cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1786p
title: Data from: Potential effects of an invasive bivalve, Nuttallia obscurata, on select sediment attributes within the intertidal region of coastal British Columbia

description: On the west coast of British Columbia, Canada, the varnish clam, Nuttallia
 obscurata, is a rapidly spreading invasive species that can reach high
 densities (i.e. 800 individuals m− 2). A field survey (Tier I) and an in
 situ mesocosm density manipulation experiment (Tier II) were applied to
 determine the potential effects of this invasive bivalve on select
 sediment attributes within the intertidal zone. In situ experiments
 involved seeding 1 m2 mesocosms with varnish clams at four densities; 0
 (control), 200 (low), 500 (mid) and 800 (high). Sediment samples were
 taken 7 times over a three week period and analyzed for organic matter,
 ammonium and grain size (gravel, coarse silt, fine silt and silt) at three
 different depths, 0–3 cm (surface), 3–6 cm (intermediate) and 6–9 cm
 (bottom). Field surveys demonstrated that at natural densities bivalve
 distribution was best explained by sediment grain size. Contrary to
 expectations, the in situ manipulations indicated that at high densities
 varnish clams did not significantly increase sediment organic matter
 concentrations. Their ability to deposit feed and re-ingest biodeposits
 may have prevented accumulations. High densities of varnish clams did
 however result in significantly higher concentrations of sediment ammonium
 and percent silt, but mostly within the lower sections of the sediment
 core. Reworking of the surficial sediments due to intense storm activity
 likely obscured any differences in determined sediment attributes among
 the 4 treatments. Nitrogen is a limiting nutrient with ammonium
 preferentially used by phytoplankton and microphytobenthos. These primary
 producers form the basis of all marine food webs thus increases in amounts
 of ammonium to shallow coastal seas as a result of high densities of an
 invasive bivalve within intertidal zones could result in an increased risk
 of eutrophication within these sensitive regions.
description: Nutrient concentration
 and density data; A Canadian Healthy Oceans Network Ecosystem Function
 Project, EF-03Excel file with all
 nutrient concentrations determined in laboratory from sediment samples as
 well as bivalve densities from Tier I & II experiments. NA denotes
 samples that were not collected or missing due to procedural errors in
 laboratory. Blank cells are outliers that have been removed from
 statistical analysis. Tier III abbreviations are as follows: s =
 sterilized treatments; sv = sterilized treatments + varnish clams; us =
 unsterilized treatments; usv = unsterilized treatments + varnish
 clams.CHONe_EF-03_ChanK_Data.xlsxDiscovery metadata, A Canadian Healthy Oceans Network Ecosystem Function Project, EF-03Excel discovery metadata fileCHONe_EF-03_ChanK_DiscoveryMetadata v4-5.xlsxData report, A Canadian Healthy Oceans Network Ecosystem Function Project, EF-03Data report file in MS WordCHONe_EF-03_CHANK.docx
DOI: 10.5061/dryad.n3373
title: Data from: A positively selected APOBEC3H haplotype is associated with natural resistance to HIV-1 infection

description: APOBEC3 genes encode cytidine deaminases endowed with the ability to
 inhibit retroviruses and retrotransposons. These genes have been targets
 of natural selection throughout primate evolutionary history. We analysed
 their selection pattern in human populations observing that APOBEC3F and
 3G are neutrally evolving. Conversely, nucleotide diversity was extremely
 high for APOBEC3H, and most tests rejected the hypothesis of selective
 neutrality in Eurasian populations. Haplotype analysis and the derived
 intra-allelic nucleotide diversity test indicated that positive selection
 has driven the increase in frequency of one haplotype (Hap I) outside
 Africa. Consistently, population genetic differentiation between African
 and non-African populations was higher than expected under neutrality. A
 case/control association analysis indicated that Hap I is associated with
 protection from sexually transmitted HIV-1 infection. Hap I carries a
 protein-destabilizing variant and a residue conferring resistance to
 Vif-mediated degradation. Data herein suggest that lower protein stability
 might have been traded-off with a higher ability to circumvent
 Vif-mediated hijacking. Alternatively, transcription regulatory variants
 might represent the selection target. Our data represent an example of how
 the selective pressures exerted by extinct or unknown viral agents can be
 exploited to provide valuable information on the allelic determinants of
 susceptibility to modern infections.
description: Samples, methods and
 supporting analysescagliani_evo.zip
DOI: 10.18150/yhfco1
title: Multilayered TiO2/Ni/Ag cathode for efficient and long lifetime high temperature fuel cells

description: This work introduces a multilayer TiO₂/Ni/Ag cathode engineered to simultaneously suppress nickel dissolution and significantly enhance the electrochemical efficiency of molten carbonate fuel cells (MCFCs). The cathode architecture is built on a tape-cast catalytic layer supported by nickel foam, providing a robust and highly conductive backbone. The TiO₂ layer was selectively applied to the electrolyte-facing side of the cathode, while a thin, 300 nm silver film was sputtered onto the interconnector side to boost electronic transport. To directly address one of the most critical degradation mechanisms in MCFCs, a dedicated experimental protocol was developed to quantify nickel solubility in the molten electrolyte under realistic operating conditions. Single-cell tests incorporating various cathode configurations were performed at 650°C under different gas flow rates.
DOI: 10.5061/dryad.s3m5s
title: Data from: Expression of taste signal transduction molecules in the caecum of common marmosets

description: The extraoral presence of taste signal transduction proteins has recently
 been reported in rodents and humans. Here, we report for the first time
 the presence of these signal transduction proteins in the caecum of a
 non-human primate, the common marmoset. Quantitative RT-PCR data on the
 gene expression of taste signal transduction molecules (gustducin and
 TRPM5) in common marmosets suggested high expression in the caecum, which
 was not observed in other non-human primates. Immunohistochemical analysis
 confirmed the specific presence of gustducin and taste receptors in
 marmoset caecal cells. These results may relate to the specific feeding
 behaviour of marmosets, which consume plant exudates, primarily gums.
description: Gonda_SampleList_EnglishRT-qPCR gustducin_EnglishRT-qPCR TRPM5_EnglishRT-qPCR T1RsT2Rs_English
DOI: 10.5061/dryad.s791pg03
title: Data from: Molecular phylogeny and biogeography of Malagasy frogs of the genus Gephyromantis

description: The genus Gephyromantis is a clade within the Malagasy–Comoroan family
 Mantellidae composed of rainforest frogs that live and breed to varying
 degrees independently from water. Based on DNA sequences of five
 mitochondrial and five nuclear genes we inferred the phylogeny of these
 frogs with full taxon coverage at the species level. Our preferred
 consensus tree from a partitioned Bayesian analysis of 5843 base pairs of
 51 nominal and candidate species supports various major clades within the
 genus although the basal relationships among these remain unresolved. The
 data provide strong evidence for the monophyly of the subgenera
 Gephyromantis (after exclusion of Gephyromantis klemmeri), Laurentomantis,
 Vatomantis, and Phylacomantis. Species assigned to the subgenus
 Duboimantis belong to two strongly supported clades of uncertain
 relationships. G. klemmeri, previously in the subgenus Gephyromantis, was
 placed with high support sister to the Laurentomantis clade, and the
 Laurentomantis + G. klemmeri clade was sister to Vatomantis. A
 reconstruction of ancestral distribution areas indicates a diversification
 of several subgenera in the northern biogeographic regions of Madagascar
 and the dispersal out of northern Madagascar for several clades.
description: Kaffenberger_Gephyromantis_maxpart_alignmentInterleaved alignment of all genes in Nexus format, with exclusion settings and partition scheme as used in the final Bayesian analysis.
DOI: 10.5061/dryad.fm0g3m5
title: Data from: Hybridization could be a common phenomenon within the highly diverse lizard genus Liolaemus

description: Hybridization is likely to occur more often between closely related taxa
 that have had insufficient time to diverge to the point of reproductive
 incompatibility; hybridization between deeply divergent lineages is rare.
 In squamate reptiles, hybridization has been proposed as a possible
 explanation for the extensive paraphyly observed in mitochondrial gene
 trees in several species complexes of the South American lizard genus
 Liolaemus. One of the best-documented cases is within the L. boulengeri
 and L. rothi complexes, which diverged ~5.5 million years ago. Here we
 describe a comprehensive study for approaching the hybridization
 hypothesis between these lizard species complexes. We explored the level
 of gene tree discordance using the novel “extra lineage contribution”
 statistics (XLC, presented in this study), that quantifies the level of
 gene tree discordance contribution per individual within a species. We
 included molecular data (12 nuclear and 2 mitochondrial genes) from 127
 individuals, and results of a coalescent model-based analysis show that
 the most likely explanation for the gene tree-species tree discordance is
 interspecific hybridization. Our best-supported hypothesis suggests
 current and past hybridization between L. rothi (rothi complex) and L.
 tehuelche (boulengeri complex), and independently between L. rothi and L.
 boulengeri and L. telsen (boulengeri complex). The hybrid descendants are
 characterized by intermediate phenotypes between the parental species, but
 are more similar to L. rothi in body size. We discuss the possible role of
 hybridization in Liolaemus evolution.
description: fasta-matricesindividual DNA sequence matrices in fasta format.Imapmapping file for individual - species associationsSupplementary material 1Supplementary material 1 "Extended materials and methods and results"Species tree (supplementary material 2)Species tree of the ingroup taxa in newick formatSupp.Mat2-sp_tree.species.newick
DOI: 10.5061/dryad.mn65t
title: Data from: Parapatric speciation in three islands: dynamics of geographical configuration of allele sharing

description: We studied the time to speciation by geographical isolation for a species
 living on three islands connected by rare migration. We assumed that
 incompatibility was controlled by a number of quantitative loci and that
 individuals differing in loci by more than a threshold did not mix
 genetically with each other. For each locus, we defined the geographical
 configuration (GC), which specifies islands with common alleles, and
 traced the stochastic transitions between different GCs. From these
 results, we calculated the changes in genetic distances. As a single
 migration event provides an opportunity for transitions in multiple loci,
 the GCs of different loci are correlated, which can be evaluated by
 constructing the stochastic differential equations of the number of loci
 with different GCs. Our model showed that the low number of
 incompatibility loci facilitates parapatric speciation and that migrants
 arriving as a group shorten the waiting time to speciation compared with
 the same number of migrants arriving individually. We also discuss how
 speciation rate changes with geographical structure.
description: SDE_3islandsThis is the simulation code written in C.Simulation_code_of_SDE_for_3-island_model.cSDE_3islands_result exampleA simulated result of three-island SDE.
DOI: 10.5061/dryad.s654mf6
title: Data from: Characterizing morphological (co)variation using structural equation models: body size, allometric relationships and evolvability in a house sparrow metapopulation

description: Body size plays a key role in the ecology and evolution of all organisms.
 Therefore, quantifying the sources of morphological (co)variation,
 dependent and independent of body size, is of key importance when trying
 to understand and predict responses to selection. We combine structural
 equation modeling with quantitative genetics analyses to study
 morphological (co)variation in a meta-population of house sparrows (Passer
 domesticus). As expected, we found evidence of a latent variable ‘body
 size’, causing genetic and environmental covariation between morphological
 traits. Estimates of conditional evolvability show that allometric
 relationships constrain the independent evolution of house sparrow
 morphology. We also found spatial differences in general body size and its
 allometric relationships. On islands where birds are more dispersive and
 mobile, individuals were smaller and had proportionally longer wings for
 their body size. While in islands where sparrows are more sedentary and
 nest in dense colonies, individuals were larger and had proportionally
 longer tarsi for their body size. We corroborated these results using
 simulations and show that our analyses produce unbiased allometric slope
 estimates. This study highlights that in the short term allometric
 relationships may constrain phenotypic evolution, but that in the long
 term selection pressures can also shape allometric relationships.
description: Morphological
 dataData containing
 morphological measurements of house sparrows in 11 islands of the
 Helgeland archipelago in Northern Norway.dryad.csv
DOI: 10.5061/dryad.8gv43s53
title: Data from: Population structure and genetic diversity among eelgrass (Zostera marina) beds and depths in San Francisco Bay

description: The seagrass Zostera marina is widely distributed in coastal regions
 throughout much of the northern hemisphere, forms the foundation of an
 important ecological habitat, and is suffering population declines.
 Studies in the Atlantic and Pacific oceans indicate the degree of
 population genetic differentiation is location-dependent. San Francisco
 Bay, California, USA, is a high-current, high-wind environment where
 rafting of seed-bearing shoots has the potential to enhance genetic
 connectivity among Z. marina populations. We tested Z. marina from six
 locations, including one annual population, within the bay to assess
 population differentiation and to compare levels of within-population
 genetic diversity. Using seven microsatellite loci, we found significant
 differentiation among all populations. The annual population had
 significantly higher clonal diversity than the others but showed no
 detectible differences in heterozygosity or allelic richness. There
 appears to be sufficient input of genetic variation through sexual
 reproduction or immigration into the perennial populations to prevent
 significant declines in the number and frequency of alleles. In additional
 depth comparisons, we found differentiation among deep and shallow
 portions in one of three beds evaluated. Genetic drift, sweepstakes
 recruitment, dispersal limitation, and possibly natural selection may have
 combined to produce genetic differentiation over a spatial scale of 3 – 30
 km in Z. marina. This implies the scale of genetic differentiation may be
 smaller than expected for seagrasses in other locations, too. We suggest
 that populations in close proximity may not be interchangeable for use as
 restoration material.
description: Supplementary Figures
 & TablesSaturation curves of
 pairwise genetic distances calculated in GenClone. Graphs of
 log-likelihood and delta K across varying numbers of genetic clusters,
 from STRUCTURE. Supplementary tables 1 & 2 showing results when all
 but one one copy of each identical genotype was removed from the data
 set.ORT_SupMat_Figures&Tables.pdf
DOI: 10.5061/dryad.s55c4
title: Data from: Rapid and unpredictable changes of the G-matrix in a natural bird population over 25 years

description: Knowledge of the genetic variances and covariances of traits (the
 G-matrix) is fundamental for the understanding of evolutionary dynamics of
 populations. Despite its essential importance in evolutionary studies,
 empirical tests of the temporal stability of the G-matrix in natural
 populations are few. We used a 25-year-long individual-based field study
 on almost 7000 breeding attempts of the collared flycatcher (Ficedula
 albicollis) to estimate the stability of the G-matrix over time. Using
 animal models to estimate G for several time periods, we show that the
 structure of the time-specific G-matrices changed significantly over time.
 The temporal changes in the G-matrix were unpredictable, and the structure
 at one time period was not indicative of the structure at the next time
 period. Moreover, we show that the changes in the time-specific G-matrices
 were not related to changes in mean trait values or due to genetic drift.
 Selection, differences in acquisition/allocation patterns or
 environment-dependent allelic effects are therefore likely explanations
 for the patterns observed, probably in combination. Our result cautions
 against assuming constancy of the G-matrix and indicates that even
 short-term evolutionary predictions in natural populations can be very
 challenging.
description: Bjorklund et al Dryad
 explanationsExplanations to the data
 filesBjorklund_et_al_dataDataBjorklund_et_al_dryad_pedigreePedigree
DOI: 10.5061/dryad.8nj00
title: Data from: Molecular phylogeny and pollen evolution of Euphorbiaceae tribe Plukenetieae

description: Tribe Plukenetieae (Euphorbiaceae, Acalyphoideae) is a pantropical lineage
 of mostly stinging, twining vines and lianas with diverse floral and
 pollen morphology. To elucidate generic relationships in the tribe and
 examine patterns of pollen morphology evolution, we conducted phylogenetic
 analyses of nuclear ribosomal ITS and plastid psbA-trnH DNA sequence and
 indel gap-scored data. We sampled all genera in subtribes Dalechampiinae
 and Tragiinae, and most in Plukenetiinae; species sampling was broad in
 the latter two subtribes. Our efforts produced a 2,207 character dataset
 of 154 terminals (representing ca. 93 species). Analyses of these data
 support the monophyly of each subtribe and weakly suggest Dalechampiinae
 (Dalechampia) is sister to Plukenetiinae + Tragiinae. Within
 Plukenetiinae, Haematostemon is resolved as sister to Romanoa +
 Plukenetia, and Plukenetia is divided into five subclades that mostly
 correspond to the current infrageneric classification. Tragiinae is
 resolved into an Old World lineage and a mostly New World lineage, and is
 divided into ten subclades also supported by floral and/or pollen
 morphology. Species-rich Tragia is recovered as para- or polyphyletic and
 intermixed with all other currently recognized Tragiinae genera. The
 recently segregated genera, Bia, Ctenomeria, and Zuckertia, are upheld,
 and Gitara is resurrected from Acidoton, resulting in two new
 combinations: Gitara nicaraguensis and Zuckertia manuelii. Pollen aperture
 and exine morphology are largely correlated with phylogeny. The loss of
 pollen endopores is a potential synapomorphy of Plukenetiinae + Tragiinae,
 and we hypothesize that weakly defined apertures and inaperturate pollen
 originated independently four and three times, respectively.
description: Plukenetieae combined
 partitioned dataset154 terminal, 2381
 character, combined psbA-trnH, psbA-trnH indels, and ITS dataset of tribe
 Plukenetieae and outgroups (Euphorbiaceae). This nexus file includes the
 full alignment, exclusion sets, and partitions.Plukenetieae.nex
DOI: 10.5061/dryad.mg0jb
title: Data from: Genetic basis for variation in salinity tolerance between stickleback ecotypes

description: Adaptation to different salinities can drive and maintain divergence
 between populations of aquatic organisms. Anadromous and stream ecotypes
 of threespine stickleback (Gasterosteus aculeatus) are an excellent model
 to explore the genetic mechanisms underlying osmoregulation divergence.
 Using a parapatric pair of anadromous and stream stickleback ecotypes, we
 employed an integrated genomic approach to identify candidate genes
 important for adaptation to different salinity environments. Quantitative
 trait loci (QTL) mapping of plasma sodium concentrations under a seawater
 challenge experiment identified a significant QTL on chromosome 16. To
 identify candidate genes within this QTL, we first conducted RNA-seq and
 microarray analysis on gill tissue to find ecotypic differences in gene
 expression that were associated with plasma Na+ levels. This resulted in
 the identification of ten candidate genes. Quantitative PCR analysis on
 gill tissue of additional Japanese stickleback populations revealed that
 the majority of the candidate genes showed parallel divergence in
 expression levels. Second, we conducted whole-genome sequencing and found
 five genes that are predicted to have functionally important amino acid
 substitutions. Finally, we conducted genome scan analysis and found that
 eight of these candidate genes were located in genomic islands of high
 differentiation, suggesting that they may be under divergent selection.
 The candidate genes included those involved in ATP synthesis and hormonal
 signalling, whose expression or amino acid changes may underlie the
 variation in salinity tolerance. Further functional molecular analysis of
 these genes will reveal the causative genetic and genomic changes
 underlying divergent adaptation.
description: SNP list of threespine
 sticklebackWe selected SNPs that
 met the following three criteria: (1) 50-bp flanking regions on both sides
 of the SNP were conserved between anadromous and stream resident
 populations, (2) the Illumina designability rank score was one, (3) the
 SNP was located within coding regions if available. We chose 278 SNPs that
 were evenly distributed across the reference genome sequence (average
 distance of 1.56 Mb). Ten SNPs were chosen from the regions within or near
 five genes that are known to be or potentially important for freshwater
 adaptation.Ga_SNPList.xlsxQTL input dataThe data sheet includes SNP information (A=anadromous, B=stream resident, H=heterozygote) with sex, body weight and plasma Na+ values.lcf2sw_input.csv95%BI2A list of genes located within the 95% bayesian credible intervals (95%BI) of QTL peak positions.