cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1g3v3
title: Data from: Divergence with gene flow in a population of thermophilic bacteria: a potential role for spatially varying selection

description: A fundamental goal of evolutionary biology is to understand how ecological
 diversity arises and is maintained in natural populations. We have
 investigated the contributions of gene flow and divergent selection to the
 distribution of genetic variation in an ecologically-differentiated
 population of a thermophilic cyanobacterium (Mastigocladus laminosus)
 found along the temperature gradient of a nitrogen-limited stream in
 Yellowstone National Park. For most loci sampled, gene flow appears to be
 sufficient to prevent substantial genetic divergence. However, one locus
 (rfbC) exhibited a comparatively low migration rate as well as other
 signatures expected for a gene experiencing spatially varying selection,
 including an excess of common variants, an elevated level of polymorphism
 and extreme genetic differentiation along the gradient. rfbC is part of an
 expression island involved in the production of the polysaccharide
 component of the protective envelope of the heterocyst, the specialized
 nitrogen-fixing cell of these bacteria. SNP-genotyping in the vicinity of
 rfbC revealed a ~5 kbp region including a gene content polymorphism that
 is tightly associated with environmental temperature and therefore likely
 contains the target of selection. Two genes have been deleted both in the
 predominant haplotype found in the downstream region of White Creek and in
 strains from other Yellowstone populations of M. laminosus, which may
 result in the production of heterocysts with different envelope
 properties. This study implicates spatially varying selection in the
 maintenance of variation related to thermal performance at White Creek
 despite on-going or recent gene flow.
description: Aligned sequence data
 for Table 1 multilocus data set, White Creek population of M.
 laminosusFASTA-formatted, aligned
 DNA sequence data for laboratory strains of the cyanobacterium
 Mastigocladus laminosus isolated from along the temperature gradient of
 White Creek, Lower Geyser Basin, Yellowstone NP.Sequence
 alignments.tarGenome sequence assembly
 draft for the pooled sample of M. laminosus strains WC111, WC344 and
 WC542Velvet de novo genome
 assembly of 2x60 Illumina sequence reads. Includes all contigs greater
 than 1 kbp in length.Mlam.Sequence_Assembly.txtSNP genotype data for Figure 1 and Figure 3 data sets, White Creek M. laminosus strain collectionIncludes SNP genotype scores for the White Creek M. laminosus strain collection for SNP markers used in Figure 1 and figure 3.SNP_genotypes.xlsx
DOI: 10.5061/dryad.47jh1
title: Data from: A unifying framework for quantifying the nature of animal interactions

description: Collective phenomena, whereby agent-agent interactions determine spatial
 patterns, are ubiquitous in the animal kingdom. On the other hand,
 movement and space use are also greatly influenced by the interactions
 between animals and their environment. Despite both types of interaction
 fundamentally influencing animal behaviour, there has hitherto been no
 unifying framework for the models proposed in both areas. Here, we
 construct a general method for inferring population-level spatial patterns
 from underlying individual movement and interaction processes, a key
 ingredient in building a statistical mechanics for ecological systems. We
 show that resource selection functions, as well as several examples of
 collective motion models, arise as special cases of our framework, thus
 bringing together resource selection analysis and collective animal
 behaviour into a single theory. In particular, we focus on combining the
 various mechanistic models of territorial interactions in the literature
 with step selection functions, by incorporate interactions into the step
 selection framework and demonstrating how to derive territorial patterns
 from the resulting models. We demonstrate the efficacy of our model by
 application to a population of insectivore birds in the Amazon rainforest.
description: Data on Amazonian bird
 positionsEach spreadsheet
 contains a different flock. Positions as grid references are in the first
 two columns, times in the third.SI_data.zip
DOI: 10.5061/dryad.74j06
title: Data from: Stick insect genomes reveal natural selection's role in parallel speciation

description: Natural selection can drive the repeated evolution of reproductive
 isolation, but the genomic basis of parallel speciation remains poorly
 understood. We analyzed whole-genome divergence between replicate pairs of
 stick insect populations that are adapted to different host plants and
 undergoing parallel speciation. We found thousands of modest-sized genomic
 regions of accentuated divergence between populations, most of which are
 unique to individual population pairs. We also detected parallel genomic
 divergence across population pairs involving an excess of coding genes
 with specific molecular functions. Regions of parallel genomic divergence
 in nature exhibited exceptional allele frequency changes between hosts in
 a field transplant experiment. The results advance understanding of
 biological diversification by providing convergent observational and
 experimental evidence for selection’s role in driving repeatable genomic
 divergence.
description: bgsr.tarC++ source code to analyze the transplant experimetns. This program analyzes allele frequency changes in experimental populations. The model assumes a set of experimental populations were founded from a single source population and that a sample of individuals from the source population exist. Further, the model assumes that individuals are sampled from each experimental population after a single generation. This software requires the GSL and HDF5. To compile the software try: h5c++ -O3 -o bgsr main.C mcmc.C func.C -lm -lgsl -lgslcblasfstanalysisR code to calculate SNP-specific Fst.fitHmmR code to fit and summarize the HMM for divergence state based on SNP Fst estimates.annotationScriptsThis compressed directory contains perl scripts to retrieve gene annotation information for focal loci, an R script for an annotation-based randomization test, example files, and a README file.
DOI: 10.5061/dryad.20152
title: Data from: Female-limited colour polymorphism in the crab spider Synema globosum (Araneae: Thomisidae)

description: Conspicuous colour variation, caused by the influence of the environment
 on phenotype or by genetic differences among individuals, is frequently
 observed in nature. If genetic in origin, colour variation can facilitate
 the study of mechanisms that contribute to the maintenance of true
 polymorphisms. Here we describe, for the first time, the female-limited
 colour polymorphism in the crab spider, Synema globosum. We looked for
 associations between life-history traits and female colour morph, and
 identified potential agents of selection that could influence the
 maintenance of the polymorphism. Our results showed that the polymorphism
 is discrete and heritable, and that differences in colour among morphs are
 likely to be detectable by honeybees, birds, and conspecifics. We found
 limited evidence of differences among morphs in morphology and ecology,
 and found no differences in components of reproduction. Based on the lines
 of evidence obtained in this study, we suggest that selection exerted by
 prey, predators, and/or mates is likely to influence the maintenance of
 the polymorphism observed in S. globosum.
description: Reflectance spectra of
 S. globosum colour morphsAverage percentage
 reflectance spectra measured from three different standardised locations
 within the colour area of the opisthosoma of each spider from the three
 colour morphs.ReflectanceSpectra.xlsxData of heritability of S. globosum colour morphsNumber of daughters of each colour morph, males, and undetermined offspring scored from each clutch produced by mothers of known colour morphs in the laboratory.Hertability.xlsxData on life history traits of S. globosum colour morphsFirst sheet contains the data of size and weight of individuals of the three colour morphs. The second sheet shows the data on the behaviour of the three morphs in the field: time spent in a patch, time spent on a flower, and number of flowers occupied. The third sheet shows the data on the probability of an individual found in a habitat patch at the beginning of the survey to be missing at the end for each morph (1 = missing, 0 = not missing). The fourth sheet shows the number of females from each morph that produced one, two, and three clutches of eggs in the laboratory. The fifth sheet contains the data on the number of clutch and the days to hatching for each morph. The sixth sheet shows cephalothorax length (for those females that were measured) and clutch size for each morph. The seventh sheet contains the data of mother cephalothorax length, and individual spiderling weight and length for each mother morph. The eighth sheet shows the data of mother cephalothorax length and spiderling survival for each mother colour morph (1 = survived, 0 = not survived).LifeHistoryTraits.xlsx
DOI: 10.5061/dryad.4g5gb
title: Data from: Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange, and distinct demographic histories

description: Widely distributed taxa provide an opportunity to compare biogeographic
 responses to climatic fluctuations on multiple continents and to
 investigate speciation. We conducted the most geographically and
 genomically comprehensive study to date of the red fox (Vulpes vulpes),
 the world's most widely distributed wild terrestrial carnivore.
 Analyses of 697 bp of mitochondrial sequence in ~1000 individuals
 suggested an ancient Middle Eastern origin for all extant red foxes and a
 400 kya (SD = 139 kya) origin of the primary North American (Nearctic)
 clade. Demographic analyses indicated a major expansion in Eurasia during
 the last glaciation (~50 kya), coinciding with a previously described
 secondary transfer of a single matriline (Holarctic) to North America. In
 contrast, North American matrilines (including the transferred portion of
 Holarctic clade) exhibited no signatures of expansion until the end of the
 Pleistocene (~12 kya). Analyses of 11 autosomal loci from a subset of
 foxes supported the colonization timeframe suggested by mtDNA (and the
 fossil record) but, in contrast, reflected no detectable secondary
 transfer, resulting in the most fundamental genomic division of red foxes
 at the Bering Strait. Endemic continental Y-chromosome clades further
 supported this pattern. Thus, intercontinental genomic exchange was
 overall very limited, consistent with long-term reproductive isolation
 since the initial colonization of North America. Based on continental
 divergence times in other carnivoran species pairs, our findings support a
 model of peripatric speciation and are consistent with the previous
 classification of the North American red fox as a distinct species, V.
 fulva.
description: Statham_nuclear_species_tree_800millionStatham_MrBayes_tree_12millionStatham_Beast_mtDNA_modern_only_100millionStatham_Beast_mtDNA_modern+ancient_100MStatham_Beast_Input_Nuclear_strict_800M_20131127ii*Beast input fileStatham_mtDNA_unique_haplotypes_alignmentStatham_Fox_mtDNA_datasetRed fox mtDNA dataStatham_Fox_Autosomal_Y_and_mtDNAcombinations
DOI: 10.5061/dryad.vp645
title: Data from: Speciation and introgression between Mimulus nasutus and Mimulus guttatus

description: Mimulus guttatus and M. nasutus are an evolutionary and ecological model
 sister species pair differentiated by ecology, mating system, and partial
 reproductive isolation. Despite extensive research on this system, the
 history of divergence and differentiation in this sister pair is unclear.
 We present and analyze a population genomic data set which shows that M.
 nasutus budded from a central Californian M. guttatus population within
 the last 200 to 500 thousand years. In this time, the M. nasutus genome
 has accrued genomic signatures of the transition to predominant selfing,
 including an elevated proportion of nonsynonymous variants, an
 accumulation of premature stop codons, and extended levels of linkage
 disequilibrium. Despite clear biological differentiation, we document
 genomic signatures of ongoing, bidirectional introgression. We observe a
 negative relationship between the recombination rate and divergence
 between M. nasutus and sympatric M. guttatus samples, suggesting that
 selection acts against M. nasutus ancestry in M. guttatus.
description: HMM_and_other_major_analysesThis set of scripts recreates most major analyses from our manuscript. This includes PCA analyses, the distribution of nj tress, the distribution of diversity and our hidden Markov Model. This all works with our associated data file.recreateAnalysesANDfigures.RProcessed_dataAn R-object containing 'nj.pca.snps' and 'pairwise.focal.mim'. pairwise.focal.mim is a matrix with genotypes for all samples at all SNPS used in nj and PCA analyses. 'pairwise.focal.mim' a list containing 'comps' and 'bounds.' 'comps' - itself a list of all pairwise comparisons between focal samples. For each pairwise comparison between focal samples the number of sites compared & differences between two samples in 1kb windows is contained in a matrix. 'bound' a matrix describing the location of each 1 kb region.brandainEtAlPLoSGen2014.Robj
DOI: 10.5061/dryad.cp325
title: Data from: Perturbing the cellular cevels of steroid receptor coactivator-2 impairs murine endometrial function

description: As pleiotropic coregulators, members of the p160/steroid receptor
 coactivator (SRC) family control a broad spectrum of transcriptional
 responses that underpin a diverse array of physiological and
 pathophysiological processes. Because of their potent coregulator
 properties, strict controls on SRC expression levels are required to
 maintain normal tissue functionality. Accordingly, an unwarranted increase
 in the cellular levels of SRC members has been causally linked to the
 initiation and/or progression of a number of clinical disorders. Although
 knockout mouse models have underscored the critical non-redundant roles
 for each SRC member in vivo, there are surprisingly few mouse models that
 have been engineered to overexpress SRCs. This deficiency is significant
 since SRC involvement in many of these disorders is based on unscheduled
 increases in the levels (rather than the absence) of SRC expression. To
 address this deficiency, we used recent mouse technology that allows for
 the targeted expression of human SRC-2 in cells which express the
 progesterone receptor. Through cre-loxP recombination driven by the
 endogenous progesterone receptor promoter, a marked elevation in
 expression levels of human SRC-2 was achieved in endometrial cells that
 are positive for the progesterone receptor. As a result of this increase
 in coregulator expression, female mice are severely subfertile due to a
 dysfunctional uterus, which exhibits a hypersensitivity to estrogen
 exposure. Our findings strongly support the proposal from clinical
 observations that increased levels of SRC-2 are causal for a number of
 endometrial disorders which compromise fertility. Future studies will use
 this mouse model to decipher the molecular mechanisms that underpin the
 endometrial defect. We believe such mechanistic insight may provide new
 molecular descriptors for diagnosis, prognosis, and/or therapy in the
 clinical management of female infertility.
description: Data from: Perturbing
 the cellular levels of steroid receptor coactivator-2 impairs murine
 endometrial functionZiped folder containing
 all files. named according to figure number. See README.TXT for
 detailsSzwarc PLOS ONE
 data.zip
DOI: 10.5061/dryad.7th55
title: Data from: Exploring Symbiodinium diversity and host specificity in Acropora corals from geographical extremes of Western Australia with 454 amplicon pyrosequencing

description: Scleractinian corals have demonstrated the ability to shuffle their
 endosymbiotic dinoflagellate communities (genus Symbiodinium) during
 periods of acute environmental stress. This has been proposed as a
 mechanism of acclimation, which would be increased by a diverse and
 flexible association with Symbiodinium. Conventional molecular techniques
 used to evaluate Symbiodinium diversity lack the sensitivity to capture
 accurate estimates of diversity and are unable to identify genetic
 lineages present at background levels below 10%. Next generation
 sequencing (NGS) offers a solution to this problem and can resolve
 microorganism diversity at much finer scales. Here we apply NGS to
 evaluate Symbiodinium diversity and host specificity in Acropora corals
 from contrasting regions of Western Australia. The application of 454
 pyrosequencing allowed for detection of Symbiodinium operational taxonomic
 units (OTUs) occurring at frequencies as low as 0.001%, offering a 10
 000-fold increase in sensitivity compared to traditional methods. All
 coral species from both regions were overwhelmingly dominated by a single
 clade C OTU (accounting for 98% of all recovered sequences). Only 8.5% of
 colonies associated with multiple clades (clades C and D, or C and G),
 suggesting a high level of symbiont specificity in Acropora assemblages in
 Western Australia. This contrasts with recent literature that have applied
 highly-sensitive molecular techniques and identified widespread
 flexibility in symbiont associations across a number of coral taxa in
 other geographic regions. While only 40% of the OTUs were shared between
 regions, the dominance of a single OTU resulted in no significant
 difference in Symbiodinium community structure, demonstrating that the
 coral-algal symbiosis can remain stable across more than 15° of latitude
 and a range of sea surface temperature profiles. This study validates the
 use of NGS platforms as tools for providing fine-scale estimates of
 Symbiodinium diversity and can offer critical insight into the flexibility
 of the coral-algal symbiosis.
description: OTU sequences 454 data
 cp23s HVR gene33 OTUs identified from
 samples based on clustering at 97% similarity using average neighbor
 algorithm in mothurOTU sequences
 cp23s.fastaHAI cp23s sanger
 sequencesAbrolhos Islands sanger
 sequences cp23sKIM cp23s sanger
 sequencesKimberley sanger
 sequences cp23sKIM sanger sequence
 cp23s.fastaOTU sequences 454 data
 ITS2 gene454 data from Acropora
 clustered into OTUs based on 97% similarity using average neighbour
 algorithmITS2 OTU
 alignment.fasta454 sequence
 data454 sequence data of
 Acropora colonies from Kimberley and Abrolhos454
 data.fastaR
 scriptfigures 2 and
 3OTU distribution for
 each colonyOTU distribution for
 each colonycolonies.csvanalysis pipelinesteps for analysis pipeline in Mothur
DOI: 10.5061/dryad.qk60s
title: Data from: Use of genotyping-by-sequencing data to develop a high-throughput and multi-functional SNP panel for conservation applications in Pacific lamprey

description: Next generation sequencing data can be mined for highly informative single
 nucleotide polymorphisms (SNPs) to develop high-throughput genomic assays
 for non-model organisms. However, choosing a set of SNPs to address a
 variety of objectives can be difficult because SNPs are often not equally
 informative. We developed an optimal combination of 96 high-throughput SNP
 assays from a total of 4,439 SNPs identified in a previous study of
 Pacific lamprey (Entosphenus tridentatus), and used them to address four
 disparate objectives: parentage analysis, species identification, and
 characterization of neutral and adaptive variation. Nine of these SNPs are
 FST outliers, and five of these outliers are localized within genes and
 significantly associated with geography, run-timing, and dwarf life
 history. Two of the 96 SNPs were diagnostic for two other lamprey species
 which are morphologically indistinguishable at early larval stages and are
 sympatric in the Pacific Northwest. The majority (85) of SNPs in the panel
 were highly informative for parentage analysis- i.e. putatively neutral
 with high minor allele frequency across the species’ range. Results from
 three case studies are presented to demonstrate the broad utility of this
 panel of SNP markers in this species. As Pacific lamprey populations are
 undergoing rapid decline, these SNPs provide an important resource to
 address critical uncertainties associated with the conservation and
 recovery of this imperiled species.
description: IdentifyLoci_SpeciesDiagnostic Perl ScriptThe "IdentifyLoci.pl" PERL script (original script described by Hecht et al. 2013) was modified such that it only identified SNP variations among but not within species collections, effectively ignoring within species variations. Hecht BC, Campbell NR, Holecek DE, Narum SR (2013) Genome-wide association reveals genetic basis for the propensity to migrate in wild populations of rainbow and steelhead trout. Molecular Ecology, 22, 3061–3076 doi: 10.1111/mec.12082.IdentifyLoci_SpeciesDiagnostic.plEtrMERdryad_96SNPdatasetThe individuals from collections described in Table S2 are included with all details of their relevant metadata and 96 SNP genotypic data. SNP data is in raw 2 column format in which the nucleotide of allele 1 and allele 2 are shown.
DOI: 10.7927/khbw-9920
title: IPCC AR6 Synthesis Report SPM.4 (c) and LR Figure 3.3 (c) (Burning Embers): Risks to coastal geographies increase with sea level rise and depend on responses

description: Assessment of the combined risk of coastal flooding, erosion and salinization for four illustrative coastal geographies in 2100, due to changing mean and extreme sea levels, under two response scenarios, with respect to the SROCC baseline period (1986-2005). The assessment does not account for changes in extreme sea level beyond those directly induced by mean sea level rise; risk levels could increase if other changes in extreme sea levels were considered (e.g., due to changes in cyclone intensity). “No-to-moderate response” describes efforts as of today (i.e. no further significant action or new types of actions). “Maximum potential response” represent a combination of responses implemented to their full extent and thus significant additional efforts compared to today, assuming minimal financial, social and political barriers. (In this context, ‘today’ refers to 2019.) The assessment criteria include exposure and vulnerability, coastal hazards, in-situ responses and planned relocation. Planned relocation refers to managed retreat or resettlements. The term response is used here instead of adaptation because some responses, such as retreat, may or may not be considered to be adaptation.