175 Works

Unifying community detection across scales from genomes to landscapes

Andrii Zaiats, Stephanie F. Hudon, Anna Roser, Anand Roopsind, Cristina Barber, Brecken C. Robb, Britt A. Pendleton, Meghan J. Camp, Patrick E. Clark, Merry M. Davidson, Jonas Frankel-Bricker, Marcella Fremgen-Tarantino, Jennifer Sorensen Forbey, Eric J. Hayden, Lora A. Richards, Olivia K. Rodrigues & T. Trevor Caughlin
Biodiversity science encompasses multiple disciplines and biological scales from molecules to landscapes. Nevertheless, biodiversity data are often analyzed separately with discipline-specific methodologies, constraining resulting inferences to a single scale. To overcome this, we present a topic modeling framework to analyze community composition in cross-disciplinary datasets, including those generated from metagenomics, metabolomics, field ecology, and remote sensing. Using topic models, we demonstrate how community detection in different datasets can inform the conservation of interacting plants and...

Data from: Restoring dryland old fields with native shrubs and grasses: does facilitation and seed source matter?

Shauna M. Uselman, Jay Davison, Owen W Baughman, Benjamin W. Sullivan, W. Wally Miller, Elizabeth A. Leger & Owen W. Baughman
Restoration of agricultural fields is challenging, especially in arid and semi-arid ecosystems. We conducted experiments in two fields in the Great Basin, USA, which differed in cultivation history and fertility. We tested the effects of different levels of functional diversity (planting grasses and shrubs together, vs. planting shrubs alone), seed source (cultivars, local or distant wild-collections), and irrigation regime (spring or fall and spring) on restoration outcomes. We sowed either: 1) grasses and shrubs in...

Data from: A pollen fatty acid enhances learning and survival in bumblebees

Felicity Muth, Phillip R. Breslow, Pavel Masek & Anne S. Leonard
Learning associations between food-related stimuli and nutrients allows foragers to collect resources efficiently. In turn, the nutrients foragers consume can themselves affect learning performance, through innate preferences for pre-ingestive stimuli, as well as post-ingestive reinforcement. Bees are insect models of learning and memory, yet the vast majority of this research concerns nectar (carbohydrate) rather than pollen (protein/lipid) rewards, despite the fact that many bees collect both simultaneously. We asked how one component of pollen surface...

Data from: A likelihood-based approach for assessment of extra-pair paternity and conspecific brood parasitism in natural populations

Patrick R. Lemons, Tristan C. Marshall, Sarah E. McCloskey, Suresh A. Sethi, Joel A. Schmutz & Jim S. Sedinger
Genotypes are frequently used to assess alternative reproductive strategies such as extra-pair paternity and conspecific brood parasitism in wild populations. However, such analyses are vulnerable to genotyping error or molecular artefacts that can bias results. For example, when using multilocus microsatellite data, a mismatch at a single locus, suggesting the offspring was not directly related to its putative parents, can occur quite commonly even when the offspring is truly related. Some recent studies have advocated...

Data from: Range and niche shifts in response to past climate change in the desert horned lizard (Phrynosoma platyrhinos)

Tereza Jezkova, Jef Jaeger, Viktoria Oláh-Hemmings, K. Bruce Jones, Rafael A. Lara-Resendiz, Daniel G. Mulcahy, Brett R. Riddle & Jef R. Jaeger
During climate change, species are often assumed to shift their geographic distributions (geographic ranges) in order to track environmental conditions – niches – to which they are adapted. Recent work, however, suggests that the niches do not always remain conserved during climate change but shift instead, allowing populations to persist in place or expand into new areas. We assessed the extent of range and niche shifts in response to the warming climate after the Last...

Data from: Host conservatism, geography, and elevation in the evolution of a Neotropical moth radiation

Joshua P. Jahner, Matthew L. Forister, Thomas L. Parchman, Angela M. Smilanich, James S. Miller, Joseph S. Wilson, Thomas R. Walla, Eric J. Tepe, Lora A. Richards, Mario A. Quijano-Abril, Andrea E. Glassmire & Lee A. Dyer
The origins of evolutionary radiations are often traced to the colonization of novel adaptive zones, including unoccupied habitats or unutilized resources. For herbivorous insects, the predominant mechanism of diversification is typically assumed to be a shift onto a novel lineage of host plants. However, other drivers of diversification are important in shaping evolutionary history, especially for groups residing in regions with complex geological histories. We evaluated the contributions of shifts in host plant clade, bioregion,...

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...

Data from: Spatial phylogenetics of the North American flora

Brent Mishler, Robert Guralnick, Pamela Soltis, Stephen Smith, Douglas Soltis, Narayani Barve, Julie Allen & Shawn Laffan
North America is a large continent with extensive climatic, geological, soil, and biological diversity. That biota is under threat from habitat destruction and climate change, making a quantitative assessment of biodiversity of critical importance. Rapid digitization of plant specimen records and accumulation of DNA sequence data enable a much-needed broad synthesis of species occurrences with phylogenetic data. Here we attempted the first such synthesis of a flora from such a large and diverse part of...

Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

Kelly B. Klingler, Joshua P. Jahner, Thomas L. Parchman, Chris Ray & Mary M. Peacock
Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use...

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...

Changes in tree community structures in defaunated forests are not driven only by dispersal limitation

Kirstie Hazelwood, C. E. Timothy Paine, Fernando H. Cornejo-Valverde, Elizabeth G. Pringle, Harald Beck & John Terborgh
1. Bushmeat hunting has reduced population sizes of large frugivorous vertebrates throughout the tropics, thereby reducing the dispersal of seeds. This is believed to affect tree population dynamics, and therefore community composition, because the seed dispersal of large-seeded trees depends upon large-bodied vertebrates. 2. We report on a long-running study of the effect of defaunation on a tropical tree community. In three censuses over 11 years, we compared sapling recruitment between a hunted and a...

Evaluating multiple historical climate products in ecological models under current and projected temperatures

Giancarlo Sadoti, Stephanie McAfee, E. Nicklen, Pamela Sousanes & Carl Roland
Gridded historical climate products (GHCPs) are employed with increasing frequency when modeling ecological phenomena across large scales and predicting ecological responses to projected climate changes. Concurrently, there is an increasing acknowledgement of the need to account for uncertainty when employing climate projections from ensembles of global circulation models (GCMs) and emissions scenarios. Despite the growing usage and documented differences among GHCPs, uncertainty characterization has primarily focused on the roles of GCM and emissions scenario choice,...

The promise and the perils of resurveying to understand global change impacts

Katharine Stuble, Sharon Bewick, Mark Fisher, Matthew Forister, Susan Harrison, Arthur Shapiro, Andrew Latimer & Laurel Fox
Historical datasets can be useful tools to aid in understanding the impacts of global change on natural ecosystems. Resampling of historically sampled sites (“snapshot resampling”) has often been used to detect long-term shifts in ecological populations and communities, because it allows researchers to avoid long-term monitoring costs and investigate a large number of potential trends. But recent simulation-based research has called the reliability of resampling into question, and its utility has not been comprehensively evaluated....

Data from: Ecology shapes epistasis in a genotype-phenotype-fitness map for stick insect colour

Zachariah Gompert, Patrik Nosil, Romain Villoutreix, Clarissa De Carvalho, Jeffrey Feder & Thomas Parchman
Genetic interactions such as epistasis are widespread in nature and can shape evolutionary dynamics. Epistasis occurs due to non-linearity in biological systems, which can arise via cellular processes that convert genotype to phenotype and via selective processes that connect phenotype to fitness. Few studies in nature have connected genotype to phenotype to fitness for multiple potentially interacting genetic variants. Thus, the causes of epistasis in the wild remain poorly understood. Here, we show that epistasis...

Latitudinal gradients in population growth do not reflect demographic responses to climate

Megan Peterson, Graham Bailes, Lauren Hendricks, Laurel Pfeifer-Meister, Paul Reed, Scott Bridgham, Bart Johnson, Robert Shriver, Ellen Waddle, Hannah Wroton, Daniel Doak, Bitty Roy & William Morris
Spatial gradients in population growth, such as across latitudinal or elevational gradients, are often assumed to primarily be driven by variation in climate, and are frequently used to infer species’ responses to climate change. Here, we use a novel demographic, mixed model approach to dissect the contributions of climate variables vs. other latitudinal or local site effects on spatiotemporal variation in population performance in three perennial bunchgrasses. For all three species, we find that performance...

The influence of history, geography and environment on patterns of diversification in the western terrestrial garter snake

Joshua Hallas, Thomas Parchman & Chris Feldman
Aim: A central aim of biogeography is to understand how biodiversity is generated and maintained across landscapes. Here, we establish phylogenetic and population genetic patterns in a widespread reptile to quantify the influence of historical biogeography and current environmental variation on patterns of genetic diversity. Location: Western North America. Taxon: Western terrestrial garter snake, Thamnophis elegans. Methods: We used double-digest RADseq to estimate phylogenetic relationships and characterize population genetic structure across the three widespread subspecies...

Disentangling lousy relationships: Comparative phylogenomics of two sucking louse lineages parasitizing chipmunks

Kayce Bell, Julie M. Allen, Kevin P. Johnson, John R. Demboski & Joseph A. Cook
The evolution of obligate parasites is often interpreted in light of their hosts’ evolutionary history. An expanded approach is to examine the histories of multiple lineages of parasites that inhabit similar environments on a particular host lineage. Western North American chipmunks (genus Tamias) have a broad distribution, a history of divergence with gene flow, and host two species of sucking lice (Anoplura), Hoplopleura arboricola and Neohaematopinus pacificus. From total genomic sequencing, we obtained sequences of...

Artificial nightlight alters the predator-prey dynamics of an apex carnivore

Mark Ditmer, David Stoner, Clinton D. Francis, Jesse Barber, James Forester, David Choate, Kirsten Ironside, Kathleen Longshore, Kent Hersey, Randy Larsen, Brock McMillan, Daniel Olson, Alyson Andreasen, Jon Beckmann, Brandon Holton, Terry Messmer & Neil Carter
Artificial nightlight is increasingly recognized as an important environmental disturbance that influences the habitats and fitness of numerous species. However, its effects on wide-ranging vertebrates and their interactions remain unclear. Light pollution has the potential to amplify land-use change, and as such, answering the question of how this sensory stimulant affects behavior and habitat use of species valued for their ecological roles and economic impacts is critical for conservation and land-use planning. Here, we combined...

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: 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...

Thistle-down velvet ants in the Desert Mimicry Ring and the evolution of white coloration: Müllerian mimicry, camouflage, and thermal ecology

Joseph Wilson, Jeni Sidwell, Matthew Forister, Kevin Williams & James Pitts
Adaptive coloration among animals is one of the most recognizable outcomes of natural selection. Here we investigate evolutionary drivers of white coloration in velvet ants (Hymenoptera: Mutillidae), which has previously been considered camouflage with the fruit of creosote bush. Our analyses indicate instead that velvet ants evolved white coloration millions of years before creosote bush was widespread in North America’s hot deserts. Furthermore, velvet ants and the creosote fruit exhibit different spectral reflectance patterns, which...

Audio recordings of Atelpus varius calls from Panama

Justin Kitzes, Samuel Lapp, Corinne Richards-Zawacki, Jamie Voyles, Keely Michelle Rodriguez & Tianhao Wu
Anurans (frogs and toads) are among the most globally threatened taxonomic groups. Successful conservation of anurans will rely on improved data on the status and changes in local populations, particularly for rare and threatened species. Automated sensors, such as acoustic recorders, have the potential to provide such data by massively increasing the spatial and temporal scale of population sampling efforts. We used AudioMoth autonomous recorders to survey for the critically endangered Harlequin toad (Atelopus varius)...

A likelihood-ratio test for lumpability of phylogenetic data: Is the Markovian property of an evolutionary process retained in recoded DNA?

Lars Jermiin, John Robinson & Victor Vera-Ruiz
In molecular phylogenetics, it is typically assumed that the evolutionary process for DNA can be approximated by independent and identically distributed Markovian processes at the variable sites and that these processes diverge over the edges of a rooted bifurcating tree. Sometimes the nucleotides are transformed from a 4-state alphabet to a 3- or 2-state alphabet by a procedure that is called recoding, lumping, or grouping of states. Here, we introduce a likelihood-ratio test for lumpability...

Data from: The genetic legacy of 50 years of desert bighorn sheep translocations

Joshua P. Jahner, Marjorie D. Matocq, Jason L. Malaney, Mike Cox, Peregrine Wolff, Mitchell A. Gritts & Thomas L. Parchman
Conservation biologists have increasingly used translocations to mitigate population declines and restore locally extirpated populations. Genetic data can guide the selection of source populations for translocations and help evaluate restoration success. Bighorn sheep (Ovis canadensis) are a managed big game species that suffered widespread population extirpations across western North America throughout the early 1900’s. Subsequent translocation programs have successfully re-established many formally extirpated bighorn herds, but most of these programs pre-date genetically-informed management practices. The...

Data from: Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus

Therese A. Catanach, Andrew D. Sweet, Nam-Phuong D. Nguyen, Rhiannon M. Peery, Andrew H. Debevec, Andrea K. Thomer, Amanda C. Owings, Bret M. Boyd, Aron D. Katz, Felipe N. Soto-Adames & Julie M. Allen
Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However,...

Registration Year

  • 2021
  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013
  • 2012

Resource Types

  • Dataset


  • University of Nevada Reno
  • Utah State University
  • University of Wyoming
  • University of Montana
  • United States Geological Survey
  • University of Michigan-Ann Arbor
  • Texas State University
  • University of California, Davis
  • University of Virginia
  • University of Tennessee at Knoxville