fortran program to perform the CLIP test
NEXUS file: 40 taxa, 164 proteins, 43,300 unambiguously aligned amino acid positions. Ribosomal dataset (11,571 positions and 4.7 % of missing data) and non-ribosomal dataset (31,729 positions and 24.1 % of missing data).
NEXUS files: 164 orthologous genes before the use of SCaFoS (selection of sequences, species and genes).
Figures S55-109: Single gene phylogenies used for the congruence test.
U.S. North American Bird Conservation Initiative Committee. 2000. North American Bird Conservation Initiative (NABCI) Bird Conservation Region Descriptions: A Supplement to the North American Bird Conservation Initiative Bird Conservation Regions Map. U.S. Fish & Wildlife Service, Migratory Birds, Arlington VA USA. http://www.nabci-us.org/aboutnabci/bcrdescrip.pdf .
The Final Environmental Impact Statement written by the USFWS on Canada Goose management.
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Code for simulation and diversity estimation. NOTE: Please use revised_simul_DL.zip and not simul_DL.zip. Version 1 was uploaded by mistake, and this is not the simulation code corresponding to the published paper. Version 2 is the correct simulation code.
Usage: ./filter_fasta.py [path to input dir] [path to accepted taxon list]. Input files are expected to be in fasta format. The script will traverse all files in the input dir, so the input dir should contain only fasta files. The taxon list should be a line-delimited text file containing the names of tips as they correspond to those in the fasta alignments.
Data from: Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in ArabidopsisJun Liu, Choonkyun Jung, Jun Xu, Huan Wang, Shulin Deng, Lucia Bernad, Catalina Arenas-Huertero & Nam-Hai Chua
Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions of yeast and animal genomes play important roles in key biological processes. Yet, plant lincRNAs remain poorly characterized and how lincRNA biogenesis is regulated is unclear. Using a reproducibility-based bioinformatics strategy to analyze 200 Arabidopsis transcriptome datasets, we identified 13,230 intergenic transcripts of which 6,480 can be classified as lincRNAs. Expression of 2,708 lincRNAs was detected by RNA-seq experiments. Transcriptome profiling by custom microarrays revealed that...
Data from: The influence of geomorphic processes on plant distribution and abundance as reflected in plant tolerance curvesMarianne N. Chase, Edward A. Johnson & Yvonne E. Martin
Ecologists describe plant distribution using direct gradient analysis, by which a tolerance curve of species abundance is described along an environmental gradient (any environmental variable that affects plant distribution). Soil moisture is generally the gradient in low relief areas that explains the most variation. Traditional direct gradient analyses have used terrain structure (i.e. transects up or down hillslopes) as a correlate to soil moisture. Here we use a numerical tectonic and geomorphic process-based landscape development...
Data from: Direct sequencing of haplotypes from diploid individuals through a modified emulsion PCR-based single-molecule sequencing approachBrian Patrick Hansen Metzger, Gregory William Gelembiuk & Carol Eunmi Lee
While standard DNA sequencing approaches readily yield genotypic sequence data, haplotype information is often of greater utility for population genetic analyses. However, obtaining individual haplotype sequences can be costly and time consuming, and sometimes requires statistical reconstruction approaches that are subject to bias and error. Advancements have recently been made in determining individual chromosomal sequences in large-scale genomic studies, yet few options exist for obtaining this information from large numbers of highly polymorphic individuals in...
Data from: Dryness is accelerating degradation of vulnerable shrublands in semiarid Mediterranean environmentsSergio M. Vicente-Serrano, Aidel Zouber, Teodoro Lasanta & Yolanda Pueyo
Semiarid Mediterranean regions are highly susceptible to desertification processes. This study investigated the influence of increasing climate aridity in explaining the decline in vegetation cover in highly vulnerable gypsum semiarid shrublands of the Mediterranean region. For this purpose, we have used time series of the percentage of vegetation coverage obtained from remote sensing imagery (Landsat satellites). We found a dominant trend toward decreased vegetation cover, mainly in summer and in areas affected by the most...
Data from: Generic recircumscriptions of Oncidiinae (Orchidaceae: Cymbidieae) based on maximum likelihood analysis of combined DNA datasetsKurt M. Neubig, William Mark Whitten, Norris H. Williams, Mario A. Blanco, Lorena Endara, John Gordon Burleigh, Katia Silvera, John C. Cushman & Mark W. Chase
Phylogenetic relationships within the orchid subtribe Oncidiinae sensu Chase were inferred using maximum likelihood analyses of single and multilocus DNA sequence data sets. Analyses included both nuclear ribosomal internal transcribed spacer DNA and plastid regions (matK exon, trnH-psbA intergenic spacer and two portions of ycf1 exon) for 736 individuals representing approximately 590 species plus seven outgroup taxa. Based on the well resolved and highly supported results, we recognize 61 genera in Oncidiinae. Mimicry of oil-secreting...
Data from: Is local selection so widespread in river organisms? Fractal geometry of river networks leads to high bias in outlier detectionChristophe Lemaire
Identifying local adaptation is crucial in conservation biology in order to define ecotypes and establish management guidelines. Local adaptation is often inferred from the detection of loci showing a high differentiation between populations, the so-called FST outliers. Methods of detection of loci under selection are reputed to be robust in most spatial population models. However, using simulations we showed that FST outlier tests provided a high rate of false positives (up to 60%) in fractal...
Data from: Finite element modelling vs. classic beam theory: comparing methods for stress estimation in a morphologically diverse sample of vertebrate long bonesCharlotte A. Brassey, Lee Margetts, Andrew C. Kitchener, Philip J. Withers, Phillip L. Manning & William I. Sellers
Classic beam theory is frequently employed in biomechanics to model the stress behaviour of vertebrate long bones, particularly when creating intraspecific scaling models. Although methodologically straightforward, classic beam theory requires complex irregular bones to be approximated as slender beams, and the errors associated with simplifying complex organic structures to such an extent are unknown. Alternative approaches, such as Finite Element Analysis (FEA), whilst much more time-consuming to perform, require no such assumptions. This paper compares...
Dioecious plant species commonly exhibit deviations from the equilibrium expectation of 1:1 sex ratio, but the mechanisms governing this variation are poorly understood. Here, we use comparative analyses of 243 species, representing 123 genera and 61 families to investigate ecological and genetic correlates of variation in the operational (flowering) sex ratio. After controlling for phylogenetic non-independence, we examined the influence of growth form, clonality, fleshy fruits, pollen and seed dispersal vector, and the possession of...
Organisms respond to changes in their environment over a wide range of biological and temporal scales. Such phenotypic plasticity can involve developmental, behavioral, physiological, and genetic shifts. The adaptive value of a plastic response is known to depend on the nature of the information that is available to the organism as well as the direct and indirect costs of the plastic response. We modeled the dynamic process of simple gene regulatory networks as they responded...
Data from: Parental frequencies and spatial configuration shape bumblebee behavior and floral isolation in hybridizing RhinanthusLaurent Christian Natalis & Renate Andrea Wesselingh
To shed light on the role played by pollinators in the diversification of angiosperms, focus is needed on how floral isolation varies locally in the early stages of plant divergence. The few studies performed so far have often used species pairs with distinct pollination syndromes and contrasting floral displays. Here, we focus on a hybridizing pair (Rhinanthus minor and R. angustifolius) with strong similarities in flower morphology and pollinators (bumblebees). We examined how ethological isolation...
Data from: The HypoMethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Picea abies)Hanna Larsson, Emanuele De Paoli, Michele Morgante, Martin Lascoux & Niclas Gyllenstrand
To evaluate the usefulness of Reduced Representation Libraries (RRL) in species with large and highly repetitive genomes such as conifers, we employed Hypomethylated Partial Restriction (HMPR) on the genome of Norway spruce (Picea abies). The HMPR method preferentially removes the repetitive fraction of the genome, which is commonly hypermethylated. Hence, RRLs should be enriched for the hypomethylated gene space. For comparison a standard shotgun library was constructed and samples of the respective libraries were obtained...
Differences in rhythmicity (relative variance in cycle period) between mammal, fish, and lizard feeding systems have been hypothesized to be associated with differences in their sensorimotor control systems. We tested this hypothesis by examining whether the locomotion of tachymetabolic tetrapods (birds and mammals) is more rhythmic than that of bradymetabolic tetrapods (lizards, alligators, turtles, salamanders). Species averages of intra-individual coefficients of variation in cycle period were compared while controlling for gait and substrate. Variance in...
Uncontrolled transposable element (TE) insertions and excisions can cause chromosome breaks and mutations with dramatic deleterious effects. The PIWI interacting RNA (piRNA) pathway functions as an adaptive TE silencing system during germline development. Several essential piRNA pathway proteins appear to be rapidly evolving, suggesting that TEs and the silencing machinery may be engaged in a classical “evolutionary arms race.” Using a variety of molecular evolutionary and population genetic approaches, we find that the piRNA pathway...
French National Centre for Scientific Research39
University of British Columbia28
University of California, Davis22
University of Cambridge19
University of Lausanne19
University of Exeter19
University of California, Berkeley18
University of Edinburgh18