cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m905qfv2k
title: Reproductive skew in quasi-social parasitoids

description: Primitively social Sclerodermus parasitoids form female multi-foundress
 groups on large, paralysed hosts and then cooperatively care for large
 broods of offspring throughout their development. We identified offspring
 with microsatellite markers and found that nearly every foundress produced
 offspring, implying that overall reproductive skew was thus not extreme.
 We expected that kinship may influence skew if, for instance, relatives
 within a group collectively suppress the reproduction of a non-relative or
 if non-relatives selfishly over-exploit group reproductive optima. We
 found slight skew, in favour of the non-sibling, when two full-sibling
 foundresses brooded with one non-sibling foundress but no skew when three
 sibs brooded with one non-sibling. All foundresses made similar
 contributions to the sexual composition of broods, which were highly
 female biased. We expected body size differences might promote skew via
 physical domination of some foundresses by others or via intrinsically
 differential fecundity. We found heterogeneity in the relative
 contributions of dissimilar-sized foundresses but no skew overall.
 Nonetheless, males within these broods were more often the progeny of the
 largest foundress, suggesting that larger females are able to dominate the
 production, or the survival, of males. We expected that temporal priority
 may generate skew via early individuals having a longer period in which to
 reproduce and/or become dominant. We found that the skew indeed favoured
 foundresses that had started to reproduce before a second foundress was
 introduced. Further, if eggs laid by a first foundress had started to
 hatch before a second foundress was introduced, the second foundress
 produced female offspring only. Overall, we found that skew is not
 strongly associated with kinship among foundresses, but does appear to be
 associated with intrinsic or acquired dominance and that where skew is
 manifest it can comprise brood sex ratio effects as well as overall
 reproduction effects.
DOI: 10.15468/dl.kcb7t8
title: Occurrence Download

description: A dataset containing 253 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aphanamixis polystachya"
 ]
}

 The dataset includes 253 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003006-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ngf1vhhvt
title: Population genetic structure of wolves in the northwestern Dinaric-Balkan region

description: The Balkan Peninsula and the Dinaric Mountains possess extraordinary
 biodiversity and support one of the largest and most diverse wolf (Canis
 lupus) populations in Europe. Results obtained with diverse genetic
 markers show west-east substructure, also seen in various other species,
 despite the absence of obvious barriers to movement. However, the spatial
 extent of the genetic clusters remains unresolved, and our aim was to
 combine fine-scale sampling with population and spatial genetic analyses
 to improve resolution of wolf genetic clusters. We analyzed 16 autosomal
 microsatellites from 255 wolves sampled in Slovenia, Croatia, Bosnia and
 Herzegovina (BIH), and Serbia, and documented three genetic clusters.
 These comprised (1) Slovenia and the regions of Gorski kotar and Lika in
 Croatia, (2) the region of Dalmatia in southern Croatia and BIH, and (3)
 Serbia. When we mapped the clusters geographically, we observed west-east
 genetic structure across the study area, together with some specific
 structure in BIH – Dalmatia. We observed that cluster 1 had a smaller
 effective population size, consistent with earlier reports of population
 recovery since the 1980s. Our results provide foundation for future
 genomic studies that would further resolve the observed west-east
 population structure and its evolutionary history in wolves and other taxa
 in the region, and identify focal areas for habitat conservation. They
 also have immediate importance for conservation planning for the wolves in
 one of the most important parts of the species’ European range.
DOI: 10.5061/dryad.6djh9w12h
title: Fourier projection algorithm for calculating phonon dispersion relations of crystals

description: We propose a Fourier projection algorithm and demonstrate its superiority
 for calculation of the phonon dispersion relations of 2D and 3D crystals
 based on the atomic coordinate trajectories from supercell molecular
 dynamics/first-principle molecular dynamics simulations. The lattice
 vibration states are described in a six-dimensional phase space composed
 of lattice and wave vectors. Phonon dispersion information in the first
 Brillouin zone sampled with a k-mesh grid of N×N×N is generated by Fourier
 projection of the lattice vibration frequencies in the supercell by N×N×N
 primitive cells, the dispersion relations along high-symmetry paths are
 retrieved therefrom. Our algorithm is physically intuitive,
 computationally convenient, and universally applicable. As examples of
 application, the successful dispersion relation calculations of 2D
 graphene, 3D BCC-Fe and FCC-Cu are presented. This algorithm shows the
 correspondence between real and reciprocal lattices, that is, the spatial
 information in the states of the lattice vibration were preserved. The
 high-symmetry paths of the first Brillouin zone in the reciprocal lattice
 primitive cells of the hexagonal, BCC, and FCC lattice were also given in
 detail. In combination with first-principles molecular dynamics, as long
 as the interatomic force is accurately known, reliable and accurate
 dispersion relation can be achieved by this Fourier projection algorithm.
description: See README for file details
DOI: 10.5061/dryad.0vt4b8h1b
title: Impact of COVID-19 on international medical education

description: Purpose: To assess the impact of the coronavirus disease 2019 (COVID-19)
 pandemic on the current study methods and future plans of medical students
 compared to those in the pre-pandemic period. Materials and methods:
 Second-grade medical students reported their academic experiences, study
 methods, and future career plans before (between 2016 and 2019) and during
 the pandemic (2020) using a questionnaire-based survey at Hokkaido
 University, Japan (n = 534). Results: From 2016 to 2019, we found an
 increasing trend for participation in short-term international exchange
 programs, taking the United States Medical Licensing Examination (USMLE),
 clinical training, and undertaking research abroad among the
 students.  However, these percentages significantly declined
 (35.5%) during the COVID-19 pandemic in 2020 for all the assessed future
 plans, including short-term exchange programs (-27.9%), taking USMLE
 (-19.8%), clinical training (-24.5%), and undertaking research abroad
 (-13.2%) compared to 2019, wherein 67.9% of the students wished to have at
 least one of these four above-mentioned academic activities. Conclusions:
 The COVID-19 pandemic adversely and significantly influenced our medical
 students plans to go abroad for clinical and research training. Future
 studies are warranted to assess the long-term influence of this pandemic
 on the career planning of medical students.
DOI: 10.5061/dryad.s4mw6m97j
title: Links between boreal forest management, soil fungal communities and belowground carbon sequestration

description: Forest management has a potential to alter belowground carbon storage.
 However, the underlying mechanisms, and the relative importance of carbon
 input and decomposition in regulation of soil carbon dynamics are poorly
 understood. We examined whether interactive effects of forest
 fertilization and thinning on carbon stocks in the topsoil of boreal
 forests were linked to changes in fungal community composition, biomass,
 and enzyme activities, in a long-term fertilization and thinning
 experiment distributed across 29 Pinus sylvestris forests along a 1300 km
 latitudinal transect in Sweden. Nitrogen fertilization increased fungal
 biomass, particularly towards the north and mainly by promoting root
 associated Ascomycetes, but the response was moderated by thinning. Fungal
 biomass correlated positively with carbon stocks in the organic topsoil.
 However, ectomycorrhizal Cortinarius species were reduced in abundance by
 fertilization and correlated negatively with carbon stocks. Plausibly,
 increased soil carbon stocks after fertilization are linked to increased
 input of carbon in the form of root-associated mycelium combined with loss
 of ectomycorrhizal decomposers within the genus Cortinarius. These fungal
 responses to fertilization may mediate a natural climate solution by
 promoting carbon sequestration in the organic topsoil, but the effect of
 fertilization may also be undesired from a biodiversity perspective.
DOI: 10.5061/dryad.sj3tx9667
title: Crataegus bretschneideri (Rosaceae), a separate species endemic to Northeast of China

description: Crataegus bretschneideri is considered a variety of Crataegus pinnatifida,
 but it has also been proposed as a separate species. We used ITS and three
 cpDNA sequence fragments (psbA-trnH, trnG-trnS, trnH-trnK) to perform
 maximum parsimony, maximum likelihood, Bayesian interence and
 neighbor-joining molecular phylogenetic tree analysis with 108 individuals
 of 19 hawthorn (Crataegus) species and 4 outgroups (Malus). ITS, cpDNA and
 cpDNA-ITS molecular phylogenetic trees constructed using 4 methods have
 similar consistency respectively. In the cpDNA-ITS molecular phylogenetic
 tree, C. bretschneideri is an independent clade separated from Crataegus
 maximowiczii and C. pinnatifida, which provides a separate species
 condition. In the ITS (nuclear inheritance) molecular phylogenetic tree,
 C. bretschneideri and C. pinnatifida are closely related and are distantly
 related to C. maximowiczii. The cpDNA (maternal inheritance) molecular
 phylogenetic tree indicated that C. bretschneideri is closely related to
 C. maximowiczii but distantly related to C. pinnatifida. Furthermore, the
 108 Crataegus individuals belonged to 15 chloroplast haplotypes, as
 determined using the DNASP analysis; C. bretschneideri and C. maximowiczii
 have the same chloroplast haplotype, H1; C. pinnatifida contains three
 haplotypes, H13-H15. Taken together with previous results of our
 laboratory, we confirm that C. bretschneideri is not a variety of C.
 pinnatifida, but a separate species that gradually developed from natural
 hybrid offspring in mixed forest areas with C. maximowiczii as the female
 parent and C. pinnatifida as the male parent.
DOI: 10.5061/dryad.zcrjdfndj
title: Fungal OTUs during dead wood succession of aspen

description: During decomposition of organic matter, microbial communities may follow
 different successional trajectories depending on the initial environment
 and colonizers. The timing and order of the assembly history can lead to
 divergent communities through priority effects. We explored how assembly
 history and substrate quality affected fungal dead wood communities and
 decomposition, 1.5 and 4.5 years after tree felling. In addition, we
 investigated the effect of invertebrate exclusion during the first two
 summers. For aspen (Populus tremula) logs, we measured initial bark and
 wood resource quality, and surveyed the fungal communities by DNA
 metabarcoding at different time points during succession. We found that a
 gradient in fungal community composition was related to resource quality
 and we discuss how this may reflect tolerance-dominance trade-offs in
 fungal life history strategies. As with previous studies, the initial
 amount of bark tannins was negatively correlated with wood decomposition
 rate over 4.5 years. The latent fungal community explained variation in
 community composition after 1.5, but not after 4.5 years, of succession.
 Although the assembly history of latent fungi may cause alternate
 trajectories in successional communities, our results indicate that the
 communities may easily converge with the arrival of secondary colonizers.
 We also identified a strong invertebrate-induced priority effect of fungal
 communities, even after 4.5 years of succession, thereby adding crucial
 knowledge to the importance of invertebrates in affecting fungal community
 development. By measuring and manipulating aspects of assembly history and
 resource quality that have rarely been studied, we expand our
 understanding of the complexity of fungal community dynamics.
description: Woodchips from aspen logs at three time intervals: fresh wood,
 after 1.5 years and after 4.5 years. Analysed for DNA
 with a modified CTAB procedure, amplified with uniquely tagged primers of
 the ITS2 region, sequenced with Illumina Miseq.
 Bioinformatics with CUTADAPT, DADA2, ITSx, VSEARCH clustering and
 LULU post-curation. Taxonomic annotations from UNITE,
 functional guilds from FUNGUILD.
description: biorxiv preprint version of manuscript:
 https://www.biorxiv.org/content/10.1101/2021.12.01.470726v1
DOI: 10.5061/dryad.wwpzgmskw
title: Multiple paternity is related to adult sex ratio and sex determination system in reptiles

description: The adult sex ratio (ASR, the proportion of males in the adult population)
 is an emerging predictor of reproductive behaviour, and recent studies in
 birds and humans suggest it is a major driver of social mating systems and
 parental care. ASR may also influence genetic mating systems. For
 instance, male-skewed ASRs are expected to increase the frequency of
 multiple paternity (defined here as a clutch or litter sired by two or
 more males) due to higher rates of coercive copulations by males and/or
 due to females exploiting the opportunity of copulation with multiple
 males to increase genetic diversity of their offspring. Here we evaluate
 this hypothesis in reptiles that often exhibit high frequency of multiple
 paternity, although its ecological and life-history predictors have
 remained controversial. Using a comprehensive dataset of 81 species
 representing all four non-avian reptile orders, we show that increased
 frequency of multiple paternity is predicted by more male-skewed ASR, and
 this relationship is robust to simultaneous effects of several
 life-history predictors. Additionally, we show that the frequency of
 multiple paternity varies with the sex determination system: species with
 female heterogamety (ZZ/ZW sex chromosomes) exhibit higher levels of
 multiple paternity than species with male heterogamety (XY/XX) or
 temperature-dependent sex determination. Thus, our across-species
 comparative study provides the first evidence that genetic mating system
 depends on ASR in reptiles. We call for further investigations to uncover
 the complex evolutionary associations between mating systems, sex
 determination systems and ASR.
description: Data sets for the paper Pipoly et al. Multiple paternity is
 related to adult sex ratio and sex determination system in
 reptiles.   AVERAGE dataset.
 Used data in the analyses and their references. Average species values are
 present where relevant. MP =
 multiple paternity (ratio from 0 to 1) EC = number of
 examined clutches for paternity analyses ASR = adult
 sex ratio SDS = Sex determination system
 MBS = male body size (in grams) FBS =
 female body size (in grams) BS = body mass
 (non-sex-specific or average of male and female body size (in
 grams) SSD = sexual size dimorphism (log10(male body
 mass / female body mass) CS = clutch size
 (avg) RM = reproductive mode (VIV = viviparous, OVI =
 oviparous) LD = absolute latitudinal degree of the
 location of population(s) studied for multiple paternity (avg if
 relevant) Order3 = non-standard classification with
 separating squamates to Lizards and Snakes 
 POP dataset. Collected population-level multiple
 paternity values about reptiles and their references. The dataset includes
 the number of examined clutches, the multiple paternity in %, the method
 of paternity investigation, the ID of the population and the source study
 reference.   Cells with
 "NA" mean missing information for that cells
DOI: 10.5061/dryad.nvx0k6dtp
title: Polyploidy promotes divergent evolution across the leaf economics spectrum and plant edaphic niche in the Dianthus broteri complex

description: The evolution of the leaf economics spectrum (LES) is known to be
 constrained by genetic relatedness but also promoted at small geographic
 and phylogenetic scales. In those cases, we hypothesised that polyploidy
 would play a prominent role as an outstanding source of functional
 divergence and adaptive potential. We registered leaf-level nutrient,
 water and light economy related traits from the LES as well as edaphic
 properties in the four cytotypes of the autopolyploid Dianthus broteri
 complex (2×, 4×, 6× and 12×). We analysed the effect of ploidy level on
 the integration of the LES network, checked if concerted evolution
 occurred between LES and soil niche and tested the influence of phylogeny
 on the variables. Alternative evolutionary models for both sets of traits
 were compared. We found higher divergence of polyploids (especially 6× and
 12×) compared to diploids in the LES and soil niche, but these traits are
 not coevolving. 6× and 12× showed opposite ecological strategies regarding
 resource use and higher uncoupling of the LES network. Early divergence of
 traits prevailed in both LES and edaphic niche (supported by better fitted
 evolutionary models with one optimum per cytotype), but
 post-polyploidization processes played an important role for the
 photochemical behaviour. Synthesis. Our results indicated shifts in
 ecological strategies across D. broteri cytotypes and suggested a powerful
 role of polyploidy in overcoming constraints for the evolution of plant
 functional traits.
DOI: 10.34740/kaggle/dsv/14647977
title: Full TMDB Movies Dataset 2024 (1M Movies)
DOI: 10.5061/dryad.7d7wm37wr
title: Population genomics of a forest fungus reveals high gene flow and climate adaptation signatures

description: Genome sequencing of spatially distributed individuals sheds light on how
 evolution structures genetic variation. Populations of Phellopilus
 nigrolimitatus, a red-listed wood-inhabiting fungus associated with
 old-growth coniferous forests, have decreased in size over the last
 century due to a loss of suitable habitats. We assessed the population
 genetic structure and investigated local adaptation in P. nigrolimitatus,
 by establishing a reference genome and genotyping 327 individuals sampled
 from 24 locations in Northern Europe by RAD sequencing. We revealed a
 shallow population genetic structure, indicating large historical
 population sizes and high levels of gene flow. Despite this weak
 sub-structuring, two genetic groups were recognized; a western group
 distributed mostly in Norway and an eastern group covering most of
 Finland, Poland and Russia. This sub-structuring may reflect
 co-immigration with the main host, Norway spruce (Picea abies), into
 Northern Europe after the last ice age. We found evidence of low levels of
 genetic diversity in southwestern Finland, which has a long history of
 intensive forestry and urbanization. Numerous loci were significantly
 associated with one or more environmental factors, indicating adaptation
 to specific environments. These loci clustered into two groups with
 different associations with temperature and precipitation. Overall, our
 findings indicate that the current population genetic structure of P.
 nigrolimitatus results from a combination of gene flow, genetic drift and
 selection. The acquisition of similar knowledge especially over broad
 geographic scales, linking signatures of adaptive genetic variation to
 evolutionary processes and environmental variation, for other fungal
 species will undoubtedly be useful for assessment of the combined effects
 of habitat fragmentation and climate change on fungi strongly bound to
 old-growth forests. --
DOI: 10.5061/dryad.pzgmsbcnj
title: Data from: Improvement of genomic predictions in small breeds by construction of genomic relationship matrix through variable selection

description: Genomic selection has been increasingly implemented in the animal breeding
 industry, and it is becoming a routine method in many livestock breeding
 contexts. However, its use is still limited in several small-population
 local breeds, which are, nonetheless, an important source of genetic
 variability of great economic value. A major roadblock for their genomic
 selection is accuracy when population size is limited: to improve breeding
 value accuracy, variable selection models that assume heterogenous
 variance have been proposed over the last few years. However, while these
 models might outperform traditional and genomic predictions in terms of
 accuracy, they also carry a proportional increase of breeding value bias
 and dispersion. These mutual increases are especially striking when
 genomic selection is performed with a low number of phenotypes and high
 shrinkage value—which is precisely the situation that happens with small
 local breeds. In our study, we tested several alternative methods to
 improve the accuracy of genomic selection in a small population. First, we
 investigated the impact of using only a subset of informative markers
 regarding prediction accuracy, bias, and dispersion. We used different
 algorithms to select them, such as recursive feature eliminations,
 penalized regression, and XGBoost. We compared our results with the
 predictions of pedigree-based BLUP, single-step genomic BLUP, and weighted
 single-step genomic BLUP in different simulated populations obtained by
 combining various parameters in terms of number of QTLs and effective
 population size. We also investigated these approaches on a real data set
 belonging to the small local Rendena breed. Our results show that the
 accuracy of GBLUP in small-sized populations increased when performed with
 SNPs selected via variable selection methods both in
 simulated and real data sets. In addition, the use of variable selection
 models—especially those using XGBoost—in our real data set did not impact
 bias and the dispersion of estimated breeding values. We have discussed
 possible explanations for our results and how our study can help estimate
 breeding values for future genomic selection in small breeds.