76 Works

Data from: Biogeography of scorpions in the Pseudouroctonus minimus complex (Vaejovidae) from south-western North America: implications of ecological specialization for pre-Quaternary diversification

Robert W. Bryson, Warren E. Savary & Lorenzo Prendini
Aim: The aim of this study was to assess the impact of pre-Quaternary tectonics and orogeny relative to that of Pleistocene climate change on diversification within the Pseudouroctonus minimus complex, a group of vaejovid scorpions with stenotopic habitat requirements. Location: South-western North America (United States and Mexico). Methods: Multilocus sequence data (1899 base pairs from two mitochondrial and two nuclear genes) were generated from 65 samples of scorpions in the minimus complex. Phylogeographical structure within...

The Life Aquatic with Spiders (Araneae): Repeated Evolution of Aquatic Habitat Association in Dictynidae and Allied Taxa

Sarah Crews, Erika Garcia, Joe Spagna, Matthew Van Dam & Lauren Esposito
Despite the terrestriality of spiders, species across a diverse array of families are associated with aquatic habitats. Many species in the spider family Dictynidae are associated with water, either living near it, or in the case of Argyroneta aquatica (Clerck, 1757), in it. Previous studies have indicated that this association arose once within the family. Here we test the hypothesis of a single origin via the broadest phylogeny of dictynids and related “marronoids” to date...

Data from: Ecological continuity and transformation after the Permo-Triassic mass extinction in northeastern Panthalassa

Ashley A. Dineen, Peter D. Roopnarine & Margaret L. Fraiser
The Permo-Triassic mass extinction (PTME) is often implicated in the transition from the Paleozoic Evolutionary Fauna (PEF) to the Modern Evolutionary Fauna (MEF). However the exact timing and details of this progression are unknown, especially regarding the vacating and filling of functional ecological space after the PTME. Here we quantify the functional diversity of middle Permian and Early Triassic marine paleocommunities in the western US to determine functional re-organization in the aftermath of the PTME....

Data from: 200 million years of anuran body size evolution in relation to geography, ecology, and life history

Molly Womack & Rayna Bell
Surprisingly little is known about body-size evolution within the most diverse amphibian order, anurans (frogs and toads), despite known effects of body size on the physiological, ecological, and life-history traits of animals more generally. Here we examined anuran body-size evolution among 2434 species with over 200 million years of shared evolutionary history. We found clade-specific evolutionary shifts to new body-size optima along with numerous independent transitions to gigantic and miniature body sizes, despite the upper...

Data from: Multi-locus sequence data reveal a new species of coral reef goby (Teleostei: Gobiidae: Eviota), and evidence of Pliocene vicariance across the Coral Triangle

Luke Tornabene, Samantha Valdez, Mark V. Erdmann & Frank L. Pezold
Here, multi-locus sequence data are coupled with observations of live colouration to recognize a new species, Eviota punyit from the Coral Triangle, Indian Ocean and Red Sea. Relaxed molecular clock divergence time estimation indicates a Pliocene origin for the new species, and the current distribution of the new species and its sister species Eviota sebreei supports a scenario of vicariance across the Indo-Pacific Barrier, followed by subsequent range expansion and overlap in the Coral Triangle....

Data from: Taxonomic revision of the Malagasy Camponotus subgenus Mayria (Hymenoptera, Formicidae) using qualitative and quantitative morphology

Jean Claude Rakotonirina & Brian L. Fisher
The Camponotus subgenus Mayria is revised based on the analysis of both qualitative morphological characters and morphometric traits. The multivariate analysis combined the Nest Centroid (NC)-clustering method and Partitioning Algorithm based on Recursive Thresholding (PART) function to generate species hypotheses based on 19 continuous morphological traits of minor workers. The proposed species hypotheses were confirmed by cumulative Linear Discriminant Analysis (LDA). Morphometric ratios for the subsets of minor and major workers were used in species...

Data from: A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements

Shahan Derkarabetian, James Starrett, Nobuo Tsurusaki, Darrell Ubick, Stephanie Castillo & Marshal Hedin
Molecular phylogenetics has transitioned into the phylogenomic era, with data derived from next-generation sequencing technologies allowing unprecedented phylogenetic resolution in all animal groups, including understudied invertebrate taxa. Within the most diverse harvestmen suborder, Laniatores, most relationships at all taxonomic levels have yet to be explored from a phylogenomics perspective. Travunioidea is an early-diverging lineage of laniatorean harvestmen with a Laurasian distribution, with species distributed in eastern Asia, eastern and western North America, and south-central Europe....

Data from: Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province

, Warren E. Savary, Amanda J. Zellmer, R. Bruce Bury, John E. McCormack & Robert W. Bryson
The California Floristic Province (CFP) in western North America is a globally significant biodiversity hotspot. Elucidating patterns of endemism and the historical drivers of this diversity has been an important challenge of comparative phylogeography for over two decades. We generated phylogenomic data using ddRADseq to examine genetic structure in Uroctonus forest scorpions, an ecologically restricted and dispersal-limited organism widely distributed across the CFP north to the Columbia River. We coupled our genetic data with species...

Data from: A unified anatomy ontology of the vertebrate skeletal system

Wasila M. Dahdul, James P. Balhoff, David C. Blackburn, Alexander D. Diehl, Melissa A. Haendel, Brian K. Hall, Hilmar Lapp, John G. Lundberg, Christopher J. Mungall, Martin Ringwald, Erik Segerdell, Ceri E. Van Slyke, Matthew K. Vickaryous, Monte Westerfield & Paula M. Mabee
The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate...

Spatial phylogenomics of acrobat ants in Madagascar—mountains function as cradles for recent diversity and endemism

Gabriela P. Camacho, Ana Carolina Loss, Brian L. Fisher & Bonnie B. Blaimer
Aim: A crucial step to protecting biodiversity is assessing species diversity and endemism. We delineate spatial patterns of diversity in Malagasy ants on a phylogenetic and taxonomic level to identify centers of diversity and endemism, and evaluate the ‘museum vs cradle’ hypothesis with regard to ant endemism. Location: Madagascar Taxon: Ants, genus Crematogaster. Methods: We estimated distribution models for 33 Crematogaster species and generated a phylogeny based on ultraconserved elements. We calculated species richness (SR),...

Alignments of Sequence Data for Phylogenetic Analysis of Damsel

Emily McFarland, Carole Baldwin, D Ross Robertson, Luiz Rocha & Luke Tornabene
Initially described in 1882, Chromis enchrysurus, the Yellowtail Reeffish, was redescribed in 1982 to account for an observed color morph that possesses a white tail instead of a yellow one, but morphological and geographic boundaries between the two color morphs were not well understood. Taking advantage of newly collected material from submersible studies of deep reefs and photographs from rebreather dives, we sought to determine whether the white-tailed Chromis is actually a color morph of...

Macroevolutionary patterns of sexual size dimorphism among African tree frogs (Family: Hyperoliidae)

Daniel Portik, David Blackburn & Jimmy McGuire
Sexual size dimorphism (SSD) is shaped by multiple selective forces that drive the evolution of sex-specific body size, resulting in male or female-biased SSD. Stronger selection on one sex can result in an allometric body-size scaling relationship consistent with Rensch’s rule or its converse. Anurans (frogs and toads) generally display female-biased SSD, but there is variation across clades and the mechanisms driving the evolution of SSD remain poorly understood. We investigated these topics in a...

Data from: Why is Madagascar special? The extraordinarily slow evolution of pelican spiders (Araneae, Archaeidae)

Hannah Marie Wood, Rosemary G. Gillespie, Charles E. Griswold & Peter C. Wainwright
Although Madagascar is an ancient fragment of Gondwana, the majority of taxa studied thus far appear to have reached the island through dispersal from Cenozoic times. Ancient lineages may have experienced a different history compared to more recent Cenozoic arrivals, as such lineages would have encountered geoclimatic shifts over an extended time period. The motivation for this study was to unravel the signature of diversification in an ancient lineage by comparing an area known for...

Data from: Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes

Pablo Saenz-Agudelo, Joseph D. DiBattista, Marek J. Piatek, Michelle R. Gaither, Hugo B. Harrison, Gerrit B. Nanninga & Michael L. Berumen
Understanding the processes that shape patterns of genetic structure across space is a central aim of landscape genetics. However, it remains unclear how geographic features and environmental variables shape gene flow, particularly for marine species in large complex seascapes. Here, we evaluated the genomic composition of the two-band anemonefish Amphiprion bicinctus across its entire geographic range in the Red Sea and Gulf of Aden, as well as its close relative, Amphiprion omanensis endemic to the...

Data from: X-ray microtomography for ant taxonomy: an exploration and case study with two new Terataner (Hymenoptera, Formicidae, Myrmicinae) species from Madagascar

Francisco Hita Garcia, Georg Fischer, Cong Liu, Tracy L. Audisio, Gary D. Alpert, Brian L. Fisher & Evan P. Economo
We explore the potential of x-ray micro computed tomography (μCT) for the field of ant taxonomy by using it to enhance the descriptions of two remarkable new species of the ant genus Terataner: T. balrog sp. n. and T. nymeria sp. n.. We provide an illustrated worker-based species identification key for all species found on Madagascar, as well as detailed taxonomic descriptions, which include diagnoses, discussions, measurements, natural history data, high-quality montage images and distribution...

Data from: Angelfishes, paper tigers and the devilish taxonomy of the Centropyge flavissima complex

Joseph D. DiBattista, Michelle R. Gaither, Jean-Paul A. Hobbs, Luiz A. Rocha & Brian W. Bowen
The pygmy angelfishes (genus Centropyge) provide numerous examples of discordance between color morphology, taxonomy and evolutionary genetic lineages. This discordance is especially evident in the Centropyge flavissima complex, which includes three primary color morphs, three previously recognized species (C. flavissima, C. eibli and C. vrolikii) and three distinct mitochondrial (mtDNA) lineages that do not align with species designations. Our previous research showed that the putative C. flavissima arose independently in the Indian and Pacific Oceans,...

Data from: Taxonomic revision of the Malagasy Camponotus grandidieri and niveosetosus species groups (Hymenoptera, Formicidae) using qualitative and quantitative morphology

Jean Claude Rakotonirina, Sándor Csősz & Brian L. Fisher
The Camponotus grandidieri species group and Camponotus niveosetosus species group of the Malagasy region are revised. Species delimitation was inferred from the evidence of both qualitative morphological analysis and multivariate morphometry. The multivariate method combined the Nest Centroid (NC)-clustering method and Partitioning Algorithm based on Recursive Thresholding (PART) function to generate hypotheses about species boundaries (clusters) based on 19 continuous morphological traits of minor workers. The proposed species hypotheses were tested by cumulative cross-validated Linear...

Data from: Understanding past population dynamics: Bayesian coalescent-based modeling with covariates

Mandev S. Gill, Philippe Lemey, Shannon N. Bennett, Roman Biek & Marc A. Suchard
Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics and evolutionary biology. Kingman's coalescent process enables inference of past population dynamics directly from molecular sequence data, and researchers have developed a number of flexible coalescent-based models for Bayesian nonparametric estimation of the effective population size as a function of time. Major goals of demographic reconstruction include identifying driving factors of effective population size, and...

Data from: Mulloidichthys flavolineatus flavicaudus Fernandez-Silva & Randall subsp. n. (Perciformes: Mullidae), a new subspecies of goatfish from the Red Sea and Arabian Sea

Iria Fernandaz-Silva, John Randall, Daniel Golani, Sergey V. Bogorodsky, Iria Fernandez-Silva & John E. Randall
The number of goatfish sp­­ecies has increased recently, thanks in part to the application of molecular approaches to the taxonomy of a family with conservative morphology and widespread intraspecific color variation. A new subspecies Mulloidichthys flavolineatus flavicaudus Fernandez-Silva & Randall subsp. n. is described from the Red Sea and Arabian Sea, including Socotra and Gulf of Oman. The two subspecies are distinguished by 1.7% sequence divergence at the mitochondrial cytochrome b gene, a yellow caudal...

Data from: The rise of army ants and their relatives: diversification of specialized predatory doryline ants

Sean G. Brady, Brian L. Fisher, Ted R. Schultz & Philip S. Ward
Background Army ants are dominant invertebrate predators in tropical and subtropical terrestrial ecosystems. Their close relatives within the dorylomorph group of ants are also highly specialized predators, although much less is known about their biology. We analyzed molecular data generated from 11 nuclear genes to infer a phylogeny for the major dorylomorph lineages, and incorporated fossil evidence to infer divergence times under a relaxed molecular clock. Results Because our results indicate that one subfamily and...

Data from: Paleotropical diversification dominates the evolution of the hyperdiverse ant tribe Crematogastrini (Hymenoptera: Formicidae)

Bonnie B. Blaimer, Philip S. Ward, Ted R. Schultz, Brian L. Fisher & Seán G. Brady
Levels of diversity vary strikingly among different phylogenetic lineages of ants. Rapid radiations in early ant evolution have often proven difficult to resolve with traditional Sanger-sequencing data sets of modest size. We provide a phylogenomic perspective on the evolution of the hyperdiverse ant tribe Crematogastrini by analyzing sequence data for nearly 1800 ultraconserved element (UCE) loci from 153 species comprising 56 genera. We reconstruct a next-to-complete genus-level phylogeny using concatenated maximum-likelihood and species-tree approaches, estimate...

Data from: Brazilian marsupial frogs are diphyletic (Anura: Hemiphractidae: Gastrotheca)

David C. Blackburn & William E. Duellman
Molecular phylogenetic analyses based on expanded taxonomic and geographic sampling support the monophyly of the marsupial frog genera (family Hemiphractidae), resolve six geographically circumscribed lineages within Gastrotheca, and, for the first time, reveal that two divergent lineages of Gastrotheca inhabit the Atlantic Coastal Forests of Brazil. Within Gastrotheca, the earliest diverging clade is confined to northeastern Brazil, whereas the three subsequent diverging lineages are restricted to northern Venezuela (G. walkeri), southeastern Brazil, and northwestern South...

Data from: Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment

David Gray, David Weissman, Jeffrey Cole, Emily Lemmon & Alan Lemmon
We present the first comprehensive molecular phylogeny of Gryllus field cricket species found in the United States and Canada, select additional named Gryllus species found in Mexico and the Bahamas, plus the European field cricket G. campestris Linnaeus and the Afro-Eurasian cricket G. bimaculatus De Geer. Acheta, Teleogryllus, and Nigrogryllus were used as outgroups. Anchored hybrid enrichment was used to generate 492,531 base pairs of DNA sequence from 563 loci. RAxML analysis of concatenated sequence...

Evolutionary drivers of sexual signal variation in Amazon slender anoles

Ivan Prates, Annelise D'Angiolella, Miguel Rodrigues, Paulo Melo-Sampaio, Kevin De Queiroz & Rayna Bell
Phenotypic variation among populations, as seen in the signaling traits of many species, provides an opportunity to test whether similar factors generate repeated phenotypic patterns in different parts of a species’ range. We investigated whether genetic divergence, abiotic gradients, and sympatry with closely related species explain variation in the dewlap colors of Amazon Slender Anoles, Anolis fuscoauratus. To this aim, we characterized dewlap diversity in the field with respect to population genetic structure and evolutionary...

A target enrichment probe set for resolving the flagellate land plant tree of life

Jesse W. Breinholt, Sarah B. Carey, George P. Tiley, E. Christine Davis, Lorena Endara, Stuart F. McDaniel, Leandro Neves, Emily B. Sessa, Matt Von Konrat, Susan Fawcett, Stefanie M. Ickert-Bond, Paulo H. Labiak, Juan Larraín, Marcus Lehnert, Lily R. Lewis, Nathalie S. Nagalingum, Nikisha Patel, Stefan A. Rensing, Weston Testo, Alejandra Vasco, Juan Carlos Villarreal, Evelyn Webb Williams, J. Gordon Burleigh, Sahut Chantanaorrapint, Leandro G. Neves … & Stefanie M. Ickert‐Bond
Premise of the Study: New sequencing technologies enable the possibility of generating large-scale molecular datasets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms. Methods and Results: We leveraged existing transcriptome and genome sequence data to design a set of 56,989 probes for target...

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