22 Works

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: Ontogenetic variation in epibiont community structure in the deep-sea yeti crab, Kiwa puravida: convergence among crustaceans

Shana K. Goffredi, Ann Gregory, William Joe Jones, Norma M. Morella & Reid I. Sakamoto
Recent investigations have demonstrated that unusually ‘hairy’ yeti crabs within the family Kiwaidae associate with two predominant filamentous bacterial families, the Epsilon and Gammaproteobacteria. These analyses, however, were based on samples collected from a single body region, the setae of pereopods. To more thoroughly investigate the microbiome associated with Kiwa puravida, a yeti crab species from Costa Rica, we utilized barcoded 16S rRNA amplicon pyrosequencing, as well as microscopy and terminal restriction fragment length polymorphism...

Data for Analysis of Keystone Predation - trait based or driven by extrinsic processes?

Bruce Menge, Melissa Foley, Matthew Robart, Erin Richmond, Mae Noble & Francis Chan
Keystone predation can be a determinant of community structure, including species diversity, but factors underlying “keystoneness” have been minimally explored. Using the system in which the original keystone, the sea star Pisaster ochraceus, was discovered, we focused on two potential (but overlapping) determinants of keystoneness: intrinsic traits or state variables of the species (e.g., size, density), and extrinsic environmental parameters (e.g., prey productivity) that may provide conditions favorable for keystone predator evolution. Using a comparative-experimental...

Contrasting influences on bacterial symbiont specificity by co-occurring deep-sea mussels and tubeworms

Shana Goffredi & Camille Brzechffa
Relationships between deep-sea invertebrates and bacterial symbionts, fueled by sulfide and methane, are well known, yet factors influencing symbiont specificity remain cryptic. For animals that obtain their symbionts from the environment, both host identity and geographic location can impact the ultimate symbiont partner. Bacterial symbionts were analyzed for 3 co-occurring species each of Bathymodiolus mussels and vestimentiferan tubeworms, from three deep methane seeps off the west coast of Costa Rica. The bacterial internal transcribed spacer...

Threshold models improve estimates of molt parameters in datasets with small sample sizes

Ryan Terrill
The timing of events in birds’ annual cycles is important to understanding life history evolution and response to global climate change. Molt timing is often measured as an index of the sum of grown feather proportion or mass within the primary flight feathers. The distribution of these molt data over time has proven difficult to model with standard linear models. The parameters of interest are at change points in model fit over time, and so...

Data from: Speciation in Western Scrub-Jays, Haldane’s rule, and genetic clines in secondary contact

Fiona C. Gowen, James M. Maley, Carla Cicero, A. Townsend Peterson, Brant C. Faircloth, T. Caleb Warr & John E. McCormack
Background: Haldane’s Rule, the tendency for the heterogametic sex to show reduced fertility in hybrid crosses, can obscure the signal of gene flow in mtDNA between species where females are heterogametic. Therefore, it is important when studying speciation and species limits in female-heterogametic species like birds to assess the signature of gene flow in the nuclear genome as well. We studied introgression of microsatellites and mtDNA across a secondary contact zone between coastal and interior...

Data from: Historical species distribution models predict species limits in western Plethodon salamanders

Tara A. Pelletier, Charlie Crisafulli, Steve Wagner, Amanda J. Zellmer & Bryan C. Carstens
Allopatry is commonly used to predict boundaries in species delimitation investigations under the assumption that currently allopatric distributions are indicative of reproductive isolation; however, species ranges are known to change over time. Incorporating a temporal perspective of geographic distributions should improve species delimitation; to explore this, we investigate three species of western Plethodon salamanders that have shifted their ranges since the end of the Pleistocene. We generate species distribution models (SDM) of the current range,...

Data from: Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird

Guillermo Friis, Guillermo Fandos, Amanda J. Zellmer, John E. McCormack, Brant C. Faircloth & Borja Milá
The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic-environment association analyses (GEA)...

Data from: Sequence capture of ultraconserved elements from bird museum specimens

John E. McCormack, Whitney L. E. Tsai, Brant C. Faircloth & Whitney L.E. Tsai
New DNA sequencing technologies are allowing researchers to explore the genomes of the millions of natural history specimens collected prior to the molecular era. Yet, we know little about how well specific next-generation sequencing (NGS) techniques work with the degraded DNA typically extracted from museum specimens. Here, we use one type of NGS approach, sequence capture of ultraconserved elements (UCEs), to collect data from bird museum specimens as old as 120 years. We targeted 5060...

Data from: A phylogenomic perspective on the biogeography of skinks in the Plestiodon brevirostris group inferred from target enrichment of ultraconserved elements

, Charles W. Linkem, Carlos J. Pavón-Vázquez, Adrián Nieto-Montes De Oca, John Klicka, John E. McCormack & Robert W. Bryson
Aim: The aim of our study was to reconstruct ancestral geographic distributions from time-calibrated phylogenies generated from phylogenomic data to answer three broad questions about the biogeography of skinks in the Plestiodon brevirostris group: (1) Are biogeographic patterns correlated with the formation of the Trans-Mexican Volcanic Belt? (2) Do different methods of phylogenetic estimation result in different topologies? If so, (3) are biogeographic reconstructions impacted by the use of different phylogenetic trees? Location: Mexico. Methods:...

Data from: Diet breadth and exploitation of exotic plants shift the core microbiome of Cephaloleia, a group of tropical herbivorous beetles

Chelsea Blankenchip, Dana E Michels, H. Elizabeth Braker & Shana K. Goffredi
The beetle genus Cephaloleia has evolved in association with tropical ginger plants and for many species their specific host plant associations are known. Here we show that the core microbiome of six closely related Costa Rican Cephaloleia species comprises only eight bacterial groups, including members of the Acinetobacter, Enterobacteriacea, Pseudomonas, Lactococcus, and Comamonas. The Acinetobacter and Enterobacteriacea together accounted for 35% of the total average 16S rRNA ribotypes recovered from all specimens. Further, microbiome diversity...

Data from: High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

James Starrett, Shahan Derkarabetian, Marshal Hedin, , John E. McCormack, Brant C. Faircloth & Robert W. Bryson
Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic...

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

Sarah Hird, Darien Capunitan, Oscar Johnson & Ryan Terrill
How the microbiome interacts with hosts across evolutionary time is poorly understood. To address this question, datasets comprised of many host species are required to conduct comparative analyses. Here, we have analyzed 142 intestinal microbiome samples from 92 birds belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene. Using four definitions for microbial taxonomic units (97%OTU, 99%OTU, 99%OTU with singletons removed, ASV), we conducted alpha and beta diversity analyses and used phylogenetic...

Facultative chemosynthesis in a deep-sea anemone from hydrothermal vents in the Pescadero Basin, Gulf of California

Shana Goffredi, Cambrie Motooka, David Fike, Luciana Gusmão, Ekin Tilic, Greg Rouse & Estefanía Rodríguez
Background Numerous deep-sea invertebrates have formed symbiotic associations with internal chemosynthetic bacteria in order to harness inorganic energy sources typically unavailable to most animals. Despite success in nearly all marine habitats and their well-known associations with photosynthetic symbionts, Cnidaria remain without a clear dependence on hydrothermal vents and chemosynthetic bacterial symbionts specifically. Results A new chemosynthetic symbiosis between the sea anemone Ostiactis pearseae (Daly & Gusmão, 2007) and intracellular bacteria was discovered at ~3700 m...

Data from: Populations at risk: conservation genetics of kangaroo mice (Microdipodops) of the Great Basin Desert

John J. Andersen, David S. Portnoy, John C. Hafner & Jessica E. Light
The Great Basin Desert of western North America has experienced frequent habitat alterations due to a complex biogeographic history and recent anthropogenic impacts, with the more recent alterations likely resulting in the decline of native fauna and flora. Dark (Microdipodops megacephalus) and pallid (M. pallidus) kangaroo mice are ecological specialists found within the Great Basin Desert and are potentially ideal organisms for assessing ecosystem health and inferring the biogeographic history of this vulnerable region. Herein,...

Evolution of breeding plumages in birds: a multiple-step pathway to seasonal dichromatism in New World Warblers (Aves: Parulidae)

Ryan Terrill, Jared Wolfe & Glenn Seeholzer
Many species of birds show distinctive seasonal breeding and nonbreeding plumages. A number of hypotheses have been proposed for the evolution of this seasonal dichromatism, specifically related to the idea that birds may experience variable levels of sexual selection relative to natural selection throughout the year. However, these hypotheses have not addressed the selective forces that have shaped molt, the underlying mechanism of plumage change. Here, we examined relationships between life-history variation, the evolution of...

Methanotrophic bacterial symbionts fuel dense populations of deep-sea feather duster worms (Sabellida, Annelida) and extend the spatial influence of methane seepage

Shana Goffredi
Deep-sea methane seeps are dynamic sources of greenhouse gas production and unique habitats supporting ocean biodiversity and productivity. Here, we demonstrate new animal-bacterial symbioses fueled by methane, between two undescribed species of annelid (a serpulid Laminatubus and sabellid Bispira) and distinct methane-oxidizing Methylococcales bacteria. Worm tissue delta 13C of -44 to -58 per mil suggested methane-fueled nutrition for both species and shipboard experiments revealed active assimilation of 13C-labelled CH4 into animal biomass, occurring via engulfment...

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: 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...

Data from: Speciation in mountain refugia: phylogeography and demographic history of the pine siskin and black-capped siskin complex

Sofía Alvarez, Jessie F. Salter, John E. McCormack & Borja Milá
Following Pleistocene glacial maxima, species that adapted to temperate climates in low-latitude refugia had to modify their ranges as climate changed, expanding either latitudinally towards the poles, or altitudinally to higher elevations in mountainous regions. Within just a few thousand years, populations taking alternative routes during interglacials became isolated from each other and subjected to different selection pressures, often leading to lineage divergence and speciation. The pine siskin Spinus pinus is a common and widespread...

Genetic data and niche differences suggest that disjunct populations of Diglossa brunneiventris are not sister lineages

Juan Luis Parra, Ana Maria Gutiérrez-Zuluaga, Catalina González-Quevedo, Jessica A. Oswald, Ryan S. Terrill & Jorge L. Pérez-Emán
Disjunct distributions within a species are of great interest in systematics and biogeography. This separation can function as a barrier to gene flow when the distance among populations exceeds the dispersal capacity of individuals, and depending on the duration of the barrier, it may eventually lead to speciation. Here we describe patterns of geographic differentiation of two disjunct populations of Diglossa brunneiventris separated by approximately 1000 km along the Andes. Diglossa brunneiventris vuilleumieri is isolated...

Cryptic diversity across the Trans-Mexican Volcanic Belt of Mexico in the montane bunchgrass lizard Sceloporus subniger (Squamata: Phrynosomatidae)

Robert Bryson, Jared Grummer, Elizabeth Connors, Joseph Tirpak, John McCormack & John Klicka
Sceloporus subniger Poglaygen & Smith is a montane bunchgrass lizard distributed across pine-oak forests of central Mexico. Prompted by the discovery of a new population of this lizard in far western Mexico, and by recent studies suggesting S. subniger may be a composite of several distinct species, we examined in more detail the genetic structure of S. subniger. We generated a mitochondrial DNA (mtDNA) dataset from 81 specimens and an ultraconserved elements (UCE) dataset representing...

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