122 Works

Local adaptation constrains drought tolerance in a tropical foundation tree

Kasey Barton, Casey Jones, Kyle Edwards, Aaron Shiels & Tiffany Knight
1. Plant species with broad climatic ranges might be more vulnerable to climate change than previously appreciated due to intraspecific variation in climatic stress tolerance. In tropical forests, drought is increasingly frequent and severe, causing widespread declines and altering community dynamics. Yet, little is known about whether foundation tropical trees vary in drought tolerance throughout their distributions, and how intraspecific variation in drought tolerance might contribute to their vulnerability to climate change. 2. We tested...

Data from: The impact of prescribed burning on native bee communities (Hymenoptera: Apoidea: Anthophila) in longleaf pine savannas in the North Carolina sandhills

Heather Moylett, Elsa Youngsteadt & Clyde Sorenson
Prescribed burning is a common silvicultural practice used in the management of longleaf pine (Pinus palustris Mill.) savannas to reduce hardwood encroachment and ground cover and to maintain biodiversity. We investigated the response of the native bee community (Hymenoptera: Apoidea: Anthophila) in the Sandhills of North Carolina to prescribed burning on a three-year rotation over two consecutive years (2012 and 2013). We deployed bee bowl traps in sites that had been burned the year of...

Accuracy of genomic selection and long-term genetic gain for resistance to Verticillium wilt in a genetically diverse strawberry population

Steven Knapp, Dominique Pincot, Michael Hardigan, Glenn Cole, Peter Henry, Thomas Gordon & Randi Famula
Verticillium wilt, a soil-borne disease caused by the fungal pathogen Verticillium dahliae, threatens strawberry (Fragaria × ananassa) production worldwide. The development of resistant cultivars has been a challenge since the disease was first reported on strawberry in the early 1900s. The empirical evidence suggests that genetic gains have not been negligible and that the genetics of resistance to this pathogen is quantitative. While resistant cultivars have been developed, a comparatively small percentage are highly resistant,...

Not a melting pot: plant species aggregate in their non-native range

Gisela C. Stotz, James F. Cahill, Jonathan A. Bennett, Cameron N. Carlyle, Edward W. Bork, Diana Askarizadeh, Sandor Bartha, Carl Beierkuhnlein, Bazartseren Boldgiv, Leslie Brown, Marcelo Cabido, Giandiego Campetella, Stefano Chelli, Ofer Cohen, Sandra Díaz, Lucas Enrico, David Ensing, Batdelger Erdenetsetseg, Alessandra Fidelis, Heath W. Garris, Hugh A.L. Henry, Anke Jentsch, Mohammad Hassan Jouri, Kadri Koorem, Peter Manning … & Lauchlan H. Fraser
Aim: Plant species continue to be moved outside of their native range by human activities. Here, we aim at determining whether, once introduced, plants assimilate into native communities, or whether they aggregate, thus forming mosaics of native- and alien-rich communities. Alien species may aggregate in their non-native range due to shared habitat preferences, such as their tendency to establish in high-biomass, species-poor areas. Location: 22 herbaceous grasslands in 14 countries, mainly in the temperate zone....

A spatially explicit model to simulate the population dynamics of gypsy moth (Lymantria dispar)

Mandy C. Barron, Andrew M. Liebhold, John M. Kean, Brian Richardson & Eckehard G. Brockerhoff
Removal of host plants is a 'tool' that can be used for the eradication of invasive alien plant pests. We developed a spatially explicit agent-based population model to simulate the population dynamics of the European strain of gypsy moth, Lymantria dispar, based on Robinet et al. (2008 - Journal of Animal Ecology 77, 966–973. doi:10.1111/j.1365-2656.2008.01417.x). The model was coded in the R language (R Core Team, 2017) and is deposited in this Dryad record. A...

Conflicting signal in transcriptomic markers leads to a poorly resolved backbone phylogeny of Chalcidoid wasps

Junxia Zhang, Amelia R.I. Lindsey, Ralph S. Peters, John M. Heraty, Keith R. Hopper, John H. Werren, Ellen O. Martinson, James B. Woolley, Matt J. Yoder & Lars Krogmann
Chalcidoidea (Hymenoptera) are a megadiverse superfamily of wasps with astounding variation in both morphology and biology. Most species are parasitoids and important natural enemies of insects in terrestrial ecosystems. In this study, we explored a transcriptome-based phylogeny of Chalcidoidea and found that poorly resolved relationships could only be marginally improved by adding more genes (a total of 5,591) and taxa (a total of 65), proof-checking for errors of homology and contamination, and decreasing missing data....

Recent evolutionary history predicts population but not ecosystem level patterns

Sarah Fitzpatrick, Madison Miller & John Kronenberger
In the face of rapid anthropogenic environmental change, it is increasingly important to understand how ecological and evolutionary interactions affect the persistence of natural populations. Augmented gene flow has emerged as a potentially effective management strategy to counteract negative consequences of genetic drift and inbreeding depression in small and isolated populations. However, questions remain about the long-term impacts of augmented gene flow and whether changes in individual and population fitness are reflected in ecosystem structure,...

Extinct plants of North America north of Mexico

Wesley Knapp, Anne Frances, Reed Noss, Robert Naczi, Alan Weakley, George Gann, Bruce Baldwin, James Miller, Patrick McIntyre, Brent Mishler, Gerry Moore, Richard Olmstead, Anna Strong, Daniel Gluesenkamp & Kathryn Kennedy
The recent study by Humphreys et al., reporting extinction of almost 600 plant species globally, represents a groundbreaking effort at compiling direct data on seed plants. We applaud Humphreys et al. for quantifying plant extinctions because they formulate an important and testable hypothesis. However, their study missed many extinctions and rediscoveries of seed plants in the United States and Canada. Our team of experts has been compiling a list of extinct plants of North America...

Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus)

Paul A Maier, Amy G Vandergast, Steve M Ostoja, Andres Aguilar & Andrew J Bohonak
Species endemic to alpine environments can evolve via steep ecological selection gradients between lowland and upland environments. Additionally, many alpine environments have faced repeated glacial episodes over the past two million years, fracturing these endemics into isolated populations. In this “glacial pulse” model of alpine diversification, cycles of allopatry and ecologically divergent glacial refugia play a role in generating biodiversity, including novel admixed (“fused”) lineages. We tested for patterns of glacial pulse lineage diversification in...

Relationships among wood-boring beetles, fungal endophytes and saprotrophs, and the decomposition of forest biomass.

James Skelton, Michelle Jusino, Paige Carlson, Katherine Smith, Mark Banik, Daniel Linder, Jonathan Palmer & Jiri Hulcr
A prevailing paradigm in forest ecology is that wood-boring beetles facilitate wood decay and carbon cycling, but empirical tests have yielded mixed results. We experimentally determined the effects of wood borers on fungal community assembly and wood decay within pine trunks in the southeastern United States. Pine trunks were made either beetle-accessible or inaccessible. Fungal communities were compared using culturing and high-throughput meta-barcode sequencing of DNA and RNA. Prior to beetle infestation, living pines had...

Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts

Alyssa Burkhardt, Kevin Childs, Jie Wang, Marina Ramon & Frank Martin
Background: Macrophomina phaseolina is a fungal plant pathogen with a broad host range, but one genotype was shown to exhibit host preference/specificity on strawberry. This pathogen lacked a high-quality genome assembly and annotation, and little was known about genomic differences among isolates from different hosts. Results: We used PacBio sequencing and Hi-C scaffolding to provide nearly complete genome assemblies for M. phaseolina isolates representing the strawberry-specific genotype and another genotype recovered from alfalfa. The strawberry...

Data from: Predicting functional responses in agro-ecosystems from animal movement data to improve management of invasive pests

Mark Wilber, Sarah Chinn, James Beasley, Raoul Boughton, Ryan Brook, Stephen Ditchkoff, Justin Fischer, Steve Hartley, Lindsey Holstrom, John Kilgo, Jesse Lewis, Ryan Miller, Nathan Snow, Kurt VerCauteren, Samantha Wisely, Colleen Webb & Kim Pepin
Functional responses describe how changing resource availability affects consumer resource use, thus providing a mechanistic approach to prediction of the invasibility and potential damage of invasive alien species (IAS). However, functional responses can be context-dependent, varying with resource characteristics and availability, consumer attributes, and environmental variables. Identifying context-dependencies can allow invasion and damage risk to be predicted across different ecoregions. Understanding how ecological factors shape the functional response in agro-ecosystems can improve predictions of hotspots...

Data from: Microbial functional diversity: from concepts to applications

Arthur Escalas, Lauren Hale, James Voordeckers, Yunfeng Yang, Mary Firestone, Lisa Alvarez-Cohen & Jizhong Zhou
Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition...

Data from: Extreme site fidelity as an optimal strategy in an unpredictable and homogeneous environment

Brian D. Gerber, Mevin B. Hooten, Christopher P. Peck, Mindy B. Rice, James H. Gammonley, Anthony D. Apa & Amy J. Davis
1. Animal site fidelity structures space-use, population demography, and ultimately gene flow. Understanding the adaptive selection for site fidelity patterns provides a mechanistic understanding to both spatial and population processes. This can be achieved by linking space-use with environmental variability (spatial and temporal) and demographic parameters. However, rarely is the environmental context that drives the selection for site fidelity behavior fully considered. 2. We use ecological theory to understand whether the spatial and temporal variability...

Data from: HiMAP: robust phylogenomics from highly multiplexed amplicon sequencing

Julian R. Dupuis, Forest T. Bremer, Angela Kauwe, Michael San Jose, Luc Leblanc, Daniel Rubinoff & Scott M. Geib
High-throughput sequencing has fundamentally changed how molecular phylogenetic datasets are assembled, and phylogenomic datasets commonly contain 50-100-fold more loci than those generated using traditional Sanger-based approaches. Here, we demonstrate a new approach for building phylogenomic datasets using single tube, highly multiplexed amplicon sequencing, which we name HiMAP (Highly Multiplexed Amplicon-based Phylogenomics), and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and post-sequencing consensus calling and alignment. This method is inexpensive...

Data from: Conservation and modification of genetic and physiological toolkits underpinning diapause in bumble bee queens

Etya Amsalem, David A. Galbraith, Jonathan Cnaani, Peter E. A. Teal & Christina M. Grozinger
Diapause is the key adaptation allowing insects to survive unfavorable conditions and inhabit an array of environments. Physiological changes during diapause are largely conserved across species, and are hypothesized to be regulated by a conserved suite of genes (a “toolkit”). Furthermore, it is hypothesized that in social insects, this toolkit was co-opted to mediate caste differentiation between long-lived, reproductive, diapause-capable queens and short-lived, sterile workers. Using Bombus terrestris queens we examined the physiological and transcriptomic...

Data from: Modeling and mapping the probability of occurrence of invasive wild pigs across the contiguous United States

Meredith L. McClure, Christopher L. Burdett, Matthew L. Farnsworth, Mark W. Lutman, David M. Theobald, Philip D. Riggs, Daniel A. Grear & Ryan S. Miller
Wild pigs (Sus scrofa), also known as wild swine, feral pigs, or feral hogs, are one of the most widespread and successful invasive species around the world. Wild pigs have been linked to extensive and costly agricultural damage and present a serious threat to plant and animal communities due to their rooting behavior and omnivorous diet. We modeled the current distribution of wild pigs in the United States to better understand the physiological and ecological...

Data from: Mediating water temperature increases due to livestock and global change in high elevation meadow streams of the Golden Trout Wilderness

Sébastien Nusslé, Kathleen R. Matthews & Stephanie M. Carlson
Rising temperatures due to climate change are pushing the thermal limits of many species, but how climate warming interacts with other anthropogenic disturbances such as land use remains poorly understood. To understand the interactive effects of climate warming and livestock grazing on water temperature in three high elevation meadow streams in the Golden Trout Wilderness, California, we measured riparian vegetation and monitored water temperature in three meadow streams between 2008 and 2013, including two “resting”...

Data from: Can butterflies evade fire? Pupa location and heat tolerance in fire prone habitats of Florida

Matthew D. Thom, Jaret C. Daniels, Leda N. Kobziar & Jonathan R. Colburn
Butterflies such as the atala hairstreak, Eumaeus atala Poey, and the frosted elfin, Callophrys irus Godart, are restricted to frequently disturbed habitats where their larval host plants occur. Pupae of these butterflies are noted to reside at the base of host plants or in the leaf litter and soil, which may allow them to escape direct mortality by fire, a prominent disturbance in many areas they inhabit. The capacity of these species to cope with...

Data from: High precipitation and seeded species competition reduce seeded shrub establishment during dryland restoration

Matthew J. Rinella, Darcy H. Hammond, Ana-Elisa M. Bryant & Brian J. Kozar
Drylands comprise 40% of Earth's land mass and are critical to food security, carbon sequestration, and threatened and endangered wildlife. Exotic weed invasions, overgrazing, energy extraction, and other factors have degraded many drylands, and this has placed an increased emphasis on dryland restoration. The increased restoration focus has generated a wealth of experience, innovations and empirical data, yet the goal of restoring diverse, native, dryland plant assemblages composed of grasses, forbs, and shrubs has generally...

Data from: Genetic structure, admixture, and invasion success in a Holarctic defoliator, the gypsy moth (Lymantria dispar, Lepidoptera: Erebidae)

Yunke Wu, John J. Molongoski, Deborah F. Winograd, Steven M. Bogdanowicz, Artemis S. Louyakis, David R. Lance, Victor C. Mastro & Richard G. Harrison
Characterizing the current population structure of potentially invasive species provides a critical context for identifying source populations and for understanding why invasions are successful. Non-native populations inevitably lose genetic diversity during initial colonization events, but subsequent admixture among independently introduced lineages may increase both genetic variation and adaptive potential. Here we characterize the population structure of the gypsy moth (Lymantria dispar Linnaeus), one of the world's most destructive forest pests. Native to Eurasia and recently...

Data from: How topography induces reproductive asynchrony and alters gypsy moth invasion dynamics

Jonathan A. Walter, Marcia S. Meixler, Thomas Mueller, William F. Fagan, Patrick C. Tobin & Kyle J. Haynes
1. Reproductive asynchrony, a temporal mismatch in reproductive maturation between an individual and potential mates, may contribute to mate-finding failure and Allee effects that influence the establishment and spread of invasive species. Variation in elevation is likely to promote variability in maturation times for species with temperature-dependent development, but it is not known how strongly this influences reproductive asynchrony or the population growth of invasive species. 2. We examined whether spatial variation in reproductive asynchrony,...

Data from: Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches

Martin P. Schilling, Paul G. Wolf, Aaron M. Duffy, Hardeep S. Rai, Carol A. Rowe, Bryce A. Richardson & Karen E. Mock
Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in...

Data from: Genomics assisted ancestry deconvolution in grape

Jason K. Sawler, Bruce Reisch, Mallikarjuna K. Aradhya, Bernard Prins, Gan-Yuan Zhong, Heidi Schwaninger, Charles Simon, Edward Buckler, Sean Myles & Jason Sawler
The genus Vitis (the grapevine) is a group of highly diverse, diploid woody perennial vines consisting of approximately 60 species from across the northern hemisphere. It is the world’s most valuable horticultural crop with ~8 million hectares planted, most of which is processed into wine. To gain insights into the use of wild Vitis species during the past century of interspecific grape breeding and to provide a foundation for marker-assisted breeding programmes, we present a...

Data from: Multilocus analyses reveal little evidence for lineage wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus)

Andrew J. Eckert, Andrew D. Bower, Kathleen D. Jermstad, Jill L. Wegrzyn, Brian J. Knaus, John V. Syring & David B. Neale
Estimates from molecular data for the fraction of new nonsynonymous mutations that are adaptive vary strongly across plant species. Much of this variation is due to differences in life-history strategies as they influence the effective population size (Ne). Ample variation for these estimates, however, remains even when comparisons are made across species with similar values of Ne. An open question thus remains as to why the large disparity for estimates of adaptive evolution exists among...

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