29 Works

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,...

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...

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...

Data from: Intraspecific and biogeographic variation in foliar fungal communities and pathogen damage of native and invasive Phragmites australis

Warwick Allen, Aaron DeVries, Nicholas Bologna, Wesley Bickford, Kurt Kowalski, Laura Meyerson & James Cronin
Aim Recent research has highlighted that the relationship between species interactions and latitude can differ between native and invasive plant taxa, generating biogeographical heterogeneity in community resistance to plant invasions. In the first study with foliar pathogens, we tested whether co-occurring native and invasive lineages of common reed (Phragmites australis) exhibit nonparallel latitudinal gradients in foliar fungi communities, pathogen susceptibility and damage, and whether these biogeographic patterns can influence invasion success. Location North America. Time...

Habitat suitability modeling to predict the spatial distribution of cold-water coral communities affected by the Deepwater Horizon oil spill

Samuel Georgian, Kody Kramer, Miles Saunders, William Shedd, Harry Roberts, Christopher Lewis, Chuck Fisher & Erik Cordes
Aim: The Deepwater Horizon disaster resulted in the largest accidental marine oil spill in history and caused extensive injury to deep-sea habitats, including cold-water coral communities dominated by Paramuricea species. One of the primary difficulties in assessing the full extent of the injury to cold-water coral ecosystems is the extreme paucity of observational data and the subsequent lack of knowledge of their distribution within the affected region. The aim of this study was to use...

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

Sarah Hird, Darien Capunitan, Oscar Johnson & Ryan Terrill
How the microbiome interacts with hosts across evolutionary time is poorly understood. To address this question, datasets comprised of many host species are required to conduct comparative analyses. Here, we have analyzed 142 intestinal microbiome samples from 92 birds belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene. Using four definitions for microbial taxonomic units (97%OTU, 99%OTU, 99%OTU with singletons removed, ASV), we conducted alpha and beta diversity analyses and used phylogenetic...

Morphological, molecular, and biogeographic evidence for specific recognition of Euthamia hirtipes and Euthamia scabra (Asteraceae, Astereae)

Marisa Szubryt, Lowell Urbatsch, Yalma Vargas-Rodriguez, David Barfknecht & Kurt Neubig
The number and identity of species in the North American genus Euthamia (Asteraceae, Astereae) have varied considerably among taxonomic treatments. Euthamia graminifolia (L.) Nutt. is often treated to broadly include plants from the northern and eastern United States and Canada, including the Atlantic and Gulf Coasts. Broad-leaved, largely glabrous plants from New Jersey to the Florida Panhandle have been inconsistently treated as E. graminifolia, E. graminifolia var. hirtipes (Fernald) C.E.S. Taylor & R.J. Taylor E....

Testing for adaptive radiation: a new approach applied to Madagascar frogs

Daniel Moen, Rojo Ravelojaona, Carl Hutter & John Wiens
Adaptive radiation is a key topic at the intersection of ecology and evolutionary biology. Yet the definition and identification of adaptive radiation both remain contentious. Here, we introduce a new approach for identifying adaptive radiations which combines key aspects of two widely used definitions. Our approach compares evolutionary rates in morphology, performance, and diversification between the candidate radiation and other clades. We then apply this approach to a putative adaptive radiation of frogs from Madagascar...

Bergmann's rule is followed at multiple stages of post-embryonic development in a long-distance migratory songbird

Joseph Youtz, Kelly Miller, Emerson Bowers, Samantha Rogers, Lesley Bulluck, Matthew Johnson, Brian Peer, Katie Percy, Erik Johnson, Elizabeth Ames, Christopher Tonra & Than Boves
Aim: We assessed the presence of Bergmann’s rule in a model migratory species across all life stages on their breeding grounds. We then compared historic and contemporary egg sizes to understand if the biogeographic patterns during this developmental life stage have changed over time. Location: Eastern North America. Time period: 1865 to 2019. Major taxa: Prothonotary warbler, Protonotaria citrea Methods: We measured the size of eggs, young and old nestlings, and adults (of two age...

Comparative population genetics of the federally endangered Relict Darter, and its sister taxon the Clarks Darter (Teleostei: Percidae)

Jerry Kattawar & Kyle Piller
The southeastern United States harbors one of the most diverse temperate freshwater fish faunas of the world. Unfortunately, due to improper land use practices and habitat degradation, many of the species in this region are imperiled and may become extinct without appropriate conservation efforts. This study examined the population dynamics of an endangered endemic darter of southwest Kentucky, the Relict Darter (Etheostoma chienense) and its sister taxon, the undescribed Clarks Darter (Etheostoma cf. oophylax). Mitochondrial...

Testing the simple and complex versions of Gloger’s rule in the Variable Antshrike (Thamnophilus caerulescens, Thamnophilidae)

Rafael Marcondes
Gloger’s rule is a classic ecogeographical principle that, in its simplest version, predicts animals should be darker in warmer and wetter climates. In a rarely-tested more complex version, it also predicts animals should be more rufous in warmer and drier climates. The Variable Antshrike is a widely-distributed South American passerine that presents an impressive amount of plumage color variation and occupies a wide variety of climatic conditions. Moreover, genetic and vocal evidence indicate ongoing hybridization...

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...

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

Target-capture phylogenomics provide insights on gene and species tree discordances in Old World Treefrogs (Anura: Rhacophoridae)

Kin Onn Chan, Carl Hutter, Perry Wood, Lee Grismer & Rafe Brown
Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to utilize traditional methods such as bootstrapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore, relatively little attention is given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets...

Metapopulation dynamics and foraging plasticity in a highly vagile seabird, the southern rockhopper penguin

Nicolas Lois, Leonardo Campagna, Ulises Balza, Michael Polito, Klemens Pütz, Juliana Vianna, Annick Morgenthaler, Esteban Frere, Ricardo Saenz-Samaniego, Andrea Raya Rey & Bettina Mahler
Population connectivity is driven by individual dispersal potential and modulated by natal philopatry. In seabirds, high vagility facilitates dispersal yet philopatry is also common, with foraging area overlap often correlated with population connectivity. We assess the interplay between these processes by studying past and current connectivity and foraging niche overlap among southern rockhopper penguin colonies of the coast of southern South America using genomic and stable isotope analyses. We found two distinct genetic clusters and...

Toxin or medication? Immunotherapeutic effects of nicotine on a specialist caterpillar

Michael Garvey, Justin Bredlau, Karen Kester, Curtis Creighton & Ian Kaplan
1. A core tenant in the field of ecological immunology is that immune responses trade off with other physiological functions due to resource-allocation costs. Caterpillars, for example, tend to exhibit reduced immune responses when reared on more toxic food plants due to a cost from detoxifying or sequestering secondary metabolites, also known as the “vulnerable host hypothesis”. However, support for this hypothesis is mixed, and studies have not yet mechanistically isolated the relative contributions of...

Data from: The role of functional strategies in global plant distribution

Huixuan Liao, Daijiang Li, Ting Zhou, Bei Huang, Haijie Zhang, Baoming Chen & Shaolin Peng
Understanding the determinants of species distributions is a central topic in ecology. Competition, stress tolerance and colonization, respectively represented by Grime’s competitor (C), stress-tolerator (S) and ruderal (R) schemes, are three important functions that interactively influence plant distributions. In this study, we compiled a dataset of 2645 vascular plant species to explore the roles of the CSR strategies in global plant distribution. We analyzed the associations between the CSR scores and species range size with...

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...

Proximity to oil wells in North Dakota does not impact nest success of ducks but lowers nest densities

Kevin Ringelman, Cassandra Skaggs, Charles Loesch, Michael Szymanski, Frank Rohwer & Kaylan Kemink
Over the past decade, the United States has seen a rapid increase in oil and gas extraction from areas where resources were previously thought to be unrecoverable, particularly the Bakken shale formation in North Dakota. The Bakken overlaps with the Prairie Pothole Region, the most critical habitat in North America for breeding ducks, where oil and gas extraction through hydraulic fracturing has the potential to impact more than a million duck pairs in the United...

The bivalve shell biomineralization toolbox: bulging, not barren

Mark Duhon & Michael Hellberg
Bivalve molluscs synthesize remarkably complex shells from calcium carbonate and an organic matrix of proteins secreted from the dorsal edge of the mantle. Molecular analyses of shell matrix proteins (SMPs) have suggested high rates of gene turnover despite the conserved nature of the shell itself. Here, we used proteomic and transcriptomic data to identify the SMPs and other biomineralization proteins from seven bivalve species that diverged 3-513 Mya. Contrary to previous studies that identified only...

Data from: Lineage and latitudinal variation in Phragmites australis tolerance to herbivory: implications for invasion success

Jordan Croy, Laura Meyerson, Warwick Allen, Ganesh Bhattarai & James T. Cronin
Herbivores play a critical role in plant invasions either by facilitating or inhibiting species establishment and spread. However, relatively few studies with invasive plant species have focused on the role of plant tolerance and how it varies geographically to influence invasion success. We conducted a common garden study using two lineages (native and invasive) of the grass Phragmites australis that are prevalent in North American wetlands. Using 31 populations collected across a broad geographic range,...

A genome-wide association study of deafness in three canine breeds

Jessica Hayward, Maria Kelly-Smith, Adam Boyko, Louise Burmeister, Luisa De Risio, Cathryn Mellersh, Julia Freeman & George Strain
Congenital deafness in the domestic dog is usually related to the presence of white pigmentation, which is controlled primarily by the piebald locus on chromosome 20 and also by merle on chromosome 10. Pigment-associated deafness is also seen in other species, including cats, mice, sheep, alpacas, horses, cows, pigs, and humans, but the genetic factors determining why some piebald or merle dogs develop deafness while others do not have yet to be determined. Here we...

Data from: Seasonal dynamics of flock interaction networks across a human-modified landscape in lowland Amazonian rainforest

Cameron Rutt & Philip Stouffer
Although lowland tropical rainforests were once widely believed to be the archetype of stability, seasonal variation exists. In these environments, seasonality is defined by rainfall, leading to a predictable pattern of biotic and abiotic changes. Only the full annual cycle reveals niche breadth, yet most studies of tropical organisms ignore seasonality, thereby underestimating realized conditions. If human-modified habitats display more seasonal stress than intact habitats, then ignoring seasonality will have particularly important repercussions for conservation....

Rethinking Gloger’s Rule: climate, light environments and color in a large family of tropical birds (Furnariidae)

Rafael S. Marcondes, Jonathan A. Nations, Glenn F. Seeholzer & Robb T. Brumfield
Ecogeographic rules provide a framework within which to test evolutionary hypotheses of adaptation. Gloger’s rule predicts endothermic animals should have darker colors in warm and rainy climates. This rule also predicts animals should be redder in warm and dry climates, the so-called “complex Gloger’s rule.” Empirical studies frequently demonstrate that animals are darker in cool and wet rather than warm and wet climates. Further, sensory ecology predicts that, to enhance crypsis, animals should be darker...

Registration Year

  • 2020

Resource Types

  • Dataset


  • Louisiana State University
  • University of Minnesota
  • University of Rhode Island
  • National Institute of Amazonian Research
  • Virginia Commonwealth University
  • University of Canterbury
  • Cornell University
  • London Business School
  • University of Kansas
  • Michigan Technological University