505 Works

Data from: Vascular epiphytes show low physiological resistance and high recovery capacity to episodic, short-term drought in Monteverde, Costa Rica

Cameron Williams, Jessica Murray, Andrew Glunk, Todd Dawson, Nalini Nadkarni & Sybil Gotsch
Tropical montane cloud forests support abundant epiphytic vascular plant communities that serve important ecosystem functions, but their reliance on atmospheric inputs of water may make them susceptible to the drying effects of rising cloud bases and more frequent droughts. We conducted a common garden experiment to explore the combined effects of decreasing cloud influence—lower humidity, warmer temperature, brighter light—and meteorological drought (i.e., absence of rain) on the physiology and morphology of vascular epiphytes native to...

First come, first served: possible role for priority effects in marine populations under different degrees of dispersal potential

Christiaan De Leeuw, Katja Peijnenburg, Rosemary Gillespie, Diede Maas, Naoto Hanzawa, Yosephine Tuti, Abdul Toha, Ludi Aji & Leontine Becking
Aim Studying clearly delineated populations in marine lakes, islands of sea, we investigate the interplay of habitat size, immigration, and priority effects in shaping marine population genetic structure. Location Marine lakes and coastal locations in Indonesia, Palau, Papua New-Guinea and Australia. Taxon Mussels (Mytillidae, Brachidontes spp.) Methods Populations were sampled from four coastal locations and 22 marine lakes of similar age (~8,000 years), yet differing in size (0.04 - 4.7 km2) and degree of connection...

Data from: Complex interactions between temperature, sexual signals, and mate choice in a desert-dwelling jumping spider

Erin Brandt, Malcolm Rosenthal & Damian Elias
Environmental context is a crucial factor that influences sexual communication systems. Particularly in ectotherms, which cannot metabolically regulate their body temperature, temperature has an outsized effect on these intraspecific interactions. Using a desert-dwelling jumping spider Habronattus clypeatus, we assessed how temperature impacts various parts of the male signal and female mate choice for the signal. These spiders have multimodal, temporally-structured courtship displays that begin with visual-only “sidling” displays and proceed to multimodal visual and vibratory...

Three eco-physiological strategies of response to drought maintain the form and function of a tropical montane grassland

Ilaíne Matos
1. Ecologists seek a general scheme to classify the diversity of plant responses to environmental factors into a few strategies (e.g. competitor -C, stress-tolerant -S, ruderal-R), while plant physiologists seek a mechanistic scheme to explain such different responses (e.g. tolerance, escape, avoidance). So far, few attempts have been made to combine both perspectives into plant eco-physiological strategies. Moreover, the relative contribution of different strategies to maintain both community structure and ecosystem functioning during drought has...

Data from: Tradeoffs, spatial heterogeneity, and the maintenance of microbial diversity

Stephanie S. Porter & Kevin J. Rice
Specialization and concomitant tradeoffs are assumed to underlie the non-neutral coexistence of lineages. Tradeoffs across heterogeneous environments can promote diversity by preventing competitive exclusion. However, the importance of tradeoffs in maintaining diversity in natural microbial assemblages is unclear, as tradeoffs are frequently not detected in artificial evolution experiments. Stressful conditions associated with patches of heavy-metal enriched serpentine soils provide excellent opportunities for examining how heterogeneity may foster genetic diversity. Using a spatially-replicated design, we demonstrate...

Data from: Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

Eddy J. Dowle, Ryan R. Bracewell, Michael E. Pfrender, Karen E. Mock, Barbara J. Bentz & Gregory J. Ragland
Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and gene flow analyses revealed three distinct...

Data from: Large-scale recovery of an endangered amphibian despite ongoing exposure to multiple stressors

Roland A. Knapp, Gary M. Fellers, Patrick M. Kleeman, David A. W. Miller, Vance T. Vredenburg, Erica Bree Rosenblum & Cheryl J. Briggs
Amphibians are one of the most threatened animal groups, with 32% of species at risk for extinction. Given this imperiled status, is the disappearance of a large fraction of the Earth’s amphibians inevitable, or are some declining species more resilient than is generally assumed? We address this question in a species that is emblematic of many declining amphibians, the endangered Sierra Nevada yellow-legged frog (Rana sierrae). Based on >7,000 frog surveys conducted across Yosemite National...

Data from: Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis

Polly Y. Hsu, Lorenzo Calviello, Hsin-Yen Larry Wu, Fay-Wei Li, Carl J. Rothfels, Uwe Ohler & Philip N. Benfey
Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the periodic property of ribosome footprints could be used to identify novel translated ORFs. However, due to the limited resolution of existing methods, the 3-nt periodicity is observed mostly in a global analysis, but not in individual transcripts. Here, we report a protocol applied to Arabidopsis that maps over 90% of the footprints to the main...

Data from: Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis

Allison Q. Byrne, Andrew P. Rothstein, Thomas J. Poorten, Jesse Erens, Matthew L. Settles & Erica Bree Rosenblum
One of the most devastating emerging pathogens of wildlife is the chytrid fungus, Batrachochytrium dendrobatidis (Bd), which affects hundreds of amphibian species around the world. Genomic data from pure Bd cultures has advanced our understanding of Bd phylogenetics, genomic architecture, and mechanisms of virulence. However pure cultures are laborious to obtain and whole genome sequencing is comparatively expensive, so relatively few isolates have been genetically characterized. Thus we still know little about the genetic diversity...

Data from: Cladogenetic and anagenetic models of chromosome number evolution: a Bayesian model averaging approach

William A. Freyman, Sebastian Höhna & William A Freyman
Chromosome number is a key feature of the higher-order organization of the genome, and changes in chromosome number play a fundamental role in evolution. Dysploid gains and losses in chromosome number, as well as polyploidization events, may drive reproductive isolation and lineage diversification. The recent development of probabilistic models of chromosome number evolution in the groundbreaking work by Mayrose et al. (2010, ChromEvol) have enabled the inference of ancestral chromosome numbers over molecular phylogenies and...

Data from: Joint evolution of differential seed dispersal and self-fertilization

Ryosuke Iritani, Pierre-Olivier Cheptou, R. Iritani & P.-O. Cheptou
Differential seed dispersal, in which selfed and outcrossed seeds possess different dispersal propensities, represents a potentially important individual-level association. A variety of traits can mediate differential seed dispersal, including inflorescence and seed size variation. However, how natural selection shapes such associations is poorly known. Here, we developed theoretical models for the evolution of mating system and differential seed dispersal in metapopulations, incorporating heterogeneous pollination, dispersal cost, cost of outcrossing, and environment-dependent inbreeding depression. We considered...

Data from: Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction

Matthew J. Shurtleff, Morayma M. Temoche-Diaz, Kate V. Karfilis, Sayaka Ri, Randy Schekman, Matthew J Shurtleff, Morayma M Temoche-Diaz & Kate V Karfilis
Exosomes are small vesicles that are secreted from metazoan cells and may convey selected membrane proteins and small RNAs to target cells for the control of cell migration, development and metastasis. To study the mechanisms of RNA packaging into exosomes, we devised a purification scheme based on the membrane marker CD63 to isolate a single exosome species secreted from HEK293T cells. Using immunoisolated CD63-containing exosomes we identified a set of miRNAs that are highly enriched...

Data from: Phenotypic and genotypic variation across a stable white-eye (Zosterops sp.) hybrid zone in central South Africa

Graeme Oatley, Dawie H. De Swardt, Rick J. Nuttal, Timothy M. Crowe & Rauri C.K. Bowie
The interbreeding of two species after a period of separation (secondary contact) most often results in stable areas of hybridization or tension zones characterized by selection against hybrid individuals. Three plumage forms of Zosterops meet and interbreed in central South Africa. Here we examine how phenotypic measures (biometric and plumage) and genotypic markers (mitochondrial and nuclear DNA) change through a putative hybrid zone located in the area where the ranges of the Orange River white-eye...

Data from: Floral resource availability from groundcover promotes bee abundance in coffee agroecosystems

Kaleigh Fisher, David J. Gonthier, Katherine K. Ennis & Ivette Perfecto
Patterns of bee abundance and diversity across different spatial scales have received thorough research consideration. However, the impact of short and long term temporal resource availability on biodiversity has been less explored. This is highly relevant in tropical agricultural systems for pollinators, as many foraging periods of pollinators extend beyond flowering of any single crop species. In this study, we sought to understand how bee communities in tropical agroecosystems changed between seasons, and if short...

Data from: High throughput functional genomics identifies modulators of TCE metabolite genotoxicity and candidate susceptibility genes

Vanessa Y. De La Rosa, Jonathan Asfaha, Michael Fasullo, Alex Loguinov, Peng Li, Lee E. Moore, Nathaniel Rothman, Jun Nakamura, James A. Swenberg, Ghislaine Scelo, Luoping Zhang, Martyn T. Smith & Chris D. Vulpe
Trichloroethylene (TCE), an industrial chemical and environmental contaminant, is a human carcinogen. Reactive metabolites are implicated in renal carcinogenesis associated with TCE exposure, yet the toxicity mechanisms of these metabolites and their contribution to cancer and other adverse effects remain unclear. We employed an integrated functional genomics approach that combined functional profiling studies in yeast and avian DT40 cell models to provide new insights into the specific mechanisms contributing to toxicity associated with TCE metabolites....

Genomic differentiation and local adaptation on a microgeographic scale in a resident songbird

Jennifer Walsh, Stepfanie Aguillon, Yvonne Chan, Peter Arcese, Phred Benham, Irby Lovette & Chloe Mikles
Elucidating forces capable of driving species diversification in the face of gene flow remains a key goal in evolutionary biology. Song sparrows, Melospiza melodia, occur as 25 subspecies in diverse habitats across North America, are among the continent’s most widespread vertebrate species, and are exemplary of many highly variable species for which the conservation of locally adapted populations may be critical to their range-wide persistence. We focus here on six morphologically distinct subspecies resident in...

Data from: Validating dispersal distances inferred from autoregressive occupancy models with genetic parentage assignments

Laurie A. Hall, Nathan D. Van Schmidt & Steven R. Beissinger
1.Dispersal distances are commonly inferred from occupancy data but have rarely been validated. Estimating dispersal from occupancy data is further complicated by imperfect detection and the presence of unsurveyed patches. 2.We compared dispersal distances inferred from seven years of occupancy data for 212 wetlands in a metapopulation of the secretive and threatened California black rail (Laterallus jamaicensis coturniculus) to distances between parent-offspring dyads identified with 16 microsatellites. 3.We used a novel autoregressive multi-season occupancy model...

Data from: Scale-dependent variation in nitrogen cycling and soil fungal communities along gradients of forest composition and age in regenerating tropical dry forests

Bonnie G. Waring, Rachel Adams, Sara Branco & Jennifer S. Powers
Rates of ecosystem nitrogen (N) cycling may be mediated by the presence of ectomycorrhizal fungi, which compete directly with free‐living microbes for N. In the regenerating tropical dry forests of Central America, the distribution of ectomycorrhizal trees is affected by succession and soil parent material, both of which may exert independent influence over soil N fluxes. In order to quantify these interacting controls, we used a scale‐explicit sampling strategy to examine soil N cycling at...

Data from: Contact networks structured by sex underpin sex-specific epidemiology of infection

Matthew J. Silk, Nicola L. Weber, Lucy C. Steward, David J. Hodgson, Michael Boots, Darren P. Croft, Richard J. Delahay, Robbie A. McDonald & Mike Boots
Contact networks are fundamental to the transmission of infection and host sex often affects the acquisition and progression of infection. However, the epidemiological impacts of sex-related variation in animal contact networks have rarely been investigated. We test the hypothesis that sex-biases in infection are related to variation in multilayer contact networks structured by sex in a population of European badgers Meles meles naturally infected with Mycobacterium bovis. Our key results are that male-male and between-sex...

Data from: Black spot infection in juvenile steelhead trout increases with stream temperature in northern California

Cody J. Schaaf, Suzanne J. Kelson, Sébastien C. Nusslé & Stephanie M. Carlson
Climate change will increase water temperature in rivers and streams that provide critical habitat for imperiled species. Warmer water temperatures will influence the intensity and nature of biotic interactions, including parasitism. To better understand the factors influencing a neascus-type parasitic infection known as black spot disease, we examined the relationship between infection rate in juvenile steelhead trout (Oncorhynchus mykiss), abundance of another intermediate host (ramshorn snail, Planorbella trivolvis), and water temperature. We quantified infection patterns...

Data from: Ecological specialization, variability in activity patterns, and response to environmental change

Talisin T. Hammond, Rupert Palme & Eileen A. Lacey
Differences in temporal patterns of activity can modulate the ambient conditions to which organisms are exposed, providing an important mechanism for responding to environmental change. Such differences may be particularly relevant to ecological generalists, which are expected to encounter a wider range of environmental conditions. Here, we compare temporal patterns of activity for partially sympatric populations of a generalist (the lodgepole chipmunk, Tamias speciosus) and a more specialized congener (the alpine chipmunk, T. alpinus) that...

Data from: Legume abundance along successional and rainfall gradients in neotropical forests

Maga Gei, Danaë M. A. Rozendaal, Lourens Poorter, Frans Bongers, Janet I. Sprent, Mira D. Garner, T. Mitchell Aide, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Pedro H.S. Brancalion, George A. L. Cabral, Ricardo Gomes César, Robin L. Chazdon, Rebecca J. Cole, Gabriel Dalla Colletta, Ben De Jong, Julie S. Denslow, Daisy H. Dent, Saara J. DeWalt, Juan Manuel Dupuy, Sandra M. Durán, Mário Marcos Do Espírito Santo, G. Wilson Fernandes, Yule Roberta Ferreira Nunes … & Jennifer S. Powers
The nutrient demands of regrowing tropical forests are partly satisfied by nitrogen (N)-fixing legume trees, but our understanding of the abundance of those species is biased towards wet tropical regions. Here we show how the abundance of Leguminosae is affected by both recovery from disturbance and large-scale rainfall gradients through a synthesis of forest-inventory plots from a network of 42 Neotropical forest chronosequences. During the first three decades of natural forest regeneration, legume basal area...

Data from: Stream flow alone does not predict population structure of diving beetles across complex tropical landscapes

Athena Lam, Emmanuel F. A. Toussaint, Carolin Kindler, Matthew H. Van Dam, Rawati Panjaitan, George K. Roderick & Michael Balke
Recent theoretical advances have hypothesized a central role of habitat persistence on population genetic structure and resulting biodiversity patterns of freshwater organisms. Here, we address the hypothesis that lotic species, or lineages adapted to comparably geologically stable running water habitats (streams and their marginal habitats), have high levels of endemicity and phylogeographic structure due to the persistent nature of their habitat. We use a nextRAD sequencing approach to investigate the population structure and phylogeography of...

Data from: Lions and leopards coexist without spatial, temporal or demographic effects of interspecific competition

Jennifer R.B. Miller, Ross T. Pitman, Gareth K.H. Mann, Angela K. Fuller, Guy A. Balme, Jennifer R. B. Miller & Gareth K. H. Mann
1. Although interspecific competition plays a principle role in shaping species behaviour and demography, little is known about the population-level outcomes of competition between large carnivores, and the mechanisms that facilitate coexistence. 2. We conducted a multi-landscape analysis of two widely distributed, threatened large carnivore competitors to offer insight into coexistence strategies and assist with species-level conservation. 3. We evaluated how interference competition affects occupancy, temporal activity and population density of a dominant competitor, the...

Data from: Directional selection effects on patterns of phenotypic (co)variation in wild populations

Ana Paula A. Assis, James L. Patton, Alex Hubbe, Gabriel Marroig, J. L. Patton, G. Marroig, A. P. A. Assis & A. Hubbe
Phenotypic (co)variation is a prerequisite for evolutionary change, and understanding how (co)variation evolves is of crucial importance to the biological sciences. Theoretical models predict that under directional selection, phenotypic (co)variation should evolve in step with the underlying adaptive landscape, increasing the degree of correlation among co-selected traits as well as the amount of genetic variance in the direction of selection. Whether either of these outcomes occurs in natural populations is an open question and thus...

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