cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ff893
title: Data from: Control of hydroid colony form by surface heterogeneity

description: The colonial hydroid Podocoryna carnea grows adherent to surfaces
 progressing along them by a motile stolon tip. We here ask whether the
 stolon tip grows preferentially within grooves etched in silicon wafers.
 In a series of pilot experiments, we varied the dimensions of grooves and
 found that stolons did not utilize grooves with a width:depth of 5:5 μm or
 10:10 μm, occasionally followed grooves 25:25 μm in size, and
 preferentially grew within grooves of a width:depth of 50:50 μm and 100:50
 μm. We then grew colonies in grids, with fixed 50:50 μm width:depth
 channels intersecting at 90° every 950, 700, 450, or 150 μm. We find that
 stolons grew within grooves early in colony ontogeny, but remained
 restricted to them only in the grid pattern with channel intersections
 every 150 μm. Finally, we created a grid in the shape of the Yale Y logo,
 with channels of 50:50 μm width:depth and intersections every 100 μm. The
 resulting colonies conformed to that of the logo. Our findings demonstrate
 that stolons respond to surface heterogeneity and that surface etching can
 be used to fabricate microfluidic circuits comprised of hydroid perisarc.
description: Yale Y Replicate
 1Contains sequential
 images of Yale logo experimental treatment, replicate 1Yale Y Replicate
 2Contains sequential
 images of Yale logo experimental treatment, replicate 2Yale Y Replicate
 3Contains sequential
 images of Yale logo experimental treatment, replicate 3Yale Y Replicate
 4Contains sequential
 images of Yale logo experimental treatment, replicate 4Yale Y Replicate
 5Contains sequential
 images of Yale logo experimental treatment, replicate 5Yale Y Replicate
 6Contains sequential
 images of Yale logo experimental treatment, replicate 6Yale Y Replicate
 7Contains sequential
 images of Yale logo experimental treatment, replicate 7Yale Y Replicate
 8Contains sequential
 images of Yale logo experimental treatment, replicate 8Grid_150_Replicate
 1_(exp1_ZZ)Contains sequential
 images for replicate 1 of the grid with intersections spaced every 150
 micronsGrid_150_Replicate
 2_(exp1_12)Contains sequential
 images for replicate 2 of the grid with intersections spaced every 150
 micronsGrid_450_Replicate 1
 (exp2_4)Contains sequential
 images of replicate 1 of the grid with intersections spaced every 450
 microns.Grid_450_Replicate 2
 (exp2_6)Contains sequential
 images of replicate 2 of the grid with intersections spaced every 450
 microns.Grid_700_Replicate
 1_(exp1_5)Contains sequential
 images of replicate 1 of the grid with intersections spaced every 700
 micronsGrid_700_Replicate
 2_(exp1_14)Contains sequential
 images of replicate 2 of the grid with intersections spaced every 700
 microns.Grid_700_Replicate
 3_(exp1_XX)Contains sequential
 images of replicate 3 of the grid with intersections spaced every 700
 microns.ReadMe
DOI: 10.5281/zenodo.18382755
title: Implicit Structural Modeling via Generative Diffusion Framework

description: Implicit structural modeling provides a principled way to represent subsurface structure with a continuous scalar field, supporting interpretation of architecture, reconstruction of deformation history, and quantitative analysis of geological processes. Yet the problem is inherently challenging in tectonically complex settings. Sparse horizon and fault constraints can admit multiple plausible solutions, and standard optimization, interpolation, or regression often yields fields that violate stratigraphic continuity, distort topology near intersections and branches, or produce kinematically implausible geometries in fold-thrust belts. We address these challenges with a diffusion framework that learns a conditional distribution of admissible structural fields from simulation based examples. Despite training on stylized normal fault scenarios, the approach transfers to diverse deformation styles, including strike-slip systems and flower structures, while remaining stable in fold-thrust belts where non monotonicity and abrupt depth jumps are common. As a result, the method produces geologically coherent implicit models that better respect structural constraints and uncertainty.
DOI: 10.5061/dryad.hq228
title: Data from: Convergent morphology in Alpinieae (Zingiberaceae): recircumscribing Amomum as a monophyletic genus

description: The tropical ginger genus Amomum (Zingiberaceae) has always posed
 challenges for classification based on morphological characters. Previous
 molecular phylogenetic studies showed Amomum to be paraphyletic but
 limited sampling and absence of the data of the type Amomum subulatum made
 it impossible to resolve the paraphyly and make nomenclatural changes.
 Here, Amomum is further investigated in a multi-marker phylogenetic
 framework using matK and nrITS including multiple accessions of the type,
 the genus Elettaria and additional accessions of Amomum, Alpinia,
 Elettariopsis, Geocharis, Geostachys and Hornstedtia. Amomum is shown to
 consist of nine clades and Alpinia of six. The genera Elettaria,
 Elettariopsis, Plagiostachys, and species in Hornstedtia are nested within
 these clades. Morphological studies of species previously subsumed in
 Amomum support recognition of new genera that correspond to well-delimited
 clades in the phylogenetic framework presented here. Recircumscription of
 the paraphyletic genus Amomum facilitates identification and creates
 nomenclatural stability. Three genera, Conamomum, Meistera and Wurfbainia,
 are resurrected, and three new genera Epiamomum, Lanxangia and Sundamomum
 are described, together with a key to the genera and a nomenclatural
 synopsis placing 384 specific names (incl. all synonyms) into the new
 generic framework. Of these 129 represent new combinations and 3 are
 replacement names. Types of Geocharis and Geostachys are designated.
 Further studies and specific sampling will be needed to resolve other
 branches of Alpinioideae containing other polyphyletic genera.
description: Dryad
 Amomum
DOI: 10.5061/dryad.4k1v5
title: Data from: The relative importance of genetic and nongenetic inheritance in relation to trait plasticity in Callosobruchus maculatus

description: A trait’s response to natural selection will reflect the nature of the
 inheritance mechanisms that mediate the transmission of variation across
 generations. The relative importance of genetic and nongenetic mechanisms
 of inheritance is predicted to be related to the degree of trait
 plasticity, with nongenetic inheritance playing a greater role in the
 cross generational transmission of more plastic traits. However, this
 prediction has never been tested. We investigated the influence of genetic
 effects and nongenetic parental effects in two morphological traits
 differing in degree of plasticity by manipulating larval diet quality
 within a cross-generational split brood experiment using the seed beetle
 Callososbuchus maculatus. In line with predictions, we found that the more
 plastic trait (elytron length) is strongly influenced by parental effects
 while genetic variance is undetectable. In contrast, the less plastic
 trait (1st abdominal sternite length) is not influenced by parental
 effects but exhibits abundant genetic variance. Our findings support the
 hypothesis that environment-dependent parental effects may play a
 particularly important role in highly plastic traits, and thereby affect
 the evolutionary response of such traits.
description: JEB-2012-00598_Data_ElytraFamily = F0 family; SCP = Sex and condition of parent (F1); Repl = Replicate; Sex = Sex of offspring (F2); CondOff = Condition of offspring (F2); Ind = Individual (5 Individuals per treatment combination were measured); Elytra = Length of Elytra; Data were collected in the laboratory.JEB-2012-00598_Data_AbdomensegmentFamily = F0 family; SCP = Sex and condition of parent (F1); Repl = Replicate; Sex = Sex of offspring (F2); CondOff = Condition of offspring (F2); Ind = Individual (5 Individuals per treatment combination were measured); Abdomen = Length of Abdomen segment; Data were collected in the laboratory
DOI: 10.5061/dryad.sh1p2
title: Data from: Economy of scale: third partner strengthens a keystone ant-plant mutualism

description: While foundation species can stabilize ecosystems at landscape scales,
 their ability to persist is often underlain by keystone interactions
 occurring at smaller scales. Acacia drepanolobium is a foundation tree,
 comprising &gt;95% of woody cover in East African black-cotton savanna
 ecosystems. Its dominance is underlain by a keystone mutualistic
 interaction with several symbiotic ant species in which it provides
 housing (swollen thorns) and carbohydrate-rich nectar from extra-floral
 nectaries (EFN). In return, it gains protection from catastrophic damage
 from mega-herbivores. Crematogaster mimosae is the ecologically dominant
 symbiotic ant in this system, also providing the highest protection
 services. In addition to tending EFN, C. mimosae tend scale insects for
 carbohydrate-rich honeydew. We investigated the role of scale insects in
 this specialized ant-plant interaction. Specifically, does this putatively
 redundant third partner strengthen the ant-plant mutualism by making the
 ant a better protector of the tree? Or does it weaken the mutualism by
 being costly to the tree while providing no additional benefit to the
 ant-plant mutualism? We coupled observational surveys with two
 scale-manipulation experiments and found evidence that this third partner
 strengthens the ant-plant mutualism. Trees with scale insects
 experimentally removed experienced a 2.5X increase in elephant damage
 compared to trees with scale insects present over 10 months. Reduced
 protection was driven by scale removal causing a decrease in ant colony
 size and per capita baseline activity and defensive behavior. We also
 found that ants increased scale-tending and the density of scale insects
 on trees when EFN were experimentally reduced. Thus, in this system, scale
 insects and EFN are likely complementary, rather than redundant, resources
 with scale insects benefitting ants when EFN production is low (such as
 during annual dry periods in this semi-arid ecosystem). This study reveals
 that a third-partner strengthens an ant-plant mutualism that serves to
 stabilize a whole ecosystem.
description: Prior&Palmer
 2017_Ecology dataData: 1) short-term
 experiment (post-treatment), 2) surveys, 3) long-term experiment - growth,
 number of scale insects (pre to post-treatment), vertebrate herbivory, and
 ant counts (final experiment date post-treatment)
DOI: 10.5061/dryad.p725tq4
title: Data from: Insect outbreaks alter nutrient dynamics in a southern African savanna: patchy defoliation of Colophospermum mopane savanna by Imbrasia belina larvae

description: Severe defoliation is expected to affect nutrient cycling of an impacted
 system. Outbreaks of the lepidopteran Imbrasia belina (mopane worm) affect
 discrete patches of Colophospermum mopane trees in semi-arid savanna;
 larvae may completely defoliate trees for up to six weeks during each of
 the early and late growing seasons. We studied the impact of mopane worm
 outbreaks on the availability of nitrogen, phosphorus and potassium within
 mopane savanna by comparing defoliated with non-defoliated savanna
 patches. Individual studies conducted were production and nutrient content
 of leaf biomass and worm frass that determine nutrient input to the soil,
 and soil nutrient concentrations. Within an outbreak area 44 percent of
 trees supported ±29,000 worms/ha who deposited ±640 kg/ha dry weight of
 frass at 1.4 g of frass/day (fourth or fifth instar) compared with an
 average 1645 kg/ha dry weight of leaf on trees most of which should be
 deposited by litter fall at the end of the growing season. Nutrient
 concentrations in frass compared with senescent mopane leaves were
 two-fold higher for phosphorus, 10 percent higher for potassium, and 20
 percent less for nitrogen. Soil nutrient content beneath defoliated trees
 was higher for phosphorus and potassium but there was no difference for
 nitrogen. Invertebrate herbivory appears to be an important driver for
 mopane savanna but has been largely neglected.
description: Copy of DB de Swardt Raw
 Data
DOI: 10.5061/dryad.4kv44
title: Data from: The influence of abdominal pigmentation in desiccation and UV-resistance in two species of Drosophila

description: Drosophila yakuba and D. santomea are sister species that differ in their
 levels of abdominal pigmentation; D. yakuba shows heavily pigmented
 posterior abdominal segments in both sexes, whereas D. santomea lacks dark
 pigment anywhere on its body. Using naturally collected lines, we
 demonstrate the existence of altitudinal variation in abdominal
 pigmentation in D. yakuba but not in D. santomea. We use the variation in
 pigmentation within D. yakuba and two body-color mutants in D. yakuba to
 elucidate selective advantage of differences in pigmentation. Our results
 indicate that although differences in abdominal pigmentation have no
 effect on desiccation resistance, lighter pigmentation confers ultraviolet
 radiation resistance in this pair of species.
description: Matute_Harris_Pigmentation_ForDryadDataframes and scripts. Zip File
DOI: 10.5061/dryad.77j02
title: Data from: Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae)

description: The long generation time and large effective size of widespread forest
 tree species can result in slow evolutionary rate and incomplete lineage
 sorting, complicating species delimitation. We addressed this issue with
 the African timber tree genus Milicia that comprises two morphologically
 similar and often confounded species: M. excelsa, widespread from West to
 East Africa, and M. regia, endemic to West Africa. We combined information
 from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences,
 and morphological systematics to identify significant evolutionary units
 and infer their evolutionary and biogeographical history. We detected five
 geographically coherent genetic clusters using nSSRs and three levels of
 genetic differentiation. First, one West African cluster matched perfectly
 with the morphospecies M. regia, which formed a monophyletic clade at both
 DNA sequences. Second, a West African M. excelsa cluster formed a
 monophyletic group at plastid DNA and was more related to M. regia than to
 Central African M. excelsa, but shared many haplotypes with the latter at
 nuclear DNA. Third, three Central African clusters appeared little
 differentiated and shared most of their haplotypes. Although gene tree
 paraphyly could suggest a single species in Milicia following the
 Phylogenetic Species Concept, the existence of mutual haplotypic
 exclusivity and non-admixed genetic clusters in the contact area of the
 two taxa indicate strong reproductive isolation, and thus, two species
 following the Biological Species Concept. Molecular dating of the first
 divergence events showed that speciation in Milicia is ancient (Tertiary),
 indicating that long-living tree taxa exhibiting genetic speciation may
 remain similar morphologically.
description: Microsatellite genotypes
 (from 7 nuSSR) of 849 Milicia individualsMicrosatellite genotypes
 (from 7 nuSSR) of 849 Milicia individuals sampled in almost the entire
 range of this African genusDainou_et_al_Evolutionary_history_of_the_genus_Milicia_Dryad.xlsx
DOI: 10.5061/dryad.564ms
title: Data from: Geological and climatic changes in quaternary shaped the evolutionary history of Calibrachoa heterophylla, an endemic South-Atlantic species of petunia

description: Background: The glacial and interglacial cycles that characterized the
 Quaternary greatly affected the distribution and genetic diversity of
 plants. In the Neotropics, few phylogeographic studies have focused on
 coastal species outside of the Atlantic Rainforest. Climatic and sea level
 changes during the Quaternary played an important role in the evolutionary
 history of many organisms found in coastal regions. To contribute to a
 better understanding of plant evolution in this environment in Southern
 South America, we focused on Calibrachoa heterophylla (Solanaceae), an
 endemic and vulnerable wild petunia species from the South Atlantic
 Coastal Plain (SACP). Results: We assessed DNA sequences from two cpDNA
 intergenic spacers and analyzed them using a phylogeographic approach. The
 present phylogeographic study reveals the influence of complex geologic
 and climatic events on patterns of genetic diversification. The results
 indicate that C. heterophylla originated inland and subsequently colonized
 the SACP; the data show that the inland haplogroup is more ancient than
 the coastal one and that the inland was not affected by sea level changes
 in the Quaternary. The major diversification of C. heterophylla that
 occurred after 0.4 Myr was linked to sea level oscillations in the
 Quaternary, and any diversification that occurred before this time was
 obscured by marine transgressions that occurred before the coastal sand
 barrier’s formation. Results of the Bayesian skyline plot showed a recent
 population expansion detected in C. heterophylla seems to be related to an
 increase in temperature and humidity that occurred at the beginning of the
 Holocene. Conclusions: The geographic clades have been formed when the
 coastal plain was deeply dissected by paleochannels and these correlate
 very well with the distributional limits of the clades. The four major sea
 transgressions formed a series of four sand barriers parallel to the coast
 that progressively increased the availability of coastal areas after the
 regressions and that may have promoted the geographic structuring of
 genetic diversity observed today. The recent population expansion for the
 entire species may be linked with the event of marine regression after the
 most recent sea transgression at ~5 kya.
description: SequencesChloroplast sequences: trnH-psbA and trnS-trnG spacers. With GenBank accesion numbersAlignmenttrnH-psbA - trnS-trnG alignment [trnh-psba:1-457pb; trns-trng:458-1243pb]alignment.nex
DOI: 10.5061/dryad.j35k0
title: Data from: Sexual selection on spontaneous mutations strengthens the between-sex genetic correlation for fitness

description: A proposed benefit to sexual selection is that it promotes purging of
 deleterious mutations from populations. For this benefit to be realised,
 sexual selection, which is usually stronger on males, must purge mutations
 deleterious to both sexes. Here, we experimentally test the hypothesis
 that sexual selection on males purges deleterious mutations that affect
 both male and female fitness. We measured male and female fitness in two
 panels of spontaneous mutation-accumulation lines of the fly, Drosophila
 serrata, each established from a common ancestor. One panel of mutation
 accumulation lines limited both natural and sexual selection (LS lines),
 whereas the other panel limited natural selection, but allowed sexual
 selection to operate (SS lines). Although mutation accumulation caused a
 significant reduction in male and female fitness in both the LS and SS
 lines, sexual selection had no detectable effect on the extent of the
 fitness reduction. Similarly, despite evidence of mutational variance for
 fitness in males and females of both treatments, sexual selection had no
 significant impact on the amount of mutational genetic variance for
 fitness. However, sexual selection did reshape the between-sex correlation
 for fitness: significantly strengthening it in the SS lines. After 25
 generations, the between-sex correlation for fitness was positive but
 considerably less than one in the LS lines, suggesting that, although most
 mutations had sexually concordant fitness effects, sex-limited and/or
 sex-biased mutations contributed substantially to the mutational variance.
 In the SS lines this correlation was strong and could not be distinguished
 from unity. Individual-based simulations that mimick the experimental
 setup reveal two conditions that may drive our results: (1) a
 modest-to-large fraction of mutations have sex-limited (or highly
 sex-biased) fitness effects, and (2) the average fitness effect of
 sex-limited mutations is larger than the average fitness effect of
 mutations that affect both sexes similarly.
description: MA_fitness_dataThe data are from an assay measuring fitness as competitive reproductive success where flies from a mutation accumulation line competed against flies bearing a recessive orange-eye mutation. Fitness was quantitated using the number of red-eyed and orange-eyed offspring that emerged from each assay.MA_simulation_outputThe data are from a simulation that replicated the conditions of the mutation accumulation experiment and allowed us to determine which factor(s) could have produced the empirical results.simulation_code_for_publicationR code that simulated mutation accumulation with and without sexual selection and allowed us to vary the proportion of sex-limited mutations, the relative strength of sex-limited mutations, and the between-sex correlation for a mutation's effect.
DOI: 10.5061/dryad.8bk0rf3
title: Data from: Genetic signatures through space, time and multiple disturbances in a ubiquitous brooding coral

description: The predominance of self-recruitment in many reef-building corals has
 fundamental and complex consequences for their genetic diversity,
 population persistence and responses to climate change. Knowledge of
 genetic structure over local scales needs to be placed within a broad
 spatial context, and also integrated with genetic monitoring through time
 to disentangle these consequences. Here, we examined patterns of genetic
 diversity over multiple spatio-temporal scales across tropical Australia
 in the ubiquitous brooding coral, Seriatopora hystrix. We also analysed
 complimentary environmental and demographic data to elucidate the seascape
 drivers of these patterns. Large genetic differences was detected between
 the east versus west coasts of Australia. In northwest Australia,
 geographic differentiation dominated genetic structure over multiple
 scales. However, three sympatric lineages were detected at the largest
 offshore reef system (Scott Reef). Similar to the differences observed
 among putative species in eastern Australia, these lineages were
 associated with different levels of wave exposure. Local genetic structure
 within the Scott Reef system was relatively stable over ten years, but
 temporal differences were observed that reflected small but important
 genetic changes over a few generations during recovery after severe
 bleaching. These results highlight the importance of self-recruitment
 together with occasional longer distance connectivity for the persistence
 of a metapopulation across spatially and temporally variable environments.
 Our multidimensional research provides a foundation for further long-term
 genetic monitoring to inform conservation strategies and highlights that
 sampling scales, ecological effects and cryptic diversity are important
 considerations to develop realistic understanding of the evolutionary
 resilience of corals.
description: Underwood_hystrix@NWA_DRYAD-DATA_coral-coverincludes data on % percentage coral cover of Seriatopora corals at each site at Scott ReefUnderwood_hystrix@NWA_DRYAD-DATA_genotypesincludes microsatellite genotypes of all genets of S. hystrix from northwest Australia in GenAlex formatUnderwood_hystrix@NWA_DRYAD-DATA_mtDNA-haplotypesincludes GenBank Accession Numbers for new mtDNA sequences for S. hystrix individuals from northwest AustraliaUnderwood_hystrix@NWA_DRYAD-DATA_site-coordsincludes latitude and longitude in decimal degrees of each site, region, system and Reef of S. hystrix collectionsHystrix@NWA_DRYAD-DATAmetadata README file describing each data file for DRYAD submission to accompany Underwood et al (Submitted to Molecular Ecology 2018) Genetic signatures through space, time and multiple disturbances in a ubiquitous brooding coral