30 Works

Historical museum samples enable the examination of divergent and parallel evolution during invasion

Katarina Stuart, William Sherwin, Jeremy Austin, Melissa Bateson, Marcel Eens, Matthew Brandley & Lee Rollins
During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline, and global climate change. Concurrently, greater globalisation is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species’ ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species’ invasion success or persistence informs invasive species management, assists with native species...

Support for the habitat amount hypothesis from a global synthesis of species density studies

James Watling, Víctor Arroyo-Rodríguez, Marion Pfeifer, Lander Baeten, Cristina Banks-Leite, Laura Cisneros, Rebecca Fang, Caroli Hamel-Leigue, Thibault Lachat, Inara Leal, Luc Lens, Hugh Possingham, Dinarzarde Raheem, Danilo Ribeiro, Eleanor Slade, Nicolas Urbina-Cardona, Eric Wood & Lenore Fahrig
Decades of research suggest that species richness depends on spatial characteristics of habitat patches, especially their size and isolation. In contrast, the habitat amount hypothesis predicts that: 1) species richness in plots of fixed size (species density) is more strongly and positively related to the amount of habitat around the plot than to patch size or isolation; 2) habitat amount better predicts species density than patch size and isolation combined, 3) there is no effect...

Reevaluating claims of ecological speciation in Halichoeres bivittatus

Dan Warren, Ron Eytan, Alex Dornburg, Teresa Iglesias, Matt Brandley & Peter Wainwright
Allopatry has traditionally been viewed as the primary driver of speciation in marine taxa, but the geography of the marine environment and the larval dispersal capabilities of many marine organisms render this view somewhat questionable. In marine fishes, one of the earliest and most highly cited empirical examples of ecological speciation with gene flow is the slippery dick wrasse, Halichoeres bivittatus. Evidence for this cryptic or incipient speciation event was primarily in the form of...

Data from: Shifts to earlier selfing in sympatry may reduce costs of pollinator sharing

April M. Randle, Rachel B. Spigler & Susan Kalisz
Coexisting plant congeners often experience strong competition for resources. Competition for pollinators can result in direct fitness costs via reduced seed set or indirect costs via heterospecific pollen transfer (HPT), causing subsequent gamete loss and unfit hybrid offspring production. Autonomous selfing may alleviate these costs, but to preempt HPT, selfing should occur early, before opportunities for HPT occur (i.e. “preemptive selfing hypothesis”). We evaluated conditions for this hypothesis in Collinsia sister species, C. linearis and...

Data from: Character Analysis in Morphological Phylogenetics: Problems and Solutions

John J. Wiens
Many aspects of morphological phylogenetics are controversial in the theoretical systematics literature and yet are often poorly explained and justified in empirical studies. In this paper, I argue that most morphological characters describe variation that is fundamentally quantitative, regardless of whether it is coded qualitatively or quantitatively by systematists. Given this view, three fundamental problems in morphological character analysis (character state definition, delimitation, and ordering) may have a common solution: coding morphological characters as continuous...

Data from: Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end

David Ben Stern, Jesse Breinholt, Carlos Pedraza-Lara, Marilú López-Mejía, Christopher L. Owen, Heather Bracken-Grissom, , Keith A. Crandall & James W. Fetzner
Caves are perceived as isolated, extreme habitats with a set of uniquely specialized biota, which long ago led to the idea that caves are ‘evolutionary dead-ends.’ This suggests that cave-adapted taxa may be doomed for extinction before they can diversify or transition to a more stable state. However, this hypothesis has not been explicitly tested in a phylogenetic framework with multiple independent cave-dwelling groups. Here we use the freshwater crayfish, a group with dozens of...

Data from: Systematics of spiny-backed treefrogs (Hylidae: Osteocephalus): an Amazonian puzzle

Karl-Heinz Jungfer, Julián Faivovich, José M. Padial, Santiago Castroviejo-Fisher, Mariana M. Lyra, Bianca Von Muller Berneck, Patricia P. Iglesias, Philippe J. R. Kok, Ross T. Macculloch, Miguel Trefaut Rodrigues, Vanessa K. Verdade, Claudia P. Torres Gastello, Juan Carlos Chaparro, Paula H. Valdujo, Steffen Reichle, Jiří Moravec, Václav Gvoždík, Giussepe Gagliardi-Urrutia, Raffael Ernst, Ignacio De La Riva, Donald Bruce Means, Albertina P. Lima, J. Celsa Señaris, Ward C. Wheeler & Célio F. B. Haddad
Spiny-backed tree frogs of the genus Osteocephalus are conspicuous components of the tropical wet forests of the Amazon and the Guiana Shield. Here, we revise the phylogenetic relationships of Osteocephalus and its sister group Tepuihyla, using up to 6134 bp of DNA sequences of nine mitochondrial and one nuclear gene for 338 specimens from eight countries and 218 localities, representing 89% of the 28 currently recognized nominal species. Our phylogenetic analyses reveal (i) the paraphyly...

Data from: A new dissorophoid temnospondyl from the Allegheny Group (Late Westphalian, Carboniferous) of Five Points, Mahoning County, Ohio (USA)

Rainer Schoch, Amy Henrici & Robert Hook
A small temnospondyl skull from the Upper Carboniferous Allegheny Group of Five Points, Ohio, is referred to a new dissorophoid, Palodromeus bairdi n. gen n. sp. The complete skull with mandibles is preserved in counterparts. It is characterized by (1) elongated slit-like choana, (2) postfrontal, postorbital, and supratemporal bearing a distinct ridge, and (3) reduced parietal only two-thirds the length of the frontal. Phylogenetic analysis confirms a dichotomy between amphibamiforms and olsoniforms and places Palodromeus...

Data from: A basal lithostrotian titanosaur (Dinosauria: Sauropoda) with a complete skull: implications for the evolution and paleobiology of Titanosauria

Rubén D. F. Martínez, Matthew C. Lamanna, Fernando E. Novas, Ryan C. Ridgely, Gabriel A. Casal, Javier E. Martínez, Javier R. Vita & Lawrence M. Witmer
We describe Sarmientosaurus musacchioi gen. et sp. nov., a titanosaurian sauropod dinosaur from the Upper Cretaceous (Cenomanian–Turonian) Lower Member of the Bajo Barreal Formation of southern Chubut Province in central Patagonia, Argentina. The holotypic and only known specimen consists of an articulated, virtually complete skull and part of the cranial and middle cervical series. Sarmientosaurus exhibits the following distinctive features that we interpret as autapomorphies: (1) maximum diameter of orbit nearly 40% rostrocaudal length of...

Data from: Life history trait divergence among populations of a non-palatable species reveals strong non-trophic indirect effects of an abundant herbivore

Christopher D. Heckel & Susan Kalisz
When large herbivores exert selection on their prey plant species, co-occurring, non-prey species may experience selection through non-trophic indirect effects. Such selection is likely common where herbivores are overabundant. Yet, empirical studies of non-trophic indirect effects as drivers of non-prey trait evolution are lacking. Here we test for adaptive shifts in life history traits in an unpalatable species, Arisaema triphyllum, a common forest perennial that is unique because it exhibits size-dependent sex switching. We collected...

Data from: Delimiting Species Using DNA and Morphological Variation and Discordant Species Limits in Spiny Lizards (Sceloporus)

John J. Wiens & Tonya A. Penkrot
Haplotype phylogenies based on DNA sequence data are increasingly being used to test traditional species-level taxonomies based on morphology. However, few studies have critically compared species limits based on morphological and DNA data, and the methods used to delimit species using either type of data are only rarely explained. In this paper, we review three approaches for species delimitation (tree-based with DNA data and tree-based and character-based with morphological data) and propose explicit protocols for...

Data for: Two is better than one: Coupling DNA metabarcoding and stable isotope analysis improves dietary characterizations for a riparian-obligate, migratory songbird

Brandon Hoenig, Brian Trevelline, Andrea Kautz, Steven Latta & Brady Porter
While an increasing number of studies are adopting molecular and chemical methods for dietary characterization, these studies often employ only one of these laboratory-based techniques; an approach which may yield an incomplete, or even biased, understanding of diet due to each method’s inherent limitations. To explore the utility of coupling molecular and chemical techniques for dietary characterizations, we applied DNA metabarcoding alongside stable isotope analysis to characterize the dietary niche of breeding Louisiana waterthrush (Parkesia...

Using convolutional neural networks to efficiently extract immense phenological data from community science images

Rachel Reeb, Naeem Aziz, Samuel Lapp, Justin Kitzes, J. Mason Heberling & Sara Kuebbing
Community science image libraries offer a massive, but largely untapped, source of observational data for phenological research. The iNaturalist platform offers a particularly rich archive, containing more than 49 million verifiable, georeferenced, open access images, encompassing seven continents and over 278,000 species. A critical limitation preventing scientists from taking full advantage of this rich data source is labor. Each image must be manually inspected and categorized by phenophase, which is both time-intensive and costly. Consequently,...

Clinging performance on natural substrates predicts habitat use in anoles and geckos

Amber Wright, Stevie Kennedy-Gold, Emily Naylor, Robyn Screen, Carla Piantoni & Timothy Higham
1. For arboreal lizards, the ability to cling or adhere to the substrate is critical for locomotion during prey capture, predator escape, thermoregulation, and social interactions. Thus, selection on traits related to clinging is likely strong. 2. Correlations between morphology, performance, and habitat use have been documented in arboreal lizards, providing a framework for using functional traits to predict habitat use in the field. 3. We tested the hypothesis that clinging performance predicts habitat use...

Anatomy of the neural endocranium and stapes of Diadectes absitus (Diadectomorpha) from the early Permian of Germany based on the high‐resolution X‐ray microcomputed tomography

Jozef Klembara, Miroslav Hain, Andrej Čerňanský, David S Berman & Amy C. Henrici
A detailed anatomy of the braincase and stapes of the subadult specimen of Diadectes absitus from early Permian sediments of Germany based on the high-resolution X-ray microcomputed tomography are described for the first time. In contrast to previous studies of Diadectes, the bones of the braincase (opisthotic, prootic, supraoccipital, basioccipital, exoccipital, basisphenoid, sphenethmoid), and parasphenoid of D. absitus are not co-ossified, but suturally defined. This has allowed for a reconstruction of a complete braincase with...

Data from: Aboveground biomass is driven by mass-ratio effects and stand structural attributes in a temperate deciduous forest

Alexander T. Fotis, Stephen J. Murphy, Raleigh D. Ricart, Meghna Krishnadas, James Whitacre, John W. Wenzel, Simon A. Queenborough & Liza S. Comita
1.Forest ecosystems are critical for the global regulation of carbon (C), a substantial portion of which is stored in aboveground biomass (AGB). While it is well understood that taxonomic and functional composition, stand structure, and environmental gradients influence spatial variation in AGB, the relative strengths of these drivers at landscape-scales has not been investigated in temperate forests. Furthermore, when biodiversity enhances C storage, it is unclear whether it is through mass-ratio effects (i.e., the dominant...

Data from: Testing Phylogenetic Methods with Tree Congruence: Phylogenetic Analysis of Polymorphic Morphological Characters in Phrynosomatid Lizards

John J. Wiens
Congruence between trees from separately analyzed data sets is a powerful approach for assessing the performance of phylogenetic methods but has been applied primarily to the analysis of molecular data. In this study, different methods for treating polymorphic characters were compared using morphological data from phrynosomatid lizards. Clades were identified that are both traditionally recognized and supported by recent molecular analyses, and species were sampled from these clades to make three RknownS phylogenies of eight...

Data from: Phenological mismatch with trees reduces wildflower carbon budgets

J. Mason Heberling, Caitlin McDonough MacKenzie, Jason D. Fridley, Susan Kalisz & Richard B. Primack
Interacting species can respond differently to climate change, causing unexpected consequences. Many understory wildflowers in deciduous forests leaf out and flower in the spring when light availability is highest before overstory canopy closure. Therefore, different phenological responses by understory and overstory species to increased spring temperature could have significant ecological implications. Pairing contemporary data with historical observations initiated by Henry David Thoreau (1850s), we found that overstory tree leaf out is more responsive to increased...

Data from: Nonnative old-field species inhabit early-season phenological niches and exhibit unique sensitivity to climate

Rachel Reeb, Isabel Acevedo, Mason Heberling & Sara Kuebbing
Native and nonnative plant species can exhibit differences in the timing of their reproductive phenology as well as their phenological sensitivity to climate. These contrasts may influence species’ interactions and the invasion potential of nonnative species; however, a limited number of phenology studies expressly consider phenological mismatches among native and nonnative species over broad spatial or temporal scales. To fill this knowledge gap, we used two complementary approaches: first, we quantified the flowering phenology of...

Data from: Tuberculosis-like respiratory infection in 245-million-year-old marine reptile suggested by bone pathologies

Dawid Surmik, Tomasz Szczygielski, Katarzyna Janiszewska & Bruce M. Rothschild
An absence of archaeological and palaeontological evidence of pneumonia in the remote past contrasts with its recognition in the more recent archaeologic record. We document an apparent infection-mediated periosteal reaction affecting the dorsal ribs in a Middle Triassic eosauropterygian historically referred to as ‘Proneusticosaurus’ silesiacus. High-resolution X-ray microtomography (XMT) and histological studies of the pathologically-altered ribs revealed the presence of a continuous solid periosteal reaction with multiple superficial blebs (protrusions) on the visceral surfaces of...

Data from: A passerine bird's evolution corroborates the geologic history of the island of New Guinea

Kristy Deiner, Alan R. Lemmon, Andrew L. Mack, Robert C. Fleischer & John P. Dumbacher
New Guinea is a biologically diverse island, with a unique geologic history and topography that has likely played a role in the evolution of species. Few island-wide studies, however, have examined the phylogeographic history of lowland species. The objective of this study was to examine patterns of phylogeographic variation of a common and widespread New Guinean bird species (Colluricincla megarhyncha). Specifically, we test the mechanisms hypothesized to cause geographic and genetic variation (e.g., vicariance, isolation...

Data from: Inner ear morphology of diadectomorphs and seymouriamorphs (Tetrapoda) uncovered by high‐resolution x‐ray microcomputed tomography, and the origin of the amniote crown group

Jozef Klembara, Miroslav Hain, Marcello Ruta, David S. Berman, Stephanie E. Pierce & Amy C. Henrici
The origin of amniotes was a key event in vertebrate evolution, enabling tetrapods to break their ties with water and invade terrestrial environments. Two pivotal clades of early tetrapods, the diadectomorphs and the seymouriamorphs, have played an unsurpassed role in debates about the ancestry of amniotes for over a century, but their skeletal morphology has provided conflicting evidence for their affinities. Using high-resolution X-ray microcomputed tomography, we reveal the three-dimensional architecture of the well preserved...

Feedbacks between forest structure and an opportunistic fungal pathogen

Christopher Lee, Ricardo Holdo & Rose-Marie Muzika
Abiotic stresses, physiological dysfunction, forest stand dynamics, and primary tree attackers (native and non-native) are all recognized as important contributors to both anomalous tree mortality and background tree mortality, and thus as important influences on biogeochemical cycling and habitat for associated terrestrial organisms. Opportunistic and latent tree pathogens and insect pests have largely been left out of this discussion, probably because they are difficult to monitor and their effects sometimes more diffuse, yet they play...

Data from: Linking phenological events in migratory passerines with a changing climate: 50 years in the Laurel Highlands of Pennsylvania

Molly E. McDermott & Lucas W. DeGroote
Advanced timing of both seasonal migration and reproduction in birds has been strongly associated with a warming climate for many bird species. Phenological responses to climate linking these stages may ultimately impact fitness. We analyzed five decades of banding data from 17 migratory bird species to investigate 1) how spring arrival related to timing of breeding, 2) if the interval between arrival and breeding has changed with increasing spring temperatures, and 3) whether arrival timing...

Transcript- and annotation-guided genome assembly of the European starling

Katarina Stuart, Richard Edwards, Yuanyuan Cheng, Wes Warren, Dave Burt, William Sherwin, Natalie Hofmeister, Scott Werner, Gregory Ball, Melissa Bateson, Matthew Brandley, Katherine Buchanan, Phillip Cassey, David Clayton, Tim De Meyer, Simone Meddle & Lee Rollins
The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second North American genome (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterisation. S. vulgaris vAU combined 10x Genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length...

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