cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t1g1jwt1x
title: Nucleotide substitutions during speciation may explain substitution rate variation

description: Although molecular mechanisms associated with the generation of mutations
 are highly conserved across taxa, there is widespread variation in
 mutation rates between evolutionary lineages. When phylogenies are
 reconstructed based on nucleotide sequences, such variation is typically
 accounted for by the assumption of a relaxed molecular clock, which is
 just a statistical distribution of mutation rates without much underlying
 biological mechanism. Here, we propose that variation in accumulated
 mutations may be partly explained by an elevated mutation rate during
 speciation. Using simulations, we show how shifting mutations from
 branches to speciation events impacts inference of branching times in
 phylogenetic reconstruction. Furthermore, the resulting nucleotide
 alignments are better described by a relaxed than by a strict molecular
 clock. Thus, elevated mutation rates during speciation potentially explain
 part of the variation in substitution rates that is observed across the
 tree of life.
description: The file "Supplementary information.pdf" contains all
 supplementary results, as indicated in the main text. 
 The associated R package 'nodeSub' has been attached as
 tar.gz file, from which it can be installed. Alternatively, the package
 can be installed from GitHub using:
 devtools::install_github("thijsjanzen/nodeSub"), or obtained
 from CRAN: https://CRAN.R-project.org/package=nodeSub A tarball of the package phangorn as used for Figure 5 has been included for reference. Furthermore, two example XML files as used by BEAST2 are included for inference of a full tree ('tree_inference_example.xml') and for obtaining the marginal likelihoods of the different substitution models ('example_marginal.xml'). The files "scripts.zip" and "code.zip" contain code and data used for each figure in the main text and the supplement. After unzipping and combining, each folder contains 4 files: - simulate.R  - R code used to simulate alignments, perform inference and calculate summary statistics<br> - plot_figure.R - R code used to plot the figure<br> - simulated_data.txt - summary information of the simulated data. Because the BEAST chains are huge, in order to be able to handle the output data, we have summarized the posterior distributions of summary statistics and collected them. We have included an example collection script (called collect.R) that demonstrates how we obtained these data files.<br> - Figure_*.pdf  - the resulting figure in high resolution<br>
DOI: 10.5061/dryad.cfxpnvx4r
title: Supplementary information for: From scales to armour: scale losses and trunk bony plate gains in ray-finned fishes

description: Actinopterygians (ray-finned fishes) are the most diversified group of
 vertebrates and are characterized by a variety of protective structures
 covering their integument, the evolution of which has intrigued biologists
 for decades. Paleontological records showed that the first mineralized
 vertebrate skeleton was composed of dermal bony plates covering the body,
 including odontogenic and skeletogenic components. Later in evolution, the
 exoskeleton of actinopterygian's trunk was composed of scale
 structures. Although scales are nowadays a widespread integument cover,
 some contemporary lineages do not have scales but bony plates covering
 their trunk, whereas other lineages are devoid of any such structures. To
 understand the evolution of the integument coverage and particularly the
 transition between different structures, we investigated the pattern of
 scale loss events along actinopterygian evolution and addressed the
 functional relationship between the scaleless phenotype and the ecology of
 fishes. Furthermore, we examined whether the emergence of trunk bony
 plates was dependent over the presence or absence of scales. To this aim,
 we used two recently published actinopterygian phylogenies, one including
 &gt; 11,600 species, and by using stochastic mapping and Bayesian
 methods, we inferred scale loss events and trunk bony plate acquisitions.
 Our results reveal that a scaled integument is the most frequent state in
 actinopterygians, but multiple independent scale loss events occurred
 along their phylogeny with essentially no scale re-acquisition. Based on
 linear mixed models, we found evidence supporting that after a scale loss
 event, fishes tend to change their ecology and adopt a benthic lifestyle.
 Furthermore, we show that trunk bony plates appeared independently
 multiple times along the phylogeny. By using fitted likelihood models for
 character evolution, we show that trunk bony plate acquisitions were
 dependent on a previous scale loss event. Overall, our findings support
 the hypothesis that integument cover is a key evolutionary trait
 underlying actinopterygian radiation.
description: The
 datasets were collected compiling different sources from
 litterature.
DOI: 10.5061/dryad.51c59zw7z
title: Data from: Variations of trophic structure and niche space in fish community along a highly regulated subtropical large river

description: The trophic interactions between consumers and resources play a vital role
 in the stability of communities. In river systems, fragmentation of
 natural habitats and environmental changes alters the energy basis and
 community composition, consequently leading to variations in the
 community's trophic structure and niche space. However, our
 understanding of how the trophic structure responds to environmental
 changes is still very limited. Here, based on stable isotope data, we
 explored and compared trophic positions (TPs), community-wide trophic
 metrics, and isotope niche space of fish communities in three reaches with
 different hydrogeomorphic conditions along a highly regulated subtropical
 river over three seasons. The community trophic structure and niche space
 showed notable spatiotemporal variations. Overall, the downstream reach
 had lower TPs and trophic diversity but higher trophic redundancy. The
 middle reach occupied a wider isotope niche space than other reaches, with
 the largest niche size during autumn. Furthermore, the niche overlap was
 relatively high in winter between reaches and in the downstream between
 seasons. The results implied a homogenization of feeding functional groups
 and energy flow pathways of species in the downstream community associated
 with the change of energy source and stability of hydrological conditions.
 The relationship between trophic structure and environmental factors
 suggested that the dam-induced alteration in hydrological-related aspects
 may drive the changes in the functional group composition, together with
 changes in energy basis, resulting in differences in the trophic structure
 of the community. The results of the present study deepen our
 understanding of how ecosystem functions respond to disturbance, thus
 contributing to an improved ability to conserve river ecosystems.
description: The dataset is composed of two Excel files:(1) LJSR Fish stable
 isotope data.xlsx file that contain information on C and N stable isotope
 values, body size and trophic categories of fish collected from the Lower
 Jinsha River and (2) LJSR Environmental variables data.xlsx file that
 contain information the environmental variables collected synchronously
 from the Lower Jinsha River as described in manuscript of Huijun Ru et al.
 in Ecology and Evolution.
DOI: 10.5061/dryad.1vhhmgqs7
title: Species composition and functional trait data for wet pine savannas

description: Trait differences among plant species can favor species coexistence. The
 role that such differences play in the assembly of diverse plant
 communities maintained by frequent fires remains unresolved. This lack of
 resolution results in part from the possibility that species with similar
 traits may coexist because none has a significant fitness advantage and in
 part from the difficulty of experimental manipulation of highly diverse
 assemblages dominated by perennial species. We examined a 65-year
 chronosequence of losses of herbaceous species following fire suppression
 (and subsequent encroachment by Pinus elliottii) in three wet longleaf
 pine savannas. We used cluster analysis, similarity profile permutation
 tests and k-R cluster analysis to identify statistically significant
 functional groups. We then used randomization tests to determine if the
 absence of functional groups near pines was greater (or less) than
 expected by chance. We also tested whether tolerant and sensitive species
 were less (or more) likely to co-occur by chance in areas in savannas away
 from pines in accordance with predictions of modern coexistence theory.
 Functional group richness near pines was lower than expected from random
 species extirpations. Wetland perennials with thick rhizomes and high leaf
 water content, spring-flowering wetland forbs (including Drosera tracyi),
 orchids, Polygala spp., and club mosses were more likely to be absent near
 pines than expected by chance. C3 grasses and sedges with seed banks and
 tall, fall-flowering C4 grasses were less likely to be absent near pines
 than expected by chance. Species sensitive to pine encroachment were more
 likely to co-occur with other such species away from pines at two of the
 three sites. Results suggest that herb species diversity in
 frequently-burned wet savannas is maintained in part by a weak fitness
 (e.g., competitive) hierarchy among herbs, and not as a result of trait
 differences among co-occurring species.
description: Data for the chronosequence study come from measurements of plant
 species richness and composition (presence/absence) in 1997 at three sites
 in Desoto National Forest in southeastern Mississippi, USA. Root porosity
 and length data collected in May and October of 2009. Other trait data
 were collected in July 2018. All data are stored on Brewer's
 university-issued computer and backed up using Carbonite.
description: See uploaded readme text file called FUNCTDATAreadme.
DOI: 10.5061/dryad.kh1893253
title: Data from: Sixteen in one: white-belted Megaselia Rondani (Diptera: Phoridae) from the New World challenge species concepts

description: We review the species of Megaselia similar to M. sulphurizona Borgmeier. A
 close examination of M. sulphurizona indicates that its current concept
 includes at least 16 species, 15 of which- M. albizona, M. borealizona, M.
 colombizona, M. cryptizona, M. danizona, M. guanizona, M. marizona, M.
 nivizona, M. oklizona, M. paulizona, M. reductizona, M. solizona, M.
 tropizona, M. wendizona, and M. winnizona are described as new, based
 primarily on molecular data. The identity of the holotype of the species
 M. sulphurizona is clarified through wing vein morphometrics. Two
 of the new species, Megaselia albizona and M. cryptizona, are the 47th and
 48th new species of phorid fly described from the BioSCAN project, an
 urban biodiversity study in Los Angeles, California, USA.
description: .DAT file: Data were collected by landmarking wings using the
 program TPSdig2. They are formatted for analysis using the program
 PAST. .FAS file: Data downloaded from BOLD and
 aligned.
DOI: 10.5061/dryad.dfn2z350x
title: Rapid evolution of sexual size dimorphism facilitated by Y-linked genetic variance data set

description: The three datasets were collected to study the genetic architecture of
 sexual size dimorphism in the seed beetle Callosobruchus maculatus
 (Quantitative_genetics_data_set), the response of sexual dimorphism to
 artificial selection (artificial_selection_data_set) and to isolate and
 quantify the effect of Y haplotypes on male body size
 (Y_introgression_data_set). Quantitative genetics: A four generation
 breeding design with pedigree information for 8022 individuals and body
 size measurements for 7356 individuals. The breeding design and sample
 size of the study allows to partition genetic variances into additive
 autosomal, additive sex-linked, autosomal dominance and X-linked dominance
 variance. Artificial selection: Family level phenotypic data over 10
 generations of artificial selection using direct progenitors of the
 quantitative genetics experiment in 5 different selection regimes (random
 selection [C], sexually antagonistic selection, for increased sexual
 dimorphism [SA], sex limited selection; for small males [SL1], for large
 females [SL2], for large males [SL3]), each selection regime was
 replicated by two replicate lines, resulting in 10 selection lines. Y
 introgression: We followed the Y lineage (paternal founder line) from the
 quantitative genetics experiment over the course of the artificial
 selection, and after the selection we introgressed each remaining Y
 lineage into an isogenic background, by 13 generations of backcrossing of
 males with the isogenic females in order to isolate the Y-linked effect on
 male body size.
description: Quantitative genetics: Individual body weight measurments [mg] for individuals of grandparental (GP), parental (P), F1 offspring (F1) and F2 offspring (F2) generation. Artificial selection: Family average body weight, by measuring 7 pooled females for female weight [mg], or 7 pooled males for male weight [mg] Y introgression: Indicudual body weight measurment [mg] at the final generation of introgression
description: Column description provided
 in the .xls in the README file
DOI: 10.5061/dryad.15dv41nwr
title: Lampsilis siliquoidea and L. radiata seven microsatellite loci data set

description: The data set corresponds to genotypes of individuals belonging
 to Lampsilis siliquoidea and L. radiata which
 are two closely related freshwater mussel species [Bivalvia:
 Unionidae]. Individual genotypes consist of seven microsatellite
 loci developed by Eackles and King 2002. Genotypes were used to
 asses population genetic structure above and below waterfalls in the lower
 Great Lakes (USA) and to investigate the degree
 of hybridization between these two species. 
description: <i>Lampsilis siliquoidea</i> and <i>L.
 radiata</i> tissue samples from sites across much of their
 geographic ranges were collected by the authors or kindly provided by
 colleagues from various agencies and institutions in the USA and
 Canada. Genomic DNA was extracted from 0.10-0.25
 cm<sup>3</sup> of tissue or from 200 ml of lysis buffer from
 each sample using a modified alcohol extraction method following Wilson
 (1997). Seven microsatellite loci developed for <i>L. abrupta
 </i>(Eackles and King 2002) that amplify across
 <i>Lampsilis</i> species were used. Each microsatellite locus
 was amplified via a polymerase chain reaction (PCR) in a 10 ml reaction
 containing the following concentrations: 10.0-20.0 ng/ml of extracted
 genomic DNA, 0.3 mM dNTPs, 10mM Tris-HCl buffer (pH 8.3), 2.5-3 mM
 MgCl<sub>2</sub>, 0.2 mM each fluorescently-labeled primer and
 1U Taq polymerase. The amplification conditions as follows: initial
 heating at 94°C for 2 min, then 30 cycles of 94°C for 40 s, annealing at
 53-57°C for 40 s, and a 1 min extension time at 72°C followed by a final
 extension of 10 min at 72°C. All PCR products were screened on 7%
 polyacrylamide gels in a LI-COR NEN® Global IR2 DNA Sequencer System,
 using fluorescently labeled primers. Allele size was determined by
 comparing amplified products to 50-350 bp size standards (LI-COR
 Biotechnology Division).Locus C2 (Eackles and King 2002) has a compound
 trinucleotide repeat motif and it showed two alleles that only differed in
 length by one base-pair (scored in this study as 157 and 158; these
 alleles are 19 bp longer than the length reported by Eackles and King
 (2002) due to an M13 tail that is added with florescent dye). These
 alleles were cloned using TOPO TA Cloning kit (ThermoFisher Scientific)
 following the manufacturer’s manual. Transformed clones were sequenced
 using Sanger sequencing by TACGen, CA. That demonstrated that they are two
 different alleles, identified as 157 and 160.
DOI: 10.5061/dryad.bg79cnp9t
title: Specialized spatial cognition is associated with reduced cognitive senescence in a food-caching bird

description: Senescence, the gradual reduction and loss of function as organisms age,
 is a widespread process that is especially pronounced in cognitive
 abilities. Senescence appears to have a genetic basis and can be affected
 by evolutionary processes. If cognitive senescence is shaped by natural
 selection, it may be linked with selection on cognitive abilities needed
 for survival and reproduction, such that species in which fitness is
 directly related to cognitive abilities should evolve delayed cognitive
 senescence. We used wild food-caching mountain chickadees, which rely on
 specialized spatial cognition to recover thousands of food caches
 annually, to test for cognitive senescence in spatial learning and memory
 and reversal spatial learning and memory abilities. We detected no signs
 of age-related senescence in spatial cognitive performance on either task
 in birds ranging from 1 to 6 years old; older birds actually performed
 better on spatial learning and memory tasks than younger birds. Our
 results, therefore, suggest that cognitive senescence may be either
 delayed or negligible in species with strong selection on cognitive
 abilities and that food-caching species may present a useful novel model
 to investigate genetic and molecular mechanisms associated with cognitive
 senescence.
description: See VariableKey file for explanation of values.
DOI: 10.5061/dryad.jdfn2z39z
title: Data from: Telomere length is highly heritable and independent of growth rate manipulated by temperature in field crickets

description: Many organisms are capable of growing faster than they do. Restrained
 growth rate has functionally been explained by negative effects on
 lifespan of accelerated growth. However, the underlying mechanisms remain
 elusive. Telomere attrition has been proposed as a causal agent and has
 been mostly studied in endothermic vertebrates. We established that
 telomeres exist as chromosomal-ends in a model insect, the field cricket
 G. campestris, using terminal restriction fragment and Bal 31 methods.
 Telomeres comprised TTAGGn repeats of 38kb on average, more than four
 times longer than the telomeres of human infants. Bal 31 assays confirmed
 that telomeric repeats were located at the chromosome-ends. We tested
 whether rapid growth between day 1, day 65, day 85, and day 125 is
 achieved at the expense of telomere length by comparing nymphs reared at
 23°C with their siblings reared at 28°C, which grew three times faster in
 the initial 65 days. Surprisingly, neither temperature treatment nor age
 affected average telomere length. Concomitantly, the broad sense
 heritability of telomere length was remarkably high at ~100%. Despite high
 heritability, the evolvability (a mean-standardized measure of genetic
 variance) was low relative to that of body mass. We discuss our findings
 in the context of telomere evolution. Some important features of
 vertebrate telomere biology are evident in an insect species dating back
 to the Triassic. The apparent lack of an effect of growth rate on telomere
 length is puzzling, suggesting strong telomere length maintenance during
 the growth phase. Whether such maintenance of telomere length is adaptive
 remains elusive and requires further study investigating the links with
 fitness in the wild.
description: The methods are described, in detail, in the
 associated paper.
DOI: 10.5061/dryad.wm37pvmmn
title: Details of the clinical and CSF findings in the enrolled patients with time-matched paired serum and CSF samples

description: Demographics and clinical features of the enrolled patients with either of
 the three demyelinating neurological diseases according to the presence of
 disease-specific antibody (MOG-IgG, AQP4-IgG), confirmed by
 a live cell-based assay method, are shown in the dataset.
 Patients treated in our facility (Tohoku University, Japan) with acute
 neurological episodes in whom time-matched paired serum and CSF MOG-IgG
 and AQP4-IgG titers were simultaneously evaluated during the acute phase
 of the neurological episodes between 2006 and 2020 were initially
 recruited. To increase the sample size, eligible data of the
 patients from other facilities in Japan were additionally collected. Based
 on the results of the MOG-IgG and AQP4-IgG titrations for their serum and
 CSF samples, patients were divided into the following four disease groups:
 MOG-IgG-associated disease (MOGAD), AQP4-IgG-positive neuromyelitis optica
 spectrum disorder (anti-AQP4-positive NMOSD), multiple sclerosis
 (MS) without these antibodies, and other conditions. Patients with the
 first three disease groups were included for the study.
description: Anti-AQP4(+)NMOSD, anti-aquaporin-4 antibodies-positive
 neuromyelitis optica spectrum disorder; F, female; M, male; MOGAD,
 anti-myelin oligodendrocyte glycoprotein-associated disease; MS, multiple
 sclerosis; OCB, oligoclonal bands; ON, optic neuritis; PSL,
 prednisolone.
DOI: 10.5061/dryad.d51c5b02r
title: Human-associated microbiota suppress invading bacteria even under disruption by antibiotics

description: In light of their adverse impacts on resident microbial communities, it is
 widely predicted that broad-spectrum antibiotics can promote the spread of
 resistance by releasing resistant strains from competition with other
 strains and species. We investigated the competitive suppression of a
 resistant strain of Escherichia coli inoculated into human-associated
 communities in the presence and absence of the broad and narrow spectrum
 antibiotics rifampicin and polymyxin B, respectively. We found strong
 evidence of community-level suppression of the resistant strain in the
 absence of antibiotics and, despite large changes in community composition
 and abundance following rifampicin exposure, suppression of the invading
 resistant strain was maintained in both antibiotic treatments. Instead,
 the strength of competitive suppression was more strongly associated with
 the source community (stool sample from individual human donor). This
 suggests microbiome composition strongly influences the competitive
 suppression of antibiotic-resistant strains, but at least some
 antibiotic-associated disruption can be tolerated before competitive
 release is observed. A deeper understanding of this association will aid
 the development of ecologically-aware strategies for managing antibiotic
 resistance.
description: Please see: Letten, A.D., Baumgartner, M., Pfrunder-Cardozo,
 K.R., Levine, J.M. and Hall, A.R. 2021. Human-associated microbiota
 suppress invading bacteria even under disruption by antibiotics.
 <em>The ISME Journal</em>
description: otufile.txt - OTU abundance and taxonomic identification
 file<br> mapfile.txt - Metadata mapping file containing sequencing
 and experimental info for each sample<br> cfu_counts.csv - Counts of
 colony forming units across each treatment See
 readme.txt for an explanation of all variables