cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3s92c
title: Data from: The Rift Valley is a major barrier to dispersal of African clawed frogs (Xenopus) in Ethiopia

description: The Ethiopian highlands – home to striking species diversity and endemism
 – are bisected by the Rift Valley, a zone of tectonic divergence. Using
 molecular data we examined the evolutionary history of two co-distributed
 species of African clawed frog (Xenopus clivii and X. largeni) that are
 endemic to this region. Our field collections substantially extend the
 known distribution of X. largeni, a species formerly known from highlands
 southeast of the Rift, but that also occurs to the northwest. In both
 species, analysis of mitochondrial DNA and 19 autosomal loci identifies
 significant population structure, suggests little or no recent migration
 across the Rift Valley, and provides divergence time estimates across the
 Rift of ∼1–3.5 million years. These results indicate that the Ethiopian
 Rift Valley is a major obstacle to dispersal of highland-adapted
 amphibians.
description: Dryad_infoExplanation of filesIM_clivii_small"Small" IMa2 input file for X. clivii with non-neutral loci removedIM_cliviiIMa2 input file for X. cliviiIM_largeniIMa2 input file for X. largeniclivii_inMIMAR input file for X. cliviilargeni_INMIMAR input file for X. largenixen12s16s_MrBayesMitochondrial DNA sequence alignment for MrBayescliv_struct_reduceStructurama input file for X. clivii with some individuals with lots of missing data removed.cliv_struct.inStructurama input file for X. cliviilarg_struct.inStructurama input file for X. largenicliv_struct_reduceStructure input file for X. clivii with some individuals with lots of missing data removedcliv_structStructure input file for X. cliviilarg_structStructure input file for X. largeni
DOI: 10.3886/e240311
title: Climate Change Has Already Made the United States Poorer

description: code.zip: Stata code. See the readme in there.data.zip: Files called in the Stata code, some of which are also generated by the Stata codeoutputdir.zip: Complete set of results files from running Stata code<br>Paper abstract: The climate is already changing. The present study shows that these changes have already affected the U.S. economy. It develops a formal framework that accounts for how climate change has affected each county's economy by altering current and past weather, both locally and elsewhere around the country. The results show that climate change is already reducing annual U.S. income by 0.32% [95% confidence interval: -0.17--0.82%] by altering counties' current, local temperatures, with losses concentrated in the Great Plains and Midwest. Accounting for effects on past temperatures and on temperatures in other counties increases income losses to 12% [2.0--22%] and makes them more widely distributed, with suggestive evidence that trade networks propagate effects around the U.S. Central estimates can change with different indices of nonlocal weather or models of cross-county heterogeneity. Calculations like those developed here could be updated annually as a way of measuring and communicating the progress of climate change.
DOI: 10.15468/dl.73sygw
title: Occurrence Download

description: A dataset containing 680 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lampanyctodes hectoris",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 680 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001711-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e240311v2
title: Climate Change Has Already Made the United States Poorer

description: code.zip: Stata code. See the readme in there.data.zip: Files called in the Stata code, some of which are also generated by the Stata codeoutputdir.zip: Complete set of results files from running Stata code<br>Paper abstract: The climate is already changing. The present study shows that these changes have already affected the U.S. economy. It develops a formal framework that accounts for how climate change has affected each county's economy by altering current and past weather, both locally and elsewhere around the country. The results show that climate change is already reducing annual U.S. income by 0.32% [95% confidence interval: -0.17--0.82%] by altering counties' current, local temperatures, with losses concentrated in the Great Plains and Midwest. Accounting for effects on past temperatures and on temperatures in other counties increases income losses to 12% [2.0--22%] and makes them more widely distributed, with suggestive evidence that trade networks propagate effects around the U.S. Central estimates can change with different indices of nonlocal weather or models of cross-county heterogeneity. Calculations like those developed here could be updated annually as a way of measuring and communicating the progress of climate change.
DOI: 10.5061/dryad.kg68d
title: Data from: Mauve assembly metrics

description: High throughput DNA sequencing technologies have spurred the development
 of numerous novel methods for genome assembly. With few exceptions, these
 algorithms are heuristic and require one or more parameters to be manually
 set by the user. One approach to parameter tuning involves assembling data
 from an organism with an available high quality reference genome, and
 measuring assembly accuracy using some metrics. We developed a system to
 measure assembly quality under several scoring metrics, and to compare
 assembly quality across a variety of assemblers, sequence data types, and
 parameter choices. When used in conjunction with training data such as a
 high quality reference genome and sequence reads from the same organism,
 our program can be used to manually identify an optimal sequencing and
 assembly strategy for de novo sequencing of related organisms.
 Availability: GPL source code and a usage tutorial is at
 http://ngopt.googlecode.com
description: assembly1Assembly of Haloferax volcanii DS2 based on 454 FLX Titanium reads to 25x coverage, sequenced at Roche Inc. The assembly was carried out by Roche Inc, using the newbler assemblerassembly2Assembly of Haloferax volcanii DS2 using 100nt paired-end Illumina reads and 50nt mate-pair reads with 6.5kbp insert size.assembly3Assembly of Haloferax volcanii DS2 using 78nt paired-end Illumina reads and 50nt mate-pair reads with 6.5kbp insert size. Assembly was computed using REPTILE error correction, IDBA assembler for contig generation, and SSPACE scaffolding.
DOI: 10.5061/dryad.6hf21
title: Data from: Recently-formed polyploid plants diversify at lower rates

description: Polyploidy, the doubling of genomic content, is a widespread feature,
 especially among plants, yet its macro-evolutionary impacts are
 contentious. Traditionally, polyploidy has been considered an evolutionary
 dead-end, whereas recent genomic studies suggest that polyploidy has been
 a key driver of macro-evolutionary success. Here we examine the
 consequences of polyploidy on the time scale of genera across a diverse
 set of vascular plants, encompassing hundreds of inferred polyploidization
 events. Likelihood-based analyses indicate that polyploids generally
 exhibit lower speciation rates and higher extinction rates than diploids,
 providing the first quantitative corroboration of the dead-end hypothesis.
 The increased speciation rates of diploids can, in part, be ascribed to
 their capacity to speciate via polyploidy. Only particularly “fit”
 lineages of polyploids may persist to enjoy longer term evolutionary
 success.
description: polyploidy_databaseThe database include 63 plant phylogenies in which ploidy variation is present. Most phylogenies are at the genus or subgenus level. Each folder contains five files: the phylogeny and associated data.
DOI: 10.5061/dryad.2d1b8
title: Data from: Climate effects on life cycle variation and population genetic architecture of the black bean aphid, Aphis fabae

description: Aphid species commonly have different reproductive modes ranging from
 cyclical to obligate parthenogenesis. The distribution of life cycle
 variation in aphids is generally determined by ecological forces, mainly
 climate, because only sexually produced diapausing eggs can survive harsh
 winters. Aphids are thus interesting models to investigate intrinsic and
 environmental factors shaping the competition among sexual and asexual
 lineages. We conducted a Europe-wide sampling of black bean aphids, Aphis
 fabae, and combined population genetic analyses based on microsatellite
 data with an experimental determination of life cycle strategies. Aphids
 were collected from broad beans (Vicia faba) as well as some
 Chenopodiaceae, but we detected no genetic differentiation between aphids
 from different host plants. Consistent with model predictions, life cycle
 variation was related to climate, with aphids from areas with cold winters
 investing more in sexual reproduction than aphids from areas with mild
 winters. Accordingly, only populations from mild areas exhibited a clear
 genetic signature of clonal reproduction. These differences arise despite
 substantial gene flow over large distances, which was evident from a very
 low geographic population structure and a lack of isolation-by-distance
 among 18 sites across distances of more than 1000 kilometres. There was
 virtually no genetic differentiation between aphids with different
 reproductive modes, suggesting that new asexual lineages are formed
 continuously. Indeed, a surprising number of A. fabae genotypes even from
 colder climates produced some parthenogenetic offspring under simulated
 winter conditions. From this we predict that a shift to predominantly
 asexual reproduction could take place rapidly in under climate warming.
description: Aphis_fabae_microsatellite_and_sampling_dataSampling details (locations, dates and host plants) of 655 European Aphis fabae specimens and the corresponding data for eight microsatellite loci.
DOI: 10.5061/dryad.gv1t0
title: Data from: Population genomic tests of models of adaptive radiation in Lake Victoria region cichlid fish.

description: Adaptive radiation is usually thought to be associated with speciation,
 but the evolution of intraspecific polymorphisms without speciation is
 also possible. The radiation of cichlid fish in Lake Victoria is perhaps
 the most impressive example of a recent rapid adaptive radiation, with
 600+ very young species. Key questions about its origin remain poorly
 characterized, such as the importance of speciation versus polymorphism,
 whether species persist on evolutionary time scales, and if speciation
 happens more commonly in small isolated or in large connected populations.
 We used 320 individuals from 105 putative species from Lakes Victoria,
 Edward, Kivu, Albert, Nabugabo and Saka, in a radiation-wide AFLP genome
 scan to address some of these questions. We demonstrate pervasive
 signatures of speciation supporting the classical model of adaptive
 radiation associated with speciation. A positive relationship between the
 age of lakes and the average genomic differentiation of their species, and
 a significant fraction of molecular variance explained by above-species
 level taxonomy suggest the persistence of species on evolutionary time
 scales, with radiation through sequential speciation rather than a single
 starburst. Finally the large gene diversity retained from colonization to
 individual species in every radiation suggests large effective population
 sizes and makes speciation in small geographical isolates unlikely.
description: Bezault_LVRS-AFLP_EVOL-10-0838Matrix of AFLP Genotypes. Individuals by lines and loci genotype (presence/absence) in column.
DOI: 10.5061/dryad.r044b
title: Data from: QTL linkage mapping of zebra finch beak color shows an oligogenic control of a sexually selected trait

description: Mate choice based on sexual ornaments can impose strong selection, which
 raises the question of how genetic variation in ornaments is maintained.
 One mechanism that has been proposed is genic capture. If ornament
 expression is influenced by general condition and condition is under
 polygenic control, selection will be inefficient in removing genetic
 variation. Here we analyze whether the genetic architecture of beak color
 in a population of zebra finches supports this hypothesis. Zebra finch
 beak color is commonly assumed to be under strong selection by mate
 choice, although some of the evidence is ambiguous. We show that beak
 redness has a heritability of 34% in our population and that it is
 strongly genetically correlated between the sexes, suggesting that it is
 largely controlled by the same genes in males and females. We mapped
 variation in beak redness based on 1,404 SNP markers genotyped in a large
 pedigree. We find evidence for linkage on four chromosomes (Tgu1, Tgu5,
 Tgu13, Tgu21), which together explain a large part of the additive genetic
 variance. Our finding of genomic regions with major additive effects is
 not consistent with directional selection and genic capture, but rather
 suggests a role of antagonistic pleiotropy in maintaining genetic
 variation.
description: data_phenotypesThe table contains data on phenotypes for all individuals (IndID). Columns mUVhalf, nmUVmax, nmRedhalf, res358, res570 and res707 show data from spectrometric beak colour measurements (for details see publication). DimDAad is the discriminant function score that was used for QTL mapping. F_Gen, FBroodID, Wline and Session are the identifiers for the mother, the brood of rearing, the maternal line and the measuring session, respectively. Age120 is an age identifier (in days). F is the inbreeding coefficient. Sex is the sex of the subject (0=females, 1=males).data_genotypesGenotype data for all successfully genotyped loci.data_linkagemapGenetic positions of SNP markers on the linkage map. Physical positions are published in Backström, N., Forstmeier, W., Schielzeth, H., Mellenius, H., Nam, K., Bolund, E., Webster, M. T., Öst, T., Schneider, M., Kempenaers, B., Ellegren, H., 2010. The recombinational landscape of the zebra finch Taeniopygia guttata genome. Genome Research. 20, 485-495. doi: 10.1101/gr.101410.109.data_pedigreeAll individuals in the pedigree and their parents. Unknown parents are shown as NA.
DOI: 10.5061/dryad.dv5dn
title: Data from: Patterns of interventions and the effect of coalitions and sociality on male fitness

description: In group living animals, especially among primates, there is consistent
 evidence that high-ranking males gain a higher reproductive output than
 low-ranking males. Primate studies have shown that male coalitions and
 sociality can impact male fitness; however, it remains unclear whether
 males could potentially increase their fitness by preferentially
 supporting and socializing with females. Here we investigate patterns of
 male interventions and the effect of coalitions and sociality on male
 fitness in rhesus macaques (Macaca mulatta) with particular focus on
 male-female interactions. We combined behavioral collected on Cayo
 Santiago with genetic data analyzed for male reproductive output and
 relatedness. Our results revealed that the ten top-ranking males provided
 the majority of all male support observed. In contrast to other primates,
 male rhesus macaques mainly formed all-down coalitions suggesting that
 coalitions are less likely used to enhance male dominance. Males
 supporting females during and before their likely conception were not more
 likely to fertilize those females. We also found no evidence that males
 preferably support their offspring or other close kin. Interestingly, the
 most important predictor of male support was sociality, since opponents
 sharing a higher sociality index with a given male were more likely to be
 supported. Furthermore, a high sociality index of a given male-female dyad
 resulted in a higher probability of paternity. Overall, our results
 strengthen the evidence that sociality affects fitness in male primates,
 but also suggest that in species in which males queue for dominance, it is
 less likely that males derive fitness benefits from coalitions.
description: data_model_1Input data for model 1.data_model_2Input data for model 2.data_model_3Input data for model 3.data_model_4Input data for model 4.data_model_5Input data for model 5.
DOI: 10.5061/dryad.8bb43
title: Data from: UV photoreceptors and UV-yellow wing pigments in Heliconius butterflies allow a color signal to serve both mimicry and intraspecific communication

description: Mimetic wing coloration evolves in butterflies in the context of predator
 confusion. Unless butterfly eyes have adaptations for discriminating
 mimetic color variation, mimicry also carries a risk of confusion for the
 butterflies themselves. Heliconius butterfly eyes, which express recently
 duplicated UV opsins, have such an adaptation. To examine bird and
 butterfly color vision as sources of selection on butterfly coloration we
 studied yellow wing pigmentation in the tribe Heliconiini. We confirmed
 using reflectance and mass spectrometry that only Heliconius use
 3-hydroxy-DL kynurenine (3-OHK) as a wing pigment. 3-OHK looks yellow to
 humans but it reflects both UV- and long-wavelength light whereas
 butterflies in related genera have chemically unknown yellow pigments
 mostly lacking UV-reflectance. Modeling of these color signals reveals
 that the two UV photoreceptors of Heliconius are better suited to
 separating 3-OHK from non-3-OHK spectra compared to the photoreceptors of
 related genera or birds. The co-occurrence of potentially enhanced
 UV-vision and a UV-reflecting ‘yellow’ wing pigment could allow
 unpalatable Heliconius private intraspecific communication in the presence
 of mimics. Our results are the best available evidence for the correlated
 evolution of a color signal and color vision. They also suggest that
 predator visual systems are error-prone in the context of mimicry.
description: Reflectance spectra of
 Heliconiine butterfly yellow wing pigmentsReflectance spectra of
 yellow wing colors of Heliconius butterflies and their relatives used in
 the color space model of birds and butterflies shown in Figure 4 of Bybee
 et al. Averaged reflectances and location of individual measurements on
 the wings are shown in Appendix.Bybee_et_al_reflectance_spectra.xlsAppendix: Wing photomicrographs and averaged yellow reflectance spectraPhotomicrographs of butterfly wings and averaged yellow reflectance spectra. Color-coded circles indicate the location from which the associated reflectance spectra were sampled. N=number of individual specimens measured. Left column: Dorsal wings and dorsal reflectance spectra, Right column: Ventral wings and ventral reflectance spectra. FD, forewing dorsal; FV, forewing ventral; HD, hindwing dorsal; HV, hindwing ventral.Appendix.pdfUV opsin nucleotide sequencesFasta file for UV opsin gene tree.Bybee_et_al.fasta
DOI: 10.15468/dl.zryfav
title: Occurrence Download

description: A dataset containing 14009 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Material sample, Specimen, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Paratrechina longicornis",
 "Year 1000-2025"
 ]
}

 The dataset includes 14009 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001713-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f40d8
title: Data from: Evidence for morphological and adaptive genetic divergence between lake and stream habitats in European minnows (Phoxinus phoxinus, Cyprinidae)

description: Natural selection drives local adaptation, potentially even at small
 temporal and spatial scales. As a result, adaptive genetic and phenotypic
 divergence can occur among populations living in different habitats. We
 investigated patterns of differentiation between contrasting lake and
 stream habitats in the cyprinid fish European minnow (Phoxinus phoxinus)
 at both the morphological and genomic level using geometric morphometrics
 and AFLP markers, respectively. We also used a spatial correlative
 approach to identify AFLP loci associated with environmental variables
 representing potential selective forces responsible for adaptation to
 divergent habitats. Our results identified two morphotypes between lakes
 and streams, with lake fish presenting a deeper body and caudal peduncle
 compared to stream fish. Differences between these morphotypes conformed
 to a priori predictions concerning biomechanics and swimming performance
 in lakes versus streams. Moreover, morphological differentiation was found
 to be associated to several environmental variables, which could affect
 body and caudal peduncle shape. We found adaptive genetic divergence
 between these contrasting habitats in the form of a few
 "outlier" loci (2.9%) whose genetic divergence exceeded neutral
 expectations. We also detected additional loci (6.6%) not associated with
 habitat type (lake versus stream), but contributing to adaptive genetic
 divergence between populations. Specific environmental variables related
 to trophic dynamics, landscape topography and geography were associated
 with several neutral and outlier loci. These results provide new insights
 into the morphological divergence and genetic basis of adaptation to
 differentiated habitats in European minnows.
description: aflpdata_Collin&FumagalliThis table contains 1930 AFLP markers from Phoxinus phoxinus. Population number, and individual ID are indicated. Individual IDs correspond to the first 2 letters of the population name, followed by the individual number. AFLP data are coded as: 0=recessive allele, 1= dominant allele
DOI: 10.7266/e7q8740e
title: Survey for Parents of OCEAN Kids Participants