180 Works

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...

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...

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...

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...

Data from: Diversification rates have no effect on the convergent evolution of foraging strategies in the most speciose genus of bats, Myotis

Ariadna E Morales, Manuel Ruedi, Kathryn Field & Bryan C Carstens
Adaptive radiations are defined as rapid diversification with phenotypic innovation led by colonization to new environments. Notably, adaptive radiations can occur in parallel when habitats with similar selective pressures are accessible promoting convergent adaptions. While convergent evolution appears to be a common process, it is unclear what are the main drivers leading the reappearance of morphologies or ecological roles. We explore this question in Myotis bats, the only Chiropteran genus with a worldwide distribution. Three...

Data from: From refugia to rookeries: phylogeography of Atlantic green turtles

Eugenia Naro-Maciel, Brendan N. Reid, S. Elizabeth Alter, George Amato, Karen A. Bjorndal, Alan B. Bolten, Meredith Martin, Campbell J. Nairn, Brian Shamblin & Oscar Pineda-Catalan
Investigating species’ distribution and abundance over time is central to evolutionary biology, and provides important context for conservation and management. With respect to population genetic structure in green sea turtles (Chelonia mydas), certain processes such as female philopatry to natal rookeries are well understood, while others, such as male philopatry and historical changes in distribution and abundance, remain relatively understudied. Further, although inferences from mitochondrial DNA and nuclear microsatellites have both been critical in identifying...

Data from: Clonal reproduction shapes evolution in the lizard malaria parasite Plasmodium floridense

Bryan G. Falk, Richard E. Glor & Susan L. Perkins
The preponderant clonal evolution hypothesis (PCE) predicts that frequent clonal reproduction (sex between two clones) in many pathogens capable of sexual recombination results in strong linkage disequilibrium and the presence of discrete genetic subdivisions characterized by occasional gene flow. We expand on the PCE and predict that higher rates of clonal reproduction will result in: (1) morphologically cryptic species that exhibit (2) low within-species variation and (3) recent between-species divergence. We tested these predictions in...

Data from: Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes

Sara Ruane, Christopher J. Raxworthy, Alan R. Lemmon, Emily Moriarty Lemmon & Frank T. Burbrink
Background: Using molecular data generated by high throughput next generation sequencing (NGS) platforms to infer phylogeny is becoming common as costs go down and the ability to capture loci from across the genome goes up. While there is a general consensus that greater numbers of independent loci should result in more robust phylogenetic estimates, few studies have compared phylogenies resulting from smaller datasets for commonly used genetic markers with the large datasets captured using NGS....

Data from: Fifty thousand years of arctic vegetation and megafaunal diet

Eske Willerslev, John Davison, Mari Moora, Martin Zobel, Eric Coissac, Mary E. Edwards, Eline D. Lorenzen, Mette Vestergård, Galina Gussarova, James Haile, Joseph Craine, Gaddy Bergmann, Ludovic Gielly, Sanne Boessenkool, Laura S. Epp, Peter B. Pearman, Rachid Cheddadi, David Murray, Karri Anne Bråthen, Nigel Yoccoz, Heather Binney, Corinne Cruaud, Patrick Wincker, Tomasz Goslar, Inger Greve Alsos … & Pierre Taberlet
Although it is generally agreed that the arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we additionally explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many...

Data from: Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms

Ronald M. Clouse, Gregorio V. Linchangco, Alexander M. Kerr, Robert W. Reid & Daniel A. Janies
Tissue inhibitors of metalloproteinases (TIMPs) help regulate the extracellular matrix (ECM) in animals, mostly by inhibiting matrix metalloproteinases (MMPs). They are important activators of mutable collagenous tissue (MCT), which have been extensively studied in echinoderms, and the four TIMP copies in humans have been studied for their role in cancer. To understand the evolution of TIMPs, we combined 405 TIMPs from an echinoderm transcriptome dataset built from 41 specimens representing all five classes of echinoderms...

Data from: A multilocus molecular phylogeny for the avian genus Liocichla (Passeriformes: Leiothrichidae: Liocichla)

Herman L. Mays, Bailey D. McKay, Dieter Thomas Tietze, Cheng-Te Yao, Lindsey N. Miller, Kathleen N. Moreland & Fumin Lei
Background: Historically the babblers have been assigned to the family Timaliidae but several recent studies have attempted to rest the taxonomy of this diverse passerine assemblage on a more firm evolutionary footing. The result has been a major rearrangement of the group. A well-supported and comprehensive phylogeny for this widespread avian group is an important part of testing evolutionary and biogeographic hypotheses, especially in Asia where the babblers are a key component of many forest...

Data from: Challenging the inbreeding hypothesis in a eusocial mammal: population genetics of the naked mole-rat, Heterocephalus glaber.

Colleen M. Ingram, Nicholas J. Troendle, Clare A. Gill, Stanton Braude & Rodney L. Honeycutt
The role of genetic relatedness in the evolution of eusociality has been the topic of much debate, especially when contrasting eusocial insects with vertebrates displaying reproductive altruism. The naked mole-rat, Heterocephalus glaber, was the first described eusocial mammal. Although this discovery was based on an ecological constraints model of eusocial evolution, early genetic studies reported high levels of relatedness in naked mole-rats, providing a compelling argument that low dispersal rates and consanguineous mating (inbreeding as...

Data from: Bayesian hierarchical models suggest oldest known plant-visiting bat was omnivorous

Laurel R. Yohe, Paúl M. Velazco, Danny Rojas, Beth E. Gerstner, Nancy B. Simmons & Liliana M. Dávalos
The earliest record of plant visiting in bats dates to the Middle Miocene of La Venta, the world's most diverse tropical palaeocommunity. Palynephyllum antimaster is known from molars that indicate nectarivory. Skull length, an important indicator of key traits such as body size, bite force and trophic specialization, remains unknown. We developed Bayesian models to infer skull length based on dental measurements. These models account for variation within and between species, variation between clades, and...

Data from: Description of a soft-bodied invertebrate with microcomputed tomography and revision of the genus Chtonobdella (Hirudinea: Haemadipsidae)

Michael Tessler, Amalie Barrio, Elizabeth Borda, Rebecca Rood-Goldman, Morgan Hill & Mark E. Siddall
Two-jawed (duognathous) terrestrial leeches in the Haemadipsidae are major pests across their wide geographic range, represented by numerous endemic species in Australia and across many islands in the Indian and Pacific Oceans. However, haemadipsid taxonomy, based largely on externally visible characters, remains in conflict with phylogenetic relationships. We capitalize on the power of microcomputed tomography (μCT), allowing for the first description of an extant soft-bodied species – Chtonobdella tanae sp. n. – using this technology....

Data from: The aggregate site frequency spectrum (aSFS) for comparative population genomic inference

Alexander T. Xue & Michael J. Hickerson
Understanding how assemblages of species responded to past climate change is a central goal of comparative phylogeography and comparative population genomics, and an endeavor that has increasing potential to integrate with community ecology. New sequencing technology now provides the potential to gain complex demographic inference at unprecedented resolution across assemblages of non-model species. To this end, we introduce the aggregate site frequency spectrum (aSFS), an expansion of the site frequency spectrum to use single nucleotide...

Data from: Population structure of a widespread bat (Tadarida brasiliensis) in an island system

Kelly A. Speer, Brandi Jo Petronio, Nancy B. Simmons, Rebecca Richey, Kristin Magrini, J. Angel Soto-Centeno & David L. Reed
Dispersal is a driving factor in the creation and maintenance of biodiversity, yet little is known about the effects of habitat variation and geography on dispersal and population connectivity in most mammalian groups. Bats of the family Molossidae are fast-flying mammals thought to have potentially high dispersal ability, and recent studies have indicated gene flow across hundreds of kilometers in continental North American populations of the Brazilian free-tailed bat, Tadarida brasiliensis. We examined the population...

Data from: Structure-function covariation with nonfeeding ecological variables influences evolution of feeding specialization in Carnivora

Jack Tseng & John J. Flynn
Skull shape convergence is pervasive among vertebrates. Although this is frequently inferred to indicate similar functional underpinnings, neither the specific structure-function linkages nor the selective environments in which the supposed functional adaptations arose are commonly identified and tested. We demonstrate that nonfeeding factors relating to sexual maturity and precipitation-related arboreality also can generate structure-function relationships in the skulls of carnivorans (dogs, cats, seals, and relatives) through covariation with masticatory performance. We estimated measures of masticatory...

Data from: Proteroctopus ribeti in coleoid evolution

Isabelle Kruta, Isabelle Rouget, Sylvain Charbonnier, Jérémie Bardin, Vincent Fernandez, Damien Germain, Arnaud Brayard & Neil Landman
Palaeontological data are key elements for inferring ancestral character states and the assembly of character complexes, but cephalopod fossils preserving soft tissues are very rare. The exceptionally well-preserved, unique specimen of Jurassic Proteroctopus ribeti Fischer & Riou from the Lagerstätte of La-Voulte-sur-Rhône (c. 165 Ma, France) is one of the few fossil octopod related taxa, but is rarely considered in evolutionary studies. In this paper, we used synchrotron microtomography to reappraise its external characters and...

Data from: How well does a part represent the whole? A comparison of cranidial shape evolution with exoskeletal character evolution in the trilobite family Pterocephaliidae

Melanie Jane Hopkins
For taphonomic and practical reasons, our understanding of morphological evolution within and among species is based primarily on measurements taken from one or a few morphological traits. However, patterns can be highly dependent on trait choice, making it difficult to draw conclusions about evolution of species or clades as a whole. In this paper, I test whether patterns of evolutionary change in the shape of a part are coincident with patterns of evolutionary change based...

Data from: Archaeogenomic evidence reveals prehistoric matrilineal dynasty

Douglas J. Kennett, Stephen Plog, Richard J. George, Brendan J. Culleton, Adam S. Watson, Pontus Skoglund, Nadin Rohland, Swapan Mallick, Kristin Stewardson, Logan Kistler, Steven A. LeBlanc, Peter M. Whiteley, David Reich & George H. Perry
For societies with writing systems, hereditary leadership is documented as one of the hallmarks of early political complexity and governance. In contrast, it is unknown whether hereditary succession played a role in the early formation of prehistoric complex societies that lacked writing. Here we use an archaeogenomic approach to identify an elite matriline that persisted between 800 and 1130 CE in Chaco Canyon, the centre of an expansive prehistoric complex society in the Southwestern United...

Data from: How many more? Sample size determination in studies of morphological integration and evolvability

Mark Grabowski & Arthur Porto
The variational properties of living organisms are an important component of current evolutionary theory. As a consequence, researchers working on the field of multivariate evolution have increasingly used integration and evolvability statistics as a way of capturing the potentially complex patterns of trait association and their effects over evolutionary trajectories. Little attention has been paid, however, to the cascading effects that inaccurate estimates of trait covariance have on these widely used evolutionary statistics. Here, we...

Data from: Bioclimatic variables derived from remote sensing: assessment and application for species distribution modeling

Eric Waltari, Ronny Schroeder, Kyle McDonald, Robert P. Anderson & Ana Carnaval
Remote sensing techniques offer an opportunity to improve biodiversity modeling and prediction worldwide. Yet, to date, the weather-station based WorldClim dataset has been the primary source of temperature and precipitation information used in correlative species distribution models. WorldClim consists of grids interpolated from in situ station data recorded primarily from 1960 to 1990. Those datasets suffer from uneven geographic coverage, with many areas of Earth poorly represented. Here, we compare two remote sensing data sources...

Data from: Simple versus complex models of trait evolution and stasis as a response to environmental change

Gene Hunt, Melanie J. Hopkins & Scott Lidgard
Previous analyses of evolutionary patterns, or modes, in fossil lineages have focused overwhelmingly on three simple models: stasis, random walks, and directional evolution. Here we use likelihood methods to fit an expanded set of evolutionary models to a large compilation of ancestor–descendant series of populations from the fossil record. In addition to the standard three models, we assess more complex models with punctuations and shifts from one evolutionary mode to another. As in previous studies,...

Data from: Disentangling the genetic effects of refugial isolation and range expansion in a trans-continentally distributed species

Brendan N. Reid, Jamie M. Kass, Seth Wollney, Evelyn L. Jensen, Michael A. Russello, Ella M. Viola, Jenna Pantophlet, John B. Iverson, Marcus Z. Peery, Christopher J. Raxworthy & Eugenia Naro-Maciel
In wide-ranging taxa with historically dynamic ranges, past allopatric isolation and range expansion can both influence the current structure of genetic diversity. Considering alternate historical scenarios involving expansion from either a single refugium or from multiple refugia can be useful in differentiating the effects of isolation and expansion. Here, we examined patterns of genetic variability in the trans-continentally distributed painted turtle (Chrysemys picta). We utilized an existing phylogeographic dataset for the mitochondrial control region and...

Data from: Genomic divergence in allopatric Northern Cardinals of the North American warm deserts is linked to behavioral differentiation

Kaiya L. Provost, & Brian T Smith
Biogeographic barriers are thought to be important in initiating speciation through geographic isolation, but they rarely indiscriminately and completely reduce gene flow across the entire community. Understanding which species’ attributes regulate a barrier could help elucidate how speciation is initiated and isolation maintained. Here, we investigated the association of behavioral isolation on population differentiation in Northern Cardinals (Cardinalis cardinalis) distributed across the Cochise Filter Barrier, a region of transitional habitat which separates the Sonoran and...

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