cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ffbg79cz0
title: Greater variability in rhesus macaque (Macaca mulatta) endocranial volume among males than females

description: The greater male variability (GMV) hypothesis proposes that traits are
 more variable among males than females, and is supported by numerous
 empirical studies. Interestingly, GMV is also observed for human brain
 size and internal brain structure, a pattern which may have implications
 for sex-biased neurological and psychiatric conditions. A better
 understanding of neuroanatomical variability in nonhuman primates may
 illuminate whether certain species are appropriate models for these
 conditions. Here, we tested for sex differences in the variability of
 endocranial volume (ECV, a proxy for brain size) in a sample 542 rhesus
 macaques (Macaca mulatta) from a large pedigreed free-ranging population.
 We also examined the components of phenotypic variance (additive genetic
 and residual variance) to tease apart the potential drivers of sex
 differences in variability. Our results suggest that males exhibit more
 variable ECVs, and that this pattern reflects either balancing/disruptive
 selection on male behaviour (associated with alternative male mating
 strategies) or sex chromosome effects (associated with mosaic patterns of
 X chromosome gene expression in females), rather than extended
 neurodevelopment among males. This represents evidence of GMV for brain
 size in a nonhuman primate species and highlights the potential of rhesus
 macaques as a model for sex-biased brain-based disorders.
DOI: 10.5061/dryad.ht76hdrjs
title: The phylogeny of Errazurizia (Fabaceae: Amorpheae) and description of the new monotypic genus Pictarena

description: Errazurizia (Fabaceae) is a genus comprised of four species of New World
 desert shrubs with an ambiguous evolutionary history. Prior studies
 determined the North American species of Errazurizia were polyphyletic and
 the relationship of E. rotundata with other genera in the tribe Amorpheae
 remained undetermined. The sole South American species, which is also the
 type species, has never been included in a molecular study. We inferred
 the phylogenetic relationships of Errazurizia and six closely related
 genera using data from the cpDNA genome and nrDNA cistron from
 reference-guided assemblies. Maximum likelihood and Bayesian analyses
 found two of the North American and the South American species were a
 monophyletic group, but that E. rotundata was sister to the monotypic
 genus Parryella. Gland and pollen surface characters confirm the close
 relationship between P. filifolia and E. rotundata. Cytonuclear
 discordance yielded partially incongruent tree topologies, and while the
 cpDNA phylogeny indicated a monophyletic Amorpha was sister to the E.
 rotundata and P. filifolia clade, the nrDNA cistron phylogeny recovered a
 paraphyletic Amorpha, with A. californica sister to the E. rotundata and
 P. filifolia clade. Molecular and morphological evidence support the
 elevation of E. rotundata to its own monotypic genus, Pictarena. The new
 genus Pictarena is defined by subsessile, suborbicular leaflets, mammiform
 leaflet glands, spicate inflorescences, and flowers with either all petals
 absent or rarely with a banner petal. Elevating E. rotundata to Pictarena
 resolves the confusing classification of the species, an imperiled endemic
 known only from four localities in northern Arizona and lends support for
 continued conservation.
DOI: 10.5061/dryad.41ns1rnhk
title: Predation and parasitism as determinants of animal personalities

description: 1. Within the same population, proactive (i.e. bolder, more exploratory,
 active and aggressive) and reactive (i.e. more timid, less exploratory,
 less active and more passive) individuals could be hypothetically
 maintained due a trade-off between foraging and anti-predator behaviour,
 provided that both phenotypes differ in their state (e.g. metabolic rates,
 body condition or energetic needs). 2. Yet, recent findings indicate that
 among-individual variation in intrinsic state can explain only a small
 proportion of variation in behaviour, meaning that other mechanisms, such
 as the presence of trophically transmitted parasites, might contribute to
 maintaining inter-individual behavioural differences. Empirical evidence,
 indeed, suggests strong relationships between certain animal personality
 traits and parasitic load within host populations. However, the direction
 of causation between these traits remains unclear: are different
 behaviours in infected hosts in contrast to uninfected ones the result of
 manipulation by parasites to increase host predation, or are some
 personalities inherently more susceptible to infection than others? 3. To
 better understand the role of parasites in shaping behavioural differences
 within host populations and examine to what extent parasite manipulation
 and/or intrinsic differences in parasite susceptibility contribute to
 maintaining behavioural differences, we used a simulation approach and
 analyzed the change in the frequencies of proactive and reactive
 individuals over time under different predation and starvation scenarios,
 when individual phenotype either affected a host’s risk of infection or
 not. 4. We found that in the absence of parasites, predation pressure
 strongly affected the expression of host personality, but trade-offs
 between foraging and anti-predator behaviour alone could not explain the
 maintenance of inter-individual behavioural differences without temporal
 variation in predation pressure. By contrast, in the presence of
 parasites, the two host phenotypes could coexist within populations even
 when individuals experienced no temporal variations in predation risk, but
 only when proactive and reactive hosts were equally susceptible to
 parasitism. 5. Our findings thus indicate that parasites can play an
 important role in maintaining genetic diversity in their host populations
 in addition to generating behavioural differences though manipulation.
description: The simulation codes were written in C++.
DOI: 10.7280/d11q30
title: Data for: Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes

description: Municipal wastewater provides a representative sample of human fecal waste
 across a catchment area and contains a wide diversity of microbes.
 Sequencing wastewater samples provides information about human-associated
 and medically-important microbial populations, and may be useful to assay
 disease prevalence and antimicrobial resistance (AMR). Here, we present a
 study in which we used untargeted metatranscriptomic sequencing on RNA
 extracted from 275 sewage influent samples obtained from eight wastewater
 treatment plants (WTPs) representing approximately 16 million people in
 Southern California between August 2020 – August 2021. We characterized
 bacterial and viral transcripts, assessed metabolic pathway activity, and
 identified over 2,000 AMR genes/variants across all samples. Because we
 did not deplete ribosomal RNA, we have a unique window into AMR carried as
 ribosomal mutants. We show that AMR diversity varied between WTPs and that
 the relative abundance of many individual AMR genes/variants increased
 over time and may be connected to antibiotic use during the
 COVID-19 pandemic. Similarly, we detected transcripts mapping to human
 pathogenic bacteria and viruses suggesting RNA sequencing is a powerful
 tool for wastewater-based epidemiology and that there are geographical
 signatures to microbial transcription. We captured the transcription of
 gene pathways common to bacterial cell processes, including central carbon
 metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We
 also posit that due to the ubiquity of many viruses and bacteria in
 wastewater, new biological targets for microbial water quality assessment
 can be developed. To the best of our knowledge, our study provides the
 most complete longitudinal metatranscriptomic analysis of a large
 population’s wastewater to date and demonstrates our ability to monitor
 the presence and activity of microbes in complex samples . By sequencing
 RNA, we can track the relative abundance of expressed AMR genes/variants
 and metabolic pathways, increasing our understanding of AMR activity
 across large human populations and sewer sheds.
DOI: 10.5061/dryad.dncjsxm2x
title: Global analysis of environmental and socioeconomic factors associated with human burden of environmentally mediated pathogens

description: This repository contains four datasets that support repeatability of the
 analyses in the Sokolow et al. paper published in Lancet Planetary Health.
 Descriptions of the four datasets are included in the metadata document.
 This study found that 80% of pathogen species known to infect humans are
 environmentally mediated, causing about 40% of contemporary
 infectious-disease burden (global loss of 130 million years of healthy
 life annually). More than 91% of this environmentally-mediated disease
 burden occurs in tropical countries, and the poorest countries carry the
 highest burdens across all latitudes. There were weak associations between
 disease burden and biodiversity or agricultural land use at the global
 scale. In contrast, the proportion of people with rural poor livelihoods
 in a country was a strong proximate indicator of environmentally mediated
 infectious disease burden there. Political stability and wealth were
 associated with improved sanitation, better health care, and lower
 proportions of rural poverty, indirectly resulting in lower burdens of
 environmentally mediated infections."
description: We started with a full list of 560 named
 pathogens (from 197 genera) associated with the World Health
 Organization’s tracked pathogens within category I.A: “Communicable,
 maternal, perinatal and nutritional conditions: Infectious and parasitic
 diseases” of the World Health Organization’s Global Burden of Disease
 Estimates from 2015. Next, to account for potential biases that result
 from the selection of pathogens that the WHO tracks, we also examined the
 transmission strategies of a random subsample of 250 pathogens (using a
 random number generator to select pathogens from the full list of 1415
 described human pathogen species) compiled by Taylor et al. in 2001, which
 is dominated by rare, opportunistic pathogens. By chance, 87 pathogens
 (from 57 genera) ended up in both the WHO and Taylor subsets (&lt;15%
 overlap) with the remaining pathogens unique to each list. Across both
 datasets, we assessed 723 unique human pathogen species (from 292 genera)
 in total. To quantify the global
 burden caused by environmentally mediated infections, we examined the WHO
 Global Health Estimates data for 2015. This dataset measures disease
 burden in all countries around the world using disability adjusted life
 years (DALYs), a standard metric for measuring the impact of disease on
 human well-being. DALYs are calculated as the sum of “years of life lost
 due to mortality” and “years of healthy life lost due to disability.”
 Burden data were available for a subset of 153 WHO pathogens, categorized
 into 51 tracked disease categories.
description: description of data reported in
 README_Metadata_for_Sokolow_et_al_LPH.rtf All the other
 files are csv format, namely: -
 723Pathogens_EMDorDTD_Sokolowetal.csv -
 SEMAnalysis_CountryLevel_Sokolowetal.csv -
 WHO_GHE_2000_2015.csv -
 WHO_GHEData_2015_Country.csv
DOI: 10.5061/dryad.547d7wmc1
title: Data from: Controlled drainage and subirrigation suitability in the United States: A meta-analysis of crop yield and soil moisture effects

description: Controlled drainage and subirrigation (CDSI) is an important water
 management strategy in many regions, but the conditions under which CDSI
 is most likely to increase crop yield and soil moisture are not
 fully understood. A meta-analysis, consisting of 154 pairwise
 observations from replicated and randomized trials in 30 peer-reviewed
 primary research articles on CDSI (6 controlled drainage, 24
 CDSI, analyzed together due to data scarcity), was conducted to
 study the responses of yield and soil moisture to CDSI, and
 investigate how crop type, soil texture, and cumulative growing
 season precipitation (PGS) influence these responses. Based
 on the yield response to these moderating factors, we used a
 fuzzy-logic approach to map potentially suitable locations for CDSI in the
 conterminous United States. On average, CDSI increased yield by
 8.0% (95% CI = 1.8–14.7%) compared with conventional free
 drainage. The yield response to CDSI did not differ among
 crops. However, a greater yield response to CDSI was observed in
 medium-textured soils (19.4% increase; 95% CI = 12.4–27.0%) than
 in coarse- or fine-textured soils. The positive effect of CDSI on
 yield increased with decreasing PGS in coarse-
 and medium-textured soils. There was no clear effect of CDSI on
 soil moisture, nor did any moderators influence this
 relationship, though this may be attributed to the scarcity of
 studies on CDSI reporting soil moisture. The fuzzy-logic-based
 approach revealed that while potentially suitable areas are
 mostly concentrated in the well studied U. S. Midwest, these
 areas also exist in other regions where CDSI may warrant further
 study.
description: This data is extracted from the published peer reviewed research
 articles on controlled drainage and subirrigation from 1990 to
 2020. Additional information can be found in Singh, N.,
 Kogan, C., Chaudhary, S., Rajagopalan, K., & LaHue, G. T. (2022).
 Controlled drainage and subirrigation suitability in the United States: A
 meta-analysis of crop yield and soil moisture effects. Vadose
 Zone Journal, e20219. https://doi.org/10.1002/vzj2.20219
description: MS-Excel R software  ArcGIS
 pro software
DOI: 10.5061/dryad.573n5tb9t
title: Data from: Phylogeography and classification of Dusty Miller (Spyridium parvifolium; Rhamnaceae): a morphologically variable shrub from south-east Australia

description: Spyridium parvifolium is a widespread and morphologically variable shrub
 from south-eastern Australia. Several varieties have been recognised and
 there is disagreement on the accepted taxonomy between Australian states.
 This study investigated the phylogeography of the species and assessed
 genetic distinctiveness of its morphological variants. Nuclear ribosomal
 DNA and complete chloroplast genomes from seventy-three samples of S.
 parvifolium and seven samples from closely related species were sequenced
 and analysed using both Bayesian and Maximum Likelihood phylogenetic
 methods. The results showed incongruence in the placement of several
 associated taxa (S. cinereum, S. obcordatum and S. daltonii), plausibly
 due to long-branch attraction, introgression or incomplete lineage
 sorting. Spyridium parvifolium was resolved as paraphyletic in both
 phylogenies, with accessions from west of the Murray Darling Depression
 divergent from those east of the Depression. We found evidence of
 isolation within S. parvifolium on the inland side of the Great Dividing
 Range, and recent gene-flow across Bass Strait. The variants of S.
 parvifolium were not supported as genetically distinct and, with the
 prevalence of several variants at single sites and morphological
 intergrades between variants, we conclude that the taxon is a single,
 morphologically variable species and that no infraspecific classification
 is warranted.
DOI: 10.15468/dl.y7vhsc
title: Occurrence Download

description: A dataset containing 4985 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((94.54239 51.42724,97.33633 51.42724,97.33633 52.54338,94.54239 52.54338,94.54239 51.42724))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingCountry is Russian Federation"
 ]
}

 The dataset includes 4985 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003175-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.gxd2547q1
title: Ecological drivers of avian diversity in a subtropical landscape: effects of habitat diversity, primary productivity and anthropogenic disturbance

description: Understanding the roles of ecological drivers in shaping biodiversity is
 fundamental for conservation practice. In this study, we explored the
 effects of elevation, conservation status, primary productivity, habitat
 diversity, and anthropogenic disturbance (represented by human population
 density and birding history) on taxonomic, phylogenetic and functional
 avian diversity in a subtropical landscape in southeastern China. We
 conducted bird surveys using 1-km transects across a total of 30 sites, of
 which 10 sites were located within a natural reserve. Metrics of
 functional diversity were calculated based on six functional traits (body
 mass, clutch size, dispersal ratio, sociality, diet and foraging stratum).
 We built simultaneous autoregression models to assess the association
 between the ecological factors and diversity of the local avian
 communities. Local avian diversity generally increased with increasing
 habitat diversity, human population density and primary productivity. We
 also detected phylogenetic and functional clustering in these communities,
 suggesting that the avian assemblages were structured mainly by
 environmental filtering, rather than interspecific competition. Compared
 to sites outside the natural reserve, sites within the natural reserve had
 relatively lower avian diversity but a higher level of phylogenetic
 heterogeneity.
DOI: 10.5061/dryad.wstqjq2px
title: Spatial and temporal resource partitioning in a mixed-species colony of avian echolocators

description: Resource partitioning may facilitate the coexistence of sympatric species
 with similar ecological requirements. Here, we study a colony of unusual
 echolocating birds called swiftlets, which nest underground on an island
 off the coast of Singapore. The colony comprises two congeneric swiftlet
 species, black-nest swiftlets (Aerodramus maximus) and edible-nest
 swiftlets (A. fuciphagus), nesting at high densities and in close
 proximity. Bioacoustic recordings and monitoring of nesting biology at the
 site across multiple seasons revealed significant differences in
 echolocation calls as well as survival rates between the species, with the
 larger black-nest swiftlet nesting at locations with the highest fledging
 rates. We also observe an additional off-season breeding peak by the
 smaller species, the edible-nest swiftlet. Unexpectedly, off-season egg
 hatching rates were significantly higher compared to rates during the
 shared breeding season (mean difference = 14%). Our study on the breeding
 biology of these echolocating cave-dwelling birds provides an example of
 spatial and temporal strategies that animals employ to partition resources
 within a confined habitat.
DOI: 10.5061/dryad.mpg4f4r2w
title: Aconitum specimens sampled in the Dolina Małej Łąki valley (ML) and Dolina Miętusia valley (DM) in the Tatra Mountains

description: In this study, our objection was to identify the extent of introgression
 between Aconitum species in a narrow mountain hybrid zone in the Tatra
 Mountains (West Carpathians, Poland). We expected that mountain topography
 may affect the genetic structure of the populations and hampered the
 interspecific gene flow. We used inter-simple sequence repeat (ISSR)
 molecular markers and chloroplast DNA (cpDNA) sequencing. The results
 revealed that the diploid and tetraploid species have different cpDNA
 haplotypes, and the triploid hybrid has a tetraploid cpDNA marker.
 Populations in adjacent mountain valleys were genetically different (FST =
 0.129, p &lt; 0.001). Principal coordinate analysis (PCoA),
 neighbor-net clustering (NN), and Bayesian inference showed genetic
 introgression between the diploid species and its taxonomic hybrid within
 the same valleys. In introgressants, no morphological changes were
 observed  compared to those of pure species. Three specimens of
 the tetraploid species (of a total of 9) had a genetic admixture of the
 diploids in an open subalpine/alpine landscape. Furthermore, in three
 diploids (of a total of 37) the introgression from the tetraploid was
 observed. We infer that the introgression between various levels of ploidy
 may have been through a triploid bridge.
description: The creation of a calibration curve based on the
 length band pattern of markers (GeneRuler TM 100 bp - Fermentas) allowed
 the determination of the molecular weight of the resulting amplification
 products. PCR products
 were analyzed with the application of sofware GelScan ver. 1.45 (Kucharczyk TE), based on this
 the  binary
 matrix of sample was
 generated (presence of PCR
 product - 1, absence of PCR product - 0).
DOI: 10.5061/dryad.4qrfj6qd0
title: Red‐backed shrike (Lanius collurio) versus common cuckoo (Cuculus canorus): An example of ineffective cuckoo–hawk mimicry

description: The red-backed shrike (Lanius collurio) used to be one of the most common
 hosts of the common cuckoo (Cuculus canorus). Nevertheless, during the
 last 30 years, there is increasing evidence from Central Europe that the
 occurrence of cuckoo chicks in shrike nests has become scarcer, and that
 in some locations they have disappeared completely. Multiple hypotheses
 have been suggested to explain this abandonment. Here, we test the
 hypothesis that shrikes vigorously attack adult cuckoos, potentially
 resulting in ineffective parasitism. Adult common cuckoos resemble in
 appearance the Eurasian sparrowhawk (Accipiter nisus), a common predator
 of small passerines. One hypothesis presumes that the cuckoo has evolved
 this mimicry to avoid attack by small passerines when searching for their
 nests. Our results show that shrikes defending their nests attacked
 cuckoos very vigorously, more often and more intensively than they did
 sparrowhawks. In the presence of a sparrowhawk dummy, parent shrikes only
 produced alarm calls and flew over the dummy. This suggests that
 cuckoo-hawk mimicry is ineffective in the case of shrikes and that they
 attack them much more often than they do any other presented intruder.
 Therefore, this activity could possibly result in the abandonment of
 shrikes as potential hosts for cuckoos.