cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/t6crfx
title: State University of New York, SUNY College of Environmental Science and Forestry Herbarium

description: The fungal collections of the College of Environmental Science and Forestry of the State University of New York emphasize wood decay fungi and fungi of the northeastern U.S. There are about 15,000 specimens pertinent to this project, including vouchers for the studies of Josiah Lowe (1938-1993) and his students (including Robert L. Gilbertson and M. J. Larsen). Based on these collections over 75 systematic papers were published (e.g. Lowe, 1963, 1975; Larsen, 1968). SYRF specimens have not yet been digitized, but the data generated by this project, will be maintained by SYRF using appropriate software. This project will not only create an electronic version of the data stored in the herbarium, but also affords the opportunity for an advanced undergraduate student or graduate student to learn digitization techniques.
DOI: 10.5061/dryad.tm33d
title: Data from: The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps

description: Climate is one of the most important drivers of local adaptation in forest
 tree species. Standing levels of genetic diversity and structure within
 and among natural populations of forest trees are determined by the
 interplay between climatic heterogeneity and the balance between selection
 and gene flow. To investigate this interplay single nucleotide
 polymorphisms (SNPs) were genotyped in 24 to 37 populations from four
 subalpine conifers, Abies alba Mill., Larix decidua L., Pinus cembra L.
 and Pinus mugo Turra, across their natural ranges in the Italian Alps and
 Apennines. Patterns of population structure were apparent using a Bayesian
 clustering program, STRUCTURE, which identified three to five genetic
 groups per species. Geographical correlates to these patterns, however,
 were only apparent for P. cembra. Multivariate environmental variables
 (i.e. principal components) were subsequently tested for association with
 SNPs using a Bayesian generalized linear mixed model. The majority of the
 SNPs, ranging from six in L. decidua to 18 in P. mugo, were associated
 with PC1, corresponding to winter precipitation and seasonal minimum
 temperature. In A. alba, four SNPs were associated with PC2, corresponding
 to the seasonal minimum temperature. Functional annotation of those genes
 with the orthologs in Arabidopsis revealed several genes involved in
 abiotic stress response. This study provides a detailed assessment of
 population structure and its association to environment and geography in
 four coniferous species in the Italian mountains.
description: Abal_mapping_OPA_analysed.annotGenotyped SNPs in Abies alba with their flanking sequencesLade_mapping_OPA_analysed.annotGenotyped SNPs in Larix decidua with their flanking sequencesPice_mapping_OPA_analysed.annotGenotyped SNPs in Pinus cembra with their flanking sequencesPimg_mapping_OPA_analysed.annotGenotyped SNPs in Pinus mugo with their flanking sequencesAbal_matrix_249SNP by sample matrix of the genotyped SNPs in Abies alba.Lade_matrix_267SNP by sample matrix of the genotyped SNPs in Larix deciduaPice_matrix_459SNP by sample matrix of the genotyped SNPs in Pinus cembraPimg_matrix_694SNP by sample matrix of the genotyped SNPs in Pinus mugoAbal_sample_dataTree by tree environmental data for Abies alba samples.Lade_sample_dataTree by tree environmental data for Larix decidua samples.Pice_sample_dataTree by tree environmental data for Pinus cembra samples.Pimg_sample_dataTree by tree environmental data for Pinus mugo samples.
DOI: 10.5061/dryad.km246
title: Data from: Glacial cycles as an allopatric speciation pump in North Eastern American freshwater fishes

description: Allopatric speciation may be the principal mechanism generating new
 species. Yet, it remains difficult to judge the generality of this process
 because few studies have provided evidence that geographic isolation has
 triggered the development of reproductive isolation over multiple species
 of a regional fauna. Here, we first combine results from new empirical
 data sets (7 taxa) and published literature (9 taxa) to show that the
 eastern Great Lakes drainage represents a multispecies suture zone for
 glacial lineages of freshwater fishes with variable levels of genetic
 divergence. Second, we performed amplified fragment length polymorphism
 analyses among four pairs of lineages. Results indicate that lineages with
 relatively deep levels of mtDNA 5′ COI (barcode) sequence divergence
 (&gt;2%) developed strong reproductive barriers, while lineages with
 lower levels of divergence show weaker reproductive isolation when found
 in sympatry. This suggests that a threshold of 2% sequence divergence at
 mtDNA could be used as a first step to flag cryptic species in North
 American freshwater fishes. By describing different levels of divergence
 and reproductive isolation in different co-occurring fishes, we offer
 strong evidence that allopatric speciation has contributed significantly
 to the diversification of north-eastern American freshwater fishes and
 confirm that Pleistocene glacial cycles can be viewed as a ‘speciation
 pump’ that played a predominant role in generating biodiversity.
description: AFLP-DATA_April-etal_MolEcol_in-press-AFLP data for 4 fish taxa (Rhinichthys, Etheostoma, Pimephales and Notemigonus) -Information on sampling sitesGenbank-numbers_AFLP-identifiersGenbank accession numbers and AFLP identifiers
DOI: 10.5061/dryad.cp00b
title: Data from: Contemporary evolution of plant growth rate following experimental removal of herbivores

description: Herbivores are credited with driving the evolutionary diversification of
 plant defensive strategies over macroevolutionary time. For this to be
 true, herbivores must also cause short-term evolution within plant
 populations, but few studies have experimentally tested this prediction.
 We addressed this gap using a long-term manipulative field experiment
 where exclosures protected 22 plant populations from natural rabbit
 herbivory for &lt;1 to 26 years. We collected seeds of Rumex acetosa
 L. (Polygonaceae) from our plots and grew them in a common greenhouse
 environment to quantify evolved differences among populations in
 individual plant growth rate, tolerance to herbivory, competitive ability,
 and the concentration of secondary metabolites (tannins and oxalate)
 implicated in defense against herbivores. In 26 years without rabbit
 herbivory, plant growth rate decreased linearly by 30%. We argue that
 plant growth rate has evolved as a defense against intense rabbit
 herbivory. In contrast, we found no change in tolerance to herbivory or
 concentrations of secondary metabolites. We also found no change in
 competitive ability, suggesting that contemporary evolution may not feed
 back to alter ecological interactions within this plant community. Our
 results combined with those of other studies show that the evolution of
 gross morphological traits such as growth rate in response to herbivory
 may be common, which calls into question assumptions about some of the
 most popular theories of plant defense.
description: all
 dataAbove and belowground
 biomass of rumex plants collected from rabbit exclusion plots at Silwood
 Park England and grown in a common garden (greenhouse) with one tab for
 all plant data and another for plot means (for regressions). A tab for
 plant oxalate concentration data measured using phtoteospectometry.
 Another tab for plant tannin concentration. Finally, another tab for
 biomass of oenothera (our competitor).all rabbit proj
 data.xls
DOI: 10.5061/dryad.pk121
title: Data from: Genetic compatibility affects division of labor in the Argentine ant Linepithema humile

description: Division of labor is central to the organization of insect societies.
 Within-colony comparisons between subfamilies of workers (patrilines or
 matrilines) revealed genetic effects on division of labor in many social
 insect species. Although this has been taken as evidence for additive
 genetic effects on division of labor, it has never been experimentally
 tested. To determine the relative roles of additive and non-additive
 genetic effects (e.g., genetic compatibility, epistasis and
 parent-of-origin imprinting effects) on worker behavior, we performed
 controlled crosses using the Argentine ant Linepithema humile. Three of
 the measured behaviors (the efficiency to collect pupae, the foraging
 propensity and the distance between non-brood-tenders and brood) were
 affected by the maternal genetic background and the two others (the
 efficiency to feed larvae and the distance between brood-tenders and
 brood) by the paternal genetic background. Moreover, there were
 significant interactions between the maternal and paternal genetic
 backgrounds for three of the five behaviors. These results are most
 consistent with parent-of-origin and genetic compatibility effects on
 division of labor. The finding of non-additive genetic effects is in
 strong contrast with the current view and has important consequences for
 our understanding of division of labor in insect societies.
description: Data_Libbrecht_and_Keller_2012
DOI: 10.5061/dryad.j2448
title: Data from: Recent non-hybrid origin of sunflower ecotypes in a novel habitat

description: The genomics of local adaptation is an increasingly active field,
 providing insights into the forces driving ecological speciation and the
 repeatability of evolution. Demography and gene flow play an important
 role in determining the paths by which parallel evolution occurs and the
 genomic signatures of adaptation. In the annual sunflowers, hybridization
 between species has repeatedly led to the colonization of extreme
 habitats, such as sand dunes. In a new case of adaptation to sand dunes
 that occurs in populations of H. petiolaris growing at Great Sand Dunes
 National Park and Preserve (Colorado), we wished to determine the age and
 long-term migration patterns of the system, as well as its ancestry. We
 addressed these questions with restriction-associated DNA (RAD) sequence
 data, aligned to a reference transcriptome. In an isolation with migration
 model using RAD sequences, coalescent analysis showed that the dune
 ecotype originated since the last ice age, which is very recent compared
 with the hybrid dune species, H. anomalus. Large effective population
 sizes and substantial numbers of gene migrants per generation between dune
 and nondune ecotypes explained the highly heterogeneous divergence
 observed among loci. Analysis of RAD-derived SNPs identified heterogeneous
 divergence between the dune and nondune ecotypes, as well as identifying
 its nearest relative. Our results did not support the hypothesis that the
 dune ecotype has hybrid ancestry, suggesting that adaptation of sunflowers
 to dunes has occurred by multiple mechanisms. The ancestry and long-term
 history of gene flow between incipient sunflower species provides valuable
 context for our understanding of ecological speciation and parallel
 adaptation.
description: GSD_RAD_SNPsGSD_RAD_SNPs contains SNP data, formatted as codominant nucleotide genotypes (e.g. "AT", "CC" etc.) and with missing data marked as "-"). The first two columns give the reference contig where each SNP aligned and its position. The final column gives Nei's Fst between the dune and non-dune ecotypes, estimated by the 'basic.stats' function in the HIERFSTAT package of the R statistical software. The data are sorted on this column. The data columns are as follows: 50 dune individuals, 15 intermediate, 35 non-dune, 10 H. petiolaris and 10 H. annuus.gsd_rad_structure_dataZip file containing files used for STRUCTURE analyses presented in Figures 4, S1, S2, S3 and S4.gsd75_sample100_3Data file for IMa2 analysis.
DOI: 10.5061/dryad.pf5cg
title: Data from: Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex

description: A major goal in evolutionary biology is to uncover the genetic basis of
 adaptation. Divergent selection exerted on ecological traits may result in
 adaptive population differentiation and reproductive isolation and affect
 differentially the level of genetic divergence along the genome.
 Genome-wide scan of large sets of individuals from multiple populations is
 a powerful approach to identify loci or genomic regions under ecologically
 divergent selection. Here, we focused on the pea aphid, a species complex
 of divergent host races, to explore the organization of the genomic
 divergence associated with host-plant adaptation and ecological
 speciation. We analyzed 390 microsatellite markers located at variable
 distances from predicted genes in replicate samples of sympatric
 populations of the pea aphid collected on alfalfa, red clover and pea,
 which correspond to three common host-adapted races reported in this
 species complex. Using a method that accounts for the hierarchical
 structure of our dataset, we found a set of 11 outlier loci that show
 higher genetic differentiation between host races than expected under the
 null hypothesis of neutral evolution. Two of the outliers are close to
 olfactory receptor genes and three other nearby genes encoding salivary
 proteins. The remaining outliers are located in regions with genes of
 unknown functions, or which functions are unlikely to be involved in
 interactions with the host plant. This study reveals genetic signatures of
 divergent selection across the genome and provides an inventory of
 candidate genes responsible for plant specialization in the pea aphid,
 thereby setting the stage for future functional studies.
description: Genotype_data_Jaquiery_et_al_2012_Mol_EcolMultilocus genotypes for pea aphids (Acyrthosiphon pisum) individuals sampled in France & Switzerland on three host plants. Precise sampling locations are indicated under the 'latitude' & 'longitude' columns. The 'pop_name' column indicates the population labels used during the analyses. Multilocus genotypes start from column G. For each microsatellite marker, two columns with a unique label (i.e. marker name) indicate the two alleles. Missing data are labelled '999'.Arlequin_input_Jaquiery_et_al_2012_Mol_EcolArlequin input fileStructure_input_Jaquiery_et_al_2012_Mol_EcolStructure input file.
DOI: 10.5061/dryad.hj2fk
title: Data from: Reconstructing the evolutionary history of an endangered subspecies across the changing landscape of the Great Central Valley of California.

description: Identifying historic patterns of population genetic diversity and
 connectivity is a primary challenge in efforts to re-establish the
 processes that have generated and maintained genetic variation across
 natural landscapes. The challenge of reconstructing pattern and process is
 even greater in highly altered landscapes where population extinctions and
 dramatic demographic fluctuations in remnant populations may have
 substantially altered, if not eliminated, historic patterns. Here, we seek
 to reconstruct historic patterns of diversity and connectivity in an
 endangered subspecies of woodrat that now occupies only 1-2 remnant
 locations within the highly altered landscape of the Great Central Valley
 of California. We examine patterns of diversity and connectivity using 14
 microsatellite loci and sequence data from a mitochondrial locus and a
 nuclear intron. We reconstruct temporal change in habitat availability to
 establish several historical scenarios that could have led to contemporary
 patterns of diversity, and use an approximate Bayesian computation
 approach to test which of these scenarios is most consistent with our
 observed data. We find that the Central Valley populations harbour unique
 genetic variation coupled with a history of admixture between two
 well-differentiated species of woodrats that are currently restricted to
 the woodlands flanking the Valley. Our simulations also show that certain
 commonly used analytical approaches may fail to recover a history of
 admixture when populations experience severe bottlenecks subsequent to
 hybridization. Overall our study shows the strength of combining empirical
 and simulation analyses to recover the history of populations occupying
 highly altered landscapes.
description: Matocq_MEC-12-0389_fig01_dataMatocq_Kelly_Phillips_Maldonado_2012Locality, individual, sequence and microsatellite dataset
DOI: 10.5061/dryad.vc86n
title: Data from: Re-mating across years and intra-lineage polygyny are associated with greater than expected levels of inbreeding in wild red deer

description: The interaction between philopatry and non-random mating has important
 consequences for the genetic structure of populations, influencing
 co-ancestry within social groups but also inbreeding. Here, using genetic
 paternity data, we describe mating patterns in a wild population of red
 deer (Cervus elaphus) which are associated with marked consequences for
 co-ancestry and inbreeding in the population. Around a fifth of females
 mate with a male with whom they have mated previously, and further,
 females frequently mate with a male with whom a female relative has also
 mated (intra-lineage polygyny). Both of these phenomena occur more than
 expected under random mating. Using simulations, we demonstrate that
 temporal and spatial factors, as well as skew in male breeding success,
 are important in promoting both re-mating behaviours and intra-lineage
 polygyny. However, the information modelled was not sufficent to explain
 the extent to which these behaviours occured. We show that re-mating and
 intra-lineage polygyny are associated with increased pairwise relatedness
 in the population and a rise in average inbreeding coefficients. The
 latter in particular resulted from a non-random spatial distribution of
 the rutting male population with respect to relatedness, such that related
 males were more likely to rut in proximity to one another. These patterns,
 alongside their consequences for the genetic structure of the population,
 have rarely been documented in wild polygynous mammals, yet they have
 important implications for our understanding of genetic structure,
 inbreeding avoidance and dispersal in such systems.
description: PedigreePedigree, calculated as described in the paper.Female Rut DataFemale Rut data from field observations. Please see ReadMe file.Male Rut DataMale rut data, from observations. Please see ReadMe file.
DOI: 10.5061/dryad.1117q
title: Data from: Comparing evolutionary rates for different phenotypic traits on a phylogeny using likelihood

description: In recent years, likelihood-based approaches have been used with
 increasing frequency to evaluate macroevolutionary hypotheses of
 phenotypic evolution under distinct evolutionary processes in a
 phylogenetic context (e.g., Brownian motion, Ornstein-Uhlenbeck, etc.),
 and to compare one or more evolutionary rates for the same phenotypic
 trait along a phylogeny. It is also of interest to determine whether one
 trait evolves at a faster rate than another trait. However, to date no
 study has compared phylogenetic evolutionary rates between traits using
 likelihood, because a formal approach has not yet been proposed. In this
 article, I describe a new likelihood procedure for comparing evolutionary
 rates for two or more phenotypic traits on a phylogeny. This approach
 compares the likelihood of a model where each trait evolves at a distinct
 evolutionary rate to the likelihood of a model where all traits are
 constrained to evolve at a common evolutionary rate. The method can also
 account for within-species measurement error and within-species trait
 covariation if available. Simulations revealed that the method has
 appropriate Type I error rates and statistical power. Importantly, when
 compared with existing approaches based on phylogenetically independent
 contrasts and methods that compare confidence intervals for model
 parameters, the likelihood method displays preferable statistical
 properties for a wide range of simulated conditions. Thus, this
 likelihood-based method extends the phylogenetic comparative biology
 toolkit and provides evolutionary biologists with a more powerful means of
 determining when evolutionary rates differ between phenotypic traits.
 Finally, I provide an empirical example illustrating the approach by
 comparing rates of evolution for several phenotypic traits in Plethodon
 salamanders.
description: 2012-SystBiol-Adams-Final-SuppMaterialSupplementary Material containing results from additional computer simulations that assess the Type I error rate and statistical power of the proposed likelihood method.Adams2012-SystBiolDataAverage linear measurements for three traits from each of 44 Plethodon species used in this study.
DOI: 10.5061/dryad.vt6bk
title: Data from: Temperature-dependent, behavioral, and transcriptional variability of a tritrophic interaction consisting of bean, herbivorous mite, and predator

description: Different organisms compensate for, and adapt to, environmental changes in
 different ways and therefore environmental changes affect animal–plant
 interactions. We consequently assessed the effect of temperature on a
 tritrophic system of the lima bean, the spider mite Tetranychus urticae,
 and the predatory mite Phytoseiulus persimilis. In this system the plant
 defends itself against T. urticae by emitting volatiles that attract P.
 persimilis. Over a range of 20 40°C the emission of volatiles by infested
 plants and the attraction of P. persimilis, peaked at 30°C but the number
 of eggs laid by T. urticae adults and the number of eggs consumed by P.
 persimilis, peaked at 35°C. This indicates that the spider mites and
 predatory mites performed best at a higher temperature than that at which
 most volatile attractants were produced. We used data from transcriptome
 pyrosequencing of the mites and found that P. persimilis up-regulated gene
 families for heat shock proteins (HSPs) and ubiquitin-associated proteins,
 whereas T. urticae did not. RNA interference-mediated gene suppression in
 P. persimilis, developed in the current study, revealed that predation on
 T. urticae eggs by P. persimilis fed with PpHsp70-1 dsRNA was reduced at
 35°C, when the expression level of PpHsp70-1 was greatly increased but not
 at 25°C. Overall, our molecular and behavioral approaches revealed that
 the mode and tolerance of lima bean, T. urticae, and the predatory mite P.
 persimilis are distinctly affected by temperature variability, thereby
 making their tritrophic interactions temperature dependent.
description: Volatile
 analysisvolatiles
 analysis.csvpredation
 assays454 Transcriptome
 pyrosequencing (T. urticae_contig)454 transcriptome
 pyrosequencing(T.
 urticae_contig).xlsx454 Transcriptome
 pyrosequencing (P. persimilis_contig)454 transcriptome
 pyrosequencing(P.
 persimilis_contig).xlsx454 Transcriptome
 pyrosequencing (T. urticae_single)454 transcriptome
 pyrosequencing(T.
 urticae_single).xlsx454 Transcriptome
 pyrosequencing (P. persimilis_single)454 transcriptome
 pyrosequencing(P.
 persimilis_single).xlsxQuantitative
 RT-PCRRT-qPCR.csvdsRNA predation experiment