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100 results for “DNA shape”
Hidden in the DNA: insights on how multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf-litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae).
Aim: To investigate cryptic diversity and diversification timing in the putatively low-dispersal Amazonian leaf-litter lizard Loxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation. Location: Central Amazonia, Brazil. Taxon: Squamata; Gymnophthalmidae; Loxopholis osvaldoi. Methods: We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographic distance among localities, the environment, and the position of localities in relation to main rivers were tested by Redundancy Analysis (RDA). Results: We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE, and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE, or historical factors. Main conclusions: Our results strongly suggest that L. osvaldoi is a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history of L. osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that non-linear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.
Data from: Long livestock farming history and human landscape shaping revealed by lake sediment DNA
The reconstruction of human-driven, Earth-shaping dynamics is important for understanding past human/environment interactions and for helping human societies that currently face global changes. However, it is often challenging to distinguish the effects of the climate from human activities on environmental changes. Here we evaluate an approach based on DNA metabarcoding used on lake sediments to provide the first high-resolution reconstruction of plant cover and livestock farming history since the Neolithic Period. By comparing these data with a previous reconstruction of erosive event frequency, we show that the most intense erosion period was caused by deforestation and overgrazing by sheep and cowherds during the Late Iron Age and Roman Period. Tracking plants and domestic mammals using lake sediment DNA (lake sedDNA) is a new, promising method for tracing past human practices, and it provides a new outlook of the effects of anthropogenic factors on landscape-scale changes.
DNA-guided transcription factor cooperativity shapes face and limb mesenchyme
<p>Code and processed data for "DNA-guided transcription factor cooperativity shapes face and limb mesenchyme," Kim et al, Cell 2024.</p>
Data from: Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: evidence from DNA metabarcoding
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Hidden in the DNA: insights on how multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf-litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae).
Open the record for dataset details and reuse information.
Data from: Long livestock farming history and human landscape shaping revealed by lake sediment DNA
Open the record for dataset details and reuse information.
Figure 2 from: Monjardim M, Azevedo CO, Fagundes V (2020) DNA barcoding and hypopygium shape support delimitation of sympatric Dissomphalus species (Hymenoptera, Bethylidae) from the Atlantic rainforest. ZooKeys 959: 87-97. https://doi.org/10.3897/zookeys.959.53737
Figure 2 A bayesian consensus tree generated from the 304-bp COI from 29 representatives of the species complex. Posterior probabilities (PP) and bootstrap (BT) indicated above branches. The species D. thaianus, D. wusheanus and D. chiangmaiensis were used as outgroups to root the tree B–D hypopygium magnified 9.2×, corresponding to each clade.
Figure 1 from: Monjardim M, Azevedo CO, Fagundes V (2020) DNA barcoding and hypopygium shape support delimitation of sympatric Dissomphalus species (Hymenoptera, Bethylidae) from the Atlantic rainforest. ZooKeys 959: 87-97. https://doi.org/10.3897/zookeys.959.53737
Figure 1 Locations of the samples in Brazil and Paraguay (see Appendix I for geographic coordinates).
DNA-guided transcription factor cooperativity shapes face and limb mesenchyme
GEO Series GSE230319. Mus musculus; Homo sapiens. 379 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
DNA replication initiation shapes the mutational landscape and expression of the human genome (RNA-Seq)
GEO Series GSE202798. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
DNA-guided transcription factor cooperativity shapes face and limb mesenchyme [RNA-seq]
GEO Series GSE230318. Homo sapiens. 87 samples. Type: Expression profiling by high throughput sequencing.
High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins
GEO Series GSE65692. Drosophila melanogaster. 9 samples. Type: Other.
Deconvolving the recognition of DNA shape from sequence
GEO Series GSE65073. Drosophila melanogaster. 32 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing.
Global Genome Repair factors are essential for shaping the DNA methylation landscape in Arabidopsis [BS-seq]
GEO Series GSE76648. Arabidopsis thaliana. 2 samples. Type: Methylation profiling by high throughput sequencing.
An evolutionarily conserved DNA-encoded logic shapes CpG island formation
GEO Series GSE72208. Danio rerio; Mus musculus. 17 samples. Type: Methylation profiling by high throughput sequencing.
ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo
GEO Series GSE67453. Saccharomyces cerevisiae. 57 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
DNA Methylation shapes histone modification landscape for transcription regulation in Arabidopsis [RNA-Seq]
GEO Series GSE183985. Arabidopsis thaliana. 12 samples. Type: Expression profiling by high throughput sequencing.
Global Genome Repair factors are essential for shaping the DNA methylation landscape in Arabidopsis
GEO Series GSE76651. Arabidopsis thaliana. 5 samples. Type: Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other.
Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA shape [RNA-seq]
GEO Series GSE267299. Thermococcus kodakarensis. 12 samples. Type: Expression profiling by high throughput sequencing.
Inflammatory Cytokines shape a Changing DNA Methylome in Monocytes Mirroring Disease Activity in Rheumatoid Arthritis (in vitro)
GEO Series GSE134425. Homo sapiens. 12 samples. Type: Methylation profiling by array.
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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)
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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.