cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p2b3b
title: Data from: Towards breed formation by island model divergence in Korean cattle

description: Background: The main cattle breed in Korea is the brown Hanwoo, which has
 been under artificial selection within a national breeding program for
 several decades. Varieties of the Hanwoo known as Jeju Black and Chikso
 were not included in the breeding program and remained isolated from the
 effects of recent artificial selection advancements. We analysed the Jeju
 Black and Chikso populations in regards to their genetic variability,
 state of inbreeding, as well as level of differentiation from the mainland
 Hanwoo population. Results: Jeju Black and Chikso were found to have small
 estimated effective population sizes (N e ) of only 11 and 7,
 respectively. Despite a small N e , higher than expected heterozygosity
 levels were observed (0.303 and 0.306), however, lower allelic richness
 was found for the two island populations (1.76 and 1.77) compared to the
 mainland population (1.81). The increase in heterozygosity could be due to
 environmental disease challenges that promoted maintenance of higher
 genetic variability; however, no direct proof exists. Increased
 heterozygosity due to a first generation crossing of genetically different
 populations is not recorded. The differentiation between the Korean
 populations had F ST values between 0.014 and 0.036 which is not as high
 as the differentiation within European beef or dairy cattle breeds
 (0.047–0.111). This suggests that the three populations have not separated
 into independent breeds. Conclusion: Results agree with an island model of
 speciation where the brown Hanwoo represents the ancestral breed, whilst
 the Jeju Black and Chikso diverge from this common ancestor, following
 different evolutionary trajectories. Nevertheless, differences are minor
 and whether Jeju Black and Chikso cattle will develop into discrete breeds
 or reintegrate with the main population has to be seen in the future and
 will largely depend on human management decisions. This offers a rare
 opportunity to accompany the development of new breeds but also poses
 challenges on how to preserve these incipient breeds and ensure their long
 term viability.
description: Strucken_BMCEvolBiol_Korean_Cattle_genoThis readme file describes the genotypic data file of the above publication. For any further queries please contact cgondro2@une.edu.au. The file contains: Genotypic data for 3 Korean cattle breeds. Genotypes are coded as allele counts (0,1,2) and missing data as NA. Genotypes are quality controled as outlined in publication. Rows: SNP names from Illumina Bovine SNP 50K Bead chip v1(Illumina, San Diego) Collumns: Cattle breed names (Hanwoo N=40, Jeju Black N=20, Chikso N=20)
DOI: 10.5061/dryad.vr0kc
title: Data from: Spatial patterning of prey at reproduction to reduce predation risk: what drives dispersion from groups?

description: Group-living is a widespread behaviour thought to be an evolutionary
 adaptation for reducing predation risk. Many group-living species,
 however, spend a portion of their life cycle as dispersed individuals,
 suggesting that the costs and benefits of these opposing behaviours vary
 temporally. Here, we evaluated mechanistic hypotheses for explaining
 individual dispersion as a tactic for reducing predation risk at
 reproduction (i.e. birthing) in an otherwise group-living animal. Using
 simulation analyses parameterized by empirical data, we assessed whether
 dispersion increases reproductive success by: (i) increasing predator
 search time, (ii) reducing predator encounter rates because individuals
 are inconspicuous relative to groups, or (iii) eliminating the risk of
 multiple kills per encounter. Simulations indicate that dispersion only
 becomes favourable when detectability increases with group size and there
 is risk of multiple kills per encounter. This latter effect, however, is
 likely the primary mechanism driving females to disperse at reproduction
 because group detectability effects are presumably constant year round. We
 suggest that the risk of multiple kills imposed by highly vulnerable
 offspring may be an important factor influencing dispersive behaviour in
 many species and conservation strategies for such species will require
 protecting sufficient space to allow dispersion to effectively reduce
 predation risk.
description: Wolf GPS location data
 from DeMars et al.GPS location data from
 15 wolves. This data was used to parameterize the simulation model
 contained in DeMars et al. Please read the README file for data
 attributes.DeMars_et_al_data.xlsx
DOI: 10.5061/dryad.322vn
title: Data from: A global perspective on Campanulaceae: biogeographic, genomic, and floral evolution

description: PREMISE OF THE STUDY: The Campanulaceae are a diverse clade of flowering
 plants encompassing more than 2300 species in myriad habitats from
 tropical rainforests to arctic tundra. A robust, multigene phylogeny,
 including all major lineages, is presented to provide a broad,
 evolutionary perspective of this cosmopolitan clade. METHODS: We used a
 phylogenetic framework, in combination with divergence dating, ancestral
 range estimation, chromosome modeling, and morphological character
 reconstruction analyses to infer phylogenetic placement and timing of
 major biogeographic, genomic, and morphological changes in the history of
 the group and provide insights into the diversification of this clade
 across six continents. KEY RESULTS: Ancestral range estimation supports an
 out-of-Africa diversification following the Cretaceous-Tertiary extinction
 event. Chromosomal modeling, with corroboration from the distribution of
 synonymous substitutions among gene duplicates, provides evidence for as
 many as 20 genome-wide duplication events before large radiations.
 Morphological reconstructions support the hypothesis that switches in
 floral symmetry and anther dehiscence were important in the evolution of
 secondary pollen presentation mechanisms. CONCLUSIONS: This study provides
 a broad, phylogenetic perspective on the evolution of the Campanulaceae
 clade. The remarkable habitat diversity and cosmopolitan distribution of
 this lineage appears to be the result of a complex history of genome
 duplications and numerous long-distance dispersal events. We failed to
 find evidence for an ancestral polyploidy event for this clade, and our
 analyses indicate an ancestral base number of nine for the group. This
 study will serve as a framework for future studies in diverse areas of
 research in Campanulaceae.
description: Alignment_Campanulaceae_all_genes_datasetAll_genes_dataset.fastaAlignment_Campanulaceae_coding_only_datasetCoding_only_dataset.fastaAlignment_Campanulaceae_plastid_only_datasetPlastid_only_dataset.fastaFlwrSym_MatrixPollenPresent_AntherArrangement_MatrixPollenPresent_Invagination_MatrixPollenPresent_Mechanism_MatrixPollenPresent_StylarGrowth_Matrix
DOI: 10.5061/dryad.dq666
title: Data from: Biogeographic dating of speciation times using paleogeographically informed processes

description: Standard models of molecular evolution cannot estimate absolute speciation
 times alone, and require external calibrations to do so, such as fossils.
 Because fossil calibration methods rely on the incomplete fossil record, a
 great number of nodes in the tree of life cannot be dated precisely.
 However, many major paleogeographical events are dated, and since
 biogeographic processes depend on paleogeographical conditions,
 biogeographic dating may be used as an alternative or complementary method
 to fossil dating. I demonstrate how a time-stratified biogeographic
 stochastic process may be used to estimate absolute divergence times by
 conditioning on dated paleogeographical events. Informed by the current
 paleogeographical literature, I construct an empirical dispersal graph
 using 25 areas and 26 epochs for the past 540 Ma of Earth’s history.
 Simulations indicate biogeographic dating performs well so long as
 paleogeography imposes constraint on biogeographic character evolution. To
 gauge whether biogeographic dating may be of practical use, I analyzed the
 well-studied turtle clade (Testudines) to assess how well biogeographic
 dating fares when compared to fossil-calibrated dating estimates reported
 in the literature. Fossil-free biogeographic dating estimated the age of
 the most recent common ancestor of extant turtles to be from the Late
 Triassic, which is consistent with fossil-based estimates. Dating
 precision improves further when including a root node fossil calibration.
 The described model, paleogeographical dispersal graph, and analysis
 scripts are available for use with RevBayes.
description: code.zipThis contains the scripts used to run the simulation and empirical analyses in RevBayes. They use the input files provided in the data.zip file. Updated versions of this code are available at https://github.com/mlandis/biogeo_dating.data.zipThis contains the data used to run the simulation and empirical analyses in RevBayes. To do so, use the scripts provided in the code.zip file. Updated versions of these data are available at https://github.com/mlandis/biogeo_dating.gplates.zipThis contains the files used to create the dispersal graph animation in GPlates 1.5. Updated versions of these files are available at https://github.com/mlandis/biogeo_dating.Supplementary InformationThis document contains a brief overview of how the paleogeographical dispersal graph was constructed, plus additional figures omitted from the Systematic Biology manuscript.supp_info_biogeo_dating_landis16.pdf
DOI: 10.5061/dryad.hn34m
title: Data from: The evolutionary dynamics of ribosomal genes, histone H3, and transposable Rex elements in the genome of Atlantic snappers

description: Lutjanidae is a family of primarily marine and carnivorous fishes
 distributed in the Atlantic, Indian, and Pacific oceans, with enormous
 economic and ecological importance. In order to better clarify the
 conservative chromosomal evolution of Lutjanidae, we analyzed the
 evolutionary dynamics of 5 repetitive DNA classes in 5 Lutjanus and in 1
 Ocyurus species from the Western Atlantic. The ribosomal 18S sites were
 generally located in a single chromosome pair, except for L. jocu and L.
 alexandrei where they are found in 2 pairs. In turn, the 5S rDNA sites are
 unique, terminal and nonsyntenic with the 18S rDNA sites. In 3 species
 analyzed, H3 hisDNA genes were found in 1 chromosomal pair. However, while
 L. jocu presented 2 H3 sites, O. chrysurus showed a noteworthy dispersion
 of this gene in almost all chromosomes of the karyotype. Retrotransposons
 Rex1 and Rex3 do not exhibit any association with the explosive
 distribution of H3 sequences in O. chrysurus. The low compartmentalization
 of Rex elements, in addition to the general nondynamic distribution of
 ribosomal and H3 genes, corroborate the karyotype conservatism in
 Lutjanidae species, also at the microstructural level. However, some
 “disturbing evolutionary waves” can break down this conservative scenario,
 as evidenced by the massive random dispersion of H3 hisDNA in the genome
 of O. chrysurus. The implication of the genomic expansion of H3 histone
 genes and their functionality remain unknown, although suggesting that
 they have higher evolutionary dynamics than previously thought.
description: Figure
 1Fluorescence in situ
 hybridization (FISH) in the metaphase chromosomes of snappers species
 highlighting the chromosomal location of 18S rDNA (red) and 5S rDNA
 (green) sites (left column) and of hisDNA H3 (red) sites (right column).
 Chromosomes were counterstained with DAPI (blue).
 Bar=5μm.Figure
 2Fluorescence in situ
 hybridization (FISH) in the metaphase chromosomes of snappers
 species,hybridized with Rex1 (green) and Rex3 (red) probes. Chromosomes
 were counterstained with DAPI (blue). Bar = 5μm.Figure
 3Phylogenetic
 distribution of ribosomal and hisDNA H3 sites in Lutjanidae species. The
 phylogeny and molecular clock of the divergent clades A, B and C were
 modified from Gold et al. (2011).
DOI: 10.5061/dryad.6n4fm
title: Data from: A gene associated with social immunity in the burying beetle Nicrophorus vespilloides

description: Some group-living species exhibit social immunity, where the immune
 response of one individual can protect others in the group from infection.
 In burying beetles this is part of parental care. Larvae feed on
 vertebrate carcasses which their parents smear with exudates that inhibit
 microbial growth. We have sequenced the transcriptome of the burying
 beetle Nicrophorus vespilloides and identified six genes that encode
 lysozymes – a type of antimicrobial enzyme that has previously been
 implicated in social immunity in burying beetles. When females start
 breeding and producing antimicrobial anal exudates, we found that the
 expression of one of these genes was increased by ~1000 times to become
 one of the most abundant transcripts in the transcriptome. Females varied
 considerably in the antimicrobial properties of their anal exudates, and
 this was strongly correlated with the expression of this lysozyme. We
 conclude that we have likely identified a gene encoding a key effector
 molecule in social immunity, and that it was recruited during evolution
 from a function in personal immunity.
description: data_fig3A_suppfig1Raw data from the paperRaw data.zip
DOI: 10.5061/dryad.n818s
title: Data from: Climate-related adaptive genetic variation and population structure in natural stands of Norway spruce in the South-Eastern Alps

description: Forest trees dominate many Alpine landscapes that are currently exposed to
 changing climate. Norway spruce is one of the most important conifer
 species of the Italian Alps, and natural populations are found across
 steep environmental gradients with large differences in temperature and
 moisture availability. This study seeks to determine and quantify patterns
 of genetic diversity in natural populations toward understanding adaptive
 responses to changing climate. Across the Italian species range, 24
 natural stands were sampled with a major focus on the Eastern Italian
 Alps. Sampled trees were genotyped for 384 selected single nucleotide
 polymorphisms (SNPs) from 285 genes. A wide array of potential candidate
 genes was tested for correlation with climatic parameters. To minimize
 false-positive association between genotype and climate, population
 structure was investigated. Pairwise F ST estimates between sampled
 populations ranged between 0.000 and 0.075, with the highest values
 involving the two disjoint populations, Valdieri, on the western Italian
 Alps, and Campolino, the most southern population on the Apennines.
 Despite considerable genetic admixture among populations, both Bayesian
 and multivariate approach identified four genetic clusters. Selection
 scans revealed five F ST outliers, and the environmental association
 analysis detected ten SNPs associated to one or more climatic variables.
 Overall, 13 potentially adaptive loci were identified, three of which have
 been reported in a previous study on the same species conducted on a
 broader geographical scale. In our study, precipitation, more than
 temperature, was often associated with genotype; therefore, it appears as
 the most important environmental variable associated with the high
 sensitivity of Norway spruce to soil water supply. These findings provide
 relevant information for understanding and quantifying climate change
 effects on this species and its ability to genetically adapt.
description: SNP_flanking_sequenceGenotyped SNPs names with their flanking sequencesSNP_sample_matrix.txtSNP_sample_matrixGenotyped SNPs by sample matrix with information on sample ID, sampling area, latitude and longitude
DOI: 10.5061/dryad.sd40d
title: Data from: Soil nutrients influence growth response of temperate tree species to drought

description: Soil properties can buffer forest response to global climate change.
 However, it is unclear how soil characteristics, water availability and
 their interactions can affect drought response of trees. The aim of this
 study was to assess the influence of soil nutrients and physical soil
 properties on the growth sensitivity of Fagus sylvatica, Quercus spp.,
 Fraxinus excelsior, Abies alba, Picea abies and Pinus sylvestris to
 drought in Central Europe. Yearly growth data from increment cores were
 obtained from 539 trees and combined with forest inventory and soil data
 at 52 sites covering a large gradient of water availability and C/N ratios
 in soil. Linear mixed-effects models were used to assess the
 species-specific growth responses to climate and soil properties for the
 period 1957–2006. The growth of the species was further projected across
 the full range of C/N and water availability observed at 1029 sites where
 soil and species cover-abundance data were available. Temperature, water
 and nutrient availability (C/N) were the most important factors for tree
 growth. Drought and low nutrient availability significantly reduced the
 growth of beech, ash, fir and spruce along the gradient. In contrast, the
 growth of pine and oak was little reduced on poor and dry sites, hence
 showing their competitive advantage over nutrient-demanding species under
 such conditions. The growth of ash and pine was enhanced at sites with
 high species abundance whereas an opposite response was found for spruce.
 No clear relationships between growth and species abundance were found for
 beech, oak and fir. Synthesis. Our results suggest that assessing tree
 responses to climate change without considering simultaneously soil
 properties and climate may be misleading since soil nutrients can
 influence growth response of trees to drought. A detailed analysis of the
 influence of the soil characteristics on growth responses of trees is
 necessary to understand the sensitivity of tree species to global climate
 change.
description: Mean tree growth and
 climatic data of the study sitesTreeGrowth_Clim_Soil_Sites.csvYearly tree growth and climate dataTreeGrowth_Yearly.csv
DOI: 10.5061/dryad.86fj0
title: Data from: Fitness differences between parapatric lake and stream stickleback revealed by a field transplant

description: Molecular comparisons of populations diverging into ecologically different
 environments often reveal strong differentiation in localized genomic
 regions, with the remainder of the genome being weakly differentiated.
 This pattern of heterogeneous genomic divergence, however, is rarely
 connected to direct measurements of fitness differences among populations.
 We here do so by performing a field enclosure experiment in threespine
 stickleback fish residing in a lake and in three replicate adjoining
 streams, and displaying weak yet heterogeneous genomic divergence between
 these habitats. Tracking survival over 29 weeks, we consistently find that
 lake genotypes transplanted into the streams suffer greatly reduced
 viability relative to local stream genotypes and that the performance of
 F1 hybrid genotypes is intermediate. This observed selection against
 migrants and hybrids combines to a total reduction in gene flow from the
 lake into streams of around 80%. Overall, our study identifies a strong
 reproductive barrier between parapatric stickleback populations, and
 cautions against inferring weak fitness differences between populations
 exhibiting weak overall genomic differentiation.
description: 1_No_Of_SurvivorsRead_Me.txt2_Body_MassRead_Me.txt3_No_Of_CompetitorsRead_Me.txt4_Genome_Wide_RAD_Data_Lake_NIDRead_Me.txt5_Genome_Wide_RAD_Data_Lake_BOHRead_Me.txt
DOI: 10.5061/dryad.3p2j0
title: Data from: A rigorous comparison of sexual selection indexes via simulations of diverse mating systems

description: Sexual selection is a cornerstone of evolutionary theory, but measuring it
 has proved surprisingly difficult and controversial. Various proxy
 measures—e.g., the Bateman gradient and the opportunity for sexual
 selection—are widely used in empirical studies. However, we do not know
 how reliably these measures predict the strength of sexual selection
 across natural systems, and most perform poorly in theoretical worst-case
 scenarios. Here we provide a rigorous comparison of eight commonly used
 indexes of sexual selection. We simulated 500 biologically plausible
 mating systems, based on the templates of five well-studied species that
 cover a diverse range of reproductive life histories. We compared putative
 indexes to the actual strength of premating sexual selection, measured as
 the strength of selection on a simulated “mating trait.” This method
 sidesteps a key weakness of empirical studies, which lack an appropriate
 yardstick against which proxy measures can be assessed. Our model predicts
 that, far from being useless, the best proxy measures reliably track the
 strength of sexual selection across biologically realistic scenarios. The
 maximum intensity of precopulatory sexual selection s′max (the Jones
 index) outperformed all other indexes and was highly correlated with the
 strength of sexual selection. In contrast, the Bateman gradient and the
 opportunity for sexual selection were poor predictors of sexual selection,
 despite their continuing popularity.
description: Simulation results:
 indices of sexual selection and selection differentials on the mating
 traitPlease see 'Read
 me' on first sheet of spreadsheetData from Henshaw et al (2016)
 PNAS.xlsx