cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jj68n
title: Data from: A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range

description: In tropical regions, most primary ecosystems have been replaced by mosaic
 landscapes in which species must cope with a large shift in the
 distribution of their habitat and associated food resources. Primates are
 particularly vulnerable to habitat modifications. Most species persist in
 small fragments surrounded by complex human-mediated matrices whose
 structure and connectivity may strongly influence their dispersal and
 feeding behavior. Behavioral plasticity appears to be a crucial parameter
 governing the ability of organisms to exploit the resources offered by new
 matrix habitats and thus to persist in fragmented habitats. In this study,
 we were interested in the dietary plasticity of the golden-crowned sifaka
 (Propithecus tattersalli), an endangered species of lemur, found only in
 the Daraina region in north-eastern Madagascar. We used a DNA-based
 approach combining the barcoding concept and Illumina next-generation
 sequencing to (i) describe the species diet across its entire range and
 (ii) evaluate the influence of landscape heterogeneity on diet diversity
 and composition. Faeces from 96 individuals were sampled across the entire
 species range and their contents were analyzed using the trnL
 metabarcoding approach. In parallel, we built a large DNA reference
 database based on a checklist of the plant species of the Daraina region.
 Our results suggest that golden-crowned sifakas exhibit remarkable dietary
 diversity with at least 130 plant species belonging to 80 genera and 49
 different families. We highlighted an influence of both habitat type and
 openness on diet composition suggesting a high flexibility of foraging
 strategies. Moreover, we observed the presence of numerous cultivated and
 naturalized plants in the faeces of groups living in forest edge areas.
 Overall, our findings support our initial expectation that P. tattersalli
 is able to cope with the current level of alteration of the landscape and
 confirm our previous results on the distribution and the dispersal ability
 of this species.
description: Quemere_gh_sequence_dataThis file contains all unique sequences produced by G/H primers and occurring more than once. The sequences have been produced by the Illumina technology (GA IIx platform).Quemere_gh_final_dataThis file contains the filtered sequences produced by G/H primers. The sequences have been produced by the Illumina technology (GA IIx platform).Quemere_gh_filtered_data.txtQuemere_gh_finalThis file contains the filtered sequences produced by G/H primers. The sequences have been produced by the Illumina technology (GA IIx platform).
DOI: 10.5061/dryad.r6209
title: Data from: The role of inbreeding depression and mating system in the evolution of heterostyly

description: We investigated the role of morph-based differences in the expression of
 inbreeding depression in loss of the mid-styled morph from populations of
 tristylous Oxalis alpina as proposed by theoretical analyses. The extent
 of self-compatibility of reproductive morphs, the degree of
 self-fertilization, and the magnitude of inbreeding depression were
 investigated in three populations of O. alpina differing in their
 tristylous incompatibility relationships. All three populations exhibited
 significant inbreeding depression. In two populations with highly modified
 tristylous incompatibility, manifested as increased reciprocal
 compatibility between short- and long-styled morphs, substantial
 self-compatibility and self-fertilization of mid-styled morphs was
 detected, and expected to result in expression of inbreeding depression in
 the progeny of mid-styled morphs in the natural populations. In contrast,
 significant self-fertility of the mid-styled morph was absent from the
 population with typical tristylous incompatibility, and no
 self-fertilization could be detected. Although self-fertilization and
 expression of inbreeding depression should result in selection against the
 mid-styled morph in the later stages of the transition from tristyly to
 distyly, in O. alpina selection against the mid-styled morph in the early
 phases of the evolution of distyly is likely due to genic selection
 against mid alleles associated with modified tristylous incompatibility,
 rather than expression of inbreeding depression.
description: 727_MorseCanyon_fitnessInbreeding depression and seed files for greenhouse study on Morse Canyon population960_LaMariquita_fitnesInbreeding depression and seed data for the populations from La Mariquita971_PinosAltos_fitnessInbreeding depression and seed data for the population from Pinos AltosreoutcrossingfilesFiles for analyses in MLTET - mating system analyses of tetraploids.
DOI: 10.5061/dryad.481
title: Data from: A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs

description: The different environments that humans experience are likely to impact
 physiology and disease susceptibility. In order to estimate the magnitude
 of the impact of environment on transcript abundance, we examined gene
 expression in peripheral blood leukocyte samples from 46 desert nomadic,
 mountain agrarian and coastal urban Moroccan Amazigh individuals. Despite
 great expression heterogeneity in humans, as much as one third of the
 leukocyte transcriptome was found to be associated with differences among
 regions. Genome-wide polymorphism analysis indicates that genetic
 differentiation in the total sample is limited and is unlikely to explain
 the expression divergence. Methylation profiling of 1,505 CpG sites
 suggests limited contribution of methylation to the observed differences
 in gene expression. Genetic network analysis further implies that specific
 aspects of immune function are strongly affected by regional factors and
 may influence susceptibility to respiratory and inflammatory disease. Our
 results show a strong genome-wide gene expression signature of regional
 population differences that presumably include lifestyle, geography, and
 biotic factors, implying that these can play at least as great a role as
 genetic divergence in modulating gene expression variation in humans.
description: Supplementary
 FiguresMoroccoSuppFig.pdfSupplementary TablesMoroccoSuppTables.pdfZipped Extra Supplementary TablesIdaghdourextsupptables.zipSupplementary Table S2IdaghdourTableS2.xlsSupplementary Table S3IdaghdourTableS3.xlsSupplementary Table S4IdaghdourTableS4.xlsCombined DatasetCombined_Morocco.xls
DOI: 10.5061/dryad.c0164
title: Data from: Effects on population divergence of within-generational learning about prospective mates

description: Although learned mate preferences are suspected to have important effects
 during speciation, theoretical models have largely neglected the effects
 on speciation and population divergence of within-generational learning,
 that is, learning based upon prior experience with potential mates. Here
 we use population genetic models to address this deficit. Focussing on the
 situation of secondary contact between populations that still hybridize,
 we consider models of learning by females and by males under polygyny. We
 assess the effects of learning to prefer conspecifics from previous
 conspecific encounters, learning to avoid heterospecifics from previous
 heterospecific encounters, and learning to prefer familiar types. We
 examine the amount of population divergence that results from learning in
 these models. We also assess the effect of learning on the spread of an
 allele that strengthens assortative mating in both models. We find that
 learning can have counterintuitive, but logical and understandable effects
 that differ with the version of the model assessed. In general, population
 divergence is expected to increase most consistently when females learn to
 strengthen their preferences for conspecifics from previous encounters
 with conspecifics. Our results also suggest that within-generational
 learning will generally inhibit the spread of alleles strengthening
 assortative mating.
description: female reinf learn loop
 programProgram for section in
 the paper titled "Female learning model: Learning increases bias
 towards conspecifics and against heterospecifics"female reinf learn loop
 prog familiarityProgram for the section
 of the paper titled "Female learning model: Preference for familiar
 types"female reinf learn loop
 prog eigProgram for the female
 learning model that calculates the eigenvalues describing the rate of
 spread of an allele for assortative mating.male reinf learn loop
 programProgram for the section
 of the paper titled "Male learning model: Learning increases bias
 towards conspecifics and against heterospecifics I: Male learning from
 female identity"male reinf learn loop
 prog - corr pref strengthProgram for the section
 of the paper titled "Male learning model: Learning increases bias
 towards conspecifics and against heterospecifics II: learning is
 positively correlated with female preference
 strength"male reinf learn loop
 prog - female mat success prop to freqsProgram for the section
 of the paper titled "Male learning model: Learning increases bias
 towards conspecifics and against heterospecifics III: Variation in female
 mating success"male reinf learn loop
 prog familiarityProgram for the section
 of the paper titled "Male learning model: Preferences for familiar
 types"male reinf learn loop
 prog eigProgram for the male
 learning model that calculates the eigenvalues describing the rate of
 spread of an allele for assortative mating.
DOI: 10.5061/dryad.4f46b
title: Data from: Fine-scale genetic structure in a wild bird population: the role of limited dispersal and environmentally-based selection as causal factors

description: Individuals are typically not randomly distributed in space; consequently
 ecological and evolutionary theory depends heavily on understanding the
 spatial structure of populations. The central challenge of landscape
 genetics is therefore to link spatial heterogeneity of environments to
 population genetic structure. Here, we employ multivariate spatial
 analyses to identify environmentally induced genetic structures in a
 single breeding population of 1174 great tits Parus major genotyped at
 4701 single-nucleotide polymorphism (SNP) loci. Despite the small spatial
 scale of the study relative to natal dispersal we found multiple axes of
 genetic structure. We built distance-based Moran's eigenvector maps
 to identify axes of pure spatial variation, which we used for spatial
 correction of regressions between SNPs and various external traits known
 to be related to fitness components (avian malaria infection risk, local
 density of conspecifics, oak tree density and altitude). We found clear
 evidence of fine-scale genetic structure, with 21, 7 and 9 significant
 SNPs respectively associated with infection risk by two species of avian
 malaria (Plasmodium circumflexum and P. relictum) and local conspecific
 density. Such fine-scale genetic structure relative to dispersal
 capabilities suggests ecological and evolutionary mechanisms maintain
 within-population genetic diversity in this population with the potential
 to drive micro-evolutionary change.
description: Environmental
 dataEnvironmental data
 associated with individual great tits and coordinates for their breeding
 nest boxenvironmental_data.csvgenetic_dataIndividual great tits with associated SNPS
DOI: 10.34740/kaggle/dsv/14639926
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.9cs2v
title: Data from: Multigenerational hybridisation and its consequences for maternal effects in Atlantic salmon

description: Outbreeding between segregating populations can be important from an
 evolutionary, conservation, and economical- agricultural perspective.
 Whether and how outbreeding influences maternal effects in wild
 populations has rarely been studied, despite both the prominent maternal
 influence on early offspring survival and the known presence of fitness
 effects resulting from outbreeding in many taxa. We studied several traits
 during the yolk-feeding stage in multigenerational crosses between a wild
 and a domesticated Atlantic salmon (Salmo salar) population up to their
 third-generation hybrid in a common laboratory environment. Using
 cross-means analysis, we inferred that maternal additive outbreeding
 effects underlie most offspring traits, but that yolk mass also underlies
 maternal dominant effects. As a consequence of the interplay between
 additive and dominant maternally controlled traits, offspring from
 first-generation hybrid mothers expressed an excessive proportion of
 residual yolk mass, relative to total mass, at time of first feeding.
 Their residual yolk mass was 23-97% greater than those of other crosses
 and 31% more than that predicted by a purely additive model. Offspring
 additive, epistatic, and epistatic offspring-by-maternal outbreeding
 effects appeared to further modify this largely maternally controlled
 cross-means pattern, resulting in an increase in offspring size with the
 percentage of domesticated alleles. Fitness implications remain elusive
 because of unknown phenotype- by-environment interactions. However, these
 results suggest how mechanistically co-adapted genetic maternal control on
 early offspring development can be disrupted by the effects of combining
 alleles from divergent populations. Complex outbreeding effects at both
 the maternal and offspring levels make the prediction of hybrid phenotypes
 difficult.
description: Offspring_DataDam_DataPedigree_ALEVINpedigree for offspring at stage = 02_AlevinPedigree_FRYpedigree for offspring at stage = 03_FryOffspring Survival Data
DOI: 10.5061/dryad.b8842
title: Data from: Current approaches using genetic distances produce poor estimates of landscape resistance to interindividual dispersal

description: Landscape resistance reflects how difficult it is for genes to move across
 an area with particular attributes (e.g., land cover, slope). An
 increasingly popular approach to estimate resistance uses Mantel and
 partial Mantel tests or causal modeling to relate observed genetic
 distances to effective distances under alternative sets of resistance
 parameters. Relatively few alternative sets of resistance parameters are
 tested, leading to relatively poor coverage of the parameter space.
 Although this approach does not explicitly model key stochastic processes
 of gene flow, including mating, dispersal, drift, and inheritance, bias
 and precision of the resulting resistance parameters have not been
 assessed. We formally describe the most commonly used model as a set of
 equations and provide a formal approach for estimating resistance
 parameters. Our optimization finds the maximum Mantel r when an optimum
 exists, and identifies the same resistance values as current approaches
 when the alternatives evaluated are near the optimum. Unfortunately, even
 where an optimum existed, estimates from the most commonly used model were
 imprecise and were typically much smaller than the simulated true
 resistance to dispersal. Causal modeling using Mantel significance tests
 also typically failed to support the true resistance to dispersal values.
 For a large range of scenarios, current approaches using a simple
 correlational model between genetic and effective distances do not yield
 accurate estimates of resistance to dispersal. We suggest that analysts
 consider the processes important to gene flow for their study species,
 model those processes explicitly, and evaluate the quality of estimates
 resulting from their model.  
description: Simulation
 FilesSims900inds_L3Thresh250i.csv is CDPOP input file. C2C2_900Inds64PixelsIDXY.csv is file of individual locations used in CDPOP. CD3_900Inds64Pixels_R20.csv is input file of cost distances with b1=1 and b2=20. GDmatrix.csv is an output file from the 100th generation simulated by CDPOP.Archive.zip
DOI: 10.5061/dryad.4js80
title: Data from: The impact of paralogy on phylogenomic studies - a case study on annelid relationships

description: Phylogenomic studies based on hundreds of genes derived from expressed
 sequence tags libraries are increasingly used to reveal the phylogeny of
 taxa. A prerequisite for these studies is the assignment of genes into
 clusters of orthologous sequences. Sophisticated methods of orthology
 prediction are used in such analyses, but it is rarely assessed whether
 paralogous sequences have been erroneously grouped together as orthologous
 sequences after the prediction, and whether this had an impact on the
 phylogenetic reconstruction using a super-matrix approach. Herein, I
 tested the impact of paralogous sequences on the reconstruction of annelid
 relationships based on phylogenomic datasets. Using single-partition
 analyses, screening for bootstrap support, blast searches and pruning of
 sequences in the supermatrix, wrongly assigned paralogous sequences were
 found in eight partitions and the placement of five taxa (the annelids
 Owenia, Scoloplos, Sthenelais and Eurythoe and the nemertean Cerebratulus)
 including the robust bootstrap support could be attributed to the presence
 of paralogous sequences in two partitions. Excluding these sequences
 resulted in a different, weaklier supported placement for these taxa.
 Moreover, the analyses revealed that paralogous sequences impacted the
 reconstruction when only a single taxon represented a previously supported
 higher taxon such as a polychaete family. One possibility of a priori
 detection of wrongly assigned paralogous sequences could to combine 1) a
 screening of single-partition analyses based on criteria such as nodal
 support or internal branch length with 2) blast searches of suspicious
 cases as presented herein. Also possible are a posteriori approaches in
 which support for specific clades is investigated by comparing alternative
 hypotheses based on differences in per-site likelihoods. Increasing the
 sizes of EST libraries will also decrease the likelihood of wrongly
 assigned paralogous sequences, and in the case of orthology prediction
 methods like HaMStR it is likewise decreased by using more than one
 reference taxon.
description: Struck_PLOSone2013This file contains the datasets for both concatenated and single partitions, used for phylogenetic analyses in phylip-format. In addition the file also contans the Perl scripts used for the screening procedure.
DOI: 10.5061/dryad.qd19h
title: Data from: Repeated origin of three-dimensional leaf venation releases constraints on the evolution of succulence in plants

description: Succulent water storage is a prominent feature among plants adapted to
 arid zones, but we know little about how succulence evolves and how it is
 integrated into organs already tasked with multiple functions. Increased
 volume in succulent leaves, for example, may result in longer transport
 distances between veins and the cells that they supply, which in turn
 could negatively impact photosynthesis [1, 2, 3 and 4]. We quantified
 water storage [5] in a group of 83 closely related species to examine the
 evolutionary dynamics of succulence and leaf venation. In most leaves,
 vein density decreased with increasing succulence, resulting in
 significant increases in the path length of water from veins to
 evaporative surfaces. The most succulent leaves, however, had a distinct
 three-dimensional (3D) venation pattern, which evolved 11–12 times within
 this small lineage, likely via multiple developmental pathways. 3D
 venation “resets” internal leaf distances, maintaining moderate vein
 density in extremely succulent tissues and suggesting that the evolution
 of extreme succulence is constrained by the need to maintain an efficient
 leaf hydraulic system. The repeated evolution of 3D venation decouples
 leaf water storage from hydraulic path length, facilitating the
 evolutionary exploration of novel phenotypic space.
description: leaf_anatomyPrimary measurements on leaf anatomical cross sectionsmatK_ndhF_phyC_240_MCC240-taxon BEAST maximum clade credibility tree, Portulacineae + Molluginaceae and outgroups. Newick format, edited so that node posterior probabilities will be recognized by the ape package in RmatK_ndhF_phyC_treedist1000 trees sampled from the BEAST posterior tree distribution, newick formatmatK_ndhF_phyCAligned fasta file. Genbank accession numbers can be found in Table S1.
DOI: 10.5061/dryad.4gv88
title: Data from: Ontogenetic sequence reconstruction and sequence polymorphism in extinct taxa: an example using early tetrapods (Tetrapoda: Lepospondyli)

description: Ontogenetic sequence reconstruction is challenging particularly for
 extinct taxa because of when, where, and how fossils preserve. Different
 methods of reconstruction exist, but the effects of preservational bias,
 the applicability of size-independent methods, and the prevalence of
 sequence polymorphism (intraspecific variation) remain unexplored for
 paleontological data. Here I compare five different methods of ontogenetic
 sequence reconstruction and their effects on the detection of sequence
 polymorphism, using a large collection of the extinct vertebrates
 Microbrachis pelikani and Hyloplesion longicostatum. The postcranial
 ossification sequences presented here for those taxa are the first
 examples known for extinct lepospondyls. Sequences were reconstructed
 according to skull length, trunk length, increasing number of ontogenetic
 events, majority-rule consensus, and Ontogenetic Sequence Analysis (OSA).
 Results generally were in agreement, demonstrating that paleontological
 data may be used to robustly reconstruct developmental patterns. When
 reconstructing sequences based on fossils, size-based methods and OSA are
 more objective and less dependent on preservational bias than other
 techniques. Apart from the other methods, OSA also allows for statistical
 analysis of observed and predicted polymorphism. However, OSA requires a
 large sample size to yield meaningful results, and size-based methods are
 justified in paleontological studies when sample size is limited by poor
 preservation. Different methods of reconstruction detected different
 patterns of sequence polymorphism, although across all methods the
 magnitude of sequence variation for M. pelikani and H. longicostatum
 (1.3−3.4%) was within the lower range of values reported for extant
 vertebrates. Compared with other extinct and extant tetrapods, all
 sequence reconstruction methods consistently showed that M. pelikani and
 H. longicostatum exhibit advanced ossification of the pubis and delayed
 ossification of the scapula. However, the postcranial ossification
 sequences of these two taxa largely are congruent with those of other
 tetrapods, suggesting an underlying conservative ancestral pattern that
 evolved early in tetrapod history.
description: Olori_12031__Supplement_RThis file includes data tables of observations made directly from museum specimens, as well as appendices containing data resulting from Ontogenetic Sequence Analysis (OSA).