cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v07j0t0
title: Data from: The effect of rhizosphere microbes outweighs host plant genotype in reducing insect herbivory

description: Rhizosphere microbes affect plant performance, including plant resistance
 against insect herbivores; yet, a direct comparison of the relative
 influence of rhizosphere microbes vs. plant genotype on herbivory levels
 and on metabolites related to defense is lacking. In the crucifer Boechera
 stricta, we tested the effects of rhizosphere microbes and plant genotype
 on herbivore resistance, the primary metabolome, and select secondary
 metabolites. Plant populations differed significantly in the
 concentrations of 6 glucosinolates (GLS), secondary metabolites known to
 provide herbivore resistance in the Brassicaceae. The population with
 lower GLS levels experienced ~60% higher levels of aphid (Aphis spp.)
 attack; no association was observed between GLS and damage by a second
 herbivore, flea beetles (Altica spp.). Rhizosphere microbiome (disrupted
 vs. intact native microbiome) had no effect on plant GLS concentrations.
 However, aphid number and flea beetle damage were respectively ~3-fold and
 7-fold higher among plants grown in the disrupted vs. intact native
 microbiome treatment. These differences may be attributable to shifts in
 primary metabolic pathways previously implicated in host defense against
 herbivores, including increases in pentose and glucoronate interconversion
 among plants grown with an intact microbiome. Further, native microbiomes
 with distinct community composition (as estimated from 16s rRNA amplicon
 sequencing) differed 2-fold in their effect on host plant susceptibility
 to aphids. The findings suggest that rhizosphere microbes, including
 distinct native microbiomes, can play a greater role than plant genotype
 in defense against insect herbivores, and act through metabolic mechanisms
 independent of plant genotype.
description: Flea_Beetle_DamageFlea Beetle damage data and metadataHerbivory_Data.csvAphid_Data_Exp1Aphid and performance data from the first aphid experimentBGP4_Aphids.csvseqtab_finalASV table from DADA2 pipelinetax_finalMicrobial Taxa table from DADA2 pipelineAphid_Expt_2Data from second aphid experiment
DOI: 10.5281/zenodo.18382490
title: Saccharification Index Data for MyDFF Study - Supplementary Figures S2 and S3

description: This dataset contains Saccharification Index (SI) values from in vitro fermentation experiments conducted as part of the My Dietary Fiber Finder (MyDFF) validation study. The data supports Figure S2 and Figure S3 in the supplementary materials of the manuscript titled "A personalized microbiota screening platform for optimizing individual volatile fatty acid production - A proof-of-concept study", which has been submitted to the journal Microbiome.

Study Design:- Cross-sectional analysis: 10 healthy adult donors (A-J) at baseline- Longitudinal analysis: 4 donors (B, C, I, J) with follow-up samples over 3-9 months

Data Collection:SI values were measured from in vitro fermentation of fecal microbiota samples with 17 different dietary fiber products representing 6 categories: resistant starch (n=4), resistant dextrin (n=3), α-cyclodextrin (n=3), isomaltodextrin (n=2), partially hydrolyzed guar gum (n=2), and inulin (n=3).

Each SI measurement represents the mean of triplicate fermentation experiments and is calculated as:SI = (pH_control - pH_sample) / (pH_control - pH_glucose)

Files Included:- FigS2_S3_Saccharification_Index_Data.csv: Plain text CSV file with all SI measurements- FigS2_S3_Saccharification_Index_Data.xlsx: Excel workbook with formatted data and detailed notes- README.md: Comprehensive documentation of the dataset
DOI: 10.5281/zenodo.18382491
title: Saccharification Index Data for MyDFF Study - Supplementary Figures S2 and S3

description: This dataset contains Saccharification Index (SI) values from in vitro fermentation experiments conducted as part of the My Dietary Fiber Finder (MyDFF) validation study. The data supports Figure S2 and Figure S3 in the supplementary materials of the manuscript titled "A personalized microbiota screening platform for optimizing individual volatile fatty acid production - A proof-of-concept study", which has been submitted to the journal Microbiome.

Study Design:- Cross-sectional analysis: 10 healthy adult donors (A-J) at baseline- Longitudinal analysis: 4 donors (B, C, I, J) with follow-up samples over 3-9 months

Data Collection:SI values were measured from in vitro fermentation of fecal microbiota samples with 17 different dietary fiber products representing 6 categories: resistant starch (n=4), resistant dextrin (n=3), α-cyclodextrin (n=3), isomaltodextrin (n=2), partially hydrolyzed guar gum (n=2), and inulin (n=3).

Each SI measurement represents the mean of triplicate fermentation experiments and is calculated as:SI = (pH_control - pH_sample) / (pH_control - pH_glucose)

Files Included:- FigS2_S3_Saccharification_Index_Data.csv: Plain text CSV file with all SI measurements- FigS2_S3_Saccharification_Index_Data.xlsx: Excel workbook with formatted data and detailed notes- README.md: Comprehensive documentation of the dataset
DOI: 10.5061/dryad.nq7c845
title: Data from: The influence of developmental environment on courtship song in cactophilic Drosophila

description: Closely related species often differ in the signals involved in sexual
 communication and mate recognition. Determining the factors influencing
 signal quality (i.e. signal's content and conspicuousness) provides
 an important insight into the potential pathways by which these
 interspecific differences evolve. Host specificity could bias the
 direction of the evolution of sexual communication and the mate
 recognition system, favoring sensory channels that work best in the
 different host conditions. In this study, we focus on the cactophilic
 sibling species Drosophila buzzatii and D. koepferae that have diverged
 not only in the sensory channel used for sexual communication and mate
 recognition but also in the cactus species that use as primary hosts. We
 evaluate the role of the developmental environment in generating courtship
 song variation using an isofemale line design. Our results show that host
 environment during development induces changes in the courtship song of D.
 koepferae males, but not in D. buzzatii males. Moreover, we report for the
 first time that host rearing environment affects the conspicuousness of
 courtship song (i.e. song volume). Our results are mainly discussed in the
 context of the sensory drive hypothesis.
description: Iglesias et al. 2018
 DATA_JEBCourtship song
 parameters and wing centroid size data of D. buzzatii and D.
 koepferae.
DOI: 10.5061/dryad.615
title: Data from: A partitioned likelihood analysis of swallowtail butterfly phylogeny (Lepidoptera: Papilionidae)

description: Although it is widely agreed that data from multiple sources are necessary
 to confidently resolve phylogenetic relationships, procedures for
 accommodating and incorporating heterogeneity in such data remain
 underdeveloped. We explored the use of partitioned, model-based analyses
 of heterogeneous molecular data in the context of a phylogenetic study of
 swallowtail butterflies (Lepidoptera: Papilionidae). Despite substantial
 basic and applied study, phylogenetic relationships among the major
 lineages of this prominent group remain contentious. We sequenced 3.3 kb
 of mitochondrial (COI/COII α 2.3 kb) and nuclear (EF-1α 1.0 kb) DNA for 22
 swallowtails, including representatives of Baroniinae, Parnassiinae, and
 Papilioninae, and several moth and butterfly outgroups. Parsimony
 encountered considerable difficulty in resolving the deepest splits among
 these taxa. We therefore chose two outgroups whose relationships to each
 other and to Papilionidae were undisputed and undertook detailed
 likelihood analyses of alternative topologies. Following previous studies
 that have demonstrated substantial heterogeneity in the evolutionary
 dynamics among process partitions of these genes, we estimated
 evolutionary parameters separately for gene-based and codon-based
 partitions. These values were then used as the basis for examining the
 likelihoods of possible resolutions and rootings under several partitioned
 and unpartitioned likelihood models. Partitioned models gave significantly
 better fits to the data than did unpartitioned models, and supported
 different topologies. However, the most likely topology varied from model
 to model. The most likely ingroup topology under the best-fitting, six
 partition GTR + Γ model favors a paraphyletic Parnassiinae. However, when
 examining the likelihoods of alternative rootings of this tree relative to
 rootings of the classical hypothesis two rootings of the latter emerge as
 most likely. Of these two, the most likely rooting is within the
 Papilioninae, although a rooting between Baronia and the remaining
 Papilionidae is only nonsignificantly less likely.
description: Caterino et al Data
 SetCaterino.nexus
DOI: 10.5061/dryad.5615g
title: Data from: Aphid specialization on different summer hosts is associated with strong genetic differentiation and unequal symbiont communities despite a common mating habitat

description: Specialization on different host plants can promote evolutionary
 diversification of herbivorous insects. Work on pea aphids (Acyrthosiphon
 pisum) has contributed significantly to the understanding of this process,
 demonstrating that populations associated with different host plants
 exhibit performance trade-offs across hosts, show adaptive host choice and
 genetic differentiation, and possess different communities of bacterial
 endosymbionts. Populations specialized on different secondary host plants
 during the parthenogenetic summer generations are also described for the
 black bean aphid (Aphis fabae complex) and are usually treated as
 different (morphologically cryptic) subspecies. In contrast to pea aphids,
 however, host choice and mate choice are decoupled in black bean aphids,
 because populations from different summer hosts return to the same primary
 host plant to mate and lay overwintering eggs. This could counteract
 evolutionary divergence, and it is currently unknown to what extent black
 bean aphids using different summer hosts are indeed differentiated. We
 addressed this question by microsatellite genotyping and endosymbiont
 screening of black bean aphids collected in summer from the goosefoot
 Chenopodium album (subspecies A. f. fabae) and from thistles of the genus
 Cirsium (subspecies A. f. cirsiiacanthoides) across numerous sites in
 Switzerland and France. Our results show clearly that aphids from Cirsium
 and Chenopodium show strong and geographically consistent genetic
 differentiation, and that they differ in their frequencies of infection
 with particular endosymbionts. The dependence on a joint winter host has
 thus not prevented the evolutionary divergence into summer host-adapted
 populations that appear to have evolved mechanisms of reproductive
 isolation within a common mating habitat.
description: microsat_data_for_dryadendosymbiont_data_for_dryadendo_data_for_dryad.txt
DOI: 10.5061/dryad.97q0th1
title: Data from: Sex differences but no evidence of quantitative honesty in the warning signals of six-spot burnet moths (Zygaena filipendulae L.)

description: The distinctive black and red wing pattern of six-spot burnet moths
 (Zygaena filipendulae, L.) is a classic example of aposematism,
 advertising their potent cyanide-based defences. While such warning
 signals provide a qualitatively honest signal of unprofitability, the
 evidence for quantitative honesty, whereby variation in visual traits
 could provide accurate estimates of individual toxicity, is more
 equivocal. Combining sophisticated measures of cyanogenic glucoside
 content and wing colour from the perspective of avian predators, we
 investigate the relationship between coloration and defences in Z.
 filipendulae, to test signal honesty both within and across populations.
 Mean cyanogenic glucoside concentration was not correlated with wing
 coloration across populations in males, yet in females higher cyanogenic
 glucoside levels were associated with smaller and lighter red forewing
 markings. Trends within populations were similarly indicative of
 quantitative dishonesty, and consistent differences between the sexes were
 apparent: larger females, carrying a greater total cyanogenic glucoside
 load, displayed larger but less conspicuous markings than smaller males,
 according to several colour metrics. The overall high aversiveness of
 cyanogenic glucosides and fluctuations in colour and toxin levels during
 an individual’s lifetime may contribute to these results, highlighting
 generally important reasons why signal honesty should not always be
 expected in aposematic species.
description: Toxicity and colour data
 for all samples, UVS visual systemThis data file contains
 the toxicity (cyanogenic glucoside concentrations) and colour measurements
 (from cone catch data to luminance, saturation and hue values) for all
 samples. Colour measurements are based on the UVS (blue tit) visual
 system.Briolat_Zfilipendulae_UVSsystem.csvToxicity and colour data for all samples, VS visual systemThis data file contains the colour and toxicity measurements for all samples, with the colour measurements based on the VS (peafowl) visual system.Briolat_Zfilipendulae_VSsystem.csvContrast (JNDs) between moth red forewing areas and natural backgroundsThis file contains the chromatic and luminance just noticeable differences (JNDs) calculated between the colours of the moths' red forewings and three plant types (Lotus corniculatus [Lc] leaves, Lotus corniculatus flowers and Knautia arvensis [Ka] flowers), for both the UVS and VS visual systems.Briolat_Zfilipendulae_ContrastToPlants.csv
DOI: 10.5061/dryad.8nb7v
title: Data from: Phylogeography and niche modelling of the relict plant Amborella trichopoda (Amborellaceae) reveal multiple Pleistocene refugia in New Caledonia

description: Amborella trichopoda Baill. (Amborellaceae, Amborellales), the sole living
 member of the sister group to all other extant Angiosperms, is endemic to
 New Caledonia. We addressed the intraspecific phylogeography of Amborella
 by investigating whether its present population genetic structure could be
 related to its current and past habitats. We found moderate range-wide
 genetic diversity based on nuclear microsatellite data, and detected four
 well-differentiated, geographically distinct genetic groups using Bayesian
 clustering analyses. We modeled the ecological niche of Amborella based on
 current climatic and environmental conditions. The predictive ability of
 the model was very good throughout the Central East mainland zone, but
 Amborella was predicted in the northern part of the island where this
 plant has not been reported. Furthermore, no significant barrier was
 detected based on habitat suitability that could explain the genetic
 differentiation across the area. Conversely, we found that the main
 genetic clusters could be related to the distribution of suitable habitat
 at the last glacial maximum (LGM, ca. 21 000 years BP), when Amborella
 experienced a dramatic 96.5% reduction in suitable area. At least two
 lineages survived in distinct putative refugia located in the Massif des
 Lèvres and in the vicinity of Mount Aoupinié. Our findings finally
 confirmed the importance of LGM rainforest refugia in shaping the current
 intra- and inter-specific diversity in New Caledonian plants, and revealed
 the possibility of an as-yet unreported refugium. The combination of niche
 modelling and population genetics thereby offered novel insight into the
 biogeographic history of an emblematic taxon.
description: Amborella-Maxent-dataAmborella localities and corresponding environmental information used for Maxent modelling. Localities are in decimal degrees (UTM58S and WGS84 Coordinate System). Description, abbreviations and source of environmental variables is given in the paper and in Table S7Amborella-nSSR-data-dryadMicrosatellite genotypes for 12 Amborella trichopodia populations sampled across New Caledonia and genotyped at 10 SSR loci
DOI: 10.5061/dryad.f82ns
title: Data from: Adaptive contraction of diet breadth affects sexual maturation and specific nutrient consumption in an extreme generalist omnivore

description: Animals balance their intake of specific nutrients, but little is known
 about how they do so when foraging in an environment with toxic resources
 and whether toxic foods promote adaptations that affect life history
 traits. In German cockroach (Blattella germanica) populations, glucose
 aversion has evolved in response to glucose-containing insecticidal baits.
 We restricted newly eclosed glucose averse (GA) and wild type (WT) female
 cockroaches to nutritionally defined diets varying in
 protein-to-carbohydrate (P:C) ratio (3:1, 1:1, or 1:3) or gave them free
 choice of the 3:1 and 1:3 diets, with either glucose or fructose as the
 sole carbohydrate source. We measured consumption of each diet over six
 days and then dissected the females to measure the length of basal oocytes
 in their ovaries. Our results showed significantly lower consumption by GA
 compared to WT cockroaches when restricted to glucose-containing diets,
 but also lower fructose intake by GA compared to WT cockroaches when
 restricted to high fructose diets or given choice of fructose-containing
 diets. Protein intake was regulated tightly regardless of carbohydrate
 intake, except by GA cockroaches restricted to glucose-containing diets.
 Oocyte growth was completely suppressed in GA females restricted to
 glucose-containing diets, but also significantly slower in GA than in WT
 females restricted to fructose-containing diets. Our findings suggest that
 GA cockroaches have adapted to reduced diet breadth through endocrine
 adjustments which reduce requirements for energetic fuels. Our study
 illustrates how an evolutionary change in the chemosensory system may
 affect the evolution of other traits that govern animal life histories.
description: Data - Sexual maturation
 and specific nutrient consumption in female glucose averse and wild type
 German cockroachesStartmess, dietary
 intake, dry mass intake, protein intake, carbohydrate intake, and average
 oocyte length for the female glucose averse and wild type German
 cockroaches when sexually maturing on diets differing in protein to
 carbohydrate ratio and carbohydrate source (glucose or
 fructose).Data - Sexual maturation and
 specific nutrient consumption.xls
DOI: 10.5061/dryad.18v6q
title: Data from: Heterospecific aggression bias towards a rarer colour morph

description: Colour polymorphisms are a striking example of phenotypic diversity, yet
 the sources of selection that allow different morphs to persist within
 populations remain poorly understood. In particular, despite the
 importance of aggression in mediating social dominance, few studies have
 considered how heterospecific aggression might contribute to the
 maintenance or divergence of different colour morphs. To redress this gap,
 we carried out a field-based study in a Nicaraguan crater lake to
 investigate patterns of heterospecific aggression directed by the cichlid
 fish, Hypsophrys nicaraguensis, towards colour polymorphic cichlids in the
 genus Amphilophus. We found that H. nicaraguensis was the most frequent
 territorial neighbour of the colour polymorphic A. sagittae. Furthermore,
 when manipulating territorial intrusions using models, H. nicaraguensis
 were more aggressive towards the gold than dark colour morph of the
 sympatric Amphilophus species, including A. sagittae. Such a pattern of
 heterospecific aggression should be costly to the gold colour morph,
 potentially accounting for its lower than expected frequency and, more
 generally, highlighting the importance of considering heterospecific
 aggression in the context of morph frequencies and coexistence in the
 wild.
description: Aggression
 dataThe table shows the
 number of aggressive events by focal Hypsophrys nicaraguensis territory
 owners. The ID of the territory, sex of each focal individual, stimulus
 type, order of presentation, stimulus species (when not P. managuensis),
 depth at the focal territory and breeding season (by year) are also
 given.Nearest neighbour
 distribution: A. sagittaeThe table shows the
 nearest neighbours of the focal Amphilophus sagittae territory owners. The
 ID of each focal territory, focal pair colour type, and breeding season
 (year) are also given.Neighbour distribution sagittae
 RSPB-2015-1551.xlsNearest neighbour
 distribution: H. nicaraguensisThe table shows the
 nearest neighbours of the focal H. nicaraguensis territories by species.
 The ID of each focal territory, neighbouring pair colour type (when
 relevant) and breeding season (by year) are also given.Neighbour distribution
 nicaraguensis RSPB-2015-1551.xls
DOI: 10.5061/dryad.61f72
title: Data from: Many paths to a common destination: morphological differentiation of a functionally convergent visual signal

description: Understanding the interacting outcomes of selection and historical
 contingency in shaping adaptive evolution remains a challenge in
 evolutionary biology. While selection can produce convergent outcomes when
 species occupy similar environments, the unique history of each species
 can also influence evolutionary trajectories and result in different
 phenotypic end points. The question is to what extent historical
 contingency places species on different adaptive pathways and, in turn,
 the extent to which we can predict evolutionary outcomes. Among lizards
 there are several distantly related genera that have independently evolved
 an elaborate extendible dewlap for territorial communication. We conducted
 a detailed morphological study and employed new phylogenetic comparative
 methods to investigate the evolution of the underlying hyoid that powers
 the extension of the dewlap. This analysis showed that there appear to
 have been multiple phenotypic pathways for evolving a functionally
 convergent dewlap. The biomechanical complexity that underlies this
 morphological structure implies that adaptation should have been
 constrained to a narrow phenotypic pathway. However, multiple adaptive
 solutions have been possible in apparent response to a common selection
 pressure. Thus, the phenotypic outcome that subsequently evolved in
 different genera seems to have been contingent on the history of the group
 in question. This blurs the distinction between convergent and
 historically contingent adaptation and suggests that adaptive phenotypic
 diversity can evolve without the need for divergent natural selection.
description: Hagman and Ord Am Nat
 Hyoid dataData collected from
 museum specimens.Hagman&Ord_AmNat_56650_data.xlsx
DOI: 10.5061/dryad.8296
title: Data from: Nested polymerase chain reaction–based detection of Dothistroma septosporum, red band needle blight of pine, a tool in support of phytosanitary regimes

description: Red band needle blight is one of the most important foliar diseases of
 Pinus species and is of increasing international forest health and
 biosecurity concern. To provide a rapid identification technique for this
 pathogen in support of official control measures, a nested polymerase
 chain reaction–based diagnostic assay that employs species-specific primer
 sets has been developed. The assay is able to detect the presence of the
 pathogen direct from pine needles, irrespective of host species, to within
 10 fg of target DNA, the equivalent of approximately 2–3 ascospores or
 hyphael cells.
description: Dryad supplement info
 for MER. septosporum MER-10-0451.R1The 67 D. septosporum
 sensu stricto ITS sequences that were either generated in this study or
 accessed via public databases that were used in the identification and
 further evaluation of primers. The accession numbers themselves are
 hyperlinked to their database of origin.Supplemental_data_for_Langrell.docSupplemental_data_for_Langrell.rtf