184 Works

Data from: Centromere–associated meiotic drive and female fitness variation in Mimulus

Lila Fishman & John Kennedy Kelly
Female meiotic drive, in which chromosomal variants preferentially segregate to the egg pole during asymmetric female meiosis, is a theoretically pervasive but still mysterious form of selfish evolution. Like other selfish genetic elements, driving chromosomes may be maintained as balanced polymorphisms by pleiotropic or linked fitness costs. A centromere-associated driver (D) with a ∼58:42 female-specific transmission advantage occurs at intermediate frequency (32-40%) in the Iron Mountain population of the yellow monkeyflower, Mimulus guttatus. Previously determined...

Data from: Age, state, environment and season dependence of senescence in body mass

Svenja B. Kroeger, Daniel T. Blumstein, Kenneth B. Armitage, Jane M. Reid, Julien G.A. Martin & Julien G. A. Martin
Data file in csv formatBMdata.csvRcode

Data from: Negative plant-phyllosphere feedbacks in native Asteraceae hosts – a novel extension of the plant-soil feedback framework

Briana K. Whitaker, Jonathan T. Bauer, James D. Bever & Keith Clay
Over the past 25 years, the plant-soil feedback (PSF) framework has catalyzed our understanding of how belowground microbiota impact plant fitness and species coexistence. Here, we apply a novel extension of this framework to microbiota associated with aboveground tissues, termed ‘plant-phyllosphere feedback (PPFs)’. In parallel greenhouse experiments, rhizosphere and phyllosphere microbiota of con- and heterospecific hosts from four species were independently manipulated. In a third experiment, we tested the combined effects of soil and phyllosphere...

Data from: Transient synchrony among populations of five foliage-feeding Lepidoptera

Maartje J. Klapwijk, Jonathan A. Walter, Aniko Hirka, György Csóka, Christer Björkman & Andrew M. Liebhold
1. Studies of transient population dynamics have largely focused on temporal changes in dynamical behavior, such as the transition between periods of stability and instability. The present study explores a related dynamic pattern, namely transient synchrony during a 49-year period among populations of five sympatric species of forest insects that share host tree resources. The long time-series allows a more comprehensive exploration of transient synchrony patterns than most previous studies. Considerable variation existed in the...

Data from: Ancient genomes revisit the ancestry of domestic and Przewalski’s horses

Charleen Gaunitz, Antoine Fages, Kristian Hanghøj, Anders Albrechtsen, Naveed Khan, Mikkel Schubert, Andaine Seguin-Orlando, Ivy J. Owens, Sabine Felkel, Olivier Bignon-Lau, Peter De Barros Damgaard, Alissa Mittnik, Azadeh F. Mohaseb, Hossein Davoudi, Saleh Alquraishi, Ahmed H. Alfarhan, Khaled A. S. Al-Rasheid, Eric Crubézy, Norbert Benecke, Sandra Olsen, Dorcas Brown, David Anthony, Ken Massy, Vladimir Pitulko, Aleksei Kasparov … & Ludovic Orlando
The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski’s horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago...

Data from: Spatial analysis of anthropogenic landscape disturbance and Buruli ulcer disease in Benin

Lindsay P. Campbell, Andrew O. Finley, Mark Eric Benbow, Jenni Gronseth, Pamela Small, Roch Christian Johnson, Ghislain E. Sopoh, Richard M. Merritt, Heather Williamson & Jiaguo Qi
Background: Land use and land cover (LULC) change is one anthropogenic disturbance linked to infectious disease emergence. Current research has focused largely on wildlife and vector-borne zoonotic diseases, neglecting to investigate landscape disturbance and environmental bacterial infections. One example is Buruli ulcer (BU) disease, a necrotizing skin disease caused by the environmental pathogen Mycobacterium ulcerans (MU). Empirical and anecdotal observations have linked BU incidence to landscape disturbance, but potential relationships have not been quantified as...

A morphometric assessment of species boundaries in a widespread anole lizard (Squamata: Dactyloidae)

Tanner Myers, Pietro De Mello & Richard Glor
Cryptic species - genetically distinct species that are morphologically difficult to distinguish - present challenges to systematists. Operationally, cryptic species are very difficult to identify and sole usage of genetic data or morphological data can fail to recognize evolutionarily isolated lineages. We use morphometric data to test species boundaries hypothesized with genetic data in the North Caribbean Bark Anole (Anolis distichus), a suspected species complex. We use univariate and multivariate analyses to test if candidate...

Quantifying shell outline variability in extant and fossil Laqueus (Brachiopoda: Terebratulida): are outlines good proxies for long-looped brachidial morphology and can they help us characterize species?

Natalia Lopez Carranza & Sandra Carlson
Extant and extinct terebratulide brachiopod species have been defined primarily on the basis of morphology. What is the fidelity of morphological species to biological species? And how can we test this fidelity with fossils? Taxonomically and phylogenetically, the most informative internal feature in the brachiopod suborder Terebratellidina is the geometrically complex long-looped brachidium, which, given their fragile nature, are not commonly preserved in the fossil record. In their absence, it is essential to test other...

Supplementary information for: The effects of geographic range size and abundance on extinction during a time of ‘sluggish’ evolution

Michelle Casey, Erin Saupe & Bruce Lieberman
Geographic range size and abundance are important determinants of extinction risk in fossil and extant taxa. However, the relationship between these variables and extinction risk has not been tested extensively during evolutionarily ‘quiescent’ times of low extinction and speciation in the fossil record. Here we examine the influence of geographic range size and abundance on extinction risk during the late Paleozoic (Mississippian–Permian), a time of ‘sluggish’ evolution when global rates of origination and extinction were...

Codes: A new approach to interspecific synchrony in population ecology using tail association

Shyamolina Ghosh, Lawrence W. Sheppard, Philip C. Reid & Daniel C. Reuman
Standard methods for studying the association between two ecologically important variables provide only a small slice of the information content of the association, but statistical approaches are available that provide comprehensive information. In particular, available approaches can reveal tail associations, i.e., accentuated or reduced associations between the more extreme values of variables. We here study the nature and causes of tail associations between phenological or population-density variables of co-located species, and their ecological importance. We...

Data from: Temporal scale of environmental correlations affects ecological synchrony

Robert A. Desharnais, Daniel C. Reuman, Robert F. Costantino & Joel E. Cohen
Population densities of a species, measured in different locations are often correlated over time, a phenomenon referred to as synchrony. Synchrony results from dispersal of individuals among locations and spatially correlated environmental variation, among other causes. Synchrony is often measured by a correlation coefficient. However, synchrony can vary with timescale. We demonstrate theoretically and experimentally that the timescale-specificity of environmental correlation affects the overall magnitude and timescale-specificity of synchrony, and that these effects are modified...

Data from: Species delimitation with gene flow: a methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs

Kin Onn Chan, Alana M. Alexander, Jesse L. Grismer, Yong-Chao Su, Evan S.H. Quah, Rafe M. Brown, Evan S. H. Quah & L. Lee Grismer
Accurately delimiting species boundaries is a non-trivial undertaking that can have significant effects on downstream inferences. We compared the efficacy of commonly-used species delimitation methods (SDMs) and a population genomics approach based on genome-wide single nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent Frog Complex currently recognized as a single species (Amolops larutensis). First, we used morphological, mitochondrial DNA and genome-wide SNPs to identify putative species boundaries by implementing non-coalescent and coalescent-based...

Data from: Interglacial microrefugia and diversification of a cactus species complex: phylogeography and palaeodistributional reconstructions for Pilosocereus aurisetus and allies

Isabel A. S. Bonatelli, Manolo F. Perez, A. Townsend Peterson, Nigel P. Taylor, Daniela C. Zappi, Marlon C. Machado, Ingrid Koch, Adriana H. C. Pires & Evandro M. Moraes
The role of Pleistocene climate changes in promoting evolutionary diversification in global biota is well documented, but the great majority of data regarding this subject come from North America and Europe, which were greatly affected by glaciation. The effects of Pleistocene changes on cold- and/or dry-adapted species in tropical areas where glaciers were not present remain sparsely investigated. Many such species are restricted to small areas surrounded by unfavourable habitats, which may represent potential interglacial...

Data from: The generification of the fossil record

Jonathan R. Hendricks, Erin E. Saupe, Corinne E. Myers, Elizabeth J. Hermsen & Warren D. Allmon
Many modern paleobiological analyses are conducted at the generic level, a practice predicated on the validity of genera as meaningful proxies for species. Uncritical application of genera in such analyses, however, has led, perhaps inadvertently, to the unjustified reification of genera in an evolutionary context. While the utility of genera as proxies for species in evolutionary studies should be evaluated as an empirical issue, in practice it is increasingly assumed (rather than demonstrated) that genera...

Data from: SATé-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees

Kevin Liu, Tandy J. Warnow, Mark T. Holder, Serita M. Nelesen, Jiaye Yu, Alexandros P. Stamatakis & C. Randal Linder
Highly accurate estimation of phylogenetic trees for large datasets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Co-estimation of alignments and trees has been attempted, but currently only SATé estimates reasonably accurate trees and alignments for large datasets in practical time frames (Liu et al., 2009b). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I)...

Data from: Stochastic faunal exchanges drive diversification in widespread Wallacean and Pacific island lizards (Squamata: Scincidae: Lamprolepis smaragdina)

Charles W. Linkem, Rafe M. Brown, Cameron D. Siler, Ben J. Evans, Christopher C. Austin, Djoko T. Iskandar, Arvin C. Diesmos, Jatna Supriatna, Noviar Andayani, Jimmy A. McGuire & Malte Ebach
Aim: Widespread species found in disturbed habitats are often expected to be human commensals. In island systems, this association predicts that dispersal will be mediated by humans. We investigated the biogeographical relationships among populations of a widespread tree skink that inhabits coastal forest and human-cultivated plantations in Southeast Asia. We sought to determine whether populations of the emerald tree skink, Lamprolepis smaragdina, dis- persed via mechanisms that were not human-mediated (‘natural’ dispersal) or whether dispersal...

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...

Extensive paraphyly in the typical owl family (Strigidae)

Jessie F Salter, Carl H Oliveros, Peter A Hosner, Joseph D Manthey, Mark B Robbins, Robert G Moyle, Robb T Brumfield & Brant C Faircloth
The typical owl family (Strigidae) comprises 194 species in 28 genera, 14 of which are monotypic. Relationships within and among genera in the typical owls have been challenging to discern because mitochondrial data have produced equivocal results and because many monotypic genera have been omitted from previous molecular analyses. Here, we collected and analyzed DNA sequences of ultraconserved elements (UCEs) from 43 species of typical owls to produce concatenated and multispecies coalescent-based phylogenetic hypotheses for...

Data from: Rates of niche and phenotype evolution lag behind diversification in a temperate radiation

Ryan A. Folk, Rebecca L. Stubbs, Mark E. Mort, Nico Cellinese, Julie M. Allen, Pamela S. Soltis, Douglas E. Soltis & Robert P. Guralnick
Environmental change can create opportunities for increased rates of lineage diversification, but continued species accumulation has been hypothesized to lead to slowdowns via competitive exclusion and niche partitioning. Such density-dependent models imply tight linkages between diversification and trait evolution, but there are plausible alternative models. Little is known about the association between diversification and key ecological and phenotypic traits at broad phylogenetic and spatial scales. Do trait evolutionary rates coincide with rates of diversification, are...

Data from: Phenology of Drosophila species across a temperate growing season and implications for behavior

J.M. Gleason, Paula R. Roy, Elizabeth R. Everman, Terry C. Gleason & Theodore J. Morgan
Drosophila community composition is complex in temperate regions with different abundance of flies and species across the growing season. Monitoring Drosophila populations provides insights into the phenology of both native and invasive species. Over a single growing season, we collected Drosophila at regular intervals and determined the number of individuals of the nine species we found in Kansas, USA. Species varied in their presence and abundance through the growing season with peak diversity occurring after...

Data from: Quantifying cryptic function loss during community disassembly

Akira Terui, Jacques Finlay, Amy Hansen & Jessica Kozarek
1. Emerging theory suggests that the ecosystem-level consequences of anthropogenic pressures depend on how species will be disassembled from ecological communities (i.e., the disassembly rule). Species loss, however, is not the sole ecological cause of ecosystem function loss: behaviors underpinning ecosystem function can also be disrupted by anthropogenic pressures without detectable declines of component species (“cryptic function loss”). 2. Here, we introduce a novel framework that integrates behavioral responses into community disassembly metrics. We applied...

New exceptionally-preserved panarthropods from the Drumian Wheeler Konservat-Lagerstätte of the House Range of Utah

Rudy Lerosey-Aubril, Julien Kimmig, Stephen Pates, Jacob Skabelund, Andries Weug & Javier Ortega-Hernández
The Drumian Wheeler Konservat-Lagerstätte of the House Range of Utah (Wheeler-HR) has yielded one of the most diverse exceptionally-preserved Cambrian biotas of North America. The discovery of soft-bodied fossils invariably provides precious insights on this remarkable Miaolingian biota, for most of its non-biomineralizing components are known from very few specimens. This contribution describes some 30 new exceptionally-preserved fossils of Wheeler panarthropods. Two new species are recognized, the radiodont Hurdia sp. nov. A and the megacheiran...

The role of evolutionary time, diversification rates and dispersal in determining the global diversity of a large radiation of passerine birds

Tianlong Cai, Shimiao Shao, Jonathan Kennedy, Per Alström, Robert Moyle, Yanhua Qu, Fumin Lei & Jon Fjeldså
Aim: Variation in species diversity among different geographic areas may result from differences in speciation and extinction rates, immigration and time for diversification. An area with high species diversity may be the result of a high net diversification rate, multiple immigration events from adjacent regions,anda long time available for the accumulation of species (know as the “time-for-speciation effect”). Here, we examine the relative importance of the three aforementionedprocesses in shaping the geographic diversity patterns of...

Repeated fire shifts carbon and nitrogen cycling by changing plant inputs and soil decomposition across ecosystems

Adam Francis Pellegrini, Sarah Hobbie, Peter Reich, Ari Jumpponen, Jack Brookshire, Anthony Caprio, Corli Coetsee & Robert Jackson
Fires shape the biogeochemistry and functioning of many ecosystems, and fire frequencies are changing across much of the globe. Frequent fires can change soil carbon (C) and nitrogen (N) storage by altering the quantity and chemistry of plant inputs through changes in plant biomass and composition as well as altering decomposition of soil organic matter. How decomposition rates change with shifting inputs remains uncertain because most studies focus on the effects of single fires, where...

Data from: Multilocus phylogenetic analyses of Hispaniolan and Bahamian trunk anoles (distichus species group)

Anthony J. Geneva, Jared Hilton, Sabina Noll & Richard E. Glor
The distichus species group includes six species and 21 subspecies of trunk ecomorph anoles distributed across Hispaniola and its satellite islands as well as the northern Bahamas. Although this group has long served as a model system for studies of reproductive character displacement, adaptation, behavior and speciation, it has never been the subject of a comprehensive phylogenetic analysis. Our goal here is to generate a multilocus phylogenetic dataset (one mitochondrial and seven nuclear loci) and...

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