cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.08kprr510
title: Raw fitness data (offspring number and weight), main dataset for manuscript: Female-specific resource limitation does not make the opportunity for selection more female biased

description: The present dataset contains the entirety of the raw empirical data used
 in the manuscript entitled: "Female-specific resource limitation does
 not make the opportunity for selection more female biased". This data
 is composed of offspring count and weight, which represent proxys of
 fitness. Fitness was assessed for males and females independently, and
 across three different experimental treatments. These fitness measures are
 used to calculate the opportunity for selection, as the variance in
 realtive fitness. Detailed methods regarding data collection can be found
 in the main manuscript.
description: See manuscript "Female-specific resource limitation does not
 make the opportunity for selection more female biased", method
 section.
description: Data: raw fitness data (offspring count and weight)
 ################################### Page1
 (Raw): Raw data as collected Page2 (no_NAS): Raw data
 with NAs removed and additional columns (see description of headers
 below). NAs correspond to assays where less than 4 individuals were found,
 which are automatically considered faulty assays (a normal assay contains
 4 parental individuals at least).
 ###################################
 Description of data headers Page 1:
 -Type_id:unique identifier for each data point.
 -Treatment: Experimental treatment (see manuscript for more
 details) -Sex: Type of assay, "f" for female,
 "m" for male. -date: Unique identifier for
 the day a particular assay was set up. -Weight: Total
 weight of individuals in the assay. -Offspring: Total
 number of individuals in the assay.
 ###################################
 Description of data headers Page2: -Type_id,
 treatment, sex, date, weight: same as Page1.
 -Ind_weight: Total offspring weight divided by offspring
 number=individual offspring weight. -individuals (eq.
 to offspring from Page 1): number of individuals counted in the assay,
 which should be 4 parent individuals + offspring.
 -offspring: actual number of offspring= number of individuals-4
 (removing 4 parents) -reloff_sex_trt: Relative
 offspring count (divided by the mean to obtain an average of 1) per sex
 per treatment. -relw_sex_trt: Relative offspring weight
 per sex per treatment.
 #################################
 #################################
DOI: 10.5061/dryad.bzkh1896w
title: Data from: Nasal compartmentalization in Kogiidae (Cetacea, Physeteroidea): Insights from a new late Miocene dwarf sperm whale from the Pisco Formation

description: Facial compartmentalization in the skull of extant pygmy whales (Kogiidae)
 is a unique feature among cetaceans that allows the housing of a wide
 array of organs responsible for echolocation. Recent fossil findings
 depict a remarkable disparity of the facial bone organization in Miocene
 kogiids, but the significance of such a rearrangement for the evolution of
 the clade has been barely explored. Here we describe Kogia
 danomurai sp. nov., a late Miocene (ca. 5.8 Ma) taxon from the
 Pisco Formation (Peru), based on a partially preserved skull with a new
 facial bone pattern. Our phylogenetic analysis recovers K.
 danomurai as the most basal representative of the extant
 genus Kogia, displaying a combination of derived (incipiently
 developed and excavated sagittal facial crest) and plesiomorphic features
 (high position of the temporal fossa and antorbital notch not transformed
 into a narrow slit). Furthermore, when compared with the
 extant Kogia, the facial patterning found in K.
 danomurai indicates differential development among the facial
 organs, implying different capabilities of sound production relative to
 extant Kogia spp. Different facial bone patterns are
 particularly notable within the multi-species kogiid assemblage of the
 Pisco Formation, which suggests causal connections between different
 patterns and feeding ecologies (e.g., nekton piscivory and benthic
 foraging). At about 5.8 Ma, K. danomurai was part of a
 cetacean community composed by clades typical of the late Miocene as well
 as other early representatives of extant taxa, a mixture probably
 depicting the initial faunal change toward the coastal ecosystem dynamics
 of the present-day Southeastern Pacific.
description: This dataset contains the character-taxon matrix (.nex file)
 and the complete list of characters (.pdf file)
DOI: 10.5061/dryad.1vhhmgqr5
title: Experimentally measured group direct benefits according to worker density explain group living of the termite Reticulitermes chinensis

description: The evolution of cooperation requires more benefits of group living than
 solitary lifestyle. However, to some degree, our understanding about the
 benefits is hindered by abstract debates over theoretical and experimental
 evidences of individual selection or group selection because it is
 difficult to examine the actual benefits at the group level. Moreover,
 group density is a crucial ecological factor which deeply affects group
 reproduction and survival, few studies have been performed in social
 insects. Here, we study the effects of worker density on group direct
 benefits in the termite species Reticulitermes chinensis. The termite R.
 chinensis is an ideal model which lives with a high worker density in
 wood. We used the quantity of eggs and the total biomass (biomass of all
 group members) accumulation as two components of group benefits. We
 investigated the group benefits in the context of worker density according
 to eleven worker densities. And we measured the group benefits and the
 resource consumption with the same group members in two types of
 artificial nest areas. Moreover, we counted the stomodeal trophallaxis
 occurrences from any workers to queens under three worker densities to
 explore the degree of cooperation according to worker density. We found
 that both the number of eggs and the total biomass accumulation
 significantly increased with increasing worker density in groups.
 Furthermore, the consumption of resources was similar between groups with
 the same number of individuals gathered in small or large nest areas, but
 the production of eggs and the biomass accumulation were higher in groups
 of small nest areas than in large nest areas. Additionally, we found the
 stomodeal trophallaxis behavior significantly increased in higher worker
 density groups. Our results suggest that the group benefits influenced by
 the high worker density may at least partially explain the group living of
 eusocial insects in ecology.
DOI: 10.5061/dryad.nk98sf7rr
title: Data from: A new dissorophoid temnospondyl from the Allegheny Group (Late Westphalian, Carboniferous) of Five Points, Mahoning County, Ohio (USA)

description: A small temnospondyl skull from the Upper Carboniferous Allegheny Group of
 Five Points, Ohio, is referred to a new dissorophoid, Palodromeus bairdi
 n. gen n. sp. The complete skull with mandibles is preserved in
 counterparts. It is characterized by (1) elongated slit-like choana, (2)
 postfrontal, postorbital, and supratemporal bearing a distinct ridge, and
 (3) reduced parietal only two-thirds the length of the frontal.
 Phylogenetic analysis confirms a dichotomy between amphibamiforms and
 olsoniforms and places Palodromeus bairdi at the base of the olsoniforms,
 revealing an early stage in the evolution of that clade.
description: Schoch_etal_Appendix REVISION.doc
DOI: 10.5061/dryad.2jm63xsmz
title: Supplementary materials for: Long term effects of cholinesterase inhibitors on cognitive decline and mortality

description: Objective: Cholinesterase inhibitors (ChEIs) are the mainstay treatment of
 Alzheimer’s dementia (AD), but their long-term effectiveness is uncertain.
 This study aims is to investigate whether ChEIs are associated with slower
 cognitive decline in AD, and decreased risk of severe dementia or death.
 Methods: AD patients from the Swedish Dementia Registry (SveDem) starting
 on ChEIs within three months of the dementia diagnosis were included and
 compared to non-treated AD patients. In a propensity score matched cohort,
 the association between ChEI-use and cognitive trajectories assessed by
 MMSE scores were examined with a mixed model, and severe dementia
 (MMSE&lt;10) or death as outcomes with Cox proportional hazards
 models. Results: The matched cohort included 11,652 ChEI-use and 5,826
 non-users. During an average of 5 years follow up, 255 cases developed
 severe dementia and 6,055 (35%) died. ChEI-use was associated with higher
 MMSE at each visit (0.13 MMSE points/year; 95% confidence interval-CI
 0.06, 0.20). ChEI-use had a 27% lower risk of death (0.73; CI 0.69, 0.77)
 compared with non-users. Galantamine was associated with lower risk of
 death (0.71; CI 0.65, 0.76), lower risk of severe dementia (0.69; CI
 0.47-1.00), and had the strongest effect on cognitive decline of all the
 ChEIs (0.18 MMSE points/year, CI 0.07, 0.28). Conclusions: ChEIs are
 associated with cognitive benefits which are modest but persist over time
 and with reduced mortality risk, which could be explained partly by their
 cognitive effects. Galantamine was the only ChEI demonstrating a
 significant reduction in the risk of developing severe dementia.
 Classification of Evidence: This study provides Class III evidence that
 for patients with AD, ChEIs decrease long term cognitive decline and risk
 of death, and that galantamine decreases the risk of severe dementia.
DOI: 10.5061/dryad.stqjq2c21
title: A study of tactical and sexual dimorphism in cognition with insights for sexual conflict

description: The sexes may have different optima in cognitive traits due to differences
 in life history strategies and the expense of investing in metabolically
 costly brain tissue. However, given genetic correlations, each sex could
 be constrained from reaching its cognitive optimum due to intralocus
 sexual conflict. We compared learning performance of two male alternative
 reproductive tactics and females from known genotypes (both sire and dam)
 in the livebearing fish Xiphophorus multilineatus. We predicted that
 females’ learning performance would align with the learning performance of
 their sire’s genotype due to genetic correlation of cognitive traits.
 Using a classical conditioning assessment (associating a flashing light
 with a food reward), we detected mating tactic dimorphism in learning
 performance, with the behaviourally plastic sneaker males outperforming
 the behaviourally fixed courter males. Unexpectedly, females
 sired by the faster-learning sneaker males performed significantly worse
 than sneaker males. We also detected an influence of brain size on female
 learning performance. Previous studies have found that females invest more
 in offspring sired by courter males, and we therefore hypothesize
 that maternal effects could potentially mitigate the influence of sexual
 conflict on a cognitive trait.
DOI: 10.5061/dryad.cvdncjt2r
title: Data from: Four myriapod relatives – but who are sisters? No end to debates on relationships among the four major myriapod subgroups

description: Background: Phylogenetic relationships among the myriapod subgroups
 Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly
 resolved. The first phylogenomic study covering all subgroups resolved
 phylogenetic relationships congruently to morphological evidence but is in
 conflict with most previously published phylogenetic trees based on
 diverse molecular data. Outgroup choice and long-branch attraction effects
 were stated as possible explanations for these incongruencies. In this
 study, we addressed these issues by extending the myriapod and outgroup
 taxon sampling using transcriptome data. Results: We generated new
 transcriptome data of 42 panarthropod species, including all four myriapod
 subgroups and additional outgroup taxa. Our taxon sampling was
 complemented by published transcriptome and genome data resulting in a
 supermatrix covering 59 species. We compiled two data sets, the first with
 a full coverage of genes per species (292 single-copy protein-coding
 genes), the second with a less stringent coverage (988 genes). We inferred
 phylogenetic relationships among myriapods using different data types,
 tree inference, and quartet computation approaches. Our results
 unambiguously support monophyletic Mandibulata and Myriapoda. Our analyses
 clearly showed that there is strong signal for a single unrooted topology,
 but a sensitivity of the position of the internal root on the choice of
 outgroups. However, we observe strong evidence for a clade
 Pauropoda+Symphyla, as well as for a clade Chilopoda+Diplopoda.
 Conclusions: Our best quartet topology is incongruent with current
 morphological phylogenies which were supported in another phylogenomic
 study. AU tests and quartet mapping reject the quartet topology congruent
 to trees inferred with morphological characters. Moreover, quartet mapping
 shows that confounding signal present in the data set is sufficient to
 explain the weak signal for the quartet topology derived from
 morphological characters. Although outgroup choice affects results, our
 study could narrow possible trees to derivatives of a single quartet
 topology. For highly disputed relationships, we propose to apply a series
 of tests (AU and quartet mapping), since results of such tests allow to
 narrow down possible relationships and to rule out confounding signal.
description: Material collection, generation of RNASeqdata and processing was
 done as described in the corresponding paper and supplementary text.
 Details are provided in the README.
DOI: 10.5061/dryad.fbg79cnsp
title: Supplementary materials: RADseq phylogenetics in two frog clades

description: Restriction-site associated DNA sequencing (RADseq) has become an
 accessible way to obtain genome-wide data in the form of single nucleotide
 polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how
 differences in RADseq methods influence phylogenetic estimation is poorly
 understood because most comparisons have largely relied on conceptual
 predictions rather than empirical tests. We examine how differences in
 ddRAD and 2bRAD data influence phylogenetic estimation in two non-model
 frog groups. We compare the impact of method choice on phylogenetic
 information, missing data, and allelic dropout, considering different
 sequencing depths. Given that researchers must balance input (funding,
 time) with output (amount and quality of data), we also provide
 comparisons of laboratory effort, computational time, monetary costs, and
 the repeatability of library preparation and sequencing. Both 2bRAD and
 ddRAD methods estimated well-supported trees, even at low sequencing
 depths, and had comparable amounts of missing data, patterns of allelic
 dropout, and phylogenetic signal. Compared to ddRAD, 2bRAD produced more
 repeatable datasets, had simpler laboratory protocols, and an overall
 faster bioinformatics assembly. However, many fewer parsimony-informative
 sites per SNP were obtained from 2bRAD data when using native pipelines,
 highlighting a need for further investigation into the effects of each
 pipeline on resulting datasets. Our study underscores the importance of
 comparing RADseq methods, such as expected results and theoretical
 performance using empirical datasets, before undertaking costly
 experiments.
description: <strong>Samples</strong>: 5 species of dendrobatid
 frog (n=12; two biological replicate samples) and 5 species of ranid frog
 (n=12; two biological replicate samples); total number of samples =
 24 <strong>Sequencing</strong>: 2bRAD and
 ddRAD for all samples (fastq files available on SRA)
 <strong>Bioinformatics assembly</strong>: iPyrad (for
 both ddRAD and 2bRAD) and Matz Lab native pipeline (for both ddRAD and
 2bRAD)  <strong>Analyses</strong>: RAxML
 tree reconstruction, calculation of shared sites (unambiguous
 synapomorphies), missing data, read depth, repeatability (based on
 biological replicate samples)
DOI: 10.5061/dryad.d7wm37q01
title: Canis dirus and Smilodon Procrustes coordinates

description: The primary goal of this paper is to examine and rationalize different
 integration metrics used in geometric morphometrics, in an attempt to
 arrive at a common basis for the characterization of phenotypic covariance
 in landmark data. We begin with a model system; two populations of
 Pleistocene dire wolves from Rancho La Brea that we examine from a
 data-analytic perspective to produce candidate models of integration. We
 then test these integration models using the appropriate statistics and
 extend this characterization to measures of whole-shape integration. We
 demonstrate that current measures of whole-shape integration fail to
 capture differences in the strength and pattern of integration. We trace
 this failure to the fact that current whole-shape integration metrics
 purport to measure only the pattern of inter-trait covariance, while
 ignoring the dimensionality across which trait variance is distributed. We
 suggest a modification to current metrics based on consideration of the
 Shannon, or information, entropy, and demonstrate that this metric
 successfully describes differences in whole shape integration patterns.
 Our new metric allows detailed comparison of the hyperellipses occupied by
 the two populations in morphospace (which is a form of covariance space).
 Finally, the information entropy approach allows comparison of whole shape
 integration in a dense semilandmark environments, and we demonstrate that
 the metric introduced here allows comparison of shape spaces that differ
 arbitrarily in their dimensionality and landmark membership.
description: These data comprise two dimensional landmark data from left jaws
 of the dire wolf, Canis dirus, from Rancho La Brea, California. The
 landmarks were digitized from photographs of the specimens.
description: The data set contains the following fields:
 <strong>Genus: </strong>This is Canis dirus, or
 Smilodon. Most the analyses in the paper concern Canis dirus, but we
 discuss the Smilodon data briefly in the discussion.
 <strong>Specimen/Photograph ID</strong>: This is the
 specimen number of the fossil photographed for Canis dirus. For Smilodon
 it is the photograph number indexed to data in:
 Meachen, J.A., O'Keefe, F.R. and Sadleir, R.W., 2014.
 Evolution in the sabre‐tooth cat, S milodon fatalis, in response to P
 leistocene climate change. <i>Journal of Evolutionary
 Biology</i>, <i>27</i>(4), pp.714-723.
 <strong>Pit:</strong> The Rancho La Brea pit deposit
 of origin for each fossil.
 <strong>LMnx,y</strong>: Original digitized landmark
 coordinates for Canis dirus jaws. These data are not included for Smilodon
 because we do not use them in the paper.
 <strong>1.x,y</strong>: Generalized Procrustes
 Analysis (GPA) transformed coordinates for Canis dirus and
 Smilodon. <strong>Centroid Size</strong>:
 This is the centroid size vector yielded by the GPA analysis.
DOI: 10.5061/dryad.9s4mw6mdr
title: Data from: Drivers of spatiotemporal variation in survival in a flyway population: a multi-colony study

description: 1. Spatio-temporal variation in population dynamics of migratory
 populations is shaped by exposure to different environments during the
 annual cycle. Hence, exposure to similar environments should translate
 into synchrony in vital rates. Despite a wide-ranging breeding population,
 the Baltic/Wadden Sea flyway population of eiders (Somateria m.
 mollissima) shares wintering grounds in the southern Baltic Sea, inner
 Danish waters and the Wadden Sea; different colonies within this flyway
 population are therefore likely to exhibit some degree of synchrony in
 vital rates. 2. Here we used capture-recapture-recovery data to
 investigate the impact of hunting, winter climate (the North-Atlantic
 Oscillation Index), winter temperature, nitrogen runoff, autumn-winter
 body condition of blue mussels Mytilus spp., natural predation and
 epidemic disease (avian cholera) on annual survival of adult females in
 ten study colonies distributed between the Netherlands and Finland.
 Moreover, we tested how the degree of similarity in spatial winter
 distributions affected the degree of similarity in annual survival among
 colonies. 3. None of the covariates universally affected female survival.
 While the quality of blue mussels in the wintering area explained almost
 40 % of the variation in survival of eiders breeding on Christiansø in the
 south-western Baltic Sea, incidence of epidemic disease explained &gt;
 60 % in two affected colonies. Furthermore, the spatial winter
 distribution did not appreciably influence annual survival rates in these
 ten colonies. 4. The lack of universal effects of spatial winter
 distribution and winter conditions on survival suggests that local
 breeding conditions may be more important, and hence prime targets for
 conservation efforts. Better monitoring of e.g. food quality, predation
 pressure and epidemic disease at the time of breeding could be the key to
 better understand the population dynamics in this endangered flyway
 population.
description: Long-term capture-recapture-recovery data on eider females from
 ten different colonies belonging to the Baltic-Wadden Sea flyway
 population. Encounter histories were compiled and prepared in a Live-Dead
 format for Program MARK. Environmental covariate data
 is in the Covariates_DRYAD.xlsx-file. Spatial recovery
 data of eider females in Recoveries_DRYAD.shp.
description: Notes on the CMR data is stated as a comment at the beginning of
 the inp.file. A README file is provided for the
 dataset Covariates_DRYAD.xlsx-file. A README file is
 provided for the dataset Recoveries_DRYAD.shp.
DOI: 10.5061/dryad.6wwpzgmwt
title: Generation of Propulsive Force via Vertical Undulations in Snakes

description: Lateral undulation is the most widespread mode of terrestrial vertebrate
 limbless locomotion, in which posteriorly propagating horizontal waves
 press against environmental asperities (e.g. grass, rocks) and generate
 propulsive reaction forces. We hypothesized that snakes can generate
 propulsion using a similar mechanism of posteriorly propagating vertical
 waves pressing against suitably oriented environmental asperities. Using
 an array of horizontally oriented cylinders, one of which was equipped
 with force sensors, and a motion capture system, we found snakes generated
 substantial propulsive force and propulsive impulse with minimal
 contribution from lateral undulation. Additional tests showed that snakes
 could propel themselves via vertical undulations from a single suitable
 contact point, and this mechanism was replicated in a robotic model.
 Vertical undulations can provide snakes a valuable locomotor tool for
 taking advantage of vertical asperities in a variety of habitats,
 potentially in combination with lateral undulation,  to fully
 exploit the 3D structure of the habitat.
description: This dataset was collected using a 248 cm long trackway with
 eleven horizontal oak dowels with one dowel equipped with two six-axis
 force sensors on either end. Four corn snakes (<em>Pantherophis
 guttatus</em>) were encouraged to traverse the trackway with six
 motion capture cameras set up to track their progress and obtain
 kinematics. Data was analyzed using a custom-written script in MATLAB. An
 ANOVA and Tukey's post-hoc statistical tests were carried out also
 using custom-written scripts in MATLAB. Two additional tests were
 conducted with an 8° (insufficient angle for vertical undulation) and 30º
 (sufficient angle for verticl undulation) sloped wedge to determine
 whether the snake could traverse a tunnel using vertical undulation.
 Finally, a snake-like robot, made of 3D printed parts and servo
 motors, was used to confirm whether vertical undulation alone can propel a
 snake-like robot through our experimental setup.