cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pp0jp
title: Data from: Subdivision design and stewardship affect bird and mammal use of conservation developments

description: Developing effective tools for conservation on private lands is
 increasingly important for global biodiversity conservation; private lands
 are located in more productive and biologically diverse areas, and they
 face accelerated rates of land conversion. One strategy is conservation
 development (CD) subdivisions, which cluster houses in a small portion of
 a property and preserve the remaining land as protected open space.
 Despite widespread use, the characteristics that make CD more or less
 effective at achieving biodiversity conservation are not well understood.
 We investigated CD's ability to successfully protect animal
 populations by examining bird and mammal occurrences in 14 CD subdivisions
 and 4 undeveloped areas (range: 14-432 ha) in northern Colorado, USA.
 Using point count and camera trap data in an occupancy modeling framework,
 we evaluated the relative importance of 9 subdivision design factors
 (e.g., housing density, proportion of CD protected) and 14 stewardship
 factors (e.g., presence of livestock, % native vegetation cover) in
 influencing the overall community composition and the probability of use
 by 16 birds and 6 mammals. We found that habitat use by 75% of birds and
 83% of mammals was associated with design characteristics that maximized
 the natural or undisturbed land area both within and near the development
 (e.g., proportion of CD protected, total area of protected open space,
 proportion of natural land cover in the surrounding landscape). These
 factors were also associated with an increasing dominance of
 human-sensitive bird species, larger-bodied mammals, and mammals with
 larger home ranges. Habitat use by birds was also influenced by local land
 use composition and quality, and use by several bird and mammal species
 decreased with increased localized disturbances. We found few differences
 in habitat use between sampling sites in undeveloped areas and in CD
 subdivisions. These similarities indicate that, if CDs are large enough or
 located within a matrix of undeveloped land, they can provide habitat that
 supports similar use patterns as protected areas without housing
 development. By incorporating characteristics that promote the persistence
 of sensitive birds and mammals on private lands, CDs have potential to
 preserve native biodiversity in areas threatened by expanding residential
 development.
description: CDBird_OccupancyAnalysis_DataCDMammal_OccupancyAnalysis_DataCDBird_CDUndevelopedComparison_DataCDMammal_CDUndevelopedComparison_DataCDBird_CommunityComposition_DataCD_Mammal_CommunityComposition_Data
DOI: 10.5061/dryad.bb702
title: Data from: Mlh3 mutations in baker's yeast alter meiotic recombination outcomes by increasing noncrossover events genome-wide

description: Mlh1-Mlh3 is an endonuclease hypothesized to act in meiosis to resolve
 double Holliday junctions into crossovers. It also plays a minor role in
 eukaryotic DNA mismatch repair (MMR). To understand how Mlh1-Mlh3
 functions in both meiosis and MMR, we analyzed in baker's yeast 60
 new mlh3 alleles. Five alleles specifically disrupted MMR, whereas one
 (mlh3-32) specifically disrupted meiotic crossing over. Mlh1-mlh3
 representatives for each class were purified and characterized. Both
 Mlh1-mlh3-32 (MMR+, crossover-) and Mlh1-mlh3-45 (MMR-, crossover+)
 displayed wild-type endonuclease activities in vitro. Msh2-Msh3, an MSH
 complex that acts with Mlh1-Mlh3 in MMR, stimulated the endonuclease
 activity of Mlh1-mlh3-32 but not Mlh1-mlh3-45, suggesting that
 Mlh1-mlh3-45 is defective in MSH interactions. Whole genome recombination
 maps were constructed for wild-type and MMR+ crossover-, MMR- crossover+,
 endonuclease defective and null mlh3 mutants in an S288c/YJM789 hybrid
 background. Compared to wild-type, all of the mlh3 mutants showed
 increases in the number of noncrossover events, consistent with
 recombination intermediates being resolved through alternative
 recombination pathways. Our observations provide a structure-function map
 for Mlh3 that reveals the importance of protein-protein interactions in
 regulating Mlh1-Mlh3's enzymatic activity. They also illustrate how
 defective meiotic components can alter the fate of meiotic recombination
 intermediates, providing new insights for how meiotic recombination
 pathways are regulated.
description: Raw groupEvents and
 ReCombine data and Custom R scripts for genome wide recombination analysis
 of mlh3 separation of function mutantseric-dryad-final_Aug16.zip
DOI: 10.5061/dryad.9677h
title: Data from: Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons

description: Background: The vaginal microbiome is an important site of
 bacterial-mammalian symbiosis. This symbiosis is currently best
 characterized for humans, where lactobacilli dominate the microbial
 community and may help defend women against infectious disease. However,
 lactobacilli do not dominate the vaginal microbiota of any other mammal
 studied to date, raising key questions about the forces that shape the
 vaginal microbiome in non-human mammals. Results: We used Illumina
 sequencing of the bacterial 16S rRNA gene to investigate variation in the
 taxonomic composition of the vaginal microbiota in 48 baboons (Papio
 cynocephalus), members of a well-studied wild population in Kenya. Similar
 to prior studies, we found that the baboon vaginal microbiota was not
 dominated by lactobacilli. Despite this difference, and similar to humans,
 reproductive state was the dominant predictor of baboon vaginal
 microbiota, with pregnancy, postpartum amenorrhea, and ovarian cycling
 explaining 18% of the variance in community composition. Furthermore,
 among cycling females, a striking 39% of variance in community composition
 was explained by ovarian cycle phase, with an especially distinctive
 microbial community around ovulation. Peri-ovulatory females exhibited the
 highest relative abundance of lactic acid-producing bacteria compared to
 any other phase, with a mean relative abundance of 44%. To a lesser
 extent, sexual behavior, especially a history of shared sexual partners,
 also predicted vaginal microbial similarity between baboons. Conclusions:
 Despite striking differences in their dominant microbes, both human and
 baboon vaginal microbiota exhibit profound changes in composition in
 response to reproductive state, ovarian cycle phase, and sexual behavior.
 We found major shifts in composition during ovulation, which may have
 implications for disease risk and conception success. These findings
 highlight the need for future studies to account for fine-scale
 differences in reproductive state, particularly differences between the
 various phases of the ovarian cycle. Overall, our work contributes to an
 emerging understanding of the forces that explain intra- and
 inter-individual variation in the mammalian vaginal microbiome, with
 particular emphasis on its role in host health and disease risk.
description: baboon_metadata_alpha_diversityMetadata, number of reads, estimated sample coverage, and alpha diversity metrics (Shannon's diversity index and OTU richness) for each vaginal sample included in this study.unrarefied_OTU_tableUnrarefied OTU table with taxonomic classifications in the last column. All OTUs that occurred in only one sample are not included.
DOI: 10.5061/dryad.bp20p
title: Data from: Rates of hypoxia induction alter mechanisms of O2 uptake and the critical O2 tension of goldfish

description: The rate of hypoxia induction (RHI) is an important but overlooked
 dimension of environmental hypoxia that may affect an organism’s survival.
 We hypothesized that, compared with rapid RHI, gradual RHI will afford an
 organism more time to alter plastic phenotypes associated with O2 uptake
 and subsequently reduce the critical O2 tension (Pcrit) of O2 uptake rate
 (ṀO2). We investigated this by determining Pcrit values for goldfish
 exposed to short (∼24 min), typical (∼84 min) and long (∼480 min) duration
 Pcrit trials to represent different RHIs. Consistent with our predictions,
 long duration Pcrit trials yielded significantly lower Pcrit values
 (1.0-1.4 kPa) than short and typical duration trials, which did not differ
 (2.6±0.3 and 2.5±0.2 kPa, respectively). Parallel experiments revealed
 these time-related shifts in Pcrit were associated with changes in aspects
 of the O2 transport cascade: gill surface areas and haemoglobin-O2 binding
 affinities were significantly higher in fish exposed to gradual RHIs over
 480 min than fish exposed to rapid RHIs over 60 min. Our results also
 revealed that the choice of respirometric technique (i.e., closed versus
 intermittent) does not affect Pcrit or routine ṀO2, despite the
 significantly reduced water pH and elevated CO2 and ammonia levels
 measured following closed-circuit Pcrit trials of ∼90 min. Together, our
 results demonstrate that gradual RHIs result in alterations to
 physiological parameters that enhance O2 uptake in hypoxic environments.
 An organism’s innate Pcrit is therefore most accurately determined using
 rapid RHIs (&lt;90 min) so as to avoid the confounding effects of
 hypoxic acclimation.
description: JEXBIO_154948Spreadsheets containing raw data files for Regan and Richards (2016)
DOI: 10.5061/dryad.mm856
title: Data from: Chromosomal speciation in the genomics era: disentangling phylogenetic evolution of rock-wallabies

description: The association of chromosome rearrangements with speciation is well
 established, and there is a long history of theory and evidence relating
 to “chromosomal speciation”. Genomic sequencing has the potential to
 provide new insights into how reorganization of genome structure promotes
 divergence, and in model systems has demonstrated reduced gene flow in
 rearranged segments. However, there are limits to what we can understand
 from a small number of model systems, which each only tell us about one
 episode of chromosomal speciation. Progressing from patterns of
 association between chromosome (and genic) change, to understanding
 processes of speciation requires both comparative studies across diverse
 systems and integration of genome-scale sequence comparisons with other
 lines of evidence. Here we showcase a promising example of chromosomal
 speciation in a non-model organism, the endemic Australian marsupial genus
 Petrogale. We present initial phylogenetic results from exon-capture that
 resolve a history of divergence associated with extensive and repeated
 chromosome rearrangements. Yet it remains challenging to disentangle gene
 tree heterogeneity caused by recent divergence and gene flow in this and
 other such recent radiations. We outline a way forward for better
 integration of comparative genomic sequence data with evidence from
 molecular cytogenetics, and analyses of shifts in the recombination
 landscape and potential disruption of meiotic segregation and epigenetic
 programming. In all likelihood, chromosome rearrangements impact multiple
 cellular processes and these effects need to be considered together, along
 with those of genic divergence. Understanding the effects of chromosome
 rearrangements together with genic divergence will require development of
 more integrative theory and inference methods. Together, new data and
 analysis tools will combine to shed light on long standing questions of
 how chromosome and genic divergence promote speciation.
description: Chromosomal speciation
 and phylogenetics of PetrogaleThis repository contains
 three directories, containing data, code and workflows for phylogenetic
 analysis and chromosome mapping of ~2000 exons for
 Petrogale.Dryad archive
 Petrogale.zip
DOI: 10.5061/dryad.g3fn8
title: Data from: Predicting evolution in response to climate change: the example of sprouting probability in three dormancy-prone orchid species

description: Although many ecological properties of species respond to climate change,
 their evolutionary responses are poorly understood. Here, we use data from
 long-term demographic studies to predict evolutionary responses of three
 herbaceous perennial orchid species, Cypripedium parviflorum, C. candidum
 and Ophrys sphegodes, to predicted climate changes in the habitats they
 occupy. We focus on the evolution of sprouting probability, because all
 three species exhibit long-term vegetative dormancy, i.e. individual
 plants may not emerge above-ground, potentially for several consecutive
 years. The drivers of all major vital rates for populations of the species
 were analysed with general linear mixed models (GLMMs).
 High-dimensionality function-based matrix projection models were then
 developed to serve as core elements of deterministic and stochastic
 adaptive dynamics models used to analyse the adaptive context of sprouting
 in all populations. We then used regional climate forecasts, derived from
 high-resolution general atmospheric circulation models, of increased mean
 annual temperatures and spring precipitation at the occupied sites, to
 predict evolutionary trends in sprouting. The models predicted that C.
 parviflorum and O. sphegodes will evolve higher and lower probabilities of
 sprouting, respectively, by the end of the twenty-first century, whereas,
 after considerable variation, the probability of sprouting in C. candidum
 will return to its current level. These trends appear to be driven by
 relationships between mortality and size: in C. parviflorum and C.
 candidum, mortality is negatively related to size in the current year but
 positively related to growth since the previous year, whereas in O.
 sphegodes, mortality is positively related to size.
description: Main matrices used in
 adaptive dynamics analysesThis Excel file contains
 population projection matrices used in the adaptive dynamics analyses
 covering the observed monitoring periods, as well as for the projected
 future period (1975-2099). Two matrices are included per species
 (Cypripedium candidum, Cypripedium parviflorum, and Ophrys sphegodes), and
 two additional matrices are provided as legends (one covering both
 Cypripedium species, and one covering Ophrys
 sphegodes).Matrices.xlsxClimate data used in adaptive dynamics analysesThis Excel file contains two spread sheets. The first contains observed and projected climate data for Gavin Prairie, the site of the Cypripedium candidum and C. parviflorum populations, while the second contains observed and projected climate data for the Ophrys sphegodes site. Legends are included on each spreadsheet.Climate Data.xlsx
DOI: 10.5061/dryad.6806c
title: Data from: Oscillatory signatures underlie growth regimes in Arabidopsis pollen tubes: computational methods to estimate tip location, periodicity and synchronization in growing cells

description: Oscillations in pollen tubes have been reported for many cellular
 processes, including growth, extracellular ion fluxes, and cytosolic ion
 concentrations. However, there is a shortage of quantitative methods to
 measure and characterize the different dynamic regimes observed. Herein, a
 suite of open-source computational methods and original algorithms were
 integrated into an automated analysis pipeline that we employed to
 characterize specific oscillatory signatures in pollen tubes of
 Arabidopsis thaliana (Col-0). Importantly, it enabled us to detect and
 quantify a Ca2+ spiking behaviour upon growth arrest and synchronized
 oscillations involving growth, extracellular H+ fluxes, and cytosolic
 Ca2+, providing the basis for novel hypotheses. Our computational approach
 includes a new tip detection method with subpixel resolution using linear
 regression, showing improved ability to detect oscillations when compared
 to currently available methods. We named this data analysis pipeline
 ‘Computational Heuristics for Understanding Kymographs and aNalysis of
 Oscillations Relying on Regression and Improved Statistics’, or
 CHUKNORRIS. It can integrate diverse data types (imaging,
 electrophysiology), extract quantitative and time-explicit estimates of
 oscillatory characteristics from isolated time series (period and
 amplitude) or pairs (phase relationships and delays), and evaluate their
 synchronization state. Here, its performance is tested with ratiometric
 and single channel kymographs, ion flux data, and growth rate analysis.
description: Ratiometric kymographs
 of growing pollen tubesKymographs of
 Arabidopsis pollen tubes growing in vitro, featuring two channels (YFP and
 CFP) of the genetically encoded ratiometric calcium probe
 YC3.6.ratiometric_kymographs.zipMetaMorph tracking of the pollen tube tipTracking and growth rate series of the of the same growing pollen tubes where the ratiometric kymographs where extracted, performed with the 'Track Object' routine in MetaMorph with 3 different ROI sizes.MetaMorph_Tracking.zipSynchronized oscillations in growth, H+ flux and intracellular Ca2+Growth rate series from a tracking software (MetaMorph) is provided, together with a kymograph with fluorescence of a calcium reporter (Yellow Cameleon 3.6) and extracellular H+ flux measurements at the pollen tube tip from an ion-selective vibrating probe. A video with the tracking trace also used as midline to produce the kymograph is also included.Sync.zip
DOI: 10.5061/dryad.g62f6
title: Data from: Inferential biases linked to unobservable states in complex occupancy models

description: Modeling of species distributions has undergone a shift from relying on
 equilibrium assumptions to recognizing transient system dynamics
 explicitly. This shift has necessitated more complex modeling techniques,
 but the performance of these dynamic models has not yet been assessed for
 systems where unobservable states exist. Our work is motivated by the
 impacts of the emerging infectious disease chytridiomycosis, a disease of
 amphibians that associated with declines of many species worldwide. Using
 this host-pathogen system as a general example, we first illustrate how
 misleading inferences can result from failing to incorporate pathogen
 dynamics into the modeling process, especially when the pathogen is
 difficult or impossible to survey in the absence of a host species. We
 found that traditional modeling techniques can underestimate the effect of
 a pathogen on host species occurrence and dynamics when the pathogen can
 only be detected in the host, and pathogen information is treated as a
 covariate. We propose a dynamic multistate modeling approach that is
 flexible enough to account for the detection structures that may be
 present in complex multistate systems, especially when the sampling design
 is limited by a species’ natural history or sampling technology. When
 multistate occupancy models are used and an unobservable state is present,
 parameter estimation can be influenced by model complexity, data
 sparseness, and the underlying dynamics of the system. We show that, even
 with large sample sizes, many models incorporating seasonal variation in
 vital rates may not generate reasonable estimates, indicating parameter
 redundancy. We found that certain types of missing data can greatly hinder
 inference, and we make study design recommendations to avoid these issues.
 Additionally, we advocate the use of time-varying covariates to explain
 temporal trends in the data, and the development of sampling techniques
 that match the biology of the system to eliminate unobservable states when
 possible.
description: scen1_toadGenerated data for the SRM boreal toad scenario with 80 sites to be used with 2-species modeling.scen2_toad_2NGenerated data for the SRM boreal toad scenario with 160 sites to be used with the dynamic 2-species model.scenario_3_missingGenerated data for the SRM boreal toad scenario with 80 sites and some missing data, as described in the manuscript, to be used with the dynamic 2-species model.scen4_rare_severeGenerated data for rare and susceptible amphibian scenario with 80 sites to be used with dynamic 2-species model.ss_occ_bd_covGenerated data for the SRM boreal toad scenario with 80 sites converted to a single species format to assess how inference changes when the unobservable state is ignored.
DOI: 10.5061/dryad.ts747
title: Data from: Evolutionary history of chemosensory-related gene families across the Arthropoda

description: Chemosensory-related gene (CRG) families have been studied extensively in
 insects, but their evolutionary history across the Arthropoda had remained
 relatively unexplored. Here, we address current hypotheses and prior
 conclusions on CRG family evolution using a more comprehensive data set.
 In particular, odorant receptors were hypothesized to have proliferated
 during terrestrial colonization by insects (hexapods), but their
 association with other pancrustacean clades and with independent
 terrestrial colonizations in other arthropod subphyla have been unclear.
 We also examine hypotheses on which arthropod CRG family is most ancient.
 Thus, we reconstructed phylogenies of CRGs, including those from new
 arthropod genomes and transcriptomes, and mapped CRG gains and losses
 across arthropod lineages. Our analysis was strengthened by including
 crustaceans, especially copepods, which reside outside the
 hexapod/branchiopod clade within the subphylum Pancrustacea. We generated
 the first high-resolution genome sequence of the copepod Eurytemora
 affinis and annotated its CRGs. We found odorant receptors and odorant
 binding proteins present only in hexapods (insects) and absent from all
 other arthropod lineages, indicating that they are not universal
 adaptations to land. Gustatory receptors likely represent the oldest
 chemosensory receptors among CRGs, dating back to the Placozoa. We also
 clarified and confirmed the evolutionary history of antennal ionotropic
 receptors across the Arthropoda. All antennal ionotropic receptors in E.
 affinis were expressed more highly in males than in females, suggestive of
 an association with male mate-recognition behavior. This study is the most
 comprehensive comparative analysis to date of CRG family evolution across
 the largest and most speciose metazoan phylum Arthropoda.
description: Supplementary
 MaterialsSupplementary_Materials.pdfSUPPLEMENTAL FILE S1SUPPLEMENTAL_FILE_S1.txtSUPPLEMENTAL FILE S2SUPPLEMENTAL_FILE_S2.txtSUPPLEMENTAL FILE S3SUPPLEMENTAL_FILE_S3.txtFigure 1Figure1.pdfFigure 2Figure2.pdfFigure 2. Aligned sequences by MAFFTfigure2.faFigure 3Figure3.pdfFigure 3. Aligned sequences by MAFFTfigure3.faFigure 4Figure4.pdfFigure 5Figure5.pdfFigure 6Figure6.pdfFigure 6. Aligned sequences by MAFFTfigure6.faFigure S1FigureS1.pdfFigure S1. Aligned sequences by MAFFTFigureS1_mafft.faFigure S1. Netwick fileFigureS1_tree.newick
DOI: 10.5281/zenodo.18386949
title: Metabolome Age dependent priming in Arabidopsis

description: Raw data corresponding to the metabolome of Arabidopsis plants infected with Plectosphaerella cucumerina. Two physiological moments has been selected: adult and seddling stages. There are 4 conditions for each developmental stage (ADULTS and SEEDLINGS) with 6 replicates per condition:CONTROL, INFECTED, TREATED and TREATED AND INFECTED, in both modes of ionization (ESI+ and ESI -), using an LC-QTOF Premier (Waters) and a C18 column (for more details, check the publication when ready).
DOI: 10.5281/zenodo.18386950
title: Metabolome Age dependent priming in Arabidopsis

description: Raw data corresponding to the metabolome of Arabidopsis plants infected with Plectosphaerella cucumerina. Two physiological moments has been selected: adult and seddling stages. There are 4 conditions for each developmental stage (ADULTS and SEEDLINGS) with 6 replicates per condition:CONTROL, INFECTED, TREATED and TREATED AND INFECTED, in both modes of ionization (ESI+ and ESI -), using an LC-QTOF Premier (Waters) and a C18 column (for more details, check the publication when ready).