34 Works

Phenology-based classification of invasive annual grasses to the species level

Peter Weisberg, Thomas Dilts, Jonathan Greenberg, Kerri Johnson, Henry Pai, Chris Sladek, Christopher Kratt, Scott Tyler & Alice Ready
The ability to detect and map invasive plants to the species level, both at high resolution and over large extents, is essential for their targeted management. Yet development of such remote sensing methodology is challenged by the spectral and structural similarities among many invasive and native plant species. We developed a multi-temporal classification approach that uses unmanned aerial vehicle (UAV) imagery to map two invasive annual grasses to the species level, and to distinguish these...

Genomic and common garden approaches yield complementary results for quantifying environmental drivers of local adaptation in rubber rabbitbrush, a foundational Great Basin shrub

Trevor Faske
The spatial structure of genomic and phenotypic variation across populations reflects historical and demographic processes as well as evolution via natural selection. Characterizing such variation can provide an important perspective for understanding the evolutionary consequences of changing climate and for guiding ecological restoration. While evidence for local adaptation has been traditionally evaluated using phenotypic data, modern methods for generating and analyzing landscape genomic data can directly quantify local adaptation by associating allelic variation with environmental...

The cost of travel: how dispersal ability limits local adaptation in host-parasite interactions

Pieter Johnson, Dana Calhoun, Wynne Moss, Travis McDevitt-Galles, Tawni Riepe, Joshua Hallas, Thomas Parchman, Chris Feldman, Josh Cropanzano, Jay Bowerman, Tyler Achatz, Vasyl Tkach & Janet Koprivnikar
Classical theory suggests that parasites will exhibit higher fitness in sympatric relative to allopatric host populations (local adaptation). However, evidence for local adaptation in natural host-parasite systems is often equivocal, emphasizing the need for cross-infection experiments conducted over realistic geographic scales and comparisons among species with varied life history traits. Here, we conducted cross-infection experiments to test how two trematode (flatworm) species (Paralechriorchis syntomentera and Ribeiroia ondatrae) with differing dispersal abilities varied in the strength...

Specialized spatial cognition is associated with reduced cognitive senescence in a food-caching bird

Virginia Heinen, Angela Pitera, Ben Sonnenberg, Lauren Benedict, Carrie Branch, Eli Bridge & Vladimir Pravosudov
Senescence, the gradual reduction and loss of function as organisms age, is a widespread process that is especially pronounced in cognitive abilities. Senescence appears to have a genetic basis and can be affected by evolutionary processes. If cognitive senescence is shaped by natural selection, it may be linked with selection on cognitive abilities needed for survival and reproduction, such that species in which fitness is directly related to cognitive abilities should evolve delayed cognitive senescence....

Let it snow? Spring snowpack and microsite characterize the regeneration niche of high-elevation pines

Lacey Hankin & Sarah Bisbing
Aim: The persistence potential of forests under rapid climate change will depend on species-specific tolerances to increasing growing season soil moisture stress as snowpack declines. High-elevation tree species may be particularly vulnerable to increasing water stress and associated changes to disturbance regimes because they occur at the environmental margins of tree distributions and are considered snowpack dependent. Here, we evaluate the interacting effects of climate, disturbance, and microsite conditions on tree regeneration in high-elevation, migration-limited...

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...

Food discovery is associated with different reliance on social learning and lower cognitive flexibility across environments in a food caching bird

Virginia Heinen, Angela Pitera, Ben Sonnenberg, Lauren Benedict, Eli Bridge, Damien Farine & Vladimir Pravosudov
Social learning is a primary mechanism for information acquisition in social species. Despite many benefits, social learning may be disadvantageous when independent learning is more efficient. For example, searching independently may be more advantageous when food sources are ephemeral and unpredictable. Individual differences in cognitive abilities such as spatial memory, which affect an individual’s environmental predictability, can also be expected to influence social information use. We investigated how resident food-caching chickadees discovered multiple novel food...

Visual discomfort and variations in chromaticity in art and nature

Olivier Penacchio, Sarah Haigh, Xortia Ross, Rebecca Ferguson & Arnold Wilkins
Visual discomfort is related to the statistical regularity of visual images. The contribution of luminance contrast to visual discomfort is well understood and can be framed in terms of a theory of efficient coding of natural stimuli, and linked to metabolic demand. While colour is important in our interaction with nature, the effect of colour on visual discomfort has received less attention. In this study, we build on the established association between visual discomfort and...

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...

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)...

Stress in paradise: effects of elevated corticosterone on immunity and avian malaria resilience in a Hawaiian passerine

Gabrielle Names, Elizabeth Schultz, Jesse Krause, Thomas Hahn, John Wingfield, Molly Heal, Jamie Cornelius, Kirk Klasing & Kathleen Hunt
Vertebrates confronted with challenging environments often experience an increase in circulating glucocorticoids, which result in morphological, physiological, and behavioral changes that promote survival. However, chronically elevated glucocorticoids can suppress immunity, which may increase susceptibility to disease. Since the introduction of avian malaria to Hawaii a century ago, low elevation populations of Hawaii Amakihi (Chlorodrepanis virens) have undergone strong selection by avian malaria and evolved increased resilience (the ability to recover from infection), while populations at...

Data from: Passeridae and Cyanocitta stelleri teleport to my deck from other areas

Aaron Goetz
In neither the teleporting or the lab are they actually migrating. Yet, in the lab, they do it anyway, and the way their species does it, without having done it before. Passeridae and Cyanocitta stelleri teleport to my deck from other areas adds to the genetic difference hypothesis by saying migrating doesn’t matter, just that they have the genetic (and maybe neural) structure needed for migration, and is used for teleporting.

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, Victor A Vera-Ruiz & Lars S Jermiin
Abstract 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...

The geographic distribution of rodent granivory and cheek pouches across North America

Jacob Dittel & Stephen Vander Wall
Seeds are an important food resource for many rodents. One of the specializations that many granivorous rodents exhibit to increase their efficiency in harvesting seeds is cheek pouches. However, many rodent species lack cheek pouches. We propose that the presence or absence of cheek pouches is related to seed size and the productivity of the habitat where those rodents reside. Location North America – United States and Canada. Taxon Granivorous rodents. We divided granivorous rodents...

Code from: Realistic genetic architecture enables organismal adaptation as predicted under the folk definition of inclusive fitness

Guillermo Garcia-Costoya & Lutz Fromhage
A fundamental task of evolutionary biology is to explain the pervasive impression of organismal design in nature, including traits benefiting kin. Inclusive fitness is considered by many to be a crucial piece in this puzzle, despite ongoing discussion about its scope and limitations. Here we use individual-based simulations to study what quantity (if any) individual organisms become adapted to maximise when genetic architectures are more or less suitable for the presumed main driver of biological...

Systematics and conservation of an endemic radiation of Accipiter hawks in the Caribbean islands

Therese A. Catanach, Matthew H. Halley, Julie M. Allen, Jeff A. Johnson, Russell Thorstrom, Samantha Palhano, Chyna Poor Thunder, Julio C. Gallardo & Jason D. Weckstein
More than one third of the bird species found in the Caribbean are endemic to a set of neighboring islands or a single island. However, we have little knowledge of the evolutionary history of the Caribbean avifauna and the lack of phylogenetic studies limits our understanding of the extent of endemism in the region. The Sharp-shinned Hawk (Accipiter striatus) occurs widely across the Americas and includes three endemic Caribbean taxa: venator on Puerto Rico, striatus...

Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions

Andrew Ontano, Guilherme Gainett, Shlomi Aharon, Jesús Balesteros, Ligia Benavides, Kevin Corbett, Efrat Gavish-Regev, Mark Harvey, Scott Monsma, Carlos Santibáñez-López, Emily Setton, Jakob Zehms, Jeanne Zeh, David Zeh & Prashant Sharma
Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch...

Hierarchical genetic structure and implications for conservation of the world’s largest salmonid, Hucho taimen

Lanie M. Galland, James B. Simmons, Joshua P. Jahner, Agusto R. Luzuriaga-Neira, Matthew R. Sloat, Sudeep Chandra, Zeb Hogan, Olaf P. Jensen & Thomas L. Parchman
Population genetic analyses can evaluate how evolutionary processes shape diversity and inform conservation and management of imperiled species. Taimen (Hucho taimen), the world’s largest freshwater salmonid, is threatened, endangered, or extirpated across much of its range due to anthropogenic activity including overfishing and habitat degradation. We generated genetic data using high throughput sequencing of reduced representation libraries for taimen from multiple drainages in Mongolia and Russia. Nucleotide diversity estimates were within the range documented in...

Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition

Joshua Jahner, Thomas Parchman & Marjorie Matocq
When organisms experience secondary contact after allopatric divergence, genomic regions can introgress differentially depending on their relationships with adaptation, reproductive isolation, recombination, and drift. Analyses of genome-wide patterns of divergence and introgression could provide insight into the outcomes of hybridization and the potential relationship between allopatric divergence and reproductive isolation. Here, we generate population genetic data (26,262 SNPs; 353 individuals) using a reduced-representation sequencing approach to quantify patterns of ancestry, differentiation, and introgression between a...

Structural and compositional dimensions of phytochemical diversity in the genus Piper reflect distinct ecological modes of action

Casey Philbin, Lee Dyer, Chris Jeffrey, Andrea Glassmire & Lora Richards
Context: An increasing number of ecological studies have used chemical diversity as a functionally relevant, scalable measure of phytochemical mixtures, demanding more rigorous attention to how chemical diversity is estimated. Most studies have focused on the composition of phytochemical mixtures and have largely ignored structural concerns, which may have greater importance for ecological function. Here we explore the development of structural complexity and compositional diversity resulting from different biotic and abiotic interactions in Piper kelleyi...

Habitat structure mediates vulnerability to climate change through its effects on thermoregulatory behavior

Lauren Neel, Michael Logan, Daniel Nicholson, Christina Miller, Albert Chung, Inbar Maayan, Zach Degon, Madeline DuBois, John David Curlis, Q Taylor, Kaitlin Keegan, Owen McMillan, Jonathan Losos & Christian Cox
Tropical ectotherms are thought to be especially vulnerable to climate change because they are thermal specialists, having evolved in aseasonal thermal environments. However, even within the tropics, habitat structure can influence opportunities for behavioral thermoregulation. Open (and edge) habitats likely promote more effective thermoregulation due to the high spatial heterogeneity of the thermal landscape, while forests are thermally homogenous and may constrain opportunities for behavioral buffering of environmental temperatures. Nevertheless, the ways in which behavior...

Differences in dietary composition and preference maintained despite gene flow across a woodrat hybrid zone

Daniel Nielsen & Marjorie Matocq
1. Hybridization can homogenize the gene pools of species that come into secondary contact. Alternatively, species differentiation can persist despite hybridization and interspecific gene flow. When hybridization occurs across sharp environmental transitions (i.e. ecotones), spatial variation in selection may reduce interspecific gene flow through pre- and post-zygotic isolating mechanisms. Ecotones, characterized by adjacent yet distinct biotic communities, provide natural laboratories in which to investigate how environmental selection influences the ecology and evolution of organisms. For...

Spatial phylogenetics of butterflies in relation to environmental drivers and angiosperm diversity across North America

Chandra Earl, Michael W. Belitz, Shawn W. Laffan, Vijay Barve, Narayani Barve, Douglas E. Soltis, Julie M. Allen, Pamela S. Soltis, Brent D. Mishler, Akito Y. Kawahara & Robert Guralnick
Broad-scale quantitative assessments of biodiversity and the factors shaping it remain particularly poorly explored in insects. Here, we undertook a spatial phylogenetic analysis of North American butterflies via assembly of a time-calibrated phylogeny of the region coupled with a unique, complete range assessment for ~75% of the known species. We utilized a suite of phylodiversity metrics and associated environmental data to test whether climate stability and temperature gradients have shaped North American butterfly phylogenetic diversity...

Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs

Kathryn Uckele, Joshua Jahner, Eric Tepe, Lora Richards, Lee Dyer, Kaitlin Ochsenrider, Casey Philbin, Massuo Kato, Lydia Yamaguchi, Matthew Forister, Angela Smilanich, Craig Dodson, Christopher Jeffrey & Thomas Parchman
Foundational hypotheses addressing plant-insect codiversification and plant defense theory typically assume a macroevolutionary pattern whereby closely related plants have similar chemical profiles. However, numerous studies have documented variation in the degree of phytochemical trait lability, raising the possibility that phytochemical evolution is more nuanced than initially assumed. We utilize proton nuclear magnetic resonance (1H NMR) data, chemical classification, and double digest restriction-site associated DNA sequencing (ddRADseq) to resolve evolutionary relationships and characterize the evolution of...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of Nevada Reno
  • University of Oklahoma
  • University of Michigan-Ann Arbor
  • Oregon State University
  • University of Wisconsin-Madison
  • Harvard University
  • Wittenberg University
  • University of California, Davis
  • Denver Museum of Nature and Science
  • Baylor University