cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kg495
title: Data from: Ocean-scale prediction of whale shark distribution

description: Aim: Predicting distribution patterns of whale sharks (Rhincodon typus,
 Smith 1828) in the open ocean remains elusive owing to few pelagic
 records. We developed multivariate distribution models of seasonally
 variant whale shark distributions derived from tuna purse-seine fishery
 data. We tested the hypotheses that whale sharks use a narrow temperature
 range, are more abundant in productive waters and select sites closer to
 continents than the open ocean. Location: Indian Ocean. Methods: We
 compared a 17-year time series of observations of whale sharks associated
 with tuna purse-seine sets with chlorophyll a concentration and sea
 surface temperature data extracted from satellite images. Different sets
 of pseudoabsences based on random distributions, distance to shark
 locations and tuna catch were generated to account for spatiotemporal
 variation in sampling effort and probability of detection. We applied
 generalized linear, spatial mixed-effects and Maximum Entropy models to
 predict seasonal variation in habitat suitability and produced maps of
 distribution. Results: The saturated generalized linear models including
 bathymetric slope, depth, distance to shore, the quadratic of mean sea
 surface temperature, sea surface temperature variance and chlorophyll a
 had the highest relative statistical support, with the highest percent
 deviance explained when using random pseudoabsences with fixed effect-only
 models and the tuna pseudo-absences with mixedeffects models (e.g. 58% and
 26% in autumn, respectively). Maximum Entropy results suggested that whale
 sharks responded mainly to variation in depth, chlorophyll a and
 temperature in all seasons. Bathymetric slope had only a minor influence
 on the presence. Main conclusions: Whale shark habitat suitability in the
 Indian Ocean is mainly correlated with spatial variation in sea surface
 temperature. The relative influence of this predictor provides a basis for
 predicting habitat suitability in the open ocean, possibly giving insights
 into the migratory behaviour of the world’s largest fish. Our results also
 provide a baseline for temperature-dependent predictions of distributional
 changes in the future.
description: Fig4_Autum_PredictionsEnsemble predictions for Autumn (9-km resolution). File headings: X - longitude, Y - latitude, predP - habitat suitability, predSE - prediction error.Fig4_Spring_PredictionsEnsemble predictions for Spring (9-km resolution). File headings: X - longitude, Y - latitude, predP - habitat suitability, predSE - prediction error.Fig4_Summer_PredictionsEnsemble predictions for Summer (9-km resolution). File headings: X - longitude, Y - latitude, predP - habitat suitability, predSE - prediction error.Fig4_Winter_PredictionsEnsemble predictions for Winter (9-km resolution). File headings: X - longitude, Y - latitude, predP - habitat suitability, predSE - prediction error.
DOI: 10.5061/dryad.r0m2f
title: Data from: Population genetics of Setaria viridis, a new model system

description: An extensive survey of the standing genetic variation in natural
 populations is among the priority steps in developing a species into a
 model system. In recent years, green foxtail (Setaria viridis), along with
 its domesticated form foxtail millet (S. italica), has rapidly become a
 promising new model system for C4 grasses and bioenergy crops, due to its
 rapid life cycle, large amount of seed production, and small diploid
 genome, among other characters. However, remarkably little is known about
 the genetic diversity in natural populations of this species. In this
 study, we survey the genetic diversity of a world-wide sample of more than
 200 S. viridis accessions, using the genotyping by sequencing technique.
 Two distinct genetic groups in S. viridis and a third group resembling S.
 italica were identified, with considerable admixture among the three
 groups. We find the genetic variation of North American S. viridis
 correlates with both geography and climate, and is representative of the
 total genetic diversity in this species. This pattern may reflect several
 introduction/dispersal events of S. viridis into North America. We also
 modeled demographic history and show signal of recent population decline
 in one subgroup. Finally we show linkage disequilibrium decay is rapid
 (less then 45 kb) in our total sample and slow in genetic subgroups. These
 results together provide an in-depth understanding of the pattern of
 genetic diversity of this new model species on a broad geographic scale.
 They also provide key guidelines for on-going and future work including
 germplasm preservation, local adaptation, crossing designs and genome-wide
 association studies.
description: GBS SNP calls from Huang
 et al.variant call file is
 generated originally by GATK, SNPs are filtered and phased according to
 the description in the paper. This is the final vcf file, and most
 downstream analysis are based on this file, otherwise stated in the
 paper.Huang_etal_Sviridis_GBS.vcf.gz
DOI: 10.5061/dryad.m863j
title: Data from: Species delimitation in the ground beetle subgenus Liocosmius (Coleoptera: Carabidae: Bembidion), including standard and next-generation sequencing of museum specimens

description: The species of subgenus Liocosmius Casey of genus Bembidion Latreille are
 delimited and documented using DNA sequences from eight genes,
 morphological data, and geography. The subgenus consists of six known
 species, three of which are described as new: Bembidion orion Cooper and
 Maddison (California), B. darlingtonielum Cooper and Maddison
 (California), and B. cooperi Maddison (New Mexico and Arizona). The group
 ranges from British Columbia south to Baja California, and east to
 Colorado and New Mexico, with the centre of diversity in California. DNA
 from a pinned specimen collected in 1968 was sequenced using an Illumina
 platform, resulting in accurate data of all eight genes studied.
 Identification tools and descriptions of each species are provided.
description: Liocosmius untrimmed
 dataThis file contains all
 of the untrimmed DNA sequence data gathered for the paper. It is formatted
 as a NEXUS file, and is compatible with Mesquite version
 2.75001.Liocosmius.AllData.nexLiocosmius data with ML treesThis file contains all of the trimmed and aligned DNA sequence data that were analyzed for this paper, and the maximum likelihood trees and the ML bootstrap trees. It is formatted as a NEXUS file, and is compatible with Mesquite version 2.75002.Liocosmius.WithMLTrees.nex
DOI: 10.5061/dryad.060d2
title: Data from: Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae)

description: Understanding the drivers of population divergence, speciation and species
 persistence is of great interest to molecular ecology, especially for
 species-rich radiations inhabiting the world’s biodiversity hotspots. The
 toolbox of population genomics holds great promise for addressing these
 key issues, especially if genomic data are analyzed within a spatially and
 ecologically explicit context. We have studied the earliest stages of the
 divergence continuum in the Restionaceae, a species-rich and ecologically
 important plant family of the Cape Floristic Region (CFR) of South Africa,
 using the widespread CFR endemic Restio capensis (L.) H.P. Linder
 & C.R. Hardy as an example. We studied diverging populations of
 this morphotaxon for chloroplast (cp) DNA sequences and &gt;14 400
 nuclear DNA polymorphisms from Restriction site Associated DNA (RAD)
 sequencing and analyzed the results jointly with spatial, climatic, and
 phytogeographic data, using a Bayesian generalized linear mixed modeling
 (GLMM) approach. The results indicate that population divergence across
 the extreme environmental mosaic of the CFR is driven by
 isolation-by-environment (IBE) rather than isolation-by-distance (IBD) for
 both neutral and non-neutral markers, consistent with genome hitchhiking
 during early stages of divergence. Mixed modeling of cpDNA and single
 highly divergent outlier loci from a Bayesian genome scan confirmed the
 predominant role of climate and pointed to additional drivers of
 divergence, such as drift and ecological agents of selection captured by
 phytogeographic zones. Our study demonstrates the usefulness of population
 genomics for disentangling the effects of IBD and IBE along the divergence
 continuum often found in species radiations across heterogeneous
 ecological landscapes.
description: File S1 Pseudoreference
 part 1Pseudoreference of
 concatenated unique RAD-seq clusters, separated by a stretch of five Ns,
 pseudochromosomes 1–6. Zip-compressed fasta file
 format.FileS1_psref_pschr1-6.Rc.fas.zipFile S2 Pseudoreference part 2Pseudoreference of concatenated unique RAD-seq clusters, separated by a stretch of five Ns, pseudochromosomes 7–12. Zip-compressed fasta file format.FileS2_psref_pschr9-12.Rc.fas.zipTable S5 RAD sequencing data setRAD sequencing data set for 96 individuals from 10 populations of R. capensis from the Cape Floristic Region of South Africa.Table_S5_R.txt
DOI: 10.5061/dryad.3066j
title: Data from: Stress-induced mutagenesis and complex adaptation

description: Because mutations are mostly deleterious, mutation rates should be reduced
 by natural selection. However, mutations also provide the raw material for
 adaptation. Therefore, evolutionary theory suggests that the mutation rate
 must balance between adaptability—the ability to adapt—and adaptedness—the
 ability to remain adapted. We model an asexual population crossing a
 fitness valley and analyse the rate of complex adaptation with and without
 stress-induced mutagenesis (SIM)—the increase of mutation rates in
 response to stress or maladaptation. We show that SIM increases the rate
 of complex adaptation without reducing the population mean fitness, thus
 breaking the evolutionary trade-off between adaptability and adaptedness.
 Our theoretical results support the hypothesis that SIM promotes
 adaptation and provide quantitative predictions of the rate of complex
 adaptation with different mutational strategies.
description: Adaptation in the weak
 mutation regimeResults of simulations
 in a weak mutation regine (U&lt;adaptation_weak_mutation_15JUL14.csv.gzAdaptation in the strong mutation regimeResults of simulations in a strong mutation regine (U~s), used for Fig. 3.adaptation_strong_mutation_15JUL14.csv.gzCompetitions between mutational strategiesSimulations of competitions for Appendix F.competitions_15JUL14.csv.gzAdaptation in weak mutation regime restricted to unloaded individualsResults of simulations in a weak mutation regine (U&lt;adaptation_weak_mutation_unloaded_16JUL14.csv.gzAdaptation in the weak mutation regime with continuous SIMResults of simulations in a weak mutation regine (U&lt;adaptation_weak_mutation_simk_16JUL14.csv.gz
DOI: 10.5061/dryad.0kh88
title: Data from: A tale of two morphs: modeling pollen transfer, magic traits, and reproductive isolation in parapatry

description: The evolution of the flower is commonly thought to have spurred angiosperm
 diversification. Similarly, particular floral traits might have promoted
 diversification within specific angiosperm clades. We hypothesize that
 traits promoting the precise positional transfer of pollen between flowers
 might promote diversification. In particular, precise pollen transfer
 might produce partial reproductive isolation that facilitates adaptive
 divergence between parapatric populations differing in their
 reproductive-organ positions. We investigate this hypothesis with an
 individual-based model of pollen transfer dynamics associated with
 heterostyly, a floral syndrome that depends on precise pollen transfer.
 Our model shows that precise pollen transfer can cause sexual selection
 leading to divergence in reproductive-organ positions between populations
 served by different pollinators, pleiotropically causing an increase in
 reproductive isolation through a “magic trait” mechanism. Furthermore,
 this increased reproductive isolation facilitates adaptive divergence
 between the populations in an unlinked, ecologically selected trait. In a
 different pollination scenario, however, precise pollen transfer causes a
 decrease in adaptive divergence by promoting asymmetric gene flow. Our
 results highlight the idea that magic traits are not “magic” in isolation;
 in particular, the effect size of magic traits in speciation depends on
 the external environment, and also on other traits that modify the
 strength of the magic trait's influence on non-random mating.
 Overall, we show that the evolutionary consequences of pollen transfer
 dynamics can depend strongly on the available pollinator fauna and on the
 morphological fit between flowers and pollinators. Furthermore, our
 results illustrate the potential importance of even weak reproductive
 isolating barriers in facilitating adaptive divergence.
description: Model
 realizationsA comma-separated value
 file with all model realization datadataset.csv
DOI: 10.5061/dryad.7v8fq
title: Data from: The world’s biogeographical regions revisited: global patterns of endemism in Tipulidae (Diptera)

description: This paper explores the distributional data of 4,224 Tipulidae (Insecta:
 Diptera) species to search for endemism patterns in a worldwide scale and
 to test the extent to which the global patterns of endemism of the group
 fit into previously proposed regionalization schemes, particularly
 Wallace’s system and recent revisions of it. Large scale areas of endemism
 are assessed using the grid-based method implemented in VNDM. VNDM depends
 on the prior definition of the grid size for analysis, but a criterion for
 choosing beforehand a particular grid size is not clear. The same holds
 for the choice of the level of similarity in species composition selected
 for the calculation of consensus areas. In our study, we developed a
 methodological approach that helped defining objective criteria for
 choosing suitable values for these critical variables. Large-scale areas
 of endemism around the globe are identified and ranked according to
 endemicity levels: 1—West Palaearctic, 2—Nearctic, 3—East
 Palaearctic-Oriental, 4—West North America, 5—Australia, 6—Neotropical,
 7—Sub-Saharan Africa, 8—Palaearctic, and 9—Middle East. Our main
 conclusion is that there are still some limitations in applying
 biogeographical classifications proposed mostly on the basis of vertebrate
 distribution to other taxonomic groups, such as the Tipulidae. While there
 is a general congruence of the broad-scale areas of endemism of tipulids
 with previously proposed regionalization schemes, for some areas, the
 sharpness of boundaries between traditional regions is not so acute, due
 to a great level of overlap of part of its biotic elements.
description: Appendix S1 Tipulidae
 VNDMGeoreferenced species
 distribution database containing the distributional records of over 4,000
 Tipulidae species. It can be directly opened for analysis in the computer
 program VNDM.Appendix S2 Comparative
 ChartComparison of the
 results of the analyses in VNDM saving sets of areas with scores above 8
 and 1.
DOI: 10.82294/dvnba3yvu
title: COPUS. Territorio: Norte de Santander. Sector: Educación. Año: 2024
title: Dato. Observación estructurada con el protocolo COPUS.

description: Información recopilada durante el año 2024 a partir de observaciones estructuradas realizadas con el protocolo COPUS, dirigidas a educadores artísticos pertenecientes a programas de formación en educación artística y cultural del sector Educación (educación formal) en el departamento de Norte de Santander.
DOI: 10.5061/dryad.2mc1t
title: Data from: Model selection in historical biogeography reveals that founder-event speciation is a crucial process in island clades

description: Founder-event speciation, where a rare jump dispersal event founds a new
 genetically isolated lineage, has long been considered crucial by many
 historical biogeographers, but its importance is disputed within the
 vicariance school. Probabilistic modeling of geographic range evolution
 creates the potential to test different biogeographical models against
 data using standard statistical model choice procedures, as long as
 multiple models are available. I re-implement the
 Dispersal-Extinction-Cladogenesis (DEC) model of LAGRANGE in the R package
 BioGeoBEARS, and modify it to create a new model, DEC+J, which adds
 founder-event speciation, the importance of which is governed by a new
 free parameter, j. The identifiability of DEC and DEC+J is tested on
 datasets simulated under a wide range of macroevolutionary models where
 geography evolves jointly with lineage birth/death events. The results
 confirm that DEC and DEC+J are identifiable even though these models
 ignore the fact that molecular phylogenies are missing many cladogenesis
 and extinction events. The simulations also indicate that DEC will have
 substantially increased errors in ancestral range estimation and parameter
 inference when the true model includes +J. DEC and DEC+J are compared on
 13 empirical datasets drawn from studies of island clades. Likelihood
 ratio tests indicate that all clades reject DEC, and AICc model weights
 show large to overwhelming support for DEC+J, for the first time verifying
 the importance of founder-event speciation in island clades via
 statistical model choice. Under DEC+J, ancestral nodes are usually
 estimated to have ranges occupying only one island, rather than the
 widespread ancestors often favored by DEC. These results indicate that the
 assumptions of historical biogeography models can have large impacts on
 inference and require testing and comparison with statistical methods.
description: Supplemental Text,
 Tables, and FiguresAll supplemental text,
 tables, and figures, as one PDF.Supp_Data_Tables_Figures.pdfSupplemental Data 1: Excel file showing DEC and DEC+J weights calculationsThis excel file shows the DEC and DEC+J weights calculations for a three-area problem. Users may change the value of the j parameter and see the resulting change in the individual per-event weights of y (sympatry), s (subset sympatry), v (vicariance), and j (jump dispersal/founder-event speciation). The conditional probabilities of each individual event, used in the calculation of the likelihood, are the individual weight divided by the sum of the weights of events allowed, conditional on a particular ancestral range.ch2_SuppData_01_cladogenesis_parameterizations_v04.xlsxSuppData2_all_BioGeoBEARS_inferencesThis zipfile contains a folder and a script for each of the 53 empirical BioGeoBEARS analyses presented in the paper. Users will have to edit working directories etc. to re-run these analysis. See the BioGeoBEARS wiki page for updates to the basic example script.
DOI: 10.5061/dryad.nb5vc
title: Data from: Data-driven discovery of the spatial scales of habitat choice by elephants

description: Setting conservation goals and management objectives relies on
 understanding animal habitat preferences. Models that predict preferences
 combine location data from tracked animals with environmental information,
 usually at a spatial resolution determined by the available data. This
 resolution may be biologically irrelevant for the species in question.
 Individuals likely integrate environmental characteristics over varying
 distances when evaluating their surroundings; we call this the scale of
 selection. Even a single characteristic might be viewed differently at
 different scales; for example, a preference for sheltering under trees
 does not necessarily imply a fondness for continuous forest. Multi-scale
 preference is likely to be particularly evident for animals that occupy
 coarsely heterogeneous landscapes like savannahs. We designed a method to
 identify scales at which species respond to resources and used these
 scales to build preference models. We represented different scales of
 selection by locally averaging, or smoothing, the environmental data using
 kernels of increasing radii. First, we examined each environmental
 variable separately across a spectrum of selection scales and found peaks
 of fit. These ‘candidate’ scales then determined the environmental data
 layers entering a multivariable conditional logistic model. We used model
 selection via AIC to determine the important predictors out of this set.
 We demonstrate this method using savannah elephants (Loxodonta africana)
 inhabiting two parks in southern Africa. The multi-scale models were more
 parsimonious than models using environmental data at only the source
 resolution. Maps describing habitat preferences also improved when
 multiple scales were included, as elephants were more often in places
 predicted to have high neighborhood quality. We conclude that elephants
 select habitat based on environmental qualities at multiple scales. For
 them, and likely many other species, biologists should include multiple
 scales in models of habitat selection. Species environmental preferences
 and their geospatial projections will be more accurately represented,
 improving management decisions and conservation planning.
description: Maputo Landscape
 DataCell ID and x,y location
 for each pixel within the landscape, and the values of the habitat
 attributes in each pixel- distance from water, distance from human
 settlement, closed woodland density, and reeds density. This information
 was determined using GIS.MaputoMap2.csvEtosha Landscape DataGrid ID and x,y location for each pixel within the landscape, and the values of the habitat attributes in each pixel- distance from water during the wet season and the dry season, mopane density, Acacia nebrownii density, and Acacia-dominated savannah density. This information was determined using GIS.enpcells.csv