92 Works

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: 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: Phylogenetic community structure of North American desert bats: influence of environment at multiple spatial and taxonomic scales

Lorelei E. Patrick & Richard D. Stevens
1. Numerous processes influence community structure. The relative importance of these processes are thought to vary with spatial, temporal, and taxonomic scale: density dependent interactions are thought to be most influential at small scales, at intermediate scales environmental conditions may be the most influential factor, and biogeographic processes are thought to be of greater importance at larger scales. Additionally, the stress-dominance hypothesis suggests that communities experiencing harsher environmental conditions will be predominantly structured by habitat...

Data from: Adaptation to climate change: trade-offs among responses to multiple stressors in an intertidal crustacean

Morgan W. Kelly, Melissa B. DeBiasse, Vidal A. Villela, Hope L. Roberts & Colleen F. Cecola
Trade-offs may influence both physiological and evolutionary responses to co-occurring stressors, but their effects on both plastic and adaptive responses to climate change are poorly understood. To test for genetic and physiological trade-offs incurred in tolerating multiple stressors, we hybridized two populations of the intertidal copepod Tigriopus californicus that were divergent for both heat and salinity tolerance. Starting in the F2 generation, we selected for increased tolerance of heat, low salinity, and high salinity in...

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: Local endemism and within-island diversification of shrews illustrate the importance of speciation in building Sundaland mammal diversity

Terrence C. Demos, Anang S. Achmadi, Thomas C. Giarla, Heru Handika, , Kevin C. Rowe & Jacob A. Esselstyn
Island systems are important models for evolutionary biology because they provide convenient, discrete biogeographic units of study. Continental islands with a history of intermittent dry land connections confound the discrete definitions of islands and have led zoologists to predict (1) little differentiation of terrestrial organisms among continental shelf islands and (2) extinction, rather than speciation, to be the main cause of differences in community composition among islands. However, few continental island systems have been subjected...

Data from: Pathogen persistence in the environment and insect-baculovirus interactions: disease-density thresholds, epidemic burnout, and insect outbreaks

Emma Fuller, Bret D. Elderd & Greg Dwyer
Classical epidemic theory focuses on directly transmitted pathogens, but many pathogens are instead transmitted when hosts encounter infectious particles. Theory has shown that for such diseases pathogen persistence time in the environment can strongly affect disease dynamics, but estimates of persistence time, and consequently tests of the theory, are extremely rare. We consider the consequences of persistence time for the dynamics of the gypsy moth baculovirus, a pathogen transmitted when larvae consume foliage contaminated with...

Data from: Population structure and phylogeography of the Gentoo Penguin (Pygoscelis papua) across the Scotia Arc

Hila Levy, Gemma V. Clucas, Alex D. Rogers, Adam D. Leaché, Kate L. Ciborowski, Michael J. Polito, Heather J. Lynch, Michael J. Dunn & Tom Hart
Climate change, fisheries pressure on penguin prey, and direct human disturbance of wildlife have all been implicated in causing large shifts in the abundance and distribution of penguins in the Southern Ocean. Without mark-recapture studies, understanding how colonies form and, by extension, how ranges shift is challenging. Genetic studies, particularly focused on newly established colonies, provide a snapshot of colonisation and can reveal the extent to which shifts in abundance and occupancy result from changes...

Data from: Biogeography of a plant invasion: genetic variation and plasticity in latitudinal clines for traits related to herbivory

Ganesh P. Bhattarai, Laura A. Meyerson, Jack Anderson, David Cummings, Warwick J. Allen & James T. Cronin
The juxtaposition of plant-species invasions with latitudinal gradients in herbivore pressure is an important yet mostly unexplored issue in invasion biology. Latitudinal clines in defense and palatability to herbivores are expected to exist in native plant species but the evolution of these clines may lag behind for invasive plant species resulting in non-parallel latitudinal clines that may impact invasion success. Our study focused on a native and European invasive lineages of the common reed Phragmites...

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: 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: Environmental gradients and the evolution of successional habitat specialization: a test case with 14 Neotropical forest sites

Susan G. Letcher, Jesse R. Lasky, Robin L. Chazdon, Natalia Norden, S. Joseph Wright, Jorge A. Meave, Eduardo A. Pérez-García, Rodrigo Muñoz, Eunice Romero-Pérez, Ana Andrade, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Tony V. Bentos, Radika Bhaskar, Frans Bongers, Vanessa Boukili, Pedro H. S. Brancalion, Ricardo G. César, Deborah A. Clark, David B. Clark, Dylan Craven, Alexander DeFrancesco, Juan M. Dupuy, Bryan Finegan … & G. Bruce Williamson
1. Successional gradients are ubiquitous in nature, yet few studies have systematically examined the evolutionary origins of taxa that specialize at different successional stages. Here we quantify successional habitat specialization in Neotropical forest trees and evaluate its evolutionary lability along a precipitation gradient. Theoretically, successional habitat specialization should be more evolutionarily conserved in wet forests than in dry forests due to more extreme microenvironmental differentiation between early and late successional stages in wet forest. 2....

Data from: Co-feeding intra- and interspecific transmission of an emerging insect-borne rickettsial pathogen

Lisa D. Brown, Rebecca C. Christofferson, Kaikhushroo H. Banajee, Fabio Del Piero, Lane D. Foil & Kevin R. Macaluso
Cat fleas (Ctenocephalides felis) are known as the primary vector and reservoir of Rickettsia felis, the causative agent of flea-borne spotted fever; however, field surveys regularly report molecular detection of this infectious agent from other blood-feeding arthropods. The presence of R. felis in additional arthropods may be the result of chance consumption of an infectious bloodmeal, but isolation of viable rickettsiae circulating in the blood of suspected vertebrate reservoirs has not been demonstrated. Successful transmission...

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: Phylogenomics using formalin-fixed and 100+ year old intractable natural history specimens

Sara Ruane & Christopher C. Austin
Museum specimens provide a wealth of information to biologists, but obtaining genetic data from formalin-fixed and fluid-preserved specimens remains challenging. While DNA sequences have been recovered from such specimens, most approaches are time-consuming and produce low data quality and quantity. Here we use a modified DNA extraction protocol combined with high-throughput sequencing to recover DNA from formalin-fixed and fluid-preserved snakes that were collected over a century ago and for which little or no modern genetic...

Data from: Shared phylogeographical breaks in a Caribbean coral reef sponge and its invertebrate commensals

Melissa B. DeBiasse, Vincent P. Richards, Mahmood S. Shivji & Michael E. Hellberg
Aim: To test whether phylogeographical barriers in the brooding sponge Callyspongia vaginalis match breaks previously identified in the Caribbean. We also compared patterns of subdivision in the sponge to those of three of its commensals, the broadcast spawning brittle star Ophiothrix suensonii and the brooding amphipods Leucothoe ashleyae and L. kensleyi, and tested whether any shared breaks arose simultaneously. Location: Florida, Bahamas and the Caribbean. Methods: Subdivision of C. vaginalis populations was inferred from one...

Data from: Phylogeography and species delimitation in convict cichlids (Cichlidae: Amatitlania): implications for taxonomy and Plio–Pleistocene evolutionary history in Central America

Justin C. Bagley, Wilfredo A. Matamoros, Caleb D. McMahan, Michael Tobler, Prosanta Chakrabarty & Jerald B. Johnson
We investigate phylogeographic patterns and delimit species boundaries within Amatitlania, a genus of Central American cichlid fishes. Phylogenetic analyses of mitochondrial DNA sequences from 318 individuals spanning the geographical ranges of all three currently recognized Amatitlania species strongly supported one major clade, with a relatively diverged subclade corresponding to A. kanna samples from eastern Costa Rica and Panama. Gene trees and networks revealed marked incongruences between phylogeographic structure and morpho-species taxonomy as a result of...

Data from: Fragmentation of Atlantic Forest has not affected gene flow of a widespread seed-dispersing bat

Eve S. McCulloch, J. Sebastian Tello, Andrew Whitehead, Claudia M. J. Rolón-Mendoza, Mario C. D. Maldonado-Rodríguez & Richard D. Stevens
Habitat loss and resultant fragmentation are major threats to biodiversity, particularly in tropical and subtropical ecosystems. It is increasingly urgent to understand fragmentation effects, which are often complex and vary across taxa, time and space. We determined whether recent fragmentation of Atlantic forest is causing population subdivision in a widespread and important Neotropical seed-disperser: Artibeus lituratus (Chiroptera: Phyllostomidae). Genetic structure within highly fragmented forest in Paraguay was compared to that in mostly contiguous forest in...

Data from: Multilocus phylogeny and biogeography of the New World Pheucticus grosbeaks (Aves: Cardinalidae)

Paulo C. Pulgarín-R, Brian Tilston Smith, , Garth M. Spellman, John Klicka & Robert W. Bryson
Using a multilocus approach, we investigated the tempo and pattern of diversification in a widely distributed New World songbird, the cardinalid genus Pheucticus. Each of the three geographic groups recovered (North American, Middle American, and South American) was comprised of a pair of currently recognized species, and four, three, and three geographically and genetically distinct phylogeographic lineages respectively. Diversification within Pheucticus appears to have occurred at a relatively constant pace throughout the Pleistocene and evenly...

Data from: Pulmonary anatomy and a case of unilateral aplasia in a common snapping turtle (Chelydra serpentina): developmental perspectives on cryptodiran lungs

Emma R. Schachner, Jayc C. Sedlmayr, Renée Schott, Tyler R. Lyson, R. Kent Sanders & Markus Lambertz
The common snapping turtle (Chelydra serpentina) is a well studied and broadly distributed member of Testudines; however, very little is known concerning developmental anomalies and soft tissue pathologies of turtles and other reptiles. Here, we present an unusual case of unilateral pulmonary aplasia, asymmetrical carapacial kyphosis, and mild scoliosis in a live adult C. serpentina. The detailed three-dimensional (3D) anatomy of the respiratory system in both the pathological and normal adult C. serpentina, and a...

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: 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: A phylogenetic and morphologic context for the radiation of an endemic fauna in a long-lived lake: Corbulidae (Bivalvia; Myoida) in the Miocene Pebas Formation of western Amazonia

Laurie C. Anderson, Frank P. Wesselingh & Joseph H. Hartman
The Corbulidae are one of a handful of a primarily marine bivalve clades that exhibit a remarkable radiation, marked by increased species richness and divergent morphologies, within a long-lived lake. For corbulids, this diversification occurred within the lower to middle Miocene Pebas Formation of western Amazonia. Only one taxon associated with this radiation (Anticorbula) remains extant. We conducted a series of phylogenetic analyses to characterize diversification of Corbulidae within the Pebas Formation and relate that...

Data from: Ecological opportunity and diversification in a continental radiation of birds: climbing adaptations and cladogenesis in the Furnariidae

Santiago Claramunt, Elizabeth P. Derryberry, Robb T. Brumfield, & J. V. Remsen
Ecological theories of adaptive radiation predict that ecological opportunity stimulates cladogenesis through its effects on competitive release and niche expansion. Given that key innovations may confer ecological opportunity, we investigate the effect of the acquisition of climbing adaptations on rates of cladogenesis in a major avian radiation, the Neotropical bird family Furnariidae, using a species-level phylogeny. Morphological specializations for vertical climbing originated in the woodcreepers ca. 23 Mya, well before that adaptation occurred in woodpeckers...

Data from: Vegetation phenology and nest survival: diagnosing heterogeneous effects through time

Kevin M. Ringelman & Cassandra G. Skaggs
Birds should select nest sites that minimize predation risk, but understanding the influence of vegetation on nest survival has proven problematic. Specifically, the common practice of measuring vegetation on nest fate date can overestimate its effect on survival, simply because vegetation at hatched nests grows for a longer period of time than vegetation at nests that were depredated. Here, we sampled the literature to determine the prevalence of this bias in studies of duck breeding...

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