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197 results for “comparative genetics”
Supplementary material 1 from: Wang J-h, Zheng X-d (2017) Comparison of the genetic relationship between nine Cephalopod species based on cluster analysis of karyotype evolutionary distance. Comparative Cytogenetics 11(3): 477-494. https://doi.org/10.3897/compcytogen.v11i3.12752
Chromosome relative length, supplemental formulae : Explanation note: Chromosome relative length, supplemental formulae and all of the original images are made available under the online digital repository Figshare, and it is free to access, in adherence to the principle of open data, more details in https://figshare.com/s/8d21a0db9ffe1f17d279
A comparative evaluation of ChatGPT 3.5 and ChatGPT 4 in responses to selected genetics questions - Full study data
<p><strong>Objective</strong>:</p> <p>Our objective is to evaluate the efficacy of ChatGPT 4 in accurately and effectively delivering genetic information, building on previous findings with ChatGPT 3.5. We focus on assessing the utility, limitations, and ethical implications of using ChatGPT in medical settings.</p> <p><strong>Materials and Methods</strong>:</p> <p>A structured questionnaire, including the Brief User Survey (BUS-15) and custom questions, was developed to assess ChatGPT 4's clinical value. An expert panel of genetic counselors and clinical geneticists independently evaluated ChatGPT 4's responses to these questions. We also involved comparative analysis with ChatGPT 3.5, utilizing descriptive statistics and using R for data analysis.</p> <p><strong>Results</strong>:</p> <p>ChatGPT 4 demonstrated improvements over 3.5 in context recognition, relevance, and informativeness. However, performance variability and concerns about the naturalness of the output were noted. No significant difference in accuracy was found between ChatGPT 3.5 and 4.0. Notably, the efficacy of ChatGPT 4 varied significantly across different genetic conditions, with specific differences identified between responses related to BRCA1 and HFE.</p> <p><strong>Discussion and Conclusion</strong>:</p> <p>This study highlights ChatGPT 4's potential in genomics, noting significant advancements over its predecessor. Despite these improvements, challenges remain, including the risk of outdated information and the necessity of ongoing refinement. The variability in performance across different genetic conditions underscores the need for expert oversight and continuous AI training. ChatGPT 4, while showing promise, emphasizes the importance of balancing technological innovation with ethical responsibility in healthcare information delivery.</p>
Fig. 2 a in Does size matter? Comparative population genetics of two butterflies with different wingspans
Fig. 2 a Map showing the groups formed when individuals were divided into populations based on sampling proximity (AGA Agastyamalais, ANA Anamalais, WAC Wayanad and Coorg, and NKAR North Karnataka). b and c Spatial multivariate analysis in sPCA. Squares represent first axis sPCA scores for b ML and c YB. In this figure, the color of the squares denotes positive (black) or negative (white) spatial autocorrelation, and the size of the squares denotes the magnitude of genetic variance. Thus, squares of different sizes are used to represent different absolute values: large black squares are well differentiated from large white squares, but small squares are less differentiated
Fig. 1 Sampling locations. A in Does size matter? Comparative population genetics of two butterflies with different wingspans
Fig. 1 Sampling locations. A map of the Western Ghats showing sampling locations for both species. Inset: map of India showing the location of the Western Ghats in blue
Data from: A comparative study on genetic effects of artificial and natural habitat fragmentation on Loropetalum chinense (Hamamelidaceae) in Southeast China
Elucidating the demographic and landscape features that determine the genetic effects of habitat fragmentation has become fundamental to research in conservation and evolutionary biology. Land-bridge islands provide ideal study areas for investigating the genetic effects of habitat fragmentation at different temporal and spatial scales. In this context, we compared patterns of nuclear microsatellite variation between insular populations of a shrub of evergreen broad-leaved forest, Loropetalum chinense, from the artificially created Thousand-Island Lake (TIL) and the Holocene-dated Zhoushan Archipelago of Southeast China. Populations from the TIL region harboured higher levels of genetic diversity than those from the Zhoushan Archipelago, but these differences were not significant. There was no correlation between genetic diversity and most island features, excepting a negative effect of mainland–island distance on allelic richness and expected heterozygosity in the Zhoushan Archipelago. In general, levels of gene flow among island populations were moderate to high, and tests of alternative models of population history strongly favoured a gene flow-drift model over a pure drift model in each region. In sum, our results showed no obvious genetic effects of habitat fragmentation due to recent (artificial) or past (natural) island formation. Rather, they highlight the importance of gene flow (most likely via seed) in maintaining genetic variation and preventing inter-population differentiation in the face of habitat 'insularization' at different temporal and spatial scales.
Data from: Comparative landscape genetic analysis of three Pacific salmon species from subarctic North America
We examined the assumption that landscape heterogeneity similarly influences the spatial distribution of genetic diversity in closely related and geographically overlapping species. Accordingly, we evaluated the influence of watershed affiliation and nine habitat variables from four categories (spatial isolation, habitat size, climate, and ecology) on population divergence in three species of Pacific salmon (Oncorhynchus tshawytscha, O. kisutch, and O. keta) from three contiguous watersheds in subarctic North America. By incorporating spatial data we found that the three watersheds did not form the first level of hierarchical population structure as predicted. Instead, each species exhibited a broadly similar spatial pattern: a single coastal group with populations from all watersheds and one or more inland groups primarily in the largest watershed. These results imply that the spatial scale of conservation should extend across watersheds rather than at the watershed level which is the scale for fishery management. Three independent methods of multivariate analysis identified two variables as having influence on population divergence across all watersheds: precipitation in all species and subbasin area (SBA) in Chinook. Although we found general broad-scale congruence in the spatial patterns of population divergence and evidence that precipitation may influence population divergence in each species, we also found differences in the level of population divergence (coho > Chinook and chum) and evidence that SBA may influence population divergence only in Chinook. These differences among species support a species-specific approach to evaluating and planning for the influence of broad-scale impacts such as climate change.
Comparative genetics of Scyphozoan species reveals the geological history and contemporary processes of the Mediterranean Sea
<p>Jellyfish are attractive biological indicators of shifts in the marine environment, as they have limited mobility and they are highly exposed to the physics and chemistry of the water column. For this study, we focused on three Mediterranean macro-jellyfish - Rhizostoma pulmo, Aurelia sp. and Phyllorhiza punctata. We used comparative genomics and molecular clock (timetree) approaches to estimate occurrences of past geological events and contemporary anthropogenic effects in the Mediterranean Sea. Our results proved that these events have left their mark on the genomes of marine jellyfish. Genomic data of R. pulmo revealed a divergence point between the East and West MS populations that occurred 4.59 Ma, after the Zanclean flood, suggesting that at this time these regions had formed the two distinct ecological environments we know today. We propose that before that time (4.59 Ma), the highly mixed Atlantic and Mediterranean waters led to the wide dispersal of different species in the MS, including the ancestral R. pulmo. At 4.59 Ma, a marine barrier between the Western and Eastern MS formed, indicating the possibility of a dramatic environmental event. The Central and Western MS showed signs of separation processes only at much later stages and at much slower rates. Using comparative genomics of the Aurelia species, we examined contemporary anthropogenic impacts with a focus on migration of scyphozoa across the Suez Canal (Lessepsian migration). Aurelia sp. is among the few scyphozoa we find in both seas. DNA analysis revealed that the Red Sea Aurelia sp. is more related to the Pacific Ocean Aurelia sp. than to the Eastern MS Aurelia species, while the latter is closer to populations from Croatia and Slovenia. Therefore, we conclude that there was no Lessepsian migration of the Aurelia species. Data from P. punctata showed that this species was only recently introduced to the MS, as samples from the MS were closer to Australian populations while they were distant from Mexico and Thailand populations. The recent introduction of P. punctata, apparently, results from anthropogenic transportation activity, such as ballast water discharge, with a known migration vector from Australia to the MS. Our findings demonstrate that jellyfish genomes can be used as a phylogeographic molecular tool to trace back past events across large temporal scales and reveal invasive species introduction due to human activity.</p>
FIGURE 21. Maximum parsimony 16S rRNA phylogram for the Boophis albipunctatus group. From 485 total characters, 391 were constant and 72 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 21. Maximum parsimony 16S rRNA phylogram for the Boophis albipunctatus group. From 485 total characters, 391 were constant and 72 parsimony informative. MP searches retained 26 trees of which a strict consensus is shown. Consensus support values higher than 50, from 2000 bootstrap replicates, are shown; an asterisk indicates Bayesian posterior probabilities equal or higher than 95%. Species newly described herein are in bold.
FIGURE 27 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 27. Spectrogram and waveform of call type 1 of Boophis luciae sp. nov. from Andasibe (recorded on 1 February 1995, air temperature 22°C).
FIGURE 19 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 19. (A) Male holotype of Boophis sandrae sp. nov. (ZMA 20133) from Ranomafana; (B) female paratype of Boophis sandrae sp. nov. (ZSM 236/2006) from Ambatolahy.
FIGURE 10 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 10. Male holotype of Boophis entingae sp. nov. (ZSM 2083/2007): (A) dorsolateral view; (B) ventral view; (C) detail showing colouration of posterior surfaces of thigh.
FIGURE 8 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 8. Male of Boophis brachychir (ZSM 2157/2007) from Forêt d'Ambre Special Reserve: (A) dorsolateral view; (B) ventral view.
FIGURE 5 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 5. Spectrograms and waveforms of advertisement calls of: (A) Boophis andrangoloaka from Ambohitantely Special Reserve (recorded on 18 January 2005, air temperature app. 18°C); (B) Boophis rhodoscelis from Ranomafanakely, Ranomafana National Park (recorded on 28 January 2004, air temperature app. 21°C).
FIGURE 9 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 9. Spectrogram, corresponding waveform and expanded waveform of the advertisement call of Boophis brachychir from Manongarivo Special Reserve (recorded on 1 February 2003, air temperature 24.5°C).
FIGURE 7. Maximum parsimony 16S in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 7. Maximum parsimony 16S rRNA phylogram of species of the Boophis goudoti group. From 510 total characters, 340 were constant and 130 parsimony informative. MP searches retained 3681 trees of which a strict consensus is shown. Consensus support values higher than 50, from 2000 bootstrap replicates, are shown; an asterisk indicates Bayesian posterior probabilities equal or higher than 95%. Species newly described or resurrected herein are in bold.
FIGURE 25 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 25. Comparative waveform sections (each 2000 ms duration) of advertisement calls of species in the Boophis albipunctatus group: (A) Boophis schuboeae (Ranomafana National Park, 23°C); (B) Boophis haingana sp. nov. (Andohahela National Park, low altitude, 23.2°C); (C) Boophis haingana sp. nov. (Andohahela National Park, 1600 m a.s.l., 17.6°C); (D) Boophis ankaratra (Manjakatompo, 18°C); (E) Boophis miadana sp. nov. (Andohahela National Park, 1550 m a.s.l., 17.6°C).
FIGURE 22 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 22. Male holotype of Boophis miadana sp. nov. (ZSM 5107/2005) from Andohahela, 1550 m a.s.l.: (A) dorsolateral view; (B) ventral view.
FIGURE 23 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 23. Male holotype of Boophis haingana sp. nov. (ZSM 5109/2005) from Andohahela: (A) dorsolateral view; (B) ventral view.
FIGURE 1. Maximum parsimony 16S in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 1. Maximum parsimony 16S rRNA phylogram for species in the Boophis majori and B. microtympanum groups. From 480 total characters, 336 were constant and 129 parsimony informative. MP searches retained 39 trees of which a strict consensus is shown. Consensus support values higher than 50, from 2000 bootstrap replicates, are shown; an asterisk indicates Bayesian posterior probabilities equal or higher than 95%. Species newly described or resurrected herein are in bold.
FIGURE 18. Maximum parsimony 16S in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 18. Maximum parsimony 16S rRNA phylogram for species in the Boophis luteus group. From 470 total characters, 347 were constant and 111 parsimony informative. MP searches retained 60 trees of which a strict consensus is shown. Consensus support values higher than 50, from 2000 bootstrap replicates, are shown; an asterisk indicates Bayesian posterior probabilities equal or higher than 95%. The species newly described herein is in bold.
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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)
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.