cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z8w9ghx90
title: Diversity and predicted function of gut microbes from two species of viviparid snails

description: Animal gut bacteria are involved in numerous critical functions. In
 snails, gut bacteria play crucial roles in organic material digestion and
 nutrient production, and have been implicated in aspects of reproduction.
 Snail gut microbes are known to differ between species, and between
 anatomical compartments of the digestive tract; dietary changes are also
 known to alter snail gut flora. In an effort to better understand their
 diversity and function, we studied the gut microbial communities from two
 viviparid snails, Campeloma decisum and Cipangopaludina japonica. We were
 interested in whether significant differences in bacterial community
 composition existed between the two species, and whether differences in
 microbial diversity corresponded to differences in community function.
 Using next-generation sequencing of the bacterial 16S V4 region, we found
 no significant differences in alpha and beta diversity between Ca. decisum
 and Ci. japonica. Firmicutes and Proteobacteria were the most abundant
 bacterial phyla in both species, while Bacteroidetes had a higher mean
 abundance in Ci. japonica. Nine taxonomic groups were significantly
 different between the snail species. Pseudomonads and Enterobacteriaceae
 were notably more abundant in Ca. decisum, while Proteobacteria and
 Chitinophagaceae were more abundant in Ci. japonica. Peptidoglycan
 synthesis, pyruvate fermentation, and aerobic respiration by cytochrome c
 were the three most abundant microbial pathways represented in the
 viviparid gut. Fourteen functional pathways differed significantly between
 Ca. decisum and Ci. japonica, potentially correlated with differences in
 bacterial community composition and snail life history. Our data fill in
 data gaps regarding gut microbes in Viviparidae, and highlight future
 research paths examining the prevalence of Firmicutes and unidentified
 diversity in both snail species.
description: We acquired 14 <em>Cameploma decisum</em> and 13
 <em>Cipangopaludina japonica</em> collected from the Flat
 River in Lowell, Michigan (42.934°N, 85.339°W) that had been frozen live
 at -80°C. After removing bodies from shells, we rinsed the animals in
 deionized water and dissected out the intestines and posterior portion of
 the stomachs. We used the DNeasy PowerSoil (Qiagen) kit to extract
 microbial genomic DNA from the tissues following manufacturer’s
 directions. We sent the DNA samples to MrDNALab (Shallowater, TX) where
 the bacterial 16S V4 region was amplified by PCR (Caporaso et al. 2011)
 and sequenced on an Ion Torrent PGM (Thermo Fisher). MrDNALab performed
 the de-multiplexing, de-noising, and removal of chimeric sequences from
 the data.
description: The sequences are in FASTA format and have not been dereplicated
 or filtered. The leading characters in the title line of each sequence
 indicates the species and individual (e.g. Cd10 = <em>Ca.
 decisum</em> snail 10).
DOI: 10.5061/dryad.ngf1vhhrp
title: Association of CSF biomarkers with hippocampal-dependent memory in preclinical Alzheimer disease

description: Objective: To determine if memory tasks with demonstrated sensitivity to
 hippocampal function can detect variance related to preclinical
 Alzheimer’s disease (AD) biomarkers, we examined associations between
 performance in three memory tasks and CSF Ab42/Ab40 and p-tau181 in
 cognitively unimpaired older adults (CU). Methods: CU enrolled in the
 Stanford Aging and Memory Study (N=153; age 68.78 ± 5.81 yrs; 94 female)
 completed a lumbar puncture and memory assessments. CSF Ab42, Ab40, and
 phosopho-tau181 (p-tau181) were measured with the automated Lumipulse G
 system in a single-batch analysis. Episodic memory was assayed using a
 delayed recall composite, paired associate (word-picture) cued recall, and
 a mnemonic discrimination task that involves discrimination between
 studied ‘target’ objects, novel ‘foil’ objects, and perceptually similar
 ‘lure’ objects. Analyses examined cross-sectional relationships between
 memory performance, age, and CSF measures, controlling for sex and
 education. Results: Age and lower Ab42/Ab40 were independently associated
 with elevated p-tau181. Age, Ab42/Ab40, and p-tau181 were each associated
 with a) poorer associative memory and b) diminished improvement in
 mnemonic discrimination performance across levels of decreased task
 difficulty (i.e., target-lure similarity). P-tau mediated the effect of
 Ab42/Ab40 on memory. Relationships between CSF proteins and delayed recall
 were similar but non-significant. CSF Ab42 was not significantly
 associated with p-tau181 or memory. Conclusions: Tests designed to tax
 hippocampal function are sensitive to subtle individual differences in
 memory among CU, and correlate with early AD-associated biomarker changes
 in CSF. These tests may offer utility for identifying cognitively
 unimpaired older adults with preclinical AD pathology.
description: <strong>Supplemental Data</strong> 
 <b>Method e-1. </b>Tau PET imaging
 <b>Figure e-1: </b>SAMS Participant
 Flowchart <b>Figure e-2: </b>Gaussian
 Mixture Modelling <b>Figure e-3: </b>CSF
 Proteins vs. Medial Temporal Lobe Tau<b>  </b>
 <b>Figure e-4: </b>CSF Ab<sub>42</sub>
 Sample Characteristics<b> </b>
 <b>Figure e-5: </b>CSF Proteins vs. Associative
 <i>d’ </i>by Stimulus Category
 <b>Figure e-6: </b>CSF Proteins vs. Lure
 Discrimination Difference Scores <b>Table e-1:
 </b>Relationships between CSF Proteins and Individual Standardized
 Delayed Recall Test Scores
DOI: 10.5061/dryad.f1vhhmgtt
title: Data from: Hot spring frogs (Buergeria japonica) prefer cooler water to hot water

description: “Hot spring frog” is an informal name used for the Japanese stream tree
 frog (Buergeria japonica), which is widely distributed in Taiwan and the
 Ryukyu Archipelago in Japan. Some populations of the species are known to
 inhabit hot springs. However, water temperature can be extremely high
 around the sources of hot springs. Thus, it is questionable
 whether B. japonica selectively inhabits such dangerous
 environments. To address this question, we conducted a series of
 observations of water temperature preferences of a hot spring population
 of B. japonica in Kuchinoshima Island in Japan: (1) a
 field observation of tadpole density in water pools of different
 temperatures, (2) a field observation of water temperatures where adult
 males appear for breeding, and (3) an indoor observation of water
 temperatures selected by adult females for oviposition. As a
 result, tadpoles showed a higher density in cooler water. Adult males
 avoided water pools hotter than 37 °C, and adult females selected cooler
 pools for oviposition. Camera records also showed that adult individuals
 tend to appear around cooler pools. Thus, we did not find any support for
 the hypothesis that hot spring frogs prefer hot water. Conversely, they
 apparently tended to prefer cooler water if it was available. Water
 temperatures around the sources of the hot spring exceed thermal
 tolerances of the species and could be a strong selective pressure on the
 population. Thus, the ability to sense and avoid lethal temperatures may
 be a key ecological and physiological characteristic for the species that
 inhabit hot springs.
DOI: 10.5061/dryad.h9w0vt4g1
title: Intra-population genetic variation in the level and rhythm of daily activity in Drosophila immigrans

description: Genetic diversity within a population, such as polymorphisms and
 personality, is considered to improve population performance because such
 intraspecific variations have the potential to alleviate the competition
 for a limited resource or the risk of predation and sexual harassment at a
 population-level. Variation in the level and rhythm of daily activity in a
 population could also affect population performance by directly altering
 ecological, social, and sexual interactions among individuals. However, it
 remains to be elucidated whether such intra-population variation in the
 level and rhythms of daily activity exists in a natural population. Here,
 we investigated the genetic variation in daily activity within a single
 natural population of Drosophila immigrans. We established 21 isofemale
 lines from a single natural population, and measured larval activity level
 and the level and daily pattern of adult activity over a 24 h period.
 Larval activity level significantly varied among isofemale lines.
 Likewise, the activity level in the adult stage significantly varied among
 lines. The significant variation was also found in the daily pattern of
 adult activity; some lines showed greater activity level in the daytime,
 and others showed greater activity level in the night. Our results
 consistently suggest that there is a genetic variation in behavioral
 activity in a natural population, probably contributing to shaping the
 population performance.
DOI: 10.5061/dryad.2547d7wnq
title: Data from: Ageing and senescence across reproductive traits and survival in superb fairy-wrens (Malurus cyaneus)

description: Why do senescence rates of fitness-related traits often vary dramatically?
 By considering the full ageing trajectories of multiple traits we can
 better understand how a species’ life-history shapes the evolution of
 senescence within a population. Here, we examined age-related changes in
 sex-specific survival, reproduction, and several components of
 reproduction using a long-term study of a cooperatively-breeding songbird,
 the superb fairy-wren (Malurus cyaneus). We compared ageing patterns
 between traits by estimating standardized rates of maturation, the age of
 onset of senescence, and rates of senescence, while controlling for
 confounding factors reflecting individual variability in life-history. We
 found striking differences in ageing and senescence patterns between
 survival and reproduction, as well as between reproductive traits. In both
 sexes, survival started to decline from maturity onwards. In contrast, all
 reproductive traits showed improvements into early adulthood, and many
 showed little or no evidence of senescence. In females, despite senescence
 in clutch size, number of offspring surviving to independence did not
 decline in late life, possibly due to improvements in maternal care with
 age. Superb fairy-wrens have exceptionally high levels of extra-group
 paternity, and male extra-group reproductive success showed much greater
 changes with age than did within-group reproductive success, suggesting
 that male reproductive ageing is driven by sexual selection. We discuss
 how the superb fairy-wrens’ complex life history may contribute to the
 disparate ageing patterns across different traits.
description: This dataset has been
 collected on a wild population of superb fairy-wrens located in and around
 the Australian National Botanic Gardens, Canberra, Australia (35°16 S,
 149°06 E) that has been intensively monitored since 1988. The study site,
 approximately 60 ha in area, contains 40-90 territories encompassing
 between 120-230 year-round resident adults. In this study, we used data
 from the years 1988-2017.
DOI: 10.5061/dryad.j0zpc86bx
title: Don’t judge a lizard by its colour: no evidence for differential socio-sexual behaviour and space use in the colour morphs of the European common wall lizard (Podarcis muralis)

description: Explaining the evolutionary origin and maintenance of colour polymorphisms
 is a major challenge in evolutionary biology. Such polymorphisms are
 commonly thought to reflect the existence of alternative behavioural or
 life-history strategies under negative frequency-dependent selection. The
 European common wall lizard Podarcis muralis exhibits a striking ventral
 colour polymorphism that has been intensely studied and is often assumed
 to reflect alternative reproductive strategies, similar to the iconic
 “rock-paper-scissors” system described in the North American lizard Uta
 stansburiana. However, available studies so far have ignored central
 aspects in the behavioural ecology of this species that are crucial to
 assess the existence of alternative reproductive strategies. Here we try
 to fill this gap by studying the social behaviour, space use, and
 reproductive performance of lizards showing different colour morphs, both
 in a free-ranging population from the eastern Pyrenees and in ten
 experimental mesocosm enclosures. In the natural population, we found no
 differences between morphs in site-fidelity, space use or male-female
 spatial overlap. Likewise, colour morph was irrelevant to socio-sexual
 behaviour, space use, and reproductive success within experimental
 enclosures. Our results contradict the commonly held hypothesis that P.
 muralis morphs reflect alternative behavioural strategies, and suggest
 that we should instead turn our attention to alternative functional
 explanations.
DOI: 10.5061/dryad.qnk98sfd8
title: Data from: Latitudinal patterns of alien plant invasions

description: Latitudinal patterns of biodiversity have long been a central topic in
 ecology and evolutionary biology. However, while most previous studies
 have focused on native species, little effort has been devoted to
 latitudinal patterns of plant invasions (with a few exceptions based on
 data from sparse locations). Using the most up-to-date worldwide native
 and alien plant distribution data from 801 regions (including islands), we
 compared invasion levels (i.e. alien richness/total richness) in the
 Northern and Southern Hemispheres and across continental regions and
 islands around the globe. Results from quantile regressions using
 B-splines to model nonlinearity showed (1) declining richness with
 increasing latitude, although the highest alien richness occurs at around
 40 degrees in both hemispheres, (2) decreasing invasion levels towards
 higher latitudes on islands but a unimodal pattern in invasion level in
 continental regions in each hemisphere, (3) significantly higher invasion
 levels on islands than in continental regions, and (4) a greater
 variability in invasThrough field observations and published records
 (e.g., literature search).ion levels on islands at low latitudes than on
 high-latitude islands. In continental regions, only the mid-latitudes had
 high variability with both low and high invasion levels. Our findings
 identified latitudes with invasion hotspots where management is urgently
 needed, and latitudes with many areas of low invasions but high
 conservation potential where prevention of future invasions should be the
 priority.
description: Through field observations and published records (e.g.,
 literature search).
description: The dataset excludes the regions/islands for which the native
 species richness is not certain. Invasion level was
 calculated as "aliens/(aliens + natives)". We
 included 4 files: 1) A file with the complete dataset
 ("Appendix I_801 sites.csv"),  2) A file with
 R code ("Guo.etal2020.R.scripts"), 3) A
 file for running R ("Essl.SppRichness.csv") for richness data,
 and 4) A file for running R ("Essl.2019.csv")
 for invasion level data.
DOI: 10.5061/dryad.vhhmgqnr8
title: Macroevolutionary patterns of body plan canalization in euarthropods

description: Reconstructing patterns of macroevolution has become a central endeavor in
 palaeobiology, because it offers insight into evolutionary models shaping
 the history of life. As the most diverse and abundant animals since the
 Cambrian period, arthropods provide copious data to elucidate the
 emergence of body plans in metazoan lineages. However, information
 provided by fossils on the tempo and mode of this phenomenon has lacked a
 recent synthesis. Here, I investigate macroevolutionary patterns of
 morphological evolution in Euarthropoda using a combined extinct and
 extant dataset optimized for multivariate analyses. Overall ordination
 patterns between the main morphogroups are consistent with another,
 independently-coded, extant-only dataset providing molecular and
 morphological rates of evolution. Based on a “deep split” phylogenetic
 framework, total-group Mandibulata and Arachnomorpha emerge as directional
 morpho-anatomical lineages, with basal fossil morphogroups showing
 heterogeneously spread-out occupations of the morphospace. In addition to
 a more homogeneous morphological variation, new morphogroups arose by
 successive reductions of translation distances; this pattern was
 interrupted only by terrestrialization events and the origin of
 pancrustaceans. A displaced optimum type of model is proposed to explain
 the fast assembly of canalized body plans during the Cambrian, with basal
 fossil morphogroups fitting intermediate fitness peaks in a moving
 adaptive landscape. Given time constraints imposed by the palaeontological
 evidence, and owing to the interplay between canalization and modularity,
 as well as a decoupling between molecular and morphological rates, the
 rise of euarthropods would support the view that the swiftness of the
 Cambrian explosion was mostly associated with the build-up of genetic
 regulatory networks.
DOI: 10.5061/dryad.1g1jwstsv
title: Plant genotypic diversity effects on soil nematodes vary with trophic level

description: At local spatial scales, loss of genetic diversity within species can lead
 to species loss. Few studies, however, have examined plant genotypic
 diversity effects across trophic levels. We investigated genotypic
 diversity effects of Phragmites australis on belowground biomass and soil
 nematode communities. Our results revealed belowground plant biomass and
 nematode abundance responses to plant genotypic diversity were uncoupled.
 Decreasing plant genotypic diversity decreased the abundance of lower, but
 not higher trophic level nematodes. Low plant genotypic diversity also
 decreased the structural footprint and functional indices of nematodes,
 indicating lowered metabolic functioning of higher-trophic level nematodes
 and decreased soil food web stability. Our study suggests that plant
 genotypic diversity effects differ across trophic levels, taxonomic
 groups, and ecosystem functions and that decreasing plant genotypic
 diversity could destabilize belowground food webs. This highlights the
 importance of conserving intraspecific plant diversity.
description: Belowground plant material was washed immediately, oven dried at
 50°C to constant weight and weighed. Nematodes were counted, identified
 (100 randomly-selected individuals per plot or all individuals if fewer
 than 100) to genus level using ×1000 magnification and classified into
 four feeding groups. Nematode abundance was expressed as individuals per
 100 g dry weight (DW) soil, diversity was expressed as the genera richness
 and Shannon–Wiener Diversity Index at the genus level
 (<i>H</i>′ diversity).
DOI: 10.5061/dryad.sj3tx962p
title: Dynamic visual noise promotes social attraction in a shoaling fish

description: Gathering information from the environment allows animals to make informed
 behavioural decisions, with individuals sampling information either
 privately, or via social cues from group members. Because environmental
 noise can disrupt the ability of animals to gather information from their
 environment, social behaviour could be disrupted by environmental noise,
 or adapted to mitigate the costs and risks associated with compromised
 perception in noisy environments. Here we test how the presence of water
 caustics, a natural form of visual noise prevalent within shallow aquatic
 habitats, affects the social decisions of shoaling fish. In a classic
 experimental paradigm, individual three-spined sticklebacks (Gasterosteus
 aculeatus), were given a choice between associating with two conspecific
 shoals differing in size while immersed in different levels of visual
 noise. While the presence of visual noise did not affect the preference of
 individual fish to associate with the larger of the two shoals, fish
 showed greater social attraction to conspecifics as noise levels
 increased, measured by a reduction in the distance they kept from the
 shoals. Our findings suggest that when the ability of individuals to
 extract visual information from their environment becomes more
 challenging, fish increase their reliance on social interactions,
 potentially to mitigate the consequences of having reduced perceptual
 abilities in noisy environments.
DOI: 10.5061/dryad.3n5tb2rf3
title: Haplotype-based genome-wide association increases the predictability of leaf rust (Puccinia triticina) resistance in wheat

description: Resistance breeding is crucial for a sustainable control of wheat leaf
 rust and SNP-based genome-wide association studies (GWAS) are widely used
 to dissect leaf rust resistance. Unfortunately, GWAS based on SNPs
 explained often only a small proportion of the genetic variation. We
 compared SNP-based GWAS with a method based on functional haplotypes (FH)
 considering epistasis in a comprehensive hybrid wheat mapping population
 composed of 133 parents plus their 1,574 hybrids and characterized with
 626,245 high-quality SNPs. In total, 2,408 and 1,139,828 significant
 associations were detected in the mapping population by using SNP-based
 and FH-GWAS, respectively. These associations mapped to 25 and 69
 candidate regions, correspondingly. SNP-based GWAS highlighted two
 already-known resistance genes, i.e. Lr22a and Lr34-B, while FH-GWAS not
 only detected associations on these genes but also on two additional
 genes, i.e. Lr10 and Lr1. As revealed by a second hybrid wheat population
 for independent validation, using detected associations from SNP-based and
 FH-GWAS reached predictabilities of 11.72% and 22.86%, respectively.
 Therefore, FH-GWAS is not only more powerful to detect associations, but
 also improves the accuracy of marker-assisted selection as compared to the
 SNP-based approach.