cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fj6q573t4
title: Admixture may be extensive among hyperdominant Amazon rainforest tree species

description: Admixture is a mechanism by which species of long-lived plants may acquire
 novel alleles. However, the potential role of admixture in the origin and
 maintenance of tropical plant diversity is unclear. We ask whether
 admixture occurs in an ecologically important clade of Eschweilera
 (Parvifolia clade, Lecythidaceae), which includes some of the most
 widespread and abundant tree species in Amazonian forests. Using target
 capture sequencing, we conducted a detailed phylogenomic investigation of
 33 species in the Parvifolia clade and investigated specific hypotheses of
 admixture within a robust phylogenetic framework. We assembled target loci
 from raw sequence reads, conducted tree-based paralog trimming, and
 estimated species trees using maximum likelihood approaches. In addition,
 we called single nucleotide polymorphisms for members of the Parvifolia
 clade and used a Bayesian clustering approach to estimate the ancestry of
 individuals. We distinguished between population structure and evidence of
 admixture using a test based on rooted gene trees. We also investigated
 overlap in geographical range, phenology, and morphology of species,
 including those we found to admix. We found strong evidence of admixture
 among three ecologically dominant species, E. coriacea, E. wachenheimii
 and E. parviflora, but a lack of evidence for admixture among other
 lineages. Accepted species were largely distinguishable from one another,
 as was geographic structure within species. We show that hybridization may
 play a role in the evolution of the most widespread and ecologically
 variable Amazonian tree species. While admixture occurs among some species
 of Eschweilera, it has not led to widespread erosion of most species’
 genetic or morphological identities. Therefore, current morphological
 based species circumscriptions appear to provide a useful characterization
 of the clade’s lineage diversity.
description: The dataset is organized according to the major types of analyses
 conducted: 
 Map Information about datasets
 used to produce maps 
 SNP_calling Files relating to calling
 single nucleotide polymorphisms 
 Trimming_and_assembly Files related to read
 trimming and gene assembly 
 Phenology Dataset on flowering
 times RT_tests
 Input and output files related to rooted triplet
 tests STRUCTURE
 Input and output files related to Bayesian clustering
 analyses 
 R_scripts_and_plotting Input data for R
 scripts 
 Tree_analyses Files related to various
 stages of tree based analyses, including species trees
 Please see the included
 README file for further details.
DOI: 10.5061/dryad.rfj6q578t
title: Data from: Evolutionary constraints on tree size and aboveground biomass in tropical dry forests

description: 1. The extent (or lack) of phylogenetic signal for key ecological traits
 reveals the role of evolutionary processes on present-day ecosystem
 function and hints on future ecological trends under climate change
 scenarios. This approach has been applied to South American tropical moist
 forests, but not to the highly threatened seasonally dry tropical forests
 (SDTF), despite acknowledgement of their unique evolutionary history. To
 fill this knowledge gap, we investigated the legacy of evolutionary
 processes on vital ecological characteristics among SDTF trees: regional
 dominance, tree size and soil preference. 2. We used tree community data
 on 313 plots of SDTF (12.52 hectares) and locally collected soil data in
 central-eastern Brazil. For each assessed trait (three for regional
 dominance, three for tree size and nine for soil preference), we
 investigated the legacy of evolution using two different approaches:
 calculating the extent of phylogenetic signal and comparing the fit of
 four different models of evolution. 3. Aboveground woody biomass and tree
 size showed strong phylogenetic signal. Most of the SDTF biomass stock was
 concentrated in a few large-sized and closely related tree genera. Among
 the soil preference variables, only phosphorus displayed significant,
 albeit weak, phylogenetic signal. 4. Synthesis. Our study is the first to
 show that evolutionary constraints related to tree size significantly
 determine regional biomass stocks of SDTF in a few closely related tree
 lineages. This suggests that even isolated SDTF fragments with low
 taxonomic and phylogenetic diversity can play an important role in the
 global carbon cycle, storing disproportionally large amounts of carbon in
 trees that belong to high-biomass lineages. Whether these lineages also
 share climate change-induced mortality risk deserves future investigation,
 as they are largely responsible for the maintenance of regional SDTF
 biomass stocks.
description: This dataset is the result of multiple field trips carried out
 between 2009 and 2016 by members of the Laboratory of Phytogeography and
 Evolutionary Ecology, Department of Forest Sciences, Federal University of
 Lavras, Brazil. Tree community and soil data were pooled into the two
 spreadsheets presented here: one containing the variables related to
 ecological dominance, tree size and soil preference on the genus level and
 the other containing the same variables on the species level. We used
 these data to run phylogenetic signal analyses as described in the main
 text of the paper.
DOI: 10.5061/dryad.wpzgmsbkx
title: Antibody features towards VAR2CSA and CSA binding infected erythrocytes in a cohort of pregnant women from PNG

description: Plasmodium falciparum causes placental malaria, which results in adverse
 outcomes for mother and child. P. falciparum infected erythrocytes that
 express the parasite protein VAR2CSA on their surface can bind to
 placental chondroitin sulfate-A.  It has been hypothesized that
 naturally acquired antibodies towards VAR2CSA protect against placental
 infection, but it has proven difficult to use measures of antibody to
 identify individuals protected from disease. We used a systems serology
 approach to identify naturally acquired antibody features mid pregnancy
 that were associated with protection from placental malaria at
 delivery.  Machine learning techniques selected six out of 169
 measured antibody features towards VAR2CSA that could predict (with 86%
 accuracy) whether a woman would subsequently have active placental malaria
 infection at delivery. Selected features were associated with inhibition
 of placental binding and/or opsonic phagocytosis of infected erythrocytes,
 and network analysis indicated that there are not one but multiple
 pathways to protection from placental malaria.
description: 167 features towards chondroitin sulfate-A binding Plasmodium
 falciparum infected erythrocytes and individual domains of VAR2CSA
 recombinant protein were measured in 127 women at 14-26 gestation weeks. 
 Women were also grouped based on infection status at delivery.
 After acquisition of antibody feature measurements the data was
 processed.  The right-skewness of the distribution of the features was
 reduced by log-transformation (log(x+1)). Four antibody features that had
 negative values were right-shifted to have their minimum at zero prior to
 log-transformation. Next, the distributions of the features were centered
 and scaled to have zero mean and unit standard deviation.   0.82% of
 observations were missing and were imputed, multivariate Imputations by
 Chained Equations (van Buuren and Groothuis-Oudshoorn, 2011) with
 predictive mean matching was used to impute any missing values. The
 imputation process was repeated five times and the median of the imputed
 values across the five generated imputed datasets was finally used for
 each missing value.
description: A detailed description of all variables is included in the ReadMe
 files.
DOI: 10.25338/b8vs7t
title: Upper-tropospheric troughs and North American monsoon rainfall in a long-term track dataset

description: The North American monsoon (NAM) is frequently affected by transient,
 propagating upper tropospheric vorticity anomalies.  Sometimes
 called Tropical Upper Tropospheric Troughs (TUTTs), these features have
 been shown to episodically enhance monsoon rainfall.  Here we
 track long-lived TUTTs in 40 years of reanalysis data, producing
 composites and case studies from 340 TUTTs which last, on average, seven
 days as they move westward across the NAM region.  TUTTs are
 thought to form from midlatitude Rossby wave breaking; case studies from
 our dataset support this theory.  Composite TUTT cyclonic
 circulations are shown to stretch across about 10 degrees of longitude and
 extend from 100 hPa to 500 hPa.  In a composite sense, it is
 shown that TUTTs track westward due to interaction of the induced vertical
 wind with the vorticity structure.  Anomalous ascent wraps around
 the vortex center from the south at the surface to the east at the
 upper-tropospheric level of maximum vortex intensity.  The upper
 level ascent is consistent with that derived for an adiabatic
 quasi-geostrophic vortex at upper levels. The kinematics of TUTTs and
 their propagation in a region of climatologically strong moisture
 gradients results in a convergence of low-level moisture southeast of the
 vortex center.  TUTTs consequently can enhance anomalous
 precipitation to their southeast.  The intensity of TRMM-measured
 precipitation when precipitation occurs is higher both south and east of
 TUTTs while the likelihood of precipitation occurring is higher both south
 and northwest of TUTTs.
description: 3 files are included.  "TUTTs.mat" and
 "TUTTs.txt" are output as from TempestExtremes with all criteria
 from Igel et al. (2021) applied.  "StitchOutputfile.txt" is
 output as from the call below which includes disturbances which occur
 entirely in June and September.  
 This data was collected by running TempestExtremes with the
 following commands over the ERA5 dataset.  The TempestExtreme
 identification call is: DetectNodes --in_data_list Inputfile --out
 Outputfile --searchbymin “streamfunction” --minlat 15 --maxlat 40 --minlon
 -120 --maxlon -90 –noclosedcontourcmd “Z,325.,4.0,1.0” --mergedist 5.0 . 
 The command to stitch identified features in time is: StitchNodes --in
 Outputfile --out StitchOutputfile --maxgap 1 --minlength 67 --range
 5.0.
DOI: 10.5061/dryad.c866t1g5r
title: Weapon performance drives weapon evolution

description: Many sexually selected traits function as weapons, and these weapons can
 be incredibly diverse. However, the factors underlying weapon diversity
 among species remain poorly understood, and a fundamental hypothesis to
 explain this diversity remains untested. Although weapons can serve
 multiple functions, an undeniably important function is their role in
 fights. Thus, a crucial hypothesis is that weapon diversification is
 driven by the evolution of weapon modifications that provide an advantage
 in combat (e.g. causing more damage). Here, we test this
 fighting-advantage hypothesis using data from 17 species of coreid bugs.
 We utilize the fact that male-male combat in coreids often results in
 detectable damage, allowing us to link different weapon morphologies to
 different levels of damage among species. We find that certain weapon
 morphologies inflict much more damage than others, strongly supporting the
 fighting-advantage hypothesis. Moreover, very different weapon
 morphologies can inflict similarly severe amounts of damage, leading to a
 weapon-performance landscape with multiple performance peaks. This
 multi-peak pattern could potentially drive different lineages towards
 divergent weapon forms, further increasing weapon diversity among species.
 Overall, our results may help explain how sexually selected weapons have
 evolved into the diversity of forms seen today.
DOI: 10.5061/dryad.8931zcrpv
title: A preliminary phylogeny and review of the genus Tasmanitachoides, with descriptions of two new species (Coleoptera: Carabidae: Bembidarenini)

description: We review Tasmanitachoides Erwin, a genus of very small
 carabid beetles endemic to Australia. Although uncommon in collections, we
 found them to be abundant and diverse on banks of fine gravel or coarse
 sand next to bodies of fresh water; our samples from southeastern
 Australia suggest numerous undescribed species. We present an initial
 phylogenetic hypothesis for the genus, including 19 of the 32 species of
 which we are aware. The inferred phylogeny, based upon one mitochondrial
 and four nuclear genes, shows the kingi group to be
 sister to remaining Tasmanitachoides, with
 the wattsensis group and T.
 lutus (Darlington) also being phylogenetically isolated. We
 describe two new species: T. baehrisp. nov., from the Australian
 Capital Territory, is a member of
 the kingi group; T. erwini sp. nov.,
 from Tasmania, is a member of the wattsensis group.
 Identification tools for described and some undescribed species are
 presented, including photographs of all known
 species.   
description: Extracted DNA was subjected to PCR, and the products Sanger
 sequenced.  Maximum likelihood analysis was conducted using IQ-TREE
 .
DOI: 10.5061/dryad.8w9ghx3kz
title: Priority effects alter interaction outcomes in a legume-rhizobium mutualism

description: Priority effects occur when the order of species arrival affects final
 community structure. Mutualists often interact with multiple partners in
 different orders, but if or how priority effects alter interaction
 outcomes is an open question. In the field, we paired the legume Medicago
 lupulina with two nodulating strains of Ensifer bacteria that vary in
 nitrogen-fixing ability. We inoculated plants with strains in different
 orders and measured interaction outcomes. The first strain to arrive
 primarily determined plant performance and final relative abundances of
 rhizobia on roots. Plants that received effective microbes first and
 ineffective microbes second grew larger than plants inoculated with the
 same microbes in opposite order. Our results show that mutualism outcomes
 can be influenced not just by partner identity, but by interaction order.
 Furthermore, hosts receiving high-quality mutualists early can better
 tolerate low-quality symbionts later, indicating priority effects may help
 explain the persistence of ineffective symbionts.
description: The MedicagoJULY.csv is the main file with all data. The other
 included file has the data re-arranged (mostly in Mean and SE) for the
 purpose of making graphs. ReadMe file is included for header meanings and
 timeline of the experiment.
DOI: 10.5061/dryad.z612jm6b9
title: Factors influencing nature interactions vary between cities and types of nature interactions

description: 1. There is mounting concern that people living more urbanised, modern
 lifestyles have fewer and lower quality interactions with nature, and
 therefore have limited access to the associated health and wellbeing
 benefits. Yet, variation in the different types of nature interactions and
 the factors that influence these interactions across populations are
 poorly understood. 2. We compared four types of nature interactions by
 administering surveys across two cities that differ markedly in
 urbanisation pattern and population density—Singapore and Brisbane—: (i)
 indirect (viewing nature through a window at work or at home); (ii)
 incidental (spending time in nature as part of work); (iii) intentional
 interactions in gardens; and (iv) intentional interactions in public urban
 greenspaces. 3. Our results show that Singapore respondents spent about
 half as much time (25.8 hours per week) interacting with nature as
 Brisbane respondents (52.3 hours per week), and indirect interactions were
 the most prevalent across both cities. 4. Nature orientation, age, income
 and gender significantly predicted the duration of nature interactions in
 both cities, while self-reported health, education and ethnicity
 additionally predicted duration of nature interactions only for Brisbane.
 Also, the relationship(s) between each factor and duration could differ in
 direction and effect size between types of nature interactions. 5. As
 such, we conclude that there is much local variation in the dynamics of
 interactions between people and nature, and that focused studies are
 needed to develop effective interventions addressing declines in nature
 interactions in different locations.
description: Please refer to the readme.txt file, and the actual paper for
 more details.
DOI: 10.5061/dryad.1jwstqjtg
title: Diet variation driven by color vision phenotype in wild capuchin monkeys

description: The polymorphic color vision of platyrrhine monkeys is a fascinating
 example of balancing selection acting on multiple genetic and phenotypic
 morphs. Yet, the mechanism of natural selection maintaining this variation
 remains elusive. Past research has demonstrated task-specific foraging
 advantages to dichromatic (two-opsin vision, red-green colorblind) and
 trichromatic (three-opsin vision, human “normal”) monkeys, raising the
 potential for dietary niche differentiation. We ask whether color vision
 type influences diet variation in a population of wild, white-faced
 capuchins (Cebus imitator) in Costa Rica. To assess this, we record food
 intake during simultaneous focal follows of adult female dichromats and
 trichromats, and classify the conspicuity of diet items in capuchin visual
 space. We assess the degree of dietary and nutritional niche overlap
 during periods of high and low fruit abundance using nutritional geometry
 and Pianka’s index. We find that in months of high fruit abundance,
 trichromats have higher intake of conspicuously-colored fruits, while
 dichromats have higher intake of camouflaged invertebrates, resulting in
 lower niche overlap. These differences disappear in months of low
 habitat-wide fruit abundance, a time when overall dietary breadth
 collapses. Our results support the hypothesis that niche differentiation
 in diet contributes to maintaining color vision variation without
 compromising species-specific nutritional intake.
description: Files "Bite_data_no_fruit.csv",
 "Bite_data_fruit.csv", and
 "nutritional_intake_data.csv" are to be used in conjunction with
 the script "GLMMs_AmNat"  Files
 "nutritional_intake data.csv" and "food_RMT.csv" are
 to be used in conjunction with the script RMTs_AmNat 
 File "pianka_index_emm.csv" is to be used in
 conjunction with the script EMM_Niche_Overlap_AmNat and the EcoSimR
 Shell
DOI: 10.5061/dryad.3tx95x6fc
title: Safe abortion services during COVID pandemic in Nepal

description: Objective: To analyze the pattern of Safe Abortion Services at a
 tertiary healthcare center during the first six months of the COVID-19
 pandemic in Nepal. Study Design: This is a cross-sectional analytical
 study.We compared the pattern of safe abortion services between the first
 three months of the pandemic when a lockdown was implemented and the
 second three months when the lockdown was eased. Demographic and obstetric
 profile of women, their abortion choices, method of termination,
 difficulty in accessibility, and level of psychological distress were
 studied. Results: A total of 52 women were provided SAS during the study
 period. The number of women coming for SAS during lockdown was 47.1% less
 than that after easing of the lockdown. During the lockdown,
 women came at a later period of gestation with a mean of 9.5 weeks
 compared to 7.5 weeks in the later three months. Because of fear of
 COVID-19, 19.2% (n=10) women opted for termination of pregnancy. Increased
 need of contraception was felt but 40% (n=12) had problems of
 accessibility. More women had probable serious mental illness during the
 lockdown period (p=0.008). Conclusion: The lockdown during the pandemic
 decreased the number of women coming for SAS due to barriers in
 accessibility. Contraceptive needs are also increased but access is
 difficult. Medical abortion has been the more sought after method.
 Psychological distress is prevalent and fear of COVID-19 has become a
 common reason for termination of pregnancy.
description: Demographic
 and obstetric profile of these women, their abortion choices including
 reason fortermination of pregnancy and method of termination, difficulty
 they are facing relating to access to these services, and their level of
 psychological distress were studied. A self-designed proforma was used for
 data collection and interview technique was used. Interviews were taken by
 the attending gynecologist who underwent an orientation program before
 data collection. The Kessler psychological distress tool, “K-6
 tool,” which is a self-administered toolvalidated for Nepal, translated by
 experts in Nepali language. This tool was used to find the level of
 psychological distress. The K-6 tool is a 6-item self-report measure of
 psychological distress used to assess risk for serious mental illness in
 the general population answerable in 5 pointscale. Using a 30-day
 reference period, respondents rated how often they felt nervous, hopeless,
 restless or fidgety, so sad that nothing could cheer them up, that
 everything was an effort, and worthless. The number of women coming for SAS
 three months prior to the beginning of the lockdown was analyzed using
 hospital medical records. Data was
 entered and analyzed using Statistical Package for Social Sciences (SPSS)
 v16. Results are presented in mean and SD, percentages.Relationship
 between categorical data was analyzed using chi square test. P value of
 &lt;0.05 was considered as significant.
DOI: 10.5061/dryad.7wm37pvs3
title: Data for: Neural divergence and hybrid disruption between ecologically isolated Heliconius butterflies

description: The importance of behavioral evolution during speciation is well
 established, but we know little about how this is manifest in
 sensory and neural systems. A handful of studies have linked
 specific neural changes to divergence in host or mate preferences
 associated with speciation. However, the degree to which brains are
 adapted to local environmental conditions, and whether this contributes to
 reproductive isolation between close relatives that have diverged in
 ecology, remains unknown. Here, we examine divergence in brain morphology
 and neural gene expression between closely related, but ecologically
 distinct, Heliconius butterflies. Despite on-going gene
 flow, sympatric species pairs within
 the melpomene-cydno complex are consistently separated
 across a gradient of open to closed forest and decreasing light intensity.
 By generating quantitative neuroanatomical data for
 107 butterflies, we show that H.
 melpomene and H. cydno clades have substantial
 shifts in brain morphology across their geographic range, with divergent
 structures clustered in the visual system. These neuroanatomical
 differences are mirrored by extensive divergence in neural gene
 expression. Differences in both neural morphology and gene expression are
 heritable, exceed expected rates of neutral divergence, and
 result in intermediate traits in first generation hybrid offspring. Strong
 evidence of divergent selection implies local adaptation to distinct
 selective optima in each parental microhabitat, suggesting the
 intermediate traits of hybrids are poorly matched to either condition.
 Neural traits may therefore contribute to coincident barriers to
 gene flow, thereby helping to facilitate speciation.
description: Files provided include supplementary material from teh journal
 article, which contains volumetric data, and R scripts for replication of
 analyses and figures