cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vd158h6
title: Data from: Early-life stress strengthens trait covariance: a plastic response that results in reduced flexibility

description: Stress exposure during development can impact both the expression of
 individual traits and associations between traits, but whether stress
 results in stronger or weaker associations between traits is unclear. In
 this study, we examined within and among-trait associations for
 morphological and physiological traits in zebra finches (Taeniopygia
 guttata) exposed to corticosterone (CORT) during the nestling and
 fledgling stages, and in control birds. Birds exposed to CORT exhibited
 stronger correlations within traits and stronger associations among
 traits. We found preliminary evidence that birds that died before the
 median age of death had stronger within and among-trait correlations
 independent of treatment, and among CORT-treated birds, smaller birds were
 more likely to survive beyond the median age than larger birds. These
 findings suggest that early-life stress hormone exposure can result in
 reduced developmental flexibility, with potential fitness ramifications,
 and that these costs may be greater for larger offspring. Furthermore, our
 results provide experimental evidence for pleiotropic effects of hormones
 during development through altered patterns of phenotypic correlation.
description: Early-life stress
 strengthens trait covariance in zebra finchesData for AmNat article:
 Early-life stress strengthens trait covariance: a plastic response that
 results in reduced flexibility. All raw data included. Accompanying
 document includes key to all columns.Data for
 dryad.xlsx
DOI: 10.5061/dryad.8h8fh
title: Data from: A basin-scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: a case study of giant salamanders in Japan

description: 1. To prevent the invasion of exotic species causing a decline in an
 endangered endemic species, it is important to determine the distribution
 of both species at an early stage, when the density of the exotic species
 is still low, and to manage the invasion immediately. However,
 distinguishing between closely related species is difficult because they
 share similar characteristics. 2. The identification of DNA fragments
 sampled from a body of water (environmental DNA) has become a popular
 technique for rapidly determining the distribution of a target species. In
 this study, we analysed environmental DNA in water samples from 37 sites
 across the Katsura River basin in Japan. We used TaqMan real-time PCR to
 distinguish the Japanese giant salamander Andrias japonicus from the
 closely related Chinese giant salamander Andrias davidianus, which is
 known to invade Japanese rivers and hybridize with the Japanese species.
 3. In environmental samples, we detected mtDNA of the endemic species at
 25 sites and mtDNA of the exotic species at nine sites. The DNA detection
 sites were concentrated in the upstream region. The exotic species DNA was
 found beyond the limits of an earlier capturing survey. 4. Synthesis and
 applications. Using environmental DNA to monitor the two salamander
 species requires less time and effort than traditional surveys, so a
 wide-ranging survey can be conducted rapidly. Our results showed that
 performing three environmental DNA surveys for each site between autumn
 and winter is desirable for giant salamanders. Further collection of
 environmental DNA, in combination with conventional population surveys,
 will provide valuable information that can help protect rare endemic
 species in a variety of aquatic ecosystems and can help monitor the
 invasion of exotic species.
description: Fukumoto_et_al_2015_raw_dataThe file contains following data: 1) raw data of real-time PCR for endemic species, 2) raw data of real-time PCR for exotic species, and 3) raw
DOI: 10.5061/dryad.7fb195gg
title: Data from: The interplay of dispersal limitation, rivers, and historical events shapes the genetic structure of an Amazonian frog

description: Disentangling the impact of landscape features such as rivers and
 historical events on dispersal is a challenging but necessary task to gain
 a comprehensive picture of the evolution of diverse biota such as that
 found in Amazonia. Adenomera andreae, a small, territorial, terrestrial
 frog species of the Amazonian forest represents a good model for such
 studies. We combined Cytochrome b sequences with 12 microsatellites to
 investigate the genetic structure at two contrasted spatial scales in
 French Guiana: along a ~6 km transect to evaluate dispersal ability and
 between paired bank populations along a ~65 km stretch of the Approuague
 river to test the effect of rivers as barriers to dispersal. We observed
 significant spatial genetic structure between individuals at a remarkably
 small geographical scale and conclude that the species has a restricted
 dispersal ability likely tied to its life history traits. Mitochondrial
 and microsatellite data also indicate a high level of differentiation
 among populations on opposite banks of the river and, in some cases, among
 populations on the same riverbank. These results suggest that the observed
 population structure in A. andreae is due to restricted dispersal
 abilities combined with the action of rivers and Quaternary population
 isolation. Given that Amazonia hosts a great portion of anurans, as well
 as other small vertebrates, that display life history traits comparable to
 Adenomera andreae, we argue that our analyses provide new insights into
 the complex interactions among evolutionary processes shaping Amazonian
 biodiversity.
description: microsats
 AdenomeraMicrosatellites raw
 data
DOI: 10.5061/dryad.9vr0c
title: Data from: Comparative tests of the role of dewlap size in Anolis lizard speciation

description: Phenotypic traits may be linked to speciation in two distinct ways:
 character values may influence the rate of speciation or diversification
 in the trait may be associated with speciation events. Traits involved in
 signal transmission, such as the dewlap of Anolis lizards, are often
 involved in the speciation process. The dewlap is an important visual
 signal with roles in species recognition and sexual selection, and dewlaps
 vary among species in relative size as well as colour and pattern. We
 compile a dataset of relative dewlap size digitized from photographs of
 184 anole species from across the genus' geographical range. We use
 phylogenetic comparative methods to test two hypotheses: that larger
 dewlaps are associated with higher speciation rates, and that relative
 dewlap area diversifies according to a speciational model of evolution. We
 find no evidence of trait-dependent speciation, indicating that larger
 signals do not enhance any role the dewlap has in promoting speciation.
 Instead, we find a signal of mixed speciational and gradual trait
 evolution, with a particularly strong signal of speciational change in the
 dewlaps of mainland lineages. This indicates that dewlap size diversifies
 in association with the speciation process, suggesting that divergent
 selection may play a role in the macroevolution of this signalling trait.
description: Dewlap size
 dataData on residual dewlap
 area of Anolis species from a log-log phylogenetic regression on head
 length (cm) as a measure of body size. Standard deviations and standard
 errors are calculated for species with multiple individuals; otherwise the
 mean intraspecific standard deviation is used. Absolute log dewlap area
 (cm^2) is also provided. Sample sizes are provided, as well as a column
 for the number of individuals measured from field guides for each
 species.Dewlap_data_archive.csvSpeciational analysis scriptScript for running the "multi-psi" analysis presented in the manuscript. Functions and code are annotated to indicate the steps in a basic analysis.Speciational_analysis_script.RGamble et al MCC phylogeny of AnolisPhylogenetic tree used in the analyses. The tree is from Gamble et al. (2013) and is available elsewhere on Dryad (doi:10.5061/dryad.dp848.2), but this lightly processed version is provided for ease of running analyses while ensuring taxa names match the data set.Gamble_MCC.phy
DOI: 10.5061/dryad.9271vq7
title: Data from: Enzyme replacement therapy and white matter hyperintensity progression in Fabry disease

description: Objective: To explore the association between Enzyme Replacement Therapy
 (ERT), clinical characteristics and the rate of progression of White
 Matter Hyperintensities (WMHs) in Fabry disease (FD) patients. Methods:
 Patients with a confirmed diagnosis of FD, aged &gt;18 years,
 participating in an existing FD observational study (NCT00196742), with at
 least two serial MRI brain scans at least 2 years apart for the period
 between December 2006 and August 2016 were included in this cohort study.
 Total WMH volume was estimated for each image using a semi-automated
 procedure. We performed linear regression to calculate the primary outcome
 measure of WMH change rate for each participant. Associations between ERT,
 clinical characteristics and the primary outcome were explored using
 multiple linear regression. Results: 863 MRI time-points were analysed for
 the 149 included participants. Age (p&lt;0.0005; increasing age
 associated with faster WMH progression), total cholesterol (p=0.03;
 increasing total cholesterol associated with slower WMH progression) and a
 history of peripheral pain (p=0.02; peripheral pain associated with faster
 WMH progression) were independently associated with WMH change rate in the
 primary analysis. We did not find an association between ‘ERT at any point
 between baseline and final MRI’ and WMH change rate (p=0.22). Conclusions:
 In a large cohort of FD patients, we did not find an association between
 ERT and WMH progression, whilst higher total cholesterol was associated
 with slower WMH progression. Further research is needed into the
 pathogenesis and treatment of cerebrovascular disease in this rare
 condition.
description: Supplemental
 Data
DOI: 10.5061/dryad.v09hh
title: Data from: Calcium interacts with temperature to influence Daphnia movement rates

description: Predicting the ecological responses to climate change is particularly
 challenging, because organisms might be affected simultaneously by the
 synergistic effects of multiple environmental stressors. Global warming is
 often accompanied by declining calcium concentration in many freshwater
 ecosystems. Although there is growing evidence that these changes in water
 chemistry and thermal conditions can influence ecosystem dynamics, little
 information is currently available about how these synergistic
 environmental stressors could influence the behaviour of aquatic
 organisms. Here, we tested whether the combined effects of calcium and
 temperature affect movement parameters (average speed, mean turning
 frequency and mean-squared displacement) of the planktonic Daphnia magna,
 using a full factorial design and exposing Daphnia individuals to a range
 of realistic levels of temperature and calcium concentration. We found
 that movement increased with both temperature and calcium concentration,
 but temperature effects became considerably weaker when individuals were
 exposed to calcium levels close to survival limits documented for several
 Daphnia species, signalling a strong interaction effect. These results
 support the notion that changes in water chemistry might have as strong an
 effect as projected changes in temperature on movement rates of Daphnia,
 suggesting that even sublethal levels of calcium decline could have a
 considerable impact on the dynamics of freshwater ecosystems.
description: Betini et al. calcium
 and temperature effects on movementtemperature: temperature
 treatment used in the experiment in oC calcium: calcium level used in the
 experiment in mg/L individualID: unique id of each individual used in the
 experiment, within each temperature level start_position: position
 relative to the ruler where each individual start each step direction:
 whether individual moved to the right (R) or left (L) in each step time:
 time of each step in seconds of distance: distance of each step in
 cm
DOI: 10.5061/dryad.rg1cj
title: Data from: May gen. n. (Araneae: Sparassidae): a unique lineage from southern Africa supported by morphological and molecular features

description: A new genus of huntsman spiders, May gen. n. is described from southern
 Africa, together with four new species: M. bruno sp. n. (♂, ♀; South
 Africa), M. ansie sp. n. (♂; Namibia), M. rudy sp. n. (♂; Namibia) and M.
 norm sp. n. (♀; Namibia). Diagnostic characters proposed include not only
 those for the genus but also for the so-called African clade. Unique
 within the entire family are the reduction of the gnathocoxal serrula and
 the prolaterad embolus. Special claw tuft setae and metatarsi I to III
 with three prolateral and retrolateral spines, respectively, occur in the
 entire African clade. A proximal cymbial shoulder in the male palp, the
 fused lateral lobes of the epigyne and the prolateral proximal spine of
 leg I shifted to a median position is characteristic for May gen. n. A
 family-wide analysis of genetic distance in the nuclear 28SrDNA gene
 (28s), including M. bruno sp. n., supports its isolated placement and thus
 the genus hypothesis.
description: 28srDNA sequence
 alignment of Sparassidae species28srDNA alignment of
 select sparassid species, with a focus on African
 lineages28s_Sparassidae.fasta
DOI: 10.5061/dryad.rr36r
title: Data from: Phylogeography of Sophora moorcroftiana supports Wu’s hypothesis on the origin of Tibetan alpine flora

description: Wu hypothesized that the Tibetan flora originated mostly from the
 paleotropical Tertiary flora in the Hengduan Mountains by adapting to the
 cold and arid environments associated with the strong uplift of the
 Qinghai-Tibet Plateau (QTP). Here, we combine the phylogeographic history
 of Sophora moorcroftiana with that of S. davidii to explore the speciation
 of S. moorcroftiana to test this hypothesis. We collected 151 individuals
 from 17 populations and sequenced two chloroplast fragments and the
 internal transcribed spacer of rDNA. Five chlorotypes and nine ribotypes
 were detected but no significant phylogeographic structure was revealed.
 The integrated results of phylogeographic studies of these two species
 clearly support the progenitor-derivative relationship between them. We
 infer that the western peripheral population of S. davidii migrated
 westwards from the Hengduan Mountains to the middle reaches of the Yarlung
 Zangbo River and differentiated from its ancestor in the process of
 adaptation to increasingly cold and arid environments with the uplift of
 the QTP and finally evolved into S. moorcroftiana during the Late
 Pliocene. In addition, our findings shed light on the idea that natural
 selection, as imposed by climate differentiation (especially mean diurnal
 range and precipitation seasonality), directly drove this peripatric
 speciation event after geographic isolation. The speciation of S.
 moorcroftiana is a strong case supporting Wu’s hypothesis about the origin
 of Tibet’s flora.
description: atpB-rbcL intergenic
 spacer, partial sequence chloroplastAR1-AR8 are identified
 from Sophora davidii,AR9, AR10 and AR11 are from Sophora
 moorcroftiana,Sophora alopecuroides and Sophora
 tomentosa,respectively.AR.txtatpI-atpH intergenic spacer, partial sequence chloroplastIH1-IH7,IH8-IH11,IH12 and IH13 are from Sophora davidii,Sophora moorcroftiana,Sophora alopecuroides and Sophora tomentosa,respectively.IH.txtInternal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequenceR1-R9 are both from Sophora moorcroftianaITS.txtchloroplast glutamine synthetase(ncpGS) gene, partial cds; nuclear gene for chloroplast productN1-N22 are both from Sophora moorcroftianancpGS.txtPsbA (psbA) gene, partial cds; and psbA-trnH intergenic spacer, partial sequence; chloroplastPT1-PT9,PT10-PT11,PT12-PT18 and PT19 are from Sophora davidii,Sophora alopecuroides,Sophora moorcroftiana and Sophora tomentosa,respetively.psbA-trnH.txtribosomal protein L32 (rpl32) gene, partial cds; and rpl32-trnL intergenic spacer, partial sequence; chloroplastRT1-RT5,RT6-RT7,RT8,RT9 are from Sophora davidii，Sophora moorcroftiana，Sophora alopecuroides and Sophora tomentosa,respectivelyrpL32-trnL.txt
DOI: 10.5061/dryad.c510p
title: Data from: Experimental manipulation of floral scent bouquets restructures flower-visitor interactions in the field

description: 1. A common structural feature of natural communities is the non-random
 distribution of pairwise interactions between organisms of different
 trophic levels. For plant–animal interactions, it is predicted that both
 stochastic processes and functional plant traits that facilitate or
 prevent interactions are responsible for these patterns. 2. However,
 unbiased manipulative field experiments that rigorously test the effects
 of individual traits on community structure are lacking. We address this
 gap by manipulating floral scent bouquets in the field. 3. Manipulation of
 floral scent bouquets led to quantitative as well as qualitative
 restructuring of flower–visitor networks, making them more generalized.
 Olfactometer trials confirmed both positive and negative responses to
 scent bouquets. 5. Our results clearly show that the distribution of
 insect visitors to the two abundant study plant species reflects the
 insects' species-specific preferences for floral scents, rather than
 for visual or morphological floral traits. 5. Thus, floral scents may be
 of major importance in partitioning flower–visitor interactions.
 Integrating experimental manipulations of plant traits with field
 observations of interaction patterns thus represents a promising approach
 for revealing the processes that structure species assemblages in natural
 communities.
description: Larue et al. Floral
 scent emissions of Achillea millefolium and Cirsium
 arvenseFloral scent compounds
 emitted by Achillea millefolium and Cirsium arvense as well scent
 emissions of flowers after application of the floral extracts. Shown are
 emission rates of each compound [ng hr-1 dry weight-1].Larue et al. JAE_Tab.1_Floral
 scent_Database.xlsxLarue et al. Absolute
 interaction frequencyAbsolute frequency of
 observed interaction on control (treated with pure pentane) and treated
 (CE: Cirsium arvense extract; AE: Achillea millefolium extract) A.
 millefolium and C. arvense plants visualised in the
 network.Larue et al.
 JAE_Tab.S2_Absolute interaction
 frequency.xlsx
DOI: 10.5061/dryad.g611t
title: Data from: Inferring the mode of origin of polyploid species from next-generation sequence data

description: Many eucaryote organisms are polyploid. However, despite their importance,
 evolutionary inference of polyploid origins and modes of inheritance has
 been limited by a need for analyses of allele segregation at multiple loci
 using crosses. The increasing availability of sequence data for non-model
 species now allows the application of established approaches for the
 analysis of genomic data in polyploids. Here, we ask whether approximate
 Bayesian computation (ABC), applied to realistic traditional and
 next-generation sequence data, allows correct inference of the
 evolutionary and demographic history of polyploids. Using simulations, we
 evaluate the robustness of evolutionary inference by ABC for tetraploid
 species as a function of the number of individuals and loci sampled, and
 the presence or absence of an outgroup. We find that ABC adequately
 retrieves the recent evolutionary history of polyploid species on the
 basis of both old and new sequencing technologies. Application of ABC to
 sequence data from diploid and polyploid species of the plant genus
 Capsella confirms its utility. Our analysis strongly supports an
 allopolyploid origin of C. bursa-pastoris about 80,000 years ago. This
 conclusion runs contrary to previous findings based on the same dataset
 but using an alternative approach and is in agreement with recent findings
 based on whole-genome sequencing. Our results indicate that ABC is a
 promising and powerful method for revealing the evolution of polyploid
 species, without the need to attribute alleles to a homeologous chromosome
 pair. The approach can readily be extended to more complex scenarios
 involving higher ploidy levels.
description: Simulation of polyploid
 scenariospriorgenWGD.py is a
 python script to generate prior distribution for the nine described models
 (a detailed help-menu is available typing ./priorgenWGD.py --help),
 bpfile_test.txt is an example file used by priorgenWGD.py, and
 text_S1.docx contains the used command-lines.simulation.tar.gzCapsella_alignments.tarUsed alignements for the empirical application from Capsella. The sequences came from St Onge KR, Foxe JP, Li J et al. (2012, Molecular biology and evolution), Slotte T, Huang H, Lascoux M, Ceplitis A (2008, Molecular biology and evolution) and Foxe JP, Slotte T, Stahl EA et al. (2009, Proceedings of the National Academy of Sciences of the United States of America).
DOI: 10.5061/dryad.1556p
title: Data from: Macroevolutionary patterns of sexual size dimorphism in copepods

description: Major theories compete to explain the macroevolutionary trends observed in
 sexual size dimorphism (SSD) in animals. Quantitative genetic theory
 suggests that the sex under historically stronger directional selection
 will exhibit greater interspecific variance in size, with covariation
 between allometric slopes (male to female size) and the strength of SSD
 across clades. Rensch's rule (RR) also suggests a correlation, but
 one in which males are always the more size variant sex. Examining
 free-living pelagic and parasitic Copepoda, we test these competing
 predictions. Females are commonly the larger sex in copepod species.
 Comparing clades that vary by four orders of magnitude in their degree of
 dimorphism, we show that isometry is widespread. As such we find no
 support for either RR or for covariation between allometry and SSD. Our
 results suggest that selection on both sexes has been equally important.
 We next test the prediction that variation in the degree of SSD is related
 to the adult sex ratio. As males become relatively less abundant, it has
 been hypothesized that this will lead to a reduction in both inter-male
 competition and male size. However, the lack of such a correlation across
 diverse free-living pelagic families of copepods provides no support for
 this hypothesis. By comparison, in sea lice of the family Caligidae, there
 is some qualitative support of the hypothesis, males may suffer elevated
 mortality when they leave the host and rove for sedentary females, and
 their female-biased SSD is greater than in many free-living families.
 However, other parasitic copepods which do not appear to have obvious
 differences in sex-based mate searching risks also show similar or even
 more extreme SSD, therefore suggesting other factors can drive the
 observed extremes.
description: Hirst_Kiorboe_SSD_AppendixMale and female body sizes of copepod species, with details of length type, the ratio of these sizes in single species, and the sources of all data sets.