19 Works

Data from: The behavior of Metropolis-coupled Markov chains when sampling rugged phylogenetic distributions

Jeremy M. Brown & Robert C. Thomson
Bayesian phylogenetic inference involves sampling from posterior distributions of trees, which sometimes exhibit local optima, or peaks, separated by regions of low posterior density. Markov chain Monte Carlo (MCMC) algorithms are the most widely used numerical method for generating samples from these posterior distributions, but they are susceptible to entrapment on individual optima in rugged distributions when they are unable to easily cross through or jump across regions of low posterior density. Ruggedness of posterior...

Data from: Comprehensive MicroRNAome analysis of the relationship between Alzheimer disease and cancer in PSEN double-knockout mice

Suji Ham, Tae Kyoo Kim, Jeewon Ryu, Yong Sik Kim, Ya-Ping Tang & Heh-In Im
Purpose: Presenilins are functionally important components of γ-secretase, which cleaves a number of transmembrane proteins. Manipulations of PSEN1 and PSEN2 have been separately studied in Alzheimer disease (AD) and cancer because both involve substrates of γ-secretase. However, numerous clinical studies have reported an inverse correlation between AD and cancer. Interestingly, AD is a neurodegenerative disorder, whereas cancer is characterized by the proliferation of malignant cells. However, this inverse correlation in the PSEN double-knockout (PSEN dKO)...

Data from: Big data analysis of genes associated with neuropsychiatric disorders in an Alzheimer's disease animal model

Suji Ham, Tae Kyoo Kim, Heeok Hong, Yong Sik Kim, Ya-Ping Tang & Heh-In Im
Alzheimer’s disease is a neurodegenerative disease characterized by the impairment of cognitive function and loss of memory, affecting millions of individuals worldwide. With the dramatic increase in the prevalence of Alzheimer’s disease, it is expected to impose extensive public health and economic burden. However, this burden is particularly heavy on the caregivers of Alzheimer’s disease patients eliciting neuropsychiatric symptoms that include mood swings, hallucinations, and depression. Interestingly, these neuropsychiatric symptoms are shared across symptoms of...

Data from: Allele phasing greatly improves the phylogenetic utility of ultraconserved elements

Tobias Andermann, Alexandre M. Fernandes, Urban Olsson, Mats Töpel, Bernard Pfeil, Bengt Oxelman, Alexandre Aleixo, Brant C. Faircloth & Alexandre Antonelli
Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for non-model organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts on a selected set of targeted loci, commonly enriched using sequence capture. The advantage of this approach is that it recovers a consistent set of loci, each with high sequencing depth, which leads to more confidence in the assembly of target sequences. High...

Data from: Variation across mitochondrial gene trees provides evidence for systematic error: how much gene tree variation is biological?

Emilie J. Richards, Jeremy M. Brown, Anthony J. Barley, Rebecca A. Chong & Robert C. Thomson
The use of large genomic datasets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of biological versus methodological factors in explaining gene tree variation is a major unresolved question. Using mitochondrial genomes to control for biological causes of gene tree variation,...

Data from: Acoustic adaptation to city noise through vocal learning by a songbird

Dana Lynn Moseley, Graham Earnest Derryberry, Jennifer Nicole Phillips, Julie Elizabeth Danner, Raymond Michael Danner, David Andrew Luther & Elizabeth Perrault Derryberry
Anthropogenic noise imposes novel selection pressures, especially on species that communicate acoustically. Many animals – including insects, frogs, whales, and birds – produce sounds at higher frequencies in areas with low-frequency noise pollution. Although there is support for animals changing their vocalizations in real time in response to noise (i.e., immediate flexibility), other evolutionary mechanisms for animals that learn their vocalizations remain largely unexplored. We hypothesize that cultural selection for signal structures less masked by...

Data from: What can mixed-species flock movement tell us about the value of Amazonian secondary forests? insights from spatial behavior

Karl Mokross, Jonathan R. Potts, Cameron L. Rutt & Philip C. Stouffer
The value of secondary forest for rainforest species remains an important question for conservation in the 21st century. Here, we describe the spatial behavior of understory mixed-species flocks in a heterogeneous landscape in central Amazonia. Understory mixed-species flocks represent a diverse, highly organized component of the rich Amazonian avifauna. We recorded movements within 26 flock home ranges in primary forest, secondary forest, interfaces between forest types, and forest fragments. We describe frequency and movement orientation...

Data from: Purifying selection in the toll-like receptors of song sparrows Melospiza melodia

Martha J. Nelson-Flower, Ryan R. Germain, Elizabeth A. MacDougall-Shackleton, Sabrina S. Taylor & Peter Arcese
Variation in immune gene sequences is known to influence resistance to infectious diseases and parasites, and hence survival and mate choice, across animal taxa. Toll-like receptors (TLRs) comprise one essential gene family in the vertebrate innate immune system, and recognize evolutionarily conserved structures from all major microorganism classes. However, the causes and consequences of TLR variation in passerine birds remain largely unexplored. We examined seven TLR genes in song sparrows (Melospiza melodia), a species that...

Data from: Comparative population genomics reveals key barriers to dispersal in Southern Ocean penguins

Gemma V. Clucas, Jane L. Younger, Damian Kao, Louise Emmerson, Colin Southwell, Barbara Wienecke, Alex D. Rogers, Charles-Andre Bost, Gary D. Miller, Michael J. Polito, Patrick Lelliot, Jonathan Handley, Sarah Crofts, Richard A. Phillips, Michael J. Dunn, Karen J. Miller, Tom Hart & Patrick Lelliott
The mechanisms that determine patterns of species dispersal are important factors in the production and maintenance of biodiversity. Understanding these mechanisms helps to forecast the responses of species to environmental change. Here we used a comparative framework and genome-wide data obtained through RAD-seq to compare the patterns of connectivity among breeding colonies for five penguin species with shared ancestry, overlapping distributions, and differing ecological niches, allowing an examination of the intrinsic and extrinsic barriers governing...

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: Phenotypic and transcriptomic responses to salinity stress across genetically and geographically divergent Tigriopus californicus populations

Melissa B. De Biasse, Yasmeen Kawji, Morgan W. Kelly & Melissa B. DeBiasse
Species inhabiting the North American west coast intertidal must tolerate an extremely variable environment, with large fluctuations in both temperature and salinity. Uncovering the mechanisms for this tolerance is key to understanding species’ persistence. We tested for differences in salinity tolerance between populations of Tigriopus californicus copepods from locations in northern (Bodega Reserve) and southern (San Diego) California known to differ in temperature, precipitation, and humidity. We also tested for differences between populations in their...

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: 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: 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 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: 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: 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: 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...

Registration Year

  • 2018

Resource Types

  • Dataset


  • Louisiana State University of Alexandria
  • Louisiana State University
  • University of Hawaii at Manoa
  • American Museum of Natural History
  • Seoul National University
  • Tulane University
  • Korea Institute of Science and Technology
  • California Polytechnic State University
  • City University of New York
  • Sao Paulo State University