distances when evaluating their surroundings; we call this the scale of selection. Even a single characteristic might be viewed differently at different...

Data from: Evolution of niche preference in Sphagnum peat mosses

Matthew G. Johnson, Gustaf Granath, Teemu Tahvanainen, Remy Pouliot, Hans K. Stenøien, Line Rochefort, Håkan Rydin & A. Jonathan Shaw
Peat mosses (Sphagnum) are ecosystem engineers— species in boreal peatlands simultaneously create and inhabit narrow habitat preferences along two microhabitat gradients: an ionic gradient and a hydrological hummock-hollow gradient. In this paper we demonstrate the connections between microhabitat preference and phylogeny in Sphagnum. Using a dataset of 39 species of Sphagnum, with an 18-locus DNA alignment and an ecological dataset encompassing three large published studies, we tested for phylogenetic signal and within-genus changes in evolutionary...

Data from: The founding of Mauritian endemic coffee trees by a synchronous long-distance dispersal event

Michael D. Nowak, Benjamin C. Haller & Anne D. Yoder
The stochastic process of long-distance dispersal is the exclusive means by which plants colonize oceanic islands. Baker's rule posits that self-incompatible plant lineages are unlikely to successfully colonize oceanic islands because they must achieve a coordinated long-distance dispersal of sufficiently numerous individuals to establish an outcrossing founder population. Here, we show for the first time that Mauritian Coffea species are self-incompatible and thus represent an exception to Baker's rule. The genus Coffea (Rubiaceae) is composed...

Registration Year

  • 2014

Resource Types

  • Dataset


  • Duke University
  • Princeton University
  • University of North Carolina
  • University of Massachusetts Amherst
  • University of Michigan-Ann Arbor
  • University of Virginia
  • University of Colorado Boulder
  • Yale University
  • Notre Dame University
  • North Carolina State University