85 Works

Amino acids (AA) all genes for: Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics

Keith Bayless, Michelle Trautwein, Karen Meusemann, David Yeates & Brian Wiegmann
Background: The largest radiation of animal life since the end Cretaceous extinction event 66 million years ago is that of schizophoran flies: a third of fly diversity including Drosophila lab fruit flies, house flies, and many other well and poorly known true flies. Rapid diversification has hindered previous attempts to elucidate the phylogenetic relationships among major schizophoran clades. A robust phylogenetic hypothesis for the major lineages containing these 55,000 described species would be critical to...

Finding complexity in complexes: assessing the causes of mitonuclear discordance in a problematic species complex of Mesoamerican toads

Thomas Firneno, Justin O'Neill, Daniel Portik, Alyson Emery, Josiah Townsend & Matthew Fujita
Mitonuclear discordance is a frequently encountered pattern in phylogeographic studies and occurs when mitochondrial and nuclear DNA display conflicting signals. Discordance among these genetic markers can be caused by several factors including confounded taxonomies, gene flow, and incomplete lineage sorting. In this study, we present a strong case of mitonuclear discordance in a species complex of toads (Bufonidae: Incilius coccifer complex) found in the Chortís Block of Central America. To determine the cause of mitonuclear...

Data from: A phylogenomic resolution of the sea urchin tree of life

Nicolás Mongiardino Koch, Simon E. Coppard, Harilaos A. Lessios, Derek E.G. Briggs, Rich Mooi & Greg W. Rouse
Background: Echinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1,000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a...

Data from: Advancing mite phylogenomics: designing ultraconserved elements for Acari phylogeny

Matthew H. Van Dam, Michelle Trautwein, Greg Spicer & Lauren Esposito
Mites (Acari) are one of the most diverse groups of life on Earth, yet their evolutionary relationships are poorly understood. Also, the resolution of broader arachnid phylogeny has been hindered by an underrepresentation of mite diversity in phylogenomic analyses. To further our understanding of Acari evolution,we design targeted ultraconserved genomic elements (UCEs) probes, intended for resolving the complex relationships between mite lineages and closely related arachnids. We then test our Acari UCE baits in-silico by...

Data from: Idiosyncratic responses to climate-driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands

Rayna C. Bell, Juan L. Parra, Gabriel Badjedjea, Michael F. Barej, David C. Blackburn, Marius Burger, Alan Channing, J. Maximilian Dehling, Eli Greenbaum, Václav Gvoždík, Jos Kielgast, Chifundera Kusamba, Stefan Lötters, Patrick J. McLaughlin, Zoltán T. Nagy, Mark-Oliver Rödel, Daniel M. Portik, Bryan L. Stuart, Jeremy VanDerWal, Ange-Ghislain Zassi Boulou & Kelly R. Zamudio
Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co-distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo-Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a...

Data from: Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

Henrik Krehenwinkel, Madeline Wolf, Jun Ying Lim, Andrew J. Rominger, Warren B. Simison & Rosemary G. Gillespie
Amplicon based metabarcoding promises rapid and cost-efficient analyses of species composition. However, it is disputed whether abundance estimates can be derived from metabarcoding due to taxon specific PCR amplification biases. PCR-free approaches have been suggested to mitigate this problem, but come with considerable increases in workload and cost. Here, we analyze multilocus datasets of diverse arthropod communities, to evaluate whether amplification bias can be countered by (1) targeting loci with highly degenerate primers or conserved...

Data from: A phylogenomic analysis of turtles

Nicholas G. Crawford, James F. Parham, Anna B. Sellas, Brant C. Faircloth, Travis C. Glenn, Theodore J. Papefuss, James B. Henderson, Madison H. Hansen, W. Brian Simison & Theodore J. Papenfuss
Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2,381 ultraconserved element (UCE) loci representing a total of 1,718,154 bp of aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. This robust...

Data from: The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota

Henrik Krehenwinkel, Marisa Fong, Susan Kennedy, Edward Greg Huang, Suzuki Noriyuki, Luis Cayetano & Rosemary Gillespie
PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias...

Data from: Quantifying the dark data in museum fossil collections as palaeontology undergoes a second digital revolution

Charles R. Marshall, Seth Finnegan, Erica C. Clites, Patricia A. Holroyd, Nicole Bonuso, Crystal Cortez, Edward Davis, Gregory P. Dietl, Patrick S. Druckenmiller, Ron C. Eng, Christine Garcia, Kathryn Estes-Smargiassi, Austin Hendy, Kathy A. Hollis, Holly Little, Elizabeth A. Nesbitt, Peter Roopnarine, Leslie Skibinski, Jann Vendetti & Lisa D. White
Large-scale analysis of the fossil record requires aggregation of palaeontological data from individual fossil localities. Prior to computers these synoptic datasets were compiled by hand, a laborious undertaking that took years of effort and forced palaeontologists to make difficult choices about what types of data to tabulate. The advent of desktop computers ushered in palaeontology’s first digital revolution – online literature-based databases, such as the Paleobiology Database (PBDB). However, the published literature represents only a...

Data from: Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens

Ethan B. Linck, Zachary R. Hanna, Anna Sellas & John P. Dumbacher
Laboratory techniques for high-throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site-associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens. The hyRAD method employs fragments produced in a restriction site-associated double digestion as the basis for probes that capture orthologous loci...

Genomic characterization and curation of UCEs improves species tree reconstruction: Supplementary Material S1

Matthew Van Dam
Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while...

Data from: Two new phragmotic ant species from Africa: morphology and next-generation sequencing solve a caste association problem in the genus Carebara Westwood

Georg Fischer, Frank L. Azorsa, Francisco Hita Garcia, Alexander S. Mikheyev, Evan P. Economo, Frank Azorsa, Alexander Mikheyev & Evan Economo
Phragmotic or “door head” ants have evolved independently in several ant genera across the world, but in Africa only one case has been documented until now. Carebara elmenteitae (Patrizi) is known from only a single phragmotic major worker collected from sifted leaf-litter near Lake Elmenteita in Kenya, but here the worker castes of two species collected from Kakamega Forest, a small rainforest in Western Kenya, are studied. Phragmotic major workers were previously identified as Carebara...

Data from: Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol

Jeremy A. Miller, Kevin K. Beentjes, Peter Van Helsdingen, Steven Ijland & Jeremy Miller
We report initial results from an ongoing effort to build a library of DNA barcode sequences for Dutch spiders and investigate the utility of museum collections as a source of specimens for barcoding spiders. Source material for the library comes from a combination of specimens freshly collected in the field specifically for this project and museum specimens collected in the past. For the museum specimens, we focus on 31 species that have been frequently collected...

Data from: Spider phylogenomics: untangling the spider tree of life

Jason Bond, Nicole L. Garrison, Juanita Rodriguez, Ingi Agnarsson, Jonathan A. Coddington, Charles E. Griswold, Christopher A. Hamilton, Marshal Hedin, Kevin Kocot, Joel M. Ledford & Jason E. Bond
Spiders (Order Araneae) are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the “usual suspect” genes...

Supplementary information for aquatic and blood-feeding Diptera

Nina Pak, Allan Cabrero, Keith Bayless & Michelle Trautwein
Aquatic Diptera are some of the most diverse and notable flies, impacting human health and providing ecosystem services. Despite the importance of aquatic Diptera, the evolution of aquatic life history and blood-feeding, are not sufficiently understood. Here, we examine the evolution of aquatic life histories and their associations with blood-feeding across Diptera. Aquatic and blood-feeding Diptera are phylogenetically conserved across the fly tree of life. We found evidence that the most recent common ancestor of...

Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula

Joseph DiBattista, Pablo Saenz-Agudelo, Marek Piatek, Fernando Cagua, Brian Bowen, John Choat, Luiz Rocha, Michelle Gaither, Jean-Paul Hobbs, Tane Sinclair-Taylor, Jennifer McIlwain, Mark Priest, Camrin Braun, Nigel Hussey, Steven Kessel & Michael Berumen
Genetic structure within marine species may be driven by local adaptation to their environment, or alternatively by historical processes, such as geographic isolation. The gulfs and seas bordering the Arabian Peninsula offer an ideal setting to examine connectivity patterns in coral reef fishes with respect to environmental gradients and vicariance. The Red Sea is characterized by a unique marine fauna, historical periods of desiccation and isolation, as well as environmental gradients in salinity, temperature, and...

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: Ecological and environmental stability in offshore Southern California Marine Basins through the Holocene

Hannah Palmer, Tessa Hill, Esther Kennedy, Peter Roopnarine, Sonali Langlois, Katherine Reyes & Lowell Stott
In the face of ongoing marine deoxygenation, understanding timescales and drivers of past oxygenation change is of critical importance. Marine sediment cores from tiered silled basins provide a natural laboratory to constrain timing and implications of oxygenation changes across multiple depths. Here, we reconstruct oxygenation and environmental change over time using benthic foraminiferal assemblages from sediment cores from three basins across the Southern California Borderlands: Tanner Basin (EW9504-09PC, 1194 m water depth), San Nicolas Basin...

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),...

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...

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: 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...

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....

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