cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4mp00
title: Data from: Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies

description: Though considerable progress has been made in inferring phylogenetic
 relationships of many plant lineages, deep unresolved nodes remain a
 common problem that can impact downstream efforts, including taxonomic
 decision-making and character reconstruction. The Core Goodeniaceae is a
 group affected by this issue: data from the plastid regions trnL-trnF and
 matK have been insufficient to generate adequate support at key nodes
 along the backbone of the phylogeny. We performed genome skimming for 24
 taxa representing major clades within Core Goodeniaceae. The plastome
 coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled
 and complemented with additional accessions sequenced for nuclear G3PDH
 and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were
 analyzed independently and topology tests were used to detect the
 alignments’ ability to reject alternative topologies. The CDS, NRR, and
 G3PDH alignments independently supported a Brunonia (Scaevola s.l.
 (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia
 s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B
 (Velleia + Goodenia C))) contrasts with the poorly supported nuclear
 topology ((Goodenia A + Goodenia B) (Velleia + Goodenia C)). A fully
 resolved and maximally supported topology for Core Goodeniaceae was
 recovered from the plastome CDS, and there is excellent support for most
 of the major clades and relationships among them in all alignments. The
 composition of these seven major clades renders many of the current
 taxonomic divisions non-monophyletic, prompting us to suggest that
 Goodenia may be split into several segregate genera.
description: NGS resolution of Core
 Goodeniaceae data filesSee "Dryad
 Description" file inside zip folder.NGS resolution of Core
 Goodeniaceae.zip
DOI: 10.5061/dryad.qm1v0
title: Data from: Are generalist Aphidiinae (Hym. Braconidae) mostly cryptic species complexes?

description: Aphidiinae are mostly composed of specialist parasitoids and the few
 species described as generalist are suspected to be composed of cryptic
 specialists, almost indistinguishable based on morphological
 characteristics. The use of molecular markers has proven to be a useful
 tool for revealing cryptic species complexes and here we use seven
 mitochondrial and nuclear gene fragments to study possible genetic
 differentiation among seven Aphidiinae generalists. Maximum likelihood
 (ML) trees and Bayesian Poisson tree processes (bPTP) models were
 conducted on each gene separately and on the seven genes together. The
 standard cytochrome c oxidase I barcode region appeared to be the most
 polymorphic and probably the best marker to reveal putative cryptic
 species. However, we showed with ML trees and bPTP models that a
 complementary use of mitochondrial and nuclear genes was the most relevant
 approach to reliably identify cryptic genetic clades in the Aphidiinae.
 Overall, most of the analysed generalist morphospecies were shown to be
 composed of subgroups related to the aphid host, some of them revealed as
 cryptic species by the species delimitation analysis. Further studies are
 needed to reveal the generality of this result in Aphidiinae.
description: 16S16S alignement:
 (Hymenoptera: Aphidiinae)28S28S alignement:
 (Hymenoptera: Aphidiinae)Argk_Exon1Arginine Kinase Exon 1 alignement: (Hymenoptera: Aphidiinae)Argk_Exon2Arginine Kinase Exon 2 alignement: (Hymenoptera: Aphidiinae)COICOI alignement: (Hymenoptera: Aphidiinae)CytBCytochrome B alignement: (Hymenoptera: Aphidiinae)EFElongation factor 1 alpha alignement: (Hymenoptera: Aphidiinae)LWRhLong wavelength Rhodopsin alignement: (Hymenoptera: Aphidiinae)COI_TreeCOI Tree: (Hymenoptera: Aphidiinae)All_genes_TreeAphidiinae (Hymenoptera) Maximum Likelihood Tree based on these seven genes: Cytochrome c oxidase I, Cytochrome B, rRNA 16S, rRNA 28S, Long wavelength Rhodopsin, Arginine Kinase and Elongation factor 1 α.
DOI: 10.5061/dryad.mj17h
title: Data from: Utility of geometric morphometrics for inferring feeding habit from mouthpart morphology in insects: tests with larval Carabidae (Insecta: Coleoptera)

description: Feeding habits are important life-history traits in animals; however,
 methods for their determination are not well established in many species.
 The larvae of the beetle family Carabidae are an example. The present
 study tested the utility of geometric morphometrics of mouthpart
 morphology to infer the feeding habits of carabid larvae. Using
 Pterostichus thunbergi as a model system, larval feeding habits were
 inferred using geometric morphometrics of mouthparts and the results were
 compared with those obtained from rearing experiments. The rearing
 experiments indicated that P. thunbergi larvae are carnivores that require
 snails as an essential part of the diet. Through geometric morphometrics,
 associations between mouthpart morphology and larval feeding habits were
 confirmed for species in which these two traits are known. A discriminant
 analysis using these associations classified P. thunbergi larvae as
 snail/slug feeders, which is a result compatible with the rearing
 experiments. Geometric morphometrics also revealed that morphological
 integration and ontogenetic shape change might play roles in the
 diversification of mouthpart morphology. Overall, these results
 demonstrate the utility of the geometric morphometrics of mouthparts to
 infer feeding habit and to clarify the mechanisms of mouthpart
 morphological diversification in the study group, and the results also
 serve as a basis for future studies of other insect groups.
description: Raw coordinates of data
 set 1 (nts format)Carabidae_mandible01(TPSDIG_DigitizedRawData).ntsRaw coordinates of data set 2 (nts format)Carabidae_mandible02(TPSDIG_DigitizedRawData).ntsSliders file of data set 1 (nts format)Carabidae_mandible01(TPSRELW_SlidersFile).ntsSliders file of data set 2 (nts format)Carabidae_mandible02(TPSRELW_SlidersFile).ntsLink file of data set 1 and 2 (nts format)Carabidae_mandible01&02(TPSRELW_LinkFile).ntsRaw coordinates for analysis of the effects of measurement error in data set 1 (nts format)ME_Carabidae_mandible01(TPSDIG_DigitizedRawData).ntsRaw coordinates for analysis of the effects of measurement error in data set 2 (nts format)ME_Carabidae_mandible02(TPSDIG_DigitizedRawData).NTSScaled image for size calibrationData on rearing P.thunbergi larvae
DOI: 10.5061/dryad.4cj58
title: Data from: Machine learning biogeographic processes from biotic patterns: a new trait-dependent dispersal and diversification model with model choice by simulation-trained discriminant analysis

description: Current statistical biogeographical analysis methods are limited in the
 ways ecology can be related to the processes of diversification and
 geographical range evolution, requiring conflation of geography and
 ecology, and/or assuming ecologies that are uniform across all lineages
 and invariant in time. This precludes the possibility of studying a broad
 class of macroevolutionary biogeographical theories that relate
 geographical and species histories through lineage-specific ecological and
 evolutionary dynamics, such as taxon cycle theory. Here we present a new
 model that generates phylogenies under a complex of superpositioned
 geographical range evolution, trait evolution, and diversification
 processes that can communicate with each other. We present a
 likelihood-free method of inference under our model using discriminant
 analysis of principal components of summary statistics calculated on
 phylogenies, with the discriminant functions trained on data generated by
 simulations under our model. This approach of model selection by
 classification of empirical data with respect to data generated under
 training models is shown to be efficient, robust, and performs well over a
 broad range of parameter space defined by the relative rates of dispersal,
 trait evolution, and diversification processes. We apply our method to a
 case study of the taxon cycle, that is testing for habitat and trophic
 level constraints in the dispersal regimes of the Wallacean avifaunal
 radiation.
description: cladogenesis-model-misspecification.analysis.2015-10-10.archipelago_a2a63ae.rev_99037f0+supplementalwallacea-supplemental-results.archipelago_2c8ab2d.rev_9bc2a6fwallacea-birds-9104e5a.tarwallacea-birds-9104e5a.results.tarperformance_2015-03-17.archipelago_54fef83.rev_f49101crobustness_2015-03-19.archipelago_b198966.rev_908f161archipelago-validation-59d10e4.tar
DOI: 10.5061/dryad.7vf87
title: Data from: High atmospheric temperatures and ‘ambient incubation’ drive embryonic development and lead to earlier hatching in a passerine bird

description: Tropical and subtropical species typically experience relatively high
 atmospheric temperatures during reproduction, and are subject to
 climate-related challenges that are largely unexplored, relative to more
 extensive work conducted in temperate regions. We studied the effects of
 high atmospheric and nest temperatures during reproduction in the zebra
 finch. We characterized the temperature within nests in a subtropical
 population of this species in relation to atmospheric temperature.
 Temperatures within nests frequently exceeded the level at which embryo’s
 develop optimally, even in the absence of parental incubation. We
 experimentally manipulated internal nest temperature to demonstrate that
 an average difference of 6°C in the nest temperature during the laying
 period reduced hatching time by an average of 3% of the total incubation
 time, owing to ‘ambient incubation’. Given the avian constraint of laying
 a single egg per day, the first eggs of a clutch are subject to prolonged
 effects of nest temperature relative to later laid eggs, potentially
 increasing hatching asynchrony. While birds may ameliorate the negative
 effects of ambient incubation on embryonic development by varying the
 location and design of their nests, high atmospheric temperatures are
 likely to constitute an important selective force on avian reproductive
 behaviour and physiology in subtropical and tropical regions, particularly
 in the light of predicted climate change that in many areas is leading to
 a higher frequency of hot days during the periods when birds breed.
description: Experimental
 chambersThis file contains the
 temperature data for the experimental chambers used in the study. The
 column headings are all very self explanatory. Temperature is degrees
 Cexperimental
 chambers.csvIncubation
 lengthThis file contains the
 data regarding the incubation duration of clutches in the experimental
 treatment. Column headings are self-explanatory. The locations given in
 'Colony' are all found in the Gap Hills area, as described in
 the paper.locationThis file contains the data for the descriptive component of the paper, characterising temperatures in different types of nest and locations in vegetation as described in the paper.Natural nestsThis file contains the data that describes the variation in temperature for natural nests at Fowlers Gap with respect to environmental variables such as location, height and orientation as described in the papernatural nests.csvNormal - LethalThis data set looks at the time that the experimental nests spent at normal or lethal incubation temperatures during the experimental period (as described in the paper).normal-lethal.csvTemperature Fowlers GapThis file contains the data on maximum daily temperature from the Fowlers Gap automated weather station run by the Australian Bureau of Meteorology. This data is presented in Figure 1.temperature FG.csv
DOI: 10.5061/dryad.2dq44
title: Data from: Cushion plant morphology controls biogenic capability and facilitation effects of Silene acaulis along an elevation gradient

description: The stress-gradient hypothesis (SGH) predicts that the balance of
 plant–plant interactions shifts along abiotic environmental gradients,
 with facilitation becoming more frequent under stressful conditions.
 However, recent studies have challenged this perspective, reporting that
 positive interactions are, in some cases, more common at the intermediate
 level of environmental severity gradients. Here, we test whether and how
 neighbour effects by Silene acaulis cushions vary along a 700 m wide
 altitudinal transect, in relation to cushion morphological traits and
 environmental severity. Field measurements along the gradient, within and
 outside cushions, included (i) species richness and cover of coexisting
 vascular plants; (ii) cushion morphology; (iii) above- and below-ground
 microclimate; and (iv) soil quality. We used the relative interaction
 index to decouple neighbour trait effects and environmental severity
 effects on plant diversity at different elevations. The ability of the
 cushion plant to facilitate heterospecifics shifts considerably along the
 elevation gradient, being greatest at the intermediate level. On the other
 hand, Silene morphological traits steadily change along the gradient, from
 lax, soft and flat-shaped cushion habits at low elevation to tightly knit
 and dome-shaped habits at high elevation. Cushion morphological changes
 are associated with mitigating effects on microclimate, indicating that
 cushions effectively act as a heat-trap at medium and high elevations,
 while at low elevations the soft and flat cushions avoid excessive heat
 accumulation by tight coupling with the surrounding atmosphere. At the
 upper end of the gradient, cushion cespitose–pulvinate compactness and
 high stem density appear to be critical traits in modulating the net
 effect of plant–plant interaction, since the space available for hosting
 other vascular species is considerably reduced. In conclusion, this work
 provides a mechanistic link between plant morphological traits, associated
 biogenic microclimate changes and variation in net plant–plant
 interactions along the explored severity gradient. Our findings support an
 alternative conceptual model to SGH, with plant facilitation collapsing at
 the upper extreme of the abiotic stress gradient.
description: 1_Bonanomi_et_al_Funct_Ecol_2015_db_dryadData of plant cover, species richness, soil quality and microclimate (temperature and soil moisture) inside and outside Silene acaulis plant.
DOI: 10.5061/dryad.tk5rj
title: Data from: Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species

description: Among the 899 species of freshwater fishes reported from Sundaland
 biodiversity hotspot, nearly 50% are endemics. The functional integrity of
 aquatic ecosystems is currently jeopardized by human activities, and
 landscape conversion led to the decline of fish populations in several
 part of Sundaland, particularly in Java. The inventory of the Javanese
 ichthyofauna has been discontinuous, and the taxonomic knowledge is
 scattered in the literature. This study provides a DNA barcode reference
 library for the inland fishes of Java and Bali with the aim to streamline
 the inventory of fishes in this part of Sundaland. Owing to the lack of
 available checklist for estimating the taxonomic coverage of this study, a
 checklist was compiled based on online catalogues. A total of 95 sites
 were visited, and a library including 1046 DNA barcodes for 159 species
 was assembled. Nearest neighbour distance was 28-fold higher than maximum
 intraspecific distance on average, and a DNA barcoding gap was observed.
 The list of species with DNA barcodes displayed large discrepancies with
 the checklist compiled here as only 36% (i.e. 77 species) and 60% (i.e. 24
 species) of the known species were sampled in Java and Bali, respectively.
 This result was contrasted by a high number of new occurrences and the
 ceiling of the accumulation curves for both species and genera. These
 results highlight the poor taxonomic knowledge of this ichthyofauna, and
 the apparent discrepancy between present and historical occurrence data is
 to be attributed to species extirpations, synonymy and misidentifications
 in previous studies.
description: Sequence
 alignmentSequence alignement of
 the 1,046 DNA barcodesNeighbour joining tree
 (nwk)Neighbour joining tree
 (Newick format) of the 1,046 DNA barcodesBOLDTree.nwkNeighbour joining tree (pdf)Neighbour joining tree of the 1,046 DNA barcodesFig S1 - NJ tree.pdf
DOI: 10.5061/dryad.bc0d8
title: Data from: The measurement of selection when detection is imperfect: how good are naïve methods?

description: The life spans of animals can be measured in natural populations by
 uniquely marking individuals and then releasing them into the field.
 Selection on survival (a component of fitness) can subsequently be
 quantified by regressing the life spans of these marked individuals on
 their trait values. However, marked individuals are not always seen on
 every subsequent catching occasion, and for this reason, imperfect
 detection is considered a problem when estimating survival selection in
 natural populations. Capture–mark–recapture methods have been advocated as
 a powerful means to correct for imperfect detection. Here, we use
 simulated and field data sets to evaluate the effect of assuming perfect
 detection (‘naïve methods’), when detection is really imperfect. We
 compared the performance of the naïve methods with methods correcting for
 imperfect detection (mark–recapture methods, or MR). Although the effects
 of trait-dependent recapture probability are mitigated when recapture
 probability is high, mark–recapture methods still provide the safest
 choice when recapture probability might be trait-dependent. In our
 simulations, mark–recapture methods had a power advantage over naïve
 methods, but all methods lost statistical power at low recapture
 probabilities. The main advantage of mark–recapture methods over naïve
 methods is the ability to control for hidden trait-dependent recapture
 probability, as it is often hard to tell a priori if trait dependence is
 an issue in a particular study. However, when trait-dependent recapture
 probability is weak, naïve methods and mark–recapture methods perform
 similarly as long as recapture rates do not become too low, and the main
 problem of survival selection studies is still low statistical power. We
 provide a R package (EasyMARK) alongside with this paper to facilitate
 future integration between MR methods and classical selection studies.
 EasyMARK provides the opportunity to convert the regression coefficients
 from MR-approaches in to classical standardized selection gradients.
description: Simulation and Field
 Data, RcodeThis is field data and
 data generated from simulations. See ReadMe file for more
 information.Dryad Data
 File.zip
DOI: 10.5061/dryad.tr26k
title: Data from: The new Andean jumping spider genus Urupuyu and its placement within a revised classification of the Amycoida (Araneae: Salticidae)

description: Urupuyu gen. nov. is described for three new species of small black
 jumping spiders from the cloud forests of Ecuador: Urupuyu antisana sp.
 nov. (type species), U. edwardsi sp. nov., and U. occidentale sp. nov.
 Phylogenetic analyses with DNA sequences (28S, actin 5C, wingless, 16SND1
 and CO1) indicate Urupuyu is closely related to the huriine amycoids
 Hurius and Scoturius, a placement also supported by morphological traits.
 Our phylogenetic analysis serves to clarify the relationships within the
 Amycoida in general, leading to our proposing a revised classification for
 the group, with subfamilies Gophoinae, Sitticinae, Bredinae subfam. nov.,
 Scopocirinae, Thiodininae, Sarindinae, Huriinae, Simonellinae, and
 Amycinae. We confirm the marpissine-like Breda belongs within the
 Amycoida. The phylogeny implies that ant mimicry has evolved at least
 twice (simonellines and sarindines) and probably a third time
 (Atomosphyrus in the thiodinines) within the Amycoida. The following new
 synonymies are proposed for suprageneric names: Hyetusseae Simon, 1903 and
 Arachnomureae Mello-Leitão, 1917 = Thiodininae Simon, 1901; Zunigeae
 Simon, 1901 = Sarindinae Simon, 1901; Synemosynae Banks, 1892 =
 Simonellinae Peckham, Peckham & Wheeler, 1888; Magoninae
 Petrunkevitch, 1928 = Amycinae F.O.P.-Cambridge, 1900.
description: RuizMaddison2015-AmycoidaThis file includes the alignments of the 5 gene regions analyzed, and resulting phylogenetic trees
DOI: 10.5061/dryad.7dq0j
title: Data from: Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices

description: Implied weighting, a method for phylogenetic inference that actively seeks
 to downweight supposed homoplasy, has in recent years begun to be widely
 utilized in palaeontological datasets. Given the method's purported
 ability at handling widespread homoplasy/convergence, we investigate the
 effects of implied weighting on modelled phylogenetic data. We generated
 100 character matrices consisting of 55 characters each using a Markov
 Chain morphology model of evolution based on a known phylogenetic tree.
 Rates of character evolution in these datasets were variable and generated
 by pulling from a gamma distribution for each character in the matrix.
 These matrices were then analysed under equal weighting and four settings
 of implied weights (k = 1, 3, 5, and 10). Our results show that implied
 weighting is inconsistent in its ability to retrieve a known phylogenetic
 tree. Equally weighted analyses are found to generally be more
 conservative, retrieving higher frequency of polytomies but being less
 likely to generate erroneous topologies. Implied weighting is found to
 generally resolve polytomies while also propagating errors, resulting in
 an increase in both correctly and incorrectly resolved nodes with a
 tendency towards higher rates of error compared to equal weighting. Our
 results suggest that equal weights may be a preferable method for
 parsimony analysis.
description: Appendix S1 - TNT
 filesZip file containing all
 100 matrices generated from our MK model of morphological
 change.S1 -
 TNT files.zipAppendix S2 –
 TreesZip file containing pdfs
 of all consensus trees generated from equal and implied weighting analyses
 for all 100 matrices. The files have been commented on to denote correct
 and incorrect node relationships with checks and x's
 respectively.S2 -
 Trees.zipAppendix S3 -
 Spreadsheet of Node CountsExcel spreadsheet with
 raw counts of correct, incorrect, and unknown relationships for all runs
 of equal and implied weighting, as well standardized counts of implied
 weighting relative to equal weighting, and overall counts of the relative
 proportions of the data which increase or decrease
 error.S3 -
 Spreadsheet of Node Counts.xlsxAppendix S4 – Run Counts
 of Repeated ErrorsA checklist of the 100
 runs counting off the number of times an error in equal weighting was
 repeated in 1, 2, 3, and all 4 implied weights runs.S4 - Run Counts of repeated
 errors.xlsxAppendix S5 - Character
 Weights Test NEXUS filesZip folder containing
 all 100 nexus files used in the character weights tests. These matrices
 contain the same 4 characters (Character 56-59), generated with known
 rates of evolution.S5 - Character Weights Test
 NEXUS files.zipAppendix S6 - Character
 WeightsExcel spreadsheet of the
 weights/fits generated for our four characters in all 100 matrices for
 four values of k (1,3,5,10).S6 - Character
 Weights.xlsx