19 Works

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...

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...

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...

Extended data for: Screening for antifolate and artemisinin resistance in Plasmodium falciparum clinical isolates from three hospitals of Eritrea

Harriet Mukhongo Natabona, Johnson Kinyua Kang'ethe, Yishak Gebrekidan Weldemichael & Remmy Kasili Wekesa
Background: Antimalarial drug resistance is a major challenge hampering malaria control and elimination. Plasmodium falciparum, the leading causative parasite species, has developed resistance to basically all antimalarials. Continued surveillance of drug resistance using genetic markers provides important molecular data for treatment policies. This study sought to verify the genetic mechanism of resistance to sulfadoxine-pyrimethamine and assess the occurrence of point mutations associated with artemisinin resistance in P. falciparum clinical isolates from Eritrea. Methods: Nineteen dried...

Limited plasticity in thermally tolerant ectotherm populations: evidence for a trade-off

Jordanna Barley, Brian S. Cheng, Matthew Sasaki, Sarah Gignoux-Wolfsohn, Cynthia G. Hays, Alysha B. Putnam, Seema Sheth, Andrew Villeneuve, Morgan Kelly, Jordanna M. Barley & Andrew R. Villeneuve
Many species face extinction risks owing to climate change, and there is an urgent need to identify which species' populations will be most vulnerable. Plasticity in heat tolerance, which includes acclimation or hardening, occurs when prior exposure to a warmer temperature changes an organism's upper thermal limit. The capacity for thermal acclimation could provide protection against warming, but prior work has found few generalizable patterns to explain variation in this trait. Here, we report the...

A supergene underlies linked variation in color and morphology in a Holarctic songbird

Erik Funk, Nicholas Mason, Snæbjörn Pálsson, Tomáš Albrecht, Jeff Johnson & Scott Taylor
The genetic architecture of a phenotype can have considerable effects on the evolution of a trait or species. Characterizing genetic architecture provides insight into the complexity of a given phenotype and, potentially, the role of the phenotype in evolutionary processes like speciation. We use genome sequences to investigate the genetic basis of phenotypic variation in redpoll finches (Acanthis spp.). We demonstrate that variation in redpoll phenotype is broadly controlled by a ~55-Mb chromosomal inversion. Within...

Brown-throated parakeet vocalization data

Jessica Eberhard, Irene Zager, Jose Ferrer-Paris & Kathryn Rodriguez-Clark
Learned vocalizations play a key role in parrot social dynamics and vocal dialects have been documented for several mainland species, but to date no studies of geographically structured call variation in parrot species have examined the role of isolation on islands. In a study of the Brown-throated Parakeet (Eupsittula pertinax), which inhabits five small Caribbean islands as well as the adjacent mainland, we found that the contact calls of island and mainland parakeets show divergence...

Comparing ultraconserved elements and exons for phylogenomic analyses of Middle American cichlids: When data agree to disagree

Fernando Alda, William B. Ludt, Diego J. Elías, Caleb D. McMahan & Prosanta Chakrabarty
Choosing among types of genomic markers to be used in a phylogenomic study can have a major influence on the cost, design, and results of a study. Yet few attempts have been made to compare categories of next-generation sequence markers limiting our ability to compare the suitability of these different genomic fragment types. Here we explore properties of different genomic markers to find if they vary in the accuracy of component phylogenetic trees and to...

Data for: Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi

Gustavo Bravo, Bret Whitney, Ricardo Belmonte-Lopes, Marcos Bornschein, Natalia Aristizabal, Renata Beco, Jaqueline Battilana, Luciano Naka, Alexandre Aleixo, Marcio Pie, Luis Silveira, Elizabeth Derryberry & Robb Brumfield
The family Thamnophilidae is a species-rich Neotropical radiation of passerine birds. Current classification of its 235 species is mostly based on morphological similarities, but recent studies integrating comprehensive phenotypic and phylogenetic data have redefined taxonomic limits of several taxa. Here, we assess generic relationships of Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus using DNA sequences from the mitochondrion, nuclear exons, and ultraconserved elements (UCEs), with further attention to interspecific relationships within Herpsilochmus. We show that Herpsilochmus...

Transgenerational plasticity and the capacity to adapt to low salinity in the eastern oyster, Crassostrea virginica

Joanna Griffiths, Kevin Johnson, Kyle Sirovy, Mark Yeats, Francis Pan, Jerome La Peyre & Morgan Kelly
Salinity conditions in oyster breeding grounds in the Gulf of Mexico are expected to drastically change due to increased precipitation from climate change and anthropogenic changes to local hydrology. We determined the capacity of the eastern oyster, Crassostrea virginica, to adapt via standing genetic variation or acclimate through transgenerational plasticity. We outplanted oysters to either a low or medium salinity site in Louisiana for two years. We then crossed adult parents using a North Carolina...

Morphological consequences of climate change for resident birds in intact Amazonian rainforest

Vitek Jirinec & Philip Stouffer
First, this dataset contains morphological measurements (body mass, wing length) of birds from the Biological Dynamics of Forest Fragments Project (BDFFP), located in central Amazonia. Birds were captured using mist-nets between 1979 and 2019 in the understory of primary forest spanning ~40 km. Second, we have included climate data (precipitation, temperature) associated with this study area derived from the global EU Copernicus ERA5 climate reanalysis (https://cds.climate.copernicus.eu).

Cave-adapted evolution in the North American Amblyopsid fishes inferred using phylogenomics and geometric morphometrics

Pamela Hart, Matthew Niemiller, Edward Burress, Jonathan Armbruster, William Ludt & Prosanta Chakrabarty
Cave adaptation has evolved repeatedly across the Tree of Life, famously leading to pigmentation and eye degeneration and loss, yet its macroevolutionary implications remain poorly understood. We use the North American amblyopsid fishes, a family spanning a wide degree of cave adaptation, to examine the impact of cave specialization on the modes and tempo of evolution. We reconstruct evolutionary relationships using ultraconserved element loci, estimate the ancestral histories of eye-state, and examine the impact of...

Data from: Combining transcriptomics and physiology to characterize plastic and evolved responses of Crassostrea virginica reared in common garden at two estuaries in the northern Gulf of Mexico

Kyle Sirovy, Kevin Johnson, Sandra Casas, Jerome La Peyre & Morgan Kelly
Eastern oysters in the northern Gulf of Mexico are facing rapid environmental changes and can respond to this change via plasticity or evolution. Plasticity can act as an immediate buffer against environmental change, but by buffering the effects of selection it could impact the organism’s ability to evolve in subsequent generations. While plasticity and evolution are not mutually exclusive, the relative contribution and interaction between them remains unclear. In this study, we investigate the roles...

Light and thermal niches of ground-foraging Amazonian insectivorous birds

Vitek Jirinec, Patricia Rodrigues, Bruna Amaral & Philip Stouffer
Insectivores of the tropical rainforest floor are consistently among the most vulnerable birds to forest clearing and fragmentation. Several hypotheses attempt to explain this pattern, including sensitivity to extreme microclimates found near forest borders—particularly brighter and warmer conditions. Importantly, this “microclimate hypothesis” has additional implications for intact forest under global climate change that could be evaluated through direct assessment of the light and temperature environment of terrestrial insectivores. In this study, we harness novel technology...

Bill size, bill shape, and body size constrain bird song evolution on a macroevolutionary scale

Amelia-Juliette Demery, Kevin Burns & Nicholas Mason
Studying macroevolutionary patterns of phenotypic variation and their driving forces in large radiations can shed light on how biodiversity is generated across broad spatiotemporal scales. In this study, we integrated song and morphological variation across more than 300 species representing the largest family of songbirds, the tanagers (Thraupidae), to uncover how morphological variables of the vocal tract combine to shape vocal evolution on a macroevolutionary scale. We found that body size correlated with multiple frequency...

Data from: Accelerated diversification explains the exceptional species richness of tropical characoid fishes

Bruno Melo, Brian Sidlauskas, Thomas Near, Fabio Roxo, Ava Ghezelayagh, Luz Ochoa, Melanie Stiassny, Jairo Arroyave, Jonathan Chang, Brant Faircloth, Daniel MacGuigan, Richard Harrington, Ricardo Benine, Michael Burns, Kendra Hoekzema, Natalia Sanches, Javier Maldonado-Ocampo, Ricardo Castro, Fausto Foresti, Michael Alfaro & Claudio Oliveira
The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1288 ultraconserved element loci spanning 293 species, 211...

Data from: Disturbed Amazonian forests support diminished breeding bird communities

Cameron Rutt, Michael Kaller & Philip Stouffer
Twenty percent of the Brazilian Amazon has now been deforested, and deforestation rates are increasing. This compels us to evaluate the conservation potential of human-modified landscapes, yet the ecological value of regenerating and fragmented Amazonian forests remains poorly understood. To date, most faunal studies in disturbed forests have examined metrics derived from presence or abundance. Although valuable, these data cannot tell us how old-growth species are using disturbed forests. In this study, we complement presence...

Body size, trophic position, and the coupling of different energy pathways across a saltmarsh landscape

Friedrich Keppeler, Jill Olin, Paola López-Duarte, Michael Polito, Linda Hooper-Bùi, Sabrina Taylor, Nancy Rabalais, F Joel Fodrie, Brian Roberts, R Eugene Turner, Charles Martin & Olaf Jensen
Here, we listed the bulk stable isotope values (δ13C and δ15N) and body size measurements of organisms that were analyzed in the manuscript "Body size, trophic position, and the coupling of different energy pathways across a saltmarsh landscape", published in Limnology and Oceanography Letters. Our dataset is a compilation of samplings obtained by the Southern Louisiana marsh food webs project within the Coastal Waters Consortium (CWC) II (Lopez-Duarte et al. 2017a [https://doi.org/10.7266/N7XS5SGD], Lopez-Duarte et al....

No Escape: The Influence of Substrate Sodium on Plant Growth and Tissue Sodium Responses

Luis Santiago-Rosario, Kyle Harms, Bret Elderd, Pamela Hart & Maheshi Dassanayake
This dataset contains data from a systematic review carried out to understand substrate sodium's influence on plant growth and sodium accumulation strategies. Accordingly, we carried out a systematic review of plants’ responses to variation in substrate sodium concentrations. We compared biomass and tissue-sodium accumulation among 107 cultivars or populations (67 species in 20 plant families), broadly expanding beyond the agricultural and model taxa for which several generalizations previously had been made. We hypothesized a priori...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Louisiana State University
  • Sao Paulo State University
  • Natural History Museum of Los Angeles County
  • University of Sao Paulo
  • Cornell University
  • University of California, Davis
  • California Polytechnic State University
  • Michigan Technological University
  • University of Massachusetts Amherst
  • University of Washington