43 Works

Data from: Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing

Ya Yang, Michael J. Moore, Samuel F. Brockington, Douglas E. Soltis, Gane Ka-Shu Wong, Eric J. Carpenter, Yong Zhang, Li Chen, Zhixiang Yan, Yinlong Xie, Rowan F. Sage, Sarah Covshoff, Julian M. Hibberd, Matthew N. Nelson & Stephen A. Smith
Many phylogenomic studies based on transcriptomes have been limited to “single-copy” genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup...

Data from: Orchid phylogenomics and multiple drivers of their extraordinary diversification

Thomas J. Givnish, Daniel Spalink, Mercedes Ames, Stephanie P. Lyon, Steven J. Hunter, Alejandro Zuluaga, William J. D. Iles, Mark A. Clements, Mary T. K. Arroyo, James Leebens-Mack, Lorena Endara, Ricardo Kriebel, Kurt M. Neubig, W. Mark Whitten, Norris H. Williams & Kenneth M. Cameron
Orchids are the most diverse family of angiosperms, with over 25 000 species, more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here, we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. A supermatrix analysis places an additional 144...

Data from: Affinity for natal environments by dispersers impacts reproduction and explains geographic structure of a highly mobile bird

Robert J. Fletcher, Ellen P. Robertson, Rebecca C. Wilcox, Brian E. Reichert, Wiley M. Kitchens & James D. Austin
Understanding dispersal and habitat selection behaviours is central to many problems in ecology, evolution and conservation. One factor often hypothesized to influence habitat selection by dispersers is the natal environment experienced by juveniles. Nonetheless, evidence for the effect of natal environment on dispersing, wild vertebrates remains limited. Using 18 years of nesting and mark–resight data across an entire North American geographical range of an endangered bird, the snail kite (Rostrhamus sociabilis), we tested for natal...

Data from: Evolution and biogeography of the endemic Roucela complex (Campanulaceae: Campanula) in the eastern Mediterranean

Andrew A. Crowl, Clayton J. Visger, Guilhem Mansion, Ralf Hand, Hsin-Hui Wu, Georgia Kamari, Dimitrios Phitos & Nico Cellinese
At the intersection of geological activity, climatic fluctuations, and human pressure, the Mediterranean Basin – a hotspot of biodiversity – provides an ideal setting for studying endemism, evolution, and biogeography. Here, we focus on the Roucela complex (Campanula subgenus Roucela), a group of 13 bellflower species found primarily in the eastern Mediterranean Basin. Plastid and low-copy nuclear markers were employed to reconstruct evolutionary relationships and estimate divergence times within the Roucela complex using both concatenation...

Data from: Phylogeny of the island archipelago frog genus Sanguirana: another endemic Philippine radiation that diversified 'Out-of-Palawan'

Rafe M. Brown, Yong-Chao Su, Brenna Barger, Cameron D. Siler, Marites B. Sanguila, Arvin C. Diesmos & David C. Blackburn
Recent higher-level frog phylogenetic analyses have included a few members of the endemic Philippine frog genus Sanguirana. Although the monophyly of the group has never been disputed, the recent phylogenetically-supported inclusion of the Palawan Wood Frog (Sanguirana sanguinea) in this clade was highly unexpected. In addition, species boundaries and relationships remain unclear and new species continue to be discovered. We estimate the phylogeny for this endemic Philippine genus using two mitochondrial gene regions and six...

Data from: Differential responses of marine communities to natural and anthropogenic changes

Michal Kowalewski, Jacelyn M. Wittmer, Troy A. Dexter, Alessandro Amorosi & Daniele Scarponi
Responses of ecosystems to environmental changes vary greatly across habitats, organisms, and observational scales. The Quaternary fossil record of the Po Basin demonstrates that marine communities of Northern Adriatic reemerged unchanged following the most recent glaciation, which lasted ~100,000 years. The Late Pleistocene and Holocene interglacial ecosystems were both dominated by the same species, species turnover rates approximated predictions of resampling models of a homogenous system, and comparable bathymetric gradients in species composition, sample-level diversity,...

Data from: Rapid diversification associated with ecological specialization in Neotropical Adelpha butterflies

Emily R. Ebel, Jeffrey M. DaCosta, Michael D. Sorenson, Ryan I. Hill, Adriana D. Briscoe, Keith R. Willmott & Sean P. Mullen
Rapid diversification is often associated with morphological or ecological adaptations that allow organisms to radiate into novel niches. Neotropical Adelpha butterflies, which comprise over 200 species and subspecies, are characterized by extraordinary breadth in host plant use and wing colour patterns compared to their closest relatives. To examine the relationship between phenotypic and species diversification, we reconstructed the phylogenetic history of Adelpha and its temperate sister genus Limenitis using genomewide restriction-site-associated DNA (RAD) sequencing. Despite...

Data from: Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies

Andrew G. Gardner, Emily B. Sessa, Pryce Michener, Eden Johnson, Kelly A. Shepherd, Dianella G. Howarth & Rachel S. Jabaily
Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major...

Data from: The influence of host plant extrafloral nectaries on multitrophic interactions: an experimental investigation

Suzanne Koptur, Ian M. Jones & Jorge E. Peña
A field experiment was conducted with outplantings of the native perennial shrub Senna mexicana var. chapmanii in a semi-natural area adjacent to native pine rockland habitat in southern Florida. The presence of ants and the availability of extrafloral nectar were manipulated in a stratified random design. Insect communities were monitored and recorded over a period of six months with a view to addressing three main questions. Do ants provide biotic defense against key herbivores on...

Data from: Character evolution and the origin of Caimaninae (Crocodylia) in the New World Tropics: new evidence from the Miocene of Panama and Venezuela

Alexander K. Hastings, Moritz Reisser & Torsten M. Scheyer
Alligators and caimans share a close relationship, supported by both molecular and morphological characters. The divergence between alligators and caimans has been difficult to discern in the fossil record. Two basal taxa have recently been described from the Miocene of Panama and Venezuela but have not yet been presented in a joint phylogeny. Continued preparation of the type material of the Venezuelan Globidentosuchus brachyrostris Scheyer et al., 2013 has revealed new characters for scoring in...

Data from: Assessing reproductive behavior important to fisheries management: a case study with red drum, Sciaenops ocellatus

Susan K. Lowerre-Barbieri, Sarah Lyle Walters Burnsed & Joel William Bickford
Spawning site selection and reproductive timing affect stock productivity and structure in marine fishes but are poorly understood. Traditionally, stock assessments measure reproductive potential as spawning stock biomass or egg production and do not include other aspects of reproductive behavior. Red drum make an excellent case study to assess these other aspects, as (1) they are highly fecund, pelagic spawners, like most exploited marine fishes; (2) their life cycle is delineated between nursery (estuarine) and...

Data from: Resolving basal lamiid phylogeny and the circumscription of Icacinaceae with a plastome-scale data set

Gregory W. Stull, Rodrigo Duno De Stefano, Douglas E. Soltis & Pamela S. Soltis
PREMISE OF THE STUDY: Major relationships within Lamiidae, an asterid clade with ∼40000 species, have largely eluded resolution despite two decades of intensive study. The phylogenetic positions of Icacinaceae and other early-diverging lamiid clades (Garryales, Metteniusaceae, and Oncothecaceae) have been particularly problematic, hindering classification and impeding our understanding of early lamiid (and euasterid) character evolution. METHODS: To resolve basal lamiid phylogeny, we sequenced 50 plastid genomes using the Illumina sequencing platform and combined these with...

Data from: Comparing process-based and constraint-based approaches for modeling macroecological patterns

Xiao Xiao, James P. O'Dwyer & Ethan P. White
Ecological patterns arise from the interplay of many different processes, and yet the emergence of consistent phenomena across a diverse range of ecological systems suggests that many patterns may in part be determined by statistical or numerical constraints. Differentiating the extent to which patterns in a given system are determined statistically, and where it requires explicit ecological processes, has been difficult. We tackled this challenge by directly comparing models from a constraint-based theory, the Maximum...

Data from: Moth tails divert bat attack: evolution of acoustic deflection

Jesse R. Barber, Brian C. Leavell, Adam L. Keener, Jesse W. Breinholt, Brad A. Chadwell, Christopher J.W. McClure, Geena M. Hill & Akito Y. Kawahara
Adaptations to divert the attacks of visually guided predators have evolved repeatedly in animals. Using high-speed infrared videography, we show that luna moths (Actias luna) generate an acoustic diversion with spinning hindwing tails to deflect echolocating bat attacks away from their body and toward these nonessential appendages. We pit luna moths against big brown bats (Eptesicus fuscus) and demonstrate a survival advantage of ∼47% for moths with tails versus those that had their tails removed....

Data from: Raccoon contact networks predict seasonal susceptibility to rabies outbreaks and limitations of vaccination

Jennifer J. H. Reynolds, Ben T. Hirsch, Stanley D. Gehrt & Meggan E. Craft
1. Infectious disease transmission often depends on the contact structure of host populations. Although it is often challenging to capture the contact structure in wild animals, new technology has enabled biologists to obtain detailed temporal information on wildlife social contacts. In this study, we investigated the effects of raccoon contact patterns on rabies spread using network modelling. 2. Raccoons (Procyon lotor) play an important role in the maintenance of rabies in the United States. It...

Data from: Regional variation in Caribbean dry forest tree species composition

Janet Franklin, Julie Ripplinger, Ethan H. Freid, Humfredo Marcano-Vega & David W. Steadman
How does tree species composition vary in relation to geographical and environmental gradients in a globally rare tropical/subtropical broadleaf dry forest community in the Caribbean? We analyzed data from 153 Forest Inventory and Analysis (FIA) plots from Puerto Rico and the U.S. Virgin Islands (USVI), along with 42 plots that we sampled in the Bahamian Archipelago (on Abaco and Eleuthera Islands). FIA data were collected using published protocols. In the Bahamian Archipelago, we recorded terrain...

Data from: New mud turtles (Kinosternidae, Kinosternon) from the Middle-Late Miocene of the United States

Jason R. Bourque
Kinosternon Spix, 1824, was widespread in xeric to savanna associated paleowetlands across North America during the middle–late Miocene and steadily diversified following its first occurrences in the Hemingfordian. In the middle Miocene, Kinosternon rincon n. sp. occurred in the late Barstovian Cerro Conejo Formation of north central New Mexico, perhaps concurrently with Kinosternon pojoaque Bourque 2012a from the Tesuque Formation. Subsequent late Miocene kinosternine fossils indicate that at least three potentially contemporaneous species existed throughout...

Data from: Tempo and mode of antibat ultrasound production and sonar jamming in the diverse hawkmoth radiation

Akito Y. Kawahara & Jesse R. Barber
The bat–moth arms race has existed for over 60 million y, with moths evolving ultrasonically sensitive ears and ultrasound-producing organs to combat bat predation. The evolution of these defenses has never been thoroughly examined because of limitations in simultaneously conducting behavioral and phylogenetic analyses across an entire group. Hawkmoths include >1,500 species worldwide, some of which produce ultrasound using genital stridulatory structures. However, the function and evolution of this behavior remain largely unknown. We built...

Data from: Conservation under uncertainty: optimal network protection strategies for worst-case disturbance events

Miguel A. Acevedo, Jorge A. Sefair, J. Cole Smith, , Brian Reichert & Robert J. Fletcher
1. Conservation goals are ideally set after a thorough understanding of potential threats; however, predicting future spatial patterns of threats, such as disturbance, remains challenging. Here, we develop a novel extension of network fortification-interdiction models (NFIM) that deals with uncertainty in future spatial patterns of disturbance by optimally selecting sites that will best mitigate a worst-case scenario for a given magnitude of disturbance. 2. This approach uses information on between-patch movement probabilities and patch-specific survival,...

Data from: Evaluation of Blue Crab, Callinectes sapidus, megalopal settlement and condition during the Deepwater Horizon oil spill

Erin K. Grey, Susan C. Chiasson, Hannah G. Williams, Victoria J. Troeger & Caz M. Taylor
The Blue Crab, Callinectes sapidus, is a commercially, culturally, and ecologically significant species in the Gulf of Mexico (GOM), whose offshore stages were likely impacted by the Deepwater Horizon oil spill (DWH). To test for DWH effects and to better understand the planktonic ecology of this species, we monitored Callinectes spp. megalopal settlement and condition at sites within and outside of the spill extent during and one year after the DWH. We tested for DWH...

Data from: Inferring speciation history in the Andes with reduced-representation sequence data: an example in the bay-backed antpittas (Aves; Grallariidae; Grallaria hypoleuca s. l.)

Benjamin M. Winger, Peter A. Hosner, Gustavo A. Bravo, Andrés M. Cuervo, Natalia Aristizábal, Luis E. Cueto & John M. Bates
In the Andes, humid-forest organisms frequently exhibit pronounced genetic structure and geographic variation in phenotype, often coincident with physical barriers to dispersal. However, phylogenetic relationships of clades have often been difficult to resolve due to short internodes. Consequently, even in taxa with well-defined genetic structure, the temporal and geographic sequences of dispersal and vicariance events that led to this differentiation have remained opaque, hindering efforts to test the association between diversification and earth history and...

Data from: The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms

George Paul Tiley & J. Gordon Burleigh
Background: Although homologous recombination affects the efficacy of selection in populations, the pattern of recombination rate evolution and its effects on genome evolution across plants are largely unknown. Recombination can reduce genome size by enabling the removal of LTR retrotransposons, alter codon usage by GC biased gene conversion, contribute to complex histories of gene duplication and loss through tandem duplication, and enhance purifying selection on genes. Therefore, variation in recombination rate across species may explain...

Data from: Contact zone dynamics during early stages of speciation in a chorus frog (Pseudacris crucifer)

Kathryn A. Stewart, James D. Austin, Kelly R. Zamudio & Stephen C. Lougheed
Characterizing the genetic and behavioural consequences of contact between previously geographically isolated lineages provides insights into the mechanisms underlying diversification and ultimately speciation. The spring peeper (Pseudacris crucifer) is a widespread Nearctic chorus frog with six divergent mitochondrial DNA (mtDNA) lineages, many of which came into secondary contact during the Holocene. We examined genetics, morphology, advertisement calls and female preference for two lineages that began diverging in allopatry in the Pliocene and now overlap in...

Data from: Historical climatic variability and geographical barriers as drivers of community composition in a biodiversity hotspot

Jessica A. Oswald, J. Gordon Burleigh, David W. Steadman, Scott K. Robinson & Andrew W. Kratter
Aim: To evaluate the roles of Quaternary (< 2.6 Ma) climatic stability and geologic barriers (i.e. the Andes Mountains) in shaping the modern community composition and patterns of endemism in Neotropical dry forest bird communities. Location: Marañón Valley and Tumbes, north-western Peru. Methods: We recorded presence and abundance of species in six dry forest bird communities on either side of the Andes Mountains. We used the data to calculate the beta diversity and phylogenetic beta...

Data from: Inhibition of BTK and ITK with ibrutinib is effective in the prevention of chronic graft-versus-host disease in mice

Steven D. Schutt, Jianing Fu, Hung Nguyen, David Bastian, Jessica Heinrichs, Yongxia Wu, Chen Liu, Daniel G. McDonald, Joseph Pidala & Xue-Zhong Yu
Bruton’s Tyrosine Kinase (BTK) and IL-2 Inducible T-cell Kinase (ITK) are enzymes responsible for the phosphorylation and activation of downstream effectors in the B-cell receptor (BCR) signaling and T cell receptor (TCR) signaling pathways, respectively. Ibrutinib is an FDA-approved potent inhibitor of both BTK and ITK that impairs B-cell and T-cell function. CD4 T cells and B cells are essential for the induction of chronic graft-versus-host disease (cGVHD). We evaluated these targets by testing the...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of Florida
  • University of Kansas
  • Field Museum of Natural History
  • University of Alberta
  • Utah State University
  • Princeton University
  • University of Michigan-Ann Arbor
  • Duke University
  • University of Wyoming
  • University of California, Berkeley