19 Works

Speciation hypotheses from phylogeographic delimitation yield an integrative taxonomy for Seal Salamanders (Desmognathus monticola)

Robert Pyron, Kyle O'Connell, Sophie Duncan, Frank Burbrink & David Beamer
Significant advances have been made in species delimitation and numerous methods can test precisely defined models of speciation, though the synthesis of phylogeography and taxonomy is still sometimes incomplete. Emerging consensus treats distinct genealogical clusters in genome-scale data as strong initial evidence of speciation in most cases; a hypothesis that must therefore be falsified under an explicit evolutionary model. We can now test speciation hypotheses linking trait differentiation to specific mechanisms of divergence with increasingly...

Hair phenotype diversity across Indriidae lemurs

Elizabeth Tapanes, Rachel Jacobs, Ian Harryman, , Mitchell Irwin, Jason Kamilar & Brenda Bradley
Objectives: Hair (i.e., pelage/fur) is a salient feature of primate (including human) diversity and evolution—serving functions tied to thermoregulation, protection, camouflage, and signaling—but wild primate pelage evolution remains relatively understudied. Specifically, assessing multiple hypotheses across distinct phylogenetic scales is essential but is rarely conducted. We examine whole body hair color and density variation across Indriidae (Avahi, Indri, Propithecus)—a lineage that, like humans, exhibits vertical posture (i.e., their whole bodies are vertical to the sun). Materials...

Phylogenomics and fossil data inform the systematics and geographic range evolution of a diverse Neotropical ant lineage

Benjamin Blanchard, Shauna Price, Scott Powell, Bonnie Blaimer & Corrie Moreau
Recent advances in phylogenomics allow for the use of large amounts of genetic information in phylogenetic inference. Ideally, the increased resolution and accuracy of such inferences facilitate improved understanding of macroevolutionary processes. Here, we integrate ultraconserved elements (UCEs) with fossil and biogeographic range data to explore diversification and geographic range evolution in the diverse turtle ant genus Cephalotes. We focus on the potential role of the uplift of the Panamanian land bridge and the putative...

Partner fidelity and environmental filtering preserve stage-specific turtle ant gut symbioses for over 40 million years

Yi Hu, Catherine D’Amelio, Benoît Béchade, Christian Cabuslay, Piotr Lukasik, Jon Sanders, Shauna Price, Emily Fanwick, Scott Powell, Corrie Moreau & Jacob Russell
Sustaining beneficial gut symbioses presents a major challenge for animals, Including holometabolous insects. Social insects may meet such challenges through behavioral symbiont transfer and transgenerational inheritance through colony founders. We address such potential through colony-wide explorations across 13 eusocial, holometabolous ant species in the genus Cephalotes. Through amplicon sequencing and qPCR, we show that previously characterized worker microbiomes are largely conserved across adult castes, that adult microbiomes exhibit strong trends of phylosymbiosis, and that Cephalotes...

Nest choice in arboreal ants is an emergent consequence of network creation under spatial constraints

Matina Donaldson-Matasci, Joanna Chang, Scott Powell & Elva J. H. Robinson
Biological transportation networks must balance competing functional priorities. The self-organizing mechanisms used to generate such networks have inspired scalable algorithms to construct and maintain low-cost and efficient human-designed transport networks. The pheromone-based trail networks of ants have been especially valuable in this regard. Here, we use turtle ants as our focal system: In contrast to the ant species usually used as models for self-organized networks, these ants live in a spatially constrained arboreal environment where...

Additional file 2 of African-specific alleles modify risk for asthma at the 17q12-q21 locus in African Americans

Charles Washington, Matthew Dapas, Arjun Biddanda, Kevin M. Magnaye, Ivy Aneas, Britney A. Helling, Brooke Szczesny, Meher Preethi Boorgula, Margaret A. Taub, Eimear Kenny, Rasika A. Mathias, Kathleen C. Barnes, Gurjit K. Khurana Hershey, Carolyn M. Kercsmar, Jessica D. Gereige, Melanie Makhija, Rebecca S. Gruchalla, Michelle A. Gill, Andrew H. Liu, Deepa Rastogi, William Busse, Peter J. Gergen, Cynthia M. Visness, Diane R. Gold, Tina Hartert … & Carole Ober
Additional file 2. Region-wide eQTL results in airway epithelial cells from 189 African American children in the URECA cohort.

Stabilized morphological evolution of spiders despite mosaic changes in foraging ecology

Jonas Wolff, Kaja Wierucka, Jonathan Coddington, Gustavo Hormiga, Michael Kelly, Marie Herberstein, Martín Ramírez & Gustavo Paterno
A prominent question in animal research is how the evolution of morphology and ecology interact in the generation of phenotypic diversity. Spiders are some of the most abundant arthropod predators in terrestrial ecosystems and exhibit a diversity of foraging styles. It remains unclear how spider body size and proportions relate to foraging style, and if the use of webs as prey capture devices correlates with changes in body characteristics. Here we present the most extensive...

Candidate-species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones

Robert Pyron, Kyle O'Connell, Emily Lemmon, Alan Lemmon & Dave Beamer
Dusky Salamanders (genus Desmognathus) currently comprise only 22 described, extant species. However, recent mitochondrial and nuclear estimates indicate the presence of up to 49 candidate species based on ecogeographic sampling. Previous studies also suggest a complex history of hybridization between these lineages. Studies in other groups suggest that disregarding admixture may affect both phylogenetic inference and clustering-based species-delimitation. With a dataset comprising 233 Anchored Hybrid Enrichment (AHE) loci sequenced for 896 Desmognathus specimens from all...

Deep-sequencing of viral genomes from treatment-naive HIV-infected persons shows positive association between intrahost genetic diversity and viral load

Migle Gabrielaite, Marc Bennedbæk, Malthe Sebro Rasmussen, Virginia Kan, Hansjakob Furrer, Robert Flisiak, Marcelo Losso, Jens D. Lundgren & Rasmus L. Marvig
Background: Infection with human immunodeficiency virus type 1 (HIV) typically results from transmission of a small and genetically uniform viral population. Following transmission, the virus population becomes more diverse because of recombination and acquired mutations through genetic drift and selection. Viral intrahost genetic diversity remains a major obstacle to the cure of HIV; however, there is a disagreement whether intrahost viral genetic diversification associates positively or negatively with disease progression and progression markers. Viral load...

A new, narrowly endemic species of swamp-dwelling dusky salamander (Plethodontidae: Desmognathus) from the Gulf Coastal Plain of Mississippi and Alabama

Robert Pyron, Kyle O'Connell, Jennifer Lamb & David Beamer
We describe a new, narrowly endemic species of swamp-dwelling dusky salamander (Plethodontidae: Desmognathus pascagoula sp. nov.) from the Gulf Coastal Plain of southeastern Mississippi and southwestern Alabama based on linear morphometrics, mitochondrial DNA, and single nucleotide polymorphisms from 881 loci produced using genotype-by-sequencing. Some populations of the new species were historically referred to as D. auriculatus, a polyphyletic assemblage of at least three species in the Atlantic and Gulf Coastal Plain from Texas to North...

Islands Within Islands: Bacterial Phylogenetic Structure and Consortia in Hawaiian Lava Caves and Fumaroles

Rebecca Prescott, Tatyana Zamkovaya, Stuart Donachie, Diana Northup, Joseph Mendley, Natalia Monsalve, Jimmy Saw, Alan Decho, Patrick Chain & Penelope Boston
Lava caves, tubes, and fumaroles in Hawai‘i present a range of volcanic, oligotrophic environments from different lava flows and host unexpectedly high levels of bacterial diversity. These features provide an opportunity to study the ecological drivers that structure bacterial community diversity and assemblies in volcanic ecosystems and compare the older, more stable environments of lava tubes, to the more variable and extreme conditions of younger, geothermally active caves and fumaroles. Using 16S rRNA amplicon-based sequencing...

Anatomy and relationships of the basal Crocodylomorphs Junggarsuchus sloani and Dibothrosuchus elaphros

James Clark & Alexander Ruebenstahl
The holotype of Junggarsuchus sloani, from the early Late Jurassic of Xinjiang, China, consists of a nearly complete skull and the anterior half of an articulated skeleton, including the pectoral girdles, nearly complete forelimbs, vertebral column, and ribs. Here we describe its anatomy and compare it to other basal crocodylomorphs, based in part on CT scans of its skull and that of Dibothrosuchus elaphros from the Early Jurassic of China. Junggarsuchus shares many features with...

Spartina patens surveys of flowering density at marsh-forest ecotone

Ezra Kottler & Keryn Gedan
Climate change is driving abiotic shifts that can threaten the conservation of foundation species and the habitats they support. Range shifts are one mechanism of escape, but this requires successful colonization of habitats where interspecific interactions may differ from those to which a species has adapted. For plants with multiple reproductive strategies, these range-edge interactions may alter the investment or allocation towards a given reproductive strategy. In this study, we quantify sexual reproduction of the...

Specimen list and landmark coordinates for the palate of early salamanders

Jia Jia, Guangzhao Li & Ke-Qin Gao
Ecological preferences and life history strategies have enormous impacts on the evolution and phenotypic diversity of salamanders, but the yet established reliable ecological indicators hinder investigations on the paleobiology of early salamanders. Here we statistically demonstrate using geometric morphometric analysis that both the shape of the palate and many non-shape variables particularly associated with vomerine teeth are ecologically informative in early stem- and basal crown-group salamanders. The morphology of the palate is heavily impacted by...

Additional file 2 of African-specific alleles modify risk for asthma at the 17q12-q21 locus in African Americans

Charles Washington, Matthew Dapas, Arjun Biddanda, Kevin M. Magnaye, Ivy Aneas, Britney A. Helling, Brooke Szczesny, Meher Preethi Boorgula, Margaret A. Taub, Eimear Kenny, Rasika A. Mathias, Kathleen C. Barnes, Gurjit K. Khurana Hershey, Carolyn M. Kercsmar, Jessica D. Gereige, Melanie Makhija, Rebecca S. Gruchalla, Michelle A. Gill, Andrew H. Liu, Deepa Rastogi, William Busse, Peter J. Gergen, Cynthia M. Visness, Diane R. Gold, Tina Hartert … & Carole Ober
Additional file 2. Region-wide eQTL results in airway epithelial cells from 189 African American children in the URECA cohort.

Data from: Computed tomographic analysis of dental system of three Jurassic ceratopsians: implications for the evolution of the tooth replacement pattern and diet in early-diverging ceratopsians

Jinfeng Hu, Catherine Forster, Xing Xu, Qi Zhao, Yiming He & Fenglu Han
The dental system of ceratopsids is among the most specialized structure in Dinosauria, and includes high angled wear surfaces, split tooth roots, and multiple teeth in each tooth family. However, the early evolution of this unique dental system is generally poorly understood due to a lack of knowledge of the dental morphology and development in early-diverging ceratopsians. Here we study the dental system of three of the earliest-diverging Chinese ceratopsians: Yinlong and Hualianceratops from the...

Resolving higher-level phylogenetic networks with repeated hybridization in a complex of polytypic salamanders (Plethodontidae: Desmognathus)

Robert Pyron, Kyle O'Connell, Hector Banos, Edward Myers & David Beamer
Repeated hybridization between newly forming lineages is a common feature of ecological speciation and ecomorphological diversification. However, computational constraints currently limit our ability to reconstruct network radiations from gene-tree data. Available methods are limited to level-1 networks wherein reticulations do not share edges, and higher-level networks may be non-identifiable in many cases. We present a heuristic method for recovering information from higher-level networks across a range of potentially identifiable empirical scenarios, supported by a theorem...

The impact of paleoclimatic changes on body size evolution in marine fishes

Emily Troyer, Ricardo Betancur-R, Lily Hughes, Mark Westneat, Giorgio Carnevale, William White, John Pogonoski, James Tyler, Carole Baldwin, Guillermo Ortí, Julien Clavel, Dahiana Arcila & Andrew Brinkworth
Body size is an important species trait, correlating with lifespan, fecundity, and other ecological factors. Over Earth’s geological history, climate shifts have occurred, potentially shaping body size evolution in many clades. General rules attempting to summarize body size evolution include Bergmann’s rule, which states that species grow to larger sizes in cooler environments and smaller sizes in warmer environments; and Cope’s rule, which poses that lineages tend to increase in size over evolutionary time. Tetraodontiform...

Fruit-feeding butterfly populations respond to variation in adult food availability: evidence from longitudinal body mass and abundance data

Freerk Molleman, Jorge Granados-Tello, Colin Chapman & Toomas Tammaru
The degree to which variation in adult food availability affects the population dynamics of a species depends on its position on the capital-income breeding continuum. The long-lived butterflies that feed on fruits as adults constitute an example of Lepidoptera with a high degree of income breeding. For three species of fruit-feeding butterflies in Uganda, we assessed the contribution of the income to breeding in the wild, and the consequences of variation in fruit availability for...

Registration Year

  • 2022

Resource Types

  • Dataset


  • George Washington University
  • University of Chicago
  • Nash Community College
  • Virginia Mason Medical Center
  • University of Washington
  • Monroe Carell Jr. Children's Hospital
  • Johns Hopkins University
  • University of Pittsburgh
  • Columbia University Medical Center
  • Cincinnati Children's Hospital Medical Center