133 Works

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...

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...

Data from: Range-wide population genetic analysis of Seaside Sparrows (Ammospiza maritima) supports at least five distinct population segments that do not align with current subspecies descriptions

Amie Settlecowski, Kathryn Davis, Mackenzie Roeder, Carolyn Enloe, Thomas Virzi, Margaret Hunter, Stefan Woltmann & Sabrina Taylor
As an obligate salt marsh species, Seaside Sparrows (Ammospiza maritima) are vulnerable to numerous threats including climate change, coastal erosion, sea level rise, and both natural and anthropogenic disasters. Of the nine recognized subspecies, two are extinct and one is endangered. Previous genetic analyses of mitochondrial DNA (mtDNA) and microsatellite loci showed that current taxonomy does not accurately reflect underlying genetic diversity, with possible consequences for the distribution of conservation resources. To further inform Seaside...

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...

Data from: Incubation recess behaviors influence nest survival of Wild Turkeys

Bret Collier, Nicholas Bakner, Landon Schofield, Cody Cedotal & Michael Chamberlain
In ground nesting upland birds, reproductive activities contribute to elevated predation risk, so females presumably use multiple strategies to ensure nest success. Identification of drivers reducing predation risk have primarily focused on evaluating vegetative conditions at nest sites, but behavioral decisions manifested through movements during incubation may be additional drivers of nest survival. However, our understanding of how movements during incubation impact nest survival is limited for most ground nesting birds. Using GPS data collected...

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...

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...

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...

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 new phylogeny of Rumex (Polygonaceae) adds evolutionary context to the diversity of reproductive systems present in the genus

Kirstie Grant, Daniel Koenemann, Janet Mansaray, Aisha Ahmed, Hamid Khamar, Jalal El Oualidi & Janelle Burke
Rumex is a unique member of the Polygonaceae family of plants. A source of intrigue for Rumex lies in the diversity of the reproductive systems associated with this genus. Four previously circumscribed subgenera and some two-hundred species comprise the collective Rumex genus. These species exhibit monoecious, dioecious, synoecious (hermaphroditic), and polygamous reproductive systems. Moreover, some of the dioecious species contain heteromorphic sex chromosomes, a phenomenon that is very rare in angiosperms. Apart from these confirmed...

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....

Climate trends and behavior of a model Amazonian terrestrial insectivore, Black-faced Antthrush, indicate adjustment to hot and dry conditions

Vitek Jirinec, Elisa Elizondo, Patricia Rodrigues & Philip Stouffer
Rainforest loss threatens terrestrial insectivorous birds throughout the world’s tropics. Recent evidence suggests these birds are declining in undisturbed Amazonian rainforest, possibly due to climate change. Here, we first asked whether Amazonian terrestrial insectivorous birds were exposed to increasingly extreme ambient conditions using 38 years of climate data. We found long-term trends in temperature and precipitation at our study site, especially in the dry season, which was ~1.3 °C hotter and 21% drier in 2019...

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...

Herbivory mediates direct and indirect interactions in long-unburned chaparral

Laurel Fox & Stephen Potts
Community interaction webs describe both direct and indirect interactions among species. Changes in direct interactions often become noticeable soon after a perturbation, but time lags in responses of many species may delay the appearance of indirect effects and lead to temporal and/or spatial variation in interaction webs. Accurately identifying these shifts in the field requires time-specific, spatially-differentiated interaction webs. We explore how variation in browsing affects interaction webs in a long-unburned chaparral shrubland near the...

Data from: A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean

Matthew Friedman, Kara Feilich, Hermione Beckett, Michael Alfaro, Brant Faircloth, David Černý, Masaki Miya, Thomas Near & Richard Harrington
The fish clade Pelagiaria, which includes tunas as its most famous members, evolved remarkable morphological and ecological variety in a setting not generally considered conducive to diversification: the open ocean. Relationships within Pelagiaria have proven elusive due to short internodes subtending major lineages suggestive of rapid early divergences. Using a novel sequence dataset of over 1000 ultraconserved DNA elements (UCEs) for 94 of the 286 species of Pelagiaria (more than 70% of genera), we provide...

Data from: Avian ecological succession in the Amazon: a long-term case study following experimental deforestation

Cameron L. Rutt, Vitek Jirinec, Mario Cohn-Haft, William F. Laurance & Philip C. Stouffer
Approximately 20% of the Brazilian Amazon has now been deforested, and the Amazon is currently experiencing the highest rates of deforestation in a decade, leading to large-scale land-use changes. Roads have consistently been implicated as drivers of ongoing Amazon deforestation and may act as corridors to facilitate species invasions. Long-term data, however, are necessary to determine how ecological succession alters avian communities following deforestation and whether established roads lead to a constant influx of new...

Data from: Biotic interactions help explain variation in elevational range limits of birds among Bornean mountains

Ryan C. Burner, Andy J. Boyce, Alison Styring, Tom Martin, David Bernasconi & Frederick Sheldon
Aim Physiological tolerances and biotic interactions along habitat gradients are thought to influence species occurrence. Distributional differences caused by such forces are particularly noticeable on tropical mountains, where high species turnover along elevational gradients occurs over relatively short distances and elevational distributions of particular species can shift among mountains. Such shifts are interpreted as evidence of the importance of spatial variation in interspecific competition and habitat or climatic gradients. To assess the relative importance of...

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...

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...

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....

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...

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...

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  • Louisiana State University
  • Louisiana State University of Alexandria
  • University of Florida
  • American Museum of Natural History
  • University of Kansas
  • University of California Los Angeles
  • Louisiana State University Agricultural Center
  • Field Museum of Natural History
  • Yale University
  • Michigan Technological University