187 Works

Data from: Dragons in our midst: phyloforensics of illegally traded Southeast Asian monitor lizards

Welton J. Luke, Cameron D. Siler, Charles W. Linkem, Arvin C. Diesmos, Mae L. Diesmos, Emerson Sy, Rafe M. Brown & Luke J. Welton
We provide a phylogenetic and population genetic evaluation of the illegal pet and bush meat trade of monitor lizards in the Philippines. We use a molecular dataset assembled from vouchered samples with known localities throughout the country, as a reference for statistical phylogenetic, population genetic, and DNA barcoding analyses of genetic material obtained during a three year survey of the Manila pet trade. Our results provide the first genetic evaluation of a major Southeast Asian...

Data from: Adaptive genetic potential and plasticity of trait variation in the foundation prairie grass Andropogon gerardii across the US Great Plains’ climate gradient: Implications for climate change and restoration

Loretta C. Johnson, Matthew Galliart, Sofia Sabates, Hannah Tetreault, Angel DeLaCruz, Johnny Bryant, Jacob Alsdurf, Mary Knapp, Nora Bello, Sara Baer, Brian Maricle, David Gibson, Jesse Poland, Paul St. Amand, Natalie Unruh, Olivia Parrish & Loretta Johnson
Plant response to climate depends on a species’ adaptive potential. To address this, we used reciprocal gardens to detect genetic and environmental plasticity effects on phenotypic variation and combined with genetic analyses. Four reciprocal garden sites were planted with three regional ecotypes of Andropogon gerardii, a dominant Great Plains prairie grass, using dry, mesic, wet ecotypes originating from western KS to Illinois that span 500 to 1,200 mm rainfall year-1. We aimed to answer: (1)...

Data from: Effects of the soil microbiome on the demography of two annual prairie plants

Helen Alexander, Hannah Reynolds, Rebekah Wagner, Guangzhou Wang, Haley Burrill & James Bever
Both mutualistic and pathogenic soil microbes are known to play important roles in shaping the fitness of plants, likely affecting plants at different life cycle stages. In order to investigate the differential effects of native soil mutualists and pathogens on plant fitness, we compared survival and reproduction of two annual tallgrass prairie plant species (Chamaecrista fasciculata and Coreopsis tinctoria) in a field study using 3 soil inocula treatments containing different compositions of microbes. The soil...

Data from: Phenotypic evolution shaped by current enzyme function in the bioluminescent courtship signals of sea fireflies

Nicholai M. Hensley, Emily A. Ellis, Gretchen A. Gerrish, Elizabeth Torres, John P. Frawley, Todd H. Oakley & Trevor J. Rivers
Mating behaviours are diverse and noteworthy, especially within species radiations where they may contribute to speciation. Studying how differences in mating behaviours arise between species can help us understand how diversity is generated at multiple biological levels. The bioluminescent courtship displays of cypridinid ostracods (or sea fireflies) are an excellent system for this since amazing variety evolves while using a conserved biochemical mechanism. We find that the evolution of one aspect in this behavioural phenotype...

Data from: The plant microbiome and native plant restoration: the example of native mycorrhizal fungi

Liz Koziol, Peggy A. Schultz, Geoffrey L. House, Jonathan T. Bauer, Elizabeth L. Middleton & James D. Bever
Ecological restoration efforts can increase the diversity and function of degraded areas. However, current restoration practices cannot typically re-establish the full diversity and species composition of remnant plant communities. We present evidence that restoration quality can be improved by reintroducing key organisms from the native plant microbiome. In particular, root symbionts called arbuscular mycorrhizal fungi are critical in shaping grassland communities, but are sensitive to anthropogenic disturbance, which may pose a problem for grassland restoration....

Data from: The hatching mechanism of 130-million-year-old insects: an association of neonates, egg shells and egg bursters in Lebanese amber

Ricardo Pérez-De La Fuente, Michael S. Engel, Dany Azar & Enrique Peñalver
Hatching is a pivotal moment in the life of most animals. Diverse chemical, behavioural and mechanical methods have evolved in metazoans to break the egg membranes. Among them, many arthropod and vertebrate embryos hatch using ephemeral, frequently convergent structures known as egg bursters. However, the evolutionary processes by which hatching mechanisms and related embryonic structures became established in deep time are poorly understood due to a nearly complete absence from the fossil record. Herein we...

On Greek Row: Diversity, Socially Responsible Leadership and Fraternity and Sorority Membership

Eugene T. Parker & Ernest Pascarella

Inter- and intra-archipelago dynamics of population structure and gene flow in a Polynesian bird

Ethan Gyllenhaal, Xena Mapel, Tejashree Modak, Lucas DeCicco, Alivereti Naikatini, Ruth Utzurrum, Joshua Seamon, Jean-Claude Thibault, Alice Cibois, Michael Sorenson, Robert Moyle, Lisa Barrow & Michael Andersen
Islands are separated by natural barriers that prevent gene flow between terrestrial populations and promote allopatric diversification. Birds in the South Pacific are an excellent model to explore the interplay between isolation and gene flow due to the region’s numerous archipelagos and well-characterized avian communities. The wattled honeyeater complex (Foulehaio spp.) comprises three allopatric species that are widespread and common across Fiji, Tonga, Samoa, and Wallis and Futuna. Here, we explored patterns of diversification within...

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...

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...

Data from: Relative selectivity of plant cardenolides for Na+/K+-ATPases from the monarch butterfly and non-resistant insects

Georg Petschenka, Colleen S. Fei, Juan J. Araya, Susanne Schröder, Barbara N. Timmermann & Anurag A. Agrawal
A major prediction of coevolutionary theory is that plants may target particular herbivores with secondary compounds that are selectively defensive. The highly specialized monarch butterfly (Danaus plexippus) copes well with cardiac glycosides (inhibitors of animal Na+/K+-ATPases) from its milkweed host plants, but selective inhibition of its Na+/K+-ATPase by different compounds has not been previously tested. We applied 17 cardiac glycosides to the D. plexippus-Na+/K+-ATPase and to the more susceptible Na+/K+-ATPases of two non-adapted insects (Euploea...

Data from: The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago

Jamie R Oaks, Cameron D. Siler & Rafe M. Brown
A primary goal of biogeography is to understand how large-scale environmental processes, like climate change, affect diversification. One often-invoked but seldom tested process is the so-called ''species-pump'' model, in which repeated bouts of co-speciation is driven by oscillating climate-induced habitat connectivity cycles. For example, over the past three million years, the landscape of the Philippine Islands has repeatedly coalesced and fragmented due to sea-level changes associated with the glacial cycles. This repeated climate-driven vicariance has...

Data from: Frequent fire slows microbial decomposition of newly deposited fine fuels in a pyrophilic ecosystem

Jacob Hopkins
Frequent fires maintain nearly 50% of terrestrial ecosystems, and drive ecosystem changes that govern future fires. Since fires are dependent on available plant or fine fuels, ecosystem processes that alter fine fuel loads like microbial decomposition are particularly important and could modify future fires. We hypothesized that variation in short-term fire history would influence fuel dynamics in such ecosystems. We predicted that frequent fires within a short-time period would slow microbial decomposition of new fine...

A test of island biogeographic theory applied to estimates of gene flow in a Fijian bird is largely consistent with neutral expectations

Ethan Gyllenhaal, Xena Mapel, Alivereti Naikatini, Robert Moyle & Michael Andersen
Islands were key to the development of allopatric speciation theory because they are a natural laboratory of repeated barriers to gene flow caused by open water gaps. Despite their proclivity for promoting divergence, little empirical work has quantified the extent of gene flow among island populations. Following classic island biogeographic theory, two metrics of interest are relative island size and distance. Fiji presents an ideal system for studying these dynamics, with four main islands that...

Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex

Kin Onn Chan, Carl Hutter, Perry Lee Wood, Lee Grismer, Indraneil Das & Rafe Brown
Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic and species delimitation inferences, the influence of these processes on species estimation is not frequently evaluated. Using large amounts of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional...

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