81 Works

Tracking the Near East origins and European dispersal of the house mouse

Thomas CUCCHI, Katerina Papayianni, Sophie Cersoy, Laetitia Aznar-Cormano, Antoine Zazzo, Régis Debruyne, Rémi Berthon, Adrian Bălășescu, Alan Simmons, François Valla, Yannis Hamilakis, Fanis Mavridis, Marjan Mashkour, Jamshid Darvish, Roohollah Siahsarvi, Fereidoun Biglari, Cameron A. Petrie, Lloyd Weeks, Alireza Sardari, Sepideh Maziar, Christiane Denys, David Orton, Emma Jenkins, Melinda Zeder, Jeremy B. Searle … & Jean-Denis Vigne
The house mouse (Mus musculus) is one of the most invasive mammals and an evolutionary model. However, the timing and components of its origin and dispersal remain poorly documented. To track its synanthropisation and subsequent biological invasion during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, dating between 40,000 and 3,000 cal. BP, combining geometric morphometris numerical taxonomy with ancient mitochondrial DNA...

Transcriptomics illuminate the phylogenetic backbone of tiger beetles

Harlan Gough, Julie Allen, Emmanuel Toussaint, Caroline Storer & Akito Kawahara
Phylogenomics is progressing rapidly, allowing large strides forward into our understanding of the tree of life. In this study, we generated transcriptomes from ethanol-preserved specimens of 13 tiger beetle species (Coleoptera: Cicindelinae) and one Scaritinae outgroup. From these 14 transcriptomes and seven publicly available transcriptomes, we recovered an average of 2538 loci for phylogenetic analysis. We constructed an evolutionary tree of tiger beetles to examine deep-level relationships and examined the extent to which the composition...

Data from: Aridity Drives Spatiotemporal Patterns of Masting Across the Latitudinal Range of a Dryland Conifer

Andreas Wion, Peter Weisberg, Ian Pearse & Miranda Redmond
Masting, or the synchronous and irregular production of seed crops, is controlled by environmental cues and resource budgets. Increasing temperatures and shifting precipitation regimes may alter the frequency and magnitude of masting, especially in species that experience chronic resource stress. Yet the effects of a changing climate on seed production are unlikely to be uniform across populations, particularly those that span broad abiotic gradients. In this study, we assessed the spatiotemporal patterns of masting across...

The Bogert effect and environmental heterogeneity

Michael L. Logan, Jenna Van Berkel & Susana Clusella-Trullas
A classic question in evolutionary biology is whether behavioural flexibility hastens or hinders evolutionary change. The latter idea, that behavior reduces the number of environmental states experienced by an organism and therefore buffers that organism against selection, has been dubbed the “Bogert Effect” after Charles Bogert, the biologist who first popularized the phenomenon using data from lizards. The Bogert Effect is pervasive when traits like mean body temperature, which tend to be invariant across space...

The evolutionary potential of an insect invader under climate change

Michael Logan, Ingrid Minnaar, Kaitlin Keegan & Susana Clusella-Trullas
Although the impacts of climate change and invasive species are typically studied in isolation, they likely interact to reduce the viability of plant and animal populations. Indeed, invasive species, by definition, have succeeded in areas outside of their native range and may therefore have higher adaptive capacity relative to native species. Nevertheless, the genetic architecture of the thermal niche, which sets a limit to the potential for populations to evolve rapidly under climate change, has...

Estimating correlations among demographic parameters in population models

Thomas Riecke, Alan Leach, James Sedinger, Benjamin Sedinger & Perry Williams
Estimating correlations among demographic parameters is critical to understanding population dynamics and life-history evolution, where correlations among parameters can inform our understanding of life-history trade-offs, result in effective applied conservation actions, and shed light on evolutionary ecology. The most common approaches rely on the multivariate normal distribution, and its conjugate inverse Wishart prior distribtion. However, the inverse Wishart prior for the covariance matrix of multivariate normal distributions has a strong influence on posterior distributions. As...

Data from: Increased soil temperature and decreased precipitation during early life stages constrain grass seedling recruitment in cold desert restoration

Jeremy J. James, Roger Sheley, Elizabeth Leger, Peter B. Adler, Stuart Hardegree, Elise Gornish & Matt Rinella
1. Seed-based restoration is one of the most difficult challenges for dryland restoration. Identifying environmental conditions that drive variation in seed and seedling mortality across similar restoration efforts could increase understanding of when and where restoration outcomes are likely to be favorable and identify new tools and strategies to improve outcomes. 2. We asked how variation in a suite of environmental predictors influenced germination, emergence, seedling establishment, and juvenile survival of four commonly sown perennial...

Data from: Sperm competitive advantage of a rare mitochondrial haplogroup linked to differential expression of mitochondrial oxidative phosphorylation genes

Jeanne Zeh, Maya Zawlodzki, Melvin Bonilla, Eleanor Su-Keene, Michael Padua & David Zeh
Maternal inheritance of mitochondria creates a sex-specific selective sieve through which mitochondrial mutations harmful to males but not females accumulate and contribute to sexual differences in longevity and disease susceptibility. Because eggs and sperm are under disruptive selection, sperm are predicted to be particularly vulnerable to the genetic load generated by maternal inheritance, yet evidence for mitochondrial involvement in male fertility is limited and controversial. Here, we exploit the coexistence of two divergent mitochondrial haplogroups...

Data from: Highly variable reproductive isolation among pairs of Catostomus species

Elizabeth G. Mandeville, Thomas L. Parchman, David B. McDonald & C. Alex Buerkle
Hybridization between diverged taxa tests the strength of reproductive isolation and can therefore reveal mechanisms of reproductive isolation. However, it remains unclear how consistent reproductive isolation is across species' ranges and to what extent reproductive isolation might remain polymorphic as species diverge. To address these questions, we compared outcomes of hybridization across species pairs of Catostomus fishes in three rivers in the Upper Colorado River basin, where an introduced species, C. commersoni, hybridizes with at...

Data from: Impacts of inference method and dataset filtering on phylogenomic resolution in a rapid radiation of ground squirrels (Xerinae: Marmotini)

Bryan S. McLean, Kayce C. Bell, Julia M. Allen, Kristofer M. Helgen, Joseph A. Cook, Bryan S Mclean, Kayce C Bell, Joseph A Cook, Julie M Allen & Kristofer M Helgen
Phylogenomic datasets are illuminating many areas of the Tree of Life. However, the large size of these datasets alone may be insufficient to resolve problematic nodes in the most rapid evolutionary radiations, because inferences in zones of extraordinarily low phylogenetic signal can be sensitive to the model and method of inference, as well as the information content of loci employed. We used a dataset of >3,950 ultraconserved element (UCE) loci from a classic mammalian radiation,...

Data from: Reconstructing the evolutionary history of an endangered subspecies across the changing landscape of the Great Central Valley of California.

Marjorie D. Matocq, Patrick A. Kelly, Scott E. Phillips & Jesús E. Maldonado
Identifying historic patterns of population genetic diversity and connectivity is a primary challenge in efforts to re-establish the processes that have generated and maintained genetic variation across natural landscapes. The challenge of reconstructing pattern and process is even greater in highly altered landscapes where population extinctions and dramatic demographic fluctuations in remnant populations may have substantially altered, if not eliminated, historic patterns. Here, we seek to reconstruct historic patterns of diversity and connectivity in an...

Data from: Genetic drift or natural selection? Hybridization and asymmetric mitochondrial introgression in two Caribbean lizards (Anolis pulchellus and Anolis krugi)

Tereza Jezkova, Manuel Leal & Javier A. Rodríguez-Robles
Hybridization and gene introgression can occur frequently between closely related taxa, but appear to be rare phenomena among members of the species-rich West Indian radiation of Anolis lizards. We investigated the pattern and possible mechanism of introgression between two sister species from Puerto Rico, Anolis pulchellus and Anolis krugi, using mitochondrial (ND2) and nuclear (DNAH3, NKTR) DNA sequences. Our findings demonstrated extensive introgression of A. krugi mtDNA (k-mtDNA) into the genome of A. pulchellus in...

Data from: Functional genomic and phenotypic responses to desiccation in natural populations of a desert drosophilid

Subhash Rajpurohit, Cassia C. Oliveira, William J. Etges & Allen G. Gibbs
We used whole transcriptome microarrays to assess changes in gene expression and monitored mortality rates and epicuticular hydrocarbons (CHCs) in response to desiccation stress in four natural populations of Drosophila mojavensis from Baja California and mainland Mexico. Desiccation had the greatest effect on gene expression, followed by biogeographical variation at regional and population levels. Genes involved in environmental sensing and cuticular structure were up-regulated in dry conditions, while genes involved in transcription itself were down-regulated....

Data from: Sea level, topography, and island diversity: phylogeography of the Puerto Rican Red-eyed Coquí, Eleutherodactylus antillensis

Brittany S. Barker, Javier A. Rodríguez-Robles, Vani S. Aran, Ashley Montoya, Robert B. Waide & Joseph A. Cook
Quaternary climatic oscillations caused changes in sea level that altered the size, number, and degree of isolation of islands, particularly in land-bridge archipelagoes. Elucidating the demographic effects of these oscillations increases our understanding of the role of climate change in shaping evolutionary processes in archipelagoes. The Puerto Rican Bank (Puerto Rico and the Eastern Islands, which comprise Vieques, Culebra, the Virgin Islands, and associated islets) in the eastern Caribbean Sea periodically coalesced during glaciations and...

Data from: Genomic sequence capture of haemosporidian parasites: methods and prospects for enhanced study of host-parasite evolution

Lisa N. Barrow, Julie M. Allen, Xi Huang, Staffan Bensch & Christopher C. Witt
Avian malaria and related haemosporidians (Plasmodium, [Para]Haemoproteus, and Leucocytoozoon) represent an exciting multi-host, multi-parasite system in ecology and evolution. Global research in this field accelerated after 1) the publication in 2000 of PCR protocols to sequence a haemosporidian mitochondrial (mtDNA) barcode, and 2) the development in 2009 of an open-access database to document the geographic and host ranges of parasite mtDNA haplotypes. Isolating haemosporidian nuclear DNA from bird hosts, however, has been technically challenging, slowing...

Data from: On the importance of having a good mother: maternal investment affects duckling mortality risk in wood ducks

Benjamin S. Sedinger, Christopher A. Nicolai, Kelley M. Stewart & Kelly M. Stewart
Most avian populations experience more variation in recruitment than adult survival, and twhich drives much of the change in population growth rates from year to year. In duck species, the probability of duckling survival is an important component of recruitment into the breeding population. We investigated how variation in maternal investment in offspring by nesting female wood duck Aix sponsa affected duckling mortality (1‐survival) to 60 days of age using capture‐mark‐recapture techniques. Our primary sample...

Data from: Parameterizing the robust design in the BUGS language: lifetime carry‐over effects of environmental conditions during growth on a long‐lived bird

Thomas V. Riecke, Alan G. Leach, Dan Gibson & James S. Sedinger
1. Since the initial development of the robust design, this capture‐recapture model structure has been modified to estimate temporary emigration, and expanded to include auxiliary information such as band recovery and live resight data using maximum likelihood approaches. These developments have allowed investigators to separately assess individual and group effects on true survival, site fidelity, and temporary emigration. Additionally, recent advances in the BUGS language have allowed researchers to develop increasingly complex, user‐specified models in...

Data from: Deconstruction of a plant-arthropod community reveals influential plant traits with nonlinear effects on arthropod assemblages

Joshua G. Harrison, Casey Philbin, Zach Gompert, Glen Forister, Leonardo Hernandez, Benjamin W. Sullivan, Ian Wallace, Lyra Beltran, Craig Dodson, Jacob S. Francis, Amie Schlageter, Oren Shelef, Su'ad Yoon, Matthew L. Forister, Ian S. Wallace, Su'ad A. Yoon, Zachariah Gompert, Casey S. Philbin, Craig D. Dodson, Leonardo Hernandez-Espinoza & Glen W. Forister
1. Studies of herbivores and secondary consumer communities rarely incorporate a comprehensive characterization of primary producer trait variation, thus limiting our understanding of how plants mediate community assembly of consumers. 2. We took advantage of recent technological developments for efficient generation of phytochemical, microbial, and genomic data to characterize individual alfalfa plants (Medicago sativa; Fabaceae) growing in an old-field, semi-naturalized state for 770 traits (including 753 chemical features). Using random forest modeling, we investigated the...

Data from: Chronotype variation drives night-time sentinel-like behaviour in hunter–gatherers

David Samson, Alyssa Crittenden, Ibrahim Mabulla, Audax Mabulla, Charles Nunn, Charles L. Nunn, David R. Samson, Audax Z. P. Mabulla, Ibrahim A. Mabulla & Alyssa N. Crittenden
Sleep is essential for survival, yet it also represents a time of extreme vulnerability to predation, hostile conspecifics, and environmental dangers. To reduce the risks of sleeping, the sentinel hypothesis proposes that group-living animals share the task of vigilance during sleep, with some individuals sleeping while others are awake. To investigate sentinel-like behaviour in sleeping humans, we investigated activity patterns at night among Hadza hunter-gatherers of Tanzania. Using actigraphy, we discovered that all subjects were...

Data from: Absence of population structure across elevational gradients despite large phenotypic variation in mountain chickadees (Poecile gambeli)

Carrie L. Branch, Joshua P. Jahner, Dovid Y. Kozlovsky, Thomas L. Parchman & Vladimir V. Pravosudov
Montane habitats are characterized by predictably rapid heterogeneity along elevational gradients and are useful for investigating the consequences of environmental heterogeneity for local adaptation and population genetic structure. Food-caching mountain chickadees inhabit a continuous elevation gradient in the Sierra Nevada, and birds living at harsher, high elevations have better spatial memory ability and exhibit differences in male song structure and female mate preference compared to birds inhabiting milder, low elevations. While high elevation birds breed,...

Data from: Genome-wide differentiation in closely related populations: the roles of selection and geographic isolation

Rebecca J. Safran, Elizabeth S. C. Scordato, Matthew R. Wilkins, Joanna K. Hubbard, Brittany R. Jenkins, Tomas Albrecht, Samuel M. Flaxman, Hakan Karaardic, Yoni Vortman, Arnon Lotem, Patrik Nosil, Péter Pap, Sheng-Feng Shen, Shih-Fan Chan, Thomas L. Parchman, Nolan C. Kane, M. R. Wilkins, J. K. Hubbard, S. Shen, S.-F. Chan, P. Nosil, T.L. Parchman, R. J. Safran, E. S. C. Scordato, B. R. Jenkins … & T. Albrecht
Population divergence in geographic isolation is due to a combination of factors. Natural and sexual selection may be important in shaping patterns of population differentiation, a pattern referred to as ‘isolation by adaptation’ (IBA). IBA can be complementary to the well-known pattern of ‘isolation by distance’ (IBD), in which the divergence of closely related populations (via any evolutionary process) is associated with geographic isolation. The barn swallow Hirundo rustica complex comprises six closely related subspecies,...

Data from: Bees use the taste of pollen to determine which flowers to visit

Felicity Muth, Francis S. Jacob, Anne S. Leonard & Jacob S. Francis
Pollen plays a dual role as both a gametophyte and a nutritional reward for pollinators. Although pollen chemistry varies across plant species, its functional significance in pollination has remained obscure, in part because little is known about how floral visitors assess it. Bees rely on pollen for protein, but whether foragers evaluate its chemistry is unclear, as it is primarily consumed by larvae. We asked whether the chemical composition of pollen influences bumblebees' foraging behaviour....

Data from: Intraspecific phytochemical variation shapes community and population structure for specialist caterpillars

Andrea E. Glassmire, Christopher S. Jeffrey, Matthew L. Forister, Thomas L. Parchman, Chris C. Nice, Joshua P. Jahner, Joseph S. Wilson, Thomas R. Walla, Lora A. Richards, Angela M. Smilanich, Michael D. Leonard, Colin R. Morrison, Wilmer Simbaña, Luis A. Salagaje, Craig D. Dodson, Jim S. Miller, Eric J. Tepe, Santiago Villamarin-Cortez & Lee A. Dyer
Chemically mediated plant–herbivore interactions contribute to the diversity of terrestrial communities and the diversification of plants and insects. While our understanding of the processes affecting community structure and evolutionary diversification has grown, few studies have investigated how trait variation shapes genetic and species diversity simultaneously in a tropical ecosystem. We investigated secondary metabolite variation among subpopulations of a single plant species, Piper kelleyi (Piperaceae), using high-performance liquid chromatography (HPLC), to understand associations between plant phytochemistry...

Data from: Leaf-cutter ants engineer large nitrous oxide hot spots in tropical forests

Fiona M. Soper, Benjamin W. Sullivan, Brooke B. Osborne, Alanna N. Shaw, Laurent Philippot & Cory C. Cleveland
Though tropical forest ecosystems are among the largest natural sources of the potent greenhouse gas nitrous oxide (N2O), the spatial distribution of emissions across landscapes is often poorly resolved. Leaf-cutter ants (LCA, Atta and Acromyrmex, Myrmicinae) are dominant herbivores throughout Central and South America and influence multiple aspects of forest structure and function. In particular, their foraging creates spatial heterogeneity by concentrating large quantities of organic matter (including nitrogen, N) from the surrounding canopy into...

Data from: Spatiotemporal dynamics and genome-wide association analysis of desiccation tolerance in Drosophila melanogaster

Subhash Rajpurohit, Eran Gefen, Alan O. Bergland, Dmitri A. Petrov, Allen G. Gibbs & Paul S. Schmidt
Water availability is a major environmental challenge to a variety of terrestrial organisms. In insects, desiccation tolerance varies predictably over spatial and temporal scales and is an important physiological determinant of fitness in natural populations. Here, we examine the dynamics of desiccation tolerance in North American populations of Drosophila melanogaster using: 1) natural populations sampled across latitudes and seasons; 2) experimental evolution in field mesocosms over seasonal time; 3) genome-wide associations to identify SNPs/genes associated...

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