30 Works

Data from: Assessing support for Blaberoidea phylogeny suggests optimal locus

Dominic Evangelista, Sabrina Simon, Megan M. Wilson, Akito Y. Kawahara, Manpreet K. Kohli, Jessica L. Ware, Benjamin Wipfler, Olivier Béthoux, Grandcolas Philippe & Frédéric Legendre
Phylogenomics seeks to use next-generation data to robustly infer an organism’s evolutionary history. Yet, the practical caveats of phylogenomics motivates investigation of improved efficiency, particularly when quality of phylogenies are questionable. To achieve improvements, one goal is to maintain or enhance the quality of phylogenetic inference while severely reducing dataset size. We approach this by assessing which kinds of loci in phylogenomic alignments provide the majority of support for a phylogenetic inference of cockroaches in...

Population genetic structure of the insular Ryukyu flying fox Pteropus dasymallus

Shiang-Fan Chen, Chung-Hao Juan, Stephen J. Rossiter, Teruo Kinjo, Dai Fukui, Kuniko Kawai, Susan M. Tsang, Maria Josefa Veluz, Hiroko Sakurai, Hua-Ching Lin, Nian-Hong Jang-Liaw, Keiko Osawa, Wen-Ya Ko & Masako Izawa
Small isolated populations are vulnerable to both stochastic events and the negative consequences of genetic drift. For threatened species, the genetic management of such populations has therefore become a crucial aspect of conservation. Flying foxes (Pteropus spp, Chiroptera) are keystone species with essential roles in pollination and seed dispersal in tropical and subtropical ecosystems. However, many flying fox species are also threatened, having experienced dramatic population declines driven by habitat loss and hunting. The insular...

Ecological and evolutionary drivers of hemoplasma infection and genotype sharing in a Neotropical bat community

Daniel Becker, Kelly Speer, Alexis Brown, Alex Washburne, Brock Fenton, Sonia Altizer, Daniel Streicker, Raina Plowright, Vladimir Chizhikov, Nancy Simmons & Dmitriy Volokhov
Most emerging pathogens can infect multiple species, underscoring the importance of understanding the ecological and evolutionary factors that allow some hosts to harbor greater infection prevalence and share pathogens with other species. However, our understanding of pathogen jumps is primarily based around viruses, despite bacteria accounting for the greatest proportion of zoonoses. Because bacterial pathogens in bats (Order: Chiroptera) can have conservation and human health consequences, studies that examine the ecological and evolutionary drivers of...

Data from: Ontogeny of the trilobite Elrathia kingii (Meek, 1870), and comparison of growth rates between Elrathia kingii and Aulacopleura koninckii (Barrande, 1846)

Melanie J Hopkins
Trilobites offer almost unparalleled insight into the growth and development of fossil ecdysozoans. Here I use newly collected material of Elrathia kingii (Meek, 1870) to estimate growth rates and describe shape change over the ontogeny of E. kingii. Well-preserved, articulated specimens from all post-embryonic stages were collected from a 1.5-meter interval of the upper Wheeler Formation (Miaolingian Series, Cambrian) in western Utah (USA), and size and landmark-based shape data were digitized from photographs. Growth rates...

Data from: Redescription and phylogenetic affinities of the caimanine Eocaiman cavernensis (Crocodylia, Alligatoroidea) from the Eocene of Argentina

Pedro L. Godoy, Giovanne Cidade, Felipe Montefeltro, Max Langer & Mark Norell
Caimaninae is one of the few crocodylian lineages that still has living representatives. Today, most of its six extant species are restricted to South and Central America. However, recent discoveries revealed a more complex evolutionary history, with a fossil record richer than previously thought and a possible North American origin. Among the oldest caimanines is Eocaiman cavernensis, from the Eocene of Patagonia, Argentina. It was described by George G. Simpson in the 1930s, representing the...

Data from: Patterns of intraspecific variation through ontogeny–a case study of the Cretaceous nautilid Eutrephoceras dekayi and modern Nautilus pompilius

Amane Tajika, Neil Landman, Naoki Morimoto, Kenji Ikuno & Tom Linn
The magnitude and ontogenetic patterns of intraspecific variation can provide important insights into the evolution and development of organisms. Understanding the intraspecific variation of organisms is a key to correctly pursuing studies in major fields of palaeontology. However, intraspecific variation has been largely overlooked in ectocochleate cephalopods, particularly nautilids. Furthermore, little is known regarding the evolutionary pattern. Here, we present morphological data for the Cretaceous nautilid Eutrephoceras dekayi (Morton, 1834) and the modern nautilid Nautilus...

Shifting ecosystem connectivity during the Pleistocene drove diversification and gene-flow in a species-complex of Neotropical birds (Tityridae: Pachyramphus)

Lukas Musher, Peter Galante, Gregory Thom, Jerry Huntley & Mary Blair
Aim: We aim to test the biogeographic drivers of diversification and gene-flow at the Isthmus of Panama using a species complex of suboscine birds as a case study. We specifically evaluate whether diversification in these birds is better explained by continuous parapatry or a Refuge Model of periodic isolation and gene-flow due glacial cycling. Location: The Isthmus of Panama (Neotropics) Taxon: Pachyramphus aglaiae and P. homochrous (Aves: Tityridae) Methods: We develop an approach to distinguish...

Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes (Pantherophis obsoletus complex)

Frank Burbrink, Marcelo Gehara, Alexander McKelvy & Edward Myers
Inferring the history of divergence between species in a framework that permits the presence of gene flow has been crucial for characterizing the “gray zone” of speciation, which is the period of time where lineages have diverged but have not yet achieved strict reproductive isolation. However, estimates of both divergence times and rates of gene flow often ignore spatial information, for example when considering the location and width of hybrid zones with respect to changes...

Data from: Morphological characters can strongly influence early animal relationships inferred from phylogenomic data sets

Johannes S. Neumann, Rob Desalle, Apurva Narechania, Bernd Schierwater & Michael Tessler
There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: The sister to all other Metazoa (SOM). Here we use published phylogenomic datasets (∼45,000-400,000 characters in size with ∼15-100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological datasets (∼15-275 characters). We additionally use small exemplar datasets to quantify...

Phylogenomic resolution of sea spider diversification through integration of multiple data classes

Jesus Ballesteros, Emily Setton, Carlos Santibáñez-López, Claudia Arango, Georg Brenneis, Saskia Brix, Kevin Corbett, Esperanza Cano-Sánchez, Merai Dandouch, Geoffrey Dilly, Marc Eleaume, Guilherme Gainett, Cyril Gallut, Sean McAtee, Lauren McIntyre, Randy Moran, Pablo López-González, Gerhard Scholtz, Clay Williamson, Arthur Woods, Jakob Zehms, Ward Wheeler & Prashant Sharma
Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and three nuclear...

Data from: Carnivorous mammals from the middle Eocene Washakie Formation, Wyoming, USA, and their diversity trajectory in a post-warming world

Susumu Tomiya, Shawn Zack, Michelle Spaulding & John J. Flynn
The middle Eocene Washakie Formation of Wyoming, USA, provides a rare window, within a single depositional basin, into the faunal transition that followed the early Eocene warming events. Based on extensive examination, we report a minimum of 27 species of carnivorous mammals from this formation, more than doubling the previous taxic count. Included in this revised list are a new species of carnivoraform, Neovulpavus mccarrolli, and up to ten other possibly new taxa. Our cladistic...

Ecological divergence and the history of gene flow in the Nearctic milksnakes (Lampropeltis triangulum complex)

Frank Burbrink, Justin Bernstein, Arianna Kuhn, Marcelo Gehara & Sara Ruane
Many phylogeographic studies on species with large ranges have found genetic-geographic structure associated with changes in habitat and physical barriers to gene flow. These studies may conclude absence of population structure, lineage structure that indicates unique species have been discovered, or suggest more research is needed prior to delimitation. Comparative risks of delimiting species incorrectly or failing to delimit species are usually not weighed and a more detailed return to these problems with more data...

Genomic signatures of host-associated divergence and adaptation in a coral-eating snail, Coralliophila violacea (Kiener, 1836)

Sara Simmonds, Allison Fritts-Penniman, Samantha Cheng, Ngurah Mahardika & Paul Barber
The fluid nature of the ocean, combined with planktonic dispersal of marine larvae, lowers physical barriers to gene flow. However, divergence can still occur despite gene flow if strong selection acts on populations occupying different ecological niches. Here, we examined the population genomics of an ectoparasitic snail, Coralliophila violacea (Kiener 1836), that specializes on Porites corals in the Indo-Pacific. Previous genetic analyses revealed two sympatric lineages associated with different coral hosts. In this study, we...

An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae)

Jinmin Chen, Elizabeth Prendini, Yun-He Wu, Bao-Lin Zhang, Chatmongkon Suwannapoom, Hong-Man Chen, Jie-Qiong Jin, Emily Moriarty Lemmon, Alan R. Lemmon, Bryan L. Stuart, Christopher J. Raxworthy, Robert W. Murphy, Zhi-Yong Yuan & Jing Che
Rhacophoridae is one of the most speciose and ecologically diverse families of amphibians. Resolution of its evolutionary relationships is key to understanding the accumulation of biodiversity, yet previous hypotheses based on Sanger sequencing exhibit much discordance amongst generic relationships. This conflict precludes the making of sound macroevolutionary conclusions. Herein, we conduct the first phylogenomic study using broad-scale sampling and sequences of 352 nuclear DNA loci obtained using anchored hybrid enrichment targeted sequencing. The robust time-calibrated...

Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in corn snakes (Pantherophis guttatus complex)

Edward Myers, Alexander McKelvy & Frank Burbrink
The southeastern Nearctic is a biodiversity hotspot that is also rich in cryptic species. This richness can be explained by numerous hypotheses affecting divergence, which include biogeographic barriers, adaptation to climatic gradients across this region, and Pleistocene speciation in glacial refugia. However, previous phylogeographic studies have both supported and refuted these hypotheses. Therefore, while one or more of these hypotheses may explain diversification, it is likely that taxa are forming within this region in species-specific...

Whole feeding apparatus 3D landmarks

Marion Segall, Daniel Rhoda, P. David Polly & Christopher Raxworthy
The kinetic skull is a key innovation that allowed snakes to capture, manipulate, and swallow prey exclusively using their heads using the coordinated movement of 8 bones. Despite these unique feeding behaviors, patterns of evolutionary integration and modularity within the feeding bones of snakes in a phylogenetic framework have yet to be addressed. Here, we use a dataset of 60 µCT scanned skulls and high-density geometric morphometric methods to address the origin and patterns of...

A Hirnantian holdover from the late Ordovician mass extinction: phylogeny and biogeography of a new Anthracocrinid crinoid from Estonia

Selina Cole, William Ausich & Mark Wilson
Relatively few Hirnantian (Late Ordovician) crinoids are known, and none have been previously described from the palaeocontinent of Baltica. This has impaired our ability to understand patterns of extinction and biogeographic dispersal surrounding the Late Ordovician mass extinction, which triggered a major turnover in crinoid faunas. Here, we describe Tallinnicrinus toomae gen. et sp. nov., an anthracocrinid diplobathrid from the Hirnantian of northern Estonia. Tallinnicrinus is the youngest member of the Anthracocrinidae and the first...

Spatial predictors of genomic and phenotypic variation differ in a lowland Middle American bird (Icterus gularis)

Lucas Rocha Moreira, Blanca E. Hernandez-Baños & Brian T. Smith
Spatial patterns of intraspecific variation are shaped by factors such as geographic distance among populations, historical changes in gene flow and interactions with local environments. Although these factors are not mutually exclusive and operate on both genomic and phenotypic variation, it is unclear how they affect these two axes of variation. We address this question by exploring the predictors of genomic and phenotypic divergence in Icterus gularis, a broadly distributed Middle American bird that exhibits...

Data from: Uneven missing data skews phylogenomic relationships within the lories and lorikeets

Brian Smith, , Brett W. Benz & Michael J. Andersen
Inlcuded is the supplementary data for Smith, B. T., Mauck, W. M., Benz, B., & Andersen, M. J. (2018). Uneven missing data skews phylogenomic relationships within the lories and lorikeets. BioRxiv, 398297. The resolution of the Tree of Life has accelerated with advances in DNA sequencing technology. To achieve dense taxon sampling, it is often necessary to obtain DNA from historical museum specimens to supplement modern genetic samples. However, DNA from historical material is generally...

Host identity and symbiotic association affects the genetic and taxonomic diversity of the clownfish-hosting sea anemone microbiome

Benjamin Titus, Robert Laroche, Estafania Rodriguez, Herman Wirshing & Christopher Meyer
All eukaryotic life engages in symbioses with a diverse community of bacteria that are essential for performing basic life functions. In many cases, eukaryotic organisms form additional symbioses with other macroscopic eukaryotes. The tightly-linked physical interactions that characterize many macroscopic symbioses creates opportunities for microbial transfer, which likely affects the diversity and function of individual microbiomes, and may ultimately lead to microbiome convergence between distantly related taxa. Here, we sequence the microbiomes of five species...

Saproxylic fly diversity in a Costa Rican forest mosaic

Lance Jones & Amy Berkov
This paper presents the first assessment of the diversity of tropical saproxylic Diptera, done on the Osa Peninsula of Costa Rica. Forty-one trees representing nine species and six plant families were sampled in a rearing experiment. In total, 272 individuals attributable to 18 families of Diptera were reared. Low abundance and species richness of flies was observed overall. A majority of taxa were in saprophagous and mycophagous larval feeding guilds, followed by predators. Host associations,...

Facultative chemosynthesis in a deep-sea anemone from hydrothermal vents in the Pescadero Basin, Gulf of California

Shana Goffredi, Cambrie Motooka, David Fike, Luciana Gusmão, Ekin Tilic, Greg Rouse & Estefanía Rodríguez
Background Numerous deep-sea invertebrates have formed symbiotic associations with internal chemosynthetic bacteria in order to harness inorganic energy sources typically unavailable to most animals. Despite success in nearly all marine habitats and their well-known associations with photosynthetic symbionts, Cnidaria remain without a clear dependence on hydrothermal vents and chemosynthetic bacterial symbionts specifically. Results A new chemosynthetic symbiosis between the sea anemone Ostiactis pearseae (Daly & Gusmão, 2007) and intracellular bacteria was discovered at ~3700 m...

Paleocommunity composition, relative abundance, and new camerate crinoids from the Brechin Lagerstätte (Upper Ordovician)

Selina Cole, David Wright, William Ausich & Joseph Koniecki
The Brechin Lagerstätte of southern Ontario contains an exceptionally diverse and well-preserved Late Ordovician (Katian) crinoid fauna. Here, we describe four genera and eight species of camerate crinoids from the Brechin Lagerstätte, including six new species. Consequently, the total diversity of the fauna now stands at 27 genera and 39 nominal species, thereby making it the most taxonomically diverse Ordovician crinoid fauna known. Taxa described herein include the diplobathrid Pararchaeocrinus kiddi n. sp. and the...

Variation in brown rat cranial shape shows directional selection over 120 years in New York City

Emily Puckett, Emma Sherratt, Matthew Combs, Elizabeth Carlen, William Harcourt-Smith & Jason Munshi-South
Urbanization exposes species to novel environments and selection pressures that may change morphological traits within a population. We investigated how the shape and size of crania and mandibles changed over time within a population of brown rats (Rattus norvegicus) living in Manhattan, New York, USA, a highly urbanized environment. We measured 3D landmarks on the cranium and mandible of 62 adult individuals sampled in the 1890s and 2010s. Static allometry explained approximately 22% of shape...

Evolutionary stasis, ecophenotypy, and environmental controls on ammonite morphology in the Late Cretaceous (Maastrichtian) Western Interior Seaway, USA

James Witts, Neil Landman, Melanie Hopkins & Corinne Myers
We test for the presence of evolutionary stasis in a species of Late Cretaceous ammonoid cephalopod, Hoploscaphites nicolletii, from the North American Western Interior Seaway. A comprehensive dataset of morphological traits was compiled across the entire spatial and temporal range of this species. These were analyzed in conjunction with sedimentologically and geochemically derived palaeoenvironmental conditions hypothesized to apply selective pressures. All changes in shell shape were observed to be ephemeral and reversable, that is, no...

Registration Year

  • 2020

Resource Types

  • Dataset


  • American Museum of Natural History
  • National Museum of Natural History
  • The Ohio State University
  • University of Edinburgh
  • Western University
  • Indiana University Bloomington
  • Kyoto University
  • Montana State University
  • Fordham University
  • Stony Brook University