cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sm01b
title: Data from: Molecular paleobiology of early-branching animals integrating DNA and fossils elucidates the evolutionary history of hexactinellid sponges

description: Reconciliation of paleontological and molecular phylogenetic evidence
 holds great promise for a better understanding of the temporal succession
 of cladogenesis and character evolution, especially for taxa with a
 fragmentary fossil record and uncertain classification. In zoology,
 studies of this kind have largely been restricted to Bilateria.
 Hexactinellids (glass sponges) readily lend themselves to test such an
 approach for early-branching (non-bilaterian) animals: they have a long
 and rich fossil record, but for certain taxa paleontological evidence is
 still scarce or ambiguous. Furthermore, there is a lack of consensus for
 taxonomic interpretations, and discrepancies exist between neontological
 and paleontological classification systems. Using conservative fossil
 calibration constraints and the largest molecular phylogenetic data set
 assembled for this group, we infer divergence times of crown-group
 Hexactinellida in a Bayesian relaxed molecular clock framework. With some
 notable exceptions, our results are largely congruent with interpretations
 of the hexactinellid fossil record, but also indicate long periods of
 undocumented evolution for several groups. This study illustrates the
 potential of an integrated molecular/paleobiological approach to
 reconstructing the evolution of challenging groups of organisms.
description: TableS1Script
DOI: 10.5061/dryad.c75f6
title: Data from: Latitudinal variation in resistance and tolerance to herbivory in the perennial herb Lythrum salicaria is related to intensity of herbivory and plant phenology

description: Both the length of the growing season and the intensity of herbivory often
 vary along climatic gradients, which may result in divergent selection on
 plant phenology, and on resistance and tolerance to herbivory. In Sweden,
 the length of the growing season and the number of insect herbivore
 species feeding on the perennial herb Lythrum salicaria decrease from
 south to north. Previous common-garden experiments have shown that
 northern L. salicaria populations develop aboveground shoots earlier in
 the summer, and finish growth before southern populations do. We tested
 the hypotheses that resistance and tolerance to damage vary with latitude
 in L. salicaria, and are positively related to the intensity of herbivory
 in natural populations. We quantified resistance and tolerance of
 populations sampled along a latitudinal gradient by scoring damage from
 natural herbivores and fitness in a common-garden experiment in the field,
 and by documenting oviposition and feeding preference by specialist leaf
 beetles in a greenhouse experiment. Plant resistance decreased with
 latitude of origin, whereas plant tolerance increased. Oviposition and
 feeding preference in the greenhouse, and leaf damage in the common-garden
 experiment were negatively related to damage in the source populations.
 The latitudinal variation in resistance was thus consistent with reduced
 selection from herbivores towards the northern range margin of L.
 salicaria. Variation in tolerance may be related to differences in the
 timing of damage in relation to the seasonal pattern of plant growth, as
 northern genotypes have developed further than southern have when
 herbivores emerge in early summer.
description: JEB data Lehndal and
 Ågren 2015JEB data Lehndal and Agren
 2015.xlsx
DOI: 10.5061/dryad.rf1b3
title: Data from: Limited effects of the maternal rearing environment on the behaviour and fitness of an insect herbivore and its natural enemy

description: The maternal rearing environment can affect offspring fitness or phenotype
 indirectly via ‘maternal effects’ and can also influence a mother’s
 behaviour and fecundity directly. However, it remains uncertain how the
 effects of the maternal rearing environment cascade through multiple
 trophic levels, such as in plant-insect herbivore-natural enemy
 interactions. Pea aphids (Acyrthosiphon pisum) show differential fitness
 on host legume species, while generalist aphid parasitoids can show
 variable fitness on different host aphid species, suggesting that maternal
 effects could operate in a plant-aphid-parasitoid system. We tested
 whether the maternal rearing environment affected the behaviour and
 fitness of aphids by rearing aphids on two plant hosts that were either
 the same as or different from those experienced by the mothers. A similar
 approach was used to test the behaviour and fitness of parasitoid wasps in
 response to maternal rearing environment. Here, the host environment was
 manipulated at the plant or plant and aphid trophic levels for parasitoid
 wasps. We also quantified the quality of host plants for aphids and host
 aphids for parasitoid wasps. In choice tests, aphids and parasitoid wasps
 had no preference for the plant nor plant and aphid host environment on
 which they were reared. Aphid offspring experienced 50.8% higher intrinsic
 rates of population growth, 43.4% heavier offspring and lived 14.9% longer
 when feeding on bean plants compared to aphids feeding on pea plants, with
 little effect of the maternal rearing environment. Plant tissue nitrogen
 concentration varied by 21.3% in response to aphid mothers’ rearing
 environment, and these differences correlated with offspring fitness.
 Maternal effects in parasitoid wasps were only observed when both the
 plant and aphid host environment was changed: wasp offspring were heaviest
 by 10.9–73.5% when both they and their mothers developed in bean-reared
 pea aphids. Also, parasitoid wasp fecundity was highest by 38.4% when
 offspring were oviposited in the maternal rearing environment. These
 findings indicate that maternal effects have a relatively small
 contribution towards the outcome of plant-aphid-parasitoid interactions.
description: Data from: Does maternal
 rearing environment affect the behaviour, fecundity and fitness of an
 insect herbivore and its natural enemy?File contains data on
 pea aphid choice tests (choices made and information about the plants
 used), aphid performance data (including fecundity (rm) and survival and
 information about the plants used), parasitoid wasp choice tests (choices
 made between different host plants and different host plants and aphids
 and information about the aphids used) and parasitoid wasp performance
 data (including number of mummiesData.xlsx
DOI: 10.5061/dryad.20b01
title: Data from: Genetic diversity and population structure of the tsetse fly Glossina fuscipes fuscipes (Diptera: Glossinidae) in Northern Uganda: implications for vector control

description: Uganda is the only country where the chronic and acute forms of human
 African Trypanosomiasis (HAT) or sleeping sickness both occur and are
 separated by &lt; 100 km in areas north of Lake Kyoga. In Uganda,
 Glossina fuscipes fuscipes is the main vector of the Trypanosoma parasites
 responsible for these diseases as well for the animal African
 Trypanosomiasis (AAT), or Nagana. We used highly polymorphic
 microsatellite loci and a mitochondrial DNA (mtDNA) marker to provide fine
 scale spatial resolution of genetic structure of G. f. fuscipes from 42
 sampling sites from the northern region of Uganda where a merger of the
 two disease belts is feared. Based on microsatellite analyses, we found
 that G. f. fuscipes in northern Uganda are structured into three distinct
 genetic clusters with varying degrees of interconnectivity among them.
 Based on genetic assignment and spatial location, we grouped the sampling
 sites into four genetic units corresponding to northwestern Uganda in the
 Albert Nile drainage, northeastern Uganda in the Lake Kyoga drainage,
 western Uganda in the Victoria Nile drainage, and a transition zone
 between the two northern genetic clusters characterized by high level of
 genetic admixture. An analysis using HYBRIDLAB supported a hybrid swarm
 model as most consistent with tsetse genotypes in these admixed samples.
 Results of mtDNA analyses revealed the presence of 30 haplotypes
 representing three main haplogroups, whose location broadly overlaps with
 the microsatellite defined clusters. Migration analyses based on
 microsatellites point to moderate migration among the northern units
 located in the Albert Nile, Achwa River, Okole River, and Lake Kyoga
 drainages, but not between the northern units and the Victoria Nile
 drainage in the west. Effective population size estimates were variable
 with low to moderate sizes in most populations and with evidence of recent
 population bottlenecks, especially in the northeast unit of the Lake Kyoga
 drainage. Our microsatellite and mtDNA based analyses indicate that G. f.
 fuscipes movement along the Achwa and Okole rivers may facilitate
 northwest expansion of the Rhodesiense disease belt in Uganda. We
 identified tsetse migration corridors and recommend a rolling carpet
 approach from south of Lake Kyoga northward to minimize disease dispersal
 and prevent vector re-colonization. Additionally, our findings highlight
 the need for continuing tsetse monitoring efforts during and after
 control.
description: Opiro_etal_2017_Gff_genotypesMicrosatellite data from 16 loci used in Temporal genetic differentiation in Glossina fuscipes fuscipes from northern Uganda. Genotypes are coded with the microsatellite fragment length, and missing data is coded as -9.
DOI: 10.5061/dryad.kr8vc17
title: Data from: Weak and inconsistent associations between melanic darkness and fitness related traits in an insect

description: The idea that the fitness value of body colouration may be affected by
 biochemically mediated trade-offs has received much research attention.
 For example, melanisation is believed to interact with other
 fitness-related traits via competition for substrates, costs associated
 with the synthesis of melanin, or pleiotropic effects of the involved
 genes. However, genetic correlations between colouration and
 fitness-related traits remain poorly understood. Here we present a
 quantitative genetic study of a colouration trait correlated to
 melanin-based cuticular darkness (‘darkness’, hereafter) in a geometrid
 moth, Ematurga atomaria, which has considerable variation in larval
 appearance. We focus on correlations between larval darkness and
 fitness-related growth performance traits. Both a half-sib analysis and an
 ‘animal model’ approach revealed moderately high heritabilities of larval
 darkness and indices of growth performance. Heritability estimates of
 darkness derived from the animal model were, however, considerably higher
 than those based on the half sib model suggesting that the determination
 of colouration includes genetic interactions and epigenetic effects.
 Importantly, on the host plant with the largest sample size, we found no
 evidence for either genetic or environmental correlations between darkness
 and growth parameters. On an alternative host plant, there was some
 indication of positive genetic and negative environmental correlation
 between these traits. This shows that respective relationships are
 environment-specific. Nevertheless, the overall pattern of weak and
 inconsistent correlations between larval colouration and growth parameters
 does not support universal trade-offs between these traits, and suggests
 that physiological costs of producing colour patterns do not necessarily
 interfere with adaptive evolution of colouration.
description: Ematurga data for
 quantitative genetic analysesAn Excel file with three
 sheets Sheet 1: Pedigree data presenting the relatedness structure id
 Individual identification number (including also individuals without
 phenotype data) sire Sire identification number (zero, if unknown) dam Dam
 identification number (zero, if unknown) * * * Sheets 2 and 3:
 Heather.data & Bilberry.data: individual-based valued of the traits
 being analysed gen Generation number (1 - F1, 2 - F2) plant Plant (1 -
 heatrher, 2 - bilberry) sex Sex (1 - male, 2 - female) h_rgr & b_rgr
 Growth ratio in 5th instar on heather and on bilberry, respectively h_pupw
 & b_pupw Pupal weight (mg) on heather and on bilberry, respectively
 h_fifth & b_fifth Duration of the 5th instar (days) on heather and on
 bilberry, respectively h_dscore & b_dscore Melanic darkness MCA score
 on heather and on bilberry, respectivelydryaddata.xlsx
DOI: 10.5281/zenodo.18382389
title: Supporting datasets for dental phenotypes related to epithelial Edar in HED

description: 相关稿件目前正在《牙科研究杂志》接受同行评审。
DOI: 10.5061/dryad.td27r
title: Data from: Tovomita (Clusiaceae) from the Brazilian Atlantic Forest: taxonomy and utility of leaf venation characters at the species level

description: Tovomita comprises approximately 50 species that are mainly distributed in
 moist forests of the Neotropics. In Brazil there are 34 species, which
 occur in the Amazon region and along the Atlantic coast. We here describe
 and illustrate the Tovomita species from the Brazilian Atlantic Forest, as
 well as characterize the leaf morphology of these taxa. Leaves were
 cleared and their venation was analyzed to look for diagnostic characters
 related to architecture and the relationship between the secondary and
 intersecondary veins. Eleven species of Tovomita were recorded, which have
 distributions ranging from the state of Rio Grande do Norte to the state
 of Rio de Janeiro. An identification key, based on the analysis, and
 distribution maps are provided. Tovomita salimenae, a new and vulnerable
 species endemic to the state of Minas Gerais, is described and two
 synonyms and nine lectotypifications are proposed. This work also revealed
 that seven species have larger distributions than previously thought and
 two species are critically endangered (T. iaspidis and T. megantha). The
 most relevant characters used to identify the studied species were exudate
 color, venation pattern, and bud shape.
description: Appendix 1 - List to
 ExsiccataeAppendix 1 - List to
 Exsiccatae - Tovomita (Clusiaceae) from the Brazilian Atlantic
 ForestAppendix
 1.doc
DOI: 10.5281/zenodo.18382388
title: Supporting datasets for dental phenotypes related to epithelial Edar in HED

description: 相关稿件目前正在《牙科研究杂志》接受同行评审。
DOI: 10.5061/dryad.77t01s2
title: Data from: Living in a high CO2 world: a global meta-analysis shows multiple trait-mediated responses of fish to ocean acidification

description: Understanding how marine organisms will be affected by global change is of
 primary importance to ensure ecosystem functioning and nature
 contributions to people. This study meets the call for addressing how
 life-history traits mediate effects of ocean acidification on fish. We
 built a database of overall and trait-mediated responses of teleost fish
 to future CO2 levels by searching the scientific literature. Using a
 meta-analytical approach, we investigated the effects of projected CO2
 levels by IPCC for 2050-2070 and 2100 on fish eco-physiology and behavior
 from 320 contrasts on 42 species, stemming from polar to tropical regions.
 Moreover, since organisms may experience a mosaic of carbonate chemistry
 in coastal environments (e.g. in estuaries, upwelling zones and intertidal
 habitats), which may have higher pCO2 values than open ocean waters, we
 assessed responses from additional 103 contrasts on 21 fish species using
 pCO2 levels well above IPCC projections. Under mid- and end-of-century CO2
 emission scenarios, we found multiple CO2-dose dependent effects on
 calcification, resting metabolic rate, yolk, behavioral performances,
 along with increased predation risk and decreased foraging, particularly
 for larvae. Importantly, many of the traits considered will not confer
 fish tolerance to elevated CO2 and far-reaching ecological consequences on
 fish population replenishment and community structure will likely occur.
 Extreme CO2 levels well above IPCC projections showed effects on fish
 mortality and calcification, while growth, metabolism and yolk were
 unaffected. CO2 exposures in short-term experiments increased fish
 mortality, which in turn decreased in longer-term exposures. Whatever the
 elevated CO2 levels considered, some key biological processes (e.g.
 reproduction, development, habitat choice) resulted critically
 understudied. Fish are an important resource for livelihoods in coastal
 communities and a key component for stability of marine ecosystems. Given
 the multiple trait-mediated effects evidenced here, we stress the need to
 fill the knowledge gap on important eco-physiological processes and to
 expand the number and duration of ocean acidification studies to
 multi-generational, multiple stressor (e.g. warming, hypoxia, fishing) and
 species interactions experiments to better elucidate complex
 ecosystem-level changes and how these changes might alter provisioning of
 ecosystem services.
description: Appendices 2-5 Cattano
 et al DRYADLiterature data used for
 the meta-analyses to assess eco-physiological and behavioural responses,
 along with response variables, category levels, CO2 treatment (range),
 duration, metrics and effect sizes. File type: .xls. Data are presented in
 four different excel sheets: Ap 2 Summary table; Ap 3 Ecophysiological
 response; Ap 4 Behavioral response; Ap 5 extreme pCO2
DOI: 10.5061/dryad.8054
title: Data from: Genetic signature of population fragmentation varies with mobility in seven bird species of a fragmented Kenyan cloud forest

description: Habitat fragmentation can restrict geneflow, reduce neighbourhood
 effective population size, and increase genetic drift and inbreeding in
 small, isolated habitat remnants. The extent to which habitat
 fragmentation leads to population fragmentation, however, differs among
 landscapes and taxa. Commonly, researchers use information on the current
 status of a species to predict population effects of habitat
 fragmentation. Such methods, however, do not convey information on
 species-specific responses to fragmentation. Here we compare levels of
 past population differentiation, estimated from microsatellite genotypes,
 with contemporary dispersal rates, estimated from multi-strata
 capture-recapture models, to infer changes in mobility over time in seven
 sympatric, forest-dependent bird species of a Kenyan cloud forest
 archipelago. Overall, populations of sedentary species were more strongly
 differentiated and clustered compared to those of vagile ones, while
 geographic patterning suggested an important role of landscape structure
 in shaping genetic variation. However, five of seven species with broadly
 similar levels of genetic differentiation nevertheless differed
 substantially in their current dispersal rates. We conclude that
 post-fragmentation levels of vagility, without reference to past
 population connectivity, may not be the best predictor of how forest
 fragmentation affects the life-history of forest-dependent species. As
 effective conservation strategies often hinge on accurate prediction of
 shifts in ecological and genetic relationships among populations,
 conservation practices based solely upon current population abundances or
 movements may, in the long term, prove to be inadequate.
description: Microsatellite data on
 all 7 species described in the paperData are in Genalex
 format and include the microsatellite lengths. Different species can be
 found in different worksheets. CODE=unique individual SITE=fragment where
 the bird was caught All other columns are microsatellite lengths on
 different locifullmicrosatdata.xls
DOI: 10.5061/dryad.bd70m
title: Data from: Lack of spatial immunogenetic structure among wolverine (Gulo gulo) populations suggestive of broad scale balancing selection

description: Elucidating the adaptive genetic potential of wildlife populations to
 environmental selective pressures is fundamental for species conservation.
 Genes of the major histocompatibility complex (MHC) are highly
 polymorphic, and play a key role in the adaptive immune response against
 pathogens. MHC polymorphism has been linked to balancing selection or
 heterogeneous selection promoting local adaptation. However, spatial
 patterns of MHC polymorphism are also influenced by gene flow and drift.
 Wolverines are highly vagile, inhabiting varied ecoregions that include
 boreal forest, taiga, tundra, and high alpine ecosystems. Here, we
 investigated the immunogenetic variation of wolverines in Canada as a
 surrogate for identifying local adaptation by contrasting the genetic
 structure at MHC relative to the structure at 11 neutral microsatellites
 to account for gene flow and drift. Evidence of historical positive
 selection was detected at MHC using maximum likelihood codon-based
 methods. Bayesian and multivariate cluster analyses revealed weaker
 population genetic differentiation at MHC relative to the increasing
 microsatellite genetic structure towards the eastern wolverine
 distribution. Mantel correlations of MHC against geographical distances
 showed no pattern of isolation by distance (IBD: r = -0.03, p = 0.9),
 whereas for microsatellites we found a relatively strong and significant
 IBD (r = 0.54, p = 0.01). Moreover, we found a significant correlation
 between microsatellite allelic richness and the mean number of MHC
 alleles, but we did not observe low MHC diversity in small populations.
 Overall these results suggest that MHC polymorphism has been influenced
 primarily by balancing selection and to a lesser extent by neutral
 processes such as genetic drift, with no clear evidence for local
 adaptation. This study contributes to our understanding of how vulnerable
 populations of wolverines may respond to selective pressures across their
 range.
description: wolverine (Gulo gulo)
 MHC dataMHC alleles
 present/absent for 269 wolverines and nine sampling
 regions.Wolverine_MHC_binary_encoded_data.xlsWolverine (Gulo gulo) microsatellite dataData for eleven microsatellite loci (as base pair in length) for 269 wolverines and nine sampling regionsWolverine_11microsatellites_data.xls
DOI: 10.5061/dryad.3p4h2
title: Data from: Parallel emergence of negative epistasis across experimental lineages

description: Epistatic interactions can greatly impact evolutionary phenomena,
 particularly the process of adaptation. Here, we leverage four parallel
 experimentally evolved lineages to study the emergence and trajectories of
 epistatic interactions in the social bacterium Myxococcus xanthus. A
 social gene (pilA) necessary for effective group swarming on soft agar had
 been deleted from the common ancestor of these lineages. During selection
 for competitiveness at the leading edge of growing colonies, two lineages
 evolved qualitatively novel mechanisms for greatly increased swarming on
 soft agar, whereas the other two lineages evolved relatively small
 increases in swarming. By reintroducing pilA into different genetic
 backgrounds along the four lineages, we tested whether parallel lineages
 showed similar patterns of epistasis. In particular, we tested whether a
 pattern of negative epistasis between accumulating mutations and pilA
 previously found in the fastest lineage would be found only in the two
 evolved lineages with the fastest and most striking swarming phenotypes,
 or rather was due to common epistatic structure across all lineages
 arising from the generic fixation of adaptive mutations. Our analysis
 reveals the emergence of negative epistasis across all four independent
 lineages. Further, we present results showing that the observed negative
 epistasis is not due exclusively to evolving populations approaching a
 maximum phenotypic value that inherently limits positive effects of pilA
 reintroduction, but rather involves direct antagonistic interactions
 between accumulating mutations and the reintroduced social gene.
description: E1_DATAE1 swarming dataE2_DATAE2 swarming dataE7_DATAE7 swarming dataTOTAL-E8-PILAE8 swarming dataGVTu1_contPlasmid control dataGJV6-pilA_controlSwarming controls