cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fg49r
title: Data from: Effects of assortative mate choice on the genomic and morphological structure of a hybrid zone between two bird subspecies

description: Phenotypic differentiation plays an important role in the formation and
 maintenance of reproductive barriers. In some cases, variation in a few
 key aspects of phenotype can promote and maintain divergence; hence the
 identification of these traits and their associations with patterns of
 genomic divergence are crucial for understanding the patterns and
 processes of population differentiation. We studied hybridization between
 the alba and personata subspecies of the white wagtail (Motacilla alba),
 and quantified divergence and introgression of multiple morphological
 traits and 19,437 SNP loci on a 3000 km transect. Our goal was to identify
 traits that may contribute to reproductive barriers and to assess how
 variation in these traits corresponds to patterns of genome-wide
 divergence. Variation in only one trait – head plumage patterning – was
 consistent with reproductive isolation. Transitions in head plumage were
 steep and occurred over otherwise morphologically and genetically
 homogeneous populations, whereas cline centers for other traits and
 genomic ancestry were displaced over one hundred kilometers from the head
 cline. Field observational data show that social pairs mated assortatively
 by head plumage, suggesting that these phenotypes are maintained by
 divergent mating preferences. In contrast, variation in all other traits
 and genetic markers could be explained by neutral diffusion, although weak
 ecological selection cannot be ruled out. Our results emphasize that
 assortative mating may maintain phenotypic differences independent of
 other processes shaping genome-wide variation, consistent with other
 recent findings that raise questions about the relative importance of mate
 choice, ecological selection and selectively neutral processes for
 divergent evolution.
description: Sampling, genomic and
 morphological data used for analysesSampling details,
 morphological and genomic data used for analysis of geographic clines,
 variance analysis and individual trait distribution modeling. Also see
 SUPPORTING INFORMATION tables S1 and S2SNP
 datasetData for 19,437 SNP loci
 and 276 individuals in allelic format used for ancestry analyses.
 Individuals IDs are voucher numbers (see Sampling, genomic and
 morphological data used for analyses.xlsx for details)
DOI: 10.5061/dryad.sc1j0
title: Data from: Genomic data resolves gene tree discordance in spiderhunters (Nectariniidae, Arachnothera)

description: Reduced representation genomic sequencing methods efficiently gather
 sequence data from thousands of loci throughout the genome. These data can
 be used to test previous phylogenetic hypotheses produced from limited
 numbers of mitochondrial and nuclear loci that often reveal intriguing,
 but conflicting results. In this paper, we use phylogenomic data to
 revisit recent molecular phylogenetic work that clarified many taxonomic
 relationships within spiderhunters, but also questioned monophyly of this
 distinctive genus of sunbirds (AVES: Nectariniidae; Arachnothera). DNA
 sequence data were produced by target-capture sequencing of ultraconserved
 elements (UCEs) to infer the evolutionary history of 11 species of
 Arachnothera and six outgroups, including the Purple-naped Sunbird
 (Hypogramma hypogrammicum), which previous work suggested might lie within
 Arachnothera. Although we recovered many different gene tree topologies,
 concatenated and coalescent methods of analysis converged on a species
 tree that strongly supports the monophyly of Arachnothera, with Hypogramma
 as its sister taxon.
description: UCE_phylipThis directory contains a phylip file for each locus in the complete UCE data matrix (n = 2,107 UCE loci). Each file contains aligned sequence data for that UCE locus in phylip format. Taxon names have been shortened to first three letters of genus and first three of the specific epithet (e.g., Arachnothera longirostra = AraLon)aligned_UCE_loci.zipraxml_genetreeThis directory contains a subdirectory for each UCE locus, and within each subdirectory is the bestTree gene tree for that locus. Trees were produced in RAxML, using a GTR+Gamma substitution model.
DOI: 10.5061/dryad.1d8th
title: Data from: Phylogeny of Anophelinae using mitochondrial protein coding genes

description: Malaria is a vector-borne disease that is a great burden on the poorest
 and most marginalized communities of the tropical and subtropical world.
 About 41 species of Anopheline mosquitoes can effectively spread species
 of Plasmodium parasites that cause human malaria. Proposing a natural
 classification for the subfamily Anophelinae has been a continuous effort,
 addressed using both morphology and DNA sequence data. Monophyly of the
 genus Anopheles, and phylogenetic placement of the genus Bironella,
 subgenera Kerteszia, Lophopodomyia, and Stethomyia within the subfamily
 Anophelinae, remain in question. To understand the classification of
 Anophelinae we inferred the phylogeny of all three genera (Anopheles,
 Bironella, Chagasia) and major subgenera by analyzing the amino acid
 sequences of the 13 protein coding genes of 150 newly sequenced
 mitochondrial genomes of Anophelinae and 18 newly sequenced Culex species
 as outgroup taxa, supplemented with 23 mitogenomes from GenBank. Our
 analyses generally place genus Bironella within the genus Anopheles, which
 implies that the latter as it is currently defined is not monophyletic.
 With some inconsistencies, Bironella was placed within the major clade
 that includes Anopheles, Cellia, Kerteszia, Lophopodomyia, Nyssorhynchus,
 and Stethomyia, which were found to be monophyletic groups within
 Anophelinae. Our findings provided robust evidence for elevating the
 monophyletic groupings Kerteszia, Lophopodomyia, Nyssorhynchus, and
 Stethomyia to genus level; genus Anopheles to include subgenera Anopheles,
 Baimaia, Cellia and Christya; Anopheles parvus to be placed into a new
 genus; Nyssorhynchus to be elevated to genus level; the genus
 Nyssorhynchus to include subgenera Myzorhynchella and Nyssorhynchus;
 Anopheles atacamensis and Anopheles pictipennis to be transferred from
 subgenus Nyssorhynchus to subgenus Myzorhynchella; and subgenus
 Nyssorhynchus to encompass the remaining species of Argyritarsis and
 Albimanus Sections.
description: Sequencing information,
 gene order, and phylogenetic treesfosterAnophelinaeSupplemental13.pdfSpecimen accession numbersAccession_number_FSP-USP.xlsxExtra sequencing informationGenomeRegion_Seq.xlsSpecimen informationSpeciesUsed.xlsx
DOI: 10.5061/dryad.2sg0m
title: Data from: Bystanders intervene to impede grooming in Western chimpanzees and sooty mangabeys

description: Grooming interactions benefit groomers, but may have negative consequences
 for bystanders. Grooming limits bystanders’ grooming access and ensuing
 alliances could threaten the bystander’s hierarchy rank or their previous
 investment in the groomers. To gain a competitive advantage, bystanders
 could intervene into a grooming bout to increase their own grooming access
 or to prevent the negative impact of others’ grooming. We test the impact
 of dominance rank and social relationships on grooming intervention
 likelihood and outcome in two sympatric primate species, Western
 chimpanzees (Pan troglodytes verus) and sooty mangabeys (Cercocebus atys
 atys). In both species, rather than increasing their own access to
 preferred partners, bystanders intervened mainly when an alliance between
 groomers could have a negative impact on them: when the lower-ranking
 groomer was close to the bystander in rank, when either groomer was an
 affiliation partner whose services they could lose, or the groomers were
 not yet strongly affiliated with each other. Thus, bystanders in both
 species appear to monitor grooming interactions and intervene based on
 their own dominance rank and social relationships, as well as triadic
 awareness of the relationship between groomers. While the motivation to
 intervene did not differ between species, mangabeys appeared to be more
 constrained by dominance rank than chimpanzees.
description: Data Model
 1-1Dataset Model 1-1,
 Impact of rank on intervention likelihoodData Model
 1-2Dataset Model 1-2,
 Impact of social relationships on intervention
 likelihoodData Model
 3Dataset Model 3,
 Intervention successData Model
 2Dataset Model 2,
 Intervention target choiceModels 1, 2 and 3 R
 scriptsR scripts for models 1
 to 3
DOI: 10.5061/dryad.3jg7h
title: Data from: Phylogenomic support for evolutionary relationships of New World direct-developing frogs (Anura: Terraranae)

description: Phylogenomic approaches have proven able to resolve difficult branches in
 the tree of life. New World direct-developing frogs (Terraranae) represent
 a large evolutionary radiation in which interrelationships at key points
 in the phylogeny have not been adequately determined, affecting
 evolutionary, biogeographic, and taxonomic interpretations. We employed
 anchored hybrid enrichment to generate a data set containing 389 loci and
 &gt;600,000 nucleotide positions for 30 terraranan and several
 outgroup frog species encompassing all major lineages in the clade.
 Concatenated maximum likelihood and coalescent species-tree approaches
 recover nearly identical topologies with strong support for nearly all
 relationships in the tree. These results are similar to previous
 phylogenetic results but provide additional resolution at short
 internodes. Among taxa whose placement varied in previous analyses,
 Ceuthomantis is shown to be the sister taxon to all other terraranans,
 rather than deeply embedded within the radiation, and Strabomantidae is
 monophyletic rather than paraphyletic with respect to Craugastoridae. We
 present an updated taxonomy to reflect these results, and describe a new
 subfamily for the genus Hypodactylus.
description: Alignment from Heinicke
 et al.Concatenated alignment
 of 389 loci for 35 species of frog. File is in phylip format. Gene
 boundaries are identified in associated partition fileinfile.zip
DOI: 10.5061/dryad.s5n3c
title: Data from: Habitat risk assessment for regional ocean planning in the U.S. Northeast and Mid-Atlantic

description: Coastal habitats provide important benefits to people, including habitat
 for species targeted by fisheries and opportunities for tourism and
 recreation. Yet, such human activities also can imperil these habitats and
 undermine the ecosystem services they provide to people. Cumulative risk
 assessment provides an analytical framework for synthesizing the influence
 of multiple stressors across habitats and decision-support for balancing
 human uses and ecosystem health. To explore cumulative risk to habitats in
 the U.S. Northeast and Mid-Atlantic Ocean Planning regions, we apply the
 open-source InVEST Habitat Risk Assessment model to 13 habitats and 31
 stressors in an exposure-consequence framework. In doing so, we advance
 the science priorities of EBM and both regional planning bodies by
 synthesizing the wealth of available data to improve our understanding of
 human uses and how they affect marine resources. We find that risk to
 ecosystems is greatest first, along the coast, where a large number of
 stressors occur in close proximity and secondly, along the continental
 shelf, where fewer, higher consequence activities occur. Habitats at
 greatest risk include soft and hard-bottom nearshore areas, tidal flats,
 soft-bottom shelf habitat, and rocky intertidal zones—with the degree of
 risk varying spatially. Across all habitats, our results indicate that
 rising sea surface temperatures, commercial fishing, and shipping
 consistently and disproportionally contribute to risk. Further, our
 findings suggest that management in the nearshore will require
 simultaneously addressing the temporal and spatial overlap as well as
 intensity of multiple human activities and that management in the offshore
 requires more targeted efforts to reduce exposure from specific threats.
 We offer a transparent, generalizable approach to evaluating cumulative
 risk to multiple habitats and illustrate the spatially heterogeneous
 nature of impacts along the eastern Atlantic coast and the importance of
 spatial scale in estimating such impacts. These results offer a valuable
 decision-support tool by helping to constrain the decision space, focus
 attention on habitats and locations at the greatest risk, and highlight
 effect management strategies.
description: Exposure and consequence
 scores for each habitat-stressor combinationexposure_consequence_scores.xlsxCumulative risk for each habitat.HRA_habitat_risk.zipecorisk_ebm
DOI: 10.5061/dryad.56j2n
title: Data from: Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences

description: Accurate classification of HIV-1 group M lineages, henceforth referred to
 as subtyping, is essential for understanding global HIV-1 molecular
 epidemiology. Because most HIV-1 sequencing is done for genotypic
 resistance testing pol gene, we sought to develop a set of
 geographically-stratified pol sequences that represent HIV-1 group M
 sequence diversity. Representative pol sequences differ from
 representative complete genome sequences because not all CRFs have pol
 recombination points and because complete genome sequences may not
 faithfully reflect HIV-1 pol diversity. We developed a software pipeline
 that compiled 6,034 one-per-person complete HIV-1 pol sequences annotated
 by country and year belonging to 11 pure subtypes and 70 CRFs and selected
 a set of sequences whose average distance to the remaining sequences is
 minimized for each subtype/CRF and country to generate a
 Geographically-Stratified set of 716 Pol Subtype/CRF (GSPS) reference
 sequences. We provide extensive data on pol diversity within each
 subtype/CRF and country combination. The GSPS reference set will also be
 useful for HIV-1 pol subtyping.
description: Complete set of 6,034
 one-per-person, subtype-assigned HIV-1 group M complete pol
 sequencesComplete set of 6,034
 one-per-person, subtype-assigned HIV-1 group M complete pol sequences is
 in a tab-delimited file containing the aligned pol sequence, GenBank
 accession number, GenBank author list, GenBank submission title, PubMed
 ID, country, sample year, and assigned subtype/CRFComplete.Set.txtGeographically-Stratified Pol Subtype/CRF (GSPS) Reference SequencesTab-delimited file containing the GenBank accession number, country, sample year, PubMed ID, and assigned subtype/CRF for each of 716 GSPS reference sequencesGSPS.Set.txtGeographically-Stratified Pol Subtype/CRF (GSPS) Reference Sequences In Fasta FormatGSPS.fasta.txtGeographically-Stratified Pol Subtype/CRF (GSPS) Reference Sequences In Tree FormatGSPS.trePhylogenetic Trees for each GSPS Subtype/CRF in PDF FormatGSPS.subtype.tre.pdf.zipRelationship between k and ADCL for each of the 155 subtype/CRF/country combinations with three or more sequencesADCL.txt
DOI: 10.5061/dryad.797kg
title: Data from: Divergent brain gene expression profiles between alternative behavioural helper types in a cooperative breeder

description: Juveniles of the cooperatively-breeding cichlid fish Neolamprologus
 pulcher either consistently provide help in form of alloparental egg care
 ('cleaners') or consistently abstain from helping
 ('non-cleaners'). These phenotypes are not based on heritable
 genetic differences. Instead they arise during ontogeny, which should lead
 to differences in brain structure or physiology, a currently untested
 prediction. We compared brain gene expression profiles of cleaners and
 non-cleaners in two experimental conditions, a helping opportunity and a
 control condition. We aimed to identify (i) expression differences between
 cleaners and non-cleaners in the control, (ii) changes in gene expression
 induced by the opportunity, and (iii) differences in plasticity of gene
 expression between cleaners and non-cleaners. Control cleaners and
 non-cleaners differed in the expression of a single gene, irx2, which
 regulates neural differentiation. During the opportunity, cleaners and
 non-cleaners had three up-regulated genes in common, which were implicated
 in neuroplasticity, hormonal signalling, and cell proliferation. Thus, the
 stimulus in the opportunity was sufficiently salient. Cleaners also showed
 higher expression of seven additional genes that were unique to the
 opportunity. One of these cleaner-specific genes is implicated in
 neuropeptide metabolism, indicating that this process is associated with
 cleaning performance. This suggests that the two types employed different
 pathways to integrate social information, preparing them for accelerated
 reaction to future opportunities. Interestingly, three developmental genes
 were down-regulated between the control and the opportunity in cleaners
 only. Our results indicate that the two behavioural types responded
 differently to the helping opportunity, and that only cleaners responded
 by down-regulating developmental genes.
description: Read count matrix and
 treatment information on individualsRead count matrix from
 RNA-seq experiment of two distinct helper types in the cooperatively
 breeding cichlid fish Neolamprologus pulcher. 48 individuals in a 2x2
 full-factorial design of cleaners and non-cleaners in control and
 opportunity. 38,2425 genes expressed in the telencephalon 45 min after the
 onset of the cooperation opportunity.data_Kasper_cichlid_helping_transcriptome.xlsx
DOI: 10.5061/dryad.fb7r5
title: Data from: Biotransformation of labdane and halimane diterpenoids by two filamentous fungi strains

description: Biotransformation of natural products by filamentous fungi is a powerful
 and effective approach to achieve derivatives with valuable new chemical
 and biological properties. Despite diterpenoid substrates exhibit good
 susceptibility towards fungi enzymes, there have been no studies
 concerning the microbiological transformation of halimane-type
 diterpenoids up to now. In this work, we investigated the capability of
 Fusarium oxysporum (a fungus isolated from the rhizosphere of Senna
 spectabilis) and Myrothecium verrucaria (an endophyte) to transform
 halimane (1) and labdane (2) acids isolated from Hymenaea stigonocarpa
 (Fabaceae). Feeding experiments resulted in the production of six
 derivatives, including hydroxy, oxo, formyl, and carboxy analogues.
 Incubation of 1 with F. oxysporum afforded 2-oxo-derivative (3), while
 bioconversion with M. verrucaria provided 18,19-dihydroxy (4), 18-formyl
 (5), and 18-carboxy (6) bioproducts. Transformation of substrate 2
 mediated by F. oxysporum produced a 7-hydroxy (7) derivative, whilst M.
 verrucaria yielded 7- (7) and 3-hydroxy (8) metabolites. Unlike F.
 oxysporum, which showed a preference to transform ring B, M. verrucaria,
 exhibited the ability to hydroxylate both rings A and B from substrate 2.
 Additionally, compounds 1–8 were evaluated for inhibitory activity against
 Hr-AChE and Hu-BChE enzymes through ICER-IT-MS/MS assay.
description: Manuscript_Supplementary
 Information_Dryad
DOI: 10.5061/dryad.7jj35
title: Data from: Plant traits determine the phylogenetic structure of arbuscular mycorrhizal fungal communities

description: Functional diversity in ecosystems has traditionally been studied using
 aboveground plant traits. Despite the known effect of plant traits on the
 microbial community composition, their effects on the microbial functional
 diversity are only starting to be assessed. In this study, the
 phylogenetic structure of arbuscular mycorrhizal (AM) fungal communities
 associated to plant species differing in life cycle and growth form, i.e.
 plant life forms, was determined to unravel the effect of plant traits on
 the functional diversity of this fungal group. The results of the
 454-pyrosenquencing showed that the AM fungal community composition
 differed across plant life forms and this effect was dependent on the soil
 collection date. Plants with ruderal characteristics tended to associate
 with phylogenetically clustered AM fungal communities. By contrast, plants
 with resource-conservative traits associated with phylogenetically
 over-dispersed AM fungal communities. Additionally, the soil collected in
 different seasons yielded AM fungal communities with different
 phylogenetic dispersion. In summary, we found that the phylogenetic
 structure, and hence the functional diversity, of AM fungal communities is
 dependent on plant traits. This finding adds value to the use of plant
 traits for the evaluation of belowground ecosystem diversity, functions
 and processes.
description: Sequences Lopez-Garcia
 454This file contains the
 sequences from the experiment with indication of the sample from they were
 obtained, the OTU classification and sample associated data (plant
 species, life form and sampling date).Site by OTU
 matrixThis file contains the
 relative abundance matrix of OTU detected in the study by each sample.
 Metadata is included.Site by species matrix
 Lopez-Garcia 454 pyrosequencing.xlsx
DOI: 10.5061/dryad.70585
title: Data from: Deletion/loss of bone morphogenetic protein 7 changes tooth morphology and function in Mus musculus: implications for dental evolution in mammals

description: Quantifying regulatory gene effects on dental morphology and function has
 implications for the underlying mechanisms that generated dental diversity
 in mammals. We tested the hypothesis that regulatory gene expression
 changes lead to differences in molars using a neural crest knockout of
 bone morphogenetic protein 7 (BMP7) in Mus musculus. 3D geometric
 morphometric methods were used to quantify the shape of the molar
 toothrow. BMP7 mutants have extra cusps on the first upper and lower
 molars, and alterations in cusp orientation and morphology. Further,
 significant shape differences between control and mutant were found for
 upper and lower toothrows. Mutant mice also exhibited differences in
 attrition facets, indicating functional changes that could lead to
 advantages chewing new food resources and eventually niche
 diversification. The size ratio of the molars in the toothrow remained
 unchanged, implying that BMP7 induced changes in molar size ratio are a
 result of knocking out epithelial, rather than neural crest, expression of
 BMP7. Our results indicate that changes in BMP7 expression are sufficient
 to alter morphology and function of the toothrow, suggesting that BMP7 or
 genes affecting its function could have played a role in structuring the
 dental diversity of extinct and extant mammals.
description: PLYFILESA zip archive of .ply files, preserving the digitized 3D models of all of the mice sampled for this project.LANDMARKFILESAll of the landmark data sets corresponding to the .ply models used in the analyses.Landmarks and RcodeWord document containing R code for geometric morphometric analysis of landmark sets as outlined in the paper.