cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cg1jv
title: Data from: Speciation despite globally overlapping distributions in Penicillium chrysogenum: the population genetics of Alexander Fleming's lucky fungus

description: Eighty years ago, Alexander Fleming described the antibiotic effects of a
 fungus that had contaminated his bacterial culture, kick starting the
 antimicrobial revolution. The fungus was later ascribed to a putatively
 globally distributed asexual species, Penicillium chrysogenum. Recently,
 the species has been shown to be genetically diverse, and possess
 mating-type genes. Here, phylogenetic and population genetic analyses show
 that this apparently ubiquitous fungus is actually composed of at least
 two genetically distinct species with only slight differences detected in
 physiology. We found each species in air and dust samples collected in and
 around St Mary’s Hospital where Fleming worked. Genotyping of 30 markers
 across the genome showed that preserved fungal material from Fleming’s
 laboratory was nearly identical to derived strains currently in culture
 collections and in the same distinct species as a wild progenitor strain
 of current penicillin producing industrial strains rather than the type
 species P. chrysogenum. Global samples of the two most common species were
 found to possess mating-type genes in a near 1:1 ratio, and show evidence
 of recombination with little geographic population subdivision evident.
 However, no hybridization was detected between the species despite an
 estimated time of divergence of less than 1 MYA. Growth studies showed
 significant interspecific inhibition by P. chrysogenum of the other common
 species, suggesting that competition may facilitate species maintenance
 despite globally overlapping distributions. Results highlight
 under-recognized diversity even among the best-known fungal groups and the
 potential for speciation despite overlapping distribution.
description: Henk_Fleming_Penicillium_dataLocation, allelic profiles, and species assignment in a single datasheet. A second datasheet contains allelic size information.
DOI: 10.5061/dryad.kq7h7
title: Data from: Using greenhouse gas fluxes to define soil functional types

description: Aim: Soils provide key ecosystem services and directly control ecosystem
 functions; thus, there is a need to define the reference state of soil
 functionality. Most common functional classifications are
 vegetation-centered, such as plant functional types (PFTs), and neglect
 soil characteristics and processes. We propose Soil Functional Types
 (SFTs) as a conceptual approach to represent and describe the
 functionality of soils based on characteristics of their greenhouse gas
 (GHG) flux dynamics. Methods: We used automated measurements of CO2, CH4
 and N2O soil fluxes in a forested area to define SFTs as surface areas
 with similar GHG dynamics. We performed mixed effects models, and
 independent cluster analyses of our environmental variables and SFT
 classifications. Results Unique groupings based on SFTs, but not
 environmental variables, supported the hypothesis that SFTs provide
 additional insights on the spatial variability of soil functionality
 beyond information represented by commonly measured soil parameters (e.g.,
 soil moisture, soil temperature, litter biomass). Conclusions: This
 approach could complement vegetation-based functional classifications to
 better represent the broad range of ecosystem functions. A global
 application of the proposed SFT framework will only be possible if there
 is a community-wide effort to share data and create a global database of
 GHG emissions from soils.
description: Daily Soil GHG
 fluxesDaily measurements of
 soil GHG fluxes used to describe soil functional types in Petrakis et al.
 Fluxes are calculated as daily means and curated for QA/QC as described in
 the journal article. Measurement dates comprise from September 2014 to
 September 2015. Values as -9999 represent missing values due to QA/QC or
 instrument failure.Petrakis_et_al_data.txt
DOI: 10.5061/dryad.4m6s6
title: Data from: Maidenhair ferns, Adiantum, are indeed monophyletic and sister to shoestring ferns, vittarioids (Pteridaceae)

description: Across the tree of life, molecular phylogenetic studies often reveal
 surprising relationships between taxa with radically different
 morphologies that have long obscured their close affiliations. A
 spectacular botanical example is Rafflesia, a holoparasite that produces
 the largest flowers in the world, but that evolved from tiny-flowered
 ancestors within the Euphorbiaceae. Outside of parasitic lineages, such
 abrupt transformations are rarely seen. One exception involves the
 “maidenhair ferns” (Adiantum), which are quintessential ferns: beautifully
 dissected, terrestrial, and shade loving. The closely related “shoestring
 ferns” (vittarioids), in contrast, have an extremely simplified
 morphology, are canopy-dwelling epiphytes, and exhibit greatly accelerated
 rates of molecular evolution. While Adiantum and the vittarioids together
 have been shown to form a robust monophyletic group (adiantoids), there
 remain unanswered questions regarding the monophyly of Adiantum and the
 evolutionary history of the vittarioids. Here we review recent
 phylogenetic evidence suggesting support for the monophyly of Adiantum,
 and analyze new plastid data to confirm this result. We find that Adiantum
 is monophyletic and sister to the vittarioids. With this robust
 phylogenetic framework established for the broadest relationships in the
 adiantoid clade, we can now focus on understanding the evolutionary
 processes associated with the extreme morphological, ecological, and
 genetic transitions that took place within this lineage.
description: AlignmentsML_analysisBayesian_analysis
DOI: 10.5061/dryad.j2p4d5t4
title: Data from: Copy number polymorphism in the α-globin gene cluster of European rabbit (Oryctolagus cuniculus).

description: Comparative genomic studies have revealed that mammals typically possess
 two or more tandemly duplicated copies of the α-globin (HBA) gene. The
 domestic rabbit represents an exception to this general rule, as this
 species was found to possess a single HBA gene. Previous electrophoretic
 surveys of HBA polymorphism in natural populations of the European rabbit
 (Oryctolagus cuniculus) revealed extensive geographic variation in the
 frequencies of three main electromorphs. The variation in frequency of two
 electromorphs is mainly partitioned between two distinct subspecies of
 European rabbit, and a third is restricted to the hybrid zone between the
 two rabbit subspecies in Iberia. Here we report the results of a survey of
 nucleotide polymorphism which revealed HBA copy number polymorphism in
 Iberian populations of the European rabbit. By characterizing patterns of
 HBA polymorphism in populations from the native range of the European
 rabbit we were able to identify the specific amino acid substitutions that
 distinguish the previously characterized electromorphs. Within the hybrid
 zone, we observed the existence of a second HBA gene duplicate, named
 HBA2, that mostly represents a novel sequence haplotype which occurs in
 higher frequency within the hybrid zone and thus appears to have arisen in
 hybrids of the two distinct subspecies. While this novel gene is also
 present in other wild Iberian populations, it is almost absent from French
 populations which suggest a recent ancestry, associated with the
 establishment of the post-Pleistocene contact zone between the two
 European rabbit subspecies.
description: dbHBAduplic_allelic_distributionPCR-RFLP results databases for estimate the frequency of HBA gene-electromorph haplotypes given in Table 3 (left 3 columns) and for the distribution of the HBA gene duplication given in Figure 3 (right 3 columns).HBAalign_Oryctolagus_EMBLAlignment of HBA genes sequences from Iberian (including the Portuguese Archipelagos of Azores and Madeira) and French populations of the European rabbit (Oryctolagus cuniculus). Samples are from 51 rabbits; sequence length is 1289bp. Sample codes relate to their sampling site: Santarém (San), Alicante (Altt), Tarragona (Tar), Navarra (Nav), Versailles (Ver), Flores (Fl) and Porto Santo (Pst). Sequences are given in the same order as in Additional file 4: from Altt6_clon1 to Nav12_clon3 sequences are from gene HBA1 and from Fl13(02)_clon1 to Nav12_clon7 are from gene HBA2. Sequences were deposited in EMBL and accession numbers are given after the sequence name (EMBL accession numbers HE608516 - HE608566).HBA_sylvilagus_EMBLHBA gene sequence from the Eastern cottontail (Sylvilagus floridanus). This sequence was deposited in EBML and the accession number is given after the sequence name (EMBL accession number HE608842).
DOI: 10.5061/dryad.1jt7m
title: Data from: Mating patterns and post-mating isolation in three cryptic species of the Engystomops petersi species complex

description: Determining the extent of reproductive isolation in cryptic species with
 dynamic geographic ranges can give us important insights into the
 processes that generate and maintain genetic divergence in the absence of
 severe geographic barriers. We studied mating patterns, propensity to
 crossbreed in nature and subsequent fertilization rates, as well as
 survival and development of hybrid F1 offspring for three species of the
 E. petersi species complex in Yasuní National Park, Ecuador. We found at
 least two species in five out of seven locations sampled, and 14.3% of the
 wild pairs genotyped were heterospecific crosses. We also found reduced
 fertilization rates in hybrid crosses between E. petersi females and E.
 “magnus” males, and between E. “magnus” females and E. “selva” males but
 not in the opposite hybrid crosses, suggesting asymmetric reproductive
 isolation for these species. Larval development time decreased in F1
 hybrid crosses compared to conspecific F1s, but we did not find any
 reduction in larval survival or early metamorph survival. Our results show
 evidence of post-mating isolation for at least two hybrid crosses of the
 cryptic species we studied. The general decrease in fertilization rates in
 heterospecific crosses suggests that sexual selection and reinforcement
 might have not only contributed to the pattern of call variation and
 behavioral isolation we see between species today, but they may also
 contribute to further signal divergence and behavioral evolution,
 especially in locations where hybridization is common and fertilization
 success is diminished.
description: Trillo_Postzygotic_Data_FinalWorksheet 1 has the fertilization rates for each hybrid and conspecific pair tested. Worksheet 2 has the developmental data.Trillo_SpeciesOverlap_Data_FinalWorksheet 1 has all individuals genotyped by site and all conspecific and hybrid pairs found. Worksheet 2 shows summary tables.
DOI: 10.5061/dryad.sh811k0h
title: Data from: Motivation and moral attributes in sport

description: This research’s aim was to analyze the relation between self-determined
 motivation, sportspersonship and athletic aggression in volleyball
 players. Participated on this study 54 athletes between adults and youths
 from both genders. As measure instruments were used: Sport Motivation
 Scale (1995), Multidimensional Sportspersonship Orientations Scale (1997)
 and Bredemeier’s Athletic Aggression Inventory (1985). The data collection
 was performed during training. For the data analysis the Mann-Whitney
 test, Spearman correlation and Cronbach’s Alpha were used. The data
 evidenced that overall selfdetermined motivation was found to be a
 favorable factor in relation to a positive attitude towards sport’s social
 conventions, rules and judges influencing on the worry and compromise with
 the opponent, being able to interfere over the tendency to behave
 aggressively.
description: Motivation-Agression-MoralRaw self-determined motivation, aggressive behaviors and sportspersonship orientation data, collected in the field with Brazilian volleyball players.Todos os Dados
DOI: 10.5061/dryad.5v71p
title: Data from: Genetic architecture of the variation in male-specific ossified processes on the anal fins of Japanese medaka

description: Traits involved in reproduction evolve rapidly and show great diversity
 among closely related species. However, the genetic mechanisms that
 underlie the diversification of courtship traits are mostly unknown.
 Japanese medaka fishes (Oryzias latipes) use anal fins to attract females
 and to grasp females during courtship; the males have longer anal fins
 with male-specific ossified papillary processes on the fin rays. However,
 anal fin morphology varies between populations: the southern populations
 tend to have longer anal fins and more processes than the northern
 populations. In the present study, we conducted quantitative trait locus
 (QTL) mapping to investigate the genetic architecture underlying the
 variation in the number of papillary processes of Japanese medaka fish and
 compared the QTLs with previously identified QTLs controlling anal fin
 length. First, we found that only a few QTLs were shared between anal fin
 length and papillary process number. Second, we found that the numbers of
 papillary processes on different fin rays were often controlled by
 different QTLs. Finally, we produced another independent cross and found
 that some QTLs were repeatable between the two crosses, whereas others
 were specific to only one cross. These results suggest that variation in
 the number of papillary processes is polygenic and controlled by QTLs that
 are distinct from those controlling anal fin length. Thus, different
 courtship traits in Japanese medaka share a small number of QTLs and have
 the potential for independent evolution.
description: pheno_papil_AFOMPapillary process number on each fish ray, total papillary process number, and anal fin length, caudal fin length and dorsal fin length of AFOM family.pheno_papil_OFAMPapillary process number on each fish ray, total papillary process number, and anal fin length, caudal fin length and dorsal fin length of OFAM family.AFOM_M_SNP_autosomeGenotype data of AFOM family. Input file for r/qtl.OFAM_M_SNP_autosomeGenotype data of OFAM family. Input file for r/qtl.
DOI: 10.5061/dryad.f0q11
title: Data from: Climatic adaptation and ecological divergence between two closely related pine species in Southeast China

description: Climatic selection contributes greatly to local adaptation and
 intraspecific differentiation, but this kind of selection could have also
 promoted interspecific divergence through ecological speciation. In this
 study, we examined genetic variation within and between two closely
 related pine species, Pinus massoniana and Pinus hwangshanensis. These two
 species occur in Southeast China and exhibit contrasting ecological
 preferences, although hybrids are formed where their distributions
 overlap. We sampled 26 populations of the two species across their
 distributional ranges and sequenced 25 climate-related candidate genes and
 12 reference loci, assumed not to be related to climatic selection. More
 than half of the 25 candidate genes (17) showed signals of recent and/or
 ancient selection, as indicated by one or several robust tests at
 different evolutionary timescales, while selection signals were only
 detected at three of the 12 reference loci. The signals of recent
 selection were species specific, but signals of ancient selection were
 mostly shared by the two species likely because of the shared history. We
 compared intra- and interspecific genetic differentiation of loci detected
 under recent selection (selected loci) with those showing no signals of
 recent selection (unselected loci). Intraspecific differentiation was
 reduced, but interspecific differentiation was elevated for selected loci.
 Under the Isolation with Migration model, climate-related candidate genes
 had earlier divergence time estimates and more restricted levels of
 migration in both directions between the two species than reference loci.
 Taken together, our results suggested that climate-related candidate genes
 might be commonly shaped by climatic selection and recent divergent
 selection might have counteracted interspecific gene flow and play an
 important role during ecological divergence of these two closely related
 pine species.
description: Alignments of sequenced
 gene fragmentsThe file included
 alignments and annotations of the 37 sequenced gene
 fragments.Alignments of gene
 fragments.zipThe HKA
 testsFile includes inputs and
 outputs of the HKA tests using the HKA program
 (https://bio.cst.temple.edu/~hey/software/software.htm#HKA).HKA.zipThe MKprf testFile includes inputs and outputs of the MKprf tests (Bustamante et al. 2002).MKprf.zip
DOI: 10.5061/dryad.043tn
title: Data from: Female collared flycatchers choose neighbouring and older extra-pair partners from the pool of males around their nests

description: Extra-pair copulation is common among passerine birds. Females might
 engage in this behavior to obtain direct or indirect benefits. They may
 choose extra-pair males with larger ornaments, especially if they are
 costly to produce. Here we studied extra-pair paternity in the collared
 flycatcher. Genetic analysis allowed us to identify the presence or
 absence of extra-pair young in the focal nests, and to identify extra-pair
 fathers. We also identified potential males available as extra-pair sires
 around the nests of females who had extra-pair young. First, we tested the
 relationship between paternity in own nest and ornament size (wing patch
 and/or forehead patch), morphological traits and age of social males and
 females. Second, we compared the same suite of traits among social mates,
 extra-pair males and all potential extra-pair mates. Finally, we
 investigated the effect of the size of ornaments on the distance between
 the social nest and that of nest the extra-pair father. Contrary to our
 prediction, males with larger ornaments and longer wings lost more
 paternity in their nests. We also found that early breeders lost less
 paternity in their nests. Extra-pair males were older and had longer wings
 than social and potential extra-pair males. Females mainly obtained
 extra-pair mates near their nests but the distance did not vary according
 to ornamentation. These results could potentially be explained by
 differences in mate guarding strategy as older males may be more
 experienced in guarding their mate and attract other females more easily.
 More data about mate guarding and prospecting are needed to increase our
 understanding of mechanisms underlying the extra-pair paternity in birds.
description: script and data
 dryadeScript and data for the
 all manuscript analysisdryades
 files.zip
DOI: 10.5061/dryad.s20g8
title: Data from: Kin discrimination increases with odor distance in the German cockroach

description: Kin recognition mediates altruistic behavior and inbreeding avoidance in
 many animal societies. So far, evidence for accurate kin recognition, when
 individuals distinguish fine scale differences in genetic relatedness, in
 social insects is mixed. Although this ability should be counter selected
 to reduce risks of nepotism in eusocial colonies, accurate kin recognition
 may be beneficial in less integrated societies where genetic conflicts are
 reduced. Here we show that gregarious cockroaches Blattella germanica
 discriminate multiple levels of relatedness and identify inherited
 cuticular odors as potential kin recognition cues. When given a choice
 between aggregation sites containing either full siblings or less related
 conspecifics, cockroaches showed an increasing preference for resting with
 full siblings with increasing genetic distance between stimuli groups,
 from 50% of choices in the presence of half siblings or cousins, to 60.7%
 with less related cockroaches from the same strain, and 72.9% with
 cockroaches from a different strain. Examination of the cuticular
 hydrocarbon profiles of 288 nymphs and their 54 parents revealed that the
 chemical distance between cockroaches was negatively correlated to their
 relatedness. Using a Bayesian animal model approach for quantitative
 genetic analyses, we identified several highly heritable methyl-branched
 alkanes as good candidates for kin recognition cues. Our results suggest
 that kin recognition is based on genetically inherited odors in this
 gregarious insect and highlight mechanistic similarities with nestmate
 recognition in eusocial species.
description: CHC analysis
 R-scriptScript used in the
 program R to estimate heritability values for individual cuticular
 hydrocarbon compounds, as well as composite PCA axes. It uses a Bayesian
 animal model approach (based on the MCMCglmm package), parent-offspring
 regression, as well as paternal half-sib analysis.CHC
 analysis.RCHC
 dataFor each sampled
 individual, its age (adult or nymph), gender (female or male), strain
 (Rennes or Dijon), mother (grandmothers and mothers of the F2 generation),
 and raw cuticular hydrocarbon peak areas (25 CHCs commonly found on the
 cuticle of Blattella germanica).PedigreePedigree (P, F1, and F2) used in the animal model approach to estimate heritabilities of cuticular hydrocarbons of Blattella germanica.pedigree.txtCHC data FS HSFor each sampled individual that had both full siblings (FS) and half-siblings (HS), its age (adult or nymph), gender (female or male), strain (Rennes or Dijon), mother (grandmothers and mothers of the F2 generation), and raw cuticular hydrocarbon peak areas (25 CHCs commonly found on the cuticle of Blattella germanica).