515 Works

A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae

Johanna Jantzen, Prabha Amarasinghe, Ryan Folk, Marcelo Reginato, Fabian Michelangeli, Douglas Soltis, Nico Cellinese & Pamela Soltis
Premise of the study: Putatively single-copy nuclear (SCN) loci, identified using genomic resources of closely related species, are ideal for phylogenomic inference. However, suitable genomic resources are not available for many clades, including Melastomataceae. We introduce a versatile approach to identify SCN loci for clades with few genomic resources and use it to develop probes for target enrichment in the distantly related Memecylon and Tibouchina (Melastomataceae). Methods: We present a two-tiered pipeline. First, we identified...

Digital biodiversity datasets reveal breeding phenology and its drivers in a widespread North American mammal

Bryan McLean & Robert Guralnick
Shifts in reproductive timing are among the most commonly documented responses of organisms to global climate change. However, our knowledge of these responses is biased towards taxa that are easily observable and abundant in existing biodiversity data sets. Mammals are common subjects in reproductive biology, but mammalian phenology and its drivers in the wild remain poorly understood because many species are small, secretive, or labor-intensive to monitor. We took an informatics-based approach to reconstructing breeding...

Assessing seasonal demographic covariation to understand environmental-change impacts on a hibernating mammal

Maria Paniw, Dylan Childs, Kenneth Armitage, Daniel Blumstein, Julien Martin, Madan Oli & Arpat Ozgul
Natural populations are exposed to seasonal variation in environmental factors that simultaneously affect several demographic rates (survival, development, reproduction). The resulting covariation in these rates determines population dynamics, but accounting for its numerous biotic and abiotic drivers is a significant challenge. Here, we use a factor-analytic approach to capture partially unobserved drivers of seasonal population dynamics. We use 40 years of individual-based demography from yellow-bellied marmots (Marmota flaviventer) to fit and project population models that...

Data from: Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths

Akito Y. Kawahara, David Plotkin, Marianne Espeland, Karen Meusemann, Emmanuel F. A. Toussaint, Alexander Donath, France Gimnich, Paul B. Frandsen, Andreas Zwick, Mario Dos Reis, Jesse R. Barber, Ralph S. Peters, Shanlin Liu, Xin Zhou, Christoph Mayer, Lars Podsiadlowski, Caroline Storer, Jayne E. Yack, Bernhard Misof & Jesse W. Breinholt
Butterflies and moths (Lepidoptera) are one of the major super-radiations of insects, comprising nearly 160,000 described extant species. As herbivores, pollinators, and prey, Lepidoptera play a fundamental role in almost every terrestrial ecosystem. Lepidoptera are also indicators of environmental change and serve as model organisms for research on mimicry and genetics. They have been central to the development of co-evolutionary hypotheses, such as butterflies with flowering plants, and moths' evolutionary arms race with echolocating bats....

Relative reproductive phenology and synchrony affect neonate survival in a nonprecocial ungulate

Eric Michel, Bronson Strickland, Stephen Demarais, Jerrold Belant, Todd Kautz, Jared Duquette, Dean Beyer, Michael Chamberlain, Karl Miller, Rebecca Shuman, John Kilgo, Duane Diefenbach, Bret Wallingford, Justin Vreeland, Steve Ditchkoff, Christopher DePerno, Christopher Moorman, Michael Chitwood & Marcus Lashley
1. Degree of reproductive synchronization in prey is hypothesized as a predator defense strategy reducing prey risk via predator satiation or predator avoidance. Species with precocial young, especially those exposed to specialist predators, should be highly synchronous to satiate predators (predator satiation hypothesis), while prey with nonprecocial (i.e., altricial) young, especially those exposed to generalist predators, should become relatively asynchronous to avoid predator detection (predator avoidance hypothesis). The white-tailed deer (Odocoileus virginianus) in North America...

Screening for simple sequences repeat markers in Hemileia vastatrix

Luis A. Ramirez Camejo, Luis C. Mejía, Amnat Eamvijarn, Jorge Díaz-Valderram, Elena Karlsen-Ayala, Elizabeth Johnson, Sòlene Pruvot-Woehl, Christophe Montagnon & M. Catherine Aime
Hemileia vastatrix is the most important fungal pathogen affecting Coffea arabica and has invaded nearly every coffee-growing region in the world and the causal agent of recurrent disease epidemics. The development of resistant varieties of coffee against H. vastatrix requires fundamental understanding of the biology of the fungus. However, the complete life cycle of H. vastatrix remains unknown and conflicting studies exist as to whether the fungus is capable of sexual reproduction or not. Here...

The roles of wing color pattern and geography in the evolution of Neotropical Preponini butterflies

Elena Ortiz-Acevedo, Juan P. Gomez, Marianne Espeland, Emmanuel Toussaint & Keith R. Willmott
Diversification rates and evolutionary trajectories are known to be influenced by phenotypic traits and the geographic history of the landscapes that organisms inhabit. One of the most conspicuous traits in butterflies is their wing color pattern, which has been shown to be important in speciation. The evolution of many taxa in the Neotropics has also been influenced by major geological events. Using a dated, species-level molecular phylogenetic hypothesis for Preponini, a colorful Neotropical butterfly tribe,...

Optimizing whole-genomic prediction for autotetraploid blueberry breeding

Ivone De Bem Oliveira, Rodrigo R. Amadeu, Luis Felipe Ferrão & Patricio R. Munoz
Blueberry (Vaccinium spp.) is an important autopolyploid crop with significant benefits for human health. Apart from its genetic complexity, the feasibility of genomic prediction has been proven for blueberry, enabling a reduction in the breeding cycle time and increasing genetic gain. However, as for other polyploid crops, sequencing costs still hinder the implementation of genome-based breeding methods for blueberry. This motivated us to evaluate the effect of training population sizes and composition, as well as...

A global, cross-system meta-analysis of polychlorinated biphenyl biomagnification

Kimberly Prince
Studies evaluating the mechanisms underpinning the biomagnification of polychlorinated biphenyls (PCBs), a globally prevalent group of regulated persistent organic pollutants, commonly couple chemical and stable isotope analyses to identify bioaccumulation pathways. Due to analytical costs constraining the taxonomic and geographic scope, sample size, and the range of compounds analyzed for most studies, and study-to-study variation in methodologies and analytical resolution, how PCBs biomagnify at food web, regional, and global scales remains uncertain. To overcome these...

Data from: Ecological drivers of avian community assembly along a tropical elevation gradient

Flavia A. Montaño-Centellas, Bette A. Loiselle & Morgan W. Tingley
Community assembly theory hypothesizes that two main niche-based processes act to shape composition and organization of biological assemblages: abiotic filtering and biological interactions. Here, we conducted repeated surveys of bird abundance along an undisturbed elevational gradient in the tropical Andes to investigate (1) signals of deterministic processes driving community assembly and (2) potential mechanisms by which these forces operate (temperature, habitat complexity, fruit and insect availability), while correcting for imperfect detection and modeling species abundances...

Is sexual conflict a driver of speciation? a case study with a tribe of brush-footed butterflies

Ana Paula Dos Santos De Carvalho, Ryan St Laurent, Emmanuel Toussaint, Caroline Storer, Kelly Dexter, Kwaku Aduse-Poku & Akito Kawahara
Understanding the evolutionary mechanisms governing the uneven distribution of species richness across the tree of life is a great challenge in biology. Scientists have long argued that sexual conflict is a key driver of speciation. This hypothesis, however, has been highly debated in light of empirical evidence. Recent advances in the study of macroevolution make it possible to test this hypothesis with more data and increased accuracy. In the present study, we use phylogenomics combined...

Code for: Threshold assessment, categorical perception, and the evolution of reliable signaling

James Peniston, Patrick Green, Matthew Zipple & Stephen Nowicki
Animals often use assessment signals to communicate information about their quality to a variety of receivers, including potential mates, competitors, and predators. But what maintains reliable signaling and prevents signalers from signaling a better quality than they actually have? Previous work has shown that reliable signaling can be maintained if signalers pay fitness costs for signaling at different intensities and these costs are greater for lower quality individuals than higher quality ones. Models supporting this...

Development and field evaluation of a motion sensor activated suction trap to study vector-host interactions

Kristin Sloyer
1. Researchers elucidating vectors of zoonotic diseases encounter problems with inefficient surveillance techniques leading to underestimation of the importance of some species, and the overestimation of the importance of others. Carbon dioxide-baited light traps are the most widely used traps for sampling vector groups. However aspirating directly from the hosts is the most accurate method to incriminate vectors. 2. A novel vector trapping system was developed, consisting of a suction trap, activated by a motion...

Data from: samc: An R package for connectivity modeling with spatial absorbing Markov chains

Andrew Marx, Chao Wang, Jorge Sefair, Miguel Acevedo & Robert Fletcher
Quantifying landscape connectivity is fundamental to better understand and predict how populations respond to environmental change. Currently, popular methods to quantify landscape connectivity emphasize how landscape features provide resistance to movement. While many tools are available to quantify landscape resistance, these do not discern between two fundamentally different sources of resistance: movement behavior and mortality. To address this issue, we developed the samc package that quantifies landscape connectivity using absorbing Markov chain theory. Within this...

Data from: Higher-level phylogeny and reclassification of Lampyridae (Coleoptera: Elateroidea)

Gavin Martin, Kathrin Stanger-Hall, Marc Branham, Luiz Da Silveira, Sarah Lower, David Hall, Xue-Yan Li, Alan Lemmon, Emily Lemmon & Seth Bybee
Fireflies (Lampyridae) are a diverse family of beetles which exhibit an array of morphologies including varying antennal and photic organ morphologies. Due in part to their morphological diversity, the classification within the Lampyridae has long been in flux. Here we use an anchored hybrid enrichment approach to reconstruct the most extensive molecular phylogeny of Lampyridae to date (436 loci and 98 taxa) and to evaluate firefly higher-level classification. We propose several classification changes supported by...

The biotic interactions hypothesis partially explains bird species turnover along a lowland Neotropical precipitation gradient

Juan Pablo Gomez, Jose Ponciano, Gusatvo Londoño & Scott Robinson
Aim We evaluated the influence of climate in determining bird communities along precipitation gradients. We argue that mechanisms responsible for community turnover along precipitation gradients are similar to mechanisms operating along temperature and latitudinal gradients. We test the hypothesis that environmental conditions affect community composition in dry forests, whereas biotic interactions affect community composition in wet forests. Location Low-elevation forests along a precipitation gradient in Colombia where precipitation ranges from 700 – 4000 mm annually...

The demographic contributions of connectivity versus local dynamics to population growth of an endangered bird

Brian Reichert, Robert Fletcher & Wiley Kitchens
1. Conservation and management increasingly focus on connectivity, because connectivity driven by variation in immigration rates across landscapes is thought to be crucial for maintaining local population and metapopulation persistence. Yet, efforts to quantify the relative role of immigration on population growth across the entire range of species and over time have been lacking. 2. We assessed whether immigration limited local and range-wide population growth of the endangered snail kite (Rostrhamus sociabilis) in Florida, USA,...

Data from: From refugia to rookeries: phylogeography of Atlantic green turtles

Eugenia Naro-Maciel, Brendan N. Reid, S. Elizabeth Alter, George Amato, Karen A. Bjorndal, Alan B. Bolten, Meredith Martin, Campbell J. Nairn, Brian Shamblin & Oscar Pineda-Catalan
Investigating species’ distribution and abundance over time is central to evolutionary biology, and provides important context for conservation and management. With respect to population genetic structure in green sea turtles (Chelonia mydas), certain processes such as female philopatry to natal rookeries are well understood, while others, such as male philopatry and historical changes in distribution and abundance, remain relatively understudied. Further, although inferences from mitochondrial DNA and nuclear microsatellites have both been critical in identifying...

Data from: Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing

Ya Yang, Michael J. Moore, Samuel F. Brockington, Douglas E. Soltis, Gane Ka-Shu Wong, Eric J. Carpenter, Yong Zhang, Li Chen, Zhixiang Yan, Yinlong Xie, Rowan F. Sage, Sarah Covshoff, Julian M. Hibberd, Matthew N. Nelson & Stephen A. Smith
Many phylogenomic studies based on transcriptomes have been limited to “single-copy” genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup...

Data from: Trait-based scaling of temperature-dependent foliar respiration in a species-rich tropical forest canopy

Martijn Slot, Camilo Rey-Sánchez, Klaus Winter & Kaoru Kitajima
The scarcity of empirical data on leaf respiration (R) and its temperature sensitivity (e.g., Q10, defined as the proportional increase in R per 10°C warming) causes uncertainty in current estimates of net primary productivity of tropical forests. We measured temperature response curves of R on 123 upper-canopy leaves of 28 species of trees and lianas from a tropical forest in Panama, and analyzed variations in R and Q10 in relation to other leaf functional traits....

Data from: Population genetic structure, genetic diversity, and natural history of the South American species of Nothofagus Subgenus Lophozonia (Nothofagaceae) inferred from nuclear microsatellite data

Rodrigo Vergara, Matthew A. Gitzendanner, Douglas E. Soltis, Pam S. Soltis & Pamela S. Soltis
The effect of glaciation on levels and patterns of genetic variation has been well studied in the Northern Hemisphere. However, although glaciation has undoubtedly shaped the genetic structure of plants in the Southern Hemisphere, fewer studies have characterized the effect, and almost none of them using microsatellites. Particularly complex patterns of genetic structure might be expected in areas such as the Andes, where both latitudinal and altitudinal glacial advance and retreat have molded modern plant...

Data from: Early back-to-Africa migration into the Horn of Africa

Jason A. Hodgson, Connie J. Mulligan, Ali Al-Meeri & Ryan L. Raaum
Genetic studies have identified substantial non-African admixture in the Horn of Africa (HOA). In the most recent genomic studies, this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few thousand years. However, mitochondrial and Y chromosome data are suggestive of earlier episodes of admixture. To investigate this further, we generated new genome-wide SNP data for a Yemeni population sample and merged these new data with published genome-wide genetic data...

Data from: Orchid phylogenomics and multiple drivers of their extraordinary diversification

Thomas J. Givnish, Daniel Spalink, Mercedes Ames, Stephanie P. Lyon, Steven J. Hunter, Alejandro Zuluaga, William J. D. Iles, Mark A. Clements, Mary T. K. Arroyo, James Leebens-Mack, Lorena Endara, Ricardo Kriebel, Kurt M. Neubig, W. Mark Whitten, Norris H. Williams & Kenneth M. Cameron
Orchids are the most diverse family of angiosperms, with over 25 000 species, more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here, we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. A supermatrix analysis places an additional 144...

Data from: Affinity for natal environments by dispersers impacts reproduction and explains geographic structure of a highly mobile bird

Robert J. Fletcher, Ellen P. Robertson, Rebecca C. Wilcox, Brian E. Reichert, Wiley M. Kitchens & James D. Austin
Understanding dispersal and habitat selection behaviours is central to many problems in ecology, evolution and conservation. One factor often hypothesized to influence habitat selection by dispersers is the natal environment experienced by juveniles. Nonetheless, evidence for the effect of natal environment on dispersing, wild vertebrates remains limited. Using 18 years of nesting and mark–resight data across an entire North American geographical range of an endangered bird, the snail kite (Rostrhamus sociabilis), we tested for natal...

Data from: The Red Death meets the abdominal bristle: polygenic mutation for susceptibility to a bacterial pathogen in Caenorhabditis elegans

Veronique Etienne, Erik C. Andersen, José Miguel Ponciano, Dustin Blanton, Analucia Cadavid, Joanna Joyner-Matos, Chikako Matsuba, Brandon Tabman & Charles F. Baer
Understanding the genetic basis of susceptibility to pathogens is an important goal of medicine and of evolutionary biology. A key first step toward understanding the genetics and evolution of any phenotypic trait is characterizing the role of mutation. However, the rate at which mutation introduces genetic variance for pathogen susceptibility in any organism is essentially unknown. Here we quantify the per-generation input of genetic variance by mutation (VM) for susceptibility of Caenorhabditis elegans to the...

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