cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4m7v7
title: Data from: Mechanical sensitivity reveals evolutionary dynamics of mechanical systems

description: A classic question in evolutionary biology is how form–function
 relationships promote or limit diversification. Mechanical metrics, such
 as kinematic transmission (KT) in linkage systems, are useful tools for
 examining the evolution of form and function in a comparative context. The
 convergence of disparate systems on equivalent metric values (mechanical
 equivalence) has been highlighted as a source of potential morphological
 diversity under the assumption that morphology can evolve with minimal
 impact on function. However, this assumption does not account for
 mechanical sensitivity—the sensitivity of the metric to morphological
 changes in individual components of a structure. We examined the
 diversification of a four-bar linkage system in mantis shrimp
 (Stomatopoda), and found evidence for both mechanical equivalence and
 differential mechanical sensitivity. KT exhibited variable correlations
 with individual linkage components, highlighting the components that
 influence KT evolution, and the components that are free to evolve
 independently from KT and thereby contribute to the observed pattern of
 mechanical equivalence. Determining the mechanical sensitivity in a system
 leads to a deeper understanding of both functional convergence and
 morphological diversification. This study illustrates the importance of
 multi-level analyses in delineating the factors that limit and promote
 diversification in form–function systems.
description: Anderson&Patek2015_species_dataUsing 196 museum specimens from 36 stomatopod species, we measured morphological and biomechanical data related to the 4-bar system in the raptorial appendage. These data are divided into two files: Anderson&Patek2015_species_data contains species averages for Kinematic Transmission (KT) as well as average link lengths (Link1, Link 2, Link 3, and Link 4) and PC scores for the species (PC1-PC8). Note that in the manuscript, we divided links 1, 2 and 3 by link 4 for analyses.Anderson&Patek2015_individuals_dataUsing 196 museum specimens from 36 stomatopod species, we measured morphological and biomechanical data related to the 4-bar system in the raptorial appendage. These data are divided into two files: Anderson&Patek2015_individuals_data contains the PC scores and KT values for the 196 specimens measured. This data was used to construct the specimen-based morphospace in the manuscript.
DOI: 10.5061/dryad.n48q0
title: Data from: Genetic and phenotypic influences on copulatory plug survival in mice

description: Across a diversity of animals, male seminal fluid coagulates upon
 ejaculation to form a hardened structure known as a copulatory plug.
 Previous studies suggest that copulatory plugs evolved as a mechanism for
 males to impede remating by females, but detailed investigations into the
 time course over which plugs survive in the female’s reproductive tract
 are lacking. Here, we cross males from eight inbred strains to females
 from two inbred strains of house mice (Mus musculus domesticus). Plug
 survival was significantly affected by male genotype. Against intuition,
 plug survival time was negatively correlated with plug size: long-lasting
 plugs were small and relatively more susceptible to proteolysis. Plug size
 was associated with divergence in major protein composition of seminal
 vesicle fluid, suggesting that changes in gene expression may play an
 important role in plug dynamics. In contrast, we found no correlation to
 genetic variation in the protein-coding regions of five genes thought to
 be important in copulatory plug formation (Tgm4, Svs1, Svs2, Svs4 and
 Svs5). Our study demonstrates a complex relationship between copulatory
 plug characteristics and survival. We discuss several models to explain
 unexpected variation in plug phenotypes.
description: Experimental
 MatingsColumn headers as
 follows: Female=Female genotype; Male= Male genotype; Male No= Individual
 male's ID; Time After Split (hrs)= Time (hrs) between mating and
 dissection; Plug (Y/N)= Indicating if the plug was still present at time
 of dissection; Mating (Y/N)= Indicates if a plug was present after
 experimental cross; Weight of Plug (g)= The absolute mass of the plug (NA
 indicates non successful mating); Weight of Female (g): Weight of female
 at dissection; Female DOB: Female's date of birth; Dissection Date=
 Date female was euthanizedSuppTable1
 (1).xlsxMale morphological
 dataColumn headers are as
 follows:Male= Male genotype; Male No= Individual male's ID; Date of
 Birth= Male's date of birth; Body Weight (g)= Body weight at
 dissection; Seminal Vesicle Weight (g)=Absolute weight of the left seminal
 vesicle; Right Testis Weight (g)= Absolute weight of the right testis;
 Left Testis Weight (g)= Absolute weight of the left
 testisSuppTable2
 (1).xlsProtein quantification
 across genotypesColumn headers are as
 follows: Male=Male genotype; SVS1:SVS5=abundance of each protein band/sum
 of the abundances of the four protein bands; Total=Absolute value of
 abundance of 4protein bandsSuppTable3
 (1).xlsx
DOI: 10.5061/dryad.n8v4m
title: Data from: Functional trait differences and trait plasticity mediate biotic resistance to potential plant invaders

description: 1. Biotic resistance represents an important natural barrier to potential
 invaders throughout the world, yet the underlying mechanisms that drive
 such resistance are still debated. In theory, native communities should
 repel both functionally similar invaders which compete for the same
 resources, and invaders which possess less competitive traits. However,
 environmental stress, trade-offs across vital rates and
 competition-induced plastic trait shifts may modify expected competitive
 outcomes, thereby influencing invasion dynamics. 2. In order to test these
 theoretical links between trait distributions and biotic resistance, we
 performed a mesocosm experiment with 25 non-native ornamental species
 invading native plant communities. Each non-native species was grown with
 and without the native community under two watering treatments (regular
 and reduced). We measured biotic resistance as the difference in
 performance of non-native individuals grown with and without the community
 in terms of their survival, growth and reproduction. We quantified overall
 functional dissimilarity between non-native ornamental individuals and
 native communities based on the combination of plant height, specific leaf
 area and seed mass. Then, assuming each of these traits is also
 potentially linked to competitive ability, we measured the position of
 non-natives on trait hierarchies. While height is positively correlated
 with competitive ability for light interception, conservative leaf and
 seed characteristics provide greater tolerance to competition for other
 resources. Finally, we quantified plastic trait shifts of non-native
 individuals induced by competition. 3. Indeed, the native community
 repelled functionally similar individuals by lowering their survival rate.
 Simultaneously, shorter ornamental individuals with larger specific leaf
 areas were less tolerant to biotic resistance from the community across
 vital rates, although the effect of trait hierarchies often depended on
 watering conditions. Finally, non-natives responded to competition by
 shifting their traits. Most importantly, individuals with more competitive
 traits were able to overcome biotic resistance also through
 competition-induced plastic trait shifts. 4. Synthesis. Our results
 highlight that both functional dissimilarity and trait hierarchies mediate
 biotic resistance to ornamental plant invaders. Nevertheless,
 environmental stress as well as opposing trends across vital rates are
 also influential. Furthermore, plastic trait shifts can reinforce
 potential invaders’ competitive superiority, determining a positive
 feedback.
description: Data for Conti et al.
 2017 JofEcol
DOI: 10.5061/dryad.n6sc718
title: Data from: Prevalence and diversity of haemosporidian parasites in the yellow-rumped warbler hybrid zone

description: Parasites can play a role in speciation, by exerting different selection
 pressures on different host lineages, leading to reproductive barriers in
 regions of possible interbreeding. Hybrid zones therefore offer an ideal
 system to study the effect of parasites on speciation. Here we study a
 hybrid zone in the foothills of the Rocky Mountains where two
 yellow-rumped warbler subspecies, Setophaga coronata coronata and S. c.
 auduboni, interbreed. There is partial reproductive isolation between
 them, but no evidence of strong assortative mating within the hybrid zone,
 suggesting the existence of a postzygotic selection against hybrids. Here,
 we test whether haemosporidian parasites might play a role in selecting
 against hybrids between S. c. coronata and S. c. auduboni. We screened
 birds from 5 transects across the hybrid zone for three phylogenetic
 groupings of avian haemosporidians Plasmodium, Haemoproteus and
 Leucocytozoon parasites and quantified intensity of infection. Contrary to
 our prediction, hybrids did not have higher haemosporidian parasite
 prevalence. Variation in Haemoproteus prevalence was best explained by an
 interaction between a birds’ hybrid index and elevation, while the
 probability of infection with Leucocytozoon parasites was only influenced
 by elevation. We also found no significant difference in the diversity of
 haemosporidian lineages between the warbler subspecies and their hybrids.
 Finally, intensity of infection by Haemoproteus increased significantly
 with elevation, but was not significantly linked to birds’ hybrid index.
 In conclusion, our data suggest that haemosporidian parasites do not seem
 to play a major role in selecting against hybrids in this system.
description: Cozzarolo_et_al_2018_YRW_haemosporidiansExcel file (4 sheets) containing yellow-rumped warblers (Setophaga coronata) data collected on the field in 2005-2007 and 2015, including body measurements, as well as diagnosis of infection by haemosporidian parasites.Cozzarolo_et_al_2018_data.xlsx
DOI: 10.5061/dryad.b28k2
title: Data from: The scope for nuclear selection within Termitomyces fungi associated with fungus-growing termites is limited

description: Background: We investigate the scope for selection at the level of nuclei
 within fungal individuals (mycelia) of the mutualistic Termitomyces
 cultivated by fungus-growing termites. Whereas in most basidiomycete fungi
 the number and kind of nuclei is strictly regulated to be two per cell, in
 Termitomyces mycelia the number of nuclei per cell is highly variable. We
 hypothesised that natural selection on these fungi not only occurs between
 mycelia, but also at the level of nuclei within the mycelium. We test this
 hypothesis using in vitro tests with five nuclear haplotypes of a
 Termitomyces species. Results: First, we studied the transition from a
 mixture of five homokaryons (mycelia with identical nuclei) each with a
 different nuclear haplotype to heterokaryons (mycelia with genetically
 different nuclei). In vitro cultivation of this mixture for multiple
 asexual transfers led to the formation of multiple heterokaryotic mycelia,
 and a reduction of mycelial diversity over time. All heterokaryotic
 mycelia contained exactly two types of nucleus. The success of a
 heterokaryon during in vitro cultivation was mainly determined by spore
 production and to a lesser extent mycelial growth rate. Second,
 heterokaryons invariably produced more spores than homokaryons implying
 that homokaryons will be outcompeted. Third, no homokaryotic ‘escapes’
 from a heterokaryon via the formation of homokaryotic spores were found,
 despite extensive spore genotyping. Fourth, in contrast to most studied
 basidiomycete fungi, in Termitomyces sp. no nuclear migration occurs
 during mating, limiting the scope for nuclear competition within the
 mycelium. Conclusions: Our experiments demonstrate that in this species of
 Termitomyces the scope for selection at the level of the nucleus within an
 established mycelium is limited. Although ‘mate choice’ of a particular
 nuclear haplotype is possible during mating, we infer that selection
 primarily occurs between mycelia with two types of nucleus
 (heterokaryons).
description: data on mycelial growth,
 nodulation and genotypingThe file contains data
 on Termitomyces mycelial growth rate and asexual spore yield, and on
 genotyping data from the mixing experimentsdata_file.xlsx
DOI: 10.5061/dryad.k8m4v
title: Data from: Conservation genetics of redside dace (Clinostomus elongatus): phylogeography and contemporary spatial structure

description: Redside dace Clinostomus elongatus (Teleostei: Cyprinidae) is a species of
 conservation concern that is declining throughout its range as a result of
 habitat fragmentation, degradation and loss. We characterized the genetic
 structure and diversity of redside dace populations across the species
 range using mitochondrial and microsatellite data to inform conservation
 efforts and assess how historical and recent events have shaped genetic
 structure and diversity within and among populations. Phylogeographic
 structure among 28 redside dace populations throughout southern Ontario
 (Canada) and the United States was assessed by sequence analysis of the
 mitochondrial cytochrome b and ATPase 6 and 8 genes. Populations were also
 genotyped using 10 microsatellite loci to examine genetic diversity within
 and among populations as well as contemporary spatial structuring.
 Mitochondrial DNA sequence data revealed three geographically distinct
 lineages, which were highly concordant with groupings identified by
 microsatellite analysis. The combined genetic data refute published
 glacial refugia hypotheses of a single Mississippian refugium or of two
 lineages associated with Mississippian and Atlantic refugia. Secondary
 contact between the two eastern groups was documented in the Allegheny
 River drainage and tributaries to Lake Ontario. With the exception of
 several allopatric populations within the Allegheny watershed, high
 genetic structuring among populations suggests their isolation, indicating
 that recovery efforts should be population-based.
description: Clinostomus elongatus
 ATPase6+8 sequence alignmentsequence alignment file
 of mitochondrial ATPase 6 and 8 sequences from redside dace (Clinostomus
 elongatus), aligned using MEGA 6Clinostomus_elongatus_ATPase_seq_alignment.masClinostomus_elongatus_cytb_seq_alignmentsequence alignment file of mitochondrial cytochrome b sequences from redside dace (Clinostomus elongatus), aligned using MEGA 6Clinostomus_elongatus_microsatellite_genotypesExcel spreadsheet of genotype data for 28 populations of Redside Dace (Clinostomus elongatus) genotyped at 10 microsatellite loci. Details on sampling locations and site codes are provided in the manuscript text.
DOI: 10.5061/dryad.8fh3g
title: Data from: TAPBPR bridges UDP-glucose:glycoprotein glucosyltransferase 1 onto MHC class I to provide quality control in the antigen presentation pathway

description: Recently we revealed that TAPBPR is a peptide exchange catalyst important
 for optimal peptide selection by MHC class I molecules. Here we asked if
 any other co-factors associate with TAPBPR which would explain its effect
 on peptide selection. We identify an interaction between TAPBPR and
 UDP-glucose:glycoprotein glucosyltransferase 1 (UGT1), a folding sensor in
 the calnexin/calreticulin quality control cycle known to regenerate the
 Glc1Man9GlcNAc2 moiety on glycoproteins. Our results suggest the formation
 of a multimeric complex, dependent on a conserved cysteine at position 94
 in TAPBPR, in which TAPBPR promotes the association of UGT1 with
 peptide-receptive class I molecules. We reveal that the interaction
 between TAPBPR and UGT1 facilities the reglucosylation of the glycan on
 class I, promoting their recognition by calreticulin. Our results suggest
 that in addition to being a peptide-editor, TAPBPR improves peptide
 optimisation by promoting peptide-receptive MHC class I molecules to
 associate with the peptide-loading complex.
description: MHC I peptide elutions
 from TAPBPR-WT and TAPBPR-C94A expressing cellsPeptide list version
 2.xlsx
DOI: 10.15468/dl.jd4egd
title: Occurrence Download

description: A dataset containing 373 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Carex bohemica"
 ]
}

 The dataset includes 373 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000761-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.51j89
title: Data from: Habituation in non-neural organisms: evidence from slime moulds

description: Learning, defined as a change in behaviour evoked by experience, has
 hitherto been investigated almost exclusively in multicellular neural
 organisms. Evidence for learning in non-neural multicellular organisms is
 scant and only a few unequivocal reports of learning have been described
 in single celled organisms. Here we demonstrate habituation, an
 unmistakable form of learning, in the non-neural organism Physarum
 polycephalum. In our experiment, using chemotaxis as the behavioural
 output and quinine or caffeine as the stimulus, we showed that P.
 polycephalum learnt to ignore quinine or caffeine when the stimuli were
 repeated, but responded again when the stimulus was withheld for a certain
 time. Our results meet the principle criteria that have been used to
 demonstrate habituation: responsiveness decline and spontaneous recovery.
 To distinguish habituation from sensory adaptation or motor fatigue, we
 also show stimulus specificity. Our results point to the diversity of
 organisms lacking neurons, which likely display a hitherto unrecognized
 capacity for learning, and suggest that slime moulds may be an ideal model
 system in which to investigate fundamental mechanisms underlying learning
 processes. Besides, documenting learning in non-neural organisms such as
 slime moulds is centrally important to a comprehensive, phylogenetic
 understanding of when and where in the tree of life the earliest
 manifestations of learning evolved.
description: Full
 datasetAll variables measured
 are in this table.Data_Ms_REV.sav
DOI: 10.5061/dryad.gq429f33
title: Data from: It's a family matter: molecular phylogenetics of Atheriniformes and the polyphyly of surf silversides (Family: Notocheiridae)

description: Phylogenetic relationships among families of Atheriniformes have long been
 problematic. The affinities of one of the most enigmatic lineages, surf
 silversides (Notocheiridae), have proven particularly elusive due to this
 taxon’s unique morphology and rarity in museum collections. In this study,
 we use mitochondrial and nuclear sequence data to generate a phylogeny for
 seven of the eight families of Atheriniformes. Our results reveal that
 four families within Atheriniformes (Atherinopsidae, Notocheiridae,
 Atherinidae, Melanotaeniidae) are not monophyletic. Most notably,
 Notocheiridae is polyphyletic, with Notocheirus hubbsi nested within New
 World silversides (Atherinopsidae), while members of Iso are sister to all
 other Old World Atheriniforms. These data suggest that the unique
 morphology of Notocheirus and Iso is a result of adaptive convergent
 evolution to the high-energy surf habitat where these species live.
description: NOTORAG1CYTBNexus file of DNA sequence data from Cytochrome B and RAG1 for various Atheriniformes.
DOI: 10.5061/dryad.4nj00
title: Data from: Genetic diversity does not explain variation in extra-pair paternity in multiple populations of a songbird

description: Many songbirds are socially monogamous but genetically polyandrous, mating
 with individuals outside their pair bonds. Extra-pair paternity (EPP)
 varies within and across species, but reasons for this variation remain
 unclear. One possible source of variation is population genetic diversity,
 which has been shown in interspecific meta-analyses to correlate with EPP
 but which has limited support from intraspecific tests. Using eight
 populations of the genetically polyandrous red-winged blackbird (Agelaius
 phoeniceus), including an island population, we investigated whether
 population-level differences in genetic diversity led to differences in
 EPP. We first measured genetic diversity over ten microsatellite loci and
 found, as predicted, low genetic diversity in the island population.
 Additional structure analyses with multilocus genotypes and mtDNA showed
 the island population to be distinct from the continental populations.
 However, the island population’s EPP rate fell in the middle of the
 continental populations’ distribution, while the continental populations
 themselves showed significant variation in EPP. This result suggests that
 genetic diversity by itself is not a predictor of EPP rate. We discuss
 reasons for the departure from previous results, including hypotheses for
 EPP that do not solely implicate female-driven behavior.
description: IAL_gen_diversity_bootstrapR script using the bootstrap to estimate three measures of genetic diversity (allelic diversity, Shannon diversity, and expected heterozygosity). Requires IAL_popsim.R and an input file of microsatellite genotypes (IAL_RWBL_genotypes.csv). Written by J. Johndrow.IAL_popsimR function needed for IAL_gen_diversity_bootstrap.R. Written by J. Johndrow.IAL_random_effects_modelR script generating random-effects model. Requires input file of extra-pair paternity rates (IAL_RWBL_EPP_allpops.csv). Written by J. Johndrow.IAL_RWBL_BahMIPA_nest_genotypesGenotypes of female, social male, and chicks at nests sampled in the Bahamas, Michigan, and Pennsylvania. These data were used to measure extra-pair paternity (EPP) in the three populations.IAL_RWBL_EPP_allpopsExtra-pair paternity (EPP) data for all eight populations, as measured by number of extra-pair young and number of nests containing at least one extra-pair young. "0" and "1" indicate a negative and positive response, respectively.IAL_RWBL_genotypesGenotypes of ten microsatellite loci for 307 red-winged blackbirds across eight populations.IAL_RWBL_ND2_sequencesSequence data for the ND2 region of mtDNA for 28 individuals (14 from the Bahamas populations and two each from the seven continental populations).IAL_RWBL_Structure_mainparamsMain parameters file for Structure runs.