cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ch4dp8n
title: Data from: Non-random associations of maternally transmitted symbionts in insects: the roles of drift versus co-transmission and selection

description: Virtually all higher organisms form holobionts with associated microbiota.
 To understand the biology of holobionts we need to know how species
 assemble and interact. Controlled experiments are suited to study
 interactions between particular symbionts, but they can only inform about
 a tiny portion of the diversity within each species. Alternatively,
 interactions can be inferred from associations among symbionts in the
 field that are more or less frequent than expected under random
 assortment. However, random assortment may not be a valid null hypothesis
 for maternally transmitted symbionts in finite populations, where drift
 alone can result in associations. Here we report results from a European
 field survey of endosymbionts in the pea aphid (Acyrthosiphon pisum), and
 we develop a model to study the effect of drift on symbiont associations
 under different population sizes, considering varying rates of horizontal
 and maternal transmission. The model showed that even though horizontal
 transmissions and maternal transmission failures randomise symbiont
 associations, drift can induce significant departures from random
 assortment, at least in moderate-sized populations. Based on these
 results, we carefully interpret our field survey and we re-visit the
 association between Spiroplasma and Wolbachia in Drosophila neotestacea
 reported by Jaenike et al. (2010). For this and for several significant
 associations between symbionts in European pea aphids we conclude that
 under reasonable assumptions of effective population size, they are indeed
 likely to be maintained by biased co-transmission or selection. Our study
 shows that formulating appropriate null expectations can strengthen the
 biological inference from co-occurrence patterns in the field.
description: Data
 Wolbachia-Spiroplasma association in Drosophila
 neotestaceaTime series describing
 the evolution of the association between Wolbachia and Spiroplasma in
 Drosophila neotestacea.Table S3 Data
 Wolbachia-Spiroplasma association in Drosophila
 neotestacea.xlsxTable S4 Data Pea aphid
 symbiontsData Pea aphid symbionts
 survey in EuropeAppendix
 S1This appendix contains
 the model which is implemented in an R function.
DOI: 10.5061/dryad.n4gt2qv
title: Data from: Allopatric speciation in Asia contributed to the diversity anomaly between eastern Asia and eastern North America: evidence from anchored phylogenomics of Stewartia (Theaceae)

description: Premise of the research. The disjunct distribution of plant genera between
 eastern Asia (EA) and eastern North America (ENA) has long attracted the
 attention of biologists and biogeographers. For most genera that have been
 studied, there are more species in EA than ENA and the diversity anomaly
 may have resulted from the greater physiographical heterogeneity in
 conjunction with climate and sea level changes in EA than in ENA. However,
 few empirical studies have explicitly tested the association between
 species diversity and allopatric speciation events. The genus Stewartia
 (Theaceae) displays this diversity anomaly with two species in ENA and 21
 species in EA, but the phylogeny of this group has not been resolved due
 to insufficient data. Methodology. Here, we sampled 15 species of
 Stewartia (65%) and generated data from over 500 nuclear loci using the
 anchored phylogenomic approach to produce a robust phylogeny of Stewartia.
 In addition, biogeographical analyses were performed to elucidate the
 natural history of Stewartia including estimated times of divergence,
 ancestral areas, and speciation patterns. Pivotal results. Our parsimony,
 Bayesian, and species tree analyses produced congruent phylogenies with
 high resolution of the interspecific relationships within Stewartia.
 Speciation in Asia was mostly allopatric between the Japanese islands and
 the Asian continent during the Miocene and early Pliocene, while the two
 ENA species represent lineages from different times with S. malacodendron
 being the first lineage to split off from the remaining species and S.
 ovata coming later sister to the deciduous species of Asian Stewartia.
 Conclusions. The results provide direct evidence for the importance of
 allopatry in the differential diversity between EA and ENA.
description: Stewartia61taxa.AnchoredHybridEnrichmentDataThis is a data set of 500 nuclear loci produced via the Anchored Hybrid Enrichment method with a total of 386131sites for the genus Stewartia as the ingroup and Franklinia, Schima, and Gordonia as the outgroups.Li et tal.Stewartia61taxa.AHE.nex
DOI: 10.5061/dryad.61pm78v
title: Data from: Tissue-specific carbon concentration, carbon stock, and distribution in Cunninghamia lanceolata (Lamb.) Hookplantations at various developmental stages in subtropical China

description: Key message Carbon (C) concentrations in Cunninghamia lanceolata (Lamb.)
 Hook plantations differed significantly among tissue types and were
 greater for aboveground than belowground tissues. Plantation C stock
 increased with developmental stage from young to mature to overmature, but
 at all stages the majority occurred as soil organic carbon (SOC) and was
 more influenced by belowground fine roots than by aboveground litterfall.
 Context Failing to account for tissue-specific variation in the C
 concentration can result in inaccurate forest C stock estimates. Aims We
 aimed to quantify the relative magnitudes of C stock for Chinese fir
 plantations at different developmental stages. Specifically, we focused on
 assessing tissue-specific C concentrations and C dynamics return of above-
 and belowground litterfall. Methods Carbon traits (C concentration, C
 flux, C stock and distribution at tree and ecosystem scales) were
 quantified in a chronosequence of Chinese fir (Cunninghamia lanceolata
 (Lamb.) Hook) monoculture plantation stands at young (10), mature (22),
 and overmature (34 years old) developmental stages. Results Carbon
 concentrations differed significantly among tissue types, with mean values
 of 48.5 ± 0.1% and 42.5 ± 0.2% for above- and belowground biomass,
 respectively. The aboveground tissue C concentration, tree- and
 plantation-scale C stock, and SOC stock depended on developmental stage.
 Carbon return in litterfall, tree C stock, and SOC increased from the
 young to the overmature stage. SOC stock accounted for the majority of
 plantation C stock at all developmental stages (78.3, 59.6 and 55.7% in
 the young, mature and overmature stages, respectively) and was more highly
 influenced by belowground fine roots than aboveground litterfall. Carbon
 stocks in Chinese fir plantations were 86, 129, and 153 t ha-2 at the
 young, mature, and overmature stages. Conclusion Prolonging Chinese fir
 rotation increases C sequestration potential and should be the focus of
 forest management strategies. The tissue-specific C concentrations provide
 detailed information for more accurate biomass C stock estimates for
 Chinese fir plantations and other subtropical coniferous forest. They
 indicate that current guidelines result in an overestimation of
 belowground biomass C stocks. Using the standard 0.47 biomass to C
 conversion factor, the belowground C stock would have been overestimated
 by 7.6-13.0% for the Chinese fir developmental stages investigated, while
 tree C stock would be underestimated by 0.08-3.24%. Therefore, developing
 species- and tissue-specific conversion factors are required for
 supporting C plantation and forest C accounting strategies.
description: Primary
 dataCarbon concentration,
 carbon stock, and distribution in Cunninghamia
 lanceolataDatas-ZLL.xlsx
DOI: 10.5061/dryad.2bj22pd
title: Data from: Abnormal brain development in child and adolescent carriers of mutant huntingtin

description: Objective: The huntingtin gene is critical for the formation and
 differentiation of the central nervous system, which raises questions
 about the neurodevelopmental impact of CAG expansion mutations within this
 gene (mHTT) that cause Huntington’s Disease (HD). We sought to determine
 if child and adolescent carriers of mHTT exhibit different brain growth
 compared to peers without the mutation. To test this hypothesis, we
 conducted structural magnetic resonance imaging in children and
 adolescents who are at risk for HD. We also explored whether variation in
 the length of CAG expansion affects brain development. Methods: Children
 and adolescents (age 6 – 18) with a parent or grandparent diagnosed with
 HD underwent neuroimaging and blinded genetic testing to confirm the
 presence or absence of mHTT. Seventy-five individuals were Gene-Expanded
 (GE) and 97 individuals were Gene-Non-Expanded (GNE). The GE group was
 estimated to be on average 35 years from clinical onset. Following an
 accelerated longitudinal design, age-related change in brain regions were
 estimated. Results: Age-related striatal volume changes differed
 significantly between the GE and GNE groups, with initial hypertrophy and
 more rapid volume decline in GE. This pattern was exaggerated with CAG
 expansion length for CAG &gt; 50. A similar age-dependent group
 difference was observed for the globus pallidus, but not in other major
 regions. Conclusions: Our results suggest that pathogenesis of HD begins
 with abnormal brain development, which sets the stage for different
 trajectories of striatal growth and development. An understanding of
 potential neurodevelopmental features associated with mHTT may be needed
 for optimized implementation of preventative gene silencing therapies,
 such that normal aspects of neurodevelopment are preserved as
 neurodegeneration is forestalled.
description: Supplemental Figure1
 UHDRS total motor scorePanel A shows the
 distribution of UHDRS total motor scores across groups. Panel B
 illustrates the impact of age on total motor score. The plot was derived
 from a mixed linear model with age and group as predictor variables for
 total motor scores &gt; 0. Age was a significant predictor of total motor
 score, t (82) = -2.7, p = 0.008, but not group, t (60) = -0.08, p = 0.93.
 GE = Gene expanded; GNE = gene-non-expanded.tmp_plts.pdfSupplemental Figure e-2 Empirical cumulative scanner distributions across ROIs and groupsPanels A through H show scanner distributions denoted by colored lines, for volumes of interest assessed as part of the study (x-axes). Scanner distributions are shown for the Gene-Expanded and Gene-Non-Expanded groups separately, as listed at the right-hand side of each graph. The Kolmogorov-Smirnov D statistic and the p-value are presented at the top left corner of each plot. Non-significant p-values indicate that the populations were sampled from similar distributions.supple_scanner.pdfModel detailsvdPlas_kidsHD_BrainDevelopment_Supplement_Model_Details.pdf
DOI: 10.5061/dryad.59j72f2
title: Data from: A revision of the concept of Mago O. Pickard-Cambridge, 1882, and proposal of a new genus (Araneae: Salticidae: Amycini)

description: In this paper we redescribe the type species of Mago O. Pickard-Cambridge,
 M. intentus O. Pickard-Cambridge, and describe Mago brimodes Ruiz
 & Maddison sp. nov. from Ecuador. Based on both morphological
 features and the 16SND1 gene region, we concluded that the larger spiders
 traditionally identified as Mago, such as Mago acutidens Simon and related
 species, are not closely related to the small dark M. intentus (type
 species) and M. brimodes. Matinta Ruiz & Maddison gen. nov. is
 therefore proposed to hold most species previously included in Mago. The
 following species are transferred from Mago to the new genus: Matinta
 acutidens (Simon, 1900) comb. nov. (type species), Matinta apophysis
 (Costa & Ruiz, 2017) comb. nov., Matinta balbina (Patello
 & Ruiz, 2014) comb. nov., Matinta chickeringi (Caporiacco, 1954)
 comb. nov., Matinta delicata (Patello & Ruiz, 2014) comb. nov.,
 Matinta fasciata (Mello-Leitão, 1940) comb. nov., Matinta fonsecai (Soares
 & Camargo, 1948) comb. nov., Matinta furcata (Costa &
 Ruiz, 2017) comb. nov., Matinta jurutiensis (Patello & Ruiz, 2014)
 comb. nov., Matinta longidens (Simon, 1900) comb. nov., Matinta mimica
 (Costa & Ruiz, 2017) comb. nov., Matinta opiparis (Simon, 1900)
 comb. nov., Matinta pardo (Costa & Ruiz, 2017) comb. nov., Matinta
 procax (Simon, 1900) comb. nov., Matinta saperda (Simon, 1900) comb. nov.,
 Matinta silvae (Crane, 1943) comb. nov., Matinta similis (Patello
 & Ruiz, 2014) comb. nov., Matinta steindachneri (Taczanowski,
 1878) comb. nov. and Matinta vicana (Simon, 1900) comb. nov. Mago
 dentichelis Crane, 1949 is transferred to Noegus Simon.
description: Data for Mago/Matinta
 phylogeny (16SND1 gene and gene trees)16SND1 data used to
 demonstrate the relationship among amycines, along with resulting
 phylogenetic trees.MagoMatinta-RuizMaddison2019.nex
DOI: 10.5061/dryad.s7v164j
title: Data from: Sex-specific relationship of cardiometabolic syndrome with lower cortical thickness

description: Objective: We investigated whether cardiometabolic factors were associated
 with age-related differences in cortical thickness in relation to sex.
 Methods: In this cross-sectional study, we enrolled 1322 cognitively
 normal elderly (≥ 65 years old) individuals (774 (58.5%) men, 548 (41.5%)
 women). Cortical thickness was measured using a surface-based analysis. We
 analyzed the associations of cardiometabolic risk factors with cortical
 thickness using multivariate linear regression models after adjusting for
 possible confounders and interactions with age. Result: Among women,
 hypertension (HTN) (β = -1.119 to -0.024, p &lt;0.05) and diabetes
 mellitus (DM) (β = -0.920, p = 0.03) were independently associated with
 lower mean cortical thickness. In addition, there was an interaction
 effect between obesity (BMI ≥ 27.5 kg/m2) and age on cortical thickness in
 women (β = -0.324 to -0.010, p &lt; 0.05) suggesting that age-related
 differences in cortical thickness were more prominent in obese women
 compared to women with normal weight. Moreover, low education level
 (&lt; 6 years) was correlated with lower mean cortical thickness (β =
 -0.053 to -0.046, p &lt; 0.05). Conversely, among men, only being
 underweight (BMI≤18.5 kg/m2, β = -2.656 to -0.073, p &lt; 0.05) was
 associated with lower cortical thickness. Conclusions: Our findings
 suggest that cortical thickness is more vulnerable to cardiometabolic risk
 factors in women than in men. Therefore, sex-specific prevention
 strategies may be needed to protect against accelerated brain aging.
description: Table e-1. The final
 estimated cortical thickness modelsTable
 e-1.docx
DOI: 10.5061/dryad.r5594f0
title: Data from: Molecular evolution in immune genes across the avian tree of life

description: All organisms encounter pathogens, and birds are especially susceptible to
 infection by malaria parasites and other haemosporidians. It is important
 to understand how immune genes, primarily innate immune genes which are
 the first line of host defense, have evolved across birds, a highly
 diverse group of tetrapods. Here, we find that innate immune genes are
 highly conserved across the avian tree of life and that although most show
 evidence of positive or diversifying selection within specific lineages or
 clades, the number of sites is often proportionally low in this broader
 context of putative constraint. Rather, evidence shows a much higher level
 of negative or purifying selection in these innate immune genes – rather
 than adaptive immune genes – which is consistent with birds’ long
 coevolutionary history with pathogens and the need to maintain a rapid
 response to infection. We further explored avian responses to
 haemosporidians by comparing differential gene expression in wild birds
 (1) uninfected with haemosporidians, (2) infected with Plasmodium and (3)
 infected with Haemoproteus (Parahaemoproteus). We found patterns of
 significant differential expression with some genes unique to infection
 with each genus and a few shared between ‘treatment’ groups, but none that
 overlapped with the genes included in the phylogenetic study.
description: DE_all results by
 comparisonResults from
 differential gene expression analyses.Fasta
 FilesFasta alignments for
 gene data setsArchive.zipSupplementary Table 1
DOI: 10.5061/dryad.r492c47
title: Data from: Flying south: foraging locations of the Hutton’s shearwater (Puffinus huttoni) revealed by time-depth recorders and GPS tracking

description: 1. The Hutton’s shearwater Puffinus huttoni is an endangered seabird
 endemic to Kaikōura, New Zealand, but the spatial and temporal aspects of
 its at-sea foraging behaviour are not well known. 2. To identify foraging
 areas and estimate trip durations, we deployed Global Positioning Systems
 (GPS) devices and Time-Depth Recorders (TDR) on 26 adult Hutton’s
 shearwaters during the chick-rearing period in 2017 and 2018. 3. We found
 Hutton’s shearwaters travelled much further from their breeding grounds at
 Kaikōura than previously considered, with most individuals foraging in
 coastal and oceanic areas 125–365 km south and near Banks Peninsula. Trip
 durations varied from 1 to 15 days (mean = 5 days), and total track
 lengths varied from 264 to 2157 km (mean = 1092.9 km). 4. Although some
 diving occurred in near-shore waters near the breeding colony, most
 foraging was concentrated in four regions south of Kaikōura. Dive
 durations averaged 23.2 seconds (range 8.1 to 71.3 sec) and dive depths
 averaged 7.1 m (range 1.5 to 30 m). Foraging locations had higher
 chlorophyll a levels and shallower water depths than non-foraging
 locations. Birds did not feed at night, but tended to raft in areas with
 deeper water than foraging locations. 5. Mapping the spatial and temporal
 distribution of Hutton’s shearwaters at-sea will be fundamental to their
 conservation, as it can reveal potential areas of overlap with fisheries
 and other industrial users of the marine environment.
description: Bennet2019_GPS_TDR_Deployment_2017-18File contains the GPS and dive data for Hutton’s shearwater during 2017 and 2018 chick-rearing periods.
DOI: 10.5061/dryad.4n2fk97
title: Data from: A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

description: Premise of the study: We developed a target enrichment panel for
 phylogenomic studies of Dioscorea, an economically important genus with
 incompletely resolved relationships. Methods: Our bait panel comprises 260
 low-to-single-copy nuclear genes targeted to work in Dioscorea, and is
 assessed here using a preliminary taxon sampling that includes both
 distantly and closely related taxa, including several yam crops and
 potential crop wild relatives (CWRs). We applied coalescent-based and
 maximum-likelihood phylogenomic inference approaches to the pilot taxon
 set, incorporating new and published transcriptome data from additional
 species. Results: The custom panel retrieved ~94% of targets and
 &gt;80% of full gene length from 88% and 68% of samples, respectively.
 It has minimal gene overlap with existing panels designed for
 angiosperm-wide studies, and generally recovers longer and more variable
 targets. Pilot phylogenomic analyses consistently resolve most deep and
 recent relationships with strong support across analyses, and point to
 revised relationships between the crop species D. alata and candidate
 CWRs. Discussion: Our customized panel reliably retrieves targeted loci
 from Dioscorea, is informative for resolving relationships in denser
 samplings, and suitable for refining our understanding of the independent
 origins of cultivated yam species; the panel likely has broader promise
 for phylogenomic studies across Dioscoreales.
description: SotoGomez_Dioscorea_BaitSeqsBait sequences for a Dioscorea-specific nuclear enrichment panel to target 260 low-to-single-copy nuclear genes.SotoGomez_AppendixS1_TargetGeneCharacterizationName, length, and predicted function of the 260 low-to-single-copy nuclear genes targeted by a Dioscorea-specific target enrichment panel.SotoGomez_AppendixS4_GenePartitioningSchemeData partitioning scheme inferred using PartitionFinder2 from 264 initial gene partitions.SotoGomez_AppendixS5_Coding+NonCodingSeq_LengthAverage length of coding and non-coding sequences recovered for 25 bait-enriched Dioscoreales taxa.SotoGomez_AppendixS6_TargetGeneSummaryStatsSummary statistics for gene targets, including average alignment length, missing data and parsimony informative sites.SotoGomez_AppendixS7_DioscoreaKit_Angiosperm353kit_ComparisonComparison of target gene overlap between a Dioscorea-specific kit and the universal Angiosperm-353 kit of Johnson et al. (2018; Systematic Biology 0:1–13)SotoGomez_AppendixS8_DioscoreaKit_AngiospermV1kit_ComparisonComparison of target gene overlap between a Dioscorea-specific kit and the universal Angiosperm v. 1 kit of Buddenhagen et al. (2016; bioRxiv doi: https://doi.org/10.1101/086298)IndividualTargetGeneAlignmentsIndividual gene alignments used for coalescent-based and concatenated phylogenomic analysesSotoGomez_IndividualTargetGeneAlignments.zipSotoGomez_IndividualTargetGeneTreesIndividual gene trees used for coalescent-based phylogenomic analysis and paralog identification.