Allele identification for transcriptome-based population genomics in the invasive plant Centaurea solstitialis

Transcriptome sequences are becoming more broadly available for multiple individuals of the same species, providing opportunities to derive population genomic information from these datasets. Using the 454 Life Science Genome Sequencer FLX and FLX-Titanium next-generation platforms, we generated 11−430 Mbp of sequence for normalized cDNA for 40 wild genotypes of the invasive plant Centaurea solstitialis, yellow starthistle, from across its worldwide distribution. We examined the impact of sequencing effort on transcriptome recovery and overlap among individuals. To do this, we developed two novel publicly available software pipelines: SnoWhite for read cleaning before assembly, and AllelePipe for clustering of loci and allele identification in assembled datasets with or without a reference genome. AllelePipe is designed specifically for cases in which read depth information is not appropriate or available to assist with disentangling closely related paralogs from allelic variation, as in transcriptome or previously assembled libraries. We find that modest applications of sequencing effort recover most of the novel sequences present in the transcriptome of this species, including single-copy loci and a representative distribution of functional groups. In contrast, the coverage of variable sites, observation of heterozygosity, and overlap among different libraries are all highly dependent on sequencing effort. Nevertheless, the information gained from overlapping regions was informative regarding coarse population structure and variation across our small number of population samples, providing the first genetic evidence in support of hypothesized invasion scenarios.Fil: Dlugosch, Katrina M.. University of British Columbia; CanadáFil: Lai, Zhao. Indiana University; Estados UnidosFil: Bonin, Auélie. Indiana University; Estados UnidosFil: Hierro, Jose Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; ArgentinaFil: Rieseberg, Loren H.. University of British Columbia; Canadá. Indiana University; Estados Unido

EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics

Recent increases in the production of genomic data are yielding new opportunities and challenges for biologists. Among the chief problems posed by next-generation sequencing are assembly and analyses of these large data sets. Here we present an online server, http://EvoPipes.net, that provides access to a wide range of tools for bioinformatic analyses of genomic data oriented for ecological and evolutionary biologists. The EvoPipes.net server includes a basic tool kit for analyses of genomic data including a next-generation sequence cleaning pipeline (SnoWhite), scaffolded assembly software (SCARF), a reciprocal best-blast hit ortholog pipeline (RBH Orthologs), a pipeline for reference protein-based translation and identification of reading frame in transcriptome and genomic DNA (TransPipe), a pipeline to identify gene families and summarize the history of gene duplications (DupPipe), and a tool for developing SSRs or microsatellites from a transcriptome or genomic coding sequence collection (findSSR). EvoPipes.net also provides links to other software developed for evolutionary and ecological genomics, including chromEvol and NU-IN, as well as a forum for discussions of issues relating to genomic analyses and interpretation of results. Overall, these applications provide a basic bioinformatic tool kit that will enable ecologists and evolutionary biologists with relatively little experience and computational resources to take advantage of the opportunities provided by next-generation sequencing in their systems

Nectar and hostplant scarcity limit populations of an endangered Oregon butterfly. Oecologia

Abstract As grassland habitats become degraded, declines in juvenile and adult food resources may limit populations of rare insects. Fender's blue butter¯y (Icaricia icarioides fenderi), a species proposed for listing as endangered under the US Endangered Species Act, survives in remnants of upland prairie in western Oregon. We investigated the eects of limited larval hostplants and adult nectar sources on butter¯y population size at four sites that encompass a range of resource densities. We used coarse and detailed estimates of resource abundance to test hypotheses relating resource quantity to population size. Coarse estimates of resources (percent cover of hostplant and density of nectar¯owers) suggest that butter¯y population size is not associated with resource availability. However, more detailed estimates of resources (density of hostplant leaves and quantity of nectar from native nectar sources) suggest that butter¯y population size is strongly associated with resource availability. The results of this study suggest that restoring degraded habitat by augmenting adult and larval resources will play an important role in managing populations of this rare butter¯y

Ne.environment.data

Effective population size, climate, and age data for California and European populations of yellow starthistle

Data from: Expansion history and environmental suitability shape effective population size in a plant invasion

The margins of an expanding range are predicted to be challenging environments for adaptation. Marginal populations should often experience low effective population sizes (Ne) where genetic drift is high due to demographic expansion and/or census population size is low due to unfavorable environmental conditions. Nevertheless, invasive species demonstrate increasing evidence of rapid evolution and potential adaptation to novel environments encountered during colonization, calling into question whether significant reductions in Ne are realized during range expansions in nature. Here we report one of the first empirical tests of the joint effects of expansion dynamics and environment on effective population size variation during invasive range expansion. We estimate contemporary values of Ne using rates of linkage disequilibrium among genome-wide markers within introduced populations of the highly invasive plant Centaurea solstitialis (yellow starthistle) in North America (California, USA), and within native Eurasian populations. As predicted, we find that Ne within the invaded range is positively correlated with both expansion history (time since founding) and habitat quality (abiotic climate). History and climate had independent additive effects with similar effect sizes, indicating an important role for both factors in this invasion. These results support theoretical expectations for the population genetics of range expansion, though whether these processes can ultimately arrest the spread of an invasive species remains an unanswered question

NU-IN: Nucleotide evolution and input module for the EvolSimulator genome simulation platform

Background: There is increasing demand to test hypotheses that contrast the evolution of genes and gene families among genomes, using simulations that work across these levels of organization. The EvolSimulator program was developed recently to provide a highly flexible platform for forward simulations of amino acid evolution in multiple related lineages of haploid genomes, permitting copy number variation and lateral gene transfer. Synonymous nucleotide evolution is not currently supported, however, and would be highly advantageous for comparisons to full genome, transcriptome, and single nucleotide polymorphism (SNP) datasets. In addition, EvolSimulator creates new genomes for each simulation, and does not allow the input of user-specified sequences and gene family information, limiting the incorporation of further biological realism and/or user manipulations of the data. Findings: We present modified C++ source code for the EvolSimulator platform, which we provide as the extension module NU-IN. With NU-IN, synonymous and non-synonymous nucleotide evolution is fully implemented, and the user has the ability to use real or previously-simulated sequence data to initiate a simulation of one or more lineages. Gene family membership can be optionally specified, as well as gene retention probabilities that model biased gene retention. We provide PERL scripts to assist the user in deriving this information from previous simulations. We demonstrate the features of NU-IN by simulating genome duplication (polyploidy) in the presence of ongoing copy number variation in an evolving lineage. This example is initiated with real genomic data, and produces output that we analyse directly with existing bioinformatic pipelines. Conclusions: The NU-IN extension module is a publicly available open source software (GNU GPLv3 license) extension to EvolSimulator. With the NU-IN module, users are now able to simulate both drift and selection at the nucleotide, amino acid, copy number, and gene family levels across sets of related genomes, for user-specified starting sequences and associated parameters. These features can be used to generate simulated genomic datasets under an extremely broad array of conditions, and with a high degree of biological realism.Botany, Department ofNon UBCScience, Faculty ofReviewedFacult

Both source‐ and recipient‐range phylogenetic community structure can predict the outcome of avian introductions

Competing phylogenetic models have been proposed to explain the success of species introduced to other communities. Here, we present a study predicting the establishment success of birds introduced to Florida, Hawaii and New Zealand using several alternative models, considering species' phylogenetic relatedness to source- and recipient-range taxa, propagule pressure and traits. We find consistent support for the predictive ability of source-region phylogenetic structure. However, we find that the effects of recipient-region phylogenetic structure vary in sign and magnitude depending on inclusion of source-region phylogenetic structure, delineation of the recipient species pool and the use of phylogenetic correction in the models. We argue that tests of alternative phylogenetic hypotheses including both source and recipient community phylogenetic structure, as well as important covariates such as propagule pressure, are likely to be critical for identifying general phylogenetic patterns in introduction success, predicting future invasions and for stimulating further exploration of the underlying mechanisms of invasibility.Open access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Where we've been and where we're going: the importance of source communities in predicting establishment success from phylogenetic relationships

The last two decades have seen growing use of phylogenetic patterns to test hypotheses predicting the success of introduced species. Nearly all of these tests have focused on hypotheses pertaining to phylogenetic relatedness between introduced species and those of the recipient community, largely neglecting hypotheses regarding phylogenetic relationships in the source region. We synthesize hypotheses regarding how phylogenetic relationships of both recipient and source regions together influence establishment success. We also detail how best to account for differences in source communities within phylogenetic frameworks of invasion. Existing studies have predominantly focused on the environmental filtering and competition-relatedness hypotheses, which deal with relatedness to the recipient community. We discuss how these recipient–region hypotheses can be integrated with three hypotheses focused on the relatedness between an introduced species and the source community in which it originated: the evolutionary imbalance, universal tradeoff and competitive constraint hypotheses. We detail important issues that arise when testing alternative hypotheses and interpreting results. We highlight a lack of tests of synthetic phylogenetic hypotheses including both the source and recipient community phylogenetic structure, as well as important covariates such as propagule pressure. Such synthetic tests may be valuable for identifying general phylogenetic patterns in establishment success, predicting future invasions, and for stimulating further exploration of the underlying mechanisms of invasibility. We conclude with recommendations for future studies that use phylogenetic relationships to predict invasions: including source and recipient communities, using complete phylogenies and accounting for phylogenetic uncertainty, considering multiple stages of invasion and conducting analyses across spatial and phylogenetic scales where possible.Open access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Sample_codes

Sampling sites for seeds of yellow starthistle (*Centaurea solstitialis*) and related taxa, including sampling site information (nearest city, country/state, continent, latitude, and longitude), and year of collection. Location numbers correspond to locations depicted in Fig S1. CESO = *C. solstitialis*, CENE = *C. nicaeensis*, CEPA = *C. pallescens*, CEME = *C. melitensis*

Data from: Increased growth in sunflower correlates with reduced defenses and altered gene expression in response to biotic and abiotic stress

Cultivated plants have been selected by humans for increased yield in a relatively benign environment, where nutrient and water resources are often supplemented, and biotic enemy loads are kept artificially low. Agricultural weeds have adapted to this same benign environment as crops, and often have high growth and reproductive rates, even though they have not been specifically selected for yield. Considering the competing demands for resources in any plant, a key question is whether adaptation to agricultural environments has been accompanied by life-history trade-offs, in which resistance to (largely absent) stress has been lost in favor of growth and reproduction. The experiments reported here were designed to test for growth-defense trade-offs in agricultural weeds, crops, and native varieties of common sunflower (Helianthus annuus L., Asteraceae) by comparing their performance in the presence or absence of abiotic (drought and crowding) or biotic (simulated herbivory, insect herbivory, and fungal) stress. We found that growth, as well viability of crops and weeds, were reduced by abiotic drought stress. The weakened defense in the agricultural genotypes was further evident as increased susceptibility to fungal infection and higher level of insect palatability. To uncover molecular mechanisms underlying these trade-offs we monitored gene expression kinetics in drought-stressed plants. By correlating phenotypic observations with molecular analyses, we report the identification of several genes, including a protein phosphatase 2C and the HD-Zip transcription factor Athb-8, whose expression is associated with the observed phenotypic variation in common sunflower