cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hp388dm
title: Data from: The evolution of microendemism in a reef fish (Hypoplectrus maya)

description: Marine species tend to have extensive distributions, which are commonly
 attributed to the dispersal potential provided by planktonic larvae and
 the rarity of absolute barriers to dispersal in the ocean. Under this
 paradigm, the occurrence of marine microendemism without geographic
 isolation in species with planktonic larvae poses a dilemma. The recently
 described Maya hamlet (Hypoplectrus maya, Serranidae) is exactly such a
 case, being endemic to a 50-km segment of the Mesoamerican Barrier Reef
 System (MBRS). We use whole-genome analysis to infer the demographic
 history of the Maya hamlet and contrast it with the sympatric and
 pan-Caribbean black (H. nigricans), barred (H. puella) and butter (H.
 unicolor) hamlets, as well as the allopatric but phenotypically similar
 blue hamlet (H. gemma). We show that H. maya is indeed a distinct
 evolutionary lineage, with genomic signatures of inbreeding and a unique
 demographic history of continuous decline in effective population size
 since it diverged from congeners just ~3000 generations ago. We suggest
 that this case of microendemism may be driven by the combination of a
 narrow ecological niche and restrictive oceanographic conditions in the
 southern MBRS, which is consistent with the occurrence of an unusually
 high number of marine microendemics in this region. The restricted
 distribution of the Maya hamlet, its decline in both census and effective
 population sizes, and the degradation of its habitat place it at risk of
 extinction. We conclude that the evolution of marine microendemism can be
 a fast and dynamic process, with extinction possibly occurring before
 speciation is complete.
description: MD5This file contains the
 checksums to verify file integrity of the data files.READMEUnphased genotypes of
 Caribbean reef fishes (Hypoplectrus sp.)Genotypes of 51 hamlets
 (H. gemma, H. maya, H. nigricans, H. puella and H. unicolor). Based on
 ~24x Illumina sequencing data, created with GATK.4_bi-allelic_snps.vcf.gzPhased genotypes of Caribbean reef fishes (Hypoplectrus sp.)Genotypes of 51 hamlets (H. gemma, H. maya, H. nigricans, H. puella and H. unicolor). Based on ~24x Illumina sequencing data, created with GATK and phased using SHAPEIT.5_phased.vcf.gz
DOI: 10.5061/dryad.6p65fh1
title: Data from: Specialized roots of Velloziaceae weather quartzite rock while mobilizing phosphorus using carboxylates

description: 1.Campos rupestres is an extremely phosphorus (P)‐impoverished rocky
 ecosystem in Brazil. Velloziaceae is an important plant family in this
 environment, and some species colonize exposed quartzite rock. However, we
 know virtually nothing about their root development and nutrient
 acquisition within the rock outcrops and their possible role in rock
 weathering and landscape formation. 2.We tested the hypothesis that
 Velloziaceae dissolve P from the rock, enhancing rock‐weathering. The
 study was carried out with two Barbacenia species (Velloziaceae) that
 colonize quartzite rocks. We assessed the root specializations and
 exudates, and determined the mineralogical composition of the rocks. 3.The
 quartzite rocks contained a low concentration of total P in a matrix
 composed predominantly of silica. Using transmission electron microscopy,
 we show root growth perpendicular to the rock‐bedding planes. A micro‐XRF
 setup at the XRF beamline of a synchrotron evidenced root‐associated rock
 dissolution. 4.The investigated roots show novel morphological and
 physiological specializations, coined vellozioid roots, which are highly
 effective at P acquisition. These carboxylate‐releasing roots function
 like others specialized roots in nutrient‐depleted soils. The rocks
 represent a barrier for most species, but due to their chemical and
 physical actions inside the rocks, vellozioid roots play a pivotal role in
 rock weathering, contributing to shaping the campos rupestres landscapes.
description: Teodoro et al.
 20191. Carboxylate
 concentrations during vellozioid root development in Barbacenia tomentosa:
 immature (2-4 days), mature (6-12 days) and senescent (more than 15 days);
 2. Mineral element concentration (mg g-1) in quartzite rock in campos
 rupestres. The rock samples were collected in Itutinga, Diamantina and
 Serra do Cipó National Park (n=9), Minas Gerais, Brazil; 3. Solubilized
 phosphorus (P) from quartzite rock collected in campos rupestres as
 affected by the addition of carboxylates (malate).
DOI: 10.5061/dryad.9v2362d
title: Data from: “Balancing” balancing selection? Assortative mating at the major histocompatibility complex despite molecular signatures of balancing selection

description: In vertebrate animals, genes of the major histocompatibility complex (MHC)
 determine the set of pathogens to which an individual's adaptive
 immune system can respond. MHC genes are extraordinarily polymorphic,
 often showing elevated nonsynonymous relative to synonymous sequence
 variation and sharing presumably ancient polymorphisms between lineages.
 These patterns likely reflect pathogen‐mediated balancing selection, for
 example, rare‐allele or heterozygote advantage. Such selection is often
 reinforced by disassortative mating at MHC. We characterized exon 2 of MHC
 class II, corresponding to the hypervariable peptide‐binding region, in
 song sparrows (Melospiza melodia). We compared nonsynonymous to synonymous
 sequence variation in order to identify positively selected sites;
 assessed evidence for trans‐species polymorphisms indicating ancient
 balancing selection; and compared MHC similarity of socially mated pairs
 to expectations under random mating. Six codons showed elevated ratios of
 nonsynonymous to synonymous variation, consistent with balancing
 selection, and we characterized several alleles similar to those occurring
 in at least four other avian families. Despite this evidence for
 historical balancing selection, mated pairs were significantly more
 similar at MHC than were randomly generated pairings. Nonrandom mating at
 MHC thus appears to partially counteract, not reinforce, pathogen‐mediated
 balancing selection in this system. We suggest that in systems where
 individual fitness does not increase monotonically with MHC diversity,
 assortative mating may help to avoid excessive offspring heterozygosity
 that could otherwise arise from long‐standing balancing selection.
description: Sequences analyzed in
 Figure 3Fasta file of sequences
 analyzed in Figure 3similar_sequences.fasUniFrac DataFiles and code used to compute UniFrac in RUniFrac_Data.zip
DOI: 10.5061/dryad.3k5m7j6
title: Data from: Non-random loss of phylogenetically distinct rare species degrades phylogenetic diversity in semi-natural grasslands

description: 1. Although biodiversity loss is a critically important topic, our
 understanding of how both land abandonment and land-use intensification in
 semi-natural grasslands alters the community diversity and assembly
 mechanisms is very limited. Large-scale economic drivers of land-use
 change might inadvertently result in the loss of vulnerable species and
 reduce ecosystem services provisioning. 2. In this study, we assessed
 non-random community change by examining patterns of low-abundance species
 loss, and community assembly in semi-natural grasslands due to land
 abandonment and intensification in southwest Japan. We analyzed
 relationships between evolutionary distinctiveness and abundance for each
 species. In addition, we used metrics of species and phylogenetic
 diversity and phylogenetic structure to assess patterns of non-random
 biodiversity loss due to both abandoned and intensified land-use. 3. We
 demonstrated that low-abundance species were more evolutionarily distinct
 compared to high-abundance (i.e., dominant) species. Furthermore, land-use
 intensification resulted in further declines in low-abundance species,
 whereas land abandonment resulted in declines in all species, regardless
 of their initial abundance. 4. We found that both forms of land-use change
 (abandonment and intensification) resulted in non-random patterns of
 community change, with traditional land-use maintaining the highest
 biodiversity and land-use change coinciding with decreased species and
 phylogenetic diversity measures. Intensified land-use caused phylogenetic
 community structure to be more closely related than expected by chance,
 whereas the metrics of how distant species are from one another on average
 based on phylogenetic tree (i.e., mean pairwise phylogenetic distance) did
 not change from land abandonment. 5. Synthesis and applications. We show
 that the loss of phylogenetic diversity, and especially of low-abundance
 species with high value of phylogenetic distinctiveness, resulted in
 non-random community disassembly. Our results argue that in order to
 maintain biodiversity in these semi-natural grasslands, traditional
 management practices should be encouraged over intensification and simple
 abandonment. Government agencies should adopt policies or provide
 incentives that encourage the maintenance of traditional practices in
 rural Japan, and elsewhere where the combination of land consolidation and
 abandonment are important conservation issues.
description: Raw data and R
 scriptThis file includes raw
 data and R script for analyses of this study.raw data and R
 script.zip
DOI: 10.5061/dryad.cq11s60
title: Data from: Conservation genetics of the pond bat (Myotis dasycneme) with special focus on the populations in northwestern Germany and Jutland, Denmark

description: Conservation genetics is important in the management of endangered
 species, helping to understand their connectivity and long-term viability,
 thus identifying populations of importance for conservation. The pond bat
 (Myotis dasycneme) is a rare species classified as ‘Near threatened’ with
 a wide but patchy Palearctic distribution. A total of 277 samples
 representing populations in Denmark, Germany, Latvia, Hungary and Russia
 were used in the genetic analyses; 224 samples representing Denmark,
 Germany and Russia were analysed at 10 microsatellite loci; 241 samples
 representing all areas were analysed using mitochondrial D-loop and
 cytochrome B sequences. A Bayesian clustering approach revealed two poorly
 resolved clusters, one representing the Danish and German group and the
 other the Russian group. However, significantly, different pairwise FST
 and DEST estimates were observed between the Danish and German group, and
 between the Danish and Russian group suggesting a recent population
 structure. These conflicting results might be attributed to the effect of
 migration or low resolution due to the number of microsatellite markers
 used. After concatenating the two mitochondrial sequences, analysis
 detected significant genetic differentiation between all populations,
 probably due to genetic drift combined with a founder event. The
 phylogenetic tree suggested a closer relationship between Russian and
 Northern European populations compared to the Hungarian population,
 implying that the latter belongs to an older ancestral population. This
 was supported by the observed haplotype network and higher nucleotide
 diversity in this population. The genetic structuring observed in the
 Danish/German pond bat stresses the need for a cross border management
 between the two countries. Further, the pronounced mtDNA structuring,
 together with the indicated migration between nearby populations suggest
 philopatric female behavior but male migration, emphasizes the importance
 of protecting suitable habitat mosaics to maintain a continuum of patches
 with dense pond bat populations across the species’ distribution range.
description: MD_Microsat2019.xlsxGenotypes based on 10 microsatellite loci for 224 pond bats representing Germany, Denmark and Russia
DOI: 10.5281/zenodo.18390401
title: LINF_320010500

description: Profilin; Leishmania infantum (strain JPCM5)
DOI: 10.5281/zenodo.18390400
title: LINF_320010500

description: Profilin; Leishmania infantum (strain JPCM5)
DOI: 10.5061/dryad.rt530k9
title: Data from: Island woodiness underpins accelerated disparification in plant radiations

description: The evolution of secondary (insular) woodiness and the rapid
 disparification of plant growth forms associated with island radiations
 show intriguing parallels between oceanic islands and tropical alpine sky
 islands. However, the evolutionary significance of these phenomena remains
 poorly understood and the focus of debate. We explore the evolutionary
 dynamics of species diversification and trait disparification across
 evolutionary radiations in contrasting island systems compared to their
 non‐island relatives. We estimate rates of species diversification, growth
 form evolution, and phenotypic space saturation for the classical oceanic
 island plant radiations – the Hawaiian silverswords and Macaronesian
 Echium ‐ and the well‐studied sky island radiations of Lupinus and
 Hypericum in the Andes. We show that secondary woodiness is associated
 with dispersal to islands and with accelerated rates of species
 diversification, accelerated disparification of plant growth forms, and
 occupancy of greater phenotypic trait space for island clades than their
 non‐island relatives, on both oceanic and sky islands. We conclude that
 secondary woodiness is a prerequisite that may act as a key innovation,
 manifest as the potential to occupy greater trait space, for plant
 radiations on island systems in general, further emphasizing the
 importance of combinations of clade‐specific traits and ecological
 opportunities in driving adaptive radiations.
description: All data used in the
 study (time trees, BEAST XML files, trait data)The data (zip file)
 contains (1) the sequence alignments and XML BEAST input files for Echium
 and Madiinae (silverswords and tarweeds) (2) the time trees (BEAST MCC
 trees) for Echium (additionally the full MCC tree for Boraginaceae pp, and
 a pdf of the full tree detailing the placement of fossil constraints),
 Hypericum, Lupinus, and Madiinae, (3) trait data for Echium, Hypericum,
 Lupinus, and Madiinae detailing distribution (island/non-island), life
 form (annual or herbaceous / perennial or woody), mean plant height (in
 ln[cm]).NuerkAtchinsonHughes_NewPytol_islandRad_data.zip
DOI: 10.5061/dryad.5cr6008
title: Data from: Morphological and molecular diagnostic species characters of Staurozoa (Cnidaria) collected on the coast of Helgoland (German Bight, North Sea)

description: Scientific knowledge and records on staurozoans are limited probably
 because of their inconspicuous life habit and the small number of
 specialists for this taxon. To increase the awareness for Staurozoa, we
 identified morphological and molecular features of the three staurozoan
 species Haliclystus tenuis Kishinouye, 1910, Haliclystus auricula Clark,
 1863, and Craterolophus convolvulus (Johnston, 1835) collected on the
 coast of the island Helgoland to evaluate their suitability as diagnostic
 characters. Useful macromorphological diagnostic features were the
 patterns of white spots of nematocysts and internal arm structures,
 whereas tentacle and gonad follicle numbers showed high intraspecific
 variations. Morphometric measurements on photographs of living specimens
 provided reliable data for interspecific comparisons. Comprehensive
 nematocyst analyses revealed interspecific shape differences of isorhizas
 and three types of rhopaloids, indicating that the staurozoan cnidome is
 more diverse than previously assumed. However, the taxonomic value of
 nematocyst analyses in Staurozoa remains unclear because comprehensive
 data is still lacking for most species. Comparative molecular genetic
 sequence analyses of mitochondrial 16S and COI and nuclear 18S ribosomal
 DNA identified the three species and confirmed their morphological
 identification. In comparison to published data, our analyses indicate
 similarities between H. auricula and Haliclystus antarcticus Pfeffer,
 1889. Proteomic fingerprinting by matrix-assisted laser
 desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)
 differentiated all three species, suggesting that this technique could
 provide an alternative rapid identification method for staurozoans.
description: holst_et_alThe zip file comprises all information on the analyses of the three markers mitochondrial 16S rDNA, mitochondrial cytochrome c oxidase subunit I (COI) and nuclear 18S rDNA including multiple alignments, neighbour joining trees and maximum likelihood trees. For further information and for displaying the files, please read the README file (included in the zip file).
DOI: 10.5061/dryad.8hh028v
title: Data from: Fighting and mating success in giant Australian cuttlefish is influenced by behavioural lateralization

description: Behavioural lateralization is widespread. Yet, a fundamental question
 remains, how can lateralization be evolutionary stable when individuals
 lateralized in one direction often significantly outnumber individuals
 lateralized in the opposite direction? A recently developed game theory
 model predicts that fitness consequences that occur during intraspecific
 interactions may be driving population-level lateralization as an
 evolutionary stable strategy. This model predicts that (i) minority-type
 individuals exist because they are more likely to adopt unpredictable
 fighting behaviours during competitive interactions (e.g. fighting); and
 (ii) majority-type individuals exist because there is a fitness advantage
 in having their biases synchronized with other conspecifics during
 interactions that require coordination (e.g. mating). We tested these
 predictions by investigating biases in giant Australian cuttlefish during
 fighting and mating interactions. During fighting, most male cuttlefish
 favoured the left eye and these males showed higher contest escalation;
 but minority-type individuals with a right-eye bias achieved higher
 fighting success. During mating interactions, most male cuttlefish
 favoured the left eye to inspect females. Furthermore, most male
 cuttlefish approached the female’s right side during a mating attempt and
 these males achieved higher mating success. Our data support the
 hypothesis that population-level biases are an evolutionary consequence of
 the fitness advantages involved in intraspecific interactions.
description: ESM_R
 DataRaw data for eye
 preferences in relation to mate guarding behaviour, contest escalation,
 contest success, female approach side and mating
 success.
DOI: 10.5061/dryad.d5279d1
title: Data from: One-shot dilation versus serial dilation technique for access in percutaneous nephrolithotomy: a systematic review and meta-analysis

description: Objective: The purpose of this study was to systematically review the
 outcomes of the use of one-shot dilation (OSD) and serial tract dilation
 for percutaneous nephrolithotomy (PCNL). Methods: A systematic review and
 meta-analysis was conducted. The randomized controlled trials (RCTs)
 included in the study were identified from EMBASE, MEDLINE, and the
 Cochrane Central Register of Controlled Trials. The last search was
 performed on April 30, 2018. Summary effects were calculated as risk
 ratios (RRs) with 95% confidence intervals (CIs) or mean differences (MDs)
 with 95% CIs. The endpoints included access time, fluoroscopy time,
 successful dilation rate, stone-free rate, postoperative decrease in
 hemoglobin levels, transfusion rate, complication rate, and length of
 postoperative hospital stay. Results: A total of 7 RCTs were included in
 the study, with clinical data reported for 697 patients. The overall
 access time was approximately 110 seconds shorter in the OSD group than in
 the serial dilation group (MD, -110.14; 95% CI, -161.99 to -58.30;
 P&lt;0.0001). The fluoroscopy time was shorter with OSD in all RCTs.
 In addition, the decrease in postoperative hemoglobin levels was
 approximately 0.23 g/dl less in patients in the OSD group than in those in
 the serial dilation group (MD, -0.23; 95% CI, -0.39 to -0.07; P=0.004). No
 relationship was found between the successful dilation rate, stone-free
 rate, transfusion rate, or complication rate and the method of tract
 dilation. Conclusion: OSD is a safe and efficacious tract dilation
 technique that can reduce the access time, fluoroscopy time, and
 postoperative decrease in hemoglobin level. No difference was found in the
 successful dilation rate, stone-free rate, transfusion rate, or rate of
 complications between the OSD and serial dilation groups. The difference
 in the length of postoperative hospital stay was uncertain. OSD may be a
 better method of tract creation for PCNL.
description: DataSharing_DryadData from: One-shot dilation versus serial dilation technique for access in percutaneous nephrolithotomy: a systematic review and meta-analysis .
DOI: 10.5061/dryad.mh82kj6
title: Data from: Genetic diversity in the Dactylorhiza majalis subsp. majalis populations (Orchidaceae) in northern Poland

description: We analysed 16 populations of Dactylorhiza majalis subsp. majalis located
 in the northern Poland, simultaneously utilizing both morphological and
 molecular data. Genetic differentiation was examined using five
 microsatellite loci, and morphological variation was assessed for 23
 characters. At the species level, our results showed a moderate level of
 genetic diversity (A = 6.00; Ae = 1.86; Ho = 0.387; FIS = 0.139) which
 varied between studied populations (A = 2.60-4.20; Ae = 1.68-2.39; Ho =
 0.270-0.523; FIS = –0.064-0.355). A significant excess of homozygotes was
 detected in five population, while excess of heterozygotes was observed in
 four populations, but obtained values were statistically insignificant.
 Moderate, but clear genetic differentiation was found (FST = 0.101; P
 &lt; 0.001). Considering the obtained pairwise-FST and number of
 migrants, we indicated three population groups (I, II, III), where the
 first one can be divided into two smaller subgroups (Ia, Ib). These three
 groups differed in the gene flow values (Nm = 0.39-1.12). The highest
 number of migrants per generation was noticed in the subgroup Ia (8.58).
 It indicates a central panmictic population with free gene flow surrounded
 by peripatric local populations (Ib) with more limited gene flow.
 Geographic isolation, habitat fragmentation and limited seed dispersal
 affect limited gene flow among three indicated population groups . A weak
 but significant pattern of isolation by distance was also observed (r =
 0.351; P &lt; 0.05).
description: D.majalis_data
 (nuclear+morphology)D.majalis_data.xls