28 Works

Data from: Pan-African phylogeography of a model organism, the African clawed frog “Xenopus laevis”

Ben L.S. Furman, Adam J. Bewick, Tia L. Harrison, Eli Greenbaum, Václav Gvoždík, Chifundera Kusamba, Ben Evans, Benjamin L. S. Furman & Ben J. Evans
The African clawed frog Xenopus laevis has a large native distribution over much of sub-Saharan Africa and is a model organism for research, a proposed disease vector, and an invasive species. Despite its prominent role in research and abundance in nature, surprisingly little is known about the phylogeography and evolutionary history of this group. Here we report an analysis of molecular variation of this clade based on 17 loci (one mitochondrial, 16 nuclear) in up...

Data from: Exploring rainforest diversification using demographic model testing in the African foam-nest treefrog (Chiromantis rufescens)

Adam Leache, Daniel Portik, Danielle Rivera, Mark-Oliver Rodel, Johannes Penner, Václav Gvoždík, Eli Greenbaum, Gregory Jongsma, Caleb Ofori-Boateng, Marius Burger, Edem Eniang, Rayna Bell & Matthew Fujita
Aim: Species with wide distributions spanning the African Guinean and Congolian rainforests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rainforest species, the African Foam-nest Treefrog (Chiromantis rufescens). Location: Guinean and Congolian rainforests, West and Central Africa. Taxon: Chiromantis rufescens. Methods: We collected mitochondrial DNA (mtDNA)...

Data from: Reduced mitochondrial respiration in hybrid asexual lizards

Randy L. Klabacka, Hailey A. Parry, Kang Nian Yap, Ryan A. Cook, Victoria A. Herron, L. Miles Horne, Jose A. Maldonado, Jamie R. Oaks, Andreas N. Kavazis, Matthew K. Fujita, Tonia S. Schwartz & Matthew E. Wolak
The scarcity of asexual reproduction in vertebrates alludes to an inherent cost. Several groups of asexual vertebrates exhibit lower endurance capacity (a trait predominantly sourced by mitochondrial respiration) compared to congeneric sexual species. Here we measure endurance capacity in five species of Aspidoscelis lizards and examine mitochondrial respiration between sexual and asexual species using mitochondrial respirometry. Our results show reduced endurance capacity, mitochondrial respiration, and phenotypic variability in asexual species compared to parental sexual species...

Data from: Potential limitations of behavioral plasticity and the role of egg relocation in climate change mitigation for a thermally-sensitive endangered species

Michael J. Liles, Tarla Rai Peterson, Jeffrey A. Seminoff, Alexander R. Gaos, Eduardo Altamirano, Ana V. Henríquez, Velkiss Gadea, Sofía Chavarría, José Urteaga, Bryan P. Wallace & Markus J. Peterson
Anthropogenic climate change is widely considered a major threat to global biodiversity, such that the ability of a species to adapt will determine its likelihood of survival. Egg-burying reptiles that exhibit temperature-dependent sex determination, such as critically endangered hawksbill turtles (Eretmochelys imbricata), are particularly vulnerable to changes in thermal regimes because nest temperatures affect offspring sex, fitness, and survival. It is unclear whether hawksbills possess sufficient behavioral plasticity of nesting traits (i.e., redistribution of nesting...

Data from: A global dataset for economic losses of extreme hydrological events during 1960-2014

Bo Tao, Liping Gao, Yunxuan Miao, Lihua Zhang, Xia Song, Wei Ren, Liyuan He & Xiaofeng Xu
A comprehensive dataset of extreme hydrological events (EHEs) – floods and droughts, consisting of 2,171 occurrences worldwide, during 1960‐2014 was compiled, and then their economic losses were normalized using a price index in U.S. dollar. The dataset showed a significant increasing trend of EHEs before 2000, while a slight post‐2000 decline. Correspondingly, the EHEs‐caused economic losses increased obviously before 2000 followed by a slight decrease; the post‐2000 decline could be partially attributed to the decreases...

Data from: ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America

Philip Lavretsky, Jeffrey M. DaCosta, Michael D. Sorenson, Kevin G. McCracken & Jeffrey L. Peters
Recently evolved species typically share genetic variation across their genomes due to incomplete lineage sorting and/or ongoing gene flow. Given only subtle allele frequency differences at most loci and the expectation that divergent selection may affect only a tiny fraction of the genome, distinguishing closely related species based on multi‐locus data requires substantial genomic coverage. In this study, we used ddRAD‐seq to sample the genomes of five recently diverged, New World “mallards” (Anas spp.), a...

Persistence of an endangered native duck, feral mallards, and multiple hybrid swarms across the main Hawaiian Islands

Caitlin Wells, Philip Lavretsky, Michael Sorenson, Jeffrey Peters, Jeffrey DaCosta, Stephen Turnbull, Kimberly Uyehara, Christopher Malachowski, Bruce Dugger, John Eadie & Andrew Engilis
Interspecific hybridization is recognized as an important process in the evolutionary dynamics of both speciation and the reversal of speciation. However, our understanding of the spatial and temporal patterns of hybridization that erode versus promote species boundaries is incomplete. The endangered, endemic koloa maoli (or Hawaiian duck, Anas wyvilliana) is thought to be threatened with genetic extinction through ongoing hybridization with an introduced congener, the feral mallard (A. platyrhynchos). We investigated spatial and temporal variation...

High site fidelity does not equate to population structure for common goldeneye and Barrow’s goldeneye in North America.

Joshua Brown, Philip Lavretsky, Robert Wilson, Christy Haughey, Sean Boyd, Daniel Esler, Sandra Talbot & Sarah Sonsthagen
Delineation of population structure provides valuable information for conservation and management of species, as levels of demographic and genetic connectivity not only affect population dynamics but also have important implications for adaptability and resiliency of populations and species. Here, we measure population genetic structure and connectivity across the respective ranges of two sister species of Goldeneye, Barrow’s Goldeneye (Bucephala islandica) and Common Goldeneye (B. clangula). We use two different marker types: 7 nuclear microsatellite loci...

Data from: Above- and belowground drivers of intraspecific trait variability across subcontinental gradients for five ubiquitous forest plants in North America

Isabelle Aubin, Françoise Cardou, Alison Munson, Madhur Anand, André Arsenault, F. Wayne Bell, Yves Bergeron, Isabelle Boulangeat, Sylvain Delagrange, Nicole J. Fenton, Dominique Gravel, François Hébert, Jill Johnstone, S. Ellen Macdonald, Azim Mallik, Anne C.S. McIntosh, Jennie R. McLaren, Christian Messier, Dave Morris, Bill Shipley, Luc Sirois, Nelson Thiffault, Laura Boisvert-Marsh & Bright B. Kumordzi
Intraspecific trait variability (ITV) provides the material for species adaptation to environmental changes. To advance our understanding of how ITV can contribute to species adaptation to a wide range of environmental conditions, we studied five widespread understory forest species exposed to both continental-scale climate gradients, and local soil and disturbance gradients. We investigated the environmental drivers of between-site leaf and root trait variation, and tested whether higher between-site ITV was associated with increased trait sensitivity...

Active source seismic line near the Rio Grande in Sunland Park, NM

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In October 2015, the Advanced Exploration Seismology class at the University of Texas at El Paso together with additional volunteers acquired a 500-m active-source seismic profile across a possible andesite dike (called the River Andesite) adjacent to the Rio Grande River near Sunland Park, New Mexico. The andesite outcrops near the bank of the Rio Grande and is surrounded by Quaternary sedimentary deposition. Garcia (1970) suggests that the River Andesite is petrologically similar to the...

Allometric modelling of plant biomass from drone-acquired photographs: drone images, ground control marker coordinates and biomass data from 36 sites, 2016-2020

A. Cunliffe, K. Anderson, F. Boschetti, H. Graham, R. Brazier, I. Myers-Smith, T. Astor, M. Boer, L. Calvo, P. Clark, M. Cramer, M. Encinas-Lara, S. Escarzaga, J. Fernández-Guisuraga, A. Fisher, K. Gdulová, B. Gillespie, A. Griebel, N. Hanan, M. Hanggito, S. Haselberger, C. Havrilla, W. Ji, J. Karl, M. Kirchhoff … & R. Wojcikiewicz
This dataset contains RGB photographs acquired from drone surveys. There are 741 harvest plots from 38 surveys at 36 sites around the world. Each site was approximately 1 ha in area. Included with the photographic images are the coordinates of ground control markers, biomass, taxonomic and location data for harvest plots and ancillary metadata. The observations can be used to obtain allometric size-biomass models. This work was supported by the Natural Environment Research Council award...

Assessing changes in genomic divergence following a century of human mediated secondary contact among wild and captive-bred ducks

Philip Lavretsky, Nancy Rotzel McInerney, Jonathon Mohl, Joshua Brown, Helen James, Kevin McCracken & Robert Fleischer
Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used world-wide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary time scales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (Anas platyrhynchos) throughout North America, and two domestic mallard-types (i.e., known game-farm mallards and feral Khaki Campbell’s). We show...

Data from: When one phenotype is not enough - divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species

Giulia Zancolli, Juan J. Calvete, Michael D. Cardwell, Harry W. Greene, William K. Hayes, Matthew J. Hegarty, Hans-Werner Herrmann, Andrew T. Holycross, Dominic I. Lannutti, John F. Mulley, Libia Sanz, Zachary D. Travis, Joshua R. Whorley, Catharine E. Wüster & Wolfgang Wuster
Understanding the origin and maintenance of phenotypic variation, particularly across a continuous spatial distribution, represents a key challenge in evolutionary biology. For this, animal venoms represent ideal study systems: they are complex, variable, yet easily quantifiable molecular phenotypes with a clear function. Rattlesnakes display tremendous variation in their venom composition, mostly through strongly dichotomous venom strategies, which may even coexist within single species. Here, through dense, widespread population-level sampling of the Mojave rattlesnake, Crotalus scutulatus,...

Data from: Ecotypic differences in the phenology of the tundra species Eriophorum vaginatum reflect sites of origin

Thomas C. Parker, Jianwu Tang, Mahalia B. Clark, Michael M. Moody & Ned Fetcher
Eriophorum vaginatum is a tussock-forming sedge that contributes significantly to the structure and primary productivity of moist acidic tussock tundra. Locally adapted populations (ecotypes) have been identified across the geographical distribution of E. vaginatum; however, little is known about how their growth and phenology differ over the course of a growing season. The growing season is short in the Arctic and therefore exerts a strong selection pressure on tundra species. This raises the hypothesis that...

Data from: TipDatingBeast: an R package to assist the implementation of phylogenetic tip-dating tests using BEAST

Adrien Rieux & Camilo E. Khatchikian
Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. In this context, BEAST, a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce TipDatingBeast, an R package built to assist the implementation of various phylogenetic tip-dating tests using BEAST. TipDatingBeast currently contains two main functions....

Data from: Natal foraging philopatry in eastern Pacific hawksbill turtles

Alexander R. Gaos, Rebecca L. Lewison, Michael P. Jensen, Michael J. Liles, Ana Henriquez, Sofia Chavarria, Carlos Mario Pacheco, Melissa Valle, David Melero, Velkiss Gadea, Eduardo Altamirano, Perla Torres, Felipe Vallejo, Cristina Miranda, Carolina LeMarie, Jesus Lucero, Karen Oceguera, Didiher Chacón, Luis Fonseca, Marino Abrego, Jeffrey A. Seminoff, Eric E. Flores, Israel Llamas, Rodrigo Donadi, Bernardo Peña … & Daniela Alarcón Ruales
The complex processes involved with animal migration have long been a subject of biological interest and broad-scale movement patterns of many marine turtle populations still remain unresolved. While it is widely accepted that once marine turtles reach sexual maturity they home to natal areas for nesting or reproduction, the role of philopatry to natal areas during other life stages has received less scrutiny, despite widespread evidence across the taxa. Here we report on genetic research...

Data from: Into the light: diurnality has evolved multiple times in geckos

Tony Gamble, Eli Greenbaum, Todd R. Jackman & Aaron M. Bauer
Geckos are the only major lizard group consisting mostly of nocturnal species. Nocturnality is presumed to have evolved early in gecko evolution and geckos possess numerous adaptations to functioning in low light and at low temperatures. However, not all gecko species are nocturnal and most diurnal geckos have their own distinct adaptations to living in warmer, sunlit environments. We reconstructed the evolution of gecko activity patterns using a newly generated time-calibrated phylogeny. Our results provide...

Investigating West Texas Seismicity and Structure with Dense Geophone Arrays

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This network was designed to record seismicity near Pecos, Texas in the Delaware Basin. This temporary network was deployed from early Nov. 2018 to early Jan. 2020 with an average of ~24 Magseis Fairfield Z-Land Generation 2 seismic nodes in the field each month. The network was redeployed with more stations during Sept. and Oct. 2020.

Node deployment in Oaxaca, Mexico following the M8.1 Tehuantepec Earthquake

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Fifty Magseis Fairfield Z-Land Generation 2 5-Hz 3-component nodes were deployed in Oaxaca, Mexico following the M8.1 Tehuantepec Earthquake from roughly Oct. 1-22, 2017.

TIME Tornillo, Texas Shot Testing I

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We deployed Reftek 125A Texans and Magseis Fairfield nodes in a circle and two lines to record explosive source seismic testing including Poulter shots, detonation cord, and other shot configurations.

El Paso Iglesias

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A network of ~50 Magseis Fairfield nodes was deployed for one month at churches ("iglesias" in Spanish) across El Paso, Texas.

Data from: Evolution of gliding in Southeast Asian geckos and other vertebrates is temporally congruent with dipterocarp forest development

Matthew P. Heinicke, Eli Greenbaum, Todd R. Jackman & Aaron M. Bauer
Gliding morphologies occur in diverse vertebrate lineages in Southeast Asian rainforests, including three gecko genera, plus frogs, snakes, agamid lizards, and squirrels. It has been hypothesized that repeated evolution of gliding is related to the dominance of Asian rainforest tree floras by dipterocarps. For dipterocarps to have influenced the evolution of gliding in Southeast Asian vertebrates, gliding lineages must have Eocene or later origins. However, divergence times are not known for most lineages. To investigate...

Data from: Idenitfying hybrids & the genomics of hybridization: mallards & American black ducks of Eastern North America

Philip Lavretsky, Thijs Janzen & Kevin G. McCracken
Resolving evolutionary relationships and establishing population structure depends on molecular diagnosability that is often limited for closely related taxa. Here, we use 3,200 ddRAD-seq loci across 290 mallards, American black ducks, and putative hybrids to establish population structure and estimate hybridization rates. We test between traditional assignment probability and accumulated recombination events based analyses to assign hybrids to generational classes. For hybrid identification, we report the distribution of recombination events complements ADMIXTURE simulation by extending...

Data from: Phylogeography of the reed frog Hyperolius castaneus (Anura: Hyperoliidae) from the Albertine Rift of Central Africa: implications for taxonomy, biogeography and conservation

Eli Greenbaum, Ulrich Sinsch, Edgar Lehr, Federico Valdez & Chifundera Kusamba
We examine the systematics of multiple populations of the Albertine Rift endemic amphibian Hyperolius castaneus, which currently incorporates four subspecies. Standard morphometric data were analyzed with principal components analyses and analyses of covariance. Phylogenetic analyses of two mitochondrial (16S, cyt b) and one nuclear (RAG1) genes were analyzed from 41 samples representing three subspecies. Results indicated some significant morphometric differences between the nominate subspecies H. c. castaneus and the Itombwe Plateau subspecies H. c. constellatus,...

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....

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