22 Works

Data from: Genotyping by sequencing and genome–environment associations in wild common bean predict widespread divergent adaptation to drought

Andrés J. Cortés & Matthew W. Blair
Drought will reduce global crop production by >10% in 2050 substantially worsening global malnutrition. Breeding for resistance to drought will require accessing crop genetic diversity found in the wild accessions from the driest high stress ecosystems. Genome–environment associations in crop wild relatives reveal natural adaptation, and therefore can be used to identify adaptive variation. We explored this approach in the food crop Phaseolus vulgaris L., characterizing 86 geo-referenced wild accessions using Genotyping by Sequencing (GBS)...

Data from: Taxonomic and functional diversity of the co-flowering community differentially affect Cakile edentula pollination at different spatial scales

Cristopher Albor, José García-Franco, Victor Parra-Tabla, Cecilia Díaz-Castelazo & Gerardo Arceo-Gomez
1. The number of co-flowering species, floral density and floral trait diversity can be major determinants of pollinator-mediated plant-plant interactions in a community. However, evaluation of how each one of these co-flowering components affects the pollination success of a single focal plant species, and how these effects vary at different spatial scales, is lacking. 2. Here we evaluated the effects of functional diversity (flower morphology and colour), taxonomic diversity (reflecting potential sampling effects) and flower...

Data from: Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection

Sergey A. Naumenko, Maria D. Logacheva, Nina V. Popova, Anna V. Klepikova, Aleksey A. Penin, Georgii A. Bazykin, Anna E. Etingova, Nikolai S. Mugue, Alexey S. Kondrashov & Lev Y. Yampolsky
Endemic species flocks inhabiting ancient lakes, oceanic islands and other long-lived isolated habitats are often interpreted as adaptive radiations. Yet molecular evidence for directional selection during species flocks radiation is scarce. Using partial transcriptomes of 64 species of Lake Baikal (Siberia, Russia) endemic amphipods and two non-endemic outgroups, we report a revised phylogeny of this species flock, and analyze evidence for positive selection within the endemic lineages. We confirm two independent invasions of amphipods into...

Data from: Moving in the Anthropocene: global reductions in terrestrial mammalian movements

Marlee A. Tucker, Katrin Böhning-Gaese, William F. Fagan, John M. Fryxell, Bram Van Moorter, Susan C. Alberts, Abdullahi H. Ali, Andrew M. Allen, Nina Attias, Tal Avgar, Hattie Bartlam-Brooks, Buuveibaatar Bayarbaatar, Jerrold L. Belant, Alessandra Bertassoni, Dean Beyer, Laura Bidner, Floris M. Van Beest, Stephen Blake, Niels Blaum, Chloe Bracis, Danielle Brown, P. J. Nico De Bruyn, Francesca Cagnacci, Justin M. Calabrese, Constança Camilo-Alves … & Thomas Mueller
Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral...

Is drought tolerance a domestication trait in tepary bean?: Allelic diversity at abiotic stress responsive genes in cultivated Phaseolus acutifolius A. Gray and its wild relatives

Andres Cortes, Angélica Buitrago-Bitar, Felipe López-Hernández, Jorge Londoño-Caicedo, Jaime Muñoz-Florez, Matthew Blair & Carmenza Muñoz
Some of the major impacts of climate change are expected in the poorest regions of the world where drought stress and nutrient deficiency are already a main issue. Legumes are an essential food crop for the poorest because of their high dietary protein and micronutrient contents. However, they are generally drought susceptible. Therefore, our goal in this study was to explore allele diversity at abiotic stress responsive candidate genes in the only drought tolerant cultivated...

Increased precipitation and nitrogen addition accelerate the temporal increase of soil respiration during eight-year old-field grassland succession

Jiajia Zhang, Jingyi Ru, Jian Song, Heng Li, Xiaoming Li, Yafei Ma, Zheng Li, Yuanfang Hao, Zhensheng Chi, Dafeng Hui & Shiqiang Wan
Ecological succession after disturbance plays a vital role in influencing ecosystem structure and functioning. However, how global change factors regulate ecosystem carbon (C) cycling in successional plant communities remains largely elusive. As part of an eight-year (2012-2019) manipulative experiment, this study was designed to examine the responses of soil respiration and its heterotrophic component to simulated increases in precipitation and atmospheric nitrogen (N) deposition in an old-field grassland undergoing secondary succession. Over the eight-year experimental...

Data from: Plant functional groups regulate soil respiration responses to nitrogen addition and mowing over a decade

Yue Du, Hongyan Han, Yanfen Wang, Mingxing Zhong, Dafeng Hui, Shuli Niu & Shiqiang Wan
1. Nitrogen (N) deposition and land-use practice (e.g. mowing) could have profound effects on soil respiration. However, the changes in other ecosystem components, such as plant functional groups (PFGs), may control soil carbon (C) efflux response to long term global change. 2. A 10-year (2005-2014) field experiment was conducted with both N addition (10g N m-2 yr-1) and mowing (once a year) in a northern Chinese temperate grassland. We collected continuous data on soil respiration...

Data from: Anchored phylogenomics illuminates the skipper butterfly tree of life

Emmanuel F.A. Toussaint, Jesse W. Breinholt, Chandra Earl, Andrew D. Warren, Andrew V.Z. Brower, Masaya Yago, Kelly M. Dexter, Marianne Espeland, Naomi E. Pierce, David J. Lohman & Akito Y. Kawahara
Butterflies (Papilionoidea) are perhaps the most charismatic insect lineage, yet phylogenetic relationships among them remain incompletely studied and controversial. We sequenced nearly 400 loci using Anchored Hybrid Enrichment and sampled all tribes and more than 120 genera of skippers (Hesperiidae), one of the most species-rich and poorly studied butterfly families. Maximum-likelihood, parsimony and coalescent multi-species methods all converged on a novel, robust phylogenetic hypothesis for skippers. Different optimality criteria and methodologies recovered almost identical phylogenetic...

Asymmetric responses of resource use efficiency to previous-year precipitation in a semi-arid grassland

Juanjuan Han, Jiquan Chen, Weiyu Shi, Jian Song, Dafeng Hui, Jingyi Ru & Shiqiang Wan
1. Intensified inter-annual fluctuations in precipitation could profoundly impact terrestrial ecosystems. However, how changes previous-year precipitation influence current ecosystem functioning (e.g., resource use efficiency) in semi-arid regions remains unclear. 2. In this study, water use efficiency (WUE) and light use efficiency (LUE) were investigated in a multi-year precipitation gradient experiment with seven treatment levels: 20%, 40% and 60% decreases and 20%, 40% and 60% increases in the amount of natural rainfall plus ambient precipitation. Plots...

Long-term litter removal rather than litter addition enhances ecosystem carbon sequestration in a temperate steppe

Jing Wang, Ang Zhang, Yujin Zheng, Jian Song, Jingyi Ru, Mengmei Zheng, Dafeng Hui & Shiqiang Wan
1. Global change can greatly affect plant productivity and subsequently litter input to soil, with potential impacts on soil carbon (C) fluxes. However, the effects of litter layer in mediating C cycling and budget at an ecosystem scale is still not clear. 2. As part of a long-term litter fall manipulation experiment in a temperate steppe on the Mongolian Plateau, this study was conducted to explore effects of litter removal and addition on ecosystem C...

Data from: Incompatible ages for clearwing butterflies based on alternative secondary calibrations

Ivonne J. Garzón-Orduña, Karina L. Silva-Brandão, Keith R. Willmott, André V. L. Freitas & Andrew V. Z. Brower
The recent publication of a time-tree for the plant family Solanaceae (nightshades) provides the opportunity to use independent calibrations to test divergence times previously inferred for the diverse Neotropical butterfly tribe Ithomiini. Ithomiini includes clades that are obligate herbivores of Solanaceae, with some genera feeding on only one genus. We used 8 calibrations extracted from the plant tree in a new relaxed molecular-clock analysis to produce an alternative temporal framework for the diversification of ithomiines....

Data from: Long-term antagonistic effect of increased precipitation and nitrogen addition on soil respiration in a semiarid steppe

Hongyan Han, Yue Du, Dafeng Hui, Lin Jiang, Mingxing Zhong & Shiqiang Wan
Changes in water and nitrogen (N) availability due to climate change and atmospheric N deposition could have significant effects on soil respiration, a major pathway of carbon (C) loss from terrestrial ecosystems. A manipulative experiment simulating increased precipitation and atmospheric N deposition has been conducted for 9 years (2005–2013) in a semiarid grassland in Mongolian Plateau, China. Increased precipitation and N addition interactively affect soil respiration through the 9 years. The interactions demonstrated that N...

Data from: GloPL, a global data base on pollen limitation of plant reproduction

Joanne. M. Bennett, Janette. A. Steets, Jean. H. Burns, Walter Durka, Jana. C. Vamosi, Gerardo Arceo-Gómez, Martin Burd, Laura. A. Burkle, Allan. G Ellis, Leandro Freitas, Junmin Li, James. G. Rodger, Marina Wolowski, Jing Xia, Tia-Lynn Ashman & Tiffany. M. Knight
Plant reproduction relies on transfer of pollen from anthers to stigmas, and the majority of flowering plants depend on biotic or abiotic agents for this transfer. A key metric for characterizing if pollen receipt is insufficient for reproduction is pollen limitation, which is assessed by pollen supplementation experiments. In a pollen supplementation experiment, fruit or seed production by flowers exposed to natural pollination is compared to that following hand pollination either by pollen supplementation (i.e....

Monarch butterfly roost site variables and habitat conservation

Brandon Boxler, Cynthia Loftin & William Sutton
The criteria that Monarchs use to select specific roost sites, and the landscape context where those sites are found, have received little study. We developed ecological niche models for the Atlantic Flyway roost sites using modeling algorithms, citizen scientist observations, and environmental variables that are known to affect Monarchs in the adult stage prior to migration. These models can be used to help prioritize survey and conservation efforts for Monarchs in areas most suitable for...

Data from: Does the genomic landscape of species divergence in Phaseolus beans coerce parallel signatures of adaptation and domestication?

Andrés J. Cortés, Paola Skeen, Matthew W. Blair & María I. Chacón-Sánchez
Exploring the genomic architecture of species and populations divergence aids understanding how lineages evolve and adapt, and ultimately can show the repeatability of evolutionary processes. Yet, the genomic signatures associated with divergence are still relatively unexplored, leading to a knowledge gap on whether species divergence ultimately differs in its genetic architecture from divergence at other spatial scales (i.e., populations, ecotypes). Our goal in this research was to determine whether genomic islands of speciation are more...

Data from: The evolutionary history of dogs in the Americas

Máire Ní Leathlobhair, Angela R. Perri, Evan K. Irving-Pease, Kelsey E. Witt, Anna Linderholm, James Haile, Ophelie Lebrasseur, Carly Ameen, Jeffrey Blick, Adam R. Boyko, Selina Brace, Yahaira Nunes Cortes, Susan J. Crockford, Alison Devault, Evangelos A. Dimopoulos, Morley Eldridge, Jacob Enk, Shyam Gopalakrishnan, Kevin Gori, Vaughan Grimes, Eric Guiry, Anders J. Hansen, Ardern Hulme-Beaman, John Johnson, Andrew Kitchen … & Laurent A. F. Frantz
Dogs were present in the Americas prior to the arrival of European colonists, but the origin and fate of these pre-contact dogs are largely unknown. We sequenced 71 mitochondrial and seven nuclear genomes from ancient North American and Siberian dogs spanning ~9,000 years. Our analysis indicates that American dogs were not domesticated from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people....

Data from: Genome-wide SNP identification and association mapping for seed mineral concentration in Mung bean (Vigna radiata L.)

Andres Cortes, Xingbo Wu, Faridul Islam, Naransa Limpot, Lucas Mackasmiel, Jerzy Mierzwa & Matthew Blair
Mung bean (Vigna radiata L.) quality is dependent on seed chemical composition, which in turn determines the benefits of mung bean consumption for human health. While rich in a range of nutritional components, such as protein, macro- and micro- nutrients, carbohydrates and vitamins, mung bean remains less well studied than other legume crops. Mung bean genomics and genetic resources are relatively sparse. To further improve nutritional levels of mung bean grain requires genome-wide marker system...

Data from: Multiple constraints cause positive and negative feedbacks limiting grassland soil CO2 efflux under CO2 enrichment

Philip Fay, Dafeng Hui, Robert Jackson, Harold Collins, Lara Reichmann, Michael Aspinwall, Virginia Jin, Albina Khasanova, Robert Heckman & Wayne Polley
Terrestrial ecosystems are increasingly enriched with resources such as atmospheric CO2 that limit ecosystem processes. The consequences for ecosystem carbon cycling depend on the feedbacks from other limiting resources and plant community change, which remain poorly understood for soil CO2 efflux, JCO2, a primary carbon flux from the biosphere to the atmosphere. We applied a unique CO2 enrichment gradient (250 to 500 µL L-1) for eight years to grassland plant communities on soils from different...

Responses of soil temperature, moisture, and respiration to five-year warming and nitrogen addition in a semi-arid grassland

Jian Song, Jianyang Xia, Dafeng Hui, Mengmei Zheng, Jing Wang, Jingyi Ru, Haidao Wang, Qingshan Zhang, Chao Yang & Shiqiang Wan
How climate warming interacts with atmospheric nitrogen (N) deposition to affect carbon (C) release from soils remains largely elusive, posing a major challenge in projecting climate change‒terrestrial C feedback. As part of a five-year (2006–2010) field manipulative experiment, this study was designed to examine the effects of 24-hour continuous warming and N addition on soil respiration and explore the underlying mechanisms in a semi-arid grassland on the Mongolian Plateau, China. Across the five years and...

Aboveground herbivory causes belowground changes in twelve oak Quercus species: a phylogenetic analysis of root biomass and non‐structural carbohydrate storage

Cynthia Perkovich & David Ward
Plant ecosystem structure is understood to be a result of complex multitrophic interactions. Most multitrophic studies focus on plant aboveground adaptations to aboveground herbivore pressures, neglecting belowground adaptations in response to aboveground damage. Differential investment in root structures may allow plants to compensate for tissue loss or damage due to herbivores. Furthermore, phylogeny may constrain a plant’s ability to adapt belowground. We examined the belowground responses of 12 species of oak (Quercus) to varying locations...

Increased interannual precipitation variability enhances the carbon sink in a semiarid grassland

Jingyi Ru, Shiqiang Wan, Dafeng Hui, Jian Song & Jing Wang
1. The amplifying interannual precipitation variability has been observed globally and is projected to intensify under climate change scenarios. However, its impacts on terrestrial vegetation and carbon (C) sink have not been well investigated. 2. As part of a field manipulative experiment with three precipitation variabilities (20%, 40%, and 60%) in a semiarid grassland, this study was conducted to examine the responses of ecosystem C cycling to increased precipitation variability. 3. Across the 3 experimental...

Behavioral context affects social signal representations within single primate prefrontal cortex neurons

Adam Fishbein, Vladimir Jovanovic, Lisa De La Mothe, Kuo-Fen Lee & Cory Miller
We tested whether social signal processing in more traditional, head-restrained contexts is representative of the putative natural analog – social communication – by comparing responses to vocalizations within individual neurons in marmoset prefrontal cortex (PFC) across a series of behavioral contexts ranging from traditional to naturalistic. Although vocalization responsive neurons were evident in all contexts, cross-context consistency was notably limited. A response to these social signals when subjects were head-restrained was not predictive of a...

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