cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bg79cnp79
title: Estimating the inbreeding level and genetic relatedness in an isolated population of critically endangered Sichuan taimen (Hucho bleekeri) using genome wide SNP markers

description: Sichuan taimen (Hucho bleekeri) is critically endangered fish listed in
 The Red List of Threatened Species compiled by the International Union for
 Conservation of Nature (IUCN). Specific locus amplified fragment
 sequencing (SLAF-seq)-based genotyping was performed for Sichuan taimen
 with 43 yearling individuals from 3 locations in Taibai River (a tributary
 of Yangtze River) that has been sequestered from its access to the ocean
 for more than 30 years since late 1980s. Applying the inbreeding level and
 genetic relatedness estimation using 15,396 genome wide SNP markers, we
 found that the inbreeding level of this whole isolated population was at a
 low level (average F=2.6×10-3±0.079), and the means of coancestry
 coefficients within and between the three sampling locations were all very
 low (close to 0), too. Genomic differentiation was negatively correlated
 with the geographical distances between the sampling locations (p &lt;
 0.001) and the 43 individuals could be considered as genetically
 independent two groups. The low levels of genomic inbreeding and
 relatedness indicated a relatively large number of sexually mature
 individuals were involved in reproduction in Taibai River. This study
 suggested a genomic-relatedness-guided breeding and conservation strategy
 for wild fish species without pedigree information records.
description: <b>Table S1. Reads output and quality statistics of SLAF
 sequencing for 43 sequenced individuals<i>.</i>
 </b> <b>Table S2 Descriptive
 statistics for SLAF tags for the 43 sequenced individuals.
 </b> <b>Table S3. Descriptive
 statistics for the SNP datasets for the 43 sequenced
 individuals.</b> <b>Table S4. Descriptive
 statistics for reads mapped to </b><b><i>Hucho
 hucho</i></b><b> genome for 43
 sequenced</b><b>
 individuals<i>.</i></b> <b>Table S5. Genomic
 inbreeding coefficients of 43</b> <b>sequenced
 individuals.</b> <b>Table S6. Significance
 test for differences in average genomic inbreeding coefficients between
 three populations.</b> <b>Table S7. Estimated
 genomic relatedness and similarity measures of each individual pairs
 within and between three populations.</b> <b>Table S8. Significance
 test for differences in average genomic pairwise relatedness
 </b><b>and similarity coefficient within each of three
 populations.</b> <b>Table S9. Significance
 test for differences in average genomic pairwise relatedness
 </b><b>and similarity between different
 populations.</b> <b>Table S10. Position on
 the first three dimensions of
 multidimensional scaling (MDS) analysis for 43 sequenced
 individuals.</b>
DOI: 10.5061/dryad.r7sqv9s7p
title: Dietary morphology of two island-endemic murine rodent clades is consistent with persistent, incumbent-imposed competitive interactions

description: A lineage colonizing a geographic region with no competitors may exhibit
 rapid diversification due to greater ecological opportunity. The resultant
 species diversity of this primary-colonizing (incumbent) clade may limit
 subsequent lineages’ ability to persist unless these non-incumbent
 lineages are ecologically distinct. We compare the diversity in
 diet-related mandibular morphology of two sympatric murid rodent clades
 endemic to Luzon Island, Philippines—incumbent Phloeomyini and
 secondary-colonizing Chrotomyini—to the mandibular morphological diversity
 of Sahul Hydromyini, the sister clade of Chrotomyini and the incumbent
 murid lineage on the supercontinent of Sahul. This three-clade comparison
 allows us to test the hypothesis that incumbent lineages can force
 persistent ecological distinction of subsequent colonists at the time of
 colonization and throughout the subsequent history of the two sympatric
 clades. We find that Chrotomyini forms a subset of the diversity of their
 clade plus Sahul Hydromyini that minimizes overlap with Phloeomyini. We
 also infer that this differentiation extends to the stem ancestor of
 Chrotomyini and Sahul Hydromyini, consistent with a biotic filter imposed
 by Phloeomyini. Our work illustrates that incumbency has the potential to
 have a profound influence on the ecomorphological diversity of colonizing
 lineages at the island scale even when the traits in question are evolving
 at similar rates among independently colonizing clades.
description: This archive contains a total of 88 files in 11 directories
 detailing analyses of comparative morphological evolution of mandibular
 shape of the Luzon Old Endemics and Sahul hydromyines after landmark
 collection. Note 1: The R scripts require files from
 the Dryad archive associated with: Rowsey et al. 2019. Tempo and mode of
 mandibular shape and size evolution reveal mixed support for incumbency
 effects in two clades of island-endemic rodents (Muridae: Murinae)
 Evolution 73:1411-1427. The archive can be found here: https://doi.org/10.5061/dryad.gb7k5d1  Note 2: throughout the script we refer to Phloeomyini as cloud rats (abbreviated "cr"), Chrotomyini as earthworm mice (abbreviated "ewm"), and Sahul Hydromyini as Sahul Old Endemics (abbreviated "SOE") which are alternative names for these respective clades. Note 3: Sahul hydromyine mandible photographs will be deposited at the museums where the specimens were borrowed.
DOI: 10.5061/dryad.tx95x69sx
title: Opposite latitudinal patterns for bird and arthropod predation revealed in the experiments with differently colored artificial prey

description: The strength of biotic interactions is generally thought to increase
 towards the equator, but support for this hypothesis is contradictory. We
 explored whether predator attacks on artificial prey of eight different
 colours vary among climates and whether this variation affects the
 detection of latitudinal patterns in predation. The data set provides
 number of damage marks on each of 1320 plasticine caterpillars of eight
 different colours, which were attached to branches of woody plants and
 exposed from 10 to 118 days in 11 localities across the globe. During each
 record, all marks found on model caterpillars were attributed to a certain
 group of predators (birds, arthropods, mammals and other predators), and
 marks of each type were counted. The models that had damage marks were
 remoulded or replaced if the damage was severe. These data contribute to
 our understanding of macroecological patterns in biotic interactions.
DOI: 10.5061/dryad.tht76hdvm
title: Clinical reasoning: sudden hearing loss with vertigo in a 42-year-old woman

description: Supplemental table: Etiologies of sudden sensorineural hearing
 loss with or without vertigo
DOI: 10.5061/dryad.tx95x69sz
title: Data from: Whole-genome sequencing of 128 camels across Asia reveals origin and migration of domestic Bactrian camels

description: The domestic Bactrian camels were treated as one of the principal means of
 locomotion between the eastern and western cultures in history. However,
 whether they originated from East Asia or Central Asia remains elusive. To
 address this question, we performed whole-genome sequencing of 128 camels
 across Asia. The extant wild and domestic Bactrian camels showed
 remarkable genetic divergence since they were split from dromedaries. The
 wild Bactrian camels also contributed little to the ancestry of domestic
 ones though they share close habitat in East Asia. Interestingly, among
 the domestic Bactrian camels, those from Iran exhibited the largest
 genetic distance and the earliest split from all others in the phylogeny,
 in spite of evident admixture between domestic Bactrian camels and
 dromedaries living in Central Asia. Taken together, our study supported
 the Central Asian origin of domestic Bactrian camels, which were then
 immigrated eastward to Mongolia where native wild Bactrian camels
 inhabited.
description: <strong>sample.xlsx</strong>
 Sample information of 128 camels, including NCBI accessions,
 sample names and populations.
 <strong>variant.filtered.vcf.zip</strong>
 Variants of 128 camels aftering filtering (vcf format).
 <strong>Fig1A_diversity.zip</strong>
 Nucleotide diversity <i>π </i>of each population
 calculated with vcftools.
 <strong>Fig1B_Fst.zip</strong>
 Pairwise population differentiation
 <i>F</i>st calculated with vcftools.
 <strong>Fig2A_MDS.zip</strong> A
 pruned subset of SNPs (ped format) and MDS calculated with
 plinks.
 <strong>Fig2B_admixture.zip</strong>
 Results of Admixture anlysis (K = 3-5).
 <strong>Fig2C_treemix.zip</strong>
 Input file of Treemix analysis.
 <strong>Fig3A_Dstats.txt</strong>
 D and fd statistics for 100-kb windows across the
 genome.
 <strong>Fig3B_Fst.zip</strong>
 <i>F</i>st of regions with non-significant fd
 values.
 <strong>Fig3C_mtDNA.fasta</strong>
 Full-length mtDNA sequences (fasta format).
 <strong>Fig4_GPhoCS.zip</strong>
 Control files (.ctl), sequence files (.seq) and result files
 (.out) in GPhoCS analysis.
DOI: 10.5061/dryad.j6q573n8n
title: Data from: The preparation and characterization of uniform nanoporous structure on glass

description: A novel fabrication method of uniform porous structures on the glass
 surface is proposed. The hydrofluoric acid fog formed by air-jet
 atomization etches the glass surface to fabricate nanoporous structure
 (NPS) on glass surface. This NPS shows the enhanced average light
 transmittance of ~92.9% and the superhydrophilic property with a contact
 angle less than 1° which presents an excellent anti-fog property.
 Passivated by fluorosilane, the NPS shows nearly the superhydrophobic
 property with a contact angle of 141.2°. This fabrication method has shown
 promising application prospects due to its simplicity, low cost and
 efficiency, which can be easily applied to large-scale industrial
 production.
description: This dataset was collected by X-ray photoelectron spectroscopy
 (Kratos, AXIS Supra), it has been processed by the software named Escape.
 In this dataset, 2 is the original data of Figure 5a, 6 is the original
 data of Figure 5b.
DOI: 10.5061/dryad.hhmgqnkcj
title: Accelerated landing in a stingless bee and its unexpected benefits for traffic congestion

description: To land, flying animals must simultaneously reduce speed and control their
 path to the target. While the control of approach speed has been studied
 in many different animals, little is known about the effect of target size
 on landing, particularly for small targets that require precise trajectory
 control. To begin to explore this, we recorded the stingless bee
 Scaptotrigona depilis landing on their natural hive entrance – a narrow
 wax tube built by the bees themselves. Rather than decelerating before
 touchdown as most animals do, S. depilis accelerates in preparation for
 its high precision landings on the narrow tube of wax. A simulation of
 traffic at the hive suggests that this counterintuitive landing strategy
 could confer a collective advantage to the colony by minimising the risk
 of mid-air collisions and thus of traffic congestion. If the simulated
 size of the hive entrance increases and if traffic intensity decreases
 relative to the measured real-world values, ‘accelerated landing’ ceases
 to provide a clear benefit, suggesting that it is only a useful strategy
 when target cross-section is small and landing traffic is high. We discuss
 this strategy in the context of S. depilis’ ecology and propose that it is
 an adaptive behaviour that benefits foraging and nest defence.
DOI: 10.5061/dryad.q573n5tf5
title: Data from: Gray plumage color is more cryptic than brown in snowy landscapes in a resident color polymorphic bird

description: Camouflage may promote fitness of given phenotypes in different
 environments. The tawny owl (Strix aluco) is a colour polymorphic species
 with a grey and brown morph resident in the Western Palearctic. A strong
 selection pressure against the brown morph during snowy and cold winters
 has been documented earlier but the selection mechanisms remain
 unresolved. Here we hypothesise that selection favors the grey morph
 because it is better camouflaged against predators and mobbers in snowy
 conditions compared to the brown one. We conducted an online citizen
 science experiment where volunteers were asked to locate a grey or a brown
 tawny owl specimen from pictures taken in snowy and snowless landscapes.
 Our results show that the grey morph in snowy landscapes is the hardest to
 detect whereas the brown morph in snowy landscapes is the easiest to
 detect. With an avian vision model we show that, similar to human
 perceivers, the brown morph is more conspicuous than the grey against
 coniferous tree trunks for a mobbing passerine. We suggest that with
 better camouflage, the grey morph may avoid mobbers and predators more
 efficiently than the brown morph and thus survive better in snowy
 environments. As winters are getting milder and shorter in the species
 range, the selection periods against brown colouration may eventually
 disappear or shift poleward.
description: Dataset contains: - Data and R code
 - Pictures for online citizen science game -
 Validation study pictures
DOI: 10.5061/dryad.dz08kprt6
title: Cocoa agroforest multifunctionality and soil fertility explained by shade tree litter traits

description: Manipulating plant functional diversity to improve agroecosystem
 multifunctionality is a central challenge of agricultural systems
 worldwide. In cocoa agroforestry systems (cAFS), shade trees are used to
 supply many services to farmers, yet their impact on soil functioning and
 cocoa yields is likely to vary substantially among tree species. Here, we
 compared the impact of five shade tree species (Canarium schweinfurthii
 (Canarium), Dacryoides edulis (Safou), Milicia excelsa (Iroko), Ceiba
 pentandra (Kapok tree), Albizia adianthifolia (Albizia)) and unshaded
 conditions on the functioning of poor sandy savannah soils within eight
 cocoa farms in Central Cameroon. We assessed the effects of plant
 functional traits, leaf litterfall and fine root biomass on a range of
 soil functions and on cocoa yield. Shade trees generally improved soil pH,
 NH4+, NO3- and Olsen P content, biomass production of bioassays, and soil
 total C and N content, while leaving cocoa yields unchanged. However,
  these effects varied largely among species. Improvements of soil
 functions were low under the two fruit trees (Canarium and Dacryodes),
 medium under the legume tree Albizia, and high under the two timber trees
 (Milicia and Ceiba). Low litter recalcitrance was most strongly associated
 with increases in soil fertility indicators such as N and P availability,
 whereas soil C and N content increased with litter Ca restitution.
 Synthesis and applications. We demonstrate that cocoa agroforest
 multifunctionality is substantially influenced by the functional traits of
 shade tree species. Shade tree species with the most dissimilar traits to
 cocoa (cocoa showing the lowest leaf litter quality) showed the largest
 improvement of soil functions. Therefore, selection of shade trees based
 on their functional traits appears as a promising practice to adequately
 manage soil functioning. In order to fully assess the beneficial role of
 shade trees in these agroecosystems, future research will need to extend
 this approach to other belowground traits and other aspects of
 multifunctionality such as long-term cocoa health and yield.
DOI: 10.5061/dryad.g4f4qrfm4
title: Data from: High genetic diversity and stable Pleistocene distributional ranges in the widespread Mexican red oak Quercus castanea Née (1801) (Fagaceae)

description: The Mexican highlands are areas of high biological complexity where taxa
 of Nearctic and Neotropical origin and different population histories are
 found. To gain a more detailed view of the evolution of the biota in these
 regions, it is necessary to evaluate the effects of historical tectonic
 and climate events on species. Here, we analyzed the phylogeographic
 structure, historical demographic processes, and the contemporary period,
 Last Glacial Maximum (LGM) and Last Interglacial (LIG) ecological niche
 models of Quercus castanea, to infer the historical population dynamics of
 this oak distributed in the Mexican highlands. A total of 36 populations
 of Q. castanea were genotyped with seven chloroplast microsatellite loci
 in four recognized biogeographic provinces of Mexico: the Sierra Madre
 Occidental (western mountain range), the Central Plateau, the
 Trans-Mexican Volcanic Belt (TMVB, mountain range crossing central Mexico
 from west to east) and the Sierra Madre del Sur (SMS, southern mountain
 range). We obtained standard statistics of genetic diversity and structure
 and tested for signals of historical demographic expansions. A total of 90
 haplotypes were identified and 29 of these haplotypes were restricted to
 sngle populations. The within-population genetic diversity was high (mean
 hS = 0.72), and among-population genetic differentiation showed a strong
 phylogeographic structure (NST = 0.630 &gt; GST = 0.266; P &lt;
 0.001). Signals of demographic expansion were identified in the TMVB and
 the SMS. The ecological niche models suggested a considerable percentage
 of stable distribution area for the species during the LGM and
 connectivity between the TMVB and the SMS. High genetic diversity, strong
 phylogeographic structure and potential distribution models suggest in
 situ permanence of Q. castanea populations with large effective population
 sizes. The complex geological and climatic histories of the TMVB help to
 explain the origin and maintenance of a large proportion of the genetic
 diversity in this oak species.
DOI: 10.5061/dryad.1jwstqjqs
title: Including dynamics in the equation: Tree growth rates and host specificity of vascular epiphytes

description: 1. The forest canopy is home to a rich biota. One salient feature are the
 dynamics of the habitat-building trees, which are growing and eventually
 vanishing. Tree species strongly differ in growth rates, final size and
 longevity. Nevertheless, these inherent dynamics have been a blind spot in
 studies on host specificity of vascular epiphytes (vascular plants
 dwelling on trees without parasitizing them) – not least because tree
 growth rates and longevity are usually unknown in highly diverse tropical
 forests. The present study aims at tackling this blind spot. 2. We
 compared epiphyte abundances (&gt; 23,000 individuals) found on 285
 individuals of four focal tree species in a lowland moist forest in
 Panama. Data on repeated dbh censuses from a permanent tree plot provided
 the unique opportunity to estimate the age of our sampled trees. We
 compared the relative importance of tree longevity for host biases with
 that of other host tree characteristics, namely microclimatic conditions
 and bark acidity, rugosity and stability. 3. The studied tree species
 differ in host quality and epiphyte species partly differ in host
 preferences. The conclusions concerning relative host tree quality depend
 hugely on whether or not different tree growth rates are considered.
 Comparing these conclusions allows important insights into the role of
 tree longevity in shaping epiphyte communities. Relating tree trait
 differences to the observed distributions of epiphytes among the focal
 tree species shows how the simultaneous action of various tree
 characteristics causes host biases. 4. Synthesis. This study highlights
 the substantial but, up to now, hidden role of different tree growth rates
 for host tree specificity of vascular epiphytes. Future investigations
 need to consider this possibly confounding factor adequately to avoid
 spurious conclusions.
DOI: 10.5061/dryad.g4f4qrfm5
title: Evaluating kin and group selection as tools for quantitative analysis of microbial data

description: Kin selection and multilevel selection theory are often used to interpret
 experiments about the evolution of cooperation and social behaviour among
 microbes. But while these experiments provide rich, detailed fitness data,
 theory is mostly used as a conceptual heuristic. Here, evaluate how kin
 and multilevel selection theory perform as quantitative analysis tools. We
 reanalyse published microbial datasets and show that the canonical fitness
 models of both theories are almost always poor fits because they use
 statistical regressions misspecified for the strong selection and non-
 additive effects we show are widespread in microbial systems. We identify
 analytical practices in empirical research that suggest how theory might
 be improved and show that analysing both individual and group fitness
 outcomes helps clarify the biology of selection. A data-driven approach to
 theory thus shows how kin and multilevel selection both have untapped
 potential as tools for quantitative understanding of social evolution in
 all branches of life.
DOI: 10.5061/dryad.8w9ghx3h2
title: Interaction motifs variability in a Mediterranean palm under environmental disturbances: the mutualism‐antagonism continuum

description: The nature and the strength of plant¬ frugivore interactions often vary
 along an antagonism-mutualism continuum and are highly influenced by the
 local ecological context (e.g. level of environmental disturbances).
 However, little is known concerning how the local ecological setting where
 plant-frugivore interactions take place affects  the seed
 dispersal effectiveness (SDE) and, eventually, plant recruitment. This
 knowledge gap relates to  the scarcity of empirical
 investigations on individual-based plant-frugivore networks. We assessed
  whether the assembly of interaction modes (antagonist and
 mutualist) of the dwarf palm Chamaerops humilis (Arecaeae) affect the
 individual and the population level SDE in two Mediterranean sites
 differing in perturbation levels. We analysed the frequency distribution
 of interaction typologies and test its relationship with variation among
 individual palms in SDE. Additionally, we document how variation in
 interaction motiffrequency (e.g. overrepresented interaction typologies)
 relates to changes in the SDE landscape of both disturbed study sites. We
 found that the interaction typologies of individual palms and its
 frugivores did not occur randomly. In a more complex landscape,
 interactions were more diverse and less dominated by simpler typologies,
 which may increase the stability of the plant-disperser interaction over
 the long term. We demonstrate that plants that interact with a more
 complex assemblage of frugivores, including both mutualistic and
 antagonistic partners, had the highest probability of recruitment. We
 found that the highly variable SDE among individual palms resulted from a
 few interaction modes occurring at higher than expected frequencies. We
 suggest this may be a reasonably frequent situation in diversified
 frugivore assemblages with a high heterogeneity of functional effects
 among mutualistic and antagonistic partners.