cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1fs7c
title: Data from: Conservation genetics of Australasian sailfin lizards: flagship species threatened by coastal development and insufficient protected area coverage

description: Despite rampant coastal development throughout Southeast Asia and the
 Pacific, studies of conservation genetics and ecology of vulnerable,
 coastal species are rare. Large bodied vertebrates with highly specialized
 habitat requirements may be at particular risk of extinction due to
 habitat degradation and fragmentation, especially if these habitats are
 naturally patchily distributed, marginal, or otherwise geographically
 limited, or associated in space with high human population densities or
 heavy anthropogenic disturbance. Particularly telling examples of these
 conservation challenges are large Australasian reptiles with obligate
 habitat requirements for lowland, coastal and mangrove forests. Plagued by
 habitat destruction due to high human densities along coastlines,
 sprawling rural development, and rapidly developing estuarine fisheries
 industry, coastal forest reptiles are experiencing rapid declines. And yet
 studies of population biology, genetics, and habitat requirements of
 species depending on these environments are few. We undertook the present
 study in order to take a multifaceted approach to understanding a poignant
 conservation problem. We identify significant evolutionary units for
 conservation in large-bodied Sailfin Lizards (genus Hydrosaurus), model
 suitable habitat in the Philippines from extensive occurrence data and
 evaluate the efficacy of the current protected area network, and identify
 the source of hydrosaurs in the illegal pet trade. We determine that the
 extent of the species' habitat coincident with protected areas is
 low. Our forensic evaluation of the illegal pet trade in the Philippines
 determines the existence of a natural population that is at risk of
 systematic exploitation by traders. Together, this integrative study
 characterizes a conservation urgency of particular significance: the
 genetically distinct Sailfin lizards of the Bicol faunal region, with
 suitable habitat virtually unprotected, and clear evidence of heavy
 exploitation for illegal trade. To the best of our knowledge, our study is
 the first conservation genetic study to evaluate the potential
 effectiveness of the protected landscape coverage in the Philippines, a
 Megadiverse nation and Biodiversity Hotspot.
description: Concatenated Alignment
 FileThis file contains the
 concatenated sequence data used in this study. A character block is
 provided at the bottom outlining character sets within the
 alignment.Alignment_Combined.nexAppendixS1This Appendix S1 provides the locality data for samples used in the study as well as coordinate data for samples used for ecological modeling procedures. GenBank numbers are provided in a complete Appendix S1 published with the study, and correspond to sequences found within the concatenated alignment file submitted with this appendix to Dryad.Maximum Likelihood Bootstrap TopologyBootstrap topology resulting from partitioned Maximum Likelihood Analyses.ML1000.tre
DOI: 10.5061/dryad.rk07d
title: Data from: Selection for predation, not female fecundity, explains sexual size dimorphism in the orchid mantises

description: Here we reconstruct the evolutionary shift towards floral simulation in
 orchid mantises and suggest female predatory selection as the likely
 driving force behind the development of extreme sexual size dimorphism.
 Through analysis of body size data and phylogenetic modelling of trait
 evolution, we recovered an ancestral shift towards sexual dimorphisms in
 both size and appearance in a lineage of flower-associated praying
 mantises. Sedentary female flower mantises dramatically increased in size
 prior to a transition from camouflaged, ambush predation to a floral
 simulation strategy, gaining access to, and visually attracting, a novel
 resource: large pollinating insects. Male flower mantises, however,
 remained small and mobile to facilitate mate-finding and reproductive
 success, consistent with ancestral male life strategy. Although moderate
 sexual size dimorphisms are common in many arthropod lineages, the
 predominant explanation is female size increase for increased fecundity.
 However, sex-dependent selective pressures acting outside of female
 fecundity have been suggested as mechanisms behind niche dimorphisms. Our
 hypothesised role of predatory selection acting on females to generate
 both extreme sexual size dimorphism coupled with niche dimorphism is novel
 among arthropods.
description: Data
 matrixCombined molecular and
 morphology matrix used to generate phylogenetic trees. A data partition
 block is included at the end of the data matrix.Svenson et al Combined
 data.nexMorphological character
 descriptionsDescription of
 morphology characters used in phylogenetic analysis. Character numbers
 correspond to the order of appearance in the data matrix. Characters taken
 from Svenson et al. (2015).Morphology
 characters.docxMeasurement
 dataAll direct measurement
 data used for statistical and ratio analysis.
DOI: 10.5061/dryad.1421
title: Data from: Geographical variation in bill size across bird species provides evidence for Allen’s rule

description: Allen’s rule proposes that the appendages of endotherms are smaller,
 relative to body size, in colder climates, in order to reduce heat loss.
 Empirical support for Allen’s rule is mainly derived from occasional
 reports of geographical clines in extremity size of individual species.
 Interspecific evidence is restricted to two studies of leg proportions in
 seabirds and shorebirds. We used phylogenetic comparative analyses of 214
 bird species to examine whether bird bills, significant sites of heat
 exchange, conform to Allen’s rule. The species comprised eight diverse
 taxonomic groups - toucans, African barbets, Australian parrots and
 estrildid finches, Canadian galliforms, penguins, gulls and terns. Across
 all species there were strongly significant relationships between bill
 length and both latitude and environmental temperature, with species in
 colder climates having significantly shorter bills. Patterns supporting
 Allen’s rule in relation to latitudinal or altitudinal distribution held
 within all groups except the finches. Evidence for a direct association
 with temperature was found within four groups (parrots, galliforms,
 penguins and gulls). Support for Allen’s rule in leg elements was weaker,
 suggesting that bird bills may be more susceptible to thermoregulatory
 constraints generally. Our results provide the strongest comparative
 support yet published for Allen’s rule, and demonstrate that
 thermoregulation has been an important factor in shaping the evolution of
 bird bills.
description: Symonds & Tattersall
 data 1.xlsMorphological and
 Geographical data used in the analysesSymonds & Tattersall
 data 2.doc
DOI: 10.5061/dryad.n41nk
title: Data from: Fish population genetic structure shaped by hydroelectric power plants in the upper Rhine catchment

description: The Rhine catchment in Switzerland has been transformed by a chain of
 hydroelectric power stations. We addressed the impact of fragmentation on
 the genetic structure of fish populations by focusing on the European chub
 (Squalius cephalus). This fish species is not stocked and copes well with
 altered habitats, enabling an assessment of the effects of fragmentation
 per se. Using microsatellites, we genotyped 2133 chub from 47 sites within
 the catchment fragmented by 37 hydroelectric power stations, two weirs and
 the Rhine Falls. The shallow genetic population structure reflected
 drainage topology and was affected significantly by barriers to migration.
 The effect of power stations equipped with fishpasses on genetic
 differentiation was detectable, albeit weaker than that of man-made
 barriers without fishpasses. The Rhine Falls as the only long-standing
 natural obstacle (formed 14 000 to 17 000 years ago) also had a strong
 effect. Man-made barriers also exacerbated the upstream decrease in
 allelic diversity in the catchment, particularly when lacking fishpasses.
 Thus, existing fishpasses do have the desired effect of mitigating
 fragmentation, but barriers still reduce population connectivity in a fish
 that traverses fishpasses better than many other species. Less mobile
 species are likely to be affected more severely.
description: Allelic Richness
 AnalysisGouskov_EvolApp_October2015_DataAllelicRichness.csvAllelic Richness AnalysisGouskov_EvolApp_October2015_DataAllelicRichness.txtIBD and GLM DataGouskov_EvolApp_October2015_DataMatrices_Spreadsheet.csvIBD and GLM DataGouskov_EvolApp_October2015_DataMatrices_Spreadsheet.txtMicrosatelliteGouskov_EvolApp_October2015_Microsatellite_Spreadsheet.csvMicrosatelliteGouskov_EvolApp_October2015_Microsatellite_Spreadsheet.txt
DOI: 10.5061/dryad.8p425
title: Data from: High-throughput molecular identification of fish eggs using multiplex suspension bead arrays

description: The location and abundance of fish eggs provide information concerning the
 timing and location of spawning activities and can provide
 fishery-independent estimates of spawning biomass. However, the full value
 of egg and larval surveys is severely restricted because many species’
 eggs and larvae are morphologically similar, making species-level
 identification difficult. Recent efforts have shown that nearly all
 species of fish may be identified by mitochondrial DNA (mtDNA) sequences
 (e.g., via “DNA barcoding”). By taking advantage of a DNA barcode
 database, we have developed oligonucleotide probes for 23 marine fish
 species that produce pelagic eggs commonly found in California waters.
 Probes were coupled to fluorescent microspheres to create a suspension
 bead array. Biotin-labeled primers were used to amplify the mitochondrial
 cytochrome oxidase subunit I (COI) and 16S ribosomal rRNA genes from
 individual fish eggs. The amplicons were then hybridized to the bead array
 and after addition of a reporter fluorophore, samples were analyzed by
 flow cytometry with Luminex 100 instrumentation. Probes specifically
 targeted eggs that are abundant and/or from morphologically
 indistinguishable species pairs. Results showed the 33 different probes
 designed for this study accurately identified all samples when PCR was
 successful. Suspension bead arrays have a number of benefits over other
 methods of molecular identification; these arrays permit high
 multiplexing, simple addition of new probes, high throughput, and lower
 cost than DNA sequencing. The increasing availability of DNA barcode data
 for numerous fish faunas worldwide suggests bead arrays could be developed
 and widely used for fish egg, larval and tissue identifications.
description: Failed probe sequences
 for DryadThese are the
 oligonucleotide probe sequences (designed using Primer BLAST available
 through the NCBI website) for the 33 fish species included in this study.
 Using nucleotide BLAST in NCBI, these probe sequences were found to match
 non-target species in the GenBank database and were thus discarded and not
 utilized further in the study.
DOI: 10.5061/dryad.q1q10
title: Data from: Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition

description: Microorganisms play a crucial role in the biological decomposition of
 plant litter in terrestrial ecosystems. Due to the permanently changing
 litter quality during decomposition, studies of both fungi and bacteria at
 a fine taxonomic resolution are required during the whole process. Here we
 investigated microbial community succession in decomposing leaf litter of
 temperate beech forest using pyrotag sequencing of the bacterial 16S and
 the fungal internal transcribed spacer (ITS) rRNA genes. Our results
 reveal that both communities underwent rapid changes. Proteobacteria,
 Actinobacteria and Bacteroidetes dominated over the entire study period,
 but their taxonomic composition and abundances changed markedly among
 sampling dates. The fungal community also changed dynamically as
 decomposition progressed, with ascomycete fungi being increasingly
 replaced by basidiomycetes. We found a consistent and highly significant
 correlation between bacterial richness and fungal richness (R = 0.76, P
 &lt; 0.001) and community structure (RMantel = 0.85, P &lt;
 0.001), providing evidence of coupled dynamics in the fungal and bacterial
 communities. A network analysis highlighted nonrandom co-occurrences among
 bacterial and fungal taxa as well as a shift in the cross-kingdom
 co-occurrence pattern of their communities from the early to the later
 stages of decomposition. During this process, macronutrients,
 micronutrients, C:N ratio and pH were significantly correlated with the
 fungal and bacterial communities, while bacterial richness positively
 correlated with three hydrolytic enzymes important for C, N and P
 acquisition. Overall, we provide evidence that the complex litter decay is
 the result of a dynamic cross-kingdom functional succession.
description: Leaf litter
 physicochemical propertiesLeaf litter
 physicochemical properties of all samples.Leaflitter_physicochemical_properties_submitted.xlsxBacteria and fungal community dynamics in decomposing litterThe data files include (i) biom matrix for bacteria 16S (ii) biom matrix for fungi ITS (iii) representative sequence for bacteria (iv) representative sequence for fungi (v) bioinformatic script for bacteria and (vi) bioinformatic script for fungiPurahong_etal2016_Bacteria_Fungi(1).zip
DOI: 10.5061/dryad.j4103
title: Data from: Paleo-islands as refugia and sources of genetic diversity within volcanic archipelagos: The case of the widespread endemic Canarina canariensis (Campanulaceae)

description: Geographical isolation by oceanic barriers and climatic stability has been
 postulated as some of the main factors driving diversification within
 volcanic archipelagos. However, few studies have focused on the effect
 that catastrophic volcanic events have had on patterns of within-island
 differentiation in geological time. This study employed data from the
 chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine
 the patterns of genetic variation in Canarina canariensis, an iconic plant
 species associated with the endemic laurel forest of the Canary Islands.
 We found a strong geographical population structure, with a first
 divergence around 0.8 Ma that has Tenerife as its central axis and divides
 Canarian populations into eastern and western clades. Genetic diversity
 was greatest in the geologically stable ‘palaeo-islands’ of Anaga, Teno
 and Roque del Conde; these areas were also inferred as the ancestral
 location of migrant alleles towards other disturbed areas within Tenerife
 or the nearby islands using a Bayesian approach to phylogeographical
 clustering. Oceanic barriers, in contrast, appear to have played a lesser
 role in structuring genetic variation, with intra-island levels of genetic
 diversity larger than those between-islands. We argue that volcanic
 eruptions and landslides after the merging of the palaeo-islands 3.5 Ma
 played key roles in generating genetic boundaries within Tenerife, with
 the palaeo-islands acting as refugia against extinction, and as cradles
 and sources of genetic diversity to other areas within the archipelago.
description: Matrix AFLPs Canarina
 canariensisOriginal Matrix of
 Canarina canariensis AFLPsmatriz_595alelos.xlsxcpDNA_Canarina_canariensisNEXUS files for the concatenated cpDNA dataset of Canarina canariensis
DOI: 10.5061/dryad.5h52h
title: Data from: Reproductive phenology of the tomato frog, Dyscophus antongili, in an urban pond of Madagascar's east coast

description: Based on daily monitoring around an urban pond in the coastal town of
 Maroantsetra, from 2003-2011, we provide an analysis of the yearly
 reproductive activity of the tomato frog (Dyscophus antongilii), a
 large-sized and prominent red-coloured microhylid frog from north-eastern
 Madagascar. Frogs were observed all year round but despite the lack of
 limited climatic seasonality in the region it was possible to observe a
 high activity period between January-May and a lower activity period
 between June-December. Freshly laid eggs were found in all months except
 November, and with highest incidence between January and May, while
 calling was heard in all months. We found a positive correlation between
 daily adult counts and minimum air temperature. On the contrary rainfall
 did not significantly predict activity, although boosts of calling and
 egg-laying especially in the austral winter were observed after heavy
 rainfall events. We define D. antongilii in Maroantsetra as a sporadic wet
 season breeder that reproduces at irregular intervals following heavy rain
 events.
description: Segev_et_al_Dyscophus_phenology_dataOriginal field transect data indicating the number of adults, freshly laid eggs, and calls recorded from 2003-2010.
DOI: 10.5061/dryad.202f5
title: Data from: Effect of the MC1R gene on sexual dimorphism in melanin-based colorations

description: Variants of the melanocortin-1 receptor (MC1R) gene result in abrupt,
 naturally selected colour morphs. These genetic variants may
 differentially affect sexual dimorphism if one morph is naturally selected
 in the two sexes but another morph is naturally or sexually selected only
 in one of the two sexes (e.g. to confer camouflage in reproductive females
 or confer mating advantage in males). Therefore, the balance between
 natural and sexual selections can differ between MC1R variants, as suggest
 studies showing interspecific correlations between sexual dimorphism and
 the rate of nonsynonymous vs. synonymous amino acid substitutions at the
 MC1R. Surprisingly, how MC1R is related to within-species sexual
 dimorphism, and thereby to sex-specific selection, has not yet been
 investigated. We tackled this issue in the barn owl (Tyto alba), a species
 showing pronounced variation in the degree of reddish pheomelanin-based
 coloration and in the number and size of black feather spots. We found
 that a valine (V)-to-isoleucine (I) substitution at position 126 explains
 up to 30% of the variation in the three melanin-based colour traits and in
 feather melanin content. Interestingly, MC1R genotypes also differed in
 the degree of sexual colour dimorphism, with individuals homozygous for
 the II MC1R variant being 2 times redder and 2.5 times less sexually
 dimorphic than homozygous individuals for the VV MC1R variant. These
 findings support that MC1R interacts with the expression of sexual
 dimorphism and suggest that a gene with major phenotypic effects and
 weakly influenced by variation in body condition can participate in
 sex-specific selection processes.
description: Data from SanJose et
 alZip
 file including data on melanin content, plumage color traits per body
 part, and plumage color traits at different ages and body
 parts.Data.zipMC1R Alligment
DOI: 10.5061/dryad.8r652
title: Data from: Relative importance of pollen and seed dispersal across a Neotropical mountain landscape for an epiphtytic orchid.

description: Populations of many species are isolated within narrow elevation bands of
 Neotropical mountain habitat, and how well dispersal maintains genetic
 connectivity is unknown. We asked whether genetic structure of an
 epiphytic orchid, Epidendrum firmum, corresponds to gaps between Costa
 Rican mountain ranges, and how these gaps influence pollen and seed flow.
 We predicted that significant genetic structure exists among mountain
 ranges due to different colonization histories and limited gene flow.
 Furthermore, we predicted that pollen movement contributes more to gene
 flow than seeds because seeds are released into strong winds perpendicular
 to the narrow northwest-southeast species distribution, while the likely
 pollinators are strong fliers. Individuals from 12 populations and three
 mountain ranges were genotyped with nuclear microsatellites (nDNA) and
 chloroplast sequences (cpDNA). Genetic diversity was high for both
 markers, while nDNA genetic structure was low (FSTn = 0.020) and cpDNA
 structure was moderate (FSTc = 0.443). Significant cpDNA barriers occurred
 within and among mountain ranges, but nDNA barriers were not significant
 after accounting for geographic distance. Consistent with these
 contrasting patterns of genetic structure, pollen contributes
 substantially more to gene flow among populations than seed (mp/ms = 46).
 Pollinators mediated extensive gene flow, eroding nDNA colonization
 footprints, while seed flow was comparatively limited, possibly due to
 directional prevailing winds across linearly distributed populations.
 Dispersal traits alone may not accurately inform predictions about gene
 flow or genetic structure, supporting the need for research into the
 potentially crucial role of pollinators and landscape context in gene flow
 among isolated populations.
description: cpDNA_alignmentFASTA file containing aligned and concatenated chloroplast DNA sequences used in analysis of chloroplast genetic variation. The file contains 248 sequences of 1370 base pairs. Each sequence header lists the population ("POP") followed by a unique sample identifier ("SAMPLE").Microsatellite_dataMicrosatellite data from Epidendrum firmum. The file is in GenAlEx format. Row one lists the number of loci, the number of samples, the number of populations, and the number of samples per population. Row two lists population names in the column below each corresponding population size in row one. Row three contains column headers: Sample Identifier, Population, and each of the five microsatellite loci. Allele one and allele two for each locus are listed in separate columns. The data correspond to allele size in base pairs, including the primer sequence. Missing data are coded as zeros.microsatellites.xlsx
DOI: 10.5061/dryad.5jq64
title: Data from: Empirical evidence for large X-effects in animals with undifferentiated sex chromosomes

description: Reproductive isolation is crucial for the process of speciation to
 progress. Sex chromosomes have been assigned a key role in driving
 reproductive isolation but empirical evidence from natural population
 processes has been restricted to organisms with degenerated sex
 chromosomes such as mammals and birds. Here we report restricted
 introgression at sex-linked compared to autosomal markers in a hybrid zone
 between two incipient species of European tree frog, Hyla arborea and H.
 orientalis, whose homologous X and Y sex chromosomes are undifferentiated.
 This large X-effect cannot result from the dominance or faster-X aspects
 of Haldane’s rule, which are specific to degenerated sex chromosomes, but
 rather supports a role for faster-heterogametic-sex or faster-male
 evolutionary processes. Our data suggest a prominent contribution of
 undifferentiated sex chromosomes to speciation.
description: Mitochondrial haplotypes
 and microsatellite genotypes of tree frog samples from the Hyla arborea /
 Hyla orientalis hybrid zone in PolandThe file shows the
 mitochondrial haplotype (Hyla arborea or orientalis) and microsatellite
 genotypes of all samples included in the publication. NA: missing data.
 See the method section of the publication for further
 detailsData.xls