132 Works

Data from: Investigating the effects of Pleistocene events on genetic divergence within Richardsonius balteatus, a widely distributed western North American minnow

Derek D. Houston, Dennis K. Shiozawa, Brian Tilston Smith & Brett R. Riddle
Background: Biogeographers seek to understand the influences of global climate shifts and geologic changes to the landscape on the ecology and evolution of organisms. Across both longer and shorter timeframes, the western North American landscape has experienced dynamic transformations related to various geologic processes and climatic oscillations, including events as recently as the Last Glacial Maximum (LGM; ~20 Ka) that have impacted the evolution of the North American biota. Redside shiner is a cyprinid species...

Data from: Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae)

Mariana Vargas Cruz, Gustavo Maruyama Mori, Dong-Ha Oh, Maheshi Dassanayake, Maria Imaculada Zucchi, Rafael Silva Oliveira & Anete Pereira De Souza
Environmental variation along the geographical space can shape populations by natural selection. In the context of global warming and changing precipitation regimes, it is crucial to understand the role of environmental heterogeneity in tropical trees adaptation, given their disproportional contribution to water and carbon biogeochemical cycles. Here, we investigated how heterogeneity in freshwater availability along tropical wetlands has influenced molecular variations of the Black Mangrove (Avicennia germinans). Fifty-seven trees were sampled in seven sites differing...

Mitochondrial genomes and thousands of ultraconserved elements resolve the taxonomy and historical biogeography of the Euphonia and Chlorophonia finches (Passeriformes: Fringillidae)

Tyler Imfeld, Keith Barker & Robb Brumfield
Relationships of the Neotropical finches in the genera Euphonia and Chlorophonia (Fringillidae: Euphoniinae) have been clarified by recent molecular studies, but species-level relationships within this group have not been thoroughly addressed. In this study, we sampled specimens representing every recognized species of these genera, in addition to 2 outgroup taxa, and used target enrichment to sequence thousands of ultraconserved element (UCE) loci, as well as mitochondrial DNA reconstructed from off-target reads, from each specimen to...

Systematics of a Neotropical clade of dead-leaf-foraging antwrens (Aves: Thamnophilidae; Epinecrophylla)

Oscar Johnson, Jeffrey T. Howard & Robb T. Brumfield
The stipple-throated antwrens of the genus Epinecrophylla (Aves: Thamnophilidae) are represented by eight species primarily found in the lowlands of the Amazon Basin and the Guiana Shield. The genus has a long and convoluted taxonomic history, with many attempts made to address the taxonomy and systematics of the group. Here we employ massively parallel sequencing of thousands of ultraconserved elements (UCEs) to provide both the most comprehensive subspecies-level phylogeny of Epinecrophylla antwrens and the first...

Divergence, gene flow, and speciation in eight lineages of trans-Beringian birds

Kevin Winker, Jessica McLaughlin, Travis Glenn & Brant Faircloth
Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans-Beringian distribution, where Asian and North American populations have likely been split and reunited through multiple Pleistocene glacial cycles. Our study transects the speciation process, including eight pairwise comparisons in three orders (ducks,...

Supplementary information for: Using networks to identify structure in phylogenetic tree sets

Jeremy Brown, Melissa Marchand, Wen Huang, Guifang Zhou, Genevieve Mount, Jeremy Ash, Kyle Gallivan & James Wilgenbusch
Modern phylogenomic studies produce large sets of trees that can represent variation in inferred phylogenies across genes, uncertainty in estimated phylogenies for a given gene, or both. Standard practice is to condense this variation down to a small set of point estimates or consensus trees in order to facilitate display and interpretation. However, doing so results in the loss of enormous amounts of information about the structure of the underlying tree set. Here, we propose...

Wing and bill measurements of Tyrannus round specimens identified to subspecies

Maggie MacPherson, Alejandro Jahn & Nicholas Mason
Morphology is closely linked to locomotion and diet in animals. In animals that undertake long-distance migrations, limb-morphology is under selection to maximize mobility and minimize energy expenditure. Migratory behaviors also interact with diet, such that migratory animals tend to be dietary generalists, while sedentary taxa tend to be dietary specialists. Despite a hypothesized link between migration status and morphology, phylogenetic comparative studies have yielded conflicting findings. We tested for evolutionary associations between migratory status and...

Phylogeny of Citharexyleae

Laura Frost, Nataly O'Leary, Laura Lagomarsino, David Tank & Richard Olmstead
As a family of Neotropical origin and primarily Neotropical distribution, the Verbenaceae are a good but understudied system with which to understand Neotropical evolution. Tribe Citharexyleae comprises three genera: Baillonia, Citharexylum—one of the largest genera in Verbenaceae—and Rehdera. A molecular phylogenetic approach was taken to resolve intergeneric relationships in Citharexyleae and infrageneric relationships in Citharexylum. The phylogeny is used to elucidate character evolution in a widespread, morphologically diverse Neotropical genus. Seven plastid regions, two nuclear...

Data from: A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia

Jonathan J. Fong, Jeremy M. Brown, Matthew K. Fujita & Bastien Boussau
In resolving the vertebrate tree of life, two fundamental questions remain: 1) what is the phylogenetic position of turtles within amniotes, and 2) what are the relationships between the three major lissamphibian (extant amphibian) groups? These relationships have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, and four proposed branching patterns within Lissamphibia. We compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa) to address these outstanding...

Data from: Explosive diversification of marine fishes at the Cretaceous-Paleogene boundary

Michael E. Alfaro, Brant C. Faircloth, Richard C. Harrington, Laurie Sorenson, Matt Friedman, Christine E. Thacker, Carl H. Oliveros, David Černý & Thomas J. Near
The Cretaceous–Palaeogene (K–Pg) mass extinction is linked to the rapid emergence of ecologically divergent higher taxa (for example, families and orders) across terrestrial vertebrates, but its impact on the diversification of marine vertebrates is less clear. Spiny-rayed fishes (Acanthomorpha) provide an ideal system for exploring the effects of the K–Pg on fish diversification, yet despite decades of morphological and molecular phylogenetic efforts, resolution of both early diverging lineages and enormously diverse subclades remains problematic. Recent...

Data from: A phylogenomic rodent tree reveals the repeated evolution of masseter architectures

Mark T. Swanson, Carl H. Oliveros & Jacob A. Esselstyn
Understanding the number of times a trait has evolved is a necessary foundation for comprehending its potential relationships with selective regimes, developmental constraints, and evolutionary diversification. Rodents make up over 40% extant of mammalian species and their ecological and evolutionary success has been partially attributed to the increase in biting efficiency that resulted from a forward shift of one or two portions of the masseter muscle from the zygomatic arch onto the rostrum. This forward...

A full-size fracture of tight sandstone induced by water, N2 and CO2

Bing Yang & Bin Wang
The tight sandstone samples collected from Yanchang oil field , China are used to conduct hydraulic fracturing experiment with fluid of water, N2 and CO2. These samples are scanned by Micro-CT scanning pre and post-hydraulic fracturing experiment. All of the images are obtained on the resolution ( voxel size ) of 53 μm under working voltage of 120 KV and current of 62.5 μA. After rock was scanned, the whole-size fracture can be extracted through...

Online Appendix: Stakeholder Engagement Strategies, National Institutions, and Firm Performance: A Configurational Perspective

Kamini Gupta, Donal Crilly & Thomas Greckhamer
Online Appendix for Stakeholder Engagement Strategies, National Institutions, and Firm Performance: A Configurational Perspective Authors: Gupta, Kamini; Crilly, Donal; Greckhamer, Thomas Request from Publisher (Wiley) to state the following for forthcoming publication in Strategic Management Journal

Data from: The evolutionary relationships and age of Homo naledi: an assessment using dated Bayesian phylogenetic methods

Mana Dembo, Davorka Radovčić, Heather M. Garvin, Myra F. Laird, Lauren Schroeder, Jill E. Scott, Juliet Brophy, Rebecca R. Ackermann, Charles M. Musiba, Darryl J. De Ruiter, Arne Ø. Mooers, Mark Collard & Chares M. Musiba
Homo naledi is a recently discovered species of fossil hominin from South Africa. A considerable amount is already known about H. naledi but some important questions remain unanswered. Here we report a study that addressed two of them: “Where does H. naledi fit in the hominin evolutionary tree?” and “How old is it?” We used a large supermatrix of craniodental characters for both early and late hominin species and Bayesian phylogenetic techniques to carry out...

Data from: Coordinated dispersal and pre-Isthmian assembly of the Central American ichthyofauna

Victor A. Tagliacollo, Scott M. Duke-Sylvester, Wilfredo A. Matamoros, Prosanta Chakrabarty & James S. Albert
We document patterns of coordinated dispersal over evolutionary time frames in heroine cichlids and poeciliine live-bearers, the two most species-rich clades of freshwater fishes in the Caribbean basin. Observed dispersal rate (DO) values were estimated from time-calibrated molecular phylogenies in Lagrange+, a modified version of the ML-based parametric biogeographic program Lagrange. DO is measured in units of ‘wallaces’ (wa) as the number of biogeographic range-expansion events per million years. DO estimates were generated on a...

Data from: Phylogeography and species delimitation in convict cichlids (Cichlidae: Amatitlania): implications for taxonomy and Plio–Pleistocene evolutionary history in Central America

Justin C. Bagley, Wilfredo A. Matamoros, Caleb D. McMahan, Michael Tobler, Prosanta Chakrabarty & Jerald B. Johnson
We investigate phylogeographic patterns and delimit species boundaries within Amatitlania, a genus of Central American cichlid fishes. Phylogenetic analyses of mitochondrial DNA sequences from 318 individuals spanning the geographical ranges of all three currently recognized Amatitlania species strongly supported one major clade, with a relatively diverged subclade corresponding to A. kanna samples from eastern Costa Rica and Panama. Gene trees and networks revealed marked incongruences between phylogeographic structure and morpho-species taxonomy as a result of...

Data from: Fragmentation of Atlantic Forest has not affected gene flow of a widespread seed-dispersing bat

Eve S. McCulloch, J. Sebastian Tello, Andrew Whitehead, Claudia M. J. Rolón-Mendoza, Mario C. D. Maldonado-Rodríguez & Richard D. Stevens
Habitat loss and resultant fragmentation are major threats to biodiversity, particularly in tropical and subtropical ecosystems. It is increasingly urgent to understand fragmentation effects, which are often complex and vary across taxa, time and space. We determined whether recent fragmentation of Atlantic forest is causing population subdivision in a widespread and important Neotropical seed-disperser: Artibeus lituratus (Chiroptera: Phyllostomidae). Genetic structure within highly fragmented forest in Paraguay was compared to that in mostly contiguous forest in...

Data from: Co-feeding intra- and interspecific transmission of an emerging insect-borne rickettsial pathogen

Lisa D. Brown, Rebecca C. Christofferson, Kaikhushroo H. Banajee, Fabio Del Piero, Lane D. Foil & Kevin R. Macaluso
Cat fleas (Ctenocephalides felis) are known as the primary vector and reservoir of Rickettsia felis, the causative agent of flea-borne spotted fever; however, field surveys regularly report molecular detection of this infectious agent from other blood-feeding arthropods. The presence of R. felis in additional arthropods may be the result of chance consumption of an infectious bloodmeal, but isolation of viable rickettsiae circulating in the blood of suspected vertebrate reservoirs has not been demonstrated. Successful transmission...

Data from: Differential introgression of a female competitive trait in a hybrid zone between sex-role reversed species

Sara E. Lipshutz, Joana I. Meier, Matthew J. Miller, Graham Derryberry, Ole Seehausen & Elizabeth Perrault Derryberry
Mating behavior between recently diverged species in secondary contact can impede or promote reproductive isolation. Traditionally, researchers focus on the importance of female mate choice and male-male competition in maintaining or eroding species barriers. Although female-female competition is widespread, little is known about its role in the speciation process. Here, we investigate a case of interspecific female competition and its influence on patterns of phenotypic and genetic introgression between species. We examine a hybrid zone...

Data from: Horizontal transmission of Rickettsia felis between cat fleas, Ctenocephalides felis

Supanee Hirunkanokpun, Chutima Thepparit, Lane D. Foil & Kevin R. Macaluso
Rickettsia felis is a rickettsial pathogen primarily associated with the cat flea, Ctenocephalides felis. Although laboratory studies have confirmed that R. felis is maintained by transstadial and transovarial transmission in C. felis, distinct mechanisms of horizontal transmission of R. felis among cat fleas is undefined. Based on the inefficient vertical transmission of R. felis by cat fleas and the detection of R. felis in a variety of hematophagous arthropods, we hypothesize that R. felis is...

Data from: Nuclear and mitochondrial sequence data reveal and conceal different demographic histories and population genetic processes in Caribbean reef fishes

Ron I Eytan & Michael E Hellberg
Mitochondrial and nuclear sequence data should recover historical demographic events at different temporal scales due to differences in their effective population sizes and substitution rates. This expectation was tested for two closely related coral reef fish, the tube blennies Acanthemblemaria aspera and A. spinosa. These two have similar life histories and dispersal potentials, and co-occur throughout the Caribbean. Sequence data for one mitochondrial and two nuclear markers were collected for 168 individuals across the species'...

Data from: Ectomycorrhizas and tree seedling establishment are strongly influenced by forest edge proximity but not soil inoculum

Sara Grove, Norah P. Saarman, Gregory S. Gilbert, Brant Faircloth, Karen A. Haubensak & Ingrid M. Parker
Reforestation is challenging when timber harvested areas have been degraded, invaded by non-native species, or are of marginal suitability to begin with. Conifers form mutualistic partnerships with ectomycorrhizal fungi (EMF) to obtain greater access to soil resources, and these partnerships may be especially important in degraded areas. However, timber harvest can impact mycorrhizal fungi by removing or compacting topsoil, removing host plants, and warming and drying the soil. We used a field experiment to evaluate...

Architecture of the bronchial tree in Cuvier’s dwarf caiman (Paleosuchus palpebrosus)

Emma Schachner, , Rob Coke, M Scott Echols, Michelle Osborn & Brandon Hedrick
We imaged the lungs of five Cuvier's dwarf caiman (Paleosuchus palpebrosus) via computed tomography (CT) and micro-computed tomography (μCT) and compared these data to the lungs of the American alligator (Alligator mississippiensis). These data demonstrate anatomical commonalities between the lungs of P. palpebrosus and A. mississippiensis, and a few notable differences. The structural similarities are (a) a proximally narrow, distally widened, hook-shaped primary bronchus; (b) a cervical ventral bronchus that branches of the primary bronchus...

Summarized voucher information on vertebrate genomes

Prosanta Chakrabarty, Janet Buckner & Brant Faircloth
A voucher is a permanently preserved specimen that is maintained in an accessible collection. In genomics, vouchers serve as the physical evidence for the taxonomic identification of genome assemblies. Unfortunately, the vast majority of vertebrate genomes stored in NCBI do not refer to voucher specimens. Here, we urge researchers generating new genome assemblies to deposit voucher specimens in accessible, permanent research collections, and to link these vouchers to publications, public databases, and repositories. We also...

Data from: Long-term change in the avifauna of undisturbed Amazonian rainforest: Ground-foraging birds disappear and the baseline shifts

Cameron Rutt, Philip Stouffer, Vitek Jirinec, Richard Bierregaard, Angélica Hernández-Palma, Erik Johnson, Stephen Midway, Luke Powell, Jared Wolfe & Thomas Lovejoy
How are rainforest birds faring in the Anthropocene? We use bird captures spanning >35 years from 55 sites within a vast area of intact Amazonian rainforest to reveal reduced abundance of terrestrial and near-ground insectivores in the absence of deforestation, edge effects, or other direct anthropogenic landscape change. Because undisturbed forest includes far fewer terrestrial and near-ground insectivores than it did historically, today’s fragments and second growth are more impoverished than shown by comparisons with...

Registration Year

  • 2022
    11
  • 2021
    19
  • 2020
    29
  • 2019
    16
  • 2018
    8
  • 2017
    1
  • 2016
    12
  • 2015
    7
  • 2014
    12
  • 2013
    1

Resource Types

  • Dataset
    132

Affiliations

  • Louisiana State University
    132
  • Louisiana State University of Alexandria
    17
  • University of Florida
    9
  • American Museum of Natural History
    8
  • University of Kansas
    7
  • University of California Los Angeles
    7
  • Louisiana State University Agricultural Center
    5
  • Field Museum of Natural History
    4
  • Yale University
    4
  • Michigan Technological University
    3