cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9cnp5hqp9
title: Data for: Distance and density dependence in two native Bornean dipterocarp species

description: The Janzen-Connell hypothesis proposes that density and distance-dependent
 mortality generated by specialist natural enemies prevent competitive
 dominance. Much literature on Janzen Connell mechanisms comes from the
 neotropics, and evidence of the role of distance and density-dependence is
 still relatively sparse. We tested the predictions of the J-C hypothesis
 in a South-East Asian system dominated by mast fruiting species. We
 hypothesized that seedling survival would decrease with distance and
 density, seedling growth would increase, and herbivory would decrease,
 according to the predictions of the Janzen-Connell hypothesis. Experiments
 were conducted to determine the strength of the Janzen Connell mechanism
 by manipulating the density and identity of tree species as a function of
 the distance from parent trees. Survival of conspecific seedlings was
 reduced near adult trees of one species, but not another. High densities
 of seedlings decreased the growth of conspecific seedlings of both
 species. In both species, herbivory rates decreased with distance in
 low-density areas. This study indicates that dipterocarp species
 experienced weak Janzen-Connell effects of distance and density dependence
 at the growth stage studied. Future studies in this system might focus on
 earlier life-history stages such as seeds and small seedlings, as well as
 studying mortality during mast-seeding events.
description: This dataset was collected by data from our experiment that
 manipulated the density and type of tree species (<em>Parashorea
 malaanonan</em> and <em>Shorea johorensis</em>) as a
 function of the distance from conspecific adult trees. We experimentally
 tested the strength of the Janzen-Connell hypothesis in these two native
 dipterocarp species.
description: All statistical analyses were conducted in the statistical
 software environment R.
DOI: 10.5061/dryad.z34tmpgk2
title: Data for: Generalist invasion in a complex lake food web

description: Invasive species constitute a threat not only to native populations but
 also to the structure and functioning of entire food webs. Despite being
 considered as a global problem, only a small number of studies have
 quantitatively predicted the food web‐level consequences of invasions.
 Here, we use an allometric trophic network model parameterized using
 empirical data on species body masses and feeding interactions to predict
 the effects of a possible invasion of Amur sleeper (Perccottus glenii), on
 a well‐studied lake ecosystem. We show that the modeled establishment of
 Amur sleeper decreased the biomasses of top predator fishes by about
 10%–19%. These reductions were largely explained by increased larval
 competition for food and Amur sleeper predation on fish larvae. In
 contrast, biomasses of less valued fish of lower trophic positions
 increased by about 0.5%–9% owing to reduced predation pressure by top
 piscivores. The predicted impact of Amur sleeper establishment on the
 biomasses of native fish species vastly exceeded the impacts of
 current‐day fishing pressures.
DOI: 10.5061/dryad.jwstqjqff
title: RNA-seq data for an embryonic chicken digit tissue time-series, treated in vivo with smoothened agonist to induce ectopic feathers

description: Vertebrate skin appendage early development is mediated by conserved
 molecular signalling composing a dynamical reaction-diffusion-like system.
 Variations to such systems contribute to the remarkable diversity of skin
 appendage forms within and among species. Here, we demonstrate that
 stage-specific transient agonism of sonic hedgehog (Shh) pathway
 signalling in chicken triggers a complete and permanent transition from
 reticulate scales to feathers on the ventral surfaces of the foot and
 digits. Resulting ectopic feathers are developmentally comparable to
 feathers adorning the body, with down-type feathers transitioning into
 regenerative, bilaterally symmetric contour feathers in adult chickens.
 Crucially, this spectacular transition of skin appendage fate (from
 nodular reticulate scales to bona-fide adult feathers) does not require
 sustained treatment. Our RNA-sequencing analyses confirm that SAG
 treatment specifically promotes the expression of key Shh
 pathway-associated genes. These results indicate that variations in Shh
 pathway signalling likely contribute to the natural diversity and
 regionalisation of avian integumentary appendages.
description: Chicken embryos were injected with either SAG or DMSO as a
 control at embryonic day 11 (E11). Digits from samples were then dissected
 at E11+5 hours, E12, E14 and E16. By E16, abundant ectopic feather buds
 are observed, resulting from SAG treatment. Furthermore, both ventral and
 dorsal tissue were dissected separately from additional samples at E16, as
 the strongest SAG effect is observable on the ventral digit surface.
 Tissue samples were stored in Trizol, prior to RNA extraction, library
 preparation and Illumina sequencing. This dataset contains the raw
 sequencing reads. Please see the supplementary information of the
 published article to download the aligned reads, and see the methods
 section for further details regarding both experimentation and sequencing
 of these samples.  
description: Any RNA-sequencing alignment and analysis software can be used to
 open these data files, including both R and CLC Genomics
 Workbench.
DOI: 10.5061/dryad.rn8pk0pgw
title: Revisiting the historical scenario of a disease dissemination using genetic data and Approximate Bayesian Computation methodology: the case of Pseudocercospora fijiensis invasion in Africa

description: The reconstruction of geographic and demographic scenarios of
 dissemination for invasive pathogens of crops is a key step towards
 improving the management of emerging infectious diseases. Nowadays, the
 reconstruction of biological invasions typically uses the information of
 both genetic and historical information to test for different hypotheses
 of colonization. The Approximate Bayesian Computation framework and its
 recent Random Forest development (ABC-RF) have been successfully used in
 evolutionary biology to decipher multiple histories of biological
 invasions. Yet, for some organisms, typically plant pathogens, historical
 data may not be reliable notably because of the difficulty to identify the
 organism and the delay between the introduction and the first mention. We
 investigated the history of the invasion of Africa by the fungal pathogen
 of banana, Pseudocercospora fijiensis, by testing the historical
 hypothesis against other plausible hypotheses. We analysed the genetic
 structure of eight populations from six eastern and western African
 countries, using 20 microsatellite markers, and tested competing scenarios
 of population foundation using the ABC-RF methodology. We do find evidence
 for an invasion front consistent with the historical hypothesis, but also
 for the existence of another front never mentioned in historical records.
 We question the historical introduction point of the disease on the
 continent. Crucially, our results illustrate that even if ABC-RF
 inferences may sometimes fail to infer a single, well-supported scenario
 of invasion, they can be helpful in rejecting unlikely scenarios, which
 can prove much useful to shed light on disease dissemination routes.
DOI: 10.5061/dryad.g79cnp5v9
title: Bringing light onto the Raunkiæran shortfall: A comprehensive review of traits used in functional animal ecology

description: Trait-based approaches elucidate the mechanisms underlying biodiversity
 response to, or effects on, the environment. Nevertheless, the Raunkiæran
 shortfall – the dearth of knowledge on species traits and their
 functionality – presents a challenge in the application of these
 approaches. We conducted a systematic review to investigate the trends and
 gaps in trait-based animal ecology in terms of taxonomic resolution, trait
 selection, ecosystem type, and geographical region. In addition, we
 suggest a set of crucial steps to guide trait selection and aid future
 research to conduct within and cross-taxon comparisons. We identified
 1,655 articles using virtually all animal groups published from 1999 to
 2020. Studies were concentrated in vertebrates, terrestrial habitats, and
 the Palearctic realm, and mostly investigated trophic and habitat
 dimensions. Additionally, they focused on response traits (79.4%) and
 largely ignored intraspecific variation (94.6%). Almost 36% of the
 datasets did not provide the rationale behind the selection of
 morphological traits. The main limitations of trait-based animal ecology
 were the use of trait averages and a rare inclusion of intraspecific
 variability. Nearly one-fifth of the studies based only on response traits
 conclude that trait diversity impacts ecosystem processes or services
 without justifying the connection between them or measuring them. We
 propose a guide for standardising trait collection that includes: (i)
 determining the type of trait and the mechanism linking the trait to the
 environment, ecosystem, or the correlation between the environment, trait,
 and ecosystem, (ii) using a "periodic table of niches" to select
 the appropriate niche dimension to support a mechanistic trait selection,
 and (iii) selecting the relevant traits for each retained niche dimension.
 By addressing these gaps, trait-based animal ecology can become more
 predictive. This implies that future research will likely focus on
 collaborating to understand how environmental changes impact animals and
 their capacity to provide ecosystem services and goods.
DOI: 10.5061/dryad.cjsxksnb6
title: Phenotypic selection in natural populations: what have we learned in 40 years?

description: In 1983, Russell Lande and Stevan Arnold published “The measurement of
 selection on correlated characters,” which became a highly influential
 citation classic in evolutionary biology. This paper stimulated a cottage
 industry of field studies of natural and sexual selection in nature and
 resulted in several large-scale meta-analyses, statistical developments
 and methods papers. The statistical tools in their paper contributed to a
 breakdown of the traditional dichotomy between ecological and evolutionary
 time scales and stimulated later developments such as “eco-evolutionary
 dynamics”. However, regression-based selection analyses also became
 criticized from philosophical, methodological and statistical viewpoints
 and stimulated some still ongoing debates about causality in evolutionary
 biology. Here I return to this landmark paper by Lande and Arnold, analyse
 the controversies and debates it gave rise to and discuss the past,
 present and future of selection analyses in natural populations. A
 remaining legacy of Lande and Arnold (1983) is that studies of selection
 and inheritance can fruitfully be decoupled and be studied separately,
 since selection acts on phenotypes regardless of their genetic basis, and
 hence selection and evolutionary responses to selection are distinct
 processes.  
description: Data are accumulated citation
 statistics over different years (1979–2022) for Lande and Arnold (1983)
 and Gould and Lewontin (1979) and the influences on various fields
 (ecology, evolutionary biology, philosophy of science, etc.). These data
 were obtained from a Web of Science (WoS) citation search in November
 2022. Citation data for these two key articles are separated by year and
 by journal in which they appeared. <br>
description: Datafiles are in CSV-format and can be opened using Excel, a
 notepad or software like "R".
DOI: 10.5061/dryad.h9w0vt4nx
title: SNP datasets and genomes used to benchmark the SNPLift program

description: Motivation: The advent of high-throughput sequencing technologies and
 availability of reference genomes has provided an unprecedented
 opportunity to discover and genotype millions of genetic variants in
 hundreds or even thousands of samples. Variant calling, the identification
 of genetic variants from raw sequencing data, is a time-consuming and
 computationally expensive process. Currently, reference genomes are
 evolving very rapidly and new versions come out more and more frequently.
 To take advantage of new or improved reference genomes, raw reads
 alignments, genotype calling, and filtration must typically all be redone.
 This is a costly and time consuming operation that is not always possible
 when projects are under time constraints. Results: Here, we present
 SNPLift, a bioinformatic pipeline that can quickly transfer SNP
 coordinates from one version of a genome to another, making it possible to
 rapidly leverage the resources represented by new reference genomes. We
 tested SNPLift on nine SNP datasets in VCF format from different species
 (Homo sapiens, Arabidopsis thaliana, Coregonus clupeaformis, Medicato
 truncatula, Oriza sativa, Salvelinus namaycush, Solanum lycopersicum, Zea
 mays, and Glycine max). Depending on the species, we accurately lifted
 between 82.64% and 99.39% of the variants very quickly and efficiently,
 reducing the required computing power by multiple orders of magnitudes
 compared to a complete re-analysis using the new genome reference. SNPLift
 provides an accurate, parallelized, efficient and fast solution to update
 genome positions, for example for variant calls, based on new reference
 genomes. Availability and implementation: SNPLift is available at
 https://github.com/enormandeau/snplift with its documentation and
 installation procedure. It also contains a script that runs an automated
 test on a small dataset, composed of 190,443 SNPs in chromosome 1 of
 Medicago truncatula. SNPLift uses only common tools that are easy to
 install and works under Linux and MacOS.
description: Nine species are present in the dataset. For each species, two
 genome versions and one VCF are present. The VCF contains SNPs whose
 positions refer to the oldest reference genome.
description: The authors of SNPLift used the data of 9 species to perform
 benchmarks, as described in the project's GitHub repository (https://github.com/enormandeau/snplift). This repository in turn points to the publication where the benchmark results are presented.
DOI: 10.5061/dryad.1vhhmgqxs
title: Data from: Just add water: Rainfall-induced anther closure and color change in Ripariosida hermaphrodita (Malvaceae)

description: Anther opening has commonly been thought of as unidirectional, but reports
 of anthers closing in response to rainfall show this is not the case. In
 some species, anther closure can protect pollen from degrading or washing
 away, thus possibly enhancing male fitness. Similarly, although floral
 color is often presumed to be static, numerous floral parts may change
 color during blooming. These color changes primarily occur in response to
 pollination or aging, thus potentially increasing pollination efficiency
 by directing floral visitors to recently opened, unpollinated flowers.
 Daily observations of 364 Ripariosida hermaphrodita flowers from seven
 individuals showed that anthers which were purple, open, and shedding
 pollen became beige-colored and tightly closed after rainfall. These
 findings were further supported by observations of plants exposed to
 simulated rainfall in a greenhouse and time-lapse photography of flowers
 misted with water. To our knowledge, our work represents the first report
 of anther closure in response to rain in Malvaceae and the first report of
 floral color change induced by rainfall.
description: Data was collected through a combination of daily floral
 observations and observations of floral anthers before and after exposure
 to simulated rainfall or a control treatment.
DOI: 10.6078/d14418
title: Preliminary phylogenetic and plasmid data for microbial laccase, fluorinase, dehalogenase, and glycyl radical enzymes

description: This dataset includes preliminary raw data associated with Berkeley's
 Superfund Project 3, 2022-2024, investigating microbial enzymatic
 degradation of halogenated contaminants in situ. These
 initial data include uncurated FastTree and maximum likelihood treefiles
 for various bacterial laccases sourced from the LccED (Graff et
 al  2020), fluorinases, and dehalogenases; plasmid maps for
 laccase and glycyl radical enzyme expression; and various
 scripts/notebooks (in Python) used for data curation and
 visualization. 
description: # Preliminary SRP Pr.3 (2022-2024) data --- This dataset includes
 preliminary phylogenetic analyses of publicly-available sequences for
 laccase, fluorinase, and fluoroacetate dehalogenase enzymes. It also
 contains plasmid maps for expression of bacterial laccases and select
 glycyl radical enzymes. ## Description of the data and file structure All
 treefiles are provided in either newick (.treefile) or nexus (.FigTree)
 format. FastTree generated files contain an 'ft_' prefix and the
 corresponding laccase subfamily number as deposited/curated on the LccED
 (Graff et al 2020). ML trees are generated using IQ-Tree (Minh et al
 2020). Plasmids are provided in GenBank (.gb) file format. ##
 Sharing/Access information N/A; all preliminary data. ## Code/Software All
 scripts and notebooks are in python/jupyter. These are used for FASTA file
 renaming/cleanup (notebooks) and subsequent visualization of newick
 treefiles as taxonomically-annoted nexus files (script modified from
 original author, Dr. L. Thiberio Rangel). See inline comments for
 additional detail.
DOI: 10.5061/dryad.j0zpc86k5
title: Local habitat type influences bumble bee pathogen loads and bee species distribution

description: Bumble bees (Bombus spp.) perform important ecological services in both
 managed and natural ecosystems. Anthropogenically-induced change, however,
 has altered the availability of floral resources, climatic suitability,
 and exposure to insecticides, factors that impact overall health and
 disease levels in these bees. Habitat management presents a solution for
 improving bee health and biodiversity, but this requires better
 understanding of how different pathogens and bee species respond to
 habitat conditions. Herein, we take advantage of the washboard of repeated
 ridges (forested) and valleys (mostly unforested and developed) in central
 Pennsylvania to examine whether local variation in habitat type and other
 landscape factors influence bumble bee community composition and the
 levels of four leading pathogens in the common eastern bumble bee, Bombus
 impatiens. Loads of viral pathogens (deformed wing virus and black queen
 cell virus) were found to be lowest in forest habitats, whereas loads of a
 gut parasite, Crithidia bombi, were highest in forests. Ridgetop forests
 hosted the most diverse bumble bee communities, including several habitat
 specialists. B. impatiens was most abundant in valleys, and showed higher
 incidence in areas of greater disturbance, including more developed,
 unforested, and lower floral resource sites, a pattern that mirrors its
 success in the face of anthropogenic change. Additionally, DNA barcoding
 revealed that B. sandersoni is much more common than is apparent from
 databases, likely due to misidentification as mimics B. perplexus and B.
 vagans. Our results provide evidence that habitat type can play a large
 role in pathogen load dynamics, but in ways that differ by pathogen type,
 and point to a need for consideration of habitat at both macro-ecological
 and local spatial scale
DOI: 10.5061/dryad.pc866t1th
title: Data from: Trade-offs between baseline thermal tolerance and thermal tolerance plasticity are much less common than it appears

description: Thermal tolerance plasticity is a core mechanism by which organisms can
 mitigate the effects of climate change. As a result, there is a need to
 understand how variation in tolerance plasticity arises. The Baseline
 Tolerance/Plasticity Trade-off Hypothesis (hereafter referred to as the
 Trade-off Hypothesis, TOH) has recently emerged as a potentially powerful
 explanation. The TOH posits that organisms with high baseline thermal
 tolerance have reduced thermal tolerance plasticity relative to those with
 low baseline tolerance. Many studies have found support for the TOH.
 However, this support must be regarded cautiously because the most common
 means of testing the TOH can yield spurious ‘trade-offs’ due to regression
 to the mean. I acquired data for 25 previously-published analyses that
 supported the TOH at the intraspecific level and reanalyzed them after
 applying a method that adjusts plasticity estimates for regression to the
 mean. Only six of the 25 analyses remained statistically significant after
 adjustment, and effect size and variance explained decreased in all cases.
 The few data sets in which support for the TOH was maintained after
 adjustment point to areas of future study, but are too few to make
 generalizations at this point. In sum, regression to the mean has led to a
 substantial overestimation of support for the TOH and must be accounted
 for in future tests of the hypothesis.
DOI: 10.5061/dryad.sj3tx968z
title: Data from: Nocturnal basking in freshwater turtles: a global assessment

description: Diurnal basking (“sunning”) is common in many ectotherms and is generally
 thought to be a behavioural mechanism for thermoregulation. Recent studies
 have reported the occurrence of nocturnal basking in a few
 distantly-related species of freshwater turtles, but the true extent of
 this behaviour is unknown, and it may be underreported due to sampling
 biases (e.g., not surveying for turtles at night). Therefore, we initiated
 a global, collaborative effort to systematically document and quantify
 basking activity (diurnal and nocturnal) across a wide range of freshwater
 turtle species and locations. We conducted camera trap or manual surveys
 in North America, the Caribbean, Europe, Asia, Africa, the Seychelles, and
 Australia. We collected 873,111 trail camera photographs (25,273 hrs of
 search effort) and obtained data on 29 freshwater turtle species from
 seven families. Nocturnal basking was documented in 13 species,
 representing six families (Chelidae, Emydidae, Geoemydidae, Kinosternidae,
 Pelomedusidae, and Trionychidae), including representatives in Central
 America, Trinidad and Tobago, Africa, the Seychelles, Asia, and Australia.
 Nocturnal basking was restricted to tropical and sub-tropical locations,
 suggesting that environmental temperature plays a role in this behaviour.
 However, the primary factors driving nocturnal basking are yet to be
 determined and may vary geographically and by species. The frequency and
 duration of nocturnal basking varied among species and seasons, but
 nocturnal basking events were often substantially longer than diurnal
 events. This is the first study to document a widespread occurrence of
 nocturnal basking, and our results suggest that nocturnal basking may be a
 common, although overlooked, aspect of many species’ ecology.
description: The data were collected primarily
 from trail cameras set to time laps. Each author provided data from at
 least one (usually three) trail cameras that were deployed for (usually)
 at least two seasons. The raw data were presented as "counts"
 for all cameras (with the number of turtles of each species present in
 each photo reported), and "durations" for at least one camera
 (with the time of the first and last photo that an individual was in
 reported, so that durations of "basking events" could be
 recorded). R scripts were used to summarize those data per species per
 season per study site per day/night (all cameras combined) and per species
 per season per study site per hour (all cameras combined). Thus, if at a
 given site for a given season, three cameras were deployed for seven days
 each (and duration data were collected from each camera), then for each
 species detected on those cameras, the total number of basking events
 during the day and during the night (across all seven days and all three
 cameras) is reported, in addition to other summary statistics (likewise,
 those statistics are reported per hour).