85 Works

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...

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: Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

Nicolás Mongiardino Koch, Jeffrey R Thompson, Avery S Hatch, Marina F McCowin, A Frances Armstrong, Simon E Coppard, Felipe Aguilera, Omri Bronstein, Andreas Kroh, Rich Mooi & Greg W Rouse
Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ eighteen novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise...

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: 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: 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: 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: 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: 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: 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...

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...

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...

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...

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...

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...

Incipient speciation and secondary contact in a fossorial island endemic, the São Tomé caecilian

Kyle O'Connell, Ivan Prates, Lauren Scheinberg, Kevin Mulder & Rayna Bell
Secondary contact of lineages in the early stages of divergence can result in lineage fusion or promote reproductive isolation through reinforcement. While these processes are well studied in many taxonomic groups, we know little about their contribution to diversification of the secretive and enigmatic caecilians (Amphibia: Gymnophiona). Here, we combine genetic (mtDNA and genome-wide SNPs) and phenotypic data to investigate the divergence history of caecilians endemic to the oceanic island of São Tomé in the...

Systematic revision of the arboreal Neotropical ‘Thorellii’ clade of Centruroides Marx, 1890 bark scorpions (Buthidae c.l. Koch, 1837) with descriptions of six new species

Aaron Goodman, Lorenzo Prendini, Oscar Francke & Lauren Esposito
The arboreal Neotropical ‘thorellii’ clade of Centruroides Marx, 1890 bark scorpions (Buthidae C.L. Koch, 1837) is revised, using a novel approach to species delimitation. A phylogenetic analysis, based on 112 morphological characters and 1078 aligned DNA nucleotides from the mitochondrial Cytochrome c Oxidase Subunit I (COI) gene, provided the framework for placing singletons from geographically disparate localities (and often with suboptimal preservation) using COI minibarcodes, thereby enlarging the taxon sample for diagnosis and delimitation of...

A high-quality carabid genome provides insights into beetle genome evolution and cold adaptation

Yi-Ming Weng, Charlotte Francoeur, Cameron Currie, David Kavanaugh & Sean Schoville
The hyper-diverse order Coleoptera comprises a staggering ~25% of known species on Earth. Despite recent breakthroughs in next generation sequencing, there remains a limited representation of beetle diversity in assembled genomes. Most notably, the ground beetle family Carabidae, comprising more than 40,000 described species, has not been studied in a comparative genomics framework using whole genome data. Here we generate a high-quality genome assembly for Nebria riversi, to examine sources of novelty in the genome...

Data from: Patterns of genomic divergence and signals of selection in sympatric and allopatric northeastern Pacific and Sea of Cortez populations of the sargo (Anisotremus davidsonii) and longjaw mudsucker (Gillichthys mirabilis)

Eric Garcia, Brian Simison & Giacomo Bernardi
Studying how isolation can impact population divergence and adaptation in co-distributed species can bring us closer to understanding how landscapes affect biodiversity. The Sargo, Anisotremus davidsonii (Haemulidae), and the Longjaw mudsucker, Gillichthys mirabilis (Gobiidae), offer a notable framework to study such mechanisms as their Pacific populations cross phylogeographic breaks at Point Conception, California, USA, and Punta Eugenia, Mexico, and are separated to those in the Sea of Cortez by the Baja California peninsula. Here, thousands...

Speciation and gene flow across an elevational gradient in New Guinea kingfishers

Ethan Linck, Benjamin Freeman & John Dumbacher
Closely related species with parapatric elevational ranges are ubiquitous in tropical mountains worldwide. The gradient speciation hypothesis proposes that these series are the result of in situ ecological speciation driven by divergent selection across elevation. Direct tests of this scenario have been hampered by the difficulty inferring the geographic arrangement of populations at the time of divergence. In cichlids, sticklebacks, and Timema stick insects, support for ecological speciation driven by other selective pressures has come...

Data From: Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae)

Xuankun Li, Luisa C. Teasdale, Keith M. Bayless, Allan G. Ellis, Brian M. Wiegmann, Carlos José E. Lamas, Christine L. Lambkin, Neal L. Evenhuis, James A. Nicholls, Diana Hartley, Seunggwan Shin, Michelle Trautwein, Andreas Zwick, Bryan D. Lessard & David K. Yeates
Bombyliidae is a very species-rich and widespread family of parasitoid flies with more than 250 genera classified into 17 extant subfamilies. However, little is known about their evolutionary history or how their present-day diversity was shaped. Transcriptomes of 15 species and anchored hybrid enrichment (AHE) sequence captures of 86 species, representing 94 bee fly species and 14 subfamilies, were used to reconstruct the phylogeny of Bombyliidae. We integrated data from transcriptomes across each of the...

Drainage basins serve as multiple glacial refugia for alpine habitats in the Sierra Nevada Mountains, California

Yi-Ming Weng, Sean Schoville & David Kavanaugh
The evolutionary histories of alpine species are often directly associated with responses to glaciation. Deep divergence among populations and complex patterns of genetic variation have been inferred as consequences of persistence within glacier boundaries (i.e. on nunataks), while shallow divergence and limited genetic variation is assumed to result from expansion from large refugia at the edge of ice shields (i.e. massifs de refuge). However, for some species, dependence on specific microhabitats could profoundly influence their...

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  • California Academy of Sciences
  • University of California, Berkeley
  • University of California, Davis
  • Smithsonian Institution
  • University of Washington
  • King Abdullah University of Science and Technology
  • University of California System
  • Duke University
  • University of Queensland
  • University of Memphis