cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2z34tmpr4
title: Integrative taxonomy, larval biology and functional morphology of the little known gall-forming coral endoparasite Petrarca (Thecostraca: Ascothoracida)

description: Petrarca is an ascothoracidan endoparasite in scleratinian dendrophyllid
 corals. Petrarca can stimulate coral growth, forming a gall chamber to
 house itself inside the coral skeleton. The  diversity, molecular
 phylogeny and feeding ecology of Petrarca are understudied. This is the
 first study of Petrarca to be based on light and scanning electron
 microscopy to document the fine-scale external and functional morphology
 of its trophi  and other structures. A combined molecular and
 morphological approach revealed at least four closely related species of
 Petrarca, P. goanna, P. morula, Petrarca nozawai sp. nov. and Petrarca
 rubus sp. nov in Turbinaria and Astreopora corals in Asia. Carapace shape
 and fine morphology, ultrastructure of the antennular aesthetasc,
 morphological characteristics of the trophi and the shape and size of the
 penis rami are diagnostic characters. Several morphological characters,
 which are all probably synapomorphies, have been proposed to distinguish
 the genus Petrarca from other Ascothoracida. Mouthparts morphology of
 Petrarca are developed for cutting and chewing, rather than for piercing
 and sucking as in many other Ascothoracida. The external surface of the
 carapace of Petrarca is ornamented with densely packed secretory papillae
 used putatively for the chemical dissolution of the substrate necessary
 for the formation of the gall chamber.
description: It is a video taken under microscopic observation
 Video S1. In situ observation of the coral galls housing
 Petrarca. Video S2. Larval release of Petrarca from the
 gall surface.
description: Video player
DOI: 10.5061/dryad.5qfttdz9v
title: Thiazides attenuate insulin secretion through inhibition of mitochondrial carbonic anhydrase 5b in β-islet cells in mice

description: Background: Thiazides are associated with glucose intolerance and new
 onset diabetes mellitus. Previous studies demonstrated that thiazides
 attenuate insulin secretion, but the molecular mechanisms remain elusive.
 We hypothesized that thiazides attenuate insulin secretion via one of the
 known molecular thiazide targets in β-cells. Methods: We performed static
 insulin secretion experiments with islets of wild-type, NCC (SLC12A3) and
 NDCBE (SLC4A8) knock-out (KO) mice and with murine Min6 cells with
 individual knock-down of carbonic anhydrase (CA) isoforms to identify the
 molecular target of thiazides in β-cells. CA5b KO mice were then used to
 assess the role of the putative thiazide target CA5b in β-cell function
 and in mediating thiazide sensitivity in vitro and in vivo. Results:
 Thiazides inhibited glucose- and sulfonylurea-stimulated insulin secretion
 in islets and Min6 cells at pharmacologically relevant concentrations.
 Inhibition of insulin secretion by thiazides was CO2/HCO3--dependent, not
 additive to unselective CA inhibition with acetazolamide and independent
 of extracellular potassium. In contrast, insulin secretion was unaltered
 in islets of mice lacking the known molecular thiazide targets NCC or
 NDCBE. CA expression profiling with subsequent knock-down of individual CA
 isoforms suggested mitochondrial CA5b as molecular target. In support of
 these findings, thiazides significantly attenuated Krebs cycle anaplerosis
 through reduction of mitochondrial oxaloacetate synthesis. CA5b KO mice
 were resistant to thiazide-induced glucose intolerance, and thiazides did
 not alter insulin secretion in CA5b KO islets. Conclusions: In summary,
 our study reveals that thiazides attenuate insulin secretion via
 inhibition of the mitochondrial CA5b isoform in β-cells.
DOI: 10.5061/dryad.q573n5tnz
title: Data from: Evolutionary process of extremely twisted heteromorph ammonites from the Upper Cretaceous in Japan

description: The heteromorph ammonite Pravitoceras sigmoidale with
 extremely twisted retroversal hook and its probable
 ancestors, Didymoceras
 awajiense and D. morozumii, occur mainly in the
 Upper Cretaceous Izumi and Sotoizumi groups in southwest Japan. Their
 morphological characteristics were investigated in this study. Morphotypes
 I–II were recognized in D. morozumii. Morphotypes III–V
 were recognized in D. awajiense. Morphotypes VI–VIII
 were recognized in P. sigmoidale. Moreover, all
 morphotypes were recognized in both the dextral and sinistral forms of
 these three species. Based on the morphological and stratigraphic
 relationships, it is considered that the evolutionary process of these
 species is divided into three steps: (1) shift from morphotypes I–II to
 III; (2) increase in variation from morphotypes III to III–V; and (3)
 shift from morphotypes III–V to VI–VIII. By comparing these morphotypes
 based on the ‘growing tube model’ belonging to the moving frame analysis,
 it is seen that there are no significant gaps of coiling patterns in the
 evolutionary processes of this lineage. Meanwhile, morphotypes III–V
 of D. awajiense have a larger morphological
 variation than morphotypes I–II
 of D. morozumii and morphotypes VI–VIII
 of P. sigmoidale. These results, and the radiometric
 ages from previous studies, suggest that D. awajiense,
 with considerable variation between ancestor and descendant species,
 existed in a short interval. It seems
 that P. sigmoidale occurred after the
 continuous but rapid and drastic morphological evolution
 from D. morozumii via D. awajiense.
description: Data 1 (Material information):
 Data_S1_Material_information.csv<br>Data 2 (Parameter values of the
 growing tube model for each morphotype):
 Data_2_Parameter_values_of_the_growing_tube_model_for_each_morphotype.csv
DOI: 10.5061/dryad.d2547d86b
title: Data for: Simulation and social network analysis provide insight into the acquisition of tool behavior in hybrid macaques

description: The pathways through which primates acquire skills are a central focus of
 cultural evolution studies. The roles of social and genetic inheritance
 processes in skill acquisition are often confounded by environmental
 factors. Hybrid macaques from Koram Island, Thailand provide an
 opportunity to examine the roles of inheritance and social learning to
 skill acquisition within a single ecological setting. These hybrids are a
 cross between tool-using Burmese long-tailed (Macaca fascicularis aurea)
 and non-tool-using common long-tailed macaques (Macaca fascicularis
 fascicularis). This population provides an opportunity to explore the
 roles of social learning and inheritance processes while being able to
 exclude underlying ecological factors. Here, we investigate the roles of
 social learning and inheritance in tool use prevalence within this
 population using social network analysis and simulation. Agent-based
 modeling (ABM) is used to generate expectations for how social/asocial
 learning and inheritance structure the patterning in a social network. The
 results of the simulation show that various transmission mechanisms can be
 differentiated based on associations between individuals in a social
 network. The results provide an investigative framework for discussing
 tool-use transmission pathways in the Koram social network. By combining
 ABM, network analysis, and behavioral data from the field we can
 investigate the roles social learning and inheritance play in tool
 acquisition in wild primates. 
description: These 6 datasets associated with the paper titled,
 "Simulation and social network analysis provide insight into the
 acquisition of tool behavior in hybrid macaques" housed in this
 repository.  1) ABM_Social_Condition.csv
 2) ABM_Inheritance_Condition.csv 3)
 ABM_Asocial_na1as25_Condition.csv 4)
 ABM_Asocial_na10as25_Condition.csv 5)
 ABM_Asocial_na200as25_Condition.csv 6)
 Koram.csv Datasets 1–5 consist of simulated data
 generated by various conditions of the Agent-based model published in this
 work. A full description of the model accompanies the publication as
 supplementary material. The code for the model is actively maintained by
 the authors and can be publically accessed by following this link. Each individual is summarized by their tool user status, age, phenotype, and position in the social network (see Readme.md).  Dataset 6: Contains comparable data for individuals of hybrid macaques from Koram island, Thailand. These data were generated from observations made during focal follows over a period of 1 year and 2 months between October 2013 and December 2014. These observations were then used to characterize each individual in terms of their age, phenotype, tool user status, and position in the social network. 
description: R v4.2.2 was used to quantify and organize the data into the
 state that it is in now. All code associated with data processing is
 actively maintained at this link.
DOI: 10.57707/fmi-b2share.bff0a61a7ddc4e59a3958fcc1060a313
title: CO2, CH4 and N2O fluxes in a Nordic agricultural field growing barley intercropped with undersown species

description: This package contains data from an experimental site in southern Finland, where barley was cultivated either as a monoculture or intercropped with 1 to 8 undersown species. After the barley harvest, the undersown species remained in the field and served as a cover crop until tillage in the following spring. The field, located in Helsinki (60°13'29.4"N, 25°01'12.7"E), is classified as coarse mineral soil. Manual chamber flux measurements included NEE, TER, N₂O, and CH₄, and were conducted over a two-year period from May 2020 to May 2022.
DOI: 10.5061/dryad.w0vt4b8wg
title: Data obtained by systematic review (codified data and meta-data) for: Influence of upwelling on coral reef benthic communities: a systematic review and meta-analysis

description: Highly competitive coral reef benthic communities are acutely sensitive to
 changes in environmental parameters such as temperature and nutrient
 concentrations. Physical oceanographic processes that induce upwelling
 therefore act as drivers of community structure on tropical reefs. How
 upwelling impacts coral communities, however, is not fully understood;
 upwelling may provide a natural buffer against climate impacts and could
 potentially enhance the efficacy of spatial management and reef
 conservation efforts. This study employed a systematic review to assess
 existing literature linking upwelling with reef community structure, and a
 meta-analysis to quantify upwelling impact on the percentage cover of
 coral reef benthic groups. We show that upwelling has context-dependant
 effects on the cover of hard coral and fleshy macroalgae, with effect size
 and direction varying with depth, region and remoteness. Fleshy macroalgae
 was found to increase by 110% on inhabited reefs yet decrease by 56%
 around one well-studied remote island in response to upwelling. Hard coral
 cover was not significantly impacted by upwelling on inhabited reefs but
 increased by 150% when direct human pressures were absent.  By
 synthesising existing evidence, this review facilitates adaptive and
 nuanced reef management which considers the influence of upwelling on reef
 assemblages.
description: This dataset is the product of a systematic review assessing the
 impact of upwelling on coral reef benthic communities. Full details of the
 methodology for collating this dataset can be viewed in the associated
 manuscript.
DOI: 10.57707/fmi-b2share.c5ke5-a8653
title: CO2, CH4 and N2O fluxes in a Nordic agricultural field growing barley intercropped with undersown species

description: This package contains data from an experimental site in southern Finland, where barley was cultivated either as a monoculture or intercropped with 1 to 8 undersown species. After the barley harvest, the undersown species remained in the field and served as a cover crop until tillage in the following spring. The field, located in Helsinki (60°13'29.4"N, 25°01'12.7"E), is classified as coarse mineral soil. Manual chamber flux measurements included NEE, TER, N₂O, and CH₄, and were conducted over a two-year period from May 2020 to May 2022.
DOI: 10.5061/dryad.vq83bk3xx
title: A custom-made AAV1 variant (AAV1-T593K) enables efficient transduction of Japanese quail neurons in vitro and in vivo

description: The widespread use of rodents in neuroscience has prompted the development
 of optimized viral variants for transduction of brain cells, in vivo.
 However, many of the viruses developed are less efficient in other model
 organisms, with birds being among the most resistant to transduction by
 current viral tools. Resultantly, the use of genetically-encoded tools and
 methods in avian species is markedly lower than in rodents; likely holding
 the field back. We sought to bridge this gap by developing custom viruses
 towards the transduction of brain cells of the Japanese quail. We first
 develop a protocol for culturing primary neurons and glia from quail
 embryos, followed by characterization of cultures via immunostaining,
 single-cell mRNA sequencing, patch clamp electrophysiology and calcium
 imaging. We then leverage the cultures for the rapid screening of various
 viruses, only to find that all yielded poor to no infection of cells in
 vitro. However, few infected neurons were obtained by AAV1 and AAV2.
 Scrutiny of the sequence of the AAV receptor found in quails led us to
 rationally design a custom-made AAV variant (AAV1-T593K; AAV1*) that
 exhibits improved transduction efficiencies in vitro and in vivo (eight-
 and five-fold, respectively). Together, we present a unique culturing
 method, transcriptomic profiles of quail’s brain cells and a
 custom-tailored AAV1 for transduction of quail neurons in vitro and in
 vivo.
description: Electrophysiology, immunostaining, single-cell mRNA
 sequencing.
DOI: 10.5061/dryad.ksn02v78k
title: Code and initial metapopulation data for model construction and simulation analyses for: Genetic rescue from protected areas is modulated by migration, hunting rate and timing of harvest

description: Migrants from protected areas may buffer the risk of harvest-induced
 evolutionary changes in exploited populations that face strong selective
 harvest pressures in both terrestrial and marine ecosystems. Understanding
 the mechanisms favouring genetic rescue through migration could help
 ensure sustainable harvest outside protected areas and conserve genetic
 diversity inside those areas. We developed a stochastic individual-based
 metapopulation model to evaluate the potential for migration from
 protected areas to mitigate the evolutionary consequences of selective
 harvest. We parameterized the model with detailed data from individual
 monitoring of two populations of bighorn sheep subjected to trophy
 hunting. We tracked horn length through time in a metapopulation including
 large protected and trophy-hunted populations connected through male
 breeding migrations. We quantified and compared declines in horn length
 and rescue potential under various combinations of migration rate, hunting
 rate in hunted areas and temporal overlap in timing of harvest and
 migrations, which affects the migrants' survival and chances to breed
 within exploited areas. Our simulations suggest that the effects of
 size-selective harvest on male horn length in hunted populations can be
 dampened or avoided if harvest pressure is low, migration rate is
 substantial, and migrants have a low risk of being shot. Intense
 size-selective harvest impacts the phenotypic and genetic diversity in
 horn length, and population structure through changes in proportions of
 large-horned males, sex ratio and age structure. When hunting pressure is
 high and overlaps with male migrations, effects of selective removal also
 emerge in the protected population, so that instead of a genetic rescue of
 hunted populations, our model predicts undesirable effects inside
 protected areas. Our results stress the importance of a metapopulational
 approach to management, to promote genetic rescue from protected areas and
 limit ecological and evolutionary impacts of harvest on both harvested and
 protected populations.
description: This dataset consists of code scripts and initial file to run the
 stochastic individual-based metapopulation model we developed to evaluate
 the potential for migration from protected areas to mitigate the
 evolutionary consequences of selective harvest. All codes were implemented
 in the open-source statistical programming language R (R Core Team,
 2021).
DOI: 10.5061/dryad.jdfn2z3fp
title: Supporting Information: Measuring Functional Redundancy Using Generalized Hill Numbers

description: A number of metrics for quantifying the amount of functional redundancy in
 a community have been proposed over the years. Two of the most
 popular metrics are based on comparing a taxonomic diversity measure with
 a generalized form of the same measure that accounts for functional
 dissimilarities between taxa. These two metrics express redundancy as
 either an absolute or relative difference between the taxonomic diversity
 measure and its generalized form. Because they express the amount of
 redundancy in a community in terms of raw diversity values, both
 redundancy metrics are susceptible to the same issues that complicate the
 interpretation of most commonly used diversity indices. It is possible to
 overcome these issues by restating these two indices using a Hill numbers
 framework. As a growing number of authors have noted, these modified
 metrics provide a more intuitive quantitative definition of functional
 redundancy when used to rank communities. Beyond this intuitive
 definition, measuring redundancy in terms of Hill numbers allows
 researchers to control the influence of rare taxa on the output value,
 enabling ecologists to better predict how a community is expected to
 respond when exposed to an external perturbation that selectively
 eliminates rare or common taxa. Here I show that, of the two possible Hill
 number-based redundancy metrics, the form based on a popular absolute
 redundancy metric is extremely sensitive to differences in taxonomic
 diversity and can provide a misleading picture of how much redundancy is
 present in a community. For this reason, I argue that Hill number-based
 functional redundancy should be quantified using a relative metric that
 explicitly accounts for differences in effective taxonomic
 diversity. The proposed Hill number-based relative redundancy
 measure is shown to provide a much more complete picture of the
 distribution of redundant taxa within a community, highlighting subtle
 patterns that are completely missed by the Hill number-based absolute
 redundancy metric.
description: Hypothetical datasets generated by the author, following the
 procedure described in the main text. Three hypothetical communities, each
 composed of equally abundant species, where five species are functionally
 identical, and the remaining species are functionally unique. X contains
 10 species, Y contains 50 species, Z contains 100 species. Software (R
 code) created by Daniel G. Dick.
description: Hypothetical datasets can be opened using any text editor. R
 scripts can be opened using the most current version of R. Appendices can
 be opened in Microsoft Word or OpenOffice.
DOI: 10.5061/dryad.9kd51c5ns
title: Data for: Gene flow accelerates adaptation to a parasite

description: Gene flow into populations can increase additive genetic variation and
 introduce novel beneficial alleles, thus facilitating adaptation. However,
 gene flow may also impede adaptation by disrupting beneficial genotypes,
 introducing deleterious alleles, or creating novel dominant negative
 interactions. While theory and fieldwork have provided insight as to the
 effects of gene flow, direct experimental tests are rare. Here, we
 evaluated the effects of gene flow on adaptation in the nematode
 Caenorhabditis elegans during exposure to the bacterial parasite Serratia
 marcescens. We evolved hosts against non-evolving parasites for ten
 passages while controlling host gene flow and source population. We used
 source nematode populations with three different genetic backgrounds (one
 similar to the sink population and two different) and two evolutionary
 histories (previously adapted to S. marcescens or naïve). We found that
 populations with gene flow exhibited greater increases in parasite
 resistance than those without gene flow. Additionally, gene flow from
 adapted populations resulted in greater increases in resistance than gene
 flow from naïve populations, particularly with gene flow from novel
 genetic backgrounds. Overall, this work demonstrates that gene flow can
 facilitate adaptation and suggests that the genetic architecture and
 evolutionary history of source populations can alter the sink population’s
 response to selection.
description: The raw data was collected by methods outlined in the materials
 and methods section of the manuscript. Data was recorded into an Excel
 spreadsheet, cleaned, then uploaded into JMP Pro 14 for statistical
 analysis and figure creation.
DOI: 10.5061/dryad.n8pk0p30v
title: DNA methylation signatures of duplicate gene evolution in angiosperms

description: Gene duplication is a source of evolutionary novelty. DNA methylation may
 play a role in the evolution of duplicate genes through its association
 with gene expression. While this relationship is examined to varying
 extents in a few individual species, the generalizability of these results
 at either a broad phylogenetic scale with species of differing duplication
 histories or across a population remains unknown. We apply a comparative
 epigenomics approach to 43 angiosperm species across the phylogeny and a
 population of 928 Arabidopsis thaliana accessions, examining the
 association of DNA methylation with paralog evolution. Genic DNA
 methylation is differentially associated with duplication type, the age of
 duplication, sequence evolution, and gene expression. Whole genome
 duplicates are typically enriched for CG-only gene-body methylated or
 unmethylated genes, while single-gene duplications are typically enriched
 for non-CG methylated or unmethylated genes. Non-CG methylation, in
 particular, was characteristic of more recent single-gene duplicates. Core
 angiosperm gene families are differentiated into those which
 preferentially retain paralogs and ‘duplication-resistant’ families, which
 convergently revert to singletons following duplication.
 Duplication-resistant families which still have paralogous copies are,
 uncharacteristically for core angiosperm genes, enriched for non-CG
 methylation. Non-CG methylated paralogs have higher rates of sequence
 evolution, higher frequency of presence-absence variation, and more
 limited expression. This suggests that silencing by non-CG methylation may
 be important to maintaining dosage following duplication and be a
 precursor to fractionation. Our results indicate that genic methylation
 marks differing evolutionary trajectories and fates between paralogous
 genes and have a role in maintaining dosage following duplication.
description: This dataset includes formatted genomes and annotations for use
 with code from: https://github.com/niederhuth/DNA-methylation-signatures-of-duplicate-gene-evolution-in-angiosperms.