cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m8s502qb
title: Data from: Coral reefs as drivers of cladogenesis: expanding coral reefs, cryptic extinction events, and the development of biodiversity hotspots

description: Diversification rates within four conspicuous coral reef fish families
 (Labridae, Chaetodontidae, Pomacentridae, Apogonidae) were estimated using
 Bayesian inference. Lineage through time plots revealed a possible late
 Eocene/early Oligocene cryptic extinction event coinciding with the
 collapse of the ancestral Tethyan/Arabian hotspot. Rates of
 diversification analysis revealed elevated cladogenesis in all families in
 the Oligocene/Miocene. Throughout the Miocene, lineages with a high
 percentage of coral reef associated taxa display significantly higher net
 diversification rates than expected. The development of a complex mosaic
 of reef habitats in the Indo-Australian Archipelago (IAA) during the
 Oligocene/Miocene appears to have been a significant driver of
 cladogenesis. Patterns of diversification suggest that coral reefs acted
 as a refuge from high extinction, as reef taxa are able to sustain
 diversification at high extinction rates. The IAA appears to support both
 cladogenesis and survival in associated lineages, laying the foundation
 for the Recent IAA marine biodiversity hotspot.
description: Suppemental Material
 Appendix 1Appendix containing
 supplementary Tables, Results and DiscussionAppendix_1_Submission.pdfSuppemental Material Appendix 2Appendix containing supplemental figuresAppendix_2_submission.pdfLabridaeChronogram for family Labridae reconstructed using BEAST and compiled with TreeAnnotatorPomacentridaeChronogram of the Family Pomcentridae reconstructed using BEAST and compiled using TreeAnnotatorChaetodontidaeChronogram of the Family Chaetodontidae reconstructed using BEAST and compiled using TreeAnotatorApogonidaeChronogram of the Family Apogonidae reconstructed using BEAST and compiled using TreeAnnotator
DOI: 10.5061/dryad.7p1k8304
title: Data from: Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study

description: Phylogenomic analyses of ancient relationships are usually performed using
 amino acid data, but it is unclear whether amino acids or nucleotides
 should be preferred. With the 2-fold aim of addressing this problem and
 clarifying pancrustacean relationships, we explored the signals in the 62
 protein-coding genes carefully assembled by Regier et al. in 2010. With
 reference to the pancrustaceans, this data set infers a highly supported
 nucleotide tree that is substantially different to the corresponding, but
 poorly supported, amino acid one. We show that the discrepancy between the
 nucleotide-based and the amino acids-based trees is caused by
 substitutions within synonymous codon families (especially those of
 serine—TCN and AGY). We show that different arthropod lineages are
 differentially biased in their usage of serine, arginine, and leucine
 synonymous codons, and that the serine bias is correlated with the
 topology derived from the nucleotides, but not the amino acids. We suggest
 that a parallel, partially compositionally driven, synonymous codon-usage
 bias affects the nucleotide topology. As substitutions between serine
 codon families can proceed through threonine or cysteine intermediates,
 amino acid data sets might also be affected by the serine codon-usage
 bias. We suggest that a Dayhoff recoding strategy would partially
 ameliorate the effects of such bias. Although amino acids provide an
 alternative hypothesis of pancrustacean relationships, neither the
 nucleotides nor the amino acids version of this data set seems to bring
 enough genuine phylogenetic information to robustly resolve the
 relationships within group, which should still be considered unresolved.
description: Supplementary
 MaterialsThis file include all
 Supplementary Figures, the Supplementary Figures Captions and
 Supplementary Table 1.ser_rev_suppl.info.pdfAmino acid alignmentThis is the amino acid alignment used in Rota-Stabelli et al. (in review) Syst. Biol.aa.phyNucleotide alignmentThis is the nucleotide alignment used in Rota-Stabelli e al. (in review Syst. Biol.). It is originally from Regier et al. 2010 - Nature. See Main text for details.nn.norl12.phy
DOI: 10.5061/dryad.bf20k4q4
title: Data from: Evaluation of two approaches to genotyping MHC class I in a passerine – CE-SSCP and 454 pyrosequencing

description: Genes of the highly dynamic major histocompatibility complex (MHC) are
 directly linked to individual fitness and are of high interest in
 evolutionary ecology and conservation genetics. Gene duplication and
 positive selection usually lead to high levels of polymorphism in the MHC
 region, making genotyping of MHC a challenging task. Here, we compare the
 performance of two methods for MHC class I genotyping in a passerine with
 highly duplicated MHC class I genes: capillary electrophoresis single
 strand conformation polymorphism (CE-SSCP) analysis and 454 GS FLX
 Titanium pyrosequencing. According to our findings, the number of MHC
 variants (called alleles for simplicity) detected by CE-SSCP is
 significantly lower than detected by 454. To resolve discrepancies between
 the two methods we cloned and Sanger sequenced a MHC class I amplicon for
 an individual with high number of alleles. We found a perfect congruence
 between cloning/Sanger sequencing results and 454. Thus, in case of
 multi-locus amplification, CE-SSCP considerably underestimates individual
 MHC diversity. However, numbers of alleles detected by both methods are
 significantly correlated, although the correlation is weak (r = 0.32).
 Thus, in systems with highly duplicated MHC, 454 provides more reliable
 information on individual diversity than CE-SSCP.
description: MP_MER_supplOriginal electro-phoretograms of CE-SSCP, using ABI PRISM 3130 (Applied Biosystems). Individual ID represented by heading number.
DOI: 10.5061/dryad.227f5pn9
title: Data from: Antagonistic responses to natural and sexual selection and the sex-specific evolution of cuticular hydrocarbons in Drosophila simulans

description: Natural and sexual selection are classically thought to oppose one
 another, and while there is evidence for this, direct experimental
 demonstrations of this antagonism are largely lacking. Here we assessed
 the effects of sexual and natural selection on the evolution of cuticular
 hydrocarbons (CHCs), a character subject to both modes of selection, in
 Drosophila simulans. Natural selection and sexual selection were
 manipulated in a fully factorial design, and after 27 generations of
 experimental evolution the responses of male and female CHCs were
 assessed. The effects of natural and sexual selection differed greatly
 across the sexes. The responses of female CHCs were generally small, but
 CHCs evolved predominantly in the direction of natural selection. For
 males, profiles evolved via sexual and natural selection, as well as
 through the interaction between the two, with some male CHC components
 only evolving in the direction of natural selection when sexual selection
 was relaxed. These results indicate sex-specific responses to selection,
 and that sexual and natural selection act antagonistically for at least
 some combinations of CHCs.
description: Evolution_11-0425.R2_Dryad_UploadThis is a Microsoft Excel (c) spreadsheet containing the raw data for Evolution ID 11-0425.R2. Column headings are self explanatory. Data contained in columns K to AI represents area for CHC peaks 1-25 as quantified from chromatograms and data in columns AM to BJ is the area expressed in proportional values after dividing by the pentadecane standard (peak 1).
DOI: 10.5061/dryad.7j0b8468
title: Data from: Molecular cytogenetic and genomic insights to chromosomal evolution

description: This review summarizes aspects of the extensive literature on the patterns
 and processes underpinning chromosomal evolution in vertebrates and
 especially placental mammals. It highlights the growing synergy between
 molecular cytogenetics and comparative genomics, particularly with respect
 to fully or partially sequenced genomes, and provides novel insights into
 changes in chromosome number and structure across deep division of the
 vertebrate tree of life. The examination of basal numbers in the deeper
 branches of the vertebrate tree suggest a haploid (n) chromosome number of
 10–13 in an ancestral vertebrate, with modest increases in tetrapods and
 amniotes most probably by chromosomal fissioning. Information drawn
 largely from cross-species chromosome painting in the data-dense
 Placentalia permits the confident reconstruction of an ancestral karyotype
 comprising n=23 chromosomes that is similarly retained in Boreoeutheria.
 Using in silico genome-wide scans that include the newly released frog
 genome we show that of the nine ancient syntenies detected in conserved
 karyotypes of extant placentals (thought likely to reflect the structure
 of ancestral chromosomes), the human syntenic segmental associations
 3p/21, 4pq/8p, 7a/16p, 14/15, 12qt/22q and 12pq/22qt predate the
 divergence of tetrapods. These findings underscore the enhanced quality of
 ancestral reconstructions based on the integrative molecular cytogenetic
 and comparative genomic approaches that collectively highlight a pattern
 of conserved syntenic associations that extends back ~360 million years
 ago.
description: Supplementary File 2
 Ruiz-Herrera et alTable listing HSBs
 detected in all 14 vertebrate species analyzed in our study. The start and
 end points of each syntenic block in each species genome are
 presented.
DOI: 10.5061/dryad.p7h802r0
title: Data from: Citizen science reveals unexpected continental-scale evolutionary change in a model organism

description: Organisms provide some of the most sensitive indicators of climate change
 and evolutionary responses are becoming apparent in species with short
 generation times. Large datasets on genetic polymorphism that can provide
 an historical benchmark against which to test for recent evolutionary
 responses are very rare, but an exception is found in the brown-lipped
 banded snail (Cepaea nemoralis). This species is sensitive to its thermal
 environment and exhibits several polymorphisms of shell colour and banding
 pattern affecting shell albedo in the majority of populations within its
 native range in Europe. We tested for evolutionary changes in shell albedo
 that might have been driven by the warming of the climate in Europe over
 the last half century by compiling an historical dataset for 6,515 native
 populations of C. nemoralis and comparing this with new data on nearly
 3,000 populations. The new data were sampled mainly in 2009 through the
 Evolution MegaLab, a citizen science project that engaged thousands of
 volunteers in 15 countries throughout Europe in the biggest such exercise
 ever undertaken. A known geographic cline in the frequency of the colour
 phenotype with the highest albedo (yellow) was shown to have persisted and
 a difference in colour frequency between woodland and more open habitats
 was confirmed, but there was no general increase in the frequency of
 yellow shells. This may have been because snails adapted to a warming
 climate through behavioural thermoregulation. By contrast, we detected an
 unexpected decrease in the frequency of Unbanded shells and an increase in
 the Mid-banded morph. Neither of these evolutionary changes appears to be
 a direct response to climate change, indicating that the influence of
 other selective agents, possibly related to changing predation pressure
 and habitat change with effects on micro-climate.
description: mainanalysesV2R script used to perform the main analyses published in the paperHistorical dataThe historical data (pre-2000) and a readme file describing data cleaninghistCnem.csvmodCnemThe Modern data (post-2000)
DOI: 10.5061/dryad.8h7k64hh
title: Data from: Intrachromosomal rearrangements in avian genome evolution: evidence for regions prone to breakpoints

description: It is generally believed that the organization of avian genomes remains
 highly conserved in evolution as chromosome number is constant and
 comparative chromosome painting demonstrated there to be very few
 interchromosomal rearrangements. The recent sequencing of the zebra finch
 (Taeniopygia guttata) genome allowed an assessment of the number of
 intra-chromosomal rearrangements between it and the chicken (Gallus
 gallus) genome, revealing a surprisingly high number of intra-chromosomal
 rearrangements. With the publication of the turkey (Meleagris gallopavo)
 genome it has become possible to describe intrachromosomal rearrangements
 between these three important avian species, gain insight into the
 direction of evolutionary change and assess whether breakpoint regions are
 reused in birds. To this end, we aligned entire chromosomes between
 chicken, turkey and zebra finch, identifying syntenic blocks of at least
 250kb. Potential optimal pathways of rearrangements between each of the
 three genomes were determined, as was a potential Galliform ancestral
 organization. From this, our data suggest that around one third of
 chromosomal breakpoint regions may recur during avian evolution, with 10%
 of breakpoints apparently recurring in different lineages. This agrees
 with our previous hypothesis that mechanisms of genome evolution are
 driven by hotspots of non-allelic homologous recombination.
description: RepeatMasker
 DataOutput from
 RepeatMasker, from which repeat densities were calculated for segments and
 breakpoints.RepeatMaskerData.tar.gzSyntenyBlockData.tarThese files contain the coordinates of synteny blocks calculated from GenAlyzer match results. These were used to prepare the figures for segmentation (i.e. Figs 2, S1-S9).
DOI: 10.5061/dryad.766tk8qj
title: Data from: Pleistocene speciation in the genus Populus (Salicaceae)

description: The macro-evolutionary consequences of recent climate change remain
 controversial and there is little paleobotanical or morphological evidence
 that Pleistocene (1.8-0.12 Ma) glacial cycles acted as drivers of
 speciation, especially among lineages with long generation times, such as
 trees. We combined genetic and ecogeographic data from two closely related
 North American tree species, Populus balsamifera and P. trichocarpa
 (Salicacaeae) to determine if their divergence coincided with and was
 possibly caused by Pleistocene climatic events. We analyzed 32 nuclear
 loci from individuals of P. balsamifera and P. trichocarpa to produce
 coalescent-based estimates of the divergence time between the two species.
 We coupled the coalescent analyses with paleodistribution models to assess
 the influence of climate change on species’ range. Further, measures of
 niche overlap were used to investigate patterns of ecological
 differentiation between species. We estimated the divergence date of P.
 balsamifera and P. trichocarpa at approximately 75 Ka, during the middle
 of the Wisconsin glaciation (115–12 Ka). Significance tests of niche
 overlap, in conjunction with genetic estimates of migration, suggested
 that speciation occurred in allopatry, possibly resulting from the
 environmental effects of Pleistocene glacial cycles. Our results indicate
 the divergence of keystone tree species, that have shaped community
 diversity in northern North American ecosystems, was recent and may have
 been a consequence of Pleistocene-era glaciation and climate change.
description: Online Appendix
 1Collection and locality
 information for sampled populations of six Populus
 species.OnlineAppendix1.pdfOnline Appendix 2Primer and nucleotide substitution information for 32 nuclear loci used in the genetic study of Populus trichocarpa and P. balsamifera.OnlineAppendix2.pdfOnline Appendix 3Multivariate similarity surface and most dissimilar variable plots from species distribution models of Populus balsamifera and P. trichocarpa. They indicate novel climate conditions in the past and the climate variable responsible.OnlineAppendix3.pdfOnline Appendix 4Per locus gene statistic estimates for Populus balsamifera and P. trichocarpa.OnlineAppendix4.pdfOnline Appendix 5The predictive posterior p-values for summary statistics simulated in goodness-of-fit tests of Populus trichocarpa and P. balsamifera divergence models.OnlineAppendix5.pdf
DOI: 10.5061/dryad.22pm2619
title: Data from: Increasing temperature, not mean temperature, is a cue for avian timing of reproduction

description: Timing of reproduction in temperate zone birds is strongly correlated with
 spring temperature, with an earlier onset of breeding in warmer years.
 Females adjust their laying between years to be synchronized with local
 food sources and thereby optimize reproductive output. However, climate
 change currently disrupts the link between predictive environmental cues
 and spring phenology. To investigate direct effects of temperature on the
 decision to lay, and its genetic basis, we used pairs of Great Tits (Parus
 major) with known ancestry and exposed them to simulated spring scenarios
 in climate-controlled aviaries. In each of three years, we exposed birds
 to different patterns of changing temperature. We varied the timing of a
 temperature change, the daily temperature amplitude and the onset and
 speed of a seasonal temperature rise. We show that females fine-tune their
 laying in response to a seasonal increase in temperature, whereas mean
 temperature and daily temperature variation alone do not affect laying
 dates. Luteinizing hormone concentrations and gonadal growth in early
 spring were not influenced by temperature or temperature rise, possibly
 posing a constraint to an advancement of breeding. Similarities between
 sisters in their laying dates indicate genetic variation in cue
 sensitivity. These results refine our understanding of how changes in
 spring climate might affect the mismatch in avian timing and thereby
 population viability.
description: Schaper et al 2011 Am
 Nat file 1 laydates and physiologyFile 1 contains general
 information about the birds used in the experiment, such as weights,
 tarsus lengths and family relationships, as well as laying dates and
 physiological measurements (LH titers, gonad sizes). It contains a
 worksheet with explanations of the variables.Schaper et al 2011 Am
 Nat file 2 moltFile 2 contains
 information about the onset and duration of molt, as well as related
 information on the birds. It contains a worksheet with explanations of the
 variables.Schaper et al 2011 Am
 Nat file 3 temp 2008File 3 gives the hourly
 mean temperature in °C for each of 36 climatized aviaries in spring
 2008.Schaper et al 2011 Am
 Nat file 4 temp 2009File 4 gives the hourly
 mean temperature in °C for each of 36 climatized aviaries in spring
 2009.Schaper et al 2011 Am
 Nat file 5 temp 2010File 5 gives the hourly
 mean temperature in °C for each of 36 climatized aviaries in spring
 2010.
DOI: 10.5061/dryad.240h7g8r
title: Data from: Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood

description: Incomplete lineage sorting can cause incongruence between the phylogenetic
 history of genes (the gene tree) and that of the species (the species
 tree), which can complicate the inference of phylogenies. In this paper, I
 present a new coalescent-based algorithm for species tree inference with
 maximum likelihood. I first describe an improved method for computing the
 probability of a gene tree topology given a species tree, which is much
 faster than an existing algorithm by Degnan and Salter (2005). Based on
 this method, I develop a practical algorithm that takes a set of gene tree
 topologies and infers species trees with maximum likelihood. This
 algorithm searches for the best species tree by starting from initial
 species trees and performing heuristic search to obtain better trees with
 higher likelihood. This algorithm, called STELLS, has been implemented in
 a program that is downloadable from the author’s web page. The simulation
 results show that the STELLS algorithm is more accurate than an existing
 maximum likelihood method for many datasets, especially when there is
 noise in gene trees. I also show that the STELLS algorithm is efficient
 and can be applied to real biological datasets.
description: DataSim-Evolution2011.tarSimulation data file. It contains simulated species trees and gene trees, as well as the inferred gene trees from simulated DNA sequences. It also contains a README file.
DOI: 10.5061/dryad.tt28qk6f
title: Data from: Joint reconstruction of divergence times and life-history evolution in placental mammals using a phylogenetic covariance model

description: Violation of the molecular clock has been amply documented, and is now
 routinely taken into account by molecular dating methods. Comparative
 analyses have revealed a systematic component in rate variation, relating
 it to the evolution of life-history traits, such as body size or
 generation time. Life-history evolution can be reconstructed using
 Brownian models. However, the resulting estimates are typically uncertain,
 and potentially sensitive to the underlying assumptions. As a way of
 obtaining more accurate ancestral trait and divergence time
 reconstructions, correlations between life-history traits and substitution
 rates could be used as an additional source of information. In this
 direction, a Bayesian framework for jointly reconstructing rates, traits,
 and dates was previously introduced. Here, we apply this model to a 17
 protein-coding gene alignment for 73 placental taxa. Our analysis
 indicates that the coupling between molecules and life history can lead to
 a reevaluation of ancestral life-history profiles, in particular for
 groups displaying convergent evolution in body size. However,
 reconstructions are sensitive to fossil calibrations and to the Brownian
 assumption. Altogether, our analysis suggests that further integrating
 inference of rates and traits might be particularly useful for
 neontological macroevolutionary comparative studies.
description: Lartillot&Delsuc-Evolution_78mammalsConcatenation of 17 protein-coding nuclear genes for 78 mammals in interleaved nexus format. Each individual gene dataset has been filtered by codon using Gblocks prior to concatenation.Lartillot&Delsuc-Evolution_78mammals_intreePhylogenetic usertree for 78 mammals in Newick format. Phylogenetic relationships in this tree followed the recent litterature on placental mammal phylogenetics.Lartillot&Delsuc-Evolution_73placentalsConcatenation of 17 protein-coding nuclear genes for 73 placentals in interleaved nexus format. This dataset was obtained by extracting placental taxa from the largest 78 mammals dataset.Lartillot&Delsuc-Evolution_73placentals_intreePhylogenetic usertree for 73 placentals used for performing all analyses with the 73 placentals dataset. Phylogenetic relationships in this tree followed the recent literature on placental mammal phylogenetics.
DOI: 10.5061/dryad.792g75qr
title: Data from: Male-mediated effects on female meiotic recombination

description: Recombination rates vary owing to an individual’s genetic composition
 and/or its environmental condition. Yet, the effects of mating partner on
 recombination rates have not been considered. Here, I document a
 previously undescribed male-mediated effect on female recombination rates.
 After crossing females to males from different genetic backgrounds, I
 observed a significant difference in proportion of recombinant offspring
 based on the genetic background of the father (p=0.0292; 3 df; F=3.07).
 Genetic variation in male ability to affect recombination rate in their
 mates suggests the potential for sexual conflict on optimal proportion of
 recombinant offspring, perhaps leading to changes in population-level
 recombination rates with varying levels of sexual selection.
description: LSS_forDryadGenotypes at four markers for all individuals included in analysis and additional information on maternal/paternal genotypes, sex, etc. See paper for details of the statistical model fit to this data.