990 Works

Data from: Stage and size structure of three species of oaks in central coastal California

Ian S. Pearse, Sophie Griswold, Desirree Pizarro & Walter D. Koenig
Oaks are foundational species in much of California, and many oak populations in the state may be in jeopardy due to a lack of recruitment of young trees. Despite considerable interest in this problem, there have been few comprehensive surveys of all stages of oak development. We surveyed all stages of three oaks: Quercus lobata, Q. douglasii, and Q. agrifolia in a forest plot with mixed land-use in central coastal California. We found abundant seedlings...

Data from: Differential introgression in a mosaic hybrid zone reveals candidate barrier genes

Erica L. Larson, Jose A. Andres, Steven M. Bogdanowicz & Richard G. Harrison
Hybrid zones act as genomic sieves; although globally advantageous alleles will spread throughout the zone and neutral alleles can be freely exchanged between species, introgression will be restricted for genes that contribute to reproductive barriers or local adaptation. Seminal fluid proteins (SFPs) are known to contribute to reproductive barriers in insects and have been proposed as candidate barrier genes in the hybridizing field crickets G. pennsylvanicus and G. firmus. Here, we have used 125 SNPs...

Data from: The fate of phosphorus fertilizer in Amazon soya bean fields

Shelby H. Riskin, Stephen Porder, Christopher Neill, Adelaine Michela E Silva Figueira, Carmen Tubbesing & Natalie Mahowald
Fertilizer-intensive soya bean agriculture has recently expanded in southeastern Amazônia, and whereas intensive fertilizer use in the temperate zone has led to widespread eutrophication of freshwater ecosystems, the effects in tropical systems are less well understood. We examined the fate of fertilizer P by comparing P forms and budgets across a chronosequence of soya bean fields (converted to soya beans between 2003 and 2008) and forests on an 800 km2 soya bean farm in Mato...

Data from: Ancient host shifts followed by host conservatism in a group of ant parasitoids

Elizabeth A. Murray, Andrew E. Carmichael & John M. Heraty
While ant colonies serve as host to a diverse array of myrmecophiles, few parasitoids are able to exploit this vast resource. A notable exception is the wasp family Eucharitidae, which is the only family of insects known to exclusively parasitize ants. Worldwide, approximately 700 Eucharitidae species attack five subfamilies across the ant phylogeny. Our goal is to uncover the pattern of eucharitid diversification, including timing of key evolutionary events, biogeographic patterns and potential cophylogeny with...

Data from: The evolutionary origins of modularity

Jeff Clune, Jean-Baptiste Mouret & Hod Lipson
A central biological question is how natural organisms are so evolvable (capable of quickly adapting to new environments). A key driver of evolvability is the widespread modularity of biological networks--their organization as functional, sparsely connected subunits--but there is no consensus regarding why modularity itself evolved. While most hypotheses assume indirect selection for evolvability, here we demonstrate that the ubiquitous, direct selection pressure to reduce the cost of connections between network nodes causes the emergence of...

Data from: Biodiversity ensures plant-pollinator phenological synchrony against climate change

Ignasi Bartomeus, Mia G. Park, Jason Gibbs, Bryan N. Danforth, Alan N. Lakso & Rachael Winfree
Climate change has the potential to alter the phenological synchrony between interacting mutualists, such as plants and their pollinators. However, high levels of biodiversity might buffer the negative effects of species-specific phenological shifts and maintain synchrony at the community level, as predicted by the biodiversity insurance hypothesis. Here, we explore how biodiversity might enhance and stabilise phenological synchrony between a valuable crop, apple and its native pollinators. We combine 46 years of data on apple...

Data from: Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits

Geoffrey P. Morris, Davina H. Rhodes, Zachary Brenton, Punna Ramu, Vinayan Madhumal Thayil, Santosh Deshpande, C. Thomas Hash, Charlotte Acharya, Sharon E. Mitchell, Edward S. Buckler, Jianming Yu & Stephen Kresovich
Genome-wide association studies (GWAS) are a powerful method to dissect the genetic basis of traits, though in practice the effects of complex genetic architecture and population structure remain poorly understood. To compare mapping strategies we dissect the genetic control of flavonoid pigmentation traits in the cereal grass sorghum using high-resolution genotyping-by-sequencing (GBS) SNP markers. Studying the grain tannin trait, we find that General Linear Models (GLM) are not able to precisely map tan1-a, a known...

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: Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters

Haibin Zhang & Matthew P. Hare
Phylogeographic inferences about gene flow are strengthened through comparison of co-distributed taxa, but also depend on adequate genomic sampling. Amplified Fragment Length Polymorphisms (AFLP) provide a rapid and inexpensive source of multilocus allele frequency data for making genomically robust inferences. Every AFLP study initially generates markers with a range of locus-specific genotyping error rates and applies criteria to select a subset for analysis. However, there has been very little empirical evaluation of the best tradeoff...

Data from: The chestnut blight fungus world tour: successive introduction events from diverse origins in an invasive plant fungal pathogen.

Cyril Dutech, Benoit Barrès, Julen Bridier, Cécile Robin, Michael G. Milgroom & Virginie Ravigné
Clonal expansion has been observed in several invasive fungal plant pathogens colonizing new areas, raising the question of the origin of clonal lineages. Using microsatellite markers, we retraced the evolutionary history of introduction of the chestnut blight fungus, Cryphonectria parasitica, in North America and western Europe. Combining discriminant analysis of principal components and approximate Bayesian computation analysis, it was shown that several introduction events from genetically differentiated source populations have occurred in both invaded areas....

Data from: Range-wide population genetic structure of the Caribbean sea fan coral, Gorgonia ventalina

Jason P. Andras, Krystal L. Rypien & Catherine Drew Harvell
The population structure of benthic marine organisms is of central relevance for the conservation and management of these often threatened species as well as an accurate understanding of their ecological and evolutionary dynamics. A growing body of evidence suggests that marine populations can be structured over short distances despite theoretically high dispersal potential. Yet the proposed mechanisms governing this structure vary, and existing empirical population genetic evidence is of insufficient taxonomic and geographic scope to...

Data from: Long-term endemism of two highly divergent lineages of the amphibian-killing fungus in the Atlantic Forest of Brazil

David Rodriguez, Carlos G. Becker, Nadya C. Pupin, Célio F. B. Haddad & Kelly R. Zamudio
The recent global spread of the amphibian-killing fungus [Batrachochytrium dendrobatidis (Bd)] has been closely tied to anthropogenic activities; however, regional patterns of spread are not completely understood. Using historical samples, we can test whether Bd was a spreading or endemic pathogen in a region within a particular time frame, because those two disease states provide different predictions for the regional demographic dynamics and population genetics of Bd. Testing historical patterns of pathogen prevalence and population...

Data from: Structure of a mosaic hybrid zone between the field crickets Gryllus firmus and G. pennsylvanicus

Erica L. Larson, C. Guilherme Becker, Eliana R. Bondra & Richard G. Harrison
Hybrid zones provide insight into the nature of species boundaries and the evolution of barriers to gene exchange. Characterizing multiple regions within hybrid zones is essential for understanding both their history and current dynamics. Here, we describe a previously uncharacterized region of a well-studied hybrid zone between two species of field crickets, Gryllus pennsylvanicus and G. firmus. We use a combination of mitochondrial DNA sequencing, morphological data, and modeling of environmental variables to identify the...

Data from: Historical changes in northeastern US bee pollinators related to shared ecological traits

Ignasi Bartomeus, John S. Ascher, Jason Gibbs, Bryan N. Danforth, David L. Wagner, Shannon M. Hedtke & Rachael Winfree
Pollinators such as bees are essential to the functioning of terrestrial ecosystems. However, despite concerns about a global pollinator crisis, long-term data on the status of bee species are limited. We present a long-term study of relative rates of change for an entire regional bee fauna in the northeastern United States, based on >30,000 museum records representing 438 species. Over a 140-y period, aggregate native species richness weakly decreased, but richness declines were significant only...

Data from: Self-recruitment in a Caribbean reef fish: a method for approximating dispersal kernels accounting for seascape

Cassidy C. D'Aloia, Steven M. Bogdanowicz, John E. Majoris, Richard G. Harrison & Peter M. Buston
Characterizing patterns of larval dispersal is essential to understanding the ecological and evolutionary dynamics of marine metapopulations. Recent research has measured local dispersal within populations, but the development of marine dispersal kernels from empirical data remains a challenge. We propose a framework to move beyond point estimates of dispersal towards the approximation of a simple dispersal kernel, based on the hypothesis that the structure of the seascape is a primary predictor of realized dispersal patterns....

Data from: On the origin of a domesticated species: identifying the parent population of Russian silver foxes (Vulpes vulpes)

Mark J. Statham, Lyudmila N. Trut, Ben N. Sacks, Anastasiya V. Kharlamova, Irina N. Oskina, Rimma G. Gulevich, Jennifer L. Johnson, Svetlana V. Temnykh, Gregory M. Acland & Anna V. Kukekova
The foxes at Novosibirsk, Russia, are the only population of domesticated foxes in the world. These domesticated foxes originated from farm-bred silver foxes (Vulpes vulpes), whose genetic source is unknown. In the present study, we examined the origin of the domesticated strain of foxes and two other farm-bred fox populations (aggressive and unselected) maintained in Novosibirsk. To identify the phylogenetic origin of these populations we sequenced two regions of mitochondrial DNA, cytochrome b and d-loop,...

Data from: Ontogeny and phylogeny in the northern swordtail clade of Xiphophorus

Jeffrey M. Marcus & Amy R. McCune
It has been hypothesized than morphological diversity within clades can be generated by simple alterations of shared developmental programs. However, few studies have examined changes in heterochrony, the rate and timing of developmental events, in an explicitly phylogenetic context. We studied how developmental patterns have changed phylogenetically in the northern swordtail clade of Xiphophorus. We reared individuals of an outgroup and seven of nine species in the clade and followed their development for ~300 days....

Data from: Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies

Megan A. Supple, Heather M. Hines, Kanchon K. Dasmahapatra, James J. Lewis, Dahlia M. Nielsen, Christine Lavoie, David A. Ray, Camilo Salazar, W. Owen McMillan & Brian A. Counterman
Identifying the genetic changes driving adaptive variation in natural populations is key to understanding the origins of biodiversity. The mosaic of mimetic wing patterns in Heliconius butterflies makes an excellent system for exploring adaptive variation using next-generation sequencing. In this study, we use a combination of techniques to annotate the genomic interval modulating red color pattern variation, identify a narrow region responsible for adaptive divergence and convergence in Heliconius wing color patterns, and explore the...

Data from: Genome-environment associations in sorghum landraces predict adaptive traits

Jesse R. Lasky, Hari D. Upadhyaya, Punna Ramu, Santosh Deshpande, C. Tom Hash, Jason Bonnette, Thomas E. Juenger, Katie Hyma, Charlotte Acharya, Sharon E. Mitchell, Edward S. Buckler, Zachary Brenton, Stephen Kresovich & Geoffrey P. Morris
Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil...

Data from: Environmental drivers of mast-seeding in Mediterranean oak species: does leaf habit matter?

Ignacio M. Pérez-Ramos, Carmen M. Padilla-Díaz, Walter D. Koenig & Teodoro Marañón
Understanding the proximate factors that govern the widespread mast-seeding process is a question of considerable interest that remains poorly understood. The identity and effect of these factors may vary among coexisting species that differ in leaf habit, potentially resulting in temporally asynchronous patterns of seed production. In this study we aim to identify the proximate causes of mast-seeding using two oak species with contrasting leaf habit that coexist in southern Spain, the deciduous Quercus canariensis...

Data from: An experimental analysis of the heritability of variation in glucocorticoid concentrations in a wild avian population

Brittany R. Jenkins, Maren N. Vitousek, Joanna K. Hubbard & Rebecca J. Safran
Glucocorticoid hormones (CORT) are predicted to promote adaptation to variable environments, yet little is known about the potential for CORT secretion patterns to respond to selection in free-living populations. We assessed the heritable variation underlying differences in hormonal phenotypes using a cross-foster experimental design with nestling North American barn swallows (Hirundo rustica erythrogaster). Using a bivariate animal model, we partitioned variance in baseline and stress-induced CORT concentrations into their additive genetic and rearing environment components...

Data from: A phylogenetic backbone for Bivalvia: an RNA-seq approach

Vanessa L. González, Sónia C. S. Andrade, Rüdiger Bieler, Timothy M. Collins, Casey W. Dunn, Paula M. Mikkelsen, John D. Taylor, Gonzalo Giribet & V. L. Gonzalez
Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000–20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves as a model...

Data from: Complete dosage compensation and sex-biased gene expression in the moth Manduca sexta

Gilbert Smith, Yun-Ru Chen, Gary W. Bissard & Adriana D. Briscoe
Sex chromosome dosage compensation balances homogametic sex chromosome expression with autosomal expression in the heterogametic sex, leading to sex chromosome expression parity between the sexes. If compensation is incomplete this can lead to expression imbalance and sex-biased gene expression. Recent work has uncovered an intriguing and variable pattern of dosage compensation across species that includes a lack of complete dosage compensation in ZW species compared to XY species. This has led to the hypothesis that...

Data from: Constructing predictive models of human running

Horst-Moritz Maus, Shai Revzen, John Guckenheimer, Christian Ludwig, Johann Reger & Andre Seyfarth
Running is an essential mode of human locomotion, during which ballistic aerial phases alternate with phases when a single foot contacts the ground. The spring-loaded inverted pendulum (SLIP) provides a starting point for modelling running, and generates ground reaction forces that resemble those of the centre of mass (CoM) of a human runner. Here, we show that while SLIP reproduces within-step kinematics of the CoM in three dimensions, it fails to reproduce stability and predict...

Data from: Genetic diversity among INERA maize inbred lines with single nucleotide polymorphism (SNP) markers and their relationship with CIMMYT, IITA, and temperate lines

Abdalla Dao, Jacob Sanou, Sharon E. Mitchell, Gracen Vernon & Eric Y. Danquah
Background: Genetic diversity provides the capacity for plants to meet changing environments. It is fundamentally important in crop improvement. Fifty-nine local maize lines developed at INERA and 41 exotic (temperate and tropical) inbred lines were characterized using 1057 SNP markers to (1) analyse the genetic diversity in a diverse set of maize inbred lines; (2) determine the level of genetic diversity in INERA inbred lines and patterns of relationships of these inbred lines developed from...

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  • Cornell University
  • Zhejiang University
  • Capital Medical University
  • Chinese Academy of Agricultural Sciences
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Shandong University
  • Second Xiangya Hospital of Central South University
  • Southern Medical University
  • Sichuan University
  • Renmin Hospital of Wuhan University