cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/ry5-zzs-rgw
title: Logania kummerovi (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5061/dryad.pb5bb65m
title: Data from: Maintenance of a male-killing Wolbachia in Drosophila innubila by male-killing dependent and male-killing independent mechanisms

description: Many maternally inherited endosymbionts manipulate their host’s
 reproduction in various ways to enhance their own fitness. One such
 mechanism is male-killing, in which sons of infected mothers are killed by
 the endosymbiont during development. Several hypotheses have been proposed
 to explain the advantages of male-killing, including resource reallocation
 from sons to daughters of infected females, avoidance of inbreeding by
 infected females, and, if transmission is not purely maternal, the
 facilitation of horizontal transmission to uninfected females. We tested
 these hypotheses in Drosophila innubila, a mycophagous species infected
 with male-killing Wolbachia. There was no evidence of horizontal
 transmission in the wild and no evidence Wolbachia reduced levels of
 inbreeding. Resource reallocation does appear to be operative, as
 Wolbachia-infected females are slightly larger, on average, than
 uninfected females, although the selective advantage of larger size is
 insufficient to account for the frequency of infection in natural
 populations. Wolbachia-infected females from the wild – though not those
 from the lab – were more fecund than uninfected females. Experimental
 studies revealed that Wolbachia can boost the fecundity of
 nutrient-deprived flies and reduce the adverse effect of RNA virus
 infection. Thus, this male-killing endosymbiont can provide direct,
 male-killing-independent fitness benefits to infected female hosts in
 addition to possible benefits mediated via male-killing.
description: Wing length
 dataData for wing length
 from 2005-2008 - see figure 2.wings_edited2.csv
DOI: 10.5061/dryad.vq087
title: Data from: Antagonistic pleiotropy and mutation accumulation contribute to age-related decline in stress response

description: As organisms age, the effectiveness of natural selection weakens, leading
 to age-related decline in fitness-related traits. The evolution of
 age-related changes associated with senescence is likely influenced by
 mutation accumulation (MA) and antagonistic pleiotropy (AP). MA predicts
 that age-related decline in fitness components is driven by age-specific
 sets of alleles, non-negative genetic correlations within trait across
 age, and an increase in the coefficient of genetic variance. AP predicts
 that age-related decline in a trait is driven by alleles with positive
 effects on fitness in young individuals and negative effects in old
 individuals, and is expected to lead to negative genetic correlations
 within traits across age. We build on these predictions using an
 association mapping approach to investigate the change in additive effects
 of SNPs across age and among traits for multiple stress-response
 fitness-related traits, including cold stress with and without acclimation
 and starvation resistance. We found support for both MA and AP theories of
 aging in the age-related decline in stress tolerance. Our study
 demonstrates that the evolution of age-related decline in stress tolerance
 is driven by a combination of alleles that have age-specific additive
 effects, consistent with MA, as well as non-independent and antagonistic
 genetic architectures characteristic of AP.
description: DGRP Line Trait
 MeansMean response of one-
 and four-week old male and female flies for DGRP lines. Traits include
 acclimation survival (AC), cold stress survival (CS), rapid cold hardening
 score (RCH), and starvation resistance (S). For AC and CS, data are
 presented as proportion of flies per vial that survived the treatment. RCH
 was calculated as the difference in survival between the AC and CS
 treatments. For S, data are presented as the average time until death per
 vial in hours.Acclimation Survival of
 Chronologically Aged FliesAcclimation survival of
 DGPR lines after each line was aged until the population was half of the
 starting population. The first column contains the Bloomington stock
 identification number, the second column (long.sur) contains the average
 line acclimation survival when the population had reached 50% of the
 starting population. The third column is the average number of days until
 50% of the starting population had been reached. The fourth column is the
 average acclimation survival of each line at one week of age and the fifth
 column is the average acclimation survival of each line at four weeks of
 age. The fourth and fifth column were measured on a separate cohort of
 flies for each line.chronage.csv
DOI: 10.5061/dryad.8111
title: Data from: Sex reversal and primary sex ratios in the common frog (Rana temporaria)

description: Sex reversal has been suggested to have profound implications for the
 evolution of sex chromosomes and population dynamics in ectotherms.
 Occasional sex reversal of genetic males has been hypothesized to prevent
 the evolutionary decay of nonrecombining Y chromosomes caused by the
 accumulation of deleterious mutations. At the same time, sex reversals can
 have a negative effect on population growth rate. Here, we studied
 phenotypic and genotypic sex in the common frog (Rana temporaria) in a
 subarctic environment, where strongly female-biased sex ratios have raised
 the possibility of frequent sex reversals. We developed two novel
 sex-linked microsatellite markers for the species and used them with a
 third, existing marker and a Bayesian modelling approach to study the
 occurrence of sex reversal and to determine primary sex ratios in egg
 clutches. Our results show that a significant proportion (0.09, 95%
 credible interval: 0.04–0.18) of adults that were genetically female
 expressed the male phenotype, but there was no evidence of sex reversal of
 genetic males that is required for counteracting the degeneration of Y
 chromosome. The primary sex ratios were mostly equal, but three clutches
 consisted only of genetic females and three others had a significant
 female bias. Reproduction of the sex-reversed genetic females appears to
 create all-female clutches potentially skewing the population level adult
 sex-ratio consistent with field observations. However, based on a
 simulation model, such a bias is expected to be small and transient and
 thus does not fully explain the observed female-bias in the field.
description: Dryad
 sheet1. Adult: Genotype data
 of adult common frogs (Rana temporaria) in Kilpisjarvi Finland, using
 three microsatellite loci (RtSB03, BFG201, BFG266). 2. Tadpole: Genotype
 of tadpoles (Rana temporaria) in Kilpisjarvi Finland, using three
 microsatellite loci (RtSB03, BFG201, BFG266).
DOI: 10.3535/45g-v9n-fnl
title: Logania kummerovi (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/by4-wb2-3z1
title: Logania kummerovi (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/sy4-svq-z6p
title: Logania kummerovi (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5061/dryad.hp34m
title: Data from: Developmental dynamics of ecomorphological convergence in a transcontinental lizard radiation

description: Phenotypic convergence has confounded evolutionary biologists for
 centuries, explained as adaptations to shared selective pressures, or
 alternatively, the result of limited developmental pathways. We tested the
 relative roles of adaptation and constraint in generating convergent
 cranial morphologies across a large lizard radiation, the Lacertidae,
 whose members inhabit diverse environments throughout the Old World and
 display high amounts of homoplasy associated with ecological niche. Using
 three-dimensional X-ray computed tomography, we quantified cranial shape
 variation associated with ontogeny, allometry, and ecology, covering all
 lacertid genera and one-third of species diversity. Landmark-based
 geometric morphometrics showed that cranial shape varied significantly
 among biomes, with substantial convergence among arid-dwelling lineages.
 Comparisons of species ontogenetic growth trajectories between biomes
 revealed that allometric postdisplacement, as evidenced by decreased
 elevation of a constant slope, drives the convergent paedomorphic
 appearance of independent arid-dwelling forms. We hypothesize that
 observed heterochronic changes reflect temporal compression of ancestral
 life history in response to extreme environments, with associated
 phenotypes occurring as by-products of adaptive shifts in reproductive
 investment. Although allometry has long been considered a developmental
 constraint, our results demonstrate that allometric flexibility during
 early ontogeny produces convergent ecomorphologies over vast temporal and
 spatial scales, thus dramatically obscuring underlying phylogenetic
 signals.
description: Lacertidae phylogeny
 nexus filePhylogeny used in
 morphometric analyses of Lacertidae, based on the multigene supermatrix
 phylogeny of Hipsley CA, Miles DB, Müller J. 2014. Morphological disparity
 opposes latitudinal diversity gradient in lacertid lizards. Biology
 Letters 10:20140101.Lacertidaephylogeny.nexLacertidae size-corrected PC scoresSize-corrected PC scores for species averages (adults only)Lacertidae_sizecorrectedPCscores.xlsx
DOI: 10.5061/dryad.1kf36
title: Data from: Dendritic network structure and dispersal affect temporal dynamics of diversity and species persistence

description: Landscape connectivity structure, specifically the dendritic network
 structure of rivers, is expected to influence community diversity dynamics
 by altering dispersal patterns, and subsequently the unfolding of species
 interactions. However, previous comparative and experimental work on
 dendritic metacommunities has studied diversity mostly from an equilibrium
 perspective. Here we investigated the effect of dendritic versus linear
 network structure on local (α-diversity), among (β-diversity) and total
 (γ-diversity) temporal species community diversity dynamics. Using a
 combination of microcosm experiments, which allowed for active dispersal
 of 14 protists and a rotifer species, and numerical analyses, we
 demonstrate the general importance of spatial network configuration and
 basic life history tradeoffs as driving factors of different diversity
 patterns in linear and dendritic systems. We experimentally found that
 community diversity patterns were shaped by the interaction of dispersal
 within the networks and local species interactions. Specifically,
 α-diversity remained higher in dendritic networks over time, especially at
 highly connected sites. β-diversity was initially greater in linear
 networks, due to increased dispersal limitation, but became more similar
 to β-diversity in dendritic networks over time. Comparing the experimental
 results with a neutral metacommunity model we found that dispersal and
 network connectivity alone may, to a large extent, explain α- and
 β-diversity dynamics. However, additional mechanisms, such as variation in
 carrying capacity and competition–colonization tradeoffs, were needed in
 the model to capture the detailed temporal diversity dynamics of the
 experiments, such as a general decline in γ-diversity and long-term
 dynamics in α-diversity.
description: SeymourFronhoferAltermatt_RawData_Oikos_2015Raw species count data file with the following columns; 1)TimePoint is a factor indicating the sequential sampling time point 2)LandscapeType is a factor indicating the microcosm network type (linear or dendritic) 3)LandscapeID is a factor indicating the unique microcosm ID 4)NetworkPair is a factor indicating the Linear/Dendritic network pair - please refer to the publication for details. 5)PatchNumber is a factor indicating the sampling location within the microcosm network - please refer to the publication for details. 6)DateSampled is the date the sampling occurred in dd.mm.yy format 7-21) are the species count numbers for each sampling event with the names corresponding to Table A1 in the publication appendix. (http://www.oikosjournal.org/sites/oikosjournal.org/files/appendix/oik-02354_0.pdf)
DOI: 10.5061/dryad.m6s21
title: Data from: Social network analysis shows direct evidence for social transmission of tool use in wild chimpanzees.

description: Claims of culture in animals have been stimulated by studies on a wide
 range of taxa revealing group-specific behavior patterns that remain
 stable through generations, consistent with different behavioral
 innovations spreading within groups by social transmission in a manner
 similar to human culture. In chimpanzees, 39 behaviors have been
 identified as 'cultural', because alternative genetic and
 environmental explanations for the observed regional variation appear less
 plausible. This interpretation is supported by experimental data from
 captive chimpanzee groups. However, there is no experimental evidence for
 social learning in the wild, nor has there been direct observation of
 social diffusion of spontaneously occurring behavioral innovations. Here,
 we document the spread of two novel tool-use variants,
 'moss-sponging' and 'leaf-sponge re-use', in the Sonso
 chimpanzee community of Budongo Forest, Uganda. We use traditional
 network-based diffusion analysis (NBDA) to test whether these novel
 behaviors spread by social learning, as well as a newly developed dynamic
 version of NBDA, capable of capturing temporal aspects of acquisition,
 i.e. how each successive personal observations impact the subsequent
 acquisition of behavior. Both models provide strong evidence that
 diffusion patterns of moss-sponging, but not leaf-sponge re-use, are
 significantly better explained by social than asocial learning, therefore
 showing that wild chimpanzees socially learned moss-sponging from each
 other. The most conservative estimate of social transmission accounts for
 85% of observed events with an estimated 11-fold increase in learning rate
 for each time a novice observed an informed individual performing
 moss-sponging. We conclude that group-specific behavioral variants in
 chimpanzees can be socially learned, suggesting this prerequisite for
 culture originated in a common ancestor of great apes and humans, long
 before the advent of modern humans.
description: Data for NBDA in
 Hobaiter et al 2014The data for running the
 network based diffusion analyses described in the
 paper.Data
 for online storage.xlsx
DOI: 10.5061/dryad.dc8dq
title: Data from: Differences in male coloration are predicted by divergent sexual selection between populations of a cichlid fish

description: Female mating preferences can influence both intraspecific sexual
 selection and interspecific reproductive isolation, and have therefore
 been proposed to play a central role in speciation. Here, we investigate
 experimentally in the African cichlid fish Pundamilia nyererei if
 differences in male coloration between three para-allopatric populations
 (i.e. island populations with gene flow) of P. nyererei are predicted by
 differences in sexual selection by female mate choice between populations.
 Second, we investigate if female mating preferences are based on the same
 components of male coloration and go in the same direction when females
 choose among males of their own population, their own and other
 conspecific populations and a closely related para-allopatric
 sister-species, P. igneopinnis. Mate-choice experiments revealed that
 females of the three populations mated species-assortatively, that
 populations varied in their extent of population-assortative mating and
 that females chose among males of their own population based on different
 male colours. Females of different populations exerted directional
 intrapopulation sexual selection on different male colours, and these
 differences corresponded in two of the populations to the observed
 differences in male coloration between the populations. Our results
 suggest that differences in male coloration between populations of P.
 nyererei can be explained by divergent sexual selection and that
 population-assortative mating may directly result from intrapopulation
 sexual selection.
description: Selz et al.
 dataRaw
 data
DOI: 10.15468/dl.5jpk8c
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dalbergia latifolia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is India",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2010"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000938-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.20k7m
title: Data from: Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating

description: Background Bayesian relaxed-clock dating has significantly influenced our
 understanding of the timeline of plant evolution. This approach requires
 the use of priors on the branching process, yet little is known about
 their impact on divergence time estimates. We investigated the effect of
 branching priors using the iconic cycads. We conducted phylogenetic
 estimations for 237 cycad species using three genes and two calibration
 strategies incorporating up to six fossil constraints to (i) test the
 impact of two different branching process priors on age estimates, (ii)
 assess which branching prior better fits the data, (iii) investigate
 branching prior impacts on diversification analyses, and (iv) provide
 insights into the diversification history of cycads. Results Using Bayes
 factors, we compared divergence time estimates and the inferred dynamics
 of diversification when using Yule versus birth-death priors. Bayes
 factors were calculated with marginal likelihood estimated with
 stepping-stone sampling. We found striking differences in age estimates
 and diversification dynamics depending on prior choice. Dating with the
 Yule prior suggested that extant cycad genera diversified in the Paleogene
 and with two diversification rate shifts. In contrast, dating with the
 birth-death prior yielded Neogene diversifications, and four rate shifts,
 one for each of the four richest genera. Nonetheless, dating with the two
 priors provided similar age estimates for the divergence of cycads from
 Ginkgo (Carboniferous) and their crown age (Permian). Of these, Bayes
 factors clearly supported the birth-death prior. Conclusions These results
 suggest the choice of the branching process prior can have a drastic
 influence on our understanding of evolutionary radiations. Therefore, all
 dating analyses must involve a model selection process using Bayes factors
 to select between a Yule or birth-death prior, in particular on ancient
 clades with a potential pattern of high extinction. We also provide new
 insights into the history of cycad diversification because we found (i)
 periods of extinction along the long branches of the genera consistent
 with fossil data, and (ii) high diversification rates within the Miocene
 genus radiations.
description: Molecular dataset and
 phylogeny of CycadalesThis ZIP file contains
 two files. First, the molecular dataset (three genes, 5587 nucleotides,
 and 243 taxa) used to build the phylogeny, and to estimate origin and
 divergence times of the Cycadales. This is a NEXUS format, ready for
 MrBayes analyses. Second, the MrBayes tree obtained from the analysis
 described in the paper.Cycadales.zip
DOI: 10.5061/dryad.4ck36
title: Data from: Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection

description: Endemic species flocks inhabiting ancient lakes, oceanic islands and other
 long-lived isolated habitats are often interpreted as adaptive radiations.
 Yet molecular evidence for directional selection during species flocks
 radiation is scarce. Using partial transcriptomes of 64 species of Lake
 Baikal (Siberia, Russia) endemic amphipods and two non-endemic outgroups,
 we report a revised phylogeny of this species flock, and analyze evidence
 for positive selection within the endemic lineages. We confirm two
 independent invasions of amphipods into Baikal and demonstrate that
 several morphological features of Baikal amphipods, such as body armor and
 reduction of appendages and sensory organs, evolved in several lineages in
 parallel. Radiation of Baikal amphipods has been characterized by short
 phylogenetic branches and frequent episodes of positive selection which
 tended to be more frequent in the early phase of the second invasion of
 amphipods into Baikal when the most intensive diversification occurred.
 Notably, signatures of positive selection are frequent in genes encoding
 mitochondrial membrane proteins with electron transfer chain and ATP
 synthesis functionality. In particular, subunits of both the membrane and
 substrate-level ATP synthases show evidence of positive selection in the
 plankton species Macrohectopus branickii, possibly indicating adaptation
 to active plankton lifestyle and to survival under conditions of low
 temperature and high hydrostatic pressures known to affect membranes
 functioning. Other functional categories represented among genes likely to
 be under positive selection include Ca-binding muscle-related proteins,
 possibly indicating adaptation to Ca-deficient low mineralization Baikal
 waters.
description: Frequency of episodes of
 positive selectionBranch length, branching
 time and frequency of episodes of positive selection, per tree edge, found
 in either entire phylogeny (smaller set of COGs) or in individual clades
 (large sets of COGs).Subset4Dryad_aBSRELresultsBy(edge).xlsx
DOI: 10.5061/dryad.751p3
title: Data from: Intergametophytic selfing and microgeographic genetic structure shape populations of the intertidal red seaweed Chondrus crispus

description: Understanding how abiotic factors influence the spatial distribution of
 genetic variation provides insight into microevolutionary processes. The
 intertidal seascape is characterized by highly heterogeneous habitats
 which probably influence the partitioning of genetic variation at very
 small scales. The effects of tidal height on genetic variation in both the
 haploid (gametophytes) and diploid (tetrasporophytes) stages of the red
 alga Chondrus crispus were studied. Fronds were sampled every 25 cm within
 a 5 m × 5 m grid and along a 90-m transect at two shore heights (high and
 low) in one intertidal site in France. The multilocus genotype of 799
 fronds was determined (Nhaploid = 586; Ndiploid = 213) using eight
 microsatellite loci to test the following hypotheses: (i) high and low
 shore fronds belong to genetically differentiated populations, (ii) gene
 flow is restricted within the high shore habitat due to tidal-influenced
 isolation and (iii) significant FIS values are driven by life history
 characteristics. Pairwise FST estimates between high and low shore levels
 supported the hypothesis that high and low shore fronds were genetically
 differentiated. The high shore was characterized by the occurrence of
 within-shore genetic differentiation, reduced genetic diversity and
 increased levels of intergametophytic selfing, suggesting it is a marginal
 environment. These results suggest at fine scales within the intertidal
 seascape the same mechanisms as those over the species’ distributional
 range are at work with core and marginal population dynamics.
description: GenAlEx input files for
 transect and 5m grid gametophtyes and tetrasporophtyesGenAlEx input files with
 genotype at each locus and location in 5m grid or along
 transect.GenAlEx Input files for 5m and
 transects.xlsx