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FIGURE 34 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 34. Mantidactylus betsileanus in life, in anterior, dorsolateral, and ventral view. (a,b,c) Adult male from Andasibe, photographed in 1991. (d) Adult male from Andasibe, photographed in situ in a small cavity next to a swamp where it was emitting its call, photographed in 1991. (e,f) Adult male from Mahasoa, photographed in 2008. (g,h) Adult male from Andasibe, photographed in 1995. Note in the ventral views the relatively small femoral glands, with the distal ulcerous macroglands placed at considerable distances from each other, which constitutes a typical character state of this species; and in the frontal view (a), the white dot on the snout tip which is typical for this and several allied species.
FIGURE 10 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 10. Mantidactylus curtus in life, in dorsolateral and ventral view. (a,b) Female specimen (ZSM 768/2001 = FGMV 2001.489) from Itremo, photographed in 2001 (note the almost complete absence of femoral glands). (c,d) Probable female (note small femoral glands) from Antoetra, photographed in 2003. (e,f), Probable female (ZSM 758/2001 = FGMV 2001.423; note rather small femoral glands) from Mount Ibity/Col des Tapias, photographed in 2001.
FIGURE 8 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 8. Heat map of Brygoomantis species distribution overlap (plotted as minimum convex polygons). This map is only based on species that are recorded from more than two localities (i.e. those for which a polygon could be plotted).
FIGURE 4 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 4. Network based on sequences of the nuclear-encoded Rag-1 gene (alignment length 351 bp) from 265 specimens of Brygoomantis. The network was built from phased alleles, i.e. each sample is represented twice. The size of circles is proportional to the number of sequences with the same allele. Small black dots represent hypothetical haplotypes (not sampled or extinct) separating sampled haplotypes, when they differ by more than one mutational step.
FIGURE 7 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 7. Mantidactylus subgenus Brygoomantis species distribution based on verified records, divided by clade (Mantidactylus stelliger sp. nov. is presented alongside the inaudax clade for practicality). Colours for species correspond to those in Figs 2 and 4. Inset map shows the geographic regions of Madagascar identified by Boumans et al. (2007), referred to throughout the text.
FIGURE 6 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 6. Overview of morphometrics of Mantidactylus (Brygoomantis) species. Points and boxplots are coloured by sex (purple = female, blue = male), with sample size per sex given beside the taxon names. Species are arranged according to the main clades to which they belong according to our phylogenomic analysis. SVL is repeated in the upper and lower panels to enable the reader to access relevant information quickly.
FIGURE 5 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 5. Maximum-Likelihood tree based on a partitioned analysis of 12,818 nuclear-encoded markers obtained via the FrogCap strategy, calculated with IQ-tree, for 58 representative individuals of species-level lineages in the subgenus Mantidactylus (Brygoomantis). Note that three species are missing from this analysis (M. bletzae sp. nov., M. marintsoai sp. nov., and M. riparius sp. nov.) and the identity of the two samples of M. katae sp. nov. in this tree is uncertain. For those lineages that previously (Perl et al. 2014; Vieites et al. 2009) had candidate species numbers assigned, these are reported in parenthesis after the name used in the classification proposed herein. All branches were fully supported by SH-like approximate likelihood ratio tests with 1000 pseudoreplicates (100% support, symbolized by black dots at nodes). The tree was rooted with Mantidactylus grandidieri (subgenus Mantidactylus) as outgroup (removed from graphical representation for better visualization of ingroup relationships), with the inclusion of M. melanopleura (subgenus Chonomantis) as hierarchical outgroup. Red arrows in the M. curtus clade indicate the two reticulation events detected by a Phylonetworks analysis performed separately for this clade (note that the topology recovered by this analysis in the Phylonetworks analysis differs in the position of M. bourgati; see original results of the Phylonetworks analysis in Zenodo repository, DOI 10.5281/zenodo.668741
FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 2. Maximum Likelihood tree of 1305 sequences of a fragment of the 16S rRNA gene (alignment length 519 bp) from a RAxML analysis. Numbers at nodes are bootstrap proportions in percent (100 ML fast bootstrap replicates); not shown if <50%. A sequence of Mantidactylus melanopleura was used as the outgroup (removed from the tree after analysis for better graphical representation). Note that some of the 'Museomics' sequences (obtained by targeted capture from historical type specimens) are represented twice, after assembly with different reference sequences. Some sequences in the analysis (several 'Museomics' sequences as well as others obtained from Illumina sequencing) only partially covered the fragment analysed (226 sequences <300 bp). We emphasize that this tree is based on a single short mitochondrial marker and therefore is unlikely to represent the deep relationships among lineages correctly; for such relationships, refer to the phylogenomic tree (Fig. 5).
FIGURE 1 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 1. Graphic scheme indicating (a) regions of the body and (b) morphometrics measurements of Mantidactylus specimens of the subgenus Brygoomantis (exemplified by a specimen of M. ulcerosus), as referred to in the descriptions of morphology and tables throughout the manuscript. Labels in (a) refer to regions of the body and not necessarily to anatomical features. Femoral gland terminology as explained in the text. Measurement abbreviations in (b) are explained in the text; FORL (stretched forelimb length), HIL (stretched hindlimb length), and FOTL (foot length including tarsus) are not shown.
FIGURE 3 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 3. Distribution of uncorrected pairwise genetic distances for a fragment of the mitochondrial 16S rRNA gene, in an alignment of 976 sequences, complete or almost complete for 488 bp.
Integration of environmental DNA metabarcoding technique to reinforce fish biodiversity assessments in seagrass ecosystems: A case study of Gazi Bay Seagrass meadows
<p><span>Assessing biodiversity in marine nearshore ecosystems is crucial for effective management, especially in the context of climate change and overexploitation of marine resources. Conventional methods often fall short in providing comprehensive information for managing seagrass ecosystems. However, the emergence of environmental DNA (eDNA) techniques has transformed the field by enabling non-invasive surveys that are cost-effective and provide detailed information with high resolution. In this study, we utilized eDNA to assess fish diversity and compared its effectiveness to conventional techniques such as catch assessment surveys and underwater surveys. </span>We sampled three habitats (A: mangrove-seagrass, B: seagrass only, and C: coral-seagrass) with 4 replicates. Site A recorded 8 fish species, site B had 16 species, and site C, characterized by coral and seagrass habitats, exhibited the highest fish diversity with 45 species (mean H' index = 2.455), underscoring its ecological importance. To ensure accurate taxonomic identification, we utilized an updated MiFish reference database containing a larger number of fish species compared to the initial library. This expanded reference database with 9,569 fish species, facilitated more precise identification and enhanced the reliability of our findings. Notably, the eDNA technique outperformed conventional methods by detecting 23 additional fish species that went undetected using traditional surveys. Moreover, our study documented five fish species previously unknown to occur within the study region, further emphasizing the value of eDNA analysis in uncovering hidden biodiversity. These findings strongly advocate for integrating eDNA techniques into the monitoring and assessment of biodiversity in shallow tropical habitats of the Western Indian Ocean. By leveraging eDNA surveys, we can gain valuable insights into fish diversity, discover hidden species, and make informed decisions for the conservation and management of these ecologically significant areas.</p>
A novel method to assess the integrity of frozen archival DNA samples: Alpha-diversity ratios of short and long-read 16S rRNA gene sequences
Open the record for dataset details and reuse information.
Integration of environmental DNA metabarcoding technique to reinforce fish biodiversity assessments in seagrass ecosystems: A case study of Gazi Bay Seagrass meadows
Open the record for dataset details and reuse information.
Figure 37 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 37. Heterolepisma cooloola sp. nov. from leaf litter at Carlo Point.
Figure 1 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 1. Collection localities.
Figure 6 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 6. Heterolepisma coorongooba sp. nov. Glen Davis, NSW.
Data from: Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modeling
<p>Molecular analysis of DNA left in the environment, known as environmental DNA (eDNA), has proven to be a powerful and cost-effective approach to infer occurrence of species. Nonetheless, relating measurements of eDNA concentration to population abundance remains difficult because detailed knowledge on the processes that govern spatial and temporal distribution of eDNA should be integrated to reconstruct the underlying distribution and abundance of a target species. In this study, we propose a general framework of abundance estimation for aquatic systems on the basis of spatially replicated measurements of eDNA. The proposed method explicitly accounts for production, transport, and degradation of eDNA by utilizing numerical hydrodynamic models that can simulate the distribution of eDNA concentrations within an aquatic area. It turns out that, under certain assumptions, population abundance can be estimated via a Bayesian inference of a generalized linear model. Application to a Japanese jack mackerel (<em>Trachurus japonicus</em>) population in Maizuru Bay revealed that the proposed method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. Furthermore, the method successfully identified a source of exogenous input of eDNA (a fish market), which may render a quantitative application of eDNA difficult to interpret unless its effect is taken into account. These findings indicate the ability of eDNA to reliably reflect population abundance of aquatic macroorganisms; when the "ecology of eDNA" is adequately accounted for, population abundance can be quantified on the basis of measurements of eDNA concentration.</p>
Supplementary information associated with a "Whole-Organism Integrated DNA Methylation and Transcriptomics Analysis of Butterfly Metamorphosis".
<p>Supplementary information, annotation and code related to the manuscript studying <em>Bicyclus anynana</em> development entitled "Whole-Organism Integrated DNA Methylation and Transcriptomics Analysis of Butterfly Metamorphosis".</p>
Application of flow cytometry using advanced chromatin analyses for assessing changes in the sperm structure and DNA integrity in a porcine model
<p><span>Chromatin status is critical for sperm fertility. We tested a multivariate approach for studying pig sperm chromatin, aiming to capture the chromatin structure's complexity with a set of quick and simple techniques, not only DNA damage. Sperm doses from 36 boars (3 ejaculates/boar) were analyzed at days 0 and 11 (cooled storage). Analyses were: CASA (motility) and flow cytometry to assess sperm functionality and chromatin structure by SCSA (DNA fragmentation %DFI and chromatin maturity %HDS), monobromobimane (mBBr, tiol status/disulfide bridges between protamines), chromomycin A3 (CMA3, protamination) and 8-hydroxy-2'-deoxyguanosine (8-oxo-dG, DNA oxidative damage). Data were analyzed by linear models for effects of boar and storage, correlations, and multivariate analysis as hierarchical clustering and principal component analysis (PCA). Storage reduced sperm quality parameters, mainly motility, with no critical oxidative stress increases, while chromatin status worsened slightly (%DFI and 8-oxo-dG increased while mBBr MFI and disulfide bridges decreased). Boar significantly affected most chromatin variables except for CMA3, with storage affecting most except %HDS. At day 0, sperm chromatin variables clustered closely, except for CMA3, and %HDS and 8-oxo-dG correlated with many variables (notably, mBBr). After storage, the relation between %HDS and 8-oxo-dG remained, but correlations among other techniques disappeared, and mBBr variables clustered separately. The PCA suggested a considerable influence of mBBr on sample variance, especially regarding storage, with SCSA and 8-oxo-dG affecting between-sample variability. Overall, CMA3 was the least informative, in contrast with results in other species. The combination of DNA fragmentation, DNA oxidation, chromatin compaction, and tiol status seems a good candidate for obtaining a complete picture of the pig sperm nucleus status, raising many questions for future molecular studies and deserving further research to establish its usefulness as fertility predictors in multivariate models. The meaning of CMA3 should be clarified.</span></p>
Supplementary materials for "Integration of public DNA methylation and expression networks via eQTMs improves prediction of functional gene–gene associations"
<p>This repository contained supplementary materials in the study named: "<strong>Integration of public DNA methylation and expression networks via eQTMs improves prediction of functional gene–gene associations.</strong>"</p> <p>For extracting all files from the downloaded tar.gz file, the following commanda could be used:</p> <pre><code>tar -xf supplementary_materials.tar.gz </code></pre> <p>The supplementary_materials/data diretcory contains the following sections:</p> <p></p> <ol> <li>eqtm_predictions: This contains the training and testing datasets for the eQTM prediction procedures</li> <li>public_methylation_data_and_pca: This contains the harmonized public DNA methylation dataset and its first 100 PCA components</li> <li>cca_data: This contains the CCA components for the public DNA methylation and gene expression datasets for the negative eQTMs, and the input datasets for the functional gene pair prediction analylsis.</li> <li>gene_enrichment_results_for_cca: This contains the gene enrichment results for the CCA components for negative and positive eQTMs</li> </ol> <p>The supplementary_materials/model directory contains the following sections:</p> <ol> <li>disease_tissue_predictions: This contains the models trained for tissue prediction and disease prediction based on the PCA components from the public DNA methylation data</li> <li>eqtm_predictions: This contains models trained for eQTM prediction</li> <li>cca_transformations: This contains CCA transformation models and models for STRING gene pair predictions </li> </ol>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.