625 Works

Data from: An experimental test of the effect of predation upon behaviour and trait correlations in threespine stickleback

Sara E. Miller, Kieran M. Samuk & Diana J. Rennison
Benthic and limnetic threespine stickleback (Gasterosteus aculeatus) are a classic example of ecological speciation. Behavioural and armour divergence between these species has been predicted to be the result of divergent selection driven in part by differential predation from cutthroat trout (Oncorhynchus clarki). To experimentally test this prediction, we reared split families of benthic–limnetic hybrids in the presence or absence of trout predation. Our results show that the presence of trout had little effect upon stickleback...

Data from: Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives.

Gregory J. Baute, Nolan C. Kane, Christopher J. Grassa, Zhao Lai & Loren H. Rieseberg
• The development of modern crops typically involves both selection and hybridization, but to date most studies have focused on the former. In the present study we explore how both processes, and their interactions, have molded the genome of the cultivated sunflower, a globally important oilseed. • To identify genes targeted by selection during the domestication and improvement of sunflower, and to detect post-domestication hybridization with wild species, we analyzed transcriptome sequences of 80 genotypes,...

Data from: Adenosine receptors mediate the hypoxic ventilatory response but not the hypoxic metabolic response in the naked mole rat during acute hypoxia

Matthew E. Pamenter, Yvonne A. Dzal & William K. Milsom
Naked mole rats are the most hypoxia-tolerant mammals identified; however, the mechanisms underlying this tolerance are poorly understood. Using whole-animal plethysmography and open-flow respirometry, we examined the hypoxic metabolic response (HMR), hypoxic ventilatory response (HVR) and hypoxic thermal response in awake, freely behaving naked mole rats exposed to 7% O2 for 1 h. Metabolic rate and ventilation each reversibly decreased 70% in hypoxia (from 39.6 ± 2.9 to 12.1 ± 0.3 ml O2 min−1 kg−1,...

Data from: The importance (or lack thereof) of niche divergence to the maintenance of a northern species complex: the case of the long-toed salamander (Ambystoma macrodactylum Baird)

Julie Lee-Yaw, Darren Irwin, J. A. Lee-Yaw & D. E. Irwin
The relative importance of ecological versus non-ecological factors for the origin and maintenance of species is an open question in evolutionary biology. Young lineages—such as the distinct genetic groups that make up the ranges of many northern species—represent an opportunity to study the importance of ecological divergence during the early stages of diversification. Yet, few studies have examined the extent of niche divergence between lineages in previously glaciated regions and the role of ecology in...

Data from: Rapid increases in forest understory diversity and productivity following a mountain pine beetle (Dendroctonus ponderosae) outbreak in pine forests

Gregory J. Pec, Justine Karst, Alexandra N. Sywenky, Paul W. Cigan, Nadir Erbilgin, Suzanne W. Simard, & James F. Cahill
The current unprecedented outbreak of mountain pine beetle (Dendroctonus ponderosae) in lodgepole pine (Pinus contorta) forests of western Canada has resulted in a landscape consisting of a mosaic of forest stands at different stages of mortality. Within forest stands, understory communities are the reservoir of the majority of plant species diversity and influence the composition of future forests in response to disturbance. Although changes to stand composition following beetle outbreaks are well documented, information on...

Data from: Patterns of domestication in the Ethiopian oil-seed crop Noug (Guizotia abyssinica)

Hannes Dempewolf, Misteru Tesfaye, Abel Teshome, Anne Bjorkman, Rose L. Andrew, Moira Scascitelli, Scott Black, Endashaw Bekele, Johannes M. M. Engels, Quentin C. B. Cronk, Loren H. Rieseberg & Anne D. Bjorkman
Noug (Guizotia abyssinica) is a semi-domesticated oil-seed crop, which is primarily cultivated in Ethiopia. Unlike its closest crop relative, sunflower, noug has small seeds, small flowering heads, many branches, many flowering heads, indeterminate flowering, and it shatters in the field. Here we conducted common garden studies and microsatellite analyses of genetic variation to test whether high levels of crop-wild gene flow and/or unfavorable phenotypic correlations have hindered noug domestication. With the exception of one population,...

Data from: Growth gains from selective breeding in a spruce hybrid zone do not compromise local adaptation to climate

Ian R. MacLachlan, Sam Yeaman & Sally N. Aitken
Hybrid zones contain extensive standing genetic variation that facilitates rapid responses to selection. The Picea glauca x P. engelmannii hybrid zone in western Canada is the focus of tree breeding programs that annually produce ~90 million reforestation seedlings. Understanding the direct and indirect effects of selective breeding on adaptive variation is necessary to implement assisted gene flow polices in Alberta and British Columbia that match these seedlings with future climates. We decomposed relationships among hybrid...

Data from: Models for assessing local-scale co-abundance of animal species while accounting for differential detectability and varied responses to the environment

Jedediah F. Brodie, Olga E. Helmy, Jayasilan Mohd-Azlan, Alys Granados, Henry Bernard, Anthony J. Giordano & Elise Zipkin
We developed a new modeling framework to assess how the local abundance of one species influences the local abundance of a potential competitor while explicitly accounting for differential responses to environmental conditions. Our models also incorporate imperfect detection as well as abundance estimation error for both species. As a case study, we applied the model to four pairs of mammal species in Borneo, surveyed by extensive and spatially widespread camera trapping. We detected different responses...

Data from: Theory, practice, and conservation in the age of genomics: the Galápagos giant tortoise as a case study

Stephen J. Gaughran, Maud C. Quinzin, Joshua M. Miller, Ryan C. Garrick, Danielle L. Edwards, Michael A. Russello, Nikos Poulakakis, Claudio Ciofi, Luciano B. Beheregaray, Aldalgisa Caccone & Adalgisa Caccone
Hgh-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in non-model species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of sampling design on estimating genetic differentiation among populations that...

Data from: Using fuzzy logic to determine the vulnerability of marine species to climate change

Miranda C. Jones & William W. L. Cheung
Marine species are being impacted by climate change and ocean acidification, although their level of vulnerability varies due to differences in species' sensitivity, adaptive capacity and exposure to climate hazards. Due to limited data on the biological and ecological attributes of many marine species, as well as inherent uncertainties in the assessment process, climate change vulnerability assessments in the marine environment frequently focus on a limited number of taxa or geographic ranges. As climate change...

Data from: Fine-root exploitation strategies differ in tropical old-growth and logged-over forests in Ghana

Shalom D. Addo-Danso, Cindy E. Prescott, Stephen Adu-Bredu, Akwasi Duah-Gyamfi, Sam Moore, Robert D. Guy, David I. Forrester, Kennedy Owusu-Afriyie, Peter L. Marshall, Yadvinder Malhi. & Yadvinder Malhi
Understanding the changes in root exploitation strategies during post-logging recovery is important for predicting forest productivity and carbon dynamics in tropical forests. We sampled fine (diameter < 2 mm) roots using the soil-core method to quantify fine-root biomass, and architectural and morphological traits to determine root exploitation strategies in an old-growth forest and in a 54-year-old logged-over forest influenced by similar parent material and climate. Seven root traits were considered: four associated with resource exploitation...

Data from: The combined impacts of experimental defaunation and logging on seedling traits and diversity

Alys Granados, Henry Bernard & Jedediah F. Brodie
Animals can have both positive (e.g. via seed dispersal) and negative (e.g. via herbivory) impacts on plants. The net effects of these interactions remain difficult to predict and may be affected by overhunting and habitat disturbance, two widespread threats to tropical forests. Recent studies have documented their separate effects on plant recruitment but our understanding of how defaunation and logging interact to influence tropical tree communities is limited. From 2013-2016, we followed the fate of...

Data for: Feedback between coevolution and epidemiology can help or hinder the maintenance of genetic variation in host-parasite models

Ailene MacPherson, Matthew Keeling & Sarah Otto
Antagonistic coevolution has long been suggested to help maintain host genetic variation. While, ecological and epidemiological feedbacks are known to have important consequences on coevolutionary allele frequency dynamics, their effects on the maintenance of genetic variation remains poorly understood.Here, we extend our previous work on the maintenance of genetic variation in a classic matching-alleles coevolutionary model by exploring the effects of ecological and epidemiological feedbacks, where both allele frequencies and population sizes are allowed to...

Genomic analyses of phenotypic differences between native and invasive populations of diffuse knapweed (Centaurea diffusa)

Kathryn Turner, Kate Ostevik, Christopher Grassa & Loren Rieseberg
Invasive species represent excellent opportunities to study the evolutionary potential of traits important to success in novel environments. Although some ecologically-important traits have been identified in invasive species, little is typically known about the genetic mechanisms that underlie invasion success in non-model species. Here, we use a genome-wide association (GWAS) approach to identify the genetic basis of trait variation in the non-model, invasive, diffuse knapweed (Centaurea diffusa Lam. [Asteraceae]). To assist with this analysis, we...

Data from: Priorities and motivations of marine coastal restoration research

Elisa Bayraktarov, Shantala Brisbane, Phoebe J Stewart-Sinclair, Audrey Van Herwaarden, Keila Stark, Valerie Hagger, Carter S Smith, Kerrie A Wilson, Catherine E Lovelock, Chris Gillies, Andrew D L Steven & Megan I Saunders
Active restoration is becoming an increasingly important conservation intervention to counteract the degradation of marine coastal ecosystems. Understanding what has motivated the scientific community to research the restoration of marine coastal ecosystems and how restoration research projects are funded is essential if we want to scale-up restoration interventions to meaningful extents.Here, we systematically review and synthesize data to understand the motivations for research on the restoration of coral reefs, seagrass, mangroves, saltmarsh, and oyster reefs....

Adaptation and latitudinal gradients in species interactions: nest predation in birds

Ben Freeman, Micah Scholer, Mannfred Boehm, Julian Heavyside & Dolph Schluter
Are rates of biotic interactions are stronger in the tropics? Here we investigate nest predation rates in birds, a canonical example of a strong tropical biotic interaction. Counter to expectations, daily rates of nest predation vary minimally with latitude. However, life history traits that influence nest predation have diverged between latitudes. For example, tropical species have evolved a longer average nesting period, which is associated with reduced rates of nest attendance by parents. Daily nest...

Hidden introductions of freshwater red algae via the aquarium trade exposed by DNA barcodes

Shing Zhan, Tsai-Yin Hsieh, Lan-Wei Yeh, Ting-Chun Kuo, Shoichiro Suda & Shao-Lun Liu
The global aquarium trade can introduce alien freshwater invaders, potentially impacting local aquatic ecosystems and their biodiversity. The role of the aquarium trade in spreading freshwater red macroalgae that hitchhike on ornamental aquatic plants and animals is unassessed. We investigated this human-mediated phenomenon via a broad biodiversity survey and genetic analysis of freshwater red algae in the field and aquarium shops in East Asia. Results We found 26 molecular operational taxonomic units (mOTUs) in Taiwan,...

Data from Beyond MAP: A guide to dimensions of rainfall variability for tropical ecology

Naomi Schwartz, Benjamin R. Lintner, Xue Feng & Jennifer S. Powers
Tropical ecologists have long recognized rainfall as the key climate filter shaping tropical ecosystem structure and function across space and time. Still, tropical ecologists have historically had a limited toolkit for characterizing rainfall, largely relying on simple metrics like mean annual precipitation (MAP) and dry season length to characterize rainfall regimes that vary along many more dimensions. Here, we review methods for quantifying dimensions of rainfall variability on multiple time scales, with a focus on...

Experimental hybridization studies suggest that pleiotropic alleles commonly underlie adaptive divergence between natural populations

Ken Thompson
The alleles used for adaptation can pleiotropically affect traits under stabilizing selection. The fixation of alleles with deleterious pleiotropic effects causes compensatory alleles to be favoured by selection. Such compensatory alleles might segregate in interpopulation hybrids, resulting in segregation variance for traits where parents have indistinguishable phenotypes. If adaptation typically involves pleiotropy and compensation, then the segregation variance for traits under stabilizing selection is expected to increase with the magnitude of adaptive phenotypic divergence between...

In situ resistance, not immigration, supports invertebrate community resilience to drought intensification in a Neotropical ecosystem

Camille Bonhomme, Régis Céréghino, Jean-François Carrias, Arthur Compin, Bruno Corbara, Vincent E.J. Jassey, Joséphine Leflaive, Vinicius F. Farjalla, Nicholas A. C. Marino, Thibaut Rota, Diane S. Srivastava & Céline Leroy
While future climate scenarios predict declines in precipitations in many regions of the world, little is known of the mechanisms underlying community resilience to prolonged dry seasons, especially in “naïve” Neotropical rainforests. Predictions of community resilience to intensifying drought are complicated by the fact that the underlying mechanisms are mediated by species’ tolerance and resistance traits, as well as rescue through dispersal from source patches. We examined the contribution of in situ tolerance-resistance and immigration...

Single cell transcriptomics of of Abedinium reveals a new early-branching dinoflagellate lineage

Elizabeth Cooney, Noriko Okamoto, Anna Cho, Elisabeth Hehenberger, Thomas Richards, Alexandra Worden, Alyson Santoro, Brian Leander & Patrick Keeling
Dinoflagellates possess many unique cellular characteristics with unresolved evolutionary histories including nuclei with greatly expanded genomes and chromatin packaged using histone-like proteins and dinoflagellate-viral nucleoproteins instead of histones, highly reduced mitochondrial genomes with extensive RNA editing, a mix of photosynthetic and cryptic secondary plastids, and tertiary plastids. Resolving the evolutionary origin of these traits requires understanding their ancestral states and early intermediates. Several deep-branching dinoflagellate lineages are good candidates for such reconstruction, however they tend...

UCE and Sanger sequenced data for phylogenetic analysis of jumping spiders (Baviini and Nungia, Salticidae)

Wayne Maddison
The systematics and taxonomy of the tropical Asian jumping spiders of the tribe Baviini is reviewed, with a molecular phylogenetic study (UCE sequence capture, traditional Sanger sequencing) guiding a reclassification of the group's genera. The well-studied members of the group are placed into six genera: Bavia Simon, 1877, Indopadilla Caleb & Sankaran, 2019, Padillothorax Simon, 1901, Piranthus Thorell, 1895, Stagetillus Simon, 1885, and one new genus, Maripanthus Maddison. The identity of Padillothorax is clarified, and...

COVID-19 clinician moral injury survey

David Barbic
Background Moral injury is an emerging explanation of burnout and suicidality, but remains poorly quantified in at-risk practitioners. We hypothesized that COVID-19 pandemic-related moral injury differs between frontline clinicians, genders, age, and country of practice. Methods We conducted an online cross-sectional survey of international physicians, nurses, nurse practitioners, paramedics and respiratory therapists between April and June 2020. We included the adapted version of the Expressions of Moral Injury Scale (EMIS). The primary outcome was differences...

The sunflower (Helianthus annuusL.) genome reflects a recent history of biased accumulation of transposable elements

S. Evan Staton, Bradley H. Bakken, Benjamin K. Blackman, Mark A. Chapman, Nolan C. Kane, Shunxue Tang, Mark C. Ungerer, Steven J. Knapp, Loren H. Rieseberg & John M. Burke
Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size (∼3.5 Gb) and the well‐documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence...

Data from: Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean

Loay Jabre, Andrew E. Allen, J. Scott P. McCain, John P. McCrow, Nancy Tenenbaum, Jenna L. Spackeen, Rachel E. Sipler, Beverley R. Green, Deborah A. Bronk, David A. Hutchins & Erin M. Bertrand
The Southern Ocean (SO) harbours some of the most intense phytoplankton blooms on Earth. Changes in temperature and iron availability are expected to alter the intensity of SO phytoplankton blooms, but little is known about how environmental change will influence community composition and downstream biogeochemical processes. We performed experimental manipulations on surface ocean microbial communities from McMurdo Sound in the Ross Sea, with and without iron addition, at -0.5 °C, 3 °C, and 6 °C....

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