cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f5s90
title: Data from: Large-scale patterns of benthic marine communities in the Brazilian Province

description: As marine ecosystems are influenced by global and regional processes,
 standardized information on community structure has become crucial for
 assessing broad-scale responses to natural and anthropogenic disturbances.
 Extensive biogeographic provinces, such as the Brazilian Province in the
 southwest Atlantic, present numerous theoretical and methodological
 challenges for understanding community patterns on a macroecological
 scale. In particular, the Brazilian Province is composed of a complex
 system of heterogeneous reefs and a few offshore islands, with contrasting
 histories and geophysical-chemical environments. Despite the large extent
 of the Brazilian Province (almost 8,000 kilometers), most studies of
 shallow benthic communities are qualitative surveys and/or have been
 geographically restricted. We quantified community structure of shallow
 reef habitats from 0° to 27°S latitude using a standard photographic
 quadrat technique. Percent cover data indicated that benthic communities
 of Brazilian reefs were dominated by algal turfs and frondose macroalgae,
 with low percent cover of reef-building corals. Community composition
 differed significantly among localities, mostly because of their
 macroalgal abundance, despite reef type or geographic region, with no
 evident latitudinal pattern. Benthic diversity was lower in the tropics,
 contrary to the general latitudinal diversity gradient pattern. Richness
 peaked at mid-latitudes, between 20°S to 23°S, where it was ~3.5-fold
 higher than localities with the lowest richness. This study provides the
 first large-scale description of benthic communities along the
 southwestern Atlantic, providing a baseline for macroecological
 comparisons and evaluation of future impacts. Moreover, the new
 understanding of richness distribution along Brazilian reefs will
 contribute to conservation planning efforts, such as management strategies
 and the spatial prioritization for the creation of new marine protected
 areas.
description: Aued et
 al_databaseThis dataset is a
 summary of mean and standart deviation of benthic groups at 40 sampled
 sites along the Southwestern Atlantic. Dataset were collected from
 photoquadrats (25x25 cm) and were analysed by PhotoQuad softaware.Data are
 provided in the form of comma separated values files (csv), one for each
 of the 40 sites.compiled_quadrats_allsitesRaw data of percent cover from all sampled sites
DOI: 10.5061/dryad.s8kv6
title: Data from: The fossil record and macroevolutionary history of the beetles

description: Coleoptera (beetles) is the most species-rich metazoan order, with
 approximately 380 000 species. To understand how they came to be such a
 diverse group, we compile a database of global fossil beetle occurrences
 to study their macroevolutionary history. Our database includes 5553
 beetle occurrences from 221 fossil localities. Amber and lacustrine
 deposits preserve most of the beetle diversity and abundance. All four
 extant suborders are found in the fossil record, with 69% of all beetle
 families and 63% of extant beetle families preserved. Considerable focus
 has been placed on beetle diversification overall, however, for much of
 their evolutionary history it is the clade Polyphaga that is most
 responsible for their taxonomic richness. Polyphaga had an increase in
 diversification rate in the Early Cretaceous, but instead of being due to
 the radiation of the angiosperms, this was probably due to the first
 occurrences of beetle-bearing amber deposits in the record. Perhaps, most
 significant is that polyphagan beetles had a family-level extinction rate
 of zero for most of their evolutionary history, including across the
 Cretaceous–Palaeogene boundary. Therefore, focusing on the factors that
 have inhibited beetle extinction, as opposed to solely studying mechanisms
 that may promote speciation, should be examined as important determinants
 of their great diversity today.
description: SmithMarcot_BeetleOccurrenceDatabase of fossil beetle occurrences reported in the international paleontological and entomological literature. Fossils are from localities that range in age from the Permian through the Pliocene.SmithMarcot_BeetleCollectionsDatabase of fossil beetle collections reported in the international paleontological and entomological literature. Localities range in age from the Permian through the Pliocene.
DOI: 10.5061/dryad.365b0
title: Data from: Asthma-like symptoms in homeless children in the Greater Paris area in 2013: prevalence, associated factors and utilization of healthcare services in the ENFAMS survey

description: Asthma remains poorly studied in homeless children. We sought to estimate
 the prevalence of asthma-like symptoms (ALS) and to identify the factors
 associated with ALS and healthcare service utilisation. Materials and
 Methods: A cross-sectional survey of a random sample of sheltered homeless
 families was conducted by interviewing 801 parents of children (0–12
 years) in 17 languages. ALS were defined as wheezing or night cough
 without fever during the previous year. Poisson regression models with
 robust error variance were used to compute prevalence ratios (PR) for
 factors associated with ALS and healthcare service utilisation for ALS.
 Results: The prevalence of ALS among the children was 19.9%. Poor housing
 sanitation was significantly associated with ALS, as being born in the
 European Union. Most of the children with ALS had used healthcare services
 (85.4%). The main barriers to accessing such services were having lived in
 France for less than 49 months, having difficulties in French and living
 in poor housing conditions. Conclusion: ALS prevalence seemed lower than
 in the general child population, possibly because of the children's
 origins. Environmental factors associated with ALS point to the need to
 improve the indoor environment of family shelters. The relatively high
 rate of healthcare service utilisation should not overshadow existing
 barriers.
description: ALS_ENFAMSThis data file contains all variables used for the analyses reported in our article published in PLOS One. It is a CSV file that contains 41 variables for 801 subjects. Data originate from the ENFAMS survey, a cross-sectional survey on sheltered homeless families in the Greater Paris Area in 2013. Further description of the data is available in the ReadMe file.
DOI: 10.5061/dryad.ps173
title: Data from: Dynamics of macronutrient self-medication and illness-induced anorexia in virally-infected insects

description: 1. Some animals change their feeding behaviour when infected with
 parasites, seeking out substances that enhance their ability to overcome
 infection. This “self-medication” is typically considered to involve the
 consumption of toxins, minerals or secondary compounds. However, recent
 studies have shown that macronutrients can influence the immune response,
 and that pathogen-challenged individuals can self-medicate by choosing a
 diet rich in protein and low in carbohydrates. Infected individuals might
 also reduce food intake when infected (i.e. illness-induced anorexia). 2.
 Here, we examine macronutrient self-medication and illness-induced
 anorexia in caterpillars of the African armyworm (Spodoptera exempta) by
 asking how individuals change their feeding decisions over the time course
 of infection with a baculovirus. We measured self-medication behaviour
 across several full-sib families to evaluate the plasticity of diet choice
 and underlying genetic variation. 3. Larvae restricted to diets high in
 protein (P) and low in carbohydrate (C) were more likely to survive a
 virus challenge than those restricted to diets with a low P:C ratio. When
 allowed free choice, virus-challenged individuals chose a higher protein
 diet than controls. 4. Individuals challenged with either a lethal or
 sub-lethal dose of virus increased the P:C ratio of their chosen diets.
 This was mostly due to a sharp decline in carbohydrate intake, rather than
 an increased intake of protein, reducing overall food intake, consistent
 with an illness-induced anorexic response. Over time the P:C ratio of the
 diet decreased until it matched that of controls. 5. Our study provides
 the clearest evidence yet for dietary self-medication using
 macronutrients, and shows that the temporal dynamics of feeding behaviour
 depends on the severity and stage of the infection. The strikingly similar
 behaviour shown by different families suggests that self-medication is
 phenotypically plastic and not a consequence of genetically-based
 differences in diet choice between families.
description: Expt 1 high dose
 choiceThis is the data from
 experiment 1, self selecting treatmentExpt 2 low dose
 choiceData from experiment 2,
 self selecting treatmentExpt 1 high dose no
 choiceData from experiment 1,
 no choice treatmentExpt 2 low dose no
 choiceData from experiment 2,
 no choice treatment
DOI: 10.5061/dryad.41d7q
title: Data from: Intense selective hunting leads to artificial evolution in horn size

description: The potential for selective harvests to induce rapid evolutionary change
 is an important question for conservation and evolutionary biology, with
 numerous biological, social and economic implications. We analyze 39 years
 of phenotypic data on horn size in bighorn sheep (Ovis canadensis) subject
 to intense trophy hunting for 23 years, after which harvests nearly
 ceased. Our analyses revealed a significant decline in genetic value for
 horn length of rams, consistent with an evolutionary response to
 artificial selection on this trait. The probability that the observed
 change in male horn length was due solely to drift is 9.9%. Female horn
 length and male horn base, traits genetically correlated to the trait
 under selection, showed weak declining trends. There was no temporal trend
 in genetic value for female horn base circumference, a trait not directly
 targeted by selective hunting and not genetically correlated with male
 horn length. The decline in genetic value for male horn length stopped,
 but was not reversed, when hunting pressure was drastically reduced. Our
 analysis provides support for the contention that selective hunting led to
 a reduction in horn length through evolutionary change. It also confirms
 that after artificial selection stops, recovery through natural selection
 is slow.
description: phenotypic
 dataDescription: Phenotypic
 measurement and covariates used for animal model and for estimation of the
 genetic covariance of trait with fitness. The population of bighorn sheep
 (Ovis canadensis) is located at Ram Moutnain, Alberta, Canada(52°8’N,
 115°8’W, elevation 1082 to 2173 m). Measurements where taken between 1973
 and 2013. Animals aged 13 and older where grouped for analysis due to
 small sample size. Animals translocated from the Cadomin population where
 excluded. NA is used for missing values Columns: ID: unique identifier for
 each animal. yr: year of measurement. age: age at measurement. sex: sex of
 animal(1=male, 0=female). cohort: year of birth. hlM: horn length of males
 aged 2 to 5 in cm adjusted to 15 September. hlF: horn length of females
 aged 2 to 5 in cm adjusted to 15 September. Avhb114M: horn base of males
 aged 2 to 5 in cm adjusted to 15 September. Avhb114F: horn base of females
 in cm adjusted to 15 September. relLongM: relative longevity of males.
 Longevity divided by the mean longevity of males of the same cohort.
 relLongF: relative longevity of females. Longevity divided by the mean
 longevity of females of the same cohort.data.csvpedigreeDescription: Pedigree of the population of bighorn sheep (Ovis canadensis), located at Ram Moutnain, Alberta, Canada(52°8’N, 115°8’W, elevation 1082 to 2173 m). NA is used for missing values Columns: Id: id of the animal dam: id of the dam sire: id of the sire
DOI: 10.5061/dryad.v7000
title: Data from: Sperm production characteristics vary with level of sperm competition in Cataglyphis desert ants

description: Under polyandry, males are selected to produce more competitive
 ejaculates. Theoretical models have explored how the mechanism of sperm
 competition drives males to partition investment within an ejaculate
 between sperm quantity and quality. The raffle-based competition model
 predicts that increased level of sperm competition selects for larger
 numbers of sperm in ejaculates. Sperm competition is also thought to
 promote the evolution of longer sperm, because longer sperm could be
 faster. In eusocial Hymenoptera, the mating system imposes unique
 selective pressures on male ejaculates. Males are short lived; they reach
 adulthood with a finite amount of spermatozoa, and they mate typically
 with a single or a few females and die. The actual number of spermatozoa
 stored in their accessory testes at emergence is thus a reliable measure
 of total investment into sperm production. In a comparative study of 15
 species of Cataglyphis desert ants, we used phylogenetically controlled
 analyses to investigate relationships between levels of sperm competition,
 sperm production and sperm length. We measured sperm production by
 quantifying the number of spermatozoa present in testes, instead of using
 a proxy measure such as size of testes. Multiple queen mating is the
 ancestral state in the genus but reduction in mating frequency evolved
 secondarily and independently in some clades, providing a unique
 opportunity to examine how reduction from multiple to single mating
 influences sperm traits. Our results provide phylogenetically robust
 evidence that species experiencing greater levels of sperm competition
 produce more sperm. After controlling for male size, investment in sperm
 production decreases significantly according to the sequence obligatory
 multiple queen mating &gt; multiple–single queen mating &gt;
 single–double queen mating. Furthermore, the number of spermatozoa
 produced per male decreases significantly with reduction in paternity
 frequency for each species. In contrast, neither sperm length nor male
 size was significantly associated with the mating system classes or the
 number of patrilines. Our measures of sperm number provide the first
 direct evidence that sperm production covaries with the level of sperm
 competition in a eusocial insect. Given the reversal from multiple to
 single mating in Cataglyphis, our comparative analysis also shows
 convincingly that reduction in sperm competition influences sperm traits.
description: Sperm size and number
 produced in Cataglyphis desert antsAron et
 al._FE-2014-00943.R1.xlsx
DOI: 10.5061/dryad.h7db0
title: Data from: Multiple processes drive genetic structure of humpback whale (Megaptera novaeangliae) populations across spatial scales

description: Elucidating patterns of population structure for species with complex life
 histories, and disentangling the processes driving such patterns, remains
 a significant analytical challenge. Humpback whale (Megaptera
 novaeangliae) populations display complex genetic structures that have not
 been fully resolved at all spatial scales. We generated a data set of
 nuclear markers for 3,575 samples spanning the seven breeding stocks and
 substocks found in the South Atlantic and western and northern Indian
 Oceans. For the total sample, and males and females separately, we
 assessed genetic diversity, tested for genetic differentiation between
 putative populations and isolation by distance, estimated the number of
 genetic clusters without a priori population information, and estimated
 rates of gene flow using maximum likelihood and Bayesian approaches. At
 the ocean basin scale, structure is governed by geographic distance (IBD
 p&lt;0.05) and female fidelity to breeding areas, in line with current
 understanding of the drivers of broad-scale population structure.
 Consistent with previous studies, the Arabian Sea breeding stock was
 highly genetically differentiated (FST 0.034-0.161; p&lt;0.01 for all
 comparisons). However, the breeding stock boundary between west South
 Africa and east Africa was more porous than expected based on genetic
 differentiation, cluster, and gene flow analyses. Instances of
 male-fidelity to breeding areas and relatively high rates of dispersal for
 females were also observed between the three substocks in the western
 Indian Ocean. This mismatch between demographic units and current
 management boundaries may have ramifications for assessments of the status
 and continued protections of populations still in recovery from commercial
 whaling.
description: UsatdataHumpback whale microsatellite data set (9 loci)Kershaw_et_al_MolecularEcology_DryadSubmission.csv
DOI: 10.5281/zenodo.18381999
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by A. R. Christiaensen, http://www.wikidata.org/entity/Q108887181. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q108887181
DOI: 10.5281/zenodo.11764319
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by A. R. Christiaensen, http://www.wikidata.org/entity/Q108887181. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q108887181
DOI: 10.5061/dryad.mg76th0n
title: Data from: Gaps, an elusive source of phylogenetic information

description: Morrison (2009) raises a very fundamental question, “Why would
 phylogeneticists ignore computerized sequence alignment?” While well aware
 of the difficulties, he considers the whole issue is a ‘gaping hole that
 needs to be filled’. Particularly with the expansion of genomic-scale data
 there are many advantages to using automated alignment for phylogenetic
 analyses, the most obvious being that it is much more efficient and
 potentially less prone to experimenter bias. So yes, it is obviously
 desirable to automate data preparation as far as possible, but the
 question remains whether we are yet at the stage that automated sequence
 alignment can obtain the full and correct phylogenetic information in the
 data. In this paper we use an example shorebird dataset to explore three
 related questions regarding the interplay between alignment and phylogeny
 estimation: 1) are gap-rich alignments reliable for phylogenetic
 inference? 2) How much phylogenetic information is contained in gaps as
 compared to sequences? 3) Are models of the insertion/deletion process
 essential, and if so at what phylogenetic depths? We report that there is
 considerable information created by the indel (insertion/deletion) process
 that is potentially available for phylogenetic inference. Ideally, we
 should be able to independently obtain the same tree from both sequences
 and from gaps; however there is still considerable variability in the
 alignments produced by different programs. We predict that better and more
 computationally tractable models of the indel process will be required
 before the information in gaps can be fully exploited for phylogenetic
 inference.
description: Alignment
 filesThis .rar file contains
 all the alignments used to create Table 1, including 51 alignments in
 total. The files are organized in sub-folders firstly by taxonomic group:
 sub-order Charadrii, suborder Scolopaci, or shorebirds (which includes
 Charadrii, Scolopaci and Lari). Within taxonomic group files are organized
 by locus: Mt exon, RAG1 exon, beta-fib intron 7, and beta-fib intron 7 gap
 data. Note that the first three are sequence alignments but the last is a
 coding of the gaps in beta-fib intron 7. Within each of these folders are
 alignments for each of the methods: clustal, mafft, muscle, sate and
 t-coffee.Supplementary
 dataIncludes extra details
 on the datasets used and supplementary figure 1
DOI: 10.5061/dryad.fg7jv
title: Data from: Genetic variation but weak genetic covariation between pre- and postcopulatory episodes of sexual selection in Drosophila melanogaster

description: When females mate polyandrously, male reproductive success depends both on
 the male's ability to attain matings and his ability to outcompete
 rival males in the fertilization of ova post copulation. Increased
 investment in ejaculate components may trade-off with investment in
 precopulatory traits due to resource allocation. Alternatively, pre- and
 postcopulatory traits could be positively related if individuals can
 afford to invest heavily in traits advantageous at both episodes of
 selection. There is empirical evidence for both positive and negative
 associations between pre- and postcopulatory episodes, but little is known
 about the genetic basis of these correlations. In this study, we measured
 morphological, chemical, and behavioural precopulatory male traits and
 investigated their relationship with measures of male fitness (male mating
 success, remating inhibition and offensive sperm competitiveness) across
 40 isofemale lines of Drosophila melanogaster. We found significant
 variation among isofemale lines, indicating a genetic basis for most of
 the traits investigated. However, we found weak evidence for genetic
 correlations between precopulatory traits and our indices of male fitness.
 Moreover, pre-and postcopulatory episodes of selection were uncorrelated,
 suggesting selection may act independently at the different episodes to
 maximise male reproductive success.
description: Pre- and postcopulatory
 trait measuresSheet 1: Data. Sheet 2:
 Variable descriptionsEpisodes
 sexsel_DRYADdata.xlsx
DOI: 10.5061/dryad.4t7jk
title: Data from: The role of parasite-driven selection in shaping landscape genomic structure in red grouse (Lagopus lagopus scotica)

description: Landscape genomics promises to provide novel insights into how neutral and
 adaptive processes shape genome-wide variation within and among
 populations. However, there has been little emphasis on examining whether
 individual-based phenotype-genotype relationships derived from approaches
 such as genome-wide association (GWAS) manifest themselves as a
 population-level signature of selection in a landscape context. The two
 may prove irreconcilable as individual-level patterns may become diluted
 by high levels of gene flow and complex phenotypic or environmental
 heterogeneity. We illustrate this issue with a case study that examines
 the role of the highly prevalent gastrointestinal nematode
 Trichostrongylus tenuis in shaping genomic signatures of selection in red
 grouse (Lagopus lagopus scotica). Individual-level GWAS involving 384 SNPs
 has previously identified five SNPs that explain variation in T. tenuis
 burden. Here, we examine whether these same SNPs display population-level
 relationships between T. tenuis burden and genetic structure across a
 small-scale landscape of 21 sites with heterogeneous parasite pressure.
 Moreover, we identify adaptive SNPs showing signatures of directional
 selection using FST outlier analysis and relate population- and
 individual-level patterns of multi-locus neutral and adaptive genetic
 structure to T. tenuis burden. The five candidate SNPs for parasite-driven
 selection were neither associated with T. tenuis burden on a population
 level, nor under directional selection. Similarly, there was no evidence
 of parasite-driven selection in SNPs identified as FST outliers. We
 discuss these results in the context of red grouse ecology and highlight
 the broader consequences for the utility of landscape genomics approaches
 for identifying signatures of selection.
description: PLINK MAP file for 274
 genome-wide SNPsgrouse2012_QCpass.mapGenotype data for 231 red grouse individualsgrouse2012_QCpass.ped.txtSampling-related and phenotypic data for 231 red grouse individualsgrouse2012_metadata.txtCoordinates for 21 sampling sitespop_latlong.txt