cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g9q79
title: Data from: Impacts of genetic correlation on the independent evolution of body mass and skeletal size in mammals

description: Mammals show a predictable scaling relationship between limb bone size and
 body mass. This relationship has a genetic basis which likely evolved via
 natural selection but it is unclear how much the genetic correlation
 between these traits in turn impacts their capacity to evolve
 independently. We selectively bred laboratory mice for increases in tibia
 length independent of body mass to test the hypothesis that a genetic
 correlation with body mass constrains evolutionary change in tibia length.
 Over 14 generations we produced mean tibia length increases of 11-12%
 while mean body mass was unchanged in selectively bred mice and
 random-bred controls. Using evolutionary scenarios with different
 selection and quantitative genetic parameters we also found that this
 genetic correlation impedes the rate of evolutionary change in both traits
 slowing increases in tibia length while preventing decreases in body mass
 despite the latter's negative effect on fitness. Overall results from
 this ongoing selection experiment suggest that parallel evolution of
 relatively longer hind limbs among rodents for example in the context of
 strong competition for resources and niche partitioning in heterogeneous
 environments may have occurred very rapidly on geological timescales in
 spite of the genetic correlation between tibia length and body mass.
description: Marchini et al 2014 BMC
 EvolBio - Coevolution tibia length and body mass datasetData file of artificial
 selection containing all mice measured from generations F01-F14.
 Measurements include body mass, tibia length, age at measurement and
 litter size. Pedigree information is also provided
DOI: 10.5061/dryad.ns7pv
title: Data from: Mapping beta diversity from space: Sparse Generalized Dissimilarity Modelling (SGDM) for analysing high-dimensional data

description: 1. Spatial patterns of community composition turnover (beta diversity) may
 be mapped through Generalised Dissimilarity Modelling (GDM). While remote
 sensing data are adequate to describe these patterns, the often
 high-dimensional nature of these data poses some analytical challenges,
 potentially resulting in loss of generality. This may hinder the use of
 such data for mapping and monitoring beta-diversity patterns. 2. This
 study presents Sparse Generalised Dissimilarity Modelling (SGDM), a
 methodological framework designed to improve the use of high-dimensional
 data to predict community turnover with GDM. SGDM consists of a two-stage
 approach, by first transforming the environmental data with a sparse
 canonical correlation analysis (SCCA), aimed at dealing with
 high-dimensional datasets, and secondly fitting the transformed data with
 GDM. The SCCA penalisation parameters are chosen according to a grid
 search procedure in order to optimise the predictive performance of a GDM
 fit on the resulting components. The proposed method was illustrated on a
 case study with a clear environmental gradient of shrub encroachment
 following cropland abandonment, and subsequent turnover in the bird
 communities. Bird community data, collected on 115 plots located along the
 described gradient, were used to fit composition dissimilarity as a
 function of several remote sensing datasets, including a time series of
 Landsat data as well as simulated EnMAP hyperspectral data. 3. The
 proposed approach always outperformed GDM models when fit on
 high-dimensional datasets. Its usage on low-dimensional data was not
 consistently advantageous. Models using high-dimensional data, on the
 other hand, always outperformed those using low-dimensional data, such as
 single date multispectral imagery. 4. This approach improved the direct
 use of high-dimensional remote sensing data, such as time series or
 hyperspectral imagery, for community dissimilarity modelling, resulting in
 better performing models. The good performance of models using
 high-dimensional datasets further highlights the relevance of dense time
 series and data coming from new and forthcoming satellite sensors for
 ecological applications such as mapping species beta diversity.
description: Species and
 environmental dataThis compiled (zip) file
 consists of 7 matrices of data: one species data matrix, with abundance
 observations per visited plot; and 6 environmental data matrices,
 consisting of land cover classification (Class), simulated EnMAP and
 Landsat data (April and August), and a 6 time-step Landsat time series
 (January, March, May, June, July and September). All data is compiled to
 the 125m radius plots, as described in the paper.Leitaoetal_Mapping beta
 diversity from space_Data.zip
DOI: 10.5061/dryad.0r7g4
title: Data from: Individual genetic diversity and probability of infection by avian malaria parasites in blue tits (Cyanistes caeruleus)

description: Understanding the importance of host genetic diversity for coping with
 parasites and infectious diseases is a long-standing goal in evolutionary
 biology. Here, we study the association between probability of infection
 by avian malaria (Plasmodium relictum) and individual genetic diversity in
 three blue tit (Cyanistes caeruleus) populations that strongly differ in
 prevalence of this parasite. For this purpose, we screened avian malaria
 infections and genotyped 789 blue tits across 26 microsatellite markers.
 We used two different arrays of markers: 14 loci classified as neutral and
 12 loci classified as putatively functional. We found a significant
 relationship between probability of infection and host genetic diversity
 estimated at the subset of neutral markers that was not explained by
 strong local effects and did not differ among the studied populations.
 This relationship was not linear, and probability of infection increased
 up to values of homozygosity by locus (HL) around 0.15, reached a plateau
 at values of HL from 0.15 to 0.40 and finally declined among a small
 proportion of highly homozygous individuals (HL &gt; 0.4). We did not
 find evidence for significant identity disequilibrium, which may have
 resulted from a low variance of inbreeding in the study populations and/or
 the small power of our set of markers to detect it. A combination of
 subtle positive and negative local effects and/or a saturation threshold
 in the association between probability of infection and host genetic
 diversity in combination with increased resistance to parasites in highly
 homozygous individuals may explain the observed negative quadratic
 relationship. Overall, our study highlights that parasites play an
 important role in shaping host genetic variation and suggests that the use
 of large sets of neutral markers may be more appropriate for the study of
 heterozygosity–fitness correlations.
description: DataBaseThis file contains the genotypes (27 microsatellite loci) and infection status (Plasmodium relictum, lineage SGS1) of 789 individuals of blue tit (Cyanistes caeruleus) sampled in three populations from Central Spain
DOI: 10.5061/dryad.b66rc
title: Data from: Genetic effects of marine stock enhancement: a case study based on the highly piscivorous Japanese Spanish mackerel

description: We used a before–after control–impact design to quantify the genetic
 effects of the large piscivorous Japanese Spanish mackerel (Scomberomorus
 niphonius) stock enhancement program on wild populations in the Seto
 Inland Sea. Samples of 1424 wild and 230 hatchery fish collected from 13
 sites around Japan were genotyped using five microsatellite markers. A
 total of 758 wild and 103 hatchery fish were sequenced for the
 mitochondrial DNA D-loop region. The population structure of Japanese
 Spanish mackerel was panmictic around Japan. Hatchery fish had
 significantly lower genetic diversity indices than did wild fish. However,
 there was no significant change in any of the diversity indices in the
 Seto Inland Sea, despite the substantial genetic mixing proportion of
 hatchery-origin genes (7.8%–14.5% from releases in 2001 and 2002), a
 conclusion supported by simulations. The estimated effective population
 size was surprisingly small (∼430–970) but stable in the Seto Inland Sea
 compared with the large census size. A Ryman–Laikre effect was not likely
 in the Japanese Spanish mackerel.
description: Microsatellite genotype
 data of Japanese Spanish mackerelGenePop file: at 5 loci
 for 16 samples (1,654 individualｓ)JSM_genotypes_and
 _GSI.xlsxJapanese Spanish
 mackerel - Individual sequencesIndividual sequences in
 fasta formatJSM_individual_sequences.fasJapanese Spanish mackerel - Haplotype sequencesSequences for 94 haplotypesJSM_haplotype_sequences.txt
DOI: 10.5061/dryad.53356
title: Data from: Paternal Imprinting of Mating Preferences Between Natural Populations of House Mice (Mus musculus domesticus)

description: The evolutionary divergence of cues for mate recognition can contribute to
 early stages of population separation. We compare here two allopatric
 populations of house mice (Mus musculus domesticus) that have become
 separated about 3000 years ago. We have used paternity assignments in
 semi-natural environments to study the degree of mutual mate recognition
 according to population origin under conditions of free choice and
 overlapping generations. Our results provide insights into the divergence
 of mating cues, but also for the mating system of house mice. We find
 frequent multiple mating, occurrence of inbreeding and formation of
 extended family groups. In addition, many animals show strong mate
 fidelity, that is, frequent choice of the same mating partners in
 successive breeding cycles, indicating a role for familiarity in mating
 preference. With respect to population divergence, we find evidence for
 assortative mating, but only under conditions where the animals had time
 to familiarize themselves with mating partners from their own population.
 Most interestingly, the first-generation offspring born in the enclosure
 showed a specific mating pattern. Although matings between animals of
 hybrid population origin with animals of pure population origin should
 have occurred with equal frequency with respect to matching the paternal
 or maternal origin, paternal matching with mates from their own
 populations occurred much more often. Our findings suggest that paternally
 imprinted cues play a role in mate recognition between mice and that the
 cues evolve fast, such that animals of populations that are separated
 since not more than 3000 years can differentially recognize them.
description: datatablesExcel file with three tables; the first table lists details for all matings evaluated, including all mating partner IDs and associated information from the monitoring surveys. The second table is a subset of the first table restricted to all matings among F1 animals that were born in the enclosure. The third table is a subset of the second table, restricted to all first matings only.all mice in experimentList of all mice that were collected and genotyped. Only animals with clear assignments were used for generating the mating data presented in the file "datatables.xls"
DOI: 10.5061/dryad.mc1j9
title: Data from: Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis

description: A system-level framework of complex microbe–microbe and host–microbe
 chemical cross-talk would help elucidate the role of our gut microbiota in
 health and disease. Here we report a literature-curated interspecies
 network of the human gut microbiota, called NJS16. This is an extensive
 data resource composed of ∼570 microbial species and 3 human cell types
 metabolically interacting through &gt;4,400 small-molecule transport
 and macromolecule degradation events. Based on the contents of our
 network, we develop a mathematical approach to elucidate representative
 microbial and metabolic features of the gut microbial community in a given
 population, such as a disease cohort. Applying this strategy to microbiome
 data from type 2 diabetes patients reveals a context-specific
 infrastructure of the gut microbial ecosystem, core microbial entities
 with large metabolic influence, and frequently produced metabolic
 compounds that might indicate relevant community metabolic processes. Our
 network presents a foundation towards integrative investigations of
 community-scale microbial activities within the human gut.
description: Metabolic transport
 network of the human gut microbiota (NJS16)A global interspecies
 metabolic interaction network of the human gut microbiota (NJS16),
 composed of ~570 microbial species and 3 human cell types metabolically
 interacting through &gt;4,400 small-molecule transport and macromolecule
 degradation events. The information upon which the network architecture
 stands is primarily from literature-based annotations.NJS16_JS_PJK.xlsx
DOI: 10.5061/dryad.1sf74
title: Data from: An objective approach to select climate scenarios when projecting species distribution under climate change

description: [No abstract entered]
description: Occurrences data for
 three Northeastern-American tree speciestrees_occurrences.zip
DOI: 10.5061/dryad.8hv52
title: Data from: Is adaptation to climate change really constrained in niche specialists?

description: Species with restricted distributions make up the vast majority of
 biodiversity. Recent evidence suggests that Drosophila species with
 restricted tropical distributions lack genetic variation in the key trait
 of desiccation resistance. It has therefore been predicted that tropically
 restricted species will be limited in their evolutionary response to
 future climatic changes and will face higher risks of extinction. However,
 these assessments have been made using extreme levels of desiccation
 stress (less than 10% relative humidity (RH)) that extend well beyond the
 changes projected for the wet tropics under climate change scenarios over
 the next 30 years. Here, we show that significant evolutionary responses
 to less extreme (35% RH) but more ecologically realistic levels of
 climatic change and desiccation stress are in fact possible in two species
 of rainforest restricted Drosophila. Evolution may indeed be an important
 means by which sensitive rainforest-restricted species are able to
 mitigate the effects of climate change.
description: van Heerwaarden and Sgro
 (2014). Data from: Is adaptation to climate change really constrained in
 niche specialists? Proceedings of the Royal Society of London, series
 BExcel file containing
 desiccation data from half-sib full-sib breeding
 experiments.van Heerwaarden and Sgro
 (2014). Data from Is adaptation t climate chaneg realy constrained in
 niche specialists? Proceedings of the Royal Society of London, series
 B.xlsx
DOI: 10.5061/dryad.t34d3
title: Data from: Geographic variation in mimetic precision among different species of coral snake mimics

description: Batesian mimicry is widespread, but whether and why different species of
 mimics vary geographically in resemblance to their model is unclear. We
 characterized geographic variation in mimetic precision among four
 Batesian mimics of coral snakes. Each mimic occurs where its model is
 abundant (i.e., in “deep sympatry”), rare (i.e., at the sympatry/allopatry
 boundary or “edge sympatry”), and absent (i.e., in allopatry). Geographic
 variation in mimetic precision was qualitatively different among these
 mimics. In one mimic, the most precise individuals occurred in edge
 sympatry; in another, they occurred in deep sympatry; in the third, they
 occurred in allopatry; and in the fourth, precise mimics were not
 concentrated anywhere throughout their range. Mimicry was less precise in
 allopatry than in sympatry in only two mimics. We present several
 non-mutually exclusive hypotheses for these patterns. Generally, examining
 geographic variation in mimetic precision—within and among different
 mimics—offers novel insights into the causes and consequences of mimicry.
description: Table
 S1Phenotypic and locality
 data for museum specimens of Micrurus fulvius, Micrurus tener,
 Lampropeltis elapsoides, Lampropeltis gentilis, Cemophora coccinea, and
 Cemophora lineri.
DOI: 10.5061/dryad.dp4kt5t
title: Data from: Daytime eyeshine contributes to pupil camouflage in a cryptobenthic marine fish

description: Ocular reflectors enhance eye sensitivity in dim light, but can produce
 reflected eyeshine when illuminated. Some fish can occlude their
 reflectors during the day. The opposite is observed in cryptic
 sit-and-wait predators such as scorpionfish and toadfish, where reflectors
 are occluded at night and exposed during the day. This results in daytime
 eyeshine, proposed to enhance pupil camouflage by reducing the contrast
 between the otherwise dark pupil and the surrounding tissue. In this
 study, we test this hypothesis in the scorpionfish Scorpaena porcus and
 show that eyeshine is the result of two mechanisms: the previously
 described Stratum Argenteum Reflected (SAR) eyeshine, and Pigment
 Epithelium Transmitted (PET) eyeshine, a newly described mechanism for
 this species. We confirm that the ocular reflector is exposed only when
 the eye is light-adapted, and present field measurements to show that
 eyeshine reduces pupil contrast against the iris. We then estimate the
 relative contribution of SAR and PET eyeshine to pupil brightness. Visual
 models for different light scenarios in the field show that daytime
 eyeshine enhances pupil camouflage from the perspective of a prey fish. We
 propose that the reversed occlusion mechanism of some cryptobenthic
 predators has evolved as a compromise between camouflage and vision.
description: Raw data
 tablesRaw data. To improve
 clarity, data have been separated in different tables.
DOI: 10.5061/dryad.99n02
title: Data from: Taxonomic revision of Ectyphus Gerstaecker, 1868 and Parectyphus Hesse, 1972 with a key to world Ectyphinae (Insecta, Diptera, Mydidae)

description: The Afrotropical Mydidae genera Ectyphus Gerstaecker, 1868 and Parectyphus
 Hesse, 1972 are revised. Six species of Ectyphus are recognised (E.
 abdominalis Bezzi, 1924, E. armipes Bezzi, 1924, E. capillatus Hesse,
 1969, E. pinguis Gerstaecker, 1868, and E. pretoriensis Bezzi, 1924), of
 which one is newly described from Kenya, E. amboseli sp. n. Two species,
 E. bitaeniatus Hesse, 1969 and E. flavidorsalis Hesse, 1969, are newly
 synonymised with E. pinguis. The monotypic genus Parectyphus Hesse, 1972
 and the male of its type species P. namibiensis Hesse, 1972 are
 re-described while the female is described for the first time. Comments on
 the distribution of all species within biodiversity hotspots are given. A
 dichotomous identification key to the genera and species of world
 Ectyphinae is provided and illustrated keys to the world Ectyphinae are
 made available online in both dichotomous and multi-access, matrix-based
 formats.
description: Species descriptions of
 Ectyphus and Parectyphus in SDD formatNatural language species
 descriptions of Ectyphus and Parectyphus as exported from Lucid Builder
 3.5 in SDD format.ectyphus+parectyphus.sdd
DOI: 10.5061/dryad.b5m6g
title: Data from: The proportion of clinically relevant alarms decreases as patient clinical severity decreases in intensive care units: a pilot study

description: Objectives: To determine (1) the proportion and number of clinically
 relevant alarms based on the type of monitoring device; (2) whether
 patient clinical severity, based on the sequential organ failure
 assessment (SOFA) score, affects the proportion of clinically relevant
 alarms and to suggest; (3) methods for reducing clinically irrelevant
 alarms in an intensive care unit (ICU). Design: A prospective,
 observational clinical study. Setting: A medical ICU at the University of
 Tokyo Hospital in Tokyo, Japan. Participants: All patients who were
 admitted directly to the ICU, aged ≥18 years, and not refused active
 treatment were registered between January and February 2012. Methods: The
 alarms, alarm settings, alarm messages, waveforms and video recordings
 were acquired in real time and saved continuously. All alarms were
 annotated with respect to technical and clinical validity. Results: 18 ICU
 patients were monitored. During 2697 patient-monitored hours, 11 591
 alarms were annotated. Only 740 (6.4%) alarms were considered to be
 clinically relevant. The monitoring devices that triggered alarms the most
 often were the direct measurement of arterial pressure (33.5%), oxygen
 saturation (24.2%), and electrocardiogram (22.9%). The numbers of relevant
 alarms were 12.4% (direct measurement of arterial pressure), 2.4% (oxygen
 saturation) and 5.3% (electrocardiogram). Positive correlations were
 established between patient clinical severities and the proportion of
 relevant alarms. The total number of irrelevant alarms could be reduced by
 21.4% by evaluating their technical relevance. Conclusions: We
 demonstrated that (1) the types of devices that alarm the most frequently
 were direct measurements of arterial pressure, oxygen saturation and ECG,
 and most of those alarms were not clinically relevant; (2) the proportion
 of clinically relevant alarms decreased as the patients’ status improved
 and (3) the irrelevance alarms can be considerably reduced by evaluating
 their technical relevance.
description: BMJOpen
DOI: 10.5061/dryad.k2c2p
title: Data from: Investigating the effects of Pleistocene events on genetic divergence within Richardsonius balteatus, a widely distributed western North American minnow

description: Background: Biogeographers seek to understand the influences of global
 climate shifts and geologic changes to the landscape on the ecology and
 evolution of organisms. Across both longer and shorter timeframes, the
 western North American landscape has experienced dynamic transformations
 related to various geologic processes and climatic oscillations, including
 events as recently as the Last Glacial Maximum (LGM; ~20 Ka) that have
 impacted the evolution of the North American biota. Redside shiner is a
 cyprinid species that is widely distributed throughout western North
 America. The species’ native range includes several well-documented
 Pleistocene refugia. Here we use mitochondrial DNA sequence data to assess
 phylogeography, and to test two biogeographic hypotheses regarding
 post-glacial colonization by redside shiner: 1) Redside shiner entered the
 Bonneville Basin at the time of the Bonneville Flood (Late Pleistocene;
 14.5 Ka), and 2) redside shiner colonized British Columbia post-glacially
 from a single refugium in the Upper Columbia River drainage. Results:
 Genetic diversification in redside shiner began in the mid to late
 Pleistocene, but was not associated with LGM. Different clades of redside
 shiner were distributed in multiple glacial age refugia, and each clade
 retains a signature of population expansion, with clades having secondary
 contact in some areas. Conclusions: Divergence times between redside
 shiner populations in the Bonneville Basin and the Upper Snake/Columbia
 River drainage precedes the Bonneville Flood, thus it is unlikely that
 redside shiner invaded the Bonneville Basin during this flooding event.
 All but one British Columbia population of redside shiner are associated
 with the Upper Columbia River drainage with the lone exception being a
 population near the coast, suggesting that the province as a whole was
 colonized from multiple refugia, but the inland British Columbia redside
 shiner populations are affiliated with a refugium in the Upper Columbia
 River drainage.
description: Redside Shiner
 Concatenated Cyt B and CR Lahontan OutgroupmtDNA nexus file used
 for phylogenetic analyses and divergence time estimates