cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dz08kprvq
title: Data from: The multilocus multispecies coalescent: a flexible new model of gene family evolution

description: Incomplete lineage sorting (ILS), the interaction between coalescence and
 speciation, can generate incongruence between gene trees and species
 trees, as can gene duplication (D), transfer (T) and loss (L). These
 processes are usually modelled independently, but in reality, ILS can
 affect gene copy number polymorphism, i.e., interfere with DTL. This has
 been previously recognised, but not treated in a satisfactory way, mainly
 because DTL events are naturally modelled forward-in-time, while ILS is
 naturally modelled backwards-in-time with the coalescent. Here we consider
 the joint action of ILS and DTL on the gene tree/species tree problem in
 all its complexity. In particular, we show that the interaction between
 ILS and duplications/transfers (without losses) can result in patterns
 usually interpreted as resulting from gene loss, and that the realised
 rate of D, T and L becomes non-homogeneous in time when ILS is taken into
 account. We introduce algorithmic solutions to these problems. Our new
 model, the multilocus multispecies coalescent (MLMSC),
 which also accounts for any level of linkage between loci, generalises the
 multispecies coalescent model and offers a versatile, powerful framework
 for proper simulation and inference of gene family evolution.
description: We use the MLMSC simulator to simulate gene trees on the fungal
 species tree using three different duplication and loss rates
 (10<sup>-10</sup>, 5x10<sup>-10</sup> and
 10x10<sup>-10</sup>, duplication and loss rates are assumed to
 be equal), three effective population sizes (10<sup>7</sup>,
 5x10<sup>7</sup>, and 10x10<sup>7</sup>), and 0.9
 year per generation. For each set of parameters, we run 500 simulations
 and calculate the proportion of unilocus trees for which the haplotype
 forest contains more than one haplotype tree (i.e., copy number
 hemiplasy occurres). We also include the full model
 specification in a separate pdf file.
DOI: 10.5061/dryad.bcc2fqz9c
title: Data from: The island syndrome hypothesis is only partially validated in two rodent species in an inland-island system

description: According to the island syndrome and island rule hypotheses, island
 isolation and reduced area lead to phenotypic shifts in ecologically
 relevant traits in insular populations compared to mainland ones. These
 hypotheses have been built up with oceanic islands in mind or islands
 where isolation is high and colonization rate relatively limited. This set
 of hypotheses, however, may not be applicable to other inland-island
 systems or recently fragmented landscapes. We investigated how island life
 leads to phenotypic changes in two rodent metapopulations: deer mice and
 red-backed voles in a fragmented system on a river in Canada. From 2013 to
 2016, we sampled 454 deer mice and 665 red-backed voles spread across 10
 islands and six mainland sites on river shores. We compared body mass,
 tail and hindfoot length, exploration, and reaction towards predators,
 between individuals from island and mainland sites, and assessed the role
 of connectivity, isolation and area of islands. Insular individuals from
 both species were less aggressive towards potential predators and insular
 mice were more thorough explorers compared to mainland ones. Male mice
 were heavier and juvenile mice had longer tails on islands. However,
 contrary to expectations, we found negative relationships between
 aggressiveness and juvenile exploration score with patch connectivity for
 mice. Island connectivity significantly affected tail length of mice
 through a concave relationship. Finally, vole aggressiveness and
 exploration of male mice were positively correlated to island isolation.
 Our study supports only partially the predictions of the island syndrome
 hypothesis. It provides empirical evidence that inland-island life can
 modify traits in deer mice, but less so in red-backed voles in a
 non-oceanic system. It also raises questions about the direct causal
 factors of these changes in a naturally fragmented landscape, and urges
 for more predictive models about phenotypic/genetic divergence among
 populations in natural and artificial fragmented landscapes.
description: The study area was located within the Winnipeg River system, in
 the Minaki area (49°59′11″N 94°40′12″W), north-western Ontario,
 Canada
DOI: 10.5061/dryad.cjsxksn3t
title: Data from: Morphology, performance and fluid dynamics of the crayfish escape response

description: Sexual selection can result in an exaggerated morphology that constrains
 locomotor performance. We studied the relationship between morphology and
 the tail-flip escape response in male and female rusty crayfish (Faxonius
 rusticus), a species in which males have enlarged claws (chelae). We found
 that females had wider abdomens and longer uropods (terminal appendage of
 the tail fan) than males, while males possessed deeper abdomens and larger
 chelae, relative to total length. Chelae size was negatively associated
 with escape velocity, whereas longer abdomens and uropods were positively
 associated with escape velocity. We found no sex-specific differences in
 maximum force generated during the tail flip, but uropod length was
 strongly, positively correlated with tail-flip force in males. Particle
 image velocimetry (PIV) revealed that the formation of a vortex, rather
 than the expulsion of fluid between two closing body surfaces, generates
 propulsion in rusty crayfish. PIV also revealed that the pleopods (ventral
 abdominal appendages) contribute to the momentum generated by the tail. To
 our knowledge, this is the first confirmation of vortex formation in a
 decapod crustacean.
description: Particle image velocimetry data are not included, but can be made
 available upon request.
DOI: 10.5061/dryad.n02v6wwv6
title: Individual genotypes of 1 416 brook trout genotyped at 14 779 high-quality SNPs for studying local adaptation and maladaptation in small populations

description: Investigating the relative importance of
 neutral versus selective processes governing the
 accumulation of genetic variants is a key goal in both evolutionary and
 conservation biology. This is particularly true in the context of small
 populations, where genetic drift can counteract the effect of selection.
 Using Brook Charr (Salvelinus fontinalis) from Québec, Canada as a case
 study, we investigated the importance of
 demographic versus selective processes governing the
 accumulation of both adaptive and maladaptive mutations in
 closed versus open and connected populations to assess
 gene flow effect. This was achieved by using 14 779 high-quality filtered
 SNPs genotyped among 1 416 fish representing 50 populations from three
 life history types: lacustrine (closed populations), riverine and
 anadromous (connected populations). Using the Provean algorithm, we
 observed a considerable accumulation of putative deleterious mutations
 across populations. The absence of correlation between the
 occurrence of putatively beneficial or deleterious mutations and local
 recombination rate supports the hypothesis that genetic drift
 might be the main driver of the accumulation of such variants.
 However, despite a lower genetic diversity observed in lacustrine
 than in riverine or anadromous populations, lacustrine populations do not
 exhibit more deleterious mutations than the two other history types,
 suggesting that the negative effect of genetic drift in lacustrine
 populations may be mitigated by that of relaxed purifying
 selection. Moreover, we also identified genomic regions
 associated with anadromy, as well as an overrepresentation of transposable
 elements associated with variation in environmental variables, thus
 supporting the importance of transposable elements in
 adaptation. 
description: SNPs have been defined using ddRADsequencing following by
 subsequent filtering steps and the 14 779 in this file correspond only to
 singletons SNPs
DOI: 10.15468/dl.grf4k6
title: Occurrence Download

description: A dataset containing 1133 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Brachystegia spiciformis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1133 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002458-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.z8w9ghx8z
title: Agricultural intensification heightens food safety risks posed by wild birds

description: 1. Agricultural intensification and simplification are key drivers of
 recent declines in wild bird populations, heightening the need to better
 balance conservation with food production. This is hindered, however, by
 perceptions that birds threaten food safety. While birds are known
 reservoirs of foodborne pathogens, there remains uncertainty about the
 links between landscape context, farming practices, and actual crop
 contamination by birds. 2. Here, we examine relationships between
 landscape context, farming practices, and pathogen contamination by birds
 using a barrier-to-spillover approach. First, we censused bird communities
 using point count surveys. Second, we collected 2024 faecal samples from
 captured birds alongside 1215 faecal samples from brassica fields and food
 processing areas across 50 farms spanning the USA West Coast. We then
 estimated the prevalence of three foodborne pathogens across landscape and
 livestock intensification gradients. Finally, we quantified the number of
 plants with faeces. 3. Campylobacter spp. were detected in 10.2% of faeces
 from captured birds and 13.1% of faeces from production areas. Nonnative
 birds were 4.1 times more likely to have Campylobacter spp. than native
 birds. Salmonella spp. were detected in 0.2% of faeces from production
 areas and were never detected in captured birds. We detected evidence of
 Shiga toxigenic E. coli in 1 sample across the &gt;3200 tested. 4.
 Campylobacter spp. prevalence in faeces from production areas increased
 with increasing mammalian livestock densities in the landscape but
 decreased with increasing amounts of natural habitat. 5. We encountered
 bird faeces on 3.3% of plants examined. Despite the impact on pathogen
 prevalence, landscape context did not increase the number of plants with
 bird faeces, although on-farm mammalian livestock density slightly did. 6.
 Synthesis and applications. Food safety and wildlife conservation are
 often thought to be in conflict. However, our findings suggest that
 natural habitat around farms may reduce crop contamination rates by birds.
 This is perhaps because natural habitat can promote native birds that are
 less likely to harbour foodborne pathogens or because it decreases contact
 with livestock waste. Our results suggest that preservation of natural
 habitats around farms could benefit both conservation and food safety,
 contrary to current standards for “best practices.”
description: <b>Dataset S1. </b>Farm attributes and landscape
 variables for farms included in the study. Meta-data are provided in tab
 2. <b>Dataset S2.
 </b>Mist-net faecal sample data. Meta-data are provided in tab
 2. <b>Dataset S3.
 </b>Data for number of plants with faecal droppings. Meta-data are
 provided in tab 2. <b>Dataset S4.
 </b>Environmental faecal sample data. Meta-data are provided in tab
 2.
DOI: 10.5061/dryad.rv15dv45r
title: Dataset from: Functional divergence of mammalian TFAP2a and TFAP2b transcription factors for bidirectional sleep control

description: Sleep is a conserved behavioral state that is found in all animals that
 have a nervous system. Invertebrates typically show quiet sleep, whereas
 in mammals, sleep is more complex, and consists of periods of
 non-rapid-eye-movement sleep (NREMS) and REM sleep (REMS). We previously
 found that the transcription factor AP-2 is required for sleep in C.
 elegans and Drosophila and that the C. elegans AP-2 gene aptf-1 is
 required for sleep-active neurons to induce sleep. In mammals, several
 paralogous AP-2 transcription factors exist. Sleep-controlling genes are
 often conserved. However, little is known about how sleep genes evolved
 from controlling simpler types of sleep to govern complex mammalian sleep.
 Here, we studied the roles of Tfap2a and Tfap2b in sleep control in mice.
 Consistent with our results from C. elegans and Drosophila, the AP-2
 transcription factors Tfap2a and Tfap2b also control sleep in mice.
 Surprisingly, however, the two AP-2 paralogs play contrary roles in sleep
 control. Tfap2a reduction of function causes stronger delta and theta
 power in both baseline and homeostasis analysis, thus indicating increased
 sleep quality, but did not affect sleep quantity. By contrast, Tfap2b
 reduction of function decreased NREM sleep time specifically during the
 dark phase, reduced NREMS and REMS power, and caused a weaker response to
 sleep deprivation. Consistent with the observed signatures of decreased
 sleep quality, stress resistance and memory were impaired in Tfap2b mutant
 animals. Also, the circadian period was slightly shortened. Taken
 together, AP-2 transcription factors control sleep behavior also in mice,
 but the role of the AP-2 genes functionally diversified to allow for a
 bidirectional control of sleep quality. Divergence of AP-2 transcription
 factors might perhaps have supported the evolution of more complex types
 of sleep.
description: 1. EEG/EMG recording   2. Behavioral tests including:   2.1 Elevated plus maze (EPM)   2.2 Rotarod   2.3 Morris water maze (MWM)   2.4 Sucrose preference test (SPT)   2.5 Forced swim test (FST)   2.6 Tail suspension test (TST)   2.7 Contextual fear conditioning test (FC)   3. Wheel running   4. RNA-sequencing   5. Quantitive PCR
DOI: 10.5061/dryad.wm37pvmk7
title: Children across cultures respond emotionally to the acoustic environment

description: Among human and non-human animals, the ability to respond rapidly to
 biologically significant events in the environment is essential for
 survival and development. Research has confirmed that human adult
 listeners respond emotionally to environmental sounds just as they
 understand the emotional connotations of speech prosody and music.
 However, it is unknown whether young children also respond emotionally to
 environmental sounds. Here, we report that changes in pitch, rate (i.e.,
 playback speed), and intensity (i.e., amplitude) of environmental sounds
 trigger emotional responses in 4- and 5-year-old children, including
 sounds of human actions, animal calls, machinery, or natural phenomena
 such as wind and waves. This phenomenon was observed for children from the
 United States and China – countries with drastically different cultural
 traditions. We discuss theoretical frameworks that predict convergent
 emotional responses to music, speech, and environmental sounds, focusing
 on Charles Darwin’s hypothesis that speech and music originated from a
 common emotional signal system based on the imitation and modification of
 environmental sounds.
DOI: 10.5061/dryad.vdncjsxrp
title: Effect of gut microbiota on α-amanitin tolerance in Drosophila tripunctata

description: The bacterial gut microbiota of many animals is known to be important for
 many physiological functions including detoxification. The selective
 pressures imposed on insects by exposure to toxins may also be selective
 pressures on their symbiotic bacteria, who thus may contribute to the
 mechanism of toxin tolerance for the insect. Amatoxins are a class of
 cyclopeptide mushroom toxins that primarily act by binding to RNA
 polymerase II and inhibiting transcription. Several species of mycophagous
 Drosophila are tolerant to amatoxins found in mushrooms of the genus
 Amanita, despite these toxins being lethal to most other known eukaryotes.
 These species can tolerate amatoxins in natural concentrations to utilize
 toxic mushrooms as larval hosts, but the mechanism by which these species
 are tolerant remains unknown. Previous data has shown that a local
 population of D. tripunctata exhibits significant genetic variation in
 toxin tolerance. This study assesses the potential role of the microbiome
 in α-amanitin tolerance in six wild-derived strains of Drosophila
 tripunctata. Normal and antibiotic-treated samples of six strains were
 reared on diets with and without α-amanitin, and then scored for survival
 from the larval stage to adulthood and for development time to pupation.
 Our results show that a substantial reduction in bacterial load does not
 influence toxin tolerance in this system, while confirming genotype and
 toxin-specific effects on survival are independent of the microbiome
 composition. Thus, we conclude that this adaptation to exploit toxic
 mushrooms as a host is likely intrinsic to the fly’s genome and not a
 property of their microbiome.
DOI: 10.5061/dryad.3n5tb2rf2
title: Data from: Frequent fire slows microbial decomposition of newly deposited fine fuels in a pyrophilic ecosystem

description: Frequent fires maintain nearly 50% of terrestrial ecosystems, and drive
 ecosystem changes that govern future fires. Since fires are dependent on
 available plant or fine fuels, ecosystem processes that alter fine fuel
 loads like microbial decomposition are particularly important and could
 modify future fires. We hypothesized that variation in short-term fire
 history would influence fuel dynamics in such ecosystems. We predicted
 that frequent fires within a short-time period would slow microbial
 decomposition of new fine fuels. We expected that fire effects would
 differ based on dominant substrates and that fire history would also alter
 soil nutrient availability, indirectly slowing decomposition. We measured
 decomposition of newly deposited fine fuels in a Longleaf pine savanna,
 comparing plots that burned 0, 1, 2, or 3 times between 2014 and 2016, and
 which were located in either close proximity to or away from overstory
 pines (Longleaf pine, Pinus palustris). Microbial decomposition
 was slower in plots near longleaf pines and, as the numbers of fires
 increased, decomposition slowed. We then used structural equation modeling
 to assess pathways for these effects (number of fires, 2016 fuel/fire
 characteristics, and soil chemistry). Increased fire frequency was
 directly associated with decreased microbial decomposition. While
 increased fires decreased nutrient availability, changes in nutrients were
 not associated with decomposition. Our findings indicate that increasing
 numbers of fires over short-time intervals can slow microbial
 decomposition of newly deposited fine fuels. This could
 favor the fine fuel accumulation and drive positive
 feedbacks on future fires.
DOI: 10.5061/dryad.cjsxksn3v
title: Prevalence of Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans in thre Hoang Lien Range, northwest Vietnam

description: This study aims to investigate the presence of the amphibian chytrid
 fungi Batrachochytrium dendrobatidis (Bd) and Batrachochytrium
 salamandrivorans (Bsal) in the Hoang Lien Range, northwest
 Vietnam as well as any patterns in Bd infection in space, time
 and host species over a five-year sampling period. This study also aims to
 investigate the presence of Bsal in the Hoang Lien Range.
DOI: 10.5061/dryad.9p8cz8wd9
title: Data from: Primers to highly conserved elements optimized for qPCR-based telomere length measurements in vertebrates

description: Telomere length dynamics are an established biomarker of health and aging
 in animals. The study of telomeres in numerous species has been
 facilitated by methods to measure telomere length by real-time
 quantitative PCR (qPCR). In this method, telomere length is determined by
 quantifying the amount of telomeric DNA repeats in a sample and
 normalizing this to the total amount of genomic DNA. This normalization
 requires the development of genomic reference primers suitable for qPCR,
 which remains challenging in non-model organism with genomes that have not
 been sequenced. Here we report reference primers that can be used in qPCR
 to measure telomere lengths in any vertebrate species. We designed primer
 pairs to amplify genetic elements that are highly conserved between
 evolutionarily distant taxa and tested them in species that span the
 vertebrate tree of life. We report five primer pairs that meet the
 specificity and reproducibility standards of qPCR. In addition, we
 demonstrate an approach to choose the best primers for a given species by
 testing the primers on multiple individuals within a species and then
 applying an established computational tool. These reference primers can
 facilitate qPCR-based telomere length measurements in any vertebrate
 species of ecological or economic interest.
description: This file contains several datasets from Hudon et al. 2020 MER.
 Each tab represents a different analysis including geNorm stability
 analysis and inter-assay repeatability for four organisms with the used
 ultraconserved primer sets. Details of data collection can be found in the
 manuscript.