70 Works

Data from: Vanishing refuge? Testing the forest refuge hypothesis in coastal East Africa using genome-wide sequence data for seven amphibians

Christopher D. Barratt, Beryl A. Bwong, Robert Jehle, H. Christoph Liedtke, Peter Nagel, Renske E. Onstein, Daniel M. Portik, Jeffrey W. Streicher & Simon P. Loader
High-throughput sequencing data have greatly improved our ability to understand the processes that contribute to current biodiversity patterns. The “vanishing refuge” diversification model is speculated for the coastal forests of eastern Africa, whereby some taxa have persisted and diversified between forest refugia, while others have switched to becoming generalists also present in non-forest habitats. Complex arrangements of geographical barriers (hydrology and topography) and ecological gradients between forest and non-forest habitats may have further influenced the...

Data from: Limitations of climate data for inferring species boundaries: insights from speckled rattlesnakes

Jesse M. Meik, Jeffrey W. Streicher, A. Michelle Lawing, Oscar Flores-Villela & Matthew K. Fujita
Phenotypes, DNA, and measures of ecological differences are widely used in species delimitation. Although rarely defined in such studies, ecological divergence is almost always approximated using multivariate climatic data associated with sets of specimens (i.e., the “climatic niche”); the justification for this approach is that species-specific climatic envelopes act as surrogates for physiological tolerances. Using identical statistical procedures, we evaluated the usefulness and validity of the climate-as-proxy assumption by comparing performance of genetic (nDNA SNPs...

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)...

Evolutionary change in metabolic rate of Daphnia pulicaria following invasion by the predator Bythotrephes longimanus

Sigurd Einum, Varsha Rani, Tim Burton & Matthew Walsh
Metabolic rate is a trait that may evolve in response to the direct and indirect effects of predator-induced mortality. Predators may indirectly alter selection by lowering prey densities and increasing resource availability or by intensifying resource limitation through changes in prey behaviour (e.g. use of less productive areas). In the current study we quantify evolution of metabolic rate in the zooplankton Daphnia pulicaria following an invasive event by the predator Bythotrephes longimanus in Lake Mendota,...

Ancestral genetic variation in phenotypic plasticity underlies rapid evolutionary changes in resurrected populations of waterfleas

Matthew Walsh, J. Alex Landy, Alixander Oschmann & Stephan Munch
The role that phenotypic plasticity plays in adaptive evolution has been debated for decades. This is because the strength of natural selection is dependent upon the direction and magnitude of phenotypic responses to environmental signals. Therefore, the connection between plasticity and adaptation will depend on the patterns of plasticity harbored by ancestral populations prior to a change in the environment. Yet, few studies have directly assessed ancestral variation in plasticity and tracked phenotypic changes over...

Data from: Development of common leaf-footed bug pests depends on the presence and identity of their environmentally-acquired symbionts

Martha Hunter, Edwin Umanzor, Suzanne Kelly, Shaira Whittaker & Alison Ravenscraft
Many beneficial symbioses between bacteria and their terrestrial arthropod hosts are vertically transmitted from mother to offspring, ensuring the progeny acquire necessary partners. Unusually, in several families of coreoid and lygeoid bugs (Hemiptera), nymphs must instead ingest the beneficial symbiont, Burkholderia (sensu lato), from the environment early in development. We studied the effects of Burkholderia on development of two species of leaf-footed bug (Coreidae) in the genus Leptoglossus, L. zonatus and L. phyllopus. We found...

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: Multilocus phylogeography reveals nested endemism in a gecko across the monsoonal tropics of Australia

Craig Moritz, Matthew Fujita, Dan F. Rosauer, Rosa Agudo, Gayleen Bourke, Russell Palmer, Mitzy Pepper, Sally Potter, Renae Pratt, Mitchell Scott, Maria Tonione, Stephen Donnellan, Paul Doughty, D. Rosauer & M. K. Fujita
Multilocus phylogeography can uncover taxonomically unrecognized lineage diversity across complex biomes. The Australian monsoonal tropics includes vast, ecologically intact savanna-woodland plains interspersed with ancient sandstone uplands. Though recognized in general for its high species richness and endemism, the biodiversity of the region remains underexplored due to its remoteness. This is despite a high rate of ongoing species discovery, especially in wetter regions and for rock-restricted taxa. To provide a baseline for ongoing comparative analyses, we...

Data from: Composite measures of selection can improve the signal-to-noise ratio in genome scans

Katie E. Lotterhos, Daren C. Card, Sara M. Schaal, Liuyang Wang, Caitlin Collins & Bob Verity
The growing wealth of genomic data is yielding new insights into the genetic basis of adaptation, but it also presents the challenge of extracting the relevant signal from multi-dimensional datasets. Different statistical approaches vary in their power to detect selection depending on the demographic history, type of selection, genetic architecture and experimental design. Here, we develop and evaluate new approaches for combining results from multiple tests, including multivariate distance measures and methods for combining P-values....

Data from: Whole genome amplification and reduced-representation genome sequencing of Schistosoma japonicum miracidia

Jonathan A. Shortt, Daren C. Card, Drew R. Schield, Yang Liu, Bo Zhong, Todd A. Castoe, Elizabeth J. Carlton & David D. Pollock
Background: In areas where schistosomiasis control programs have been implemented, morbidity and prevalence have been greatly reduced. However, to sustain these reductions and move towards interruption of transmission, new tools for disease surveillance are needed. Genomic methods have the potential to help trace the sources of new infections, and allow us to monitor drug resistance. Large-scale genotyping efforts for schistosome species have been hindered by cost, limited numbers of established target loci, and the small...

Data from: Evolution of life history traits in geographically isolated populations of Vaejovis scorpions (Scorpiones: Vaejovidae)

Matthew M. Steffenson & Christopher A. Brown
Geographical isolation can over time accumulate life-history variation which can eventually lead to speciation. We used five species of Vaejovis scorpions that have been isolated from one another since the Pleistocene glaciation to identify if biogeographical patterns have allowed for the accumulation of life-history variation among species. Gravid females were captured and brought back to the lab until giving birth. Once offspring had begun to disperse, measurements of female size, reproductive investment, offspring size, offspring...

Data from: Predator-induced phenotypic plasticity within- and across-generations: a challenge for theory?

Matthew R. Walsh, Kelsey Biles, Frank Cooley & Stephan B. Munch
Much work has shown that the environment can induce non-genetic changes in phenotype that span multiple generations. Theory predicts that predictable environmental variation selects for both increased within- and across-generation responses. Yet, to the best of our knowledge, there are no empirical tests of this prediction. We explored the relationship between within- versus across-generation plasticity by evaluating the influence of predator cues on the life-history traits of Daphnia ambigua. We measured the duration of predator-induced...

Data from: Sexual differences in head form and diet in a population of Mexican Lance-headed Rattlesnakes, Crotalus polystictus

Jesse M. Meik, Kirk Setser, Estrella Mociño-Deloya & Anna Michelle Lawing
Sexual dimorphism of phenotypic traits associated with resource use is common in animals, and may result from niche divergence between sexes. Snakes have become widely used in studies of the ecological basis of sexual dimorphism because they are gape-limited predators and their head morphology is likely to be a direct indicator of the size and shape of prey consumed. We examined sexual dimorphism of body size and head morphology, and sexual differences in diet in...

Data from: Higher predation risk for insect prey at low latitudes and elevations

Tomas Roslin, Bess Hardwick, Vojtech Novotny, William K. Petry, Nigel R. Andrew, Ashley Asmus, Isabel C. Barrio, Yves Basset, Andrea Larissa Boesing, Timothy C. Bonebrake, Erin K. Cameron, Wesley Dáttilo, David A. Donoso, Pavel Drozd, Claudia L. Gray, David S. Hik, Sarah J. Hill, Tapani Hopkins, Shuyin Huang, Bonny Koane, Benita Laird-Hopkins, Liisa Laukkanen, Owen T. Lewis, Sol Milne, Isaiah Mwesige … & Eleanor M. Slade
Biotic interactions underlie ecosystem structure and function, but predicting interaction outcomes is difficult. We tested the hypothesis that biotic interaction strength increases toward the equator, using a global experiment with model caterpillars to measure predation risk. Across an 11,660-kilometer latitudinal gradient spanning six continents, we found increasing predation toward the equator, with a parallel pattern of increasing predation toward lower elevations. Patterns across both latitude and elevation were driven by arthropod predators, with no systematic...

Data from: Separate block based parameter estimation method for Hammerstein systems

Shuo Zhang, Dongqing Wang & Feng Liu
Different from the output-input representation based identification methods of two-block Hammerstein systems, this paper concerns a separate block based parameter estimation method for each block of a two-block Hammerstein CARMA system, without combining the parameters of two parts together. The idea is to consider each block as a subsystem and to estimate the parameters of the nonlinear block and the linear block separately (interactively), by using two least squares algorithms in one recursive step. The...

Data from: Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

Jared A. Grummer, Martha L. Calderón-Espinosa, Adrián Nieto-Montes De Oca, Eric N. Smith, Fausto R. Méndez De La Cruz & Adam D. Leaché
Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the overlap of ancestral populations. In this study, we performed population genetic analyses, species delimitation, simulations and a recently developed approach of species tree diffusion to infer the...

Data from: Probabilistic species tree distances: implementing the multispecies coalescent to compare species trees within the same model-based framework used to estimate them

Richard H. Adams & Todd A. Castoe
Despite the ubiquitous use of statistical models for phylogenomic and population genomic inferences, this model-based rigor is rarely applied to post-hoc comparison of trees. In a recent study, Garba and colleagues derived new methods for measuring the distance between two gene trees computed as the difference in their site pattern probability distributions. Unlike traditional metrics that compare trees solely in terms of geometry, these measures consider gene trees and associated parameters as probabilistic models that...

Data for: Transgenerational plasticity in the eye size of Daphnia

Matthew Walsh & Michael Gillis
It is well established that environmental signals can induce phenotypic responses that persist for multiple generations. The induction of such 'transgenerational plasticity' (TGP) depends upon the ability of organisms to accurately receive and process information from environmental signals. Thus, sensory systems are likely intertwined with TGP. Here we tested the link between an environmental stressor and transgenerational responses in a component of the sensory system (eye size) that is linked to enhanced vision and ecologically-relevant...

Finding complexity in complexes: assessing the causes of mitonuclear discordance in a problematic species complex of Mesoamerican toads

Thomas Firneno, Justin O'Neill, Daniel Portik, Alyson Emery, Josiah Townsend & Matthew Fujita
Mitonuclear discordance is a frequently encountered pattern in phylogeographic studies and occurs when mitochondrial and nuclear DNA display conflicting signals. Discordance among these genetic markers can be caused by several factors including confounded taxonomies, gene flow, and incomplete lineage sorting. In this study, we present a strong case of mitonuclear discordance in a species complex of toads (Bufonidae: Incilius coccifer complex) found in the Chortís Block of Central America. To determine the cause of mitonuclear...

A metacommunity approach for detecting species influenced by mass effect

Thibault Leboucher, Juliette Tison-Rosebery, William R. Budnick, Aurélien Jamoneau, Wim Vyverman, Janne Soininen, Sébastien Boutry & Sophia I. Passy
1. Mass effect, allowing species to persist in unfavourable habitats, and dispersal limitation, preventing species from reaching favourable habitats, are the two major dispersal processes. While dispersal limitation can be detected by experimental or modeling techniques, mass effect is more challenging to evaluate, which hampers our ability to disentangle the influence of the environment vs. dispersal on species distribution. This is undesirable for biomonitoring programs built on known species-environment relationships. 2. We developed an approach...

QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient

David Lowry, John Lovell, Li Zhang, Jason Bonnette, Philip Fay, Robert Mitchell, John Lloyd-Reilley, Arvid Boe, Yanqi Wu, Francis Rouquette, Richard Wynia, Xiaoyu Weng, Kathrine Behrman, Adam Healey, Kerrie Barry, Anna Lipzen, Diane Bauer, Aditi Sharma, Jerry Jenkins, Jeremy Schmutz, Felix B. Fritschi & Thomas E. Juenger
Local adaptation is the process by which natural selection drives adaptive phenotypic divergence across environmental gradients. Theory suggests that local adaptation results from genetic trade-offs at individual genetic loci, where adaptation to one set of environmental conditions results in a cost to fitness in alternative environments. However, the degree to which there are costs associated with local adaptation is poorly understood because most of these experiments rely on two-site reciprocal transplant experiments. Here, we quantify...

Phylogenomics, introgression, and demographic history of South American true toads (Rhinella)

Danielle Rivera, Ivan Prates, Thomas Firneno, Miguel Rodrigues, Janalee Caldwell & Matthew Fujita
The effects of genetic introgression on species boundaries and how they affect species’ integrity and persistence over evolutionary time have received increased attention. The increasing availability of genomic data has revealed contrasting patterns of gene flow across genomic regions, which impose challenges to inferences of evolutionary relationships and of patterns of genetic admixture across lineages. By characterizing patterns of variation across thousands of genomic loci in a widespread complex of true toads (Rhinella), we assess...

Data from: The evolution of reproductive diversity in Afrobatrachia: a phylogenetic comparative analysis of an extensive radiation of African frogs

Daniel M. Portik & David C. Blackburn
The reproductive modes of anurans (frogs and toads) are the most diverse of terrestrial vertebrates, and a major challenge is identifying selective factors that promote the evolution or retention of reproductive modes across clades. Terrestrialized anuran breeding strategies have evolved repeatedly from the plesiomorphic fully aquatic reproductive mode, a process thought to occur through intermediate reproductive stages. Several selective forces have been proposed for the evolution of terrestrialized reproductive traits, but factors such as water...

Data from: Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes

Jeffrey W. Streicher, Jay P. McEntee, Laura C. Drzich, Daren C. Card, Drew R. Schield, Utpal Smart, Christopher L. Parkinson, Tereza Jezkova, Eric N. Smith & Todd A. Castoe
Strong spatial sorting of genetic variation in contiguous populations is often explained by local adaptation or secondary contact following allopatric divergence. A third explanation, spatial sorting by stochastic effects of range expansion, has been considered less often though theoretical models suggest it should be widespread, if ephemeral. In a study designed to delimit species within a clade of venomous coralsnakes, we identified an unusual pattern within the Texas coral snake (Micrurus tener): strong spatial sorting...

Data from: Maternal diet and age alter direct and indirect relationships between life history traits across multiple generations

Jared M. Goos, Cameron J. Swain, Stephan B. Munch & Matthew R. Walsh
1. Maternal age has important consequences for offspring fitness, with influences on size, development, and reproductive schedules. Such maternal age effects may be driven by differential provisioning of resources, yet little is known about the role of environmental supply of nutritional resources in mediating such effects. 2. We tested the influence of limiting nutritional resource, dietary phosphorus (P), on maternal age effects across multiple generations by examining the potential interactive effects of maternal nutrition and...

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