92 Works

Data from: Unrecognized coral species diversity masks differences in functional ecology

Jennifer N. Boulay, Michael E. Hellberg, Jorge Cortés, Iliana B. Baums & J. Cortes
Porites corals are foundation species on Pacific reefs but a confused taxonomy hinders understanding of their ecosystem function and responses to climate change. Here, we show that what has been considered a single species in the eastern tropical Pacific, Porites lobata, includes a morphologically similar yet ecologically distinct species, Porites evermanni. While P. lobata reproduces mainly sexually, P. evermanni dominates in areas where triggerfish prey on bioeroding mussels living within the coral skeleton, thereby generating...

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: Deflating trees: improving Bayesian branch-length estimates using informed priors

Bradley J. Nelson, John J. Andersen & Jeremy M. Brown
Prior distributions can have a strong effect on the results of Bayesian analyses. However, no general consensus exists for how priors should be set in all circumstances. Branch-length priors are of particular interest for phylogenetics, because they affect many parameters and biologically relevant inferences have been shown to be sensitive to the chosen prior distribution. Here, we explore the use of outside information to set informed branch-length priors and compare inferences from these informed analyses...

Data from: Combining citizen science species distribution models and stable isotopes reveals migratory connectivity in the secretive Virginia rail

Auriel M. V. Fournier, Alexis R. Sullivan, Joseph K. Bump, Marie Perkins, Mark C. Shieldcastle & Sammy L. King
Stable hydrogen isotope (δD) methods for tracking animal movement are widely used yet often produce low resolution assignments. Incorporating prior knowledge of abundance, distribution or movement patterns can ameliorate this limitation, but data are lacking for most species. We demonstrate how observations reported by citizen scientists can be used to develop robust estimates of species distributions and to constrain δD assignments. We developed a Bayesian framework to refine isotopic estimates of migrant animal origins conditional...

Data from: Dry habitats were crucibles of domestication in the evolution of agriculture in ants

Michael G. Branstetter, Ana Ješovnik, Jeffrey Sosa-Calvo, Michael W. Lloyd, Brant C. Faircloth, Seán G. Brady & Ted R. Schultz
The evolution of ant agriculture, as practiced by the fungus-farming “attine” ants, is thought to have arisen in the wet rainforests of South America about 55-65 Ma. Most subsequent attine agricultural evolution, including the domestication event that produced the ancestor of higher attine cultivars, is likewise hypothesized to have occurred in South American rainforests. The “out-of-the-rainforest” hypothesis, while generally accepted, has never been tested in a phylogenetic context. It also presents a problem for explaining...

Data from: Fuels and fires influence vegetation via above- and below-ground pathways in a high-diversity plant community

Paul R. Gagnon, Heather A. Passmore, Matthew Slocum, Jonathan A. Myers, Kyle E. Harms, William J. Platt & C. E. Timothy Paine
1. Fire strongly influences plant populations and communities around the world, making it an important agent of plant evolution. Fire influences vegetation through multiple pathways, both above- and belowground. Few studies have yet attempted to tie these pathways together in a mechanistic way through soil heating even though the importance of soil heating for plants in fire-prone ecosystems is increasingly recognized. 2. Here we combine an experimental approach with structural equation modelling (SEM) to simultaneously...

Data from: Impact of model violations on the inference of species boundaries under the multispecies coalescent

Anthony J. Barley, Jeremy M. Brown & Robert C. Thomson
The use of genetic data for identifying species-level lineages across the tree of life has received increasing attention in the field of systematics over the past decade. The multispecies coalescent model provides a framework for understanding the process of lineage divergence, and has become widely adopted for delimiting species. However, because these studies lack an explicit assessment of model fit, in many cases, the accuracy of the inferred species boundaries are unknown. This is concerning...

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...

Data from: Adaptation to heat stress reduces phenotypic and transcriptional plasticity in a marine copepod

Morgan W. Kelly, M. Sabrina Pankey, Melissa B. DeBiasse & David C. Plachetzki
Organisms may respond to changing environments through phenotypic plasticity or adaptive evolution. These two processes are not mutually exclusive and may either dampen or strengthen each other's effects, depending on the genetic correlation between trait values and the slopes of their norms of reaction. To examine the effect of adaptation to heat stress on the plasticity of heat tolerance, we hybridized populations of the crustacean Tigriopus californicus that show divergent phenotypes for heat tolerance. We...

Data from: The negative effects of pathogen-infected prey on predators: a meta-analysis

Andrew J. Flick, Miguel A. Acevedo & Bret D. Elderd
Intra-guild predation (IGP) – where a top predator (IGPred) consumes both a basal resource and a competitor for that resource (IGPrey) – has become a fundamental part of understanding species interactions and community dynamics. IGP communities composed of intraguild predators and prey have been well studied; however, we know less about IGP communities composed of predators, pathogens, and resources. Resource quality plays an important role in community dynamics and may influence IGP dynamics as well....

Data from: Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera

Michael G. Branstetter, John T. Longino, Philip S. Ward & Brant C. Faircloth
1. Targeted enrichment of conserved genomic regions (e.g., ultraconserved elements or UCEs) has emerged as a promising tool for inferring evolutionary history in many organismal groups. Because the UCE approach is still relatively new, much remains to be learned about how best to identify UCE loci and design baits to enrich them. 2. We test an updated UCE identification and bait design workflow for the insect order Hymenoptera, with a particular focus on ants. The...

Data from: Identifying conserved genomic elements and designing universal bait sets to enrich them

Brant C. Faircloth
Targeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic and population genetic studies. For example, two available bait sets each allow enrichment of thousands of orthologous loci from >20 000 species (Faircloth et al. Systematic Biology, 61, 717–726, 2012; Molecular Ecology Resources, 15, 489–501, 2015). Unfortunately, few open-source workflows are available to identify conserved genomic elements shared among divergent taxa and...

Data from: Transcriptomics reveal transgenerational effects in purple sea urchin embryos: adult acclimation to upwelling conditions alters the response of their progeny to differential pCO2 levels

Juliet M. Wong, Kevin M. Johnson, Morgan W. Kelly & Gretchen E. Hofmann
Understanding the mechanisms with which organisms can respond to a rapidly changing ocean is an important research priority in marine sciences, especially in light of recent predictions regarding the pace of ocean change in the coming decades. Transgenerational effects, in which the experience of the parental generation can shape the phenotype of their offspring, may serve as such a mechanism. In this study, adult purple sea urchins, Strongylocentrotus purpuratus, were conditioned to regionally and ecologically...

Data from: Host-targeted RAD-Seq reveals genetic changes in the coral Oculina patagonica associated with range expansion along the Spanish Mediterranean coast

Karine Posbic Leydet, Carsten G.B. Grupstra, Rafel Coma, Marta Ribes, Michael E. Hellberg & Carsten G. B. Grupstra
Many organisms are expanding their ranges in response to changing environmental conditions. Understanding the patterns of genetic diversity and adaptation along an expansion front is crucial to assessing a species’ long-term success. While next-generation sequencing techniques can reveal these changes in fine detail, ascribing them to a particular species can be difficult for organisms that live in close association with symbionts. Using a novel modified restriction-site associated DNA sequencing (RAD-Seq) protocol to target coral DNA,...

Data from: The polyphyly of Plasmodium: comprehensive phylogenetic analyses of the malaria parasites (order Haemosporida) reveal widespread taxonomic conflict

Spencer C. Galen, Janus Borner, Ellen S. Martinsen, Juliane Schaer, Christopher C. Austin, Christopher J. West & Susan L. Perkins
The evolutionary relationships among the apicomplexan blood pathogens known as the malaria parasites (order Haemosporida), some of which infect nearly 200 million humans each year, has remained a vexing phylogenetic problem due to limitations in taxon sampling, character sampling, and the extreme nucleotide base composition biases that are characteristic of this clade. Previous phylogenetic work on the malaria parasites has often lacked sufficient representation of the broad taxonomic diversity within the Haemosporida or the multi-locus...

Data from: Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: new approaches to long-standing problems

Andrea M. Quattrini, Brant C. Faircloth, Luisa F. Dueñas, Thomas C.L. Bridge, Mercer R. Brügler, Ivan F. Calixto-Botía, Danielle M. DeLeo, Sylvain Foret, Santiago Herrera, Simon M.Y. Lee, David J. Miller, Carlos Prada, Gandhi Rádis-Baptista, Catalina Ramírez-Portilla, Juan A. Sánchez, Estefania Rodriguez, Catherine S. McFadden, Tom C. L. Bridge & Simon M. Y. Lee
Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ~7500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,308 RNA baits to capture 720 Ultraconserved Element loci and 1,071 exon loci. Library preparation and...

Data from: Loss of genetic diversity, recovery, and allele surfing in a colonizing parasite, Geomydoecus aurei

James W. Demastes, David J. Hafner, Mark S. Hafner, Jessica E. Light & Theresa A. Spradling
Understanding the genetic consequences of changes in species distributions has wide-ranging implications for predicting future outcomes of climate change, for protecting threatened or endangered populations, and for understanding the history that has led to current genetic patterns within species. Herein, we examine the genetic consequences of range expansion over a 25-year period in a parasite (Geomydoecus aurei) that is in the process of expanding its geographic range via invasion of a novel host. By sampling...

Data from: Population genetic inferences using immune gene SNPs mirror patterns inferred by microsatellites

Jean P. Elbers, Rachel W. Clostio & Sabrina S. Taylor
Single nucleotide polymorphisms (SNPs) are replacing microsatellites for population genetic analyses, but it is not apparent how many SNPs are needed or how well SNPs correlate with microsatellites. We used data from the gopher tortoise, Gopherus polyphemus—a species with small populations, to compare SNPs and microsatellites to estimate population genetic parameters. Specifically, we compared one SNP data set (16 tortoises from four populations sequenced at 17 901 SNPs) to two microsatellite data sets, a full...

Data from: Physiological plasticity and local adaptation to elevated pCO2 in calcareous algae: an ontogenetic and geographic approach

Jacqueline L. Padilla-Gamiño, Juan D. Gaitán-Espitia, Morgan W. Kelly & Gretchen E. Hofmann
To project how ocean acidification will impact biological communities in the future, it is critical to understand the potential for local adaptation and the physiological plasticity of marine organisms throughout their entire life cycle, as some stages may be more vulnerable than others. Coralline algae are ecosystem engineers that play significant functional roles in oceans worldwide, and are considered vulnerable to ocean acidification. Using different stages of coralline algae, we tested the hypothesis that populations...

Data from: Contrasting effects of nutrient enrichment on below-ground biomass in coastal wetlands

Sean A. Graham & Irving A. Mendelssohn
Anthropogenically-enhanced nutrient availability is often cited among the most important drivers of altered ecosystem function and loss of services worldwide. Although the above-ground consequences of nutrient enrichment on plant growth patterns are numerous and well-documented, below-ground impacts are less clear but nonetheless critical from a global change perspective. In coastal wetlands, for example, plant-soil-nutrient dynamics directly affect the capacity to sequester carbon as soil organic matter, keep pace with sea level rise, and resist storm-induced...

Data from: Pyrogenic fuels produced by savanna trees can engineer humid savannas

William J. Platt, Darin P. Ellair, Jean M. Huffman, Stephen E. Potts & Brian Beckage
Natural fires ignited by lightning strikes following droughts frequently are posited as the ecological mechanism maintaining discontinuous tree cover and grass-dominated ground layers in savannas. Such fires, however, may not reliably maintain humid savannas. Pyrogenic shed leaves of savanna trees, however, might engineer fire characteristics in ways that maintain humid savannas through effects on ground layer plants. We explored our hypothesis in a high-rainfall, frequently-burned pine savanna in which the dominant tree, longleaf pine (Pinus...

Data from: Re-evaluating the geological evidence for Late Holocene marine incursion events along the Guerrero Seismic Gap on the Pacific Coast of Mexico

Thomas A. Bianchette, Terrence A. McCloskey & Kam-Biu Liu
Despite the large number of tsunamis that impact Mexico's Pacific coast, stratigraphic studies focusing on geological impacts are scanty, making it difficult to assess the long-term risks for this vulnerable region. Surface samples and six cores were taken from Laguna Mitla near Acapulco to examine sedimentological and geochemical evidence for marine incursion events. Sediment cores collected from behind the beach barrier are dominated by intercalated layers of peat and inorganic sediments, mostly silt and clay,...

Data from: The effect of demographic correlations on the stochastic population dynamics of perennial plants

Aldo Compagnoni, Andrew J. Bibian, Brad M. Ochocki, Haldre S. Rogers, Emily L. Schultz, Michelle E. Sneck, Bret D. Elderd, Amy M. Iler, David W. Inouye, Hans Jacquemyn, Tom E.X. Miller & Tom E. X. Miller
Understanding the influence of environmental variability on population dynamics is a fundamental goal of ecology. Theory suggests that, for populations in variable environments, temporal correlations between demographic vital rates (e.g., growth, survival, reproduction) can increase (if positive) or decrease (if negative) the variability of year-to-year population growth. Because this variability generally decreases long-term population viability, vital rate correlations may importantly affect population dynamics in stochastic environments. Despite long-standing theoretical interest, it is unclear whether vital...

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 role of mitochondrial introgression in illuminating the evolutionary history of Nearctic treefrogs

, Brian Tilston Smith, Adrian Nieto-Montes De Oca, Uri Omar Garcia-Vazquez, Brett R. Riddle & Robert W. Bryson
Inferring the evolutionary history of lineages often becomes difficult when gene histories are in conflict with each other. Introgression, for example, can cause DNA sequences from one species to be more similar to sequences of a different species and lead to incongruence amongst gene trees. However, incorporating congruent and incongruent locus-specific phylogenetic estimates with the geographical distribution of lineages may provide valuable insight into evolutionary processes important to speciation. In this study, we investigated mitochondrial...

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