cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vv197
title: Data from: Constraints on geographic variation in fiddler crabs (Ocypodidae: Uca) from the western Atlantic

description: A key question in evolutionary biology is how intraspecific variation
 biases the evolution of a population and its divergence from other
 populations. Such constraints potentially limit the extent to which
 populations respond to selection, but may endure long enough to have
 macroevolutionary consequences. Previous studies have focused on the
 association between covariation patterns and divergence among isolated
 populations. Few have focused on geographic variation among semi-connected
 populations, however, even though this may be indicative of early
 selective pressures that could lead to long-term divergence and
 speciation. Here, we test whether covariation in the shape of the carapace
 of fiddler crabs (genus Uca Leach, 1814) is important for structuring
 geographic variation. We find that morphological divergence among
 populations is associated with evolvability in the direction of divergence
 in only a few species. The shape of the ancestral covariation matrix in
 these species differs from other species in having notably more variation
 concentrated along fewer directions (i.e., higher eccentricity). For most
 species, there is some evidence that covariation has constrained the range
 of directions into which populations have diverged but not the degree of
 divergence. These results suggest that even though fiddler crab
 populations have diverged morphologically in directions predicted by
 covariation, constraints on the extent to which divergence has occurred
 may only be manifested in species where variation patterns are eccentric
 enough to limit populations’ ability to respond effectively in many
 directions.
description: Hopkins_etal_landmarkdataLandmark data for all specimens used in analysis, and associated tables linking specimen names to populations and locality information. See published paper for figure showing placement of landmarks on the carapace. Locality table is the same as that published in the supplementary materials.
DOI: 10.25345/c5hd7p61d
title: MassIVE MSV000100596 - GNPS-Taurine supplementation in mice study
title: This dataset consists of untargeted LC-MS/MS metabolomics data from blood samples collected from mice supplemented with unlabeled and 13C-labeled taurine. MS/MS data acquisition was carried out on Thermo Q Exactive mass spectrometer in positive ionization mode, with chromatographic separation achieved using a Phenomenex Polar C18 column.
DOI: 10.5061/dryad.th2c5f7
title: Data from: Estimating sensitivity of seabed habitats to disturbance by bottom trawling based on the longevity of benthic fauna

description: Bottom fishing such as trawling and dredging may pose serious risks to the
 seabed and benthic habitats, calling for a quantitative assessment method
 to evaluate the impact and guide management to develop mitigation
 measures. We provide a method to estimate the sensitivity of benthic
 habitats based on the longevity composition of the invertebrate community.
 We hypothesize that long-lived species are more sensitive to trawling
 mortality due to their lower pace of life (i.e. slower growth, late
 maturation). We analyse data from box-core and grab samples taken from 401
 stations in the English Channel and southern North Sea to estimate the
 habitat-specific longevity composition of the benthic invertebrate
 community and of specific functional groups (i.e. suspension feeders and
 bioturbators), and examine how bottom trawling affects the longevity
 biomass composition. The longevity biomass composition differed between
 habitats governed by differences in sediment composition (gravel and mud
 content) and tidal bed-shear stress. The biomass proportion of long-lived
 species increased with gravel content and decreased with mud content and
 shear stress. Bioturbators had a higher median longevity than suspension
 feeders. Trawling, in particular by gears that penetrate the seabed
 &gt;2cm, shifted the community towards shorter-lived species. Changes
 from bottom trawling were highest in habitats with many long-lived species
 (hence increasing with gravel content, decreasing with mud content).
 Benthic communities in high shear stress habitats were less affected by
 bottom trawling. Using these relationships, we predicted the sensitivity
 of the benthic community from bottom trawling impact at large spatial
 scale (the North Sea). We derived different benthic sensitivity metrics
 that provide a basis to estimate indicators of trawling impact on a
 continuous scale for the total community and specific functional groups.
 In combination with high resolution data of trawling pressure, our
 approach can be used to monitor and assess trawling impact and seabed
 status at the scale of the region or broadscale habitat and to compare the
 environmental impact of bottom-contacting fishing gears across fisheries.
description: CumulativeBiomass_by_LongevityClass_Data_DryadSee readme
DOI: 10.5061/dryad.j18qs
title: Data from: Paleocommunity analysis of the Burgess Shale Tulip Beds, Mount Stephen, British Columbia: comparison with the Walcott Quarry and implications for community variation in the Burgess Shale

description: The Tulip Beds locality on Mount Stephen (Yoho National Park, British
 Columbia) yields one of the most abundant and diverse (~10,000 specimens
 in 110 taxa) Burgess Shale fossil assemblages in the Canadian Rockies.
 Detailed semi quantitative and quantitative analyses of this assemblage
 suggest strong similarities with the Walcott Quarry on Fossil Ridge. Both
 assemblages are dominated by epibenthic, sessile, and suspension feeding
 taxa, mostly represented by arthropods and sponges and have comparable
 diversity patterns, despite sharing only about half the genera. However,
 the Tulip Beds has a higher relative abundance of suspension feeders and
 taxa of unknown affinity compared to the Walcott Quarry. These biotic
 variations are probably largely attributable to ecological and
 evolutionary differences between the two temporally distinct communities
 that adapted to similar, but not identical, environmental settings. For
 instance, the Tulip Beds is farther away from the Cathedral Escarpment
 than the Walcott Quarry. The Tulip Beds and Walcott Quarry assemblages are
 more similar to each other than either one is to the assemblages of the
 Chengjiang biota, although the relative diversity of major taxonomic
 groups and ecological patterns are similar in all assemblages. The
 conserved diversity patterns and ecological structures among sites suggest
 that the ecological composition of Cambrian Burgess Shale-type communities
 was relatively stable across wide geographic and temporal scales.
description: Supplementary_Table_1Taxa of the Tulip Beds with their respective abundance, ecological modes (tieirng level, motility and feeding mode), and phyla (or other higher taxonomic grouping)Supplementary_Table_2Taxa of the Walcott Quarry with their respective abundance, ecological modes (tieirng level, motility and feeding mode), and phyla (or other higher taxonomic grouping). This dataset is adapted from Caron and Jackson (2008); see the original paper for details on data collection.Supplementary_Table_3Taxa of Walcott Quarry with their respective abundances for each of 26 bedding assemblages. This data has been modified from Caron and Jackson (2008); see the original paper for details on data collection.Supplementary_Table_4ASummary statistics for the co-occurrence (clustering) of specimens of the same species on a slab. See Appendix 4B for the raw data.Supplementary_Table_4BRaw data for the co-occurrence (clustering) of specimens of the same species on a slab. See Appendix 4A for the summary statistics.
DOI: 10.5061/dryad.s0vc7
title: Data from: Evolution of a mating preference for a dual-utility trait used in intrasexual competition in genetically monogamous populations

description: The selection pressures by which mating preferences for ornamental traits
 can evolve in genetically monogamous mating systems remain understudied.
 Empirical evidence from several taxa supports the prevalence of
 dual-utility traits, defined as traits used both as armaments in
 intersexual selection and ornaments in intrasexual selection, as well as
 the importance of intrasexual resource competition for the evolution of
 female ornamentation. Here, we study whether mating preferences for traits
 used in intrasexual resource competition can evolve under genetic
 monogamy. We find that a mating preference for a competitive trait can
 evolve and affect the evolution of the trait. The preference is more
 likely to persist when the fecundity benefit for mates of successful
 competitors is large and the aversion to unornamented potential mates is
 strong. The preference can persist for long periods or potentially
 permanently even when it incurs slight costs. Our results suggest that,
 when females use ornaments as signals in intrasexual resource competition,
 males can evolve mating preferences for those ornaments, illuminating both
 the evolution of female ornamentation and the evolution of male
 preferences for female ornaments in monogamous species.
description: Analytic derivations,
 simulation code and resultsThe ZIP archive contains
 a Mathematica notebook and a PDF version of the Mathematica notebook,
 showing the derivation of the model as well as the code for the
 simulations and the results of the simulations.
DOI: 10.5061/dryad.j3f08d2
title: Data from: Bryozoan genera Fenestrulina and Microporella no longer confamilial; multi-gene phylogeny supports separation

description: Bryozoans are a moderately diverse, mostly marine phylum with a fossil
 record extending to the early Ordovician. Compared to other phyla, little
 is known about their phylogenetic relationships at both lower and higher
 taxonomic levels. Hence, an effort is being made to elucidate the
 phylogenetic relationships among bryozoans. Here, we present newly
 sequenced nuclear and mitochondrial genes for 21 cheilostome bryozoans and
 compile these with existing orthologous molecular data. Using these data,
 we focus on reconstructing the phylogenetic relationships of Fenestrulina
 and Microporella, two species-rich genera. They are currently placed in a
 globally distributed family, Microporellidae, defined by having a
 semicircular primary orifice and a proximal ascopore, although there are
 indirect inferences in the morphological literature that suggest they
 might not be confamilial. Our six-gene phylogenetic analysis reveals that
 the genera Fenestrulina and Microporella are each monophyletic, with the
 sister clade to Microporella comprising non-microporellids. These genera
 thus have a polyphyletic relationship and should not be placed in the same
 family. Our result supports the reinstatement of the family
 Fenestrulinidae Jullien, 1888 for Fenestrulina and genera with comparable
 frontal shield and ooecial morphologies. Our well-supported phylogeny
 based on independent molecular data lends credit to existing phylogenetic
 hypotheses based on morphological observations but does not conform to the
 current classification of these particular bryozoans. This illustrates the
 general need for a rethink of bryozoan higher-level systematics, ideally
 based on both morphological and molecular data.
description: Fenestrulina:Microporella_18s.maskedFenestrulina:Microporella_18sFenestrulina:Microporella_CONCAT.maskedFenestrulina:Microporella_cox1.maskedFenestrulina:Microporella_cox1Fenestrulina:Microporella_cox3.maskedFenestrulina:Microporella_cox3Fenestrulina:Microporella_cytb.maskedFenestrulina:Microporella_rrnL.maskedFenestrulina:Microporella_cytbFenestrulina:Microporella_rrnLFenestrulina:Microporella_rrnS.maskedFenestrulina:Microporella_rrnS18scox1cox3cytBrrnLrrnS
DOI: 10.5061/dryad.87k57
title: Data from: Unsorted homology within locus and species trees

description: The concept of homology lies at the root of evolutionary biology. Since
 the seminal work of Fitch (1970) three main categories of homology
 relationships have been defined at the molecular level: orthology,
 paralogy and xenology. In brief, if two gene copies arose by duplication
 they are paralogs, while if they arose via speciation they are orthologs.
 If one of them was transferred from a contemporaneous species, we call
 them xenologs (Fig. S1 in doi: ; see Gray and Fitch 1983; Fitch 2000).
 Indeed, these terms were coined under a phylogenetic framework in which
 species were represented by single individuals, and as such they have
 remained very much intact during the last four decades –although
 particular cases within these categories have received specific names
 (Mindell and Meyer 2001). However, advances in sequencing technology have
 changed the field, and it is now very common to collect data sets
 containing multiple gene loci and/or multiple individuals per species. In
 general, genome-wide data sets not only have unveiled extensive
 phylogenomic incongruence (Jeffroy, Brinkmann, et al. 2006; Salichos and
 Rokas 2013) but have brought back to the spotlight the consideration of
 how ancestral polymorphisms sort within populations (Edwards 2009).
 Altogether, phylogenomic data makes imperative the explicit distinction
 between organismal and gene histories.
description: Supplementary
 MaterialSupplementary figures
 S1-S5
DOI: 10.5061/dryad.q1gb0
title: Data from: Evidence of a link between survival and pair fidelity across multiple tit populations

description: Although they have the potential to strongly influence individual fitness
 and the dynamics and productivity of populations, the survival
 consequences of pairing outcomes and the influence of current pairing
 outcomes on those in the future have rarely been addressed. Previously, we
 have shown that pair fidelity increases both survival and future pair
 fidelity in a population of great tits (Parus major). The aim of this
 study was to explore the generality of our previous findings by evaluating
 the influence of current paring outcomes on survival and on future pairing
 outcomes in two different species and in different populations. We
 addressed our aims within a multievent capture-mark-recapture (MECMR)
 statistical framework, which accounts for differences in recapture rates
 and uncertainty in the assignment of pair status (i.e. whether an
 individual is breeding with the same partner or not). We applied the
 framework to breeding records of two great tit populations and one blue
 tit (Cyanistes caeruleus) population. We detected survival benefits (i.e.
 increased survival) of pair fidelity in all three populations. These were
 similar in both great tit populations, but higher for male great tits than
 for male blue tits. We found that age-dependence in the rate of pair
 fidelity was shared between different populations and species, but did not
 detect any influence of current pair status on future pair status. Our
 study highlights the importance of considering survival when studying the
 fitness benefits of pair fidelity. Some of the differences in pair
 fidelity rates and survival benefits of pair fidelity are likely the
 result of long-term and short-term demographic and environmental factors
 in the population. We advocate the use of the MECMR framework used here
 for further exploration of these differences.
description: Capture histories used
 to model pair fidelity and survival in E_surgeData include capture
 histories (column 'H:') for a) female blue and great tits of
 Wytham woods; b) male blue and great tits of Wytham woods; c) female great
 tits of Wytham and Bagley woods; d) male great tits of Wytham and Bagley
 woods. For each dataset, the capture history is followed by the column
 'S:' (denotes number of individuals with the capture history),
 the column '$COV:Mgp' (covariate coding for age, either Juvenile
 or Adult), and the column '$COV:Sp; or ;$COV:Pop; (coding for
 Species: G - great tit, B -Blue tit; or population Bag - Bagley wood, Wyth
 = Wytham woods). These capture histories were used to model pair fidelity
 and survival in program E_Surge as described in the Supplementary material
 of the Culina et al. 2015. Capture histories consist of 6 different codes
 that describe the 'event' that happen for a particular bird in a
 particular season. The original data on breeding pairs come from the
 long-term monitored populations in these woods.Capture_histories.xlsm
DOI: 10.5061/dryad.g8140
title: Data from: Temporal dynamics of Puumala hantavirus infection in cyclic populations of bank voles

description: Understanding the dynamics of zoonotic pathogens in their reservoir host
 populations is a prerequisite for predicting and preventing human disease
 epidemics. The human infection risk of Puumala hantavirus (PUUV) is
 highest in northern Europe, where populations of the rodent host (bank
 vole, Myodes glareolus) undergo cyclic fluctuations. We conducted a 7-year
 capture-mark-recapture study to monitor seasonal and multiannual patterns
 of the PUUV infection rate in bank vole populations exhibiting a 3-year
 density cycle. Infected bank voles were most abundant in mid-winter months
 during years of increasing or peak host density. Prevalence of PUUV
 infection in bank voles exhibited a regular, seasonal pattern reflecting
 the annual population turnover and accumulation of infections within each
 year cohort. In autumn, the PUUV transmission rate tracked increasing host
 abundance, suggesting a density-dependent transmission. However,
 prevalence of PUUV infection was similar during the increase and peak
 years of the density cycle despite a twofold difference in host density.
 This may result from the high proportion of individuals carrying maternal
 antibodies constraining transmission during the cycle peak years. Our
 exceptionally intensive and long-term dataset provides a solid basis on
 which to develop models to predict the dynamic public health threat posed
 by PUUV in northern Europe.
description: Prevalence of PUUV per
 trapping sessionPrevalence of Puumala
 hantavirus infection in a cyclic, boreal bank vole population during a
 7-year capture-mark-recapture study. Prevalence per trapping session. Key
 to variable names on a separate worksheet.PUUV prevalence per trapping
 session.xlsSeroconversion rate per
 trapping sessionRate of Puumala
 hantavirus seroconversion (acquisition of specific antibodies) in a
 cyclic, boreal bank vole population during a 7-year capture-mark-recapture
 study. Rates per trapping session. Key to variable names on a separate
 worksheet.PUUV prevalence per year
 cohortPrevalence of Puumala
 hantavirus infection in a cyclic, boreal bank vole population during a
 7-year capture-mark-recapture study. Prevalences per bank vole year cohort
 and trapping session. Key to variable names on a separate
 worksheet.Seroconversion rate per
 year cohortRate of Puumala
 hantavirus seroconversion (acquisition of specific antibodies) in a
 cyclic, boreal bank vole population during a 7-year capture-mark-recapture
 study. Rates per bank vole year cohort and trapping session. Key to
 variable names on a separate worksheet.
DOI: 10.5061/dryad.b5pj61f
title: Data from: Depressed TSH level as a predictor of poststroke fatigue in patients with acute ischemic stroke

description: Objectives: To investigate whether thyroid function profiles can predict
 the poststroke fatigue (PSF) in patients with AIS. Methods: Stroke
 patients were consecutively recruited within 3 days of onset in Jinling
 hospital. Serum levels of thyroid hormones, thyroid antibodies,
 haematological indexes, and biochemical indexes were measured on
 admission. Fatigue was scored by the FSS. Association were analyzed with
 multivariate regression and restricted cubic splines. Results: Of the 704
 stroke patients, 292 (41.5%) were diagnosed with fatigue in the acute
 stage and 224 (35.3%) at 6-month of the index stroke. The serum levels of
 TSH were inversely associated with the risk of PSF in both acute phase and
 follow-up evaluations after adjusting for potential confounders (OR 0.30,
 95% CI 0.24-0.37 in the acute phase and OR 0.70, 95% CI 0.58-0.84 at
 follow-up). The subgroup analysis indicated that in acute phase of
 ischemic stroke, TSH was associated with the severity of PSF in group of
 euthyroidism (β = -0.70, p&lt;0.001), subclinical hypothyroidism (β =
 -0.44, p&lt;0.001) and low-T3 syndrome (β = -0.34, p=0.008). Higher
 TSH was associated with the better FSS scores in patients with low- T3
 syndrome at 6-month of the index stroke (β = -0.35, p=0.01). Furthermore,
 in the group of low-T3 syndrome, FT3 serum level could also indicate a
 higher risk of PSF (β = -2.54, p&lt;0.001 in the acute phase and β = -
 2.67, p&lt;0.001 at follow-up). Conclusions: Thyroid function profiles
 may predict fatigue after AIS, suggesting that neuroendocrine responses
 could play a role in PSF.
description: supplement methods and
 data
DOI: 10.5061/dryad.5b1k0
title: Data from: Many-to-one form-to-function mapping weakens parallel morphological evolution

description: Evolutionary ecologists aim to explain and predict evolutionary change
 under different selective regimes. Theory suggests that such evolutionary
 prediction should be more difficult for biomechanical systems in which
 different trait combinations generate the same functional output:
 “many-to-one mapping”. Many-to-one mapping of phenotype to function
 enables multiple morphological solutions to meet the same adaptive
 challenges. Therefore, many-to-one mapping should undermine parallel
 morphological evolution, and hence evolutionary predictability, even when
 selection pressures are shared among populations. Studying 16 replicate
 pairs of lake- and stream-adapted threespine stickleback (Gasterosteus
 aculeatus), we quantified three parts of the teleost feeding apparatus and
 used biomechanical models to calculate their expected functional outputs.
 The three feeding structures differed in their form-to-function
 relationship from one-to-one (lower jaw lever ratio) to increasingly
 many-to-one (buccal suction index, opercular 4-bar linkage). We tested for
 (1) weaker linear correlations between phenotype and calculated function,
 and (2) less parallel evolution across lake-stream pairs, in the
 many-to-one systems relative to the one-to-one system. We confirm both
 predictions, thus supporting the theoretical expectation that increasing
 many-to-one mapping undermines parallel evolution. Therefore, sole
 consideration of morphological variation within and among populations
 might not serve as a proxy for functional variation when multiple adaptive
 trait combinations exist.
description: main.cole
 Main R script to
 run first, to load packages, and set up directory structure, along with
 other housekeeping.   
 functions.cole Contains functions for analysis. Is sourced by main.cole   figures.cole Contains figure functions. Is sourced by main.R   analyses.cole_MS_161115 analysis code, used to generate the statistics, analyses, and output in the manuscript. requires main.cole to be run first.   CalculateKTCode Calculates Kinematic Transmission for the Opercular 4-bar system.   Complexity Simulation Code for the simulation that compares levels of many-to-one mapping across biomechanical systems.   03.dietCntnt_fromGitHub_161013 Gut content data.   Results_all_R_SI_KT_sexSL Biomechanical trait measurements.