189 Works

Pinus contorta landscape genetics and common garden data

Sarah Bisbing
Aim: Climate change poses significant challenges for tree species, which are slow to adapt and migrate. Insight into genetic and phenotypic variation under current landscape conditions can be used to gauge persistence potential to future conditions and determine conservation priorities, but landscape effects have been minimally tested in trees. Here, we use Pinus contorta, one of the most widely-distributed conifers in North America, to evaluate the influence of landscape heterogeneity on genetic structure as well...

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...

LeafByte: A mobile application that measures leaf area and herbivory quickly and accurately

Zoe Getman-Pickering, Adam Campbell, Julie Davis, Nicholas Aflitto, Ari Grele, Todd Ugine, Zoe L. Getman‐Pickering, Julie K. Davis & Todd A. Ugine
In both basic and applied studies, quantification of herbivory on foliage is a key metric in characterizing plant-herbivore interactions, which underpin many ecological, evolutionary, and agricultural processes. Current methods of quantifying herbivory are slow or inaccurate. We present LeafByte, a free iOS application for measuring leaf area and herbivory. LeafByte can save data automatically, read and record barcodes, handle both light and dark colored plant tissue, and be used non-destructively. We evaluate its accuracy 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: 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: 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,...

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: 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: Selection on a genetic polymorphism counteracts ecological speciation in a stick insect

Aaron A. Comeault, Samuel M. Flaxman, Rüdiger Riesch, Emma Curran, Víctor Soria-Carrasco, Zachariah Gompert, Timothy E. Farkas, Moritz Muschick, Thomas L. Parchman, Tanja Schwander, Jon Slate & Patrik Nosil
The interplay between selection and aspects of the genetic architecture of traits (such as linkage, dominance, and epistasis) can either drive or constrain speciation. Despite accumulating evidence that speciation can progress to “intermediate” stages—with populations evolving only partial reproductive isolation—studies describing selective mechanisms that impose constraints on speciation are more rare than those describing drivers. The stick insect Timema cristinae provides an example of a system in which partial reproductive isolation has evolved between populations...

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,...

Data from: Experimental evidence for ecological selection on genome variation in the wild

Zachariah Gompert, Aaron A. Comeault, Timothy E. Farkas, Jeffery L. Feder, Thomas L. Parchman, Alex C. Buerkle, Patrik Nosil & Jeffrey L. Feder
Understanding natural selection's effect on genetic variation is a major goal in biology, but the genome-scale consequences of contemporary selection are not well known. In a release and recapture field experiment we transplanted stick insects to native and novel host plants and directly measured allele frequency changes within a generation at 186 576 genetic loci. We observed substantial, genome-wide allele frequency changes during the experiment, most of which could be attributed to random mortality (genetic...

Data from: The many dimensions of diet breadth: phytochemical, genetic, behavioral, and physiological perspectives on the interaction between a native herbivore and an exotic host

Joshua G. Harrison, Zachariah Gompert, James A. Fordyce, C. Alex Buerkle, Rachel Grinstead, Joshua P. Jahner, Scott Mikel, Christopher C. Nice, Aldrin Santamaria & Matthew L. Forister
From the perspective of an herbivorous insect, conspecific host plants are not identical, and intraspecific variation in host nutritional quality or defensive capacity might mediate spatially variable outcomes in plant-insect interactions. Here we explore this possibility in the context of an ongoing host breadth expansion of a native butterfly (the Melissa blue, Lycaeides melissa) onto an exotic host plant (alfalfa, Medicago sativa). We examine variation among seven alfalfa populations that differed in terms of colonization...

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: 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: 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...

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...

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...

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...

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...

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...

Data from: Population genetic structure and its implications for adaptive variation in memory and the hippocampus on a continental scale in food-caching black-capped chickadees

Vladimir V. Pravosudov, , Matthew L. Forister, Lara D. LaDage, Theresa M. Burg, Michael J. Braun & Brian S. Davidson
Food-caching birds rely on stored food to survive the winter and spatial memory has been shown to be critical in successful cache recovery. Both spatial memory and the hippocampus, an area of the brain involved in spatial memory, exhibit significant geographic variation linked to climate-based environmental harshness and the potential reliance on food caches for survival. Such geographic variation has been suggested to have a heritable basis associated with differential selection. Here, we ask whether...

Data from: Resource stability and geographic isolation are associated with genome divergence in western Palearctic crossbills

Thomas L. Parchman, Pim Edelaar, Kathryn Uckele, Eduardo T. Mezquida, Daniel Alonso, Joshua P. Jahner, Ron W. Summers & Craig W. Benkman
While many conifers produce annually variable seed crops, serotinous species (which hold seeds in cones for multiple years) represent unusually stable food resources for seed predators. Such stability is conducive to residency and potentially population divergence of consumers as exemplified by the Cassia crossbill (Loxia sinesciuris) in North America. We used genotyping-by-sequencing to test whether three Mediterranean subspecies of common crossbills (L. curvirostra) associated with the serotinous Aleppo pine (Pinus halepensis) were more genetically distinct...

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...

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