cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h30t5
title: Data from: Ontogenetic development of intestinal length and relationships to diet in an Australasian fish family (Terapontidae)

description: Background: One of the most widely accepted ecomorphological relationships
 in vertebrates is the negative correlation between intestinal length and
 proportion of animal prey in diet. While many fish groups exhibit this
 general pattern, other clades demonstrate minimal, and in some cases
 contrasting, associations between diet and intestinal length. Moreover,
 this relationship and its evolutionary derivation have received little
 attention from a phylogenetic perspective. This study documents the
 phylogenetic development of intestinal length variability, and resultant
 correlation with dietary habits, within a molecular phylogeny of 28
 species of terapontid fishes. The Terapontidae (grunters), an ancestrally
 euryhaline-marine group, is the most trophically diverse of
 Australia's freshwater fish families, with widespread shifts away
 from animal-prey-dominated diets occurring since their invasion of fresh
 waters. Results: Description of ontogenetic development of intestinal
 complexity of terapontid fishes, in combination with ancestral character
 state reconstruction, demonstrated that complex intestinal looping
 (convolution) has evolved independently on multiple occasions within the
 family. This modification of ontogenetic development drives much of the
 associated interspecific variability in intestinal length evident in
 terapontids. Phylogenetically informed comparative analyses (phylogenetic
 independent contrasts) showed that the interspecific differences in
 intestinal length resulting from these ontogenetic developmental
 mechanisms explained ~65% of the variability in the proportion of animal
 material in terapontid diets. Conclusions: The ontogenetic development of
 intestinal complexity appears to represent an important functional
 innovation underlying the extensive trophic differentiation seen in
 Australia's freshwater terapontids, specifically facilitating the
 pronounced shifts away from carnivorous (including invertebrates and
 vertebrates) diets evident across the family. The capacity to modify
 intestinal morphology and physiology may also be an important facilitator
 of trophic diversification during other phyletic radiations.
description: tera.gut.mt.nuc.concat.ginsiNexus file used to generate phylogenetic results.tera.gutXML file used in the BEAST analysis to generate a sample of 450 trees.tera.gut.trees.450450 trees (after 10% burn-in) from the BEAST analysis.tera.gut.star.beast.174XML file used in the *BEAST species tree analysis.tera.gut.star.beast.174.species.trees2Resulting tree from the *BEAST species tree analysis.
DOI: 10.5061/dryad.h4070
title: Data from: Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach

description: Premise of the study: We sought novel evolutionary insights for the highly
 diverse Saxifragales by constructing a large phylogenetic tree
 encompassing 36.8% of the species-level biodiversity. Methods: We built a
 phylogenetic tree for 909 species of Saxifragales and used this hypothesis
 to examine character evolution for: annual or perennial habit, woody or
 herbaceous habit, ovary position, petal number, carpel number, and stamen:
 petal ratio. We employed likelihood approaches to investigate the effect
 of habit and life history on speciation and extinction within this clade.
 Key results: Two major shifts occurred from a woody ancestor to the
 herbaceous habit, with multiple secondary changes from herbaceous to
 woody. Transitions among superior, subinferior, and inferior ovaries
 appear equiprobable. A major increase in petal number is correlated with a
 large increase in carpel number; these increases have co-occurred multiple
 times in Crassulaceae. Perennial or woody lineages have higher rates of
 speciation than annual or herbaceous ones, but higher probabilities of
 extinction offset these differences. Hence, net diversification rates are
 highest for annual, herbaceous lineages and lowest for woody perennials.
 The shift from annuality to perenniality in herbaceous taxa is frequent.
 Conversely, woody perennial lineages to woody annual transitions are
 infrequent; if they occur, the woody annual state is left immediately.
 Conclusions: The large tree provides new insights into character evolution
 that are not obvious with smaller trees. Our results indicate that in some
 cases the evolution of angiosperms might be conditioned by constraints
 that have been so far overlooked.
description: Saxafragales_Supermatrix.phyThe file "Saxafragales_Supermatrix.phy" contains the full supermatrix data set in phylip format.Saxifragales.R8s.tre"Saxifragales.R8s.tre" contains the estimated ML tree and 200 ML botstrap trees for the data set. All of the trees in "Saxifragales.R8s.tre" have ultrametric branch lengths corresponding to time (in million years), obtained by penalized likelihood analysis in R8s.Saxifragales_Accession_Table"Saxifragales_Accession_Table.txt" gives the GenBank id number for each sequence used in the supermatrix.GeneLocationsInAlignmentThe file "GeneLocationsInAlignment.txt" tells which genes correspond to which parts of the alignment in the supermatrix.Saxifragales.table1(POLYMRPHS)Saxifragales.table1(POLYMRPHS).xlsb and Saxifragales.table2.(SIMPLE)_.xlsb contain the character data used in the ancestral state reconstruction analyses.Saxifragales.table2.(SIMPLE)_Saxifragales.table1(POLYMRPHS).xlsb and Saxifragales.table2.(SIMPLE)_.xlsb contain the character data used in the ancestral state reconstruction analyses.
DOI: 10.5061/dryad.s5j81
title: Data from: Social environment influences the relationship between genotype and gene expression in wild baboons

description: Variation in the social environment can have profound effects on survival
 and reproduction in wild social mammals. However, we know little about the
 degree to which these effects are influenced by genetic differences among
 individuals, and conversely, the degree to which social environmental
 variation mediates genetic reaction norms. To better understand these
 relationships, we investigated the potential for dominance rank, social
 connectedness and group size to modify the effects of genetic variation on
 gene expression in the wild baboons of the Amboseli basin. We found
 evidence for a number of gene–environment interactions (GEIs) associated
 with variation in the social environment, encompassing social environments
 experienced in adulthood as well as persistent effects of early life
 social environment. Social connectedness, maternal dominance rank and
 group size all interacted with genotype to influence gene expression in at
 least one sex, and either in early life or in adulthood. These results
 suggest that social and behavioural variation, akin to other factors such
 as age and sex, can impact the genotype–phenotype relationship. We
 conclude that GEIs mediated by the social environment are important in the
 evolution and maintenance of individual differences in wild social
 mammals, including individual differences in responses to social
 stressors.
description: Environmental_datafull_genotype_callsSummarized_ASGE_data
DOI: 10.5061/dryad.k8760
title: Data from: Gene coexpression networks reveal key drivers of phenotypic divergence in lake whitefish

description: BACKGROUND: A functional understanding of processes involved in adaptive
 divergence is one of the awaiting opportunities afforded by high
 throughput transcriptomic technologies. Functional analysis of
 co-expressed genes has succeeded in the biomedical field in identifying
 key drivers of disease pathways. However, in ecology and evolutionary
 biology, functional interpretation of transcriptomic data is still
 limited. RESULTS: Here we used Weighted Gene Co-Expression Network
 Analysis (WGCNA) to identify modules of co-expressed genes in muscle and
 brain tissue of a lake whitefish backcross progeny. Modules were connected
 to gradients of known adaptive traits involved in the ecological
 speciation process between benthic and limnetic ecotypes. Key drivers,
 i.e. hub genes of functional modules related to reproduction, growth, and
 behavior were identified, and module preservation was assessed in natural
 populations. Using this approach, we identified modules of co-expressed
 genes involved in phenotypic divergence and their key drivers, and further
 identified a module part specifically rewired in the backcross progeny.
 CONCLUSIONS: Functional analysis of transcriptomic data can significantly
 contribute to the understanding of the mechanisms underlying ecological
 speciation. Our findings point to BMP and Calcium signaling as common
 pathways involved in coordinated evolution of trophic behavior, trophic
 morphology (gill rakers), and reproduction. Results also point to pathways
 implicating hemoglobins and constitutive stress response (HSP70) governing
 growth in lake whitefish.
description: lake_whitefish_brain_transcriptome_rawlake_whitefish_brain_transcriptome_normalized
DOI: 10.5061/dryad.304dn
title: Data from: Genetic drift or natural selection? Hybridization and asymmetric mitochondrial introgression in two Caribbean lizards (Anolis pulchellus and Anolis krugi)

description: Hybridization and gene introgression can occur frequently between closely
 related taxa, but appear to be rare phenomena among members of the
 species-rich West Indian radiation of Anolis lizards. We investigated the
 pattern and possible mechanism of introgression between two sister species
 from Puerto Rico, Anolis pulchellus and Anolis krugi, using mitochondrial
 (ND2) and nuclear (DNAH3, NKTR) DNA sequences. Our findings demonstrated
 extensive introgression of A. krugi mtDNA (k-mtDNA) into the genome of A.
 pulchellus in western Puerto Rico, to the extent that k-mtDNA has mostly
 or completely replaced the native mtDNA of A. pulchellus on this part of
 the island. We proposed two not mutually exclusive scenarios to account
 for the interspecific matings between A. pulchellus and A. krugi. We
 inferred that hybridization events occurred independently in several
 populations, and determined that k-mtDNA haplotypes harboured in
 individuals of A. pulchellus can be assigned to four of the five major
 mtDNA clades of A. krugi. Further, the spatial distribution of k-mtDNA
 clades in the two species is largely congruent. Based on this evidence, we
 concluded that natural selection was the probable driving mechanism for
 the extensive k-mtDNA introgression into A. pulchellus. Our two nuclear
 data sets yielded different results. DNAH3 showed reciprocal monophyly of
 A. pulchellus and A. krugi, indicating no effect of hybridization on this
 marker. In contrast, the two species shared nine NKTR alleles, probably
 due to incomplete lineage sorting. Our study system will provide an
 excellent opportunity to experimentally assess the behavioural and
 ecological mechanisms that can lead to hybridization in closely related
 taxa.
description: A. pulchellus and A.
 krugi ND2 sequencesAlligned ND2 sequences
 in a fasta format for Anolis krugi, Anolis pulchellus and
 outgroups.ND2.txtA. pulchellus and A. krugi nuclear NKTR sequencesAlligned and phased nuclear NKTR sequences in a fasta format for A. pulchellus and A. krugiNKTR.csvA. pulchellus and A. krugi nuclear DNAH3 sequencesAlligned and phased nuclear DNAH3 sequences for A. pulchellus, A. krugi and outgroupsDNAH3.csv
DOI: 10.5061/dryad.fj8dm
title: Data from: Characterization of human cortical gene expression in relation to glucose utilization.

description: Objectives: Human brain development follows a unique pattern characterized
 by a prolonged period of postnatal growth and reorganization, and a
 postnatal peak in glucose utilization. The molecular processes underlying
 these developmental changes are poorly characterized. The objectives of
 this study were to determine developmental trajectories of gene expression
 and to examine the evolutionary history of genes differentially expressed
 as a function of age. Methods: We used microarrays to determine
 age-related patterns of mRNA expression in human cerebral cortical samples
 ranging from infancy to adulthood. In contrast to previous developmental
 gene expression studies of human neocortex that relied on postmortem
 tissue, we measured mRNA expression from the nondiseased margins of
 surgically resected tissue. We used regression models designed to identify
 transcripts that followed significant linear or curvilinear functions of
 age and used population genetics techniques to examine the evolution of
 these genes. Results: We identified 40 transcripts with significant
 age-related trajectories in expression. Ten genes have documented roles in
 nervous system development and energy metabolism, others are novel
 candidates in brain development. Sixteen transcripts showed similar
 patterns of expression, characterized by decreasing expression during
 childhood. Comparative genomic analyses revealed that the regulatory
 regions of three genes have evidence of adaptive evolution in recent human
 evolution. Conclusions: These findings provide evidence that a subset of
 genes expressed in the human cerebral cortex broadly mirror developmental
 patterns of cortical glucose consumption. Whether there is a causal
 relationship between gene expression and glucose utilization remains to be
 determined.
description: Dataset
 S1Probes significantly
 associated with age.SternerEtAl_DatasetS1.xlsDataset S2Association tests between age and medication/neuropathology variables.SternerEtAl_DatasetS2.xlsDataset S3GOTerm and Kegg Pathway analyses for probes differentially expressed by age.SternerEtAl_DatasetS3.xlsDataset S4Worksheet A. GOTerm and Gene List enrichment analyses by expression level, association with age and profile types. Worksheet B. GOTerm and Gene Lists information.SternerEtAl_DatasetS4.xlsDataset S5Intersection of 36 genes differentially expressed in the cerebral cortex with Mammalian Genome Informatics Mammalian Phenotype data.SternerEtAl_DatasetS5.xlsx
DOI: 10.5061/dryad.7k14q
title: Data from: Next-generation museomics disentangles one of the largest primate radiations

description: Guenons (tribe Cercopithecini) are one of the most diverse groups of
 primates. They occupy all of sub-Saharan Africa and show great variation
 in ecology, behavior, and morphology. This variation led to the
 description of over 60 species and subspecies. Here, using next-generation
 DNA sequencing (NGS) in combination with targeted DNA capture, we
 sequenced 92 mitochondrial genomes from museum-preserved specimens as old
 as 117 years. We infer evolutionary relationships and estimate divergence
 times of almost all guenon taxa based on mitochondrial genome sequences.
 Using this phylogenetic framework, we infer divergence dates and
 reconstruct ancestral geographic ranges. We conclude that the
 extraordinary radiation of guenons has been a complex process driven by,
 among other factors, localized fluctuations of African forest cover. We
 find incongruences between phylogenetic trees reconstructed from
 mitochondrial and nuclear DNA sequences, which can be explained by either
 incomplete lineage sorting or hybridization. Furthermore, having produced
 the largest mitochondrial DNA dataset from museum specimens, we document
 how NGS technologies can 'unlock' museum collections, thereby
 helping to unravel the tree-of-life.
description: Guschanski_et_al_SISupporting Materials and Methods and Supporting Results, Supporting table legendsFig. S1Distribution of sequenced fragment sizesFig. S2Coverage and GC contentFig. S3Chronogram of CercopithecidaeFig. S4Comparison of prior and posterior distributions for calibrated nodes based on BEAST analysesFig. S5Juxtaposed mitochondrial trees containing all available samples and only samples with at least 13kb sequenced nucleotidesFig. S6Juxtaposed mitochondrial trees calibrated using different placement of the Macaca libyca fossil: as stem macaque on the right and as crown macaque on the left.Fig. S7Log lineage through time plot.Fig. S8Range overlap analysis on nuclear data from Perelman et al. 2011.Table S1Specimen taxonomy, collection locality and GenBank accession numbersTable S2Sample source, extraction, sequencing and enrichment successTable S3Mitochondrial primersTable S4Best partitioning scheme identified with PartitionFinder for mtDNA data using only RaxML evolutionary models and all modelsTable S5Taxonomic representation of nuclear data from Perelman et al. 2011Table S6Lagrange analysis: geographic species distribution, adjacency matrix and allowed rangesTable S7Tests of diversification models in LasermtDNA_BEAST_input_file_Mlibyca_crownExample BEAST control file with Macaca libyca used as crown macaque calibration point. The file contains among other information input for substitution models.mtDNA_RaxML_input_with_patitioning_scheme
DOI: 10.5061/dryad.9sj49
title: Data from: Evidence for hearing loss in amblyopsid cavefishes

description: The constant darkness of caves and other subterranean habitats imposes
 sensory constraints that offer a unique opportunity to examine evolution
 of sensory modalities. Hearing in cavefishes has not been well explored,
 and here we show that cavefishes in the family Amblyopsidae are not only
 blind but have also lost a significant portion of their hearing range. Our
 results showed that cave and surface amblyopsids shared the same audiogram
 profile at low frequencies but only surface amblyopsids were able to hear
 frequencies higher than 800 Hz and up to 2 kHz. We measured ambient noise
 in aquatic cave and surface habitats and found high intensity peaks near 1
 kHz for streams underground, suggesting no adaptive advantage in hearing
 in those frequencies. In addition, cave amblyopsids had lower hair cell
 densities compared with their surface relative. These traits may have
 evolved in response to the loud high-frequency background noise found in
 subterranean pools and streams. This study represents the first report of
 auditory regression in a subterranean organism.
description: AmblyopsisFile contains all raw data from auditory evoked potentials as well as all worksheet files compiled in TDT BioSig from all Amblyopsis trialsForbesichthysFile includes all raw data files and all TDT BioSig worksheets from auditory evoked potentials on all Forbesichthys trialsTyphlichtysFile includes all raw data files and all TDT BioSig worksheets from auditory evoked potentials on all Typhlichtys trials
DOI: 10.7927/c2rc-7j21
title: IPCC AR6 Synthesis Report LR Figure 3.5 (b): Cumulative CO2 emissions and warming until 2050

description: This figure displays the relationship between cumulative CO2 emissions and the increase in global surface temperature. Historical data (thin black line) shows historical CO2 emissions versus observed global surface temperature increase relative to the period 1850–1900. The grey range with its central line shows a corresponding estimate of the human-caused share of historical warming. Coloured areas show the assessed very likely range of global surface temperature projections, and thick coloured central lines show the median estimate as a function of cumulative CO2 emissions for the selected scenarios SSP1-1.9, SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5. Projections until 2050 use the cumulative CO2 emissions of each respective scenario, and the projected global warming includes the contribution from all anthropogenic forcers.
DOI: 10.5061/dryad.t68f3
title: Data from: The role of local ecology during hybridisation at the initial stages of ecological speciation in a marine snail

description: Hybrid zones of ecologically divergent populations are ideal systems to
 study the interaction between natural selection and gene flow during the
 initial stages of speciation. Here we perform an AFLP genome scan in
 parallel hybrid zones between divergent ecotypes of the marine snail
 Littorina saxatilis, which is considered a model case for the study of
 ecological speciation. RB (Ridged-Banded) and SU (Smooth-Unbanded)
 ecotypes are adapted to different shore levels and microhabitats, although
 they present a sympatric distribution at the mid-shore where they meet and
 mate (partially assortatively). We used shell morphology, outlier and
 non-outlier AFLP loci from RB, SU and hybrid specimens captured in
 sympatry to determine the level of phenotypic and genetic introgression.
 We found different levels of introgression at parallel hybrid zones and
 non-outlier loci showed more gene flow with greater phenotypic
 introgression. These results were independent from the phylogeography of
 the studied populations, but not from the local ecological conditions.
 Genetic variation at outlier loci was highly correlated with phenotypic
 variation. In addition, we used the relationship between genetic and
 phenotypic variation to estimate the heritability of morphological traits
 and to identify potential QTLs to be confirmed in future crosses. These
 results suggest that ecology (exogenous selection) plays an important role
 in this hybrid zone. Thus, ecologically-based divergent natural selection
 is responsible, simultaneously, for both ecotype divergence and
 hybridisation. On the other hand, genetic introgression occurs only at
 neutral loci (non-outliers). In the future, genome-wide studies and
 controlled crosses would give more valuable information about this process
 of speciation in the face of gene flow.
description: LittorinaSaxatilis_AFLPs
DOI: 10.5061/dryad.vr7bb
title: Data from: Identifying loci under selection against gene flow in isolation with migration models

description: When divergence occurs in the presence of gene flow, there can arise an
 interesting dynamic in which selection against gene flow, at sites
 associated with population-specific adaptations or genetic
 incompatibilities, can cause net gene flow to vary across the genome. Loci
 linked to sites under selection may experience reduced gene flow and may
 experience genetic bottlenecks by the action of nearby selective sweeps.
 Data from histories such as these may be poorly fitted by conventional
 neutral model approaches to demographic inference, which treat all loci as
 equally subject to forces of genetic drift and gene flow. To allow for
 demographic inference in the face of such histories, as well as the
 identification of loci affected by selection, we developed an
 isolation-with-migration model that explicitly provides for variation
 among genomic regions in migration rates and/or rates of genetic drift.
 The method allows for loci to fall into any of multiple groups, each
 characterized by a different set of parameters, thus relaxing the
 assumption that all loci share the same demography. By grouping loci, the
 method can be applied to data with multiple loci and still have tractable
 dimensionality and statistical power. We studied the performance of the
 method using simulated data, and we applied the method to study the
 divergence of two subspecies of European rabbits (Oryctolagus cuniculus).
description: Genetics_SousaetalThe file "Genetics_Sousaetal.zip" is a compressed file with the files used for the simulation study and analysis of European rabbit (Orytolagus cuniculus cuniculus and O. c. algirus) sequence data performed in VC Sousa, M Carneiro, N Ferrand and J Hey (2013) "Identifying loci under selection against gene flow in isolation with migration models", Genetics.
DOI: 10.5281/zenodo.18390534
title: LINF_320011100

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.5281/zenodo.18390533
title: LINF_320011100

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)