123 Works

Genome-wide association mapping to identify genetic loci for cold tolerance and cold recovery during germination in rice

Michael Thomson, Ranjita Thapa & Endang Septiningsih
To investigate the genetic architecture underlying cold tolerance during germination in rice (Oryza sativa), we conducted a genome-wide association study (GWAS) using a novel diversity panel of 257 rice accessions from around the world and 5,185 SNP markers from a 7K SNP marker array. Genotyping was performed using a 7K Illumina iSelect custom-designed array by following the Infinium HD Array Ultra Protocol. The 7K array, called the C7AIR, was designed by Dr. Susan McCouch’s Lab...

Divergent neurogenomic responses shape social learning of both personality and mate preference

Pablo Delclos, Santiago Forero & Gil Rosenthal
Behavior plays a fundamental role in shaping the origin and fate of species. Mating decisions can act to promote or restrict gene flow, as can personality traits that influence dispersal and niche use. Mate choice and personality are often both learned and therefore influenced by an individual’s social environment throughout development. Likewise, the molecular pathways that shape these behaviors may also be co-expressed. In this study on swordtail fish (Xiphophorus birchmanni), we show that female...

Dityrosine formation via reactive oxygen consumption yields increasingly recalcitrant humic-like fluorescent organic matter in the ocean

Ryan Paerl, Iliana Claudio, Michael Shields, Thomas Bianchi & Christopher Osburn
Marine dissolved organic matter (DOM) is a massive elemental pool on Earth and is thought to consist of a chemically complex mixture of molecules. Part of marine DOM is fluorescent (FDOM) and includes humic-like compounds. The chemical composition of, and biochemical pathways that yield, autochthonous humic-like FDOM in the ocean is largely unknown. Inspired by medical and biochemical research detailing the formation of colored and fluorescent dityrosine via peroxidase mediated reactions, we used fluorometry and...

Emergent social cohesion for coping with community disruptions in disasters

Chao Fan, Yucheng Jiang & Ali Mostafavi
Social cohesion is an important determinant of community well-being, especially in times of distress such as disasters. This study investigates the phenomena of emergent social cohesion, which is characterized by abrupt, temporary, and extensive social ties with the goal of sharing and receiving information regarding a particular event influencing a community. In the context of disasters, emergent social cohesion, enabled by social media usage, could play a significant role in improving the ability of communities...

Utilizing field collected insects for next generation sequencing: effects of sampling, storage, and DNA extraction methods

Kimberly Ballare, Nathaniel Pope, Antonio Castilla, Sarah Cusser, Richard Metz & Shalene Jha
DNA sequencing technologies continue to advance the biological sciences, expanding opportunities for genomic studies of non-model organisms for basic and applied questions. Despite these opportunities, many next-generation sequencing protocols have been developed assuming a substantial quantity of high molecular weight DNA (>100 ng), which can be difficult to obtain for many study systems. In particular, the ability to sequence field-collected specimens that exhibit varying levels of DNA degradation remains largely unexplored. In this study we...

Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites

Stephan Funk, Jose Luis Vega-Pla, Cristina Luis, Gus Cothran & Rytis Juras
STRUCTURE remains the most applied tool aimed at recovering the true, but unknown, population structure from observed microsatellite data or other genetic markers. About 30% of STRUCTURE-based studies could not be reproduced (Gilbert et al., 2012). Here we use a large set of data from 2323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellite markers, to evaluate how program settings, in particular the so far insufficiently evaluated number of replicates,...

Conflicting signal in transcriptomic markers leads to a poorly resolved backbone phylogeny of Chalcidoid wasps

Junxia Zhang, Amelia R.I. Lindsey, Ralph S. Peters, John M. Heraty, Keith R. Hopper, John H. Werren, Ellen O. Martinson, James B. Woolley, Matt J. Yoder & Lars Krogmann
Chalcidoidea (Hymenoptera) are a megadiverse superfamily of wasps with astounding variation in both morphology and biology. Most species are parasitoids and important natural enemies of insects in terrestrial ecosystems. In this study, we explored a transcriptome-based phylogeny of Chalcidoidea and found that poorly resolved relationships could only be marginally improved by adding more genes (a total of 5,591) and taxa (a total of 65), proof-checking for errors of homology and contamination, and decreasing missing data....

Data from: Sporadic genetic connectivity among small insular populations of the rare geoendemic plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower)

A Millie Burrell, Jeffrey HR Goddardd, Paul J Greer, Ryan J Williams & Alan E Pepper
Globally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants are restricted to this harsh environment. Caulanthus ampexlicaulis var. barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to a small set of isolated serpentine outcrops in the...

Unoccupied aerial system enabled functional modeling of maize (Zea mays L.) height reveals dynamic expression of loci associated to temporal growth

Steven Anderson, Seth Murray, Yuanyuan Chen, Lonesome Malambo, Anjin Chang, Sorin Popescu, Dale Cope & Jinha Jung
Unoccupied aerial systems (UAS) were used to phenotype growth trajectories of inbred maize populations under field conditions. Three recombinant inbred line populations were surveyed on a weekly basis collecting RGB images across two irrigation regimens (irrigated and non-irrigated/rain fed). Plant height, estimated by the 95th percentile (P95) height from UAS generated 3D point clouds, exceeded 70% correlation to manual ground truth measurements and 51% of experimental variance was explained by genetics. The Weibull sigmoidal function...

Data from: External temperature and distance from nearest entrance influence microclimates of cave and culvert roosting tri-colored bats Perimyotis subflavus

Samantha Leivers, Melissa Meierhofer, Brian Pierce, Jonah Evans & Michael Morrison
Many North American bat species hibernate in both natural and artificial roosts. Although hibernacula can have high internal climate stability, they still retain spatial variability in their thermal regimes, resulting in various ‘microclimates’ throughout the roost that differ in their characteristics (e.g., temperature, air moisture). These microclimate components can be influenced by factors such as the number of entrances, the depth of the roost, and distance to the nearest entrance of the roost. Tri-colored bats...

Data from: Prediction of maize grain yield before maturity using improved temporal height estimates of unmanned aerial systems

Steven Anderson, Seth Murray, Lonesome Malambo, Colby Ratcliff, Sorin Popescu, Dale Cope, Anjin Chang, Jinha Jung & J. Thomasson
Weekly unmanned aerial system (UAS) imagery was collected over the College Station, TX, 2017 Genomes to Fields (G2F) hybrid trial, across three environmental stress treatments, using two UAS platforms. The high-altitude (120-m) fixed-wing platform increased the fraction of variation attributed to genetics and had highly repeatable (R > 60%) height estimates, increasing the genetic variance explained (10–40%) over traditional terminal plant height measurement (PHT TRML ∼30%), as well as over the low-altitude rotary-wing UAS platform...

Data from: Olfaction written in bone: cribriform plate size parallels olfactory receptor gene repertoires in Mammalia

Deborah J. Bird, William J. Murphy, Lester Fox-Rosales, Iman Hamid, Robert A. Eagle & Blaire Van Valkenburgh
The evolution of mammalian olfaction is manifested in a remarkable diversity of gene repertoires, neuroanatomy, and skull morphology across living species. Olfactory receptor genes (ORG), which initiate the conversion of odorant molecules into odor perceptions and help an animal resolve the olfactory world, range in number from a mere handful to several thousand genes across species. Within the snout, each of these ORGs is exclusively expressed by a discrete population of olfactory sensory neurons (OSN),...

Data from: Gene trees, species trees and Earth history combine to shed light on the evolution of migration in a model avian system

Gary Voelker, Rauri C. K. Bowie & John Klicka
The evolution of migration in birds has fascinated biologists for centuries. In this study, we performed phylogenetic-based analyses of Catharus thrushes, a model genus in the study of avian migration, and their close relatives. For these analyses, we used both mitochondrial and nuclear genes, and the resulting phylogenies were used to trace migratory traits and biogeographic patterns. Our results provide the first robust assessment of relationships within Catharus and relatives and indicate that both mitochondrial...

Data from: The evolutionary relationships and age of Homo naledi: an assessment using dated Bayesian phylogenetic methods

Mana Dembo, Davorka Radovčić, Heather M. Garvin, Myra F. Laird, Lauren Schroeder, Jill E. Scott, Juliet Brophy, Rebecca R. Ackermann, Charles M. Musiba, Darryl J. De Ruiter, Arne Ø. Mooers, Mark Collard & Chares M. Musiba
Homo naledi is a recently discovered species of fossil hominin from South Africa. A considerable amount is already known about H. naledi but some important questions remain unanswered. Here we report a study that addressed two of them: “Where does H. naledi fit in the hominin evolutionary tree?” and “How old is it?” We used a large supermatrix of craniodental characters for both early and late hominin species and Bayesian phylogenetic techniques to carry out...

Data from: Pulsing hydrology determines top-down control of basal resources in a tropical river-floodplain ecosystem

Kirk O. Winemiller, Jose V. Montoya, Daniel L. Roelke, James B. Cotner, Craig A. Layman, Luzmila Sanchez & Maria M. Castillo
Variable hydrology of rivers strongly affects biophysical factors that influence primary production and population densities, thereby affecting the relative influence of bottom-up and top-down processes in trophic networks. Many tropical floodplain rivers have sustained seasonal flood pulses driven by precipitation patterns of the Intertropical Convergence Zone. These changes in flow alter concentrations of dissolved nutrients, aquatic primary productivity, and per-unit-area densities of aquatic organisms. Therefore, one would predict that the strength of top-down effects of...

Data from: Northern Bobwhite (Colinus virginianus) mitochondrial population genomics reveals structure, divergence, and evidence for heteroplasmy

Yvette A. Halley, David L. Oldeschulte, Eric K. Bhattarai, Joshua Hill, Richard P. Metz, Charles D. Johnson, Steven M. Presley, Rebekah E. Ruzicka, Dale Rollins, Markus J. Peterson, WIlliam J. Murphy & Christopher M. Seabury
Herein, we evaluated the concordance of population inferences and conclusions resulting from the analysis of short mitochondrial fragments (i.e., partial or complete D-Loop nucleotide sequences) versus complete mitogenome sequences for 53 bobwhites representing six ecoregions across TX and OK (USA). Median joining (MJ) haplotype networks demonstrated that analyses performed using small mitochondrial fragments were insufficient for estimating the true (i.e., complete) mitogenome haplotype structure, corresponding levels of divergence, and maternal population history of our samples....

Data from: Exploring origins, invasion history and genetic diversity of Imperata cylindrica (L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing

A. Millie Burrell, Alan E. Pepper, George Hodnett, John A. Goolsby, William A. Overholt, Alexis E. Racelis, Rodrigo Diaz & Patricia E. Klein
Imperata cylindrica (Cogongrass, Speargrass) is a diploid C4 grass that is a noxious weed in 73 countries and constitutes a significant threat to global biodiversity and sustainable agriculture. We used a cost-effective genotyping-by-sequencing (GBS) approach to identify the reproductive system, genetic diversity and geographic origins of invasions in the south-eastern United States. In this work, we demonstrated the advantage of employing the closely related, fully sequenced crop species Sorghum bicolor (L.) Moench as a proxy...

Data from: Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle

Jared Egan Decker, Stephanie D. McKay, Megan M. Rolf, JaeWoo Kim, Antonio Molina Alcalá, Tad S. Sonstegard, Olivier Hanotte, Anders Götherström, Christopher M. Seabury, Lisa Praharani, Masroor Ellahi Babar, Luciana Correia De Almieda Regitano, Mehmet Ali Yildiz, Michael P. Heaton, Wan-Sheng Liu, Chu-Zhao Lei, James M. Reecy, Muhammad Saif-Ur-Rehman, Robert D. Schnabel, Jeremy F. Taylor, Jared E. Decker & Antonio Molina Alcalá
The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns...

Data from: Signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) revealed by a genome scan analysis of single nucleotide polymorphisms

Julio Chávez-Galarza, Dora Henriques, J. Spencer Johnston, João C. Azevedo, John C. Patton, Irene Muñoz, Pilar De La Rúa, Maria Alice Pinto & M. Alice Pinto
Understanding the genetic mechanisms of adaptive population divergence is one of the most fundamental endeavours in evolutionary biology and is becoming increasingly important as it will allow predictions about how organisms will respond to global environmental crisis. This is particularly important for the honey bee, a species of unquestionable ecological and economical importance that has been exposed to increasing human-mediated selection pressures. Here, we conducted a single nucleotide polymorphism (SNP)-based genome scan in honey bees...

Data from: Validating the use of coloration patterns for individual recognition in the worm pipefish using a novel set of microsatellite markers

Nuno M. Monteiro, Rodolfo M. Silva, Mário Cunha, Agostinho Antunes, Adam G. Jones, Maria N. Vieira, A. G. Jones, N. M. Monteiro, A. Antunes & M. N. Vieira
In studies of behaviour, ecology and evolution, identification of individual organisms can be an invaluable tool, capable of unravelling otherwise cryptic information regarding group structure, movement patterns, population size and mating strategies. The use of natural markings is arguably the least invasive method for identification. However, to be truly useful natural markings must be sufficiently variable to allow for unique identification, while being stable enough to permit long-term studies. Non-invasive marking techniques are especially important...

Data from: The rediscovery of a long described species reveals additional complexity in speciation patterns of poeciliid fishes in sulfide springs

Maura Palacios, Lenin Arias-Rodrigues, Martin Plath, Constanze Eifert, Hannes Lerp, Anton Lamboj, Gary Voelker, Michael Tobler & Lenin Arias-Rodriguez
The process of ecological speciation drives the evolution of locally adapted and reproductively isolated populations in response to divergent natural selection. In Southern Mexico, several lineages of the freshwater fish species of the genus Poecilia have independently colonized toxic, hydrogen sulfide-rich springs. Even though ecological speciation processes are increasingly well understood in this system, aligning the taxonomy of these fish with evolutionary processes has lagged behind. While some sulfide spring populations are classified as ecotypes...

Data from: Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes

Rongfeng Cui, Molly Schumer, Karla Kruesi, Ronald Brice Walter, Peter Andolfatto, Gil G. Rosenthal & Ronald Walter
Hybridization is increasingly being recognized as a widespread process, even between ecologically and behaviorally divergent animal species. Determining phylogenetic relationships in the presence of hybridization remains a major challenge for evolutionary biologists, but advances in sequencing technology and phylogenetic techniques are beginning to address these challenges. Here we reconstruct evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by remarkable morphological diversity and behavioral barriers to interspecific mating. Past attempts to...

Data from: Environmental filtering improves ecological niche models across multiple scales

Adrian A. Castellanos, Jerry W. Huntley, Gary Voelker, A. Michelle Lawing, A Michelle Lawing, Adrian A Castellanos & Jerry W Huntley
1. A clear challenge for ecological niche modeling is determining how to best mitigate the effects of sampling bias from commonly collected biodiversity data. Recent approaches have focused on filtering occurrences in overrepresented regions based on geographic or environmental proximity. 2. We tested the efficacy of filtering in geographic and environmental space using occurrence data from four species. Our evaluation strategies examined 14 distance measures in geographic and environmental spaces and eight combinations of environmental...

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, Mark S Hafner, David J Hafner, James W Demastes, Theresa A Spradling & Jessica E Light
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: Phylogeography, population genetics, and distribution modeling reveal vulnerability of Scirpus longii (Cyperaceae) and the Atlantic Coastal Plain Flora to climate change.

Daniel Spalink, Ron MacKay, Kenneth J Sytsma & Kenneth J. Sytsma
A proactive approach to conservation must be predictive, anticipating how habitats will change and which species are likely to decline or prosper. We use composite species distribution modeling to identify suitable habitats for 18 members of the North American Atlantic Coastal Plain Flora (ACPF) since the Last Glacial Maximum and project these into the future. We then use Scirpus longii (Cyperaceae), a globally imperiled ACPF sedge with many of the characteristics of extinction vulnerability, as...

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