14 Works

Data from: The earliest bird-line archosaurs and the assembly of the dinosaur body plan

Sterling J. Nesbitt, Richard J. Butler, Martin D. Ezcurra, Paul M. Barrett, Michelle R. Stocker, Kenneth D. Angielczyk, Roger M. H. Smith, Christian A. Sidor, Grzegorz Niedźwiedzki, Andrey G. Sennikov & Alan J. Charig
The relationship between dinosaurs and other reptiles is well established, but the sequence of acquisition of dinosaurian features has been obscured by the scarcity of fossils with transitional morphologies. The closest extinct relatives of dinosaurs either have highly derived morphologies or are known from poorly preserved or incomplete material. Here we describe one of the stratigraphically lowest and phylogenetically earliest members of the avian stem lineage (Avemetatarsalia), Teleocrater rhadinus gen. et sp. nov., from the...

Data from: Caves as microrefugia: Pleistocene phylogeography of the troglophilic North American scorpion Pseudouroctonus reddelli

Robert W. Bryson, Lorenzo Prendini, Warren E. Savary & Peter B. Pearman
Background: Survival in microrefugia represents an important paradigm in phylogeography for explaining rapid postglacial re-colonization by species in temperate regions. Microrefugia may allow populations to persist in areas where the climatic conditions on the surface have become unfavourable. Caves generally contain stable microclimates and may represent microrefugia for species capable of exploiting both cave and surface habitats (troglophiles). We examine the phylogeography of the troglophilic North American vaejovid scorpion Pseudouroctonus reddelli using 1,993 base pairs...

Data from: Geometric morphometric analyses of worn cheek teeth help identify extant and extinct gophers (Rodentia: Geomyidae)

Jonathan J. M. Calede & Jennifer W. Glusman
Studies of the biostratigraphy and palaeoecology of fossil vertebrate assemblages require large samples of accurately identified specimens. Such analyses can be hampered by the inability to assign isolated and worn remains to specific taxa. Entoptychine gophers are a diverse group of burrowing rodents found in Oligo-Miocene deposits of the western United States. In both entoptychines and their extant relatives the geomyines, diagnostic characters of the occlusal surface of the teeth are modified with wear, making...

Data from: Phylogeography of the Trans-Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of southeastern Mexico

Adam D. Leaché, Julia A. Palacios, Vladimir N. Minin, & Robert W. Bryson
We quantify the population divergence processes that shaped population genetic structure in the Trans-Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south-eastern Mexico. Multilocus genetic data from nine nuclear loci and mitochondrial (mt)DNA were used to estimate the population divergence history for 47 samples of S. bicanthalis. Bayesian clustering methods partitioned S. bicanthalis into three populations: (1) a southern population in Oaxaca and southern Puebla; (2) a population in western Puebla; and (3) a...

Data from: Identification of the notothenioid sister lineage illuminates the biogeographic history of an Antarctic adaptive radiation

Thomas J. Near, Alex Dornburg, Richard C. Harrington, Claudio Oliveira, Theodore W. Pietsch, Christine E. Thacker, Takashi P. Satoh, Eri Katayama, Peter C. Wainwright, Joseph T. Eastman & Jeremy M. Beaulieu
Background: Antarctic notothenioids are an impressive adaptive radiation. While they share recent common ancestry with several species-depauperate lineages that exhibit a relictual distribution in areas peripheral to the Southern Ocean, an understanding of their evolutionary origins and biogeographic history is limited as the sister lineage of notothenioids remains unidentified. The phylogenetic placement of notothenioids among major lineages of perciform fishes, which include sculpins, rockfishes, sticklebacks, eelpouts, scorpionfishes, perches, groupers and soapfishes, remains unresolved. We investigate...

Data from: Hidden histories of gene flow in highland birds revealed with genomic markers

Eugenia Zarza, Brant C. Faircloth, Whitney L. E. Tsai, , John Klicka, John E. McCormack, Whitney L.E. Tsai & Robert W. Bryson
Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species-rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well-studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial...

Data from: Bacterial endosymbiont infections in ‘living fossils’: a case study of North American vaejovid scorpions

& Robert W. Bryson
Bacterial endosymbionts are common among arthropods, and maternally inherited forms can affect the reproductive and behavioural traits of their arthropod hosts. The prevalence of bacterial endosymbionts and their role in scorpion evolution have rarely been investigated. In this study, 61 samples from 40 species of scorpion in the family Vaejovidae were screened for the presence of the bacterial endosymbionts Cardinium, Rickettsia, Spiroplasma and Wolbachia. No samples were infected by these bacteria. However, one primer pair...

Data from: Minor allele frequency thresholds strongly affect population structure inference with genomic datasets

Ethan Linck & C.J. Battey
One common method of minimizing errors in large DNA sequence datasets is to drop variable sites with a minor allele frequency below some specified threshold. Though widespread, this procedure has the potential to alter downstream population genetic inferences and has received relatively little rigorous analysis. Here we use simulations and an empirical SNP dataset to demonstrate the impacts of minor allele frequency (MAF) thresholds on inference of population structure. We find that model-based inference of...

Data from: New insights into New World biogeography: an integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies

F. Keith Barker, Kevin J. Burns, John Klicka, Scott M. Lanyon & Irby J. Lovette
Understanding the biogeographic origins and temporal sequencing of groups within a region or of lineages within an ecosystem can yield important insights into evolutionary dynamics and ecological processes. Fifty years ago, Ernst Mayr generated comprehensive—if limited—inferences about the origins of the New World avifaunas, including the importance of pre-Isthmian dispersal between North and South America. Since then, methodological advances have improved our ability to address many of the same questions, but the phylogenies upon which...

Data from: Species delimitation using Bayes factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae)

Jared A. Grummer, , Tod W. Reeder & Robert W. Bryson
Current molecular methods of species delimitation are limited by the types of species delimitation models and scenarios that can be tested. Bayes factors allow for more flexibility in testing non-nested species delimitation models and hypotheses of individual assignment to alternative lineages. Here, we examined the efficacy of Bayes factors in delimiting species through simulations and empirical data from the Sceloporus scalaris species group. Marginal likelihood scores of competing species delimitation models, from which Bayes factor...

Data from: Diversification across the New World within the ‘blue’ cardinalids (Aves: Cardinalidae)

, Jaime Chaves, Brian Tilston Smith, Matthew J. Miller, Kevin Winker, Jorge L. Pérez-Emán, John Klicka & Robert W. Bryson
Aim: To examine the history of diversification of ‘blue’ cardinalids (Cardinalidae) across North and South America. Location: North America (including Middle America) and South America. Methods: We collected 163 individuals of the 14 species of blue cardinalids and generated multilocus sequence data (3193 base pairs from one mitochondrial and three nuclear genes) to infer phylogeographical structure and reconstruct time-calibrated species trees. We then estimated the ancestral range at each divergence event and tested for temporal...

Data from: A genomic evaluation of taxonomic trends through time in coast horned lizards (genus Phrynosoma)

Adam D. Leache, Matt T. McElroy, Anna Trinh & Matthew T. McElroy
Determining the boundaries between species and deciding when to describe new species are challenging practices that are particularly difficult in groups with high levels of geographic variation. The coast horned lizards (Phrynosoma blainvillii, P. cerroense, and P. coronatum) have an extensive geographic distribution spanning many distinctive ecological regions ranging from northern California to the Cape Region of Baja California, Mexico, and populations differ substantially with respect to external morphology across much of this range. The...

Data from: Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma)

Christopher Blair, & Robert W. Bryson
Biodiversity reduction and loss continues to progress at an alarming rate, and thus there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species-delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods...

Phylogenomic assessment of biodiversity using a reference-based taxonomy: An example with Horned Lizards (Phrynosoma)

Adam Leache, Hayden Davis, Sonal Singhal, Matt Fujita & Megan Lahti
Phylogenomic investigations of biodiversity facilitate the detection of fine-scale population genetic structure and the demographic histories of species and populations. However, determining whether or not the genetic divergence measured among populations reflects species-level differentiation remains a central challenge in species delimitation. One potential solution is to compare genetic divergence between putative new species with other closely related species, sometimes referred to as a reference-based taxonomy. To be described as a new species, a population should...

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