cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18253023
title: Annotations of human skin-associated fungi

description: Description

This repository contains genome annotations for skin-associated fungi sequenced and analysed in the manuscript:Comparative Genomic Analysis of Clinically Relevant Human Skin-Associated Fungi, S. Agerbaek et al., https://doi.org/10.21203/rs.3.rs-6700810/v1 (under review)

The data provided here represent the original genome assemblies and annotations generated prior to any downstream processing, and are deposited to ensure full reproducibility of the results reported in the study.

Clean assemblies and raw reads are available under the Bioproject: PRJNA126044, which also contains metadata about the strains sequenced. Note that some genomes were excluded from the analysis following the initial upload, which is why there are fewer annotations here than assemblies in the Bioproject. 

Annotations available in this repo under Annotations/species_ID were annotated with Funannotate v1.8.13. Functional annotations were generated with Eggnog-mapper v2.1.7, InterProScan v5.56-89.0, antiSMASH v6.0.0 and SignalP v6.0. 

Content

For each genome, the following files are provided: 



.scaffolds.fa



Initial assembly 



.gff3



Structural gene annotation including gene, transcript, and CDS features



.proteins.fa



Predicted protein sequences 



.rn.proteins.fasta 



Predicted protein sequences with re-named fasta headers containing functional annotation in the format: >Species | Strain_ID | Gene accession | Gene name | Gene description | COG | Antismash | GO term | EC number(s) | Pfam term(s) | Interpro term(s) 



.cds-transcripts.fa 



Nucleotide coding sequences 



.annotations.txt



Functional annotation summary table



.stats.json



Assembly and annotation statistics generated during the annotation process




 

For questions regarding these data, please contact: 

Sofie Agerbaek, sofie.agerbaek@sund.ku.dk
DOI: 10.5061/dryad.8d0r0
title: Data from: Effects of management on aquatic tree-hole communities in temperate forests are mediated by detritus amount and water chemistry

description: 1. Arthropod communities in water-filled tree-holes may be sensitive to
 impacts of forest management, for example via changes in environmental
 conditions such as resource input. 2. We hypothesized that increasing
 forest management intensity negatively affects arthropod abundance and
 richness and shifts community composition and trophic structure of
 tree-hole communities. We predicted that this shift is caused by reduced
 habitat and resource availability at the forest stand scale as well as
 reduced tree-hole size, detritus amount and changed water chemistry at the
 tree-hole scale. 3. We mapped 910 water-filled tree-holes in two regions
 in Germany and studied 199 tree-hole inhabiting arthropod communities. 4.
 We found that increasing forest management intensity indeed significantly
 reduced arthropod abundance and richness in water-filled tree-holes. The
 most important indirect effects of management intensity on tree-hole
 community structure were the reduced amounts of detritus for the tree-hole
 inhabiting organisms and changed water chemistry at the tree-hole scale,
 both of which seem to act as a habitat filter. Although habitat
 availability at the forest stand scale decreased with increasing
 management intensity, this unexpectedly increased local arthropod
 abundance in individual tree-holes. However, regional species richness in
 tree-holes significantly decreased with increasing management intensity,
 most likely due to decreased habitat diversity. We did not find that the
 management-driven increase in plant diversity at the forest stand scale
 affected communities of individual tree-holes, for example via resource
 availability for adults. 5. Our results suggest that management of
 temperate forests has to target a number of factors at different scales to
 conserve diverse arthropod communities in water-filled tree holes.
description: Insect communities in
 water-filled tree holescollected in the
 fieldGossner_et_al_Dryad.xlsx
DOI: 10.5061/dryad.sn622
title: Data from: The consequences of facultative sex in a prey adapting to predation

description: A species reproductive mode, along with its associated costs and benefits,
 can play a significant role in its evolution and survival. Facultative
 sexuality, being able to reproduce both sexually and asexually, has been
 deemed evolutionary favourable as the benefits of either mode may be fully
 realized. In fact, many studies have focused on identifying the benefits
 of sex and/or the forces selecting for increased rates of sex using
 facultative sexual species. The costs of either mode however can also have
 a profound impact on a population's evolutionary trajectory. Here we
 used experimental evolution and fitness assays to investigate the
 consequences of facultative sexuality in prey adapting to predation.
 Specifically, we compared the adaptive response of algal prey populations
 exposed to constant rotifer predation and which had alternating cycles of
 asexual and sexual reproduction where sexual episodes were either
 facultative (sexual and asexual progeny simultaneously propagated) or
 obligate (only sexual progeny propagated). We found that prey populations
 with facultative sexual episodes reached a lower final relative fitness
 and suffered a greater trade-off in traits under selection, i.e. defense
 and competitive ability, as compared to prey populations with obligate
 sexual episodes. Our results suggest that costs associated with sexual
 reproduction (germination time) and asexual reproduction (selection
 interference) were amplified in the facultative sexual prey populations,
 leading to a reduction in the net advantage of sexuality. Additionally, we
 found evidence that the cost of sex was reduced in the obligate sexual
 prey populations because increased selection for sex was observed via the
 spontaneous production of sexual cells. These results show that certain
 costs associated with facultative sexuality can affect an organism's
 evolutionary trajectory.
description: KochBecks_JEB_Fig1Data Figure 1KochBecks_JEB_Fig2Data Figure 2KochBecks_JEB_Fig3Data Figure 3
DOI: 10.5061/dryad.rb187
title: Data from: Introgressive replacement of natives by invading Arion pest slugs

description: Hybridization with invasive species is one of the major threats to the
 phenotypic and genetic persistence of native organisms worldwide. Arion
 vulgaris (syn. lusitanicus) is a major agricultural pest slug that
 successfully invaded many European countries in recent decades, but its
 impact on closely related native species remains unclear. Here, we
 hypothesized that the regional decline of native A. rufus is connected
 with the spread of invasive A. vulgaris, and tested whether this can be
 linked to hybridization between the two species by analyzing 625 Arion sp.
 along altitudinal transects in three regions in Switzerland. In each
 region, we observed clear evidence of different degrees of genetic
 admixture, suggesting recurrent hybridization beyond the first generation.
 We found spatial differences in admixture patterns that might reflect
 distinct invasion histories among the regions. Our analyses provide a
 landscape level perspective for the genetic interactions between invasive
 and native animals during the invasion. We predict that without specific
 management action, A. vulgaris will further expand its range, which might
 lead to local extinction of A. rufus and other native slugs in the near
 future. Similar processes are likely occurring in other regions currently
 invaded by A. vulgaris.
description: Microsatellite genotypes
 - Arion rufus and A. vulgarisMicrosatellite genotypes
 of Arion rufus and Arion vulgaris individuals from three hybrid zones in
 SwitzerlandArion_transects.xlsx
DOI: 10.5061/dryad.2f0j5
title: Data from: The legacy of a vanished sea: a high level of diversification within a European freshwater amphipod species complex driven by 15 My of Paratethys regression

description: The formation of continental Europe in the Neogene was due to the
 regression of the Tethys Ocean and of the Paratethys Sea. The dynamic
 geology of the area and repetitious transitions between marine and
 freshwater conditions presented opportunities for the colonization of
 newly emerging hydrological networks and diversification of aquatic biota.
 Implementing mitochondrial and nuclear markers in conjunction with a
 large-scale sampling strategy, we investigated the impact of this
 spatiotemporal framework on the evolutionary history of a freshwater
 crustacean morphospecies. The Gammarus balcanicus species complex is
 widely distributed in the area previously occupied by the Paratethys Sea.
 Our results revealed its high diversification and polyphyly in relation to
 a number of other morphospecies. The distribution of the studied amphipod
 is generally characterized by very high local endemism and divergence. The
 Bayesian time-calibrated reconstruction of phylogeny and geographical
 distribution of ancestral nodes indicates that this species complex
 started to diversify in the Early Miocene in the central Balkans,
 partially in the shallow epicontinental sea. It is possible that there
 were several episodes of inland water colonization by local brackish water
 lineages. Subsequent diversification within clades and spread to new areas
 could have been induced by Alpine orogeny in the Miocene/Pliocene and,
 finally, by Pleistocene glaciations. The present distribution of clades,
 in many cases, still reflects Miocene palaeogeography of the area. Our
 results point out that investigations of the historical aspect of cryptic
 diversity in other taxa may help in a general understanding of the origins
 of freshwater invertebrate fauna of Europe.
description: AlignmentsAlignments of haplotype data for three genes used in analysisTreesAll trees generated for the publication in editable formats (nexus and newick). Fig. 2 The history of diversification within the G. balcanicus group. Maximum clade credibility chronogram generated with a Bayesian inference, based on the full multimarker data. Figure S1 Topology of Maximum Likelihood reconstruction of phylogeny based on the mitochondrial COI DNA marker. Figure S2 Topology of Maximum Likelihood reconstruction of phylogeny based on the mitochondrial 16S rRNA marker. Figure S3 Topology of Maximum Likelihood reconstruction of phylogeny based on the nuclear 28S rRNA marker. Figure S4 Maximum clade credibility chronogram generated using Bayesian inference and based on the full multimarker data set. Figure S5 Time calibrated phylogeny of the G. balcanicus group based on the reduced multimarker data set
DOI: 10.5061/dryad.4pq11
title: Data from: Experimental contact zones reveal causes and targets of sexual selection in hybridizing lizards

description: Divergence in sexually selected traits in allopatry should affect the
 degree and direction of hybridization. However, few studies have
 established the causes and targets of sexual selection during secondary
 contact. Common wall lizards (Podarcis muralis) from north-central Italy
 have highly exaggerated male sexual traits compared to populations in
 Western Europe. Using experimental populations, we show that this creates
 asymmetries in male dominance, spatial habitat use and reproductive
 success upon secondary contact. Hybridization occurred almost exclusively
 between males of the Italian lineage and females of the Western European
 lineage. We provide evidence to suggest stronger ongoing selection on male
 sexual traits within the dominant Italian lineage. However, these same
 characters did not predict hybridization, and hybrid matings contributed
 little to variance in male reproductive success. Instead, most hybrid
 offspring were sired by Italian males displaying phenotypes associated
 with lower within-lineage reproductive success. Thus, highly directional
 hybridization arises because some Italian males are out-competed within
 their own lineage but remain competitive relative to males of the other
 lineage. This pattern of hybridization is consistent with the direction of
 introgression in natural contact zones, but our data suggest that sexual
 selection acting through hybridization may be weak at the leading edge of
 natural hybrid zones.
description: MacGregoretal_Traits&Genotypes_FE-2016
DOI: 10.5061/dryad.93633
title: Data from: New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance

description: Studying domesticated species and their wild relatives allows
 understanding of the mechanisms of population divergence and adaptation,
 and identifying valuable genetic resources. Apricot is an important fruit
 in the Northern hemisphere, where it is threatened by the Plum pox virus
 (PPV), causing the sharka disease. The histories of apricot domestication
 and of its resistance to sharka are however still poorly understood. We
 used 18 microsatellite markers to genotype a collection of 230 wild trees
 from Central Asia and 142 cultivated apricots as representatives of the
 worldwide cultivated apricot germplasm; we also performed experimental PPV
 inoculation tests. The genetic markers revealed highest levels of
 diversity in Central Asian and Chinese wild and cultivated apricots,
 confirming an origin in this region. In cultivated apricots, Chinese
 accessions were differentiated from more Western accessions, while
 cultivated apricots were differentiated from wild apricots. An approximate
 Bayesian approach indicated that apricots likely underwent two independent
 domestication events, with bottlenecks, from the same wild population.
 Central Asian native apricots exhibited genetic subdivision and high
 frequency of resistance to sharka. Altogether, our results contribute to
 the understanding of the domestication history of cultivated apricot and
 point to valuable genetic diversity in the extant genetic resources of
 wild apricots.
description: Data for manuscript
 MEC-16-0220This file contains two
 sheets: the first one describes the samples and their locations while the
 second sheet presents the genotypes at 20 SSR and SSLP loci as they were
 used for diversity and differentiation analysis in the MEC-16-0220
 manuscript.N/A: missing data.
DOI: 10.5061/dryad.2s7nm
title: Data from: Seed perishability determines the caching behaviour of a food-hoarding bird

description: 1. Many animals hoard seeds for later consumption and establish seed
 caches that are often located at sites with specific environmental
 characteristics. One explanation for the selection of non-random caching
 locations is the avoidance of pilferage by other animals. Another possible
 hypothesis is that animals choose locations that hamper the perishability
 of stored food, allowing the consumption of unspoiled food items over long
 time periods. 2. We examined seed perishability and pilferage-avoidance as
 potential drivers for caching behaviour of Spotted nutcrackers (Nucifraga
 caryocatactes) in the Swiss Alps where the birds are specialized on
 caching seeds of Swiss stone pine (Pinus cembra). 3. We used seedling
 establishment as an inverse measure of seed perishability, as established
 seedlings cannot longer be consumed by nutcrackers. We recorded the
 environmental conditions (i.e., canopy openness and soil moisture) of seed
 caching, seedling establishment and pilferage sites. 4. Our results show
 that sites of seed caching and seedling establishment had opposed
 micro-environmental conditions. Canopy openness and soil moisture were
 negatively related to seed caching but positively related to seedling
 establishment, i.e., nutcrackers cached seeds preferentially at sites
 where seed perishability was low. We found no effects of environmental
 factors on cache pilferage, i.e. neither canopy openness nor soil moisture
 had significant effects on pilferage rates. We thus could not relate
 caching behaviour to pilferage-avoidance. 5. Our study highlights the
 importance of seed perishability as a mechanism for seed caching
 behaviour, which should be considered in future studies. Our findings
 could have important implications for the regeneration of plants whose
 seeds are dispersed by seed-caching animals, as the potential of seedlings
 to establish may strongly decrease if animals cache seeds at sites that
 favour seed perishability rather than seedling establishment.
description: seed caching, predation
 and germination of Pinus cembraThis data set contains
 data on seed caching, pilferage and the germination of Pinus cembra seeds.
 It also contains the environmental characteristics (canopy openness, soil
 moisture and dwarf shrub vegetation cover) of the caching, pilferage and
 germination sites.seedcaching_NeuschulzetalJAnimEcol.csv
DOI: 10.5061/dryad.8239h
title: Data from: Transatlantic disjunctions in fleshy fungi III: Gymnopus confluens

description: Phylogeographic data indicate that DNA differences consistently exist
 between the North American and European allopatric populations of Gymnopus
 confluens. Conversely, pairing experiments show that collections from both
 populations were sexually compatible in vitro and detailed morphological
 examinations of numerous fresh and dried basidiomata do not produce
 qualitative differences. Percent ITS sequence divergence between Europe
 and North American collections of G. confluens was 3.25%. Species
 delineation metrics including Rosenberg’s PAB statistic, PID metrics, RRD
 (randomly distributed) and PTP (Poisson Tree Processes) gave mixed
 indications that North American and European populations were distinct at
 species rank. The North American populations are described as Gymnopus
 confluens subsp. campanulatus (Peck) R.H. Petersen.
description: Gymnopus confluens and
 Gymnopus eneficola ITS sequencesAligned ITS sequence
 file with Gymnopus eneficola as the outgroup. Names are given as herbarium
 accession numbers and cultures with the culture collection designation.
 Locations are abbreviated following the name (see manuscript for
 locations). The file is a fasta file.Gymnopus_confluens_ITS.fastaGymnopus confluens and G. eneficola concatinated ITS and LSU sequencesGymnopus confluens (fungi) concatinated ITS + 5' part of ribosomal large subunit RNA sequenceConfluens_LSUplusITS.fasta
DOI: 10.5061/dryad.6m780
title: Data from: Invading Africa: a novel transoceanic dispersal by a New World ant parasitoid

description: Aim: An ant parasitoid wasp genus (Eucharitidae: Kapala) common in the New
 World exhibits the intriguing pattern of having one species distributed
 widely across tropical Africa and Madagascar. The unusual distribution
 prompted an investigation of the age, origins and diversification of the
 Afrotropical Kapala species. We evaluate a previous hypothesis that the
 species was anthropogenically introduced. Location: Africa and Madagascar
 and the Neotropics. Methods: Numerous forms of evidence are incorporated
 to explain the origin of the Afrotropical species Kapala ivorensis,
 including phylogenetic relationships, molecular dating estimates, inter-
 and intraspecific genetic distances, morphology and geography. A
 phylogenetic analysis was performed using six gene regions (18S, 28S-D2,
 28S-D3-D5, ITS2, COI and COII), and network and haplotype analyses were
 executed with subsets of the data. Two mitochondrial gene fragments were
 used to calculate divergence times under a strict clock model.
 Additionally, we tested for a correlation between genetic distance and
 geographical distance in K. ivorensis populations. Results: Phylogenetic
 analysis supports one evolutionary origin of K. ivorensis from within a
 clade of New World relatives. Network and haplotype analyses of the
 species show no biogeographical structure, and additionally, there is no
 statistical phylogeographical signal. These results, in conjunction with
 the low amount of phenotypic intraspecific variation and the genetic
 distance to the nearest New World relative, provide sufficient evidence to
 maintain the Old World Kapala as one species. Estimated mitochondrial
 mutation rates suggest that this species is over 1 Myr old, thus predating
 any potential for recent human introduction. Main conclusions: Multiple
 analytical methods indicate the Afrotropical K. ivorensis is molecularly
 distinct from the Neotropical sister species and originated from a single
 pre-human dispersal. This is the first dated example of an insect that has
 colonized Africa via trans-Atlantic dispersal from South America.
description: nexus
 fileConcatenated alignment
 of 40 taxa and 2447 characters from six gene regions. Includes MrBayes
 block.Murray_Heraty_2016.nex
DOI: 10.5061/dryad.5jc73
title: Data from: Ancient vicariance and climate-driven extinction explain continental-wide disjunctions in Africa: the case of the Rand Flora genus Canarina (Campanulaceae)

description: Transoceanic distributions have attracted the interest of scientists for
 centuries. Less attention has been paid to the evolutionary origins of
 ‘continent-wide’ disjunctions, in which related taxa are distributed
 across isolated regions within the same continent. A prime example is the
 ‘Rand Flora’ pattern, which shows sister taxa disjunctly distributed in
 the continental margins of Africa. Here, we explore the evolutionary
 origins of this pattern using the genus Canarina, with three species: C.
 canariensis, associated with the Canarian laurisilva, and C. eminii and C.
 abyssinica, endemic to the Afromontane region in East Africa, as case
 study. We infer phylogenetic relationships, divergence times and the
 history of migration events within Canarina using Bayesian inference on a
 large sample of chloroplast and nuclear sequences. Ecological niche
 modelling was employed to infer the climatic niche of Canarina through
 time. Dating was performed with a novel nested approach to solve the
 problem of using deep time calibration points within a molecular dataset
 comprising both above-species and population-level sampling. Results show
 C. abyssinica as sister to a clade formed by disjunct C. eminii and C.
 canariensis. Miocene divergences were inferred among species, whereas
 infraspecific divergences fell within the Pleistocene–Holocene periods.
 Although C. eminii and C. canariensis showed a strong genetic geographic
 structure, among-population divergences were older in the former than in
 the latter. Our results suggest that Canarina originated in East Africa
 and later migrated across North Africa, with vicariance and
 aridification-driven extinction explaining the 7000 km/7 million year
 divergence between the Canarian and East African endemics.
description: Fig2A_cpDNA_PlatycodoneaeNEXUS and tre files with the analysis settings used in MrBayes inferred from the concatenated chloroplast dataset (psbJ-petA, trnL-trnF, petB-petD) for the PlatycodoneaeFig2B_ITS_platycodoneaeNEXUS and tre files with the analysis settings used in MrBayes inferred from the nuclear ribosomal dataset (ITS) for PlatycodoneaeFig2C_ITS_4cpdnaNEXUS and tre files with the analysis settings used in MrBayes inferred from the combined nuclear and chloroplast dataset (ITS, psbJ-petA, trnL-trnF, petB-petD, trnS-trnG) for PlatycodoneaeNested-dating approach analysisScript (.xml) and tre files for the "Nested analyses" of all three linked datasets: Platycodoneae, C. eminii and C. canariensisNested Analysis.zipFigure S1Nexus and .tre files for the single-gene analyses of the Platycodoneae dataset.Figure S2Nexus and .tre files for the single-gene analyses of the Canarina dataset