cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j3f5j
title: Data from: Reconstructing ecological niche evolution when niches are incompletely characterized

description: Evolutionary dynamics of abiotic ecological niches across phylogenetic
 history can shed light on large-scale biogeographic patterns,
 macroevolutionary rate shifts, and the relative ability of lineages to
 respond to global change. An unresolved question is how best to represent
 and reconstruct evolution of these complex traits at coarse spatial scales
 through time. Studies have approached this question by integrating
 phylogenetic comparative methods with niche estimates inferred from
 correlative and other models. However, methods for estimating niches often
 produce incomplete characterizations, as they are inferred from
 present-day distributions that may be limited in full expression of the
 fundamental ecological niche by biotic interactions, dispersal
 limitations, and the existing set of environmental conditions. Here, we
 test whether incomplete niche characterizations inherent in most estimates
 of species’ niches bias phylogenetic reconstructions of niche evolution,
 using simulations of virtual species with known niches. Results establish
 that incompletely-characterized niches inflate estimates of evolutionary
 change and lead to error in ancestral state reconstructions. Our analyses
 also provide a potential mechanism to explain the frequent observation
 that maximum thermal tolerances are more conserved than minimum thermal
 tolerances: populations and species experience more spatial variation in
 minimum temperature than in maximum temperature across their
 distributions, and consequently may experience stronger diversifying
 selection for cold tolerance.
description: Supplementary
 MaterialsTable S1 & S2;
 Figures S1-S19NichePaper_Supplementary
 Materials_3.docx
DOI: 10.5061/dryad.fg12f
title: Data from: Repeated evolution and reversibility of self-fertilization in the volvocine green algae

description: Outcrossing and self-fertilization are fundamental strategies of sexual
 reproduction, each with different evolutionary costs and benefits.
 Self-fertilization is thought to be an evolutionary “dead-end” strategy,
 beneficial in the short term but costly in the long term, resulting in
 self-fertilizing species that occupy only the tips of phylogenetic trees.
 Here, we use volvocine green algae to investigate the evolution of
 self-fertilization. We use ancestral-state reconstructions to show that
 self-fertilization has repeatedly evolved from outcrossing ancestors and
 that multiple reversals from selfing to outcrossing have occurred. We use
 three phylogenetic metrics to show that self-fertilization is not
 restricted to the tips of the phylogenetic tree, a finding inconsistent
 with the view of self-fertilization as a dead-end strategy. We also find
 no evidence for higher extinction rates or lower speciation rates in
 selfing lineages. We find that self-fertilizing species have significantly
 larger colonies than outcrossing species, suggesting the benefits of
 selfing may counteract the costs of increased size. We speculate that our
 macroevolutionary results on self-fertilization (i.e. non-tippy
 distribution, no decreased diversification rates) may be explained by the
 haploid-dominant life cycle that occurs in volvocine algae, which may
 alter the costs and benefits of selfing.
description: 600 Bayesian
 treesSystematic sample of
 Bayesian trees. Every 1,000th post-burnin tree from the four runs was
 included, for a total of 600 trees.combined_chloroplast_collection.newickVolvocine tree, ultrametricVolvocine phylogenetic tree, created from the phylogram using a penalized likelihood function.combined_chloroplast.con.clado.nexVolvocine tree, phylogramBayesian phylogram of volvocine and outgroup taxa.combined_chloroplast.con.tre.nexChloroplast data matrixData matrix for volvocine chloroplast phylogenetic tree.combined_chloroplast.fasta.nexDataset S1Continuous colony size metrics and discrete character states for mating systems and associated references for volvocine taxa. For heterothallic species, only one strain of a mating pair has been given.
DOI: 10.5061/dryad.71b5t
title: Data from: Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy

description: Most HIV-1-infected individuals with virological failure (VF) on a
 pharmacologically-boosted protease inhibitor (PI)-containing regimen do
 not develop PI-resistance protease mutations. One proposed explanation is
 that mutations in HIV-1 gag or gp41 cytoplasmic domain might also reduce
 PI susceptibility. In a recent study of paired gag and gp41 sequences from
 individuals with VF on a PI-containing regimen, we did not identify
 PI-selected mutations and concluded that if such mutations existed, larger
 numbers of paired sequences from multiple studies would be needed for
 their identification. In our study, we performed dN/dS analyses and
 curated gag and gp41 sequence datasets from more than 400 published
 studies to generate site-specific amino acid profiles and to identify
 positions changing during therapy from conserved to uncommon amino acids.
 The methods used to perform the dN/dS analysis and to generate the curated
 sequence datasets and amino acid profiles will facilitate the application
 of consistent methods to a growing body of paired gag and gp41 sequence
 datasets and expedite the identification of sites under PI-selection
 pressure.
description: Data and Analysis
 Scripts for Selection Analyses of Paired HIV-1 gag and gp41 Sequences
 Obtained Before and After Antiretroviral TherapyThis file contains all
 data and analysis scripts for the selection analyses of paired HIV-1 gag
 and gp41 sequences. It is a snapshot of the Github repository
 github.com/hivdb/gag-gp41. The exact version of this snapshot is 59951f0.
 A README.md file is included in this zip file.gag-gp41-master.zip
DOI: 10.5061/dryad.gd0qc
title: Data from: The behavioural response of migrating humpback whales to a full seismic air gun array

description: Despite concerns on the effects of noise from seismic survey air guns on
 marine organisms, there remains uncertainty in the biological significance
 of any response. This study quantifies and interprets the response of
 migrating humpback whales (Megaptera novaeangliae) to a 3130 cui (51.3l)
 commercial air gun array. We compare the behavioural responses to active
 trials (array operational; n = 34 whale groups), with responses to control
 trials (source vessel towing the array while silent; n = 33) and baseline
 studies of normal behaviour in the absence of the vessel (n = 85). No
 abnormal behaviours were recorded during the trials. However, in response
 to the active seismic array and the controls, the whales displayed changes
 in behaviour. Changes in respiration rate were of a similar magnitude to
 changes in baseline groups being joined by other animals suggesting any
 change group energetics was within their behavioural repertoire. However,
 the reduced progression southwards in response to the active treatments,
 for some cohorts, was below typical migratory speeds. This response was
 more likely to occur within 4 km from the array at received levels over
 135 dB re 1µPa2.s.
description: BRAHSS1415_Dataset_ALLMeasured response variables for migrating humpback whale baseline groups and groups exposed to control (vessel only) and full array seismic air gun trials.
DOI: 10.5061/dryad.17c8h
title: Data from: Early Triassic benthic invertebrates from the Great Bank of Guizhou, South China: systematic palaeontology and palaeobiology

description: To further our understanding on the evolution, selectivity, and ecological
 composition of marine communities following the latest Permian mass
 extinction, new collections from underrepresented regions in the immediate
 extinction aftermath are required. Here, we provide new systematic data
 and the first palaeobiological account of the benthic invertebrate
 community from the Great Bank of Guizhou, South China. We systematically
 describe 3 brachiopod species, 26 bivalve species, 11 gastropod species, 1
 microconchid, and 1 crinoid species. The descriptions include five new
 species; two bivalve species (Hoernesia? danisae, Atomodesma? hautmanni)
 and three gastropod species (Donaldina erwini, Cossmannina alfischeri, and
 Vernelia samae). This is the most species-rich benthic community known so
 far from the extinction aftermath, which is typically characterised by a
 high proportion of Permian holdover genera and cosmopolitan taxa.
 Taxonomically, this community is different from coeval faunas with
 dissimilarity values &gt; 60%. Ecologically, however, this fauna is
 similar to faunas from the Dolomites (Italy), and East Greenland. This new
 data, therefore, suggests that the lower Griesbachian invertebrate faunas
 were taxonomically heterogeneous, whereas ecologically they were
 relatively homogenous. The marine community on the Great Bank of Guizhou
 records genera that survived the mass extinction event with some, but not
 all, recording a size reduction, i.e., the Lilliput effect. The absence of
 large body fossils and the preferential survival of small species suggest
 that the mass extinction event was size-selective.
description: GBG_Accession_numbersAccession numbers for the specimens identified in this study.H.parvus occurrencesOccurrences used for palaeoecological analysis
DOI: 10.5061/dryad.s59v1
title: Data from: The impact of host genetic diversity on virus evolution and emergence

description: Accumulating evidence indicates that biodiversity has an important impact
 on parasite evolution and emergence. The vast majority of studies in this
 area have only considered the diversity of species within an environment
 as an overall measure of biodiversity, overlooking the role of genetic
 diversity within a particular host species. Although theoretical models
 propose that host genetic diversity in part shapes that of the infecting
 parasite population, and hence modulates the risk of parasite emergence,
 this effect has seldom been tested empirically. Using Rabies virus (RABV)
 as a model parasite, we provide evidence that greater host genetic
 diversity increases both parasite genetic diversity and the likelihood of
 a host being a donor in RABV cross-species transmission events. We
 conclude that host genetic diversity may be an important determinant of
 parasite evolution and emergence.
description: Data_S1Accession numbers, isolate name, host of origin, and data on the year and geographical location (country) of collection of the samples that led to the Rabies virus sequences utilized in the work. Values and reference work of all host expected heterozygosity data used in the work.Rabies_ALL_SPECIES_N.FULL.DATEDAlignment of the Rabies virus N gene sequences used in the study in nexus format.Rabies_ALL_SPECIES_G.FULL.DATEDAlignment of Rabies virus G gene sequences used in the work in nexus format
DOI: 10.5061/dryad.ff072
title: Data from: Identification of genomic regions associated with sex in Pacific halibut

description: Understanding and identifying the genetic mechanisms responsible for
 sex-determination are important for species management, particularly in
 exploited fishes where sex biased harvest could have implications on
 population dynamics and long-term persistence. The Pacific halibut
 (Hippoglossus stenolepis) supports important fisheries in the North
 Pacific Ocean. The proportion of each sex in the annual harvest is
 currently estimated using growth curves, but genetic techniques may
 provide a more accurate method. We used restriction-site associated DNA
 (RAD) sequencing to identify RAD-tags that were linked to genetic sex,
 based on differentiation (FST) between the sexes. Identified RAD-tags were
 aligned to the Atlantic halibut (Hippoglossus hippoglossus) linkage map,
 the turbot (Scophthalmus maximus) genome, and the half-smooth tongue sole
 (Cynoglossus semilaevis) genome to identify genomic regions that may be
 involved in sex determination. In total, 56 RAD-tags (70 single nucleotide
 polymorphisms) were linked to sex, and three RAD-tags were identified in
 only females. Sex-linked loci aligned to three linkage groups in the
 Atlantic halibut (LG07: 7 loci, LG15: 1 locus, and LG24: 1 locus), three
 chromosomes in the turbot (LG12: 13 loci, LG01: 1 locus, and LG05: 1
 locus), and one chromosome in the half-smooth tongue sole (ChrZ: 9 loci).
 Results add support to the hypothesis that Pacific halibut genetic sex is
 determined in a ZW system. Two sex-linked loci were further developed into
 sex identification assays, and their efficacy was tested on individuals
 that had been morphologically sexed. The accuracy of each assay on its own
 was 97.5% compared to morphological sex.
description: halibut_genepopFile containing all genotypes. File in Genepop format. Locus names are formatted with an underscore between the RADtag name and SNP position.supplemental_material_199_sex_assaysResults of two TaqMan assays linked to sex.supplemental_material_primers_and_probesPrimer and probe sequences for TaqMan assays.supplemental_materials_alignmentsAlignments between Pacific halibut loci and 1) Atlantic halibut linkage map, 2) turbot genome, and 3) half-smooth tongue sole genome.
DOI: 10.5061/dryad.r6049
title: Data from: Colony personality and plant health in the Azteca-Cecropia mutualism

description: For interspecific mutualisms, the behavior of one partner can influence
 the fitness of the other, especially in the case of symbiotic mutualisms
 where partners live in close physical association for much of their lives.
 Behavioral effects on fitness may be particularly important if either
 species in these long-term relationships displays personality. We
 conducted a field study on collective personality in Azteca constructor
 colonies that live in Cecropia trees, one of the most successful and
 prominent mutualisms of the neotropics. These pioneer plants provide
 hollow internodes for nesting and nutrient-rich food bodies; in return,
 the ants provide protection from herbivores and encroaching vines. We
 tested the consistency and correlation of five colony-level behavioral
 traits, censused colonies, and measured the amount of leaf damage for each
 plant. Four of five traits were both consistent within colonies and
 correlated among colonies. This reveals a behavioral syndrome along a
 docile-aggressive axis, with higher-scoring colonies showing greater
 activity, aggression, and responsiveness. Scores varied substantially
 between colonies and were independent of colony size and age. Host plants
 of more active, aggressive colonies had less leaf damage, suggesting a
 link between a colony’s personality and effective defense of its host,
 though the directionality of this link remains uncertain. Our field study
 shows that colony personality is an ecologically relevant phenomenon and
 sheds light on the importance of behavioral differences within mutualism
 dynamics.
description: All
 SummariesAll data for average
 colony behavior and attributes, and host tree attributes (size, leaf
 damage, canopy cover, etc.).AllSummariesPub.csvResponse to intruderTime course data for each response to intruder trial - time stamp seconds indicates when an Azteca ant crossed the focal internode.AttaTime.csvPatrolling BehaviorData for each patrolling trial with total number referring to total number of ants crossing the focal internode in 5 minutes.AztecaBehavior_ActivityStats.csvResponse to Leaf DamageData for each response to leaf damage trial where the number of workers on the focal leaf are counted every minute.AztecaBehavior_LeafDamageStats.csvResponse to Vibrational DisturbanceTime course data for each response to vibrational disturbance trial - time stamp seconds indicate when an Azteca ant crossed the focal internode.DisturbanceTime.csvExplore BehaviorTime course data for each exploration trial - time stamp seconds indicates when an Azteca ant crossed the 2-cm mark on the dowel rod.ExploreTime.csv
DOI: 10.5061/dryad.7b86c
title: Data from: Marker development for phylogenomics: the case of Orobanchaceae, a plant family with contrasting nutritional modes

description: Phylogenomic approaches, employing next-generation sequencing (NGS)
 techniques, have revolutionized systematic and evolutionary biology.
 Target enrichment is an efficient and cost-effective method in
 phylogenomics and is becoming increasingly popular. Depending on
 availability and quality of reference data as well as on biological
 features of the study system, (semi-)automated identification of suitable
 markers will require specific bioinformatic pipelines. Here, we
 established a highly flexible bioinformatic pipeline, BaitsFinder, to
 identify putative orthologous single copy genes (SCGs) and to construct
 bait sequences in a single workflow. Additionally, this pipeline has been
 constructed to be able to cope with challenging data sets, such as the
 nutritionally heterogeneous plant family Orobanchaceae. To this end, we
 used transcriptome data of differing quality available for four
 Orobanchaceae species and, as reference, SCG data from monkeyflower
 (Erythranthe guttata, syn. Mimulus g.; 1,915 genes) and tomato (Solanum
 lycopersicum; 391 genes). Depending on whether gaps were permitted in
 initial blast searches of the four Orobanchaceae species against the
 reference, our pipeline identified 1,307 and 981 SCGs with average length
 of 994 bp and 775 bp, respectively. Automated bait sequence construction
 (using 2× tiling) resulted in 38,170 and 21,856 bait sequences,
 respectively. In comparison to the recently published MarkerMiner 1.0
 pipeline BaitsFinder identified about 1.6 times as many SCGs (of at least
 900 bp length). Skipping steps specific to analyses of Orobanchaceae,
 BaitsFinder was successfully used in a group of non-parasitic plants
 (three Asteraceae species and, as reference, SCG data from Arabidopsis
 thaliana based on previously compiled SCGs). Thus, BaitsFinder is expected
 to be broadly applicable in groups, where only transcriptomes or partial
 genome data of differing quality are available.
description: Reference data for
 OrobanchaceaeA compressed file (in
 zip-format) including single copy genes (cds- and fa-format) of
 Erythranthe guttata (syn. Mimulus gutattus) and, unless too similar, of
 Solanum lycopersicum used as reference data for identifying suitable loci
 in Orobanchaceae and for generating bait sequences for
 target-capture.reference_data.zip
DOI: 10.5061/dryad.3cs37
title: Data from: Are the radiations of temperate lineages in tropical alpine ecosystems pre-adapted?

description: Aim: Tropical mountains around the world harbour an extraordinarily rich
 pool of plant species and are hotspots of biodiversity. Climatically, they
 can be zoned into montane climates at mid-altitudes and tropical alpine
 climates above the tree line. Around half of the tropical alpine species
 belong to plant lineages with a temperate ancestry, although these regions
 are often geographically distant. We test the hypothesis that these
 temperate lineages are pre-adapted to the tropical alpine climate.
 Location: New World, with a focus on tropical alpine Andes. Time period:
 Miocene to present. Major taxa studied: Flowering plants. Methods: We
 build multidimensional environmental models representing the full space of
 New World climates. We quantify the environmental similarity between the
 tropical alpine ecosystem and those of potential source areas, while
 correcting for regional differences by kernel density smoothers. Based on
 spatial observations of the genus Hypericum (St John's Wort), we
 quantify niche overlap and test for niche conservatism following
 intercontinental dispersal using density-weighted nonparametric tests. A
 dated species tree, biogeographical estimation, multi-optima
 Ornstein–Uhlenbeck models and model selection approaches are used to test
 for niche shifts during establishment in the tropical alpine Andes.
 Results: The tropical alpine ecosystem is isolated by its climate from
 adjacent regions and is climatically similar to temperate lowland biomes
 of both hemispheres. Niche conservatism is evident in the study group,
 except in the tropical alpine lineage that is characterized by niche
 expansion and shifts in temperature optima. Main conclusions: Our results
 reject the pre-adaptation hypothesis and instead suggest pronounced niche
 evolution during colonization of tropical alpine ecosystems. Establishment
 involved substantial niche shifts, mainly in temperature-related
 variables, and resulted in a tremendous proliferation of species in the
 newly invaded tropical alpine ecosystem.
description: Molecular phylogenetic,
 climate data and species occurrenceThe file contains (1)
 the sequence alignments (nc, cp, and full concatenated) and the resulting
 ML and MCC trees, (2) the spatial points from the New World with climate
 data, and (3) the species occurrence datasets with environmental variables
 (all sp occurrences, max 15 occ/sp, and the species specific climate
 values as median, 5-qtl, and 95-qtl).Nuerk_etal_GEB_TrpAlpNicheShift_data.zip
DOI: 10.5061/dryad.tq221
title: Data from: Forecasting range shifts of a cold-adapted species under climate change: are genomic and ecological diversity within species crucial for future resilience?

description: Cold-adapted taxa are experiencing severe range shifts due to climate
 change and are expected to suffer a significant reduction of their
 climatically suitable habitats in the next few decades. However, it has
 been proposed that taxa with sufficient standing genetic and ecologic
 diversity will better withstand climate change. These taxa are typically
 more broadly distributed in geographic and ecological niche space,
 therefore they are likely to endure higher levels of populations loss than
 more restricted, less diverse taxa before the effects of those losses
 impact their overall diversity and resilience. Here, we explore the
 potential relationship between intraspecific genetic and ecological
 diversity and future resilience, using the cold-adapted plant Primula
 farinosa. We employ high-throughput sequencing to assess the genomic
 diversity of phylogeographic lineages in P. farinosa. Additionally, we use
 current climatic variables to define niche breadth and niche
 differentiation across lineages. Finally, we calibrate Species
 Distribution Models (SDMs) and project the climatic preferences of each
 lineage on future climate to predict lineage-specific shifts in
 climatically suitable habitats. Our study predicts relative persistence of
 future suitable habitats for the most genetically and ecologically diverse
 lineages of the cold-adapted P. farinosa, but significant reduction of
 them for two out of its four lineages. While we do not provide specific
 experiments aimed at identifying the causal links between genetic
 diversity and resilience to climate change, our results indicate that
 greater genetic diversity and wider ecological breadth may buffer species
 responses to rapid climatic changes. This study further highlights the
 importance of integrating knowledge of intraspecific diversity for
 predicting species fate in response to climate change.
description: STACKS fasta file
 outputThe fasta file
 containing all loci identified by STACKS. This file was used to asses the
 genetic diversity across the four lineages of Primula
 farinosa5x3M6n.fa.zipSTACKS VCF file outputThe VCF file containing alll SNPs identified by STACKS. This file was filtered and further used to assess genetic structure across the distribution of Primula farinosa in Europe5x3M6n.vcf.zipOccurrence records for Primula farinosaThe four csv files containing spatially filtered occurrences for the four lineages of Primula farinosa. These files were used for assessing niche breadth and conducting species distribution modellingOccurrences.zip