92 Works

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: Sequence capture and next-generation sequencing of ultraconserved elements in a large-genome salamander

Catherine E. Newman & Christopher C. Austin
Amidst the rapid advancement in next-generation sequencing (NGS) technology over the last few years, salamanders have been left behind. Salamanders have enormous genomes – up to 40 times the size of the human genome – and this poses challenges to generating NGS data sets of quality and quantity similar to those of other vertebrates. However, optimization of laboratory protocols is time-consuming and often cost prohibitive, and continued omission of salamanders from novel phylogeographic research is...

Data from: A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

John E. McCormack, Michael G. Harvey, Brant C. Faircloth, Nicholas G. Crawford, Travis C. Glenn & Robb T. Brumfield
Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed...

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: Phylogenomic insights into the evolution of stinging wasps and the origins of ants and bees

Michael G. Branstetter, Bryan N. Danforth, James P. Pitts, Brant C. Faircloth, Philip S. Ward, Matthew L. Buffington, Michael W. Gates, Robert R. Kula & Seán G. Brady
The stinging wasps (Hymenoptera: Aculeata) are an extremely diverse lineage of hymenopteran insects, encompassing over 70,000 described species and a diversity of life history traits, including ectoparasitism, cleptoparasitism, predation, pollen feeding (bees [Anthophila] and Masarinae) and eusociality (social vespid wasps, ants, and some bees) [1]. The most well-studied lineages of Aculeata are the ants, which are ecologically dominant in most terrestrial ecosystems [2], and the bees, the most important lineage of angiosperm-pollinating insects [3]. Establishing...

Data from: Soil erodibility differs according to heritable trait variation and nutrient-induced plasticity in the salt marsh engineer Spartina alterniflora

Brittany M. Bernik, John H. Pardue, Michael J. Blum, BM Bernik, MJ Blum & JH Pardue
Use of landform engineers for habitat restoration has often resulted in unanticipated outcomes. It is possible that departures from expectation arise because applications do not adequately account for the influence of heritable and non-heritable phenotypic variation on ecosystem attributes. In this study, we performed a common garden greenhouse experiment to determine whether soil shear strength—a characteristic linked to erosion resistance—varies according to heritable and plastic trait expression in Spartina alterniflora grown under contrasting nutrient regimes....

Data from: Seasonal flooding, topography, and organic debris interact to influence the emergence and distribution of seedlings in a tropical grassland

Francielli Bao, Tracy Elsey-Quirk, Marco Antonio De Assis, Rafael Arruda & Arnildo Pott
In seasonally flooded wetlands, natural disturbances such as flooding and associated organic debris deposition followed by a drawdown period provide various opportunities for plant species regeneration, which can promote plant community diversity across space and time. Specifically, regeneration may be influenced by the direct effect of flooding on seed dispersal and seedling emergence as well as the indirect effect of organic debris on seed trapping and germination. Our objective was to examine the influence of...

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: Cryptic diversity hides host and habitat specialization In a gorgonian-algal symbiosis

Carlos Prada, Shelby E. McIlroy, Diana M. Beltrán, Daniel J. Valint, Scott Alan Ford, Michael E. Hellberg & Mary Alice Coffroth
Shallow water anthozoans, the major builders of modern coral reefs, enhance their metabolic and calcification rates with algal symbionts. Controversy exists over whether these anthozoan-algae associations are flexible over the lifetimes of individual hosts, promoting acclimative plasticity, or are closely linked, such that hosts and symbionts coevolve across generations. Given the diversity of algal symbionts and the morphological plasticity of many host species, cryptic variation within either partner could potentially confound studies of anthozoan-algal associations....

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: Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae)

Gustavo A. Bravo, , Robb Thomas Brumfield & J. V. Remsen
Phylogenetic niche conservatism and convergence are contrasting evolutionary patterns that describe phenotypic similarity across independent lineages. Assessing whether and how adaptive processes give origin to these patterns represent a fundamental step toward understanding phenotypic evolution. Phylogenetic model-based approaches offer the opportunity not only to distinguish between phylogenetic niche conservatism and convergence, but also to determine the extent that adaptive processes explain phenotypic similarity. The Myrmotherula complex in the Neotropical family Thamnophilidae is a polyphyletic group...

Data from: Phylogenomics of pike cichlids (Cichlidae: Crenicichla): the rapid evolution and trophic diversification of an incipient species flock

Edward D. Burress, Fernando Alda, Alejandro Duarte, Marcelo Loureiro, Jonathan W. Armbruster & Prosanta Chakrabarty
The rapid rise of phenotypic and ecological diversity in independent lake-dwelling groups of cichlids is emblematic of the East African Great Lakes. In this study, we show that similar ecologically-based diversification has occurred in pike cichlids (Crenicichla) throughout the Uruguay River drainage of South America. We collected genomic data from nearly 500 ultraconserved element (UCEs) loci and >260,000 base pairs across 33 species, to obtain a phylogenetic hypothesis for the major species-groups and to evaluate...

Data from: Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis bats

, Brant C. Faircloth, Kevin A.M. Sullivan, Troy J. Kieran, Travis C. Glenn, Michael W. Vandewege, , Robert J. Baker, Richard D. Stevens, David A. Ray, Thomas E Lee, Roy N Platt & Kevin A M Sullivan
The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial...

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: Conservation genetics of the Philippine tarsier: cryptic genetic variation restructures conservation priorities for an island archipelago primate

Rafe M. Brown, Jennifer A. Weghorst, Karen V. Olson, Mariano R. M. Duya, Anthony J. Barley, Melizar V. Duya, Myron Shekelle, Irene Neri-Arboleda, Jacob A. Esselstyn, Nathaniel J. Dominy, Perry S. Ong, Gillian L. Moritz, Adrian Luczon, Mae Lowe L. Diesmos, Arvin C. Diesmos & Cameron D. Siler
Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies,...

Data from: Repeated evolution of carnivory among Indo-Australian rodents

Kevin C. Rowe, Anang S. Achmadi & Jacob A. Esselstyn
Convergent evolution, often observed in island archipelagos, provides compelling evidence for the importance of natural selection as a generator of species and ecological diversity. The Indo-Australian Archipelago (IAA) is the world's largest island system and encompasses distinct biogeographic units, including the Asian (Sunda) and Australian (Sahul) continental shelves, which together bracket the oceanic archipelagos of the Philippines and Wallacea. Each of these biogeographic units houses numerous endemic rodents in the family Muridae. Carnivorous murids, i.e.,...

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...

Data from: Evaluating summary statistics used to test for incomplete lineage sorting: mito-nuclear discordance in the reef sponge Callyspongia vaginalis

Melissa B. DeBiasse, Bradley J. Nelson & Michael E. Hellberg
Conflicting patterns of population differentiation between the mitochondrial and nuclear genomes (mito-nuclear discordance) have become increasingly evident as multilocus datasets have become easier to generate. Incomplete lineage sorting (ILS) of nucDNA is often implicated as the cause of such discordance, stemming from the large effective population size of nucDNA relative to mtDNA. However, selection, sex-biased dispersal, and historical demography can also lead to mito-nuclear discordance. Here we compare patterns of genetic diversity and subdivision for...

Data from: Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting

Fernando Alda, Victor A. Tagliacollo, Maxwell J. Bernt, Brandon T. Waltz, William B. Ludt, Brant C. Faircloth, Michael E. Alfaro, James S. Albert & Prosanta Chakrabarty
Resolving patterns of ancient and rapid diversifications is one of the most challenging tasks in evolutionary biology. These difficulties arise from confusing phylogenetic signals that are associated with the interplay of incomplete lineage sorting and homoplasy. Phylogenomic analyses of hundreds, or even thousands, of loci offer the potential to resolve such contentious relationships. Yet, how much useful phylogenetic information these large data sets contain remains uncertain and often goes untested. Here, we assess the utility...

Data from: Deep phylogeographic structure and environmental differentiation in the carnivorous plant Sarracenia alata

Amanda J. Zellmer, Margaret M. Hanes, Sarah M. Hird & Bryan C. Carstens
We collected ~29kb of sequence data using Roche 454 pyrosequencing in order to estimate the timing and pattern of diversification in the carnivorous pitcher plant Sarracenia alata. Utilizing modified protocols for reduced representation library construction, we generated sequence data from 86 individuals across 10 populations from throughout the range of the species. We identified 76 high quality and high coverage loci (containing over 500 SNPs) using the bioinformatics pipeline PRGmatic. Results from a Bayesian clustering...

Data from: Model selection as a tool for phylogeographic inference: an example from the willow Salix melanopsis

Bryan C. Carstens, Reid S. Brennan, Vivien Chua, Caroline V. Duffie, Michael G. Harvey, Rachel A. Koch, Caleb D. McMahan, Bradley J. Nelson, Catherine E. Newman, Jordan D. Satler, Glenn Seeholzer, Karine Posbic, David C. Tank & Jack Sullivan
Phylogeographic inference has typically relied on analyses of data from one or a few genes to provide estimates of demography and population histories. While much has been learned from these studies, all phylogeographic analysis is conditioned on the data, and thus, inferences derived from data that represent a small sample of the genome are unavoidably tenuous. Here, we demonstrate one approach for moving beyond classic phylogeographic research. We use sequence capture probes and Illumina sequencing...

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: The role of physical barriers in the location of avian suture zones in the Guiana Shield, northern Amazonia

Luciano Nicholas Naka, Catherine L. Bechtoldt, L. Magalli Pinto Henriques, Robb T. Brumfield & Luciano Nicolas Naka
Suture zones represent natural forums to examine the role of geography and ecology in the speciation process. Here, we conduct a comparative analysis designed to investigate the location of avian phylogeographic breaks and contact zones in the Guiana Shield, northern Amazonia. We use distributional and genetic data from 78 pairs of avian taxa to address whether phylogeographic breaks and contact zones are associated with contemporary landscape features. Using spatially explicit statistical models, we found that...

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: 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...

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