cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2118mj5
title: Data from: Transmission ratio distortion is frequent in Arabidopsis thaliana controlled crosses

description: The equal probability of transmission of alleles from either parent during
 sexual reproduction is a central tenet of genetics and evolutionary
 biology. Yet, there are many cases where this rule is violated. The
 preferential transmission of alleles or genotypes is termed transmission
 ratio distortion (TRD). Examples of TRD have been identified in many
 species, implying that they are universal, but the resolution of
 species-wide studies of TRD are limited. We have performed a species-wide
 screen for TRD in over 500 segregating F2 populations of Arabidopsis
 thaliana using pooled reduced-representation genome sequencing. TRD was
 evident in up to a quarter of surveyed populations. Most populations
 exhibited distortion at only one genomic region, with some regions being
 repeatedly affected in multiple populations. Our results begin to
 elucidate the species-level architecture of biased transmission of genetic
 material in A. thaliana, and serve as a springboard for future studies
 into the biological basis of TRD in this species.
description: READMESummary of scripts used
 to generate the allele frequency files found in allele_freq.zip and
 allele_freq_BSA.zip. Scripts and associated input files are located in
 code.zip.CodeDirectory containing
 scripts and associated input files.code.zipallele_freqDirectory containing genotype data for F2 pools (reduced representation sequencing).allele_freq_BSADirectory containing genotype data for F2 pools (whole genome sequencing).
DOI: 10.5061/dryad.0q7pc
title: Data from: Integrative taxonomy and preliminary assessment of species limits in the Liolaemus walkeri complex (Squamata, Liolaemidae) with descriptions of three new species from Peru

description: Species delimitation studies based on integrative taxonomic approaches
 have received considerable attention in the last few years, and have
 provided the strongest hypotheses of species boundaries. We used three
 lines of evidence (molecular, morphological, and niche envelopes) to test
 for species boundaries in Peruvian populations of the Liolaemus walkeri
 complex. Our results show that different lines of evidence and analyses
 are congruent in different combinations, for unambiguous delimitation of
 three lineages that were “hidden” within known species, and now deserve
 species status. Our phylogenetic analysis shows that L. walkeri, L. tacnae
 and the three new species are strongly separated from other species
 assigned to the alticolor-bibronii group. Few conventional morphological
 characters distinguish the new species from closely related taxa and this
 highlights the need to integrate other sources of data to erect strong
 hypothesis of species limits. A taxonomic key for known Peruvian species
 of the subgenus Lioalemus is provided.
description: Figure
 1.Concatenated maximum
 likelihood (-Log L = 8452.31415) tree based on cyt-b and 12S haplotypes of
 focal taxa (Ancash, Ayacucho Cusco) and species assigned to the alticolor
 group and outgroups. Bootstrap ≥ 70 (*) and posterior probabilities values
 are shown above and below branches respectively.Fig1.pngFigure 2.Detailed view of the cloaca region showing absence (A, D) or presence (B, C, E) of precloacal pores: (A) Ancash, (B) Ayacucho, (C) Cusco, (D) L. tacnae, and (E) L. walkeri.Fig2.pngFigure 3.Ventral view showing the color patterns of the belly and tail: (A) Ancash, (B) Ayacucho, (C) Cusco, (D) L. tacnae, and (E) L. walkeri.Fig3.pngFigure 4.Lateral view showing the color patterns of (A) Ayacucho, (B) Cusco, and (C) L. walkeri.Fig4.pngFigure 5.First and second principal components (PC) and correspondence axes (CA) of morphometric (A) and meristic (B) data of Ancash, Ayacucho, Cusco, L. tacnae and L. walkeri respectively.Fig5.pngFigure 6Predicted area and known geographic distribution (A) used to develop distributional models of Ancash (B), Ayacucho (C), Cusco (D), L. tacnae (E), and L. walkeri (F).Fig6.pngFigure 7.ROC curves and AUC values for (A) Ancash, (B) Ayacucho, (C) Cusco, (D) L. tacnae and (E) L. walkeri.Fig7.pngFigure 8.Dorsal (A) and ventral (B) views of the holotype of Liolaemus chavin sp. n. (C) Type locality.Fig8.pngFigure 9.Lateral (A), dorsal (B), and ventral (C) views of the holotype of Liolaemus pachacutec sp. n.. (D) Habitat of L. pachacutecFig9.pngFigure 10.Lateral (A), dorsal (B), and ventral (C) views of the holotype of Liolaemus wari sp. n. (D) Type locality.Fig10.pngFigure 11.Geographic distribution of L. chavin, L. pachacutec, L. tacnae, L. walkeri, and L. wari.Fig11.pngSupplementaryFile2Examined museum specimens and locality data from L. alticolor, L. chavin, L. incaicus, L. pachacutec, L. walkeri and L. wari.
DOI: 10.5061/dryad.h0dj3p3
title: Data from: Estimating mortality rates among passerines caught for ringing with mist-nets using data from previously-ringed birds

description: 1. Mist-netting is the most commonly used method for catching birds for
 scientific ringing but, despite decades of use, there have been few
 attempts to quantify the associated potential risks to the individuals
 caught. Any incidence of mortality through capture and handling, however
 low, is of potential ethical concern and may also introduce biases into
 the data. 2. We estimate the mortality rate associated with capture of
 previously ringed (recaptured) passerines from the British and Irish
 Ringing Scheme (c. 1.5 million records) caught using mist-nets. The
 importance of species, age, mass, month, time, previous captures and an
 index of predator occurrence were tested using generalised linear
 mixed-effects models. 3. The average mortality rate was 0.0011, most of
 which was reported to occur before the individuals had been extracted from
 the nets (c. 70% of incidents). Juveniles appeared to be at higher risk
 and the incidence of predation from mist-nets was seasonal, with increased
 risk during the winter. Species differed in their reported mortality rates
 with the apparent risk being greatest for Chiffchaff Phylloscopus
 collybita (0.0029) and Bullfinch Pyrrhula pyrrhula (0.0027). 4 To improve
 our understanding (and hence minimise risk in future) we recommend
 collecting more complete data on incidences of mortality, and also
 injuries; exercising increased care when the species we have identified as
 being at greater risk are likely to be captured, and ensuring there are
 robust procedures for the checking of nets (as most reported incidents of
 mortality occur before handling). We also recommend that all Ringing
 Schemes should collate and make available data on capture-related
 mortality.5. Overall rates of mortality associated with capture, though,
 were low and support the use of mist-netting as a safe capture technique,
 without undue bias from mortality, when used by appropriately trained
 individuals.
description: Data file for Clewley_et
 _alA
 csv file containing the following columns: "sq10km" - 10km
 square of UK national grid; "species" name; "sex" -
 Male/Female/Unknown; "time" - hour of day; "month";
 "year"; "casualty" - 1 yes, 0 no;
 "predated"- 1 yes, 0 no; "died_other" - 1 yes, 0 no;
 "age_class" -ad(ult), juv(enile), PJ post-jevenile [11]
 "mass" "capture_history" "sparrowhawk"
 "family"Clewley_et
 _al.csv
DOI: 10.5061/dryad.8hn63
title: Data from: Small carbonaceous fossils (SCFs) from the Terreneuvian (lower Cambrian) of Baltica

description: We describe a new assemblage of small carbonaceous fossils (SCFs) from
 diagenetically minimally altered clays and siltstones of Terreneuvian age
 from the Lontova and Voosi formations of Estonia, Lithuania and Russia.
 This is the first detailed account of an SCF assemblage from the
 Terreneuvian, and includes a number of previously undocumented Cambrian
 organisms. Recognisably bilaterian-derived SCFs include abundant
 protoconodonts (total-group Chaetognatha), and distinctive cuticular
 spines of scalidophoran worms. Alongside these metazoan remains are a
 range of protistan-grade fossils, including Retiranus balticus gen. et sp.
 nov., a distinctive funnel-shaped or sheet-like problematicum
 characterized by terminal or marginal vesicles, and Lontohystrichosphaera
 grandis gen. et sp. nov., a large (100–550 µm) ornamented vesicular
 microfossil. Together these data offer a fundamentally enriched view of
 Terreneuvian life in the epicratonic seas of Baltica, from an episode
 where records of non-biomineralized life are currently sparse. Even so,
 the recovered assemblages contain a lower diversity of metazoans than SCF
 biotas from younger (Stage 4) Baltic successions that represent broadly
 equivalent environments, echoing the diversification signal recorded in
 the coeval shelly and trace-fossil records. Close comparison to the
 biostratigraphic signal from Fortunian small shelly fossils (SSFs)
 supports a late Fortunian age for most of the Lontova/Voosi succession,
 rather than a younger (wholly Stage 2) range.
description: Protohertzina compressa
 holotypeHolotype specimen of
 Protohertzina compressa. Scale bar = 400 µm. Slide number: NRM-PZ X
 7032.Retiranus balticus
 holotypeHolotype specimen of
 Retiranus balticus. Scale bar = 400 µm. Slide number: NRM-PZ X
 7062.Lontohystrichosphaera
 grandis holotypeHolotype specimen of
 Lontohystrichosphaera grandis. Scale bar = 500 µm. Slide number: NRM-PZ X
 7023.
DOI: 10.5061/dryad.j92k8
title: Data from: Ecogeographic isolation and speciation in the genus Mimulus

description: Despite a long history of examining the geographic context of speciation,
 differences in geographic range have rarely been considered a legitimate
 isolating mechanism. This likely results from the complex relationship
 between historical and ecological processes in determining the spatial
 distribution of species. Ecogeographic isolation is the proportion of
 geographic isolation that results from genetically based ecological
 differences between taxa and should therefore be measured as an isolating
 mechanism under the biological species concept. In this study, species
 distribution modeling was used to evaluate the potential ranges of 12
 recently diverged pairs of species in the genus Mimulus. Variation in the
 distribution models showed that these species differ significantly in the
 niches they occupy. These differences result in substantial ecogeographic
 isolation, with an average strength of 0.67, revealing that, on average,
 Mimulus species exhibit only 33% overlap in the extent of suitable habitat
 with their closest relatives. Because prezygotic barriers act early in the
 life cycle of organisms, this strong barrier has the potential to
 contribute greatly to the total isolation experienced between diverging
 species. Therefore, ecogeographic isolation appears to play an important
 role in Mimulus, and estimating the strength of this barrier is essential
 to our general understanding of speciation.
description: populationsPopulation accessions used in studyenv_var_buffersenvironmental variables used in species distribution modelingmaxent_outContinuous species distribution modelsvariable_extractionsEnvironmental variable data from specific population locations
DOI: 10.5061/dryad.1mn1n
title: Data from: Fat, fibre and cancer risk in African Americans and rural Africans

description: Rates of colon cancer are much higher in African Americans (65:100,000)
 than in rural South Africans (&lt;5:100,000). The higher rates are
 associated with higher animal protein and fat, and lower fibre
 consumption, higher colonic secondary bile acids, lower colonic
 short-chain fatty acid quantities and higher mucosal proliferative
 biomarkers of cancer risk in otherwise healthy middle-aged volunteers.
 Here we investigate further the role of fat and fibre in this association.
 We performed 2-week food exchanges in subjects from the same populations,
 where African Americans were fed a high-fibre, low-fat African-style diet
 and rural Africans a high-fat, low-fibre western-style diet, under close
 supervision. In comparison with their usual diets, the food changes
 resulted in remarkable reciprocal changes in mucosal biomarkers of cancer
 risk and in aspects of the microbiota and metabolome known to affect
 cancer risk, best illustrated by increased saccharolytic fermentation and
 butyrogenesis, and suppressed secondary bile acid synthesis in the African
 Americans.
description: HITChip data
 matrixA csv file containing
 HITChip phylogenetic microarray data matrix for the study samples. The
 data provides the absolute HITChip phylogenetic microarray signal estimate
 for 130 genus-like groups, preprocessed as described in the main
 article.HITChip.csvMetadataCSV file containing the sample metadata in the HITChip data matrix. The variables are rounded or aggregated to ensure subject anonymity. 'NA' refers to missing values. The variable units and other information are as follows: - SampleID: unique sample identified corresponding to samples in the HITChip data matrix - subject: Subject identifier (some subjects have multiple time points) - bmi: Standard body-mass classification (underweight: &lt;18.5; lean: 18.5-25; overweight: 25-30; obese: 30-35; severe obese: 35-40; morbid obese 40-45; superobese &gt;45). - sex (male/female) - nationality: African American (AAM); Native African (AFR) - timepoint.group: Time point (1/2) within the group (ED/HE/DI) - timepoint.total: Time point in the overall data set (ED1 - HE1 -HE2 - DI1 - DI2 - ED2 ie. 1- 2- 3- 4- 5- 6) - group: Sample treatment group: as described in the main article; Dietary intervention (DI) / Home environment (HE) / Solid stool pre-colonoscopy (ED)NMR dataJKNCRC_JLI121127_Okeefe.zip
DOI: 10.5061/dryad.t99b1
title: Data from: Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome

description: Although common knowledge dictates that the lichen thallus is formed
 solely by a fungus (mycobiont) that develops a symbiotic relationship with
 an alga and/or cyanobacterium (photobiont), the non-photoautotrophic
 bacteria found in lichen microbiomes are increasingly regarded as integral
 components of lichen thalli. For this study, comparative analyses were
 conducted on lichen-associated bacterial communities to test for effects
 of photobiont-types (i.e., green algal vs. cyanobacterial),
 mycobiont-types, and large-scale spatial distances (from tropical to
 arctic latitudes). Amplicons of the 16S (SSU) rRNA gene were examined
 using both Sanger sequencing of cloned fragments and barcoded
 pyrosequencing. Rhizobiales is typically the most abundant and
 taxonomically diverse order in lichen microbiomes; however, overall
 bacterial diversity in lichens is shown to be much higher than previously
 reported. Members of Acidobacteriaceae, Acetobacteraceae, Brucellaceae,
 and sequence group LAR1 are the most commonly found groups across the
 phylogenetically and geographically broad array of lichens examined here.
 Major bacterial community trends are significantly correlated with
 differences in large-scale geography, photobiont-type, and mycobiont-type.
 The lichen as a microcosm represents a structured, unique microbial
 habitat with greater ecological complexity and bacterial diversity than
 previously appreciated and can serve as a model system for studying larger
 ecological and evolutionary principles.
description: Lichen-Associated
 Bacterial 16S Sequences & Analysis FilesThe archive contains 5
 major elements: [Clon16SFinal.fasta - A fasta-formatted file containing
 all cloned sequences from the order Rhizobiales generated as part of this
 study] [FIGS1.pdf - An image of a phylogeny of all cloned sequences from
 the order Rhizobiales generated as part of this study (the methodology for
 generating the figure is outlined in the associated publication)]
 [HodkinsonLichen16S_454_raw_data_archive - A directory containing archived
 fna + qual files of raw sequence data with associated oligos files (used
 for processing with Mothur 1.15)] [454_clean - A directory containing the
 cleaned sequence data set (in the form of a .fasta and a .groups file)
 after quality checks performed using Mothur 1.15] [Supporting_Information
 - A directory containing all of the supplementary files referenced in the
 text of the associated publication along with instructions for using the
 various scripts written for this study, all found within a system of
 descriptively-titled sub-directories]Hodkinson_et_al_EMI_Dryad.zip
DOI: 10.5061/dryad.s5d9q
title: Data from: Molecular characterization of copepod photoreception

description: Copepod crustaceans are an abundant and ecologically significant group
 whose basic biology is guided by numerous visually guided behaviors. These
 behaviors are driven by copepod eyes, including naupliar eyes and
 Gicklhorn’s organs, which vary widely in structure and function among
 species. Yet little is known about the molecular aspects of copepod
 vision. In this study we present a general overview of the molecular
 aspects of copepod vision by identifying phototransduction genes from
 newly generated and publicly available RNA-sequencing data and assemblies
 from 12 taxonomically diverse copepod species. We identify a set of 10
 expressed transcripts that serve as a set of target genes for future
 studies of copepod phototransduction. Our more detailed evolutionary
 analyses of the opsin gene responsible for forming visual pigments found
 that all of the copepod species investigated express two main groups of
 opsins: middle-wavelength-sensitive (MWS) opsins and pteropsins.
 Additionally, there is evidence from a few species (e.g., Calanus
 finmarchicus, Eurytemora affinis, Paracyclopina nana, and Lernaea
 cyprinacea) for the expression of two additional groups of opsins—the
 peropsins and rhodopsin 7 (Rh7) opsins—at low levels or distinct
 developmental stages. An ontogenetic analysis of opsin expression in
 Calanus finmarchicus found the expression of a single dominant MWS opsin,
 as well as evidence for differences in expression across development in
 some MWS, pteropsin, and Rh7 opsins, with expression peaking in early
 naupliar through early copepodite stages.
description: Copepod
 phototransduction transcript sequence dataSeparate nucleotide and
 amino acid sequence files for each species for contigs identified from
 RNA-seq assemblies as involved in phototransduction. All files are as
 fasta, and the transcript identity is indicated in the sequence
 header.Copepod_phototrans_transcript_seq_data.zipLernaea cyprinacea trinity assemblyTrinity assembly file with all contigs from reassembled Lernaea cyprinacea RNA-seq data.Lcyp_Trinity.fastaCopepod Opsin alignmentPhylip alignment file used to make copepod opsin phylogenyCopepodOpsins.phyCopepod Opsin Phylogeny Newick Tree fileRAxML phylogeny produced from alignment as newick tree file with branch lengths.CopepodOpsinNewick.resultCopepod_opsins_seq_databaseDatabase providing species information and accession numbers for each sequence ID used in the alignment.
DOI: 10.5061/dryad.gs51v
title: Data from: Modeling central metabolism and energy biosynthesis across microbial life

description: Background: Automatically generated bacterial metabolic models, and even
 some curated models, lack accuracy in predicting energy yields due to poor
 representation of key pathways in energy biosynthesis and the electron
 transport chain (ETC). Further compounding the problem, complex
 interlinking pathways in genome-scale metabolic models, and the need for
 extensive gapfilling to support complex biomass reactions, often results
 in predicting unrealistic yields or unrealistic physiological flux
 profiles Results: To overcome this challenge, we developed methods and
 tools (http://coremodels.mcs.anl.gov) to build high quality core metabolic
 models (CMM) representing accurate energy biosynthesis based on a well
 studied, phylogenetically diverse set of model organisms. We compare these
 models to explore the variability of core pathways across all microbial
 life, and by analyzing the ability of our core models to synthesize ATP
 and essential biomass precursors, we evaluate the extent to which the core
 metabolic pathways and functional ETCs are known for all microbes. 6,600
 (80%) of our models were found to have some type of aerobic ETC, whereas
 5,100 (62%) have an anaerobic ETC, and 1,279 (15%) do not have any ETC.
 Using our manually curated ETC and energy biosynthesis pathways with no
 gapfilling at all, we predict accurate ATP yields for nearly 5586 (70%) of
 the models under aerobic and anaerobic growth conditions. This study
 revealed gaps in our knowledge of the central pathways that result in
 2,495 (30%) CMMs being unable to produce ATP under any of the tested
 conditions. We then established a methodology for the systematic
 identification and correction of inconsistent annotations using core
 metabolic models coupled with phylogenetic analysis. Conclusions: We
 predict accurate energy yields based on our improved annotations in energy
 biosynthesis pathways and the implementation of diverse ETC reactions
 across the microbial tree of life. We highlighted missing annotations that
 were essential to energy biosynthesis in our models. We examine the
 diversity of these pathways across all microbial life and enable the
 scientific community to explore the analyses generated from this
 large-scale analysis of over 8000 microbial genomes.
description: Microbial life tree (16S
 OTU98.5)Phylogenetic tree (nwk
 format) used to show pathway conservation analysis on central
 metabolismtree.0.01Microbial life tree (16S OTU98.5) labelsFile contains the list of genomes and their RAST given idssubtree.genomes16S alignment fileSequence alignment file that has been used to generate the initial master tree. Based on this master tree, the microbial life tree that was used in this study (16S OTU98.5) was generated using a distance-based clustering algorithm.16s.ali