cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9zw3r22jj
title: Data from: The role of niche breadth in oak phylogeography: Quercus glaucoides as a study case

description: The amount of genetic diversity and its distribution among populations has
 been associated to species’ attributes such as mating system, dispersal
 ability and geographic range size. Another attribute that could contribute
 to explain intraspecific phylogeographic patterns is niche breadth, but
 this relationship barely has been tested. Here, we studied a Mexican oak
 (Quercus glaucoides) with a comparatively narrow climatic niche breadth.
 Genetic diversity and structure were assessed, as well as historical
 demography dynamics and connectivity. Then, we tested for a general
 correlation of genetic diversity and structure with niche breadth, using
 our data and previous results from other co-distributed Mexican oaks with
 variable niche breadths. Methods Descriptors of genetic diversity and
 structure were obtained from 21 Q. glaucoides populations using
 chloroplast DNA (cpDNA) and nuclear microsatellites (nSSRs). Historical
 demography dynamics were inferred with approximate Bayesian computation
 (ABC) and past potential distribution models. To test for an association
 between niche breadth and phylogeographic patterns, we used genetic
 diversity and differentiation values of Q. glaucoides plus those
 previously published for other ten species. Niche breadth was estimated
 for all species and linear regressions were performed. Results Genetic
 diversity calculated from nSSRs (HO= 0.539; HE= 0.714) was among the
 lowest, and cpDNA differentiation (NST= 0.88) was the highest so far
 obtained for comparable Mexican oaks. Moderate changes in demographic size
 and distribution shifts throughout the last glacial cycle were inferred,
 explaining some of the observed genetic patterns. A positive correlation
 of HO and a negative correlation of NST with niche breadth were detected
 across species.  Main conclusions Distinct phylogeographic
 patterns in Q. glaucoides could be explained because a narrower niche may
 cause lower historical effective population sizes and more fragmented
 distributions in comparison to species with a wider niche breadth, even
 with similar range sizes.
description: Microsatellites data was obtained through the following procedures:
 PCR reactions were performed
 using the Platinum Multiplex PCR Master Mix (Thermo Fisher Scientific) in
 a final volume of 6 uL. Four groups of primers were used for the PCR
 reaction according to the colour of the fluorescent tag and fragment size.
 The temperatures of reactions were as follows: denaturation at 95 °C for 5
 min; 40 cycles of 95 °C for 30 s, alignment between 45 and 61 °C
 (according to the primer group) for 45 s and extension at 72 °C for 1 min;
 followed by a final step at 72 °C for 10 min. PCR products were analysed
 in an ABI-PRISM 3300 Avant sequencer. Fragment sizes were determined using the program
 GeneMarker 2.6.4 (SoftGenetics) using Gene-scan-600 Liz as a size
 standard.
DOI: 10.5061/dryad.ksn02v78j
title: Data for: Latitudinal cline of death-feigning behaviour in a beetle (Tribolium castaneum)

description: Death-feigning behaviour is a phenomenon in which a prey is rendered
 motionless due to stimulation or threat from a predator. This
 anti-predator defense mechanism has been observed across numerous animal
 taxa and is considered adaptive in nature. However, longer durations of
 death feigning can result in decreased opportunities for feeding and
 reproduction, and therefore is often associated with higher fitness costs
 as compared to environments without predators. Differences have also been
 observed in the frequencies and durations of death-feigning behaviours
 within animal populations, and these differences are thought to be
 influenced by the balance between survival and other fitness costs.
 Furthermore, this balance is predicted to vary in response to changes in
 environmental conditions. In this study, we examined the frequency and
 duration of death-feigning behaviours in 38 populations of the red flour
 beetle (Tribolium castaneum). Our results demonstrate that frequencies and
 durations of the death-feigning behaviours in Tribolium castaneum show
 geographical variations and a latitude cline, indicating that this
 behaviour is influenced by location as well as latitude. This study is the
 first to demonstrate the existence of a latitudinal cline in
 death-feigning behaviour and suggests that this behavior might have
 evolved in response to environmental factors that vary with latitude.
DOI: 10.5061/dryad.18931zd2b
title: A sexually-selected male weapon characterised by strong additive genetic variance and no evidence for sexually antagonistic polyphenic maintenance

description: Sexual selection and sexual antagonism are important drivers of
 eco-evolutionary processes. The evolution of traits shaped by these
 processes depends on their genetic architecture, which remains poorly
 studied. Here, implementing a quantitative genetics approach using diallel
 crosses of the bulb mite, Rhizoglyphus robini, we investigated the genetic
 variance that underlies a sexually-selected weapon that is dimorphic among
 males and female fecundity. Previous studies indicated that a negative
 genetic correlation between these two traits likely exists. We found male
 morph showed considerable additive genetic variance, which is unlikely to
 be explained solely by mutation-selection balance, indicating the likely
 presence of large-effect loci. However, a significant magnitude of
 inbreeding depression also indicates that morph expression is likely to be
 condition-dependent to some degree and that deleterious recessives can
 simultaneously contribute to morph expression. Female fecundity also
 showed a high degree of inbreeding depression, but variance in female
 fecundity was mostly explained by epistatic effects, with very little
 contribution from additive effects. We found no significant genetic
 correlation, nor any evidence for dominance reversal, between male morph
 and female fecundity. The complex genetic architecture underlying male
 morph and female fecundity in this system has important implications for
 our understanding of the evolutionary interplay between purifying
 selection and sexually antagonistic selection.
description: Inbred lines of the bulb mite, <em>Rhizoglyphus
 robini</em>, were established from wild-caught individuals using
 full sib x sib mating for 14 generations. Males of the species are
 dimorphic, with fighter males expressing an enlarged and thickened third
 pair of legs which are used in combat with other males, in contrast,
 scrambler males have legs with all approximately equal thickness. The
 morph of each P-generation male was recorded and in subsequent generations
 of inbreeding, the same male morph was used, thus giving inbred lines
 fixed for fighter and scrambler alleles. Using diallel
 crossing, males and females from each inbred line were crossed with other
 inbred lines. The offspring produced by each cross were either 1)
 individually isolated and the fecundity of F1 females determined or 2)
 reared in small groups and the frequency of each male morph
 recorded. Using a Bayesian modeling approach, we
 partitioned the variance of each trait into additive effects, parental-sex
 effects, dominance effects and epistatic effects, plus noise. Furthermore,
 we investigated dominance relationships of these traits by calculating
 array covariances.
description: All analysis was performed in R, using packages
 <em>litterDiallel</em>, <em>MCMCglmm</em>,
 <em>ggplot2</em> and <em>lme4</em>
 (for their references
 please see main text).
DOI: 10.5281/zenodo.18323793
title: Environmental drivers of wild orchid distribution: soil properties shape habitat preferences in the Po Delta Regional Park (Italy)

description: Raw data of the article "Environmental drivers of wild orchid distribution: soil properties shape habitat preferences in the Po Delta Regional Park (Italy)", in production by PLOS ONE
DOI: 10.5281/zenodo.18323794
title: Environmental drivers of wild orchid distribution: soil properties shape habitat preferences in the Po Delta Regional Park (Italy)

description: Raw data of the article "Environmental drivers of wild orchid distribution: soil properties shape habitat preferences in the Po Delta Regional Park (Italy)", in production by PLOS ONE
DOI: 10.5061/dryad.jwstqjqf4
title: Shifts from non-obligate generalists to obligate specialists in simulations of mutualistic network assembly

description: Understanding ecosystem recovery after perturbation is crucial for
 ecosystem conservation. Mutualisms contribute key functions for plants
 such as pollination and seed dispersal. We modelled the assembly of
 mutualistic networks based on trait matching between plants and their
 animal partners that have different degrees of specialization on plant
 traits. Additionally, we addressed the role of non-obligate animal
 mutualists, including facultative mutualists or non-resident species that
 have their main resources outside the target site. Our computer
 simulations show that non-obligate animals facilitate network assembly
 during the early stages, furthering colonization by an increase in niche
 space and reduced competition. While non-obligate and generalist animals
 provide most of the fitness benefits to plants in the early stages of the
 assembly, obligate and specialist animals dominate at the end of the
 assembly. Our results thus demonstrate the combined occurrence of shifts
 from diet, trait, and habitat generalists to more specialised animals.
description: Data was generated with computer simulations. The methods are
 described in the main text and the source code is provided here and
 described in the README.md file. The data produced with the simulations
 have been processed using Python scripts, which are also provided here and
 explained in the README.md file.
DOI: 10.5061/dryad.bvq83bkdz
title: Data from: Variable ambient temperature promotes song learning and production in zebra finches

description: This data set contains the data used in the analysis of the article
 titled: Variable ambient temperature promotes song learning and production
 in zebra finches.
DOI: 10.5061/dryad.9kd51c5np
title: Genetic factors predict hybrid formation in the British flora

description: Natural hybridization can have a profound evolutionary impact, with
 consequences ranging from the extinction of rare taxa to the origin of new
 species. Natural hybridization is particularly common in plants; however,
 our understanding of the general factors that promote or prevent
 hybridization is hampered by the highly variable outcomes in different
 lineages. Here, we quantify the influence of different predictors on
 hybrid formation across species from an entire flora. We combine estimates
 of hybridization with ecological attributes and a new species-level
 phylogeny for over 1,100 UK flowering plant species. Our results show that
 genetic factors, particularly parental genetic distance, as well as
 phylogenetic position and ploidy, are key determinants of hybrid
 formation, whereas many other factors such as range overlap and genus size
 explain much less variation in hybrid formation. Overall, intrinsic
 genetic factors shape the evolutionary and ecological consequences of
 natural hybridization across species in a flora.
description: We estimated phylogenetic
 relationships from the Barcode UK dataset, which includes a three locus
 DNA barcode of <em>rbcL</em>, <em>matK</em>, and
 <em>ITS2</em> for native flowering plant species. Due to the
 different sequence diversity and alignment success of plastid and nuclear
 ribosomal DNA across flowering plants, we used a single alignment of
 plastid sequences to infer relationships between all taxa, while nuclear
 ribosomal ITS2 was aligned separately for each genus and only used to
 infer congeneric relationships. Plastid DNA was aligned for all taxa using
 Geneious, while ITS2 was aligned by genus, padded with Ns, and gapped
 using the program catfasta2phyml. Phylogenetic inferences were made using
 IQ-TREE in an analysis with three partitions allowing models of molecular
 evolution to differ between loci, and including a multifurcating
 constraint tree based on Angiosperm Phylogeny Group IV (APGIV)
 relationships generated with Phylomatic. Tree support was estimated using
 1000 ultrafast bootstrap replicates. The phylogeny was dated using treePL,
 using calibration with 30 well-spread phylogenetically assigned fossils
 across the flowering plant phylogeny.
 Tree-based genetic distances
 from the combined sequence alignment of ITS2 and plastid data were
 inferred using the R function cophenetic.phylo() from the package ape
 while separate pairwise distances for ITS2 and plastid DNA were calculated
 with the R function dist.alignment() from the seqinr package. The
 resulting distances (either tree-based distances or pairwise distances)
 were the square root of pairwise distances. Tree manipulation took place
 in R, with the circular plot made with the R package circlize; the
 phylogeny was coerced into a circular dendrogram for visualization. Other
 plots were generated with the R package ggplot2 and lattice. All other
 data manipulation took place in R version 3.6.1 using base R, and packages
 data.table and dplyr.
DOI: 10.5061/dryad.h9w0vt4np
title: Forest survey data of a landscape in Pine Mountain

description: This dataset provides the planar coordinates, height and the diameter at
 breast height (DBH) of trees with DBH &gt;= 1 cm within a landscape of
 400 m by 1000 m (made up of one-thousand 20 m by 20 m plots) in the
 Beijing Pine Mountain National Nature Reserve (40°30'50''
 N, 115°49'12'' E), which was carried out in 2014.
description: The surveyed landscape was divided into one-thousand 20 m by 20 m
 plots. For each plot, the trees with DBH &gt;= 1 cm was reorded and
 located. Please see Shi et al. (2018) for details.
 Shi, P., Gao, J., Song, Z.,
 Liu, Y., Hui, C. 2018. Spatial segregation facilitates the coexistence of
 tree species in temperate forests. Forests, 9: 768.
 https://doi.org/10.3390/f9120768
DOI: 10.5061/dryad.0vt4b8h3m
title: Orchid-mycorrhizal fungi interactions reveal a duality in their network structure in two European regions differing in climate

description: Network analysis is an effective tool to describe and quantify the
 ecological interactions between plants and root-associated fungi.
 Mycoheterotrophic plants, such as orchids, critically rely on mycorrhizal
 fungi for nutrients to survive, therefore, investigating the structure of
 those intimate interactions brings new insights into the plant community
 assembly and coexistence. So far, there is little consensus on the
 structure of those interactions, described either as nested (generalist
 interactions), modular (highly specific interactions) or of both
 topologies. Biotic factors (e.g., mycorrhizal specificity) were shown to
 influence the network structure, while there is less evidence of abiotic
 factor effects. By using next-generation sequencing of the orchid
 mycorrhizal fungal (OMF) community associated with 238 plant individuals
 belonging to 17 orchid species, we assessed the structure of four
 orchid-OMF networks in two European regions under contrasting climatic
 conditions (Mediterranean vs Continental). Each network contained four to
 12 co-occurring orchid species, including up to eight species shared among
 the sites. All four networks were both nested and modular, and fungal
 communities were different between co-occurring orchid species, despite
 multiple sharing of fungi across some orchids. Co-occurring orchid species
 growing in Mediterranean climates were associated with more dissimilar
 fungal communities, consistent with a greater modular structure compared
 to the Continental ones. The OMF diversity was comparable among orchid
 species since most orchids were associated with multiple rarer fungi and
 with only a few highly dominant ones in the roots. Our results provide
 useful highlights on potential factors involved in structuring
 plant-mycorrhizal fungi interactions in different climatic conditions.
description: To assess the fungal
 communities associated with several orchid species, root samples were
 collected from 238 plant individuals belonging to 17 orchid species in
 May-June 2018 in four species-rich grasslands located in two
 Europeans regions (Czech Republic and Southern France). Fungal DNA was
 extracted by the CTAB method, then the ITS2 nuclear rDNA region was
 amplified using two barcode-tagged primer pairs to cover the whole fungal
 diversity: the forward primer 5.8S-OF (5’-CATYGARTYKTTGAACGCA-3’)
 (Vogt-Schilb et al., 2020) complemented with the reverse primers (i)
 ITS4OF (5’-GTTACTAGGGGAATCCTTGTT-3’) and (ii) ITS4Tul
 (5’-CCGCCAGATTCACACATTGA-3’) (Taylor & McCormick, 2008). After
 bioinformatic analysis, the obtained reads were assigned to OTUs taxa when
 belonging to Ceratobasidiaceae, Tulasnellaceae and Serendipitaceae
 families with at least 85% of the similarity threshold (other fungal taxa
 known to form orchid mycorrhiza like ectomycorrhizal and saprobic fungi
 were kept for further analysis). Sequencing was performed on a MiSeq
 Illumina by the SEQme Company (Dobříš, Czech Republic).
DOI: 10.5061/dryad.g4f4qrfv3
title: Whole genome sequencing (WGS) data from invasive pine sawfly Diprion similis

description: Biological introductions are unintended “natural experiments” that provide
 unique insights into evolutionary processes. Invasive phytophagous insects
 are of particular interest to evolutionary biologists studying adaptation,
 as introductions often require rapid adaptation to novel host plants.
 However, adaptive potential of invasive populations may be limited by
 reduced genetic diversity—a problem known as the “genetic paradox of
 invasions”. One potential solution to this paradox is if there are
 multiple invasive waves that bolster genetic variation in invasive
 populations. Evaluating this hypothesis requires characterizing genetic
 variation and population structure in the invaded range. To this end, we
 assemble a reference genome and describe patterns of genetic variation in
 the introduced white pine sawfly, Diprion similis. This species was
 introduced to North America in 1914, where it has rapidly colonized the
 thin-needled eastern white pine (Pinus strobus), making it an ideal
 invasion system for studying adaptation to novel environments. To evaluate
 evidence of multiple introductions, we generated whole-genome resequencing
 data for 64 D. similis females sampled across the North American range.
 Both model-based and model-free clustering analyses supported a single
 population for North American D. similis. Within this population, we found
 evidence of isolation-by-distance and a pattern of declining
 heterozygosity with distance from the hypothesized introduction site.
 Together, these results support a single-introduction event. We consider
 implications of these findings for the genetic paradox of invasion and
 discuss priorities for future research in D. similis, a promising model
 system for invasion biology.
description: Full methods on how this data was prepared and processed can be
 found at the linked publication. In brief: Raw genetic
 material was collected from larval tissue from insects and extracted using
 Qiagen kits. DNA libraries were prepared using KAPA HyperPrep kits and was
 then sequenced on NovaSeq 6000 S4 flowcell.  vcftools
 and ANGSD programs were used to prepare the sam and beagle files
 respectively. See the paper methods for more details.
DOI: 10.5061/dryad.612jm647j
title: Data from: Comparing ant morphology measurements from microscope and online AntWeb.org 2D z-stacked images

description: Unprecedented technological advances in digitization and the steadily
 expanding open-access digital repositories are yielding new opportunities
 to quickly and efficiently measure morphological traits without
 transportation and advanced/expensive microscope machinery. A prime
 example is the AntWeb.org database, which allows researchers from all over
 the world to study taxonomic, ecological, or evolutionary questions on the
 same ant specimens with ease. However, the reproducibility and reliability
 of morphometric data deduced from AntWeb compared to traditional
 microscope measurements has not yet been tested. Here, we compared 12
 morphological traits of 46 Temnothorax ant specimens
 measured either directly by stereomicroscope on physical specimens or via
 the widely used open access software tpsDig utilizing AntWeb digital
 images. We employed a complex statistical framework to test several
 aspects of reproducibility and reliability between the methods. We
 estimated (i) the agreement between the measurement methods and (ii) the
 trait value dependence of the agreement, then (iii) compared the
 coefficients of variation produced by the different methods, and finally,
 (iv) tested for systematic bias between the methods in a mixed
 modelling-based statistical framework. The stereomicroscope measurements
 were extremely precise. Our comparisons showed that agreement between the
 two methods was exceptionally high, without trait value dependence.
 Further, the coefficients of variation did not differ between the methods.
 However, we found systematic bias in eight traits: apart from one trait
 where software measurements overestimated the microscopic measurements,
 the former underestimated the latter. Our results shed light on the fact
 that relying solely on the level of agreement between methods can be
 highly misleading. In our case, even though the software measurements
 predicted microscope measurements very well, replacing traditional
 microscope measurements with software measurements, and especially mixing
 data collected by the different methods, might result in erroneous
 conclusions. We provide guidance on the best way to utilize virtual
 specimens (2D z-stacked images) as a source of morphometric data,
 emphasizing the method’s limitations in certain fields and applications.