cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5sh77
title: Data from: Three-dimensional morphological variability of recent rhynchonellide brachiopod crura

description: Crura, the calcareous support structures of the lophophore in
 rhynchonellide brachiopods, have historically been used to justify
 higher-level rhynchonellide classification and reveal major evolutionary
 lineages within rhynchonellides. Seventeen crural types have been
 described and categorized into four groups based on variation in overall
 structure and cross-sectional shape, but not evaluated in a quantitative
 or comprehensive manner. Heterochrony has been hypothesized to play a role
 in the evolutionary transitions among some types, but the structural,
 developmental, and phylogenetic context for testing these hypotheses has
 not yet been established. In this study, we use three-dimensional
 geometric morphometric techniques to quantify morphological disparity
 among all six crural morphs in Recent adult rhynchonellides, with the goal
 of delineating more objective criteria for identifying and comparing
 crural morphs, ultimately to test hypotheses explaining morphological
 transformations in ontogeny and phylogeny. We imaged the crura of seven
 Recent rhynchonellide species, using X-ray computed microtomography. We
 used landmarks and semi-landmarks to define the dimensions and curvature
 of the crura and the surrounding hinge area. Procrustes-standardized
 landmark coordinates were analyzed using a principal component analysis to
 test the discreteness of the individual crural morphs and named groups of
 morphs, and to identify features that vary most among the crural
 configurations. Our results demonstrate that microCT imaging techniques
 provide novel ways to investigate the morphology of small features that
 may be otherwise impossible to quantify using more conventional imaging
 techniques. Although we predicted overlap among crural morphs in the 3-D
 shape space, the principal component analyses suggest that five of the six
 crural morphs differ distinctly from one another. Some but not all
 previously designated crural groups appear to exhibit morphological
 cohesion. This study establishes a quantitative morphological foundation
 necessary to begin an investigation of the phylogenetic significance of
 ontogenetic changes in crura, which will allow hypotheses of heterochrony
 to be tested.
description: Supplementary Table
 1The
 species name, crural type, crural group, collection location, and
 repository information of all adult extant rhynchonellides used in the
 analyses.Schreiber_Supplementary_Table_1.pdf
DOI: 10.5061/dryad.9k58f56
title: Data from: Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird

description: The highlands of Mesoamerica harbor some of the highest biodiversity in
 the world, especially in cloud forests, but the landscape drivers of this
 diversification are not well known. Taxonomy in this region has been
 challenging due to a lack of consensus about how to test species limits.
 We apply integrative taxonomy to an emblematic species of the Mesoamerican
 cloud forests, the Unicolored Jay (Aphelocoma unicolor). We assess
 divergence along three complementary axes – genetics, phenotype, and
 ecological niche – finding evidence for differentiation among five
 lineages, currently described as subspecies, in isolated forest patches.
 DNA suggests that lineages have long histories of divergence. Multivariate
 analysis of phenotype, along with an objective method for detecting
 phenotypic clusters, suggest that at least four of the five lineages are
 diagnosable. There was also a pattern of increasing ecological divergence
 through time. The divergence observed among lineages is comparable to
 other species-level divergences in the genus, arguing for elevation of at
 least two, and as many as four, lineages within A. unicolor to species
 rank. According to our timetree, cloud forest patches became isolated
 starting in the late Miocene, continuing into the Pleistocene, suggesting
 both tectonic activity and glacial cycles as drivers of speciation.
description: UNJA_cytbTree file from cytb mtDNA phylogenetic analyses.UNJA_uceTree file from UCE phylogenetic analyses.UNJA_phenotypic_dataMorphological and plumage reflectance data for museum specimens measured in the study. Plumage measurements include raw spectral values and three PC axes (brightness, hue, and chroma).UNJA_occurence_ptsOccurrence points used in niche differentiation analyses.READMERead me file for this data package.
DOI: 10.5061/dryad.gd3dq
title: Data from: Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli

description: Many populations live in environments subject to frequent biotic and
 abiotic changes. Nonetheless, it is interesting to ask whether an evolving
 population's mean fitness can increase indefinitely, and potentially
 without any limit, even in a constant environment. A recent study showed
 that fitness trajectories of Escherichia coli populations over 50 000
 generations were better described by a power-law model than by a
 hyperbolic model. According to the power-law model, the rate of fitness
 gain declines over time but fitness has no upper limit, whereas the
 hyperbolic model implies a hard limit. Here, we examine whether the
 previously estimated power-law model predicts the fitness trajectory for
 an additional 10 000 generations. To that end, we conducted more than 1100
 new competitive fitness assays. Consistent with the previous study, the
 power-law model fits the new data better than the hyperbolic model. We
 also analysed the variability in fitness among populations, finding
 subtle, but significant, heterogeneity in mean fitness. Some, but not all,
 of this variation reflects differences in mutation rate that evolved over
 time. Taken together, our results imply that both adaptation and
 divergence can continue indefinitely—or at least for a long time—even in a
 constant environment.
description: All.Hands.Concatenated.DataThis data file contains all of the plate counts for all of the fitness measurements within this paper.Mutation.Rate.DataThis file contains the mutation rate data from the fluctuation tests in Table S8 in the manuscript.All.Hands.Revised.SubmissionThis is the revised analysis script, adding a section at the end to include an additional analysis requested by a reviewer.
DOI: 10.5061/dryad.pr284
title: Data from: Persisting in defaunated landscapes: reduced plant population connectivity after seed dispersal collapse

description: 1. Defaunation of large-bodied frugivores could be causing severe losses
 of crucial ecosystem functions such as seed dispersal. The immediate
 ecological consequences may include alteration or even collapse of
 seed-mediated gene flow affecting plant population connectivity, with
 impacts on the regional scale distribution of genetic variation. Yet these
 far-reaching consequences of defaunation remain understudied. 2. Here we
 tested whether human-induced defaunation of the Canarian frugivorous
 lizards (Gallotia, Lacertidae) altered within-island population
 connectivity and the amount and large-scale distribution of genetic
 variation of Neochamaelea pulverulenta (Rutaceae), which relies
 exclusively on these lizards for seed dispersal. Our study system defines
 a lizard downsizing gradient with three contrasted ecological scenarios
 (islands) with relatively optimal (Gran Canaria; large-sized lizards),
 sub-optimal (Tenerife; medium) and collapsed seed dispersal processes (La
 Gomera; small). We extensively sampled individual plant genotypes from 80
 populations spanning the full geographic range of the plant to examine
 their genetic diversity, population-genetic network topologies, and the
 patterns of isolation both by distance (IBD) and resistance (IBR) across
 these three ecological scenarios. 3. Plant genetic diversity appeared
 unaffected by defaunation-mediated downsizing of frugivorous lizards.
 However, we found a reduced overall plant population connectivity together
 with an increased isolation by distance within the most defaunated islands
 (La Gomera and, to a lesser extent, Tenerife) when compared with the
 scenario preserving the functionality of lizard-mediated seed dispersal
 (Gran Canaria). The results, with a significant effect of lizard
 downsizing, were robust when controlling for biotic/abiotic differences
 among the three islands by means of isolation by resistance models (IBR).
 4. Synthesis. Our results provide valuable insights into the far-reaching
 consequences of the deterioration of mutualisms on plant population
 dynamics over very large spatial scales. Conservation of large-bodied
 frugivores is thus essential because their irreplaceable mutualistic
 dispersal services maintain an extensive movement of seeds across the
 landscape, crucial for maintaining the genetic cohesiveness of
 metapopulations and the adaptive potential of plant species across their
 entire geographic range.
description: data_PerezMendez_Neochamaelea_populations_JEcolGenetic distances among populations of N. pulverulenta in Gran Canaria, Tenerife and La Gomera (Euclidean genetic distances, GD; conditional genetic distance, cGD), and isolation by resistances values for: topographic complexity, potential and current vegetation, climate, non-resistance, and range shape of N. pulverulenta
DOI: 10.5061/dryad.g2p5g
title: Data from: Phylogeography of speciation: allopatric divergence and secondary contact between outcrossing and selfing Clarkia

description: The origins of hybrid zones between parapatric taxa have been of
 particular interest for understanding the evolution of reproductive
 isolation and the geographic context of species divergence. One challenge
 has been to distinguish between allopatric divergence (followed by
 secondary contact) versus primary intergradation (parapatric speciation)
 as alternative divergence histories. Here we use complementary
 phylogeographic and population genetic analyses to investigate the recent
 divergence of two subspecies of Clarkia xantiana and the formation of a
 hybrid zone within the narrow region of sympatry. We tested alternative
 phylogeographic models of divergence using ABC (approximate Bayesian
 computation) and found strong support for a secondary contact model and
 little support for a model allowing for gene flow throughout the
 divergence process (i.e. primary intergradation). Two independent methods
 for inferring the ancestral geography of each subspecies, one based on
 probabilistic character state reconstructions and the other on
 paleodistribution modeling, also support a model of divergence in
 allopatry and range expansion leading to secondary contact. The membership
 of individuals to genetic clusters suggests geographic substructure within
 each taxon where allopatric and sympatric samples are primarily found in
 separate clusters. We also observed coincidence and concordance of genetic
 clines across three types of molecular markers, which suggests that there
 is a strong barrier to gene flow. Taken together, our results provide
 evidence for allopatric divergence followed by range expansion leading to
 secondary contact. The location of refugial populations and the
 directionality of range expansion are consistent with expectations based
 on climate change since the last glacial maximum.
description: Microsatellite genotypes
 for Clarkia xantianamsats_archived_5_31_2012.txtphased_tempoMode_phylogeo_sequences
DOI: 10.5061/dryad.9387c
title: Data from: Nest suitability, fine-scale population structure and male-mediated dispersal of a solitary ground nesting bee in an urban landscape

description: Bees are the primary pollinators of flowering plants in almost all
 ecosystems. Worldwide declines in bee populations have raised awareness
 about the importance of their ecological role in maintaining ecosystem
 functioning. The naturally strong philopatric behavior that some bee
 species show can be detrimental to population viability through increased
 probability of inbreeding. Furthermore, bee populations found in
 human-altered landscapes, such as urban areas, can experience lower levels
 of gene flow and effective population sizes, increasing potential for
 inbreeding depression in wild bee populations. In this study, we
 investigated the fine-scale population structure of the solitary bee
 Colletes inaequalis in an urbanized landscape. First, we developed a
 predictive spatial model to detect suitable nesting habitat for this
 ground nesting bee and to inform our field search for nests. We genotyped
 18 microsatellites in 548 female individuals collected from nest
 aggregations throughout the study area. Genetic relatedness estimates
 revealed that genetic similarity among individuals was slightly greater
 within nest aggregations than among randomly chosen individuals. However,
 genetic structure among nest aggregations was low (Nei’s GST = 0.011).
 Reconstruction of parental genotypes revealed greater genetic relatedness
 among females than among males within nest aggregations, suggesting
 male-mediated dispersal as a potentially important mechanism of population
 connectivity and inbreeding avoidance. Size of nesting patch was
 positively correlated with effective population size, but not with other
 estimators of genetic diversity. We detected a positive trend between
 geographic distance and genetic differentiation between nest aggregations.
 Our landscape genetic models suggest that increased urbanization is likely
 associated with higher levels of inbreeding. Overall, these findings
 emphasize the importance of density and distribution of suitable nesting
 patches for enhancing bee population abundance and connectivity in human
 dominated habitats and highlights the critical contribution of landscape
 genetic studies for enhanced conservation and management of native
 pollinators.
description: Lopez-Uribe_etal_Colletes_inaqualisThis file contains the genotypes of 18 microsallite loci for 547 female individuals of Colletes inaequalis.
DOI: 10.5061/dryad.c9h41
title: Data from: Phenotypic integration in flowers of neotropical lianas: diversification of form with stasis of underlying patterns

description: Phenotypic integration is essential to the understanding of organismal
 evolution as a whole. In this study, a phylogenetic framework is used to
 assess phenotypic integration among the floral parts of a group of
 Neotropical lianas. Flowers consist of plant reproductive organs (carpels
 and stamens), usually surrounded by attractive whorls (petals and sepals).
 Thus, flower parts might be involved in different functions and
 developmental constraints, leading to conflicting selective forces. We
 found that Bignonieae flowers have very similar patterns of
 variance/covariance among traits and that such patterns are uncorrelated
 with the phylogenetic relationships between species. However, in spite of
 pattern stasis, our results also indicate that diversification of floral
 morphology in this group has occurred throughout the evolution of
 magnitudes of correlation among traits. Thus, we suggest that stabilizing
 selection has played an important role in phenotypic integration,
 resulting in the long-term stasis of covariance patterns underlying flower
 diversification during the ca. 50 Myr of evolution of Bignonieae. This is
 the first report of long-term stasis in the phenotypic integration of
 angiosperms, suggesting that patterns of floral morphology can be
 recognizable as specific attributes of distinct botanical families.
description: Floral traits
 measurements and phylogenetic distance matrices of
 Bignonieae.Worksheets: 1- traits
 description; 2- traits measurements (herbarium specimens;) 3- genus
 phylogenetic distances matrix; 4- species phylogenetic distances
 matrix.29262994JEB-2013-00188.R1.xlsx
DOI: 10.5061/dryad.pr1jf
title: Data from: Quantitative analysis of long-form aromatase mRNA in the male and female rat brain

description: In vitro studies show that estrogens acutely modulate synaptic function in
 both sexes. These acute effects may be mediated in vivo by estrogens
 synthesized within the brain, which could fluctuate more rapidly than
 circulating estrogens. For this to be the case, brain regions that respond
 acutely to estrogens should be capable of synthesizing them. To
 investigate this question, we used quantitative real-time PCR to measure
 expression of mRNA for the estrogen-synthesizing enzyme, aromatase, in
 different brain regions of male and female rats. Importantly, because
 brain aromatase exists in two forms, a long form with aromatase activity
 and a short form with unknown function, we targeted a sequence found
 exclusively in long-form aromatase. With this approach, we found highest
 expression of aromatase mRNA in the amygdala followed closely by the bed
 nucleus of the stria terminalis (BNST) and preoptic area (POA); we found
 moderate levels of aromatase mRNA in the dorsal hippocampus and cingulate
 cortex; and aromatase mRNA was detectable in brainstem and cerebellum, but
 levels were very low. In the amygdala, gonadal/hormonal status regulated
 aromatase expression in both sexes; in the BNST and POA, castration of
 males down-regulated aromatase, whereas there was no effect of estradiol
 in ovariectomized females. In the dorsal hippocampus and cingulate cortex,
 there were no differences in aromatase levels between males and females or
 effects of gonadal/hormonal status. These findings demonstrate that
 long-form aromatase is expressed in brain regions that respond acutely to
 estrogens, such as the dorsal hippocampus, and that gonadal/hormonal
 regulation of aromatase differs among different brain regions.
description: qPCR data (Tabatadze et
 al., 2014)Raw qPCR data (Tabatadze et
 al., 2014).xlsx
DOI: 10.5061/dryad.9f77pr0
title: Data from: Rapid evolution of generalised resistance mechanisms can constrain the efficacy of phage-antibiotic treatments

description: Antimicrobial resistance has been estimated to be responsible for over
 700,000 deaths per year, therefore new antimicrobial therapies are
 urgently needed. One way to increase the efficiency of antibiotics is to
 use them in combination with bacteria-specific parasitic viruses, phages,
 which have been shown to exert additive or synergistic effects in
 controlling bacteria. However, it is still unclear to what extent these
 combinatory effects are limited by rapid evolution of resistance,
 especially when the pathogen grows as biofilm on surfaces typical for many
 persistent and chronic infections. To study this, we used a microcosm
 system, where genetically isogenic populations of Pseudomonas aeruginosa
 PAO1 bacterial pathogen were exposed to a phage 14/1, gentamycin or a
 combination of them both in a spatially structured environment. We found
 that even though antibiotic and phage-antibiotic treatments were equally
 effective at controlling bacteria in the beginning of the experiment,
 combination treatment rapidly lost its efficacy in both planktonic and
 biofilm populations. Mechanistically, this was due to rapid resistance
 evolution: while both antibiotic and phage selected for increased
 resistance on their own, phage selection correlated positively with
 increase in antibiotic resistance, while biofilm growth, which provided
 generalised resistance mechanism, was favoured most in in the combination
 treatment. Only relatively small cost of resistance and weak evidence for
 coevolutionary dynamics were observed. Together these results suggest that
 spatial heterogeneity can promote rapid evolution of generalised
 resistance mechanisms without corresponding increase in phage infectivity,
 which could potentially limit the effectiveness of phage-antibiotic
 treatments in the evolutionary timescale.
description: Data for Rapid evolution
 of generalised resistance mechanisms can constrain the efficacy of
 phage-antibiotic treatments
DOI: 10.5061/dryad.b31h1
title: Data from: Sex differences in adult mortality rate mediated by early-life environmental conditions

description: Variation in sex differences is affected by both genetic and environmental
 variation, with rapid change in sex differences being more likely due to
 environmental change. One case of rapid change in sex differences is human
 lifespan, which has become increasingly female-biased in recent centuries.
 Long-term consequences of variation in the early-life environment may, in
 part, explain such variation in sex differences, but whether the
 early-life environment mediates sex differences in life-history traits is
 poorly understood in animals. Combining longitudinal data on 60 cohorts of
 pre-industrial Finns with environmental data, we show that the early-life
 environment is associated with sex differences in adult mortality and
 expected lifespan. Specifically, low infant survival rates and high rye
 yields (an important food source) in early-life are associated with
 female-bias in adult lifespan. These results support the hypothesis that
 environmental change has the potential to affect sex differences in
 life-history traits in natural populations of long-lived mammals.
description: Data for Griffin et al
 Ecology LettersHuman lifespan data from
 the Finnish population. Data includes lifespan on 1988 individuals from 60
 birth cohorts (R1), with environmental data (E1-E8), data on sex,
 censoring, and socioeconomic status (F1-F3). For further information
 please see the published article or contact the
 authors.dryad.txt
DOI: 10.5061/dryad.2fv7033c
title: Data from: On-farm dynamic management of genetic diversity: the impact of seed diffusions and seed saving practices on a population-variety of bread wheat

description: Since the domestication of crop species, humans have derived specific
 varieties for particular uses, and shaped the genetic diversity of these
 varieties. Here, using an interdisciplinary approach combining ethnobotany
 and population genetics, we document the within-variety genetic structure
 of a population-variety of bread wheat (Triticum aestivum L.) in relation
 to farmers practices to decipher their contribution to crop species
 evolution. Using 19 microsatellites markers, we conducted two
 complementary graph theory-based methods to analyze population structure
 and gene flow among 19 sub-populations of a single population-variety
 (Rouge de Bordeaux, RDB). The ethnobotany approach allowed us to determine
 the RDB history including diffusion and reproduction events. We found that
 the complex genetic structure among the RDB sub-populations is highly
 consistent with the structure of the seed diffusion and reproduction
 network drawn based on the ethnobotanical study. This structure
 highlighted the key role of the farmer-led seed diffusion through founder
 effects, selection and genetic drift due to human practices. An important
 result is that the genetic diversity conserved on farm is complementary to
 that found in the genebank indicating that both systems are required for a
 more efficient crop diversity conservation.
description: rdbr_19ssr_586ind