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197 results for “comparative genetics”
A Linked Application of Discrete Differential Evolution Algorithm Coupled with Simulation- Optimization Model and Comparative Analysis by Genetic Algorithm for Discrete Groundwater Management Problems
<p>Complete dataset of publication name as "The complete publication dataset is "A Discrete Differential Evolution- Linear Programming Algorithm for Groundwater Management Problems." You can find all the written codes in the zip file.</p>
Time trees and Clock genes: a Systematic Review and Comparative Analysis of Contemporary Avian Migration Genetics (Dataset)
<p>Complete dataset of <em>Clock</em> and <em>Adcyap1</em> alleles, distance matrices, and migration data used in the review and meta-analysis "<strong>Time trees and Clock genes: a Systematic Review and Comparative Analysis of Contemporary Avian Migration Genetics".</strong> </p>
Fig. 1. Collectionsitesfor 91 specimensfrom 29 locationsof Apodemusagrarius, usedin thisstudy. ThespecimennumberforeachlocationarelistedinTable 1 in Comparative Genetics Of Apodemus Agrarius (Rodentia: Mammalia) From Insular And Continental Eurasian Populations: Cytochrome B Sequence Analyses
Fig. 1. Collectionsitesfor 91 specimensfrom 29 locationsof Apodemusagrarius, usedin thisstudy. ThespecimennumberforeachlocationarelistedinTable 1, andminimum Jukes-Cantordistancesbetween 17 haplotypesfrommainlandKoreaandother 49 haplo- typesfromsevenregions (Taiwan, Jeju, northeasternChina, easternChina, centralChina, Far-easternRussia, andEurope) basedonthecytochrome b completesequencesaregiven
Data from: Comparative phylogeography, genetic differentiation, and contrasting reproductive modes in three fungal symbionts of a multipartite bark beetle symbiosis
Multipartite symbioses are complex symbiotic relationships involving multiple interacting partners. These types of partnerships provide excellent opportunities in which to apply a comparative approach to identify common historical patterns of population differentiation and species-specific life history traits. Using three symbiotic blue stain fungal species (Ophiostomatacea) associated with outbreaking populations of the mountain pine beetle (Dendroctonus ponderosae Hopkins) in western Canada, we applied phylogenetic, population genetic, and demographic approaches to clarify phylogeographic patterns among the three fungal species. Broadly, the three species showed significant population differentiation, forming northern and southern populations, despite dramatic differences in haplotype diversity. Finer scale structuring and population demographic patterns were less consistent, showing some interspecific incongruence. By contrasting these species simultaneously, we were able to identify differences in recombination rate and ecological traits that can explain the observed patterns of incongruence among the fungal species. By applying a comparative approach to partners of a multipartite symbiosis we were able to distinguish congruent population structuring and species-specific differences that help us to understand the complexity and evolution of this symbiotic system.
Data from: Comparative landscape genetics of two frugivorous bats in a biological corridor undergoing agricultural intensification
Agricultural intensification in tropical landscapes poses a new threat to the ability of biological corridors to maintain functional connectivity for native species. We use a landscape genetics approach to evaluate impacts of expanding pineapple plantations on two widespread and abundant frugivorous bats in a biological corridor in Costa Rica. We hypothesize that the larger, more mobile Artibeus jamaicensis will be less impacted by pineapple than the smaller Carollia castanea. In 2012 and 2013, we sampled 735 bats in 26 remnant forest patches surrounded by different proportions of forest, pasture, crops and pineapple. We used 10 microsatellite loci for A. jamaicensis and 16 microsatellite loci for C. castanea to estimate genetic diversity and gene flow. Canonical correspondence analyses indicate that land cover type surrounding patches has no impact on genetic diversity of A. jamaicensis. However, for C. castanea, both percentage forest and pineapple surrounding patches explained a significant proportion of the variation in genetic diversity. Least-cost transect analyses (LCTA) and pairwise G″st suggest that for A. jamaicensis, pineapple is more permeable to gene flow than expected, while as expected, forest is the most permeable land cover for gene flow of C. castanea. For both species, LCTA indicate that development may play a role in inhibiting gene flow. The current study answers the call for landscape genetic research focused on tropical and agricultural landscapes, highlights the value of comparative landscape genetics in biological corridor design and management and is one of the few studies of biological corridors in any ecosystem to implement a genetic approach to test corridor efficacy.
Data from: genetic evidence of differential dispersal pattern in Asiatic wild dog: comparing populations with different pack size and tiger densities
<p><span>Dispersal is a multi-causal, crucial life-history event in shaping the genetic and behavioral structure of mammals. We assessed the dispersal pattern of dholes aka Asiatic wild dog (<em>Cuon alpinus</em>), a social monogamous mammal at two tiger reserves of Maharashtra with different degrees of pack size and competition with tigers i.e. Tadoba-Andhari (TATR, smaller pack size, higher tiger density) and Nawegaon-Nagzira (NNTR, larger pack size, lower tiger density). We used the microsatellite data of 174 individual genotypes (98 males and 67 females) to assess the dispersal pattern of dholes from two populations with varying pack size, tiger density, and landscape connectivity using gene flow as a proxy. We compared the population structure, pairwise F statistics, assignment index, and relatedness across a spatial scale. Overall, the results suggested a difference in sex-bias dispersal pattern for the two sub-populations, exhibiting significant results for female-biased dispersal in the TATR population with a smaller pack size and higher tiger density. Our study highlights the variability in sex-biased dispersal patterns in two different populations which could be the consequence of different variables such as pack size, tiger density, and geographical scale. The study warrants further quantitative investigation including several factors including individual behavior, pack composition, pack size, tiger density, etc. In the present Anthropocene era, determining the sex bias in dispersal patterns for a short-range, pack-living carnivore will help in devising an effective conservation management plan for their long-term survival.</span></p>
Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes
<p><span><span><span>Cave-dwelling animals evolve distinct troglomorphic traits, such as loss of eyes, skin pigmentation, and augmentation of senses following long-term adaptation to the perpetual darkness. However, the molecular genetic mechanisms underlying these phenotypic variations remain unclear. In this study, we conducted comparative histology and comparative transcriptomics study of the skin of eight <i>Sinocyclocheilus</i> species (Cypriniformes: Cyprinidae) that included surface and cave-dwelling species. We analyzed four surface and four cavefish species by using next-generation sequencing, and a total of 802,798,907 clean reads were generated and assembled into 505,495,009 transcripts, which contributed to 1,037,334 unigenes. Bioinformatics comparisons of four different surface-cave fish groups revealed between 10,629 and 6442 significantly differentially expressed unigenes. Further, tens of differentially expressed genes (DEGs) potentially related to skin pigmentation were identified. Most of these DEGs (including <i>GNAQ</i>, <i>PKA</i>, <i>NRAS</i>, and <i>p38</i>) are downregulated in cavefish species. They are involved in key signaling pathways of pigment synthesis, such as the melanogenesis, Wnt, and MAPK pathways. This trend of downregulation was confirmed through qPCR experiments. This study will deepen our understanding of the formation of troglomorphic traits in cavefishes.</span></span></span></p>
Detection of genetic alterations in gastric cancer patients from Saudi Arabia using comparative genomic hybridization (CGH)
<p>Abstract</p> <p>Background: The present study was conducted to discover genetic imbalances such as DNA copy number variations (CNVs) associated with gastric cancer (GC) and to examine their association with different genes involved in the process of gastric carcinogenesis in Saudi population. </p> <p>Methods: Formalin-fixed paraffin-embedded (FFPE) tissues samples from 33 gastric cancer patients and 15 normal gastric samples were collected. Early and late stages GC samples were genotyped and CNVs were assessed by using Illumina HumanOmni1-Quad v.1.0 BeadChip. </p> <p>Results: Copy number gains were more frequent than losses throughout all GC samples compared to normal tissue samples. The mean number of the altered chromosome per case was 64 for gains and 40 for losses, and the median aberration length was 679115bp for gains and 375889bp for losses. We identified 7 high copy gain, 52 gains, 14 losses, 32 homozygous losses, and 10 copy neutral LOHs (loss of heterozygosities). Copy number gains were frequently detected at 1p36.32, 1q12, 1q22, 2p11.1, 4q23-q25, 5p12-p11, 6p21.33, 9q12-q21.11, 12q11-q12, 14q32.33, 16p13.3, 17p13.1, 17q25.3, 19q13.32, and losses at 1p36.23, 1p36.32, 1p32.1, 1q44, 3q25.2, 6p22.1, 6p21.33, 8p11.22, 10q22.1, 12p11.22, 14q32.12 and 16q24.2. We also identified 2 monosomy at chromosome 14 and 22, 52 partially trisomy and 22 whole chromosome 4 neutral loss of heterozygosities at 13q14.2-q21.33, 5p15.2-p15.1, 5q11.2-q13.2, 5q33.1-q34 and 3p14.2-q13.12. Furthermore, 11 gains and 2 losses at 1p36.32 were detected for 11 different GC samples and this region has not been reported before in other populations. Statistical analysis confirms significant association of H. pylori infection with T4 stage of GC as compare to control and other stages.</p>
Fig. 3. The contact region. Numbers designate collecting sites. Compare with figure 49 in Hybridization Among Western Whiptail Lizards (Cnemidophorus Tigris) In Southwestern New Mexico: Population Genetics, Morphology, And Ecology In Three Contact Zones
Fig. 3. The contact region. Numbers designate collecting sites. Compare with figure 49.
Unique or not unique? Comparative genetic analysis of bacterial O-antigens from the Oxalobacteraceae family.Supplementary_data
<p>This is Supplementary files for the paper "Unique or not unique? Comparative genetic analysis of bacterial O-antigens from the Oxalobacteraceae family".</p> <p>The description for each dataset is located inside files.</p>
Genomic tools for comparative conservation genetics among three recently diverged stag beetles (Lucanus, Lucanidae)
<p>We are witnessing a rapid decline in global biodiversity. International protocols and local conservation laws have been installed to counter such an unprecedented rate of decline. However, quantitatively evaluating how much biodiversity has been lost due to climatic and anthropogenic effects and how much biodiversity has been restored due to conservation efforts remain challenging. We applied a comparative conservation genomic approach to statistically and quantitatively address these questions using three geographical taxa from a stag beetle species complex. We found that the three sky-island taxa formed three independently evolving units without detectable post-divergence gene flow; furthermore, the three taxa, which have been divergent from each other since the mid-Pleistocene, have experienced episodes of demographic decline in the past. More importantly, even though idiosyncratic anthropogenic exploitations have been hypothesized to impact the recent demographic history (< 100 years) differently, we found a shared pattern of continuous decline in effective population size among the three geographical taxa. We argue that future empirical studies should include more taxa, in addition to the focal species, that may or may not be affected by the focal historical events to avoid making biased conservation plans.</p>
Comparative transmission genetics of introgressed chromatin in reciprocal advanced backcross populations in Gossypium (cotton) polyploids
<p>Introgression is a potential source of valuable genetic variation and interspecific introgression lines are important resources for plant breeders to access novel alleles. Experimental advanced-generation backcross populations contain individuals with genomic compositions similar to those resulting from natural interspecific hybridization and provide opportunities to study the nature and transmission pattern of donor chromatin in recipient genomes. Here, we analyze transmission of donor chromatin in reciprocal backcrosses between <em>G. hirsutum</em> and <em>G. barbadense</em>. Across the genome, recurrent backcrossing in both backgrounds yielded donor chromatin at slightly higher frequencies than the Mendelian expectation in BC<sub>5</sub>F<sub>1</sub> plants, while the average frequency of donor alleles in BC<sub>5</sub>F<sub>2</sub> segregating families was less than expected. In the two subgenomes of polyploid cotton, the rate of donor chromatin introgression was similar. Although donor chromatin was tolerated over much of the recipient genomes, 21 regions recalcitrant to donor alleles were identified. Only limited correspondence is observed between the recalcitrant regions in the two backgrounds, suggesting the effect of species background on introgression of donor segments. Genetic breakdown was progressive, with floral abscission and seed inviability ongoing during backcrossing cycles. Regions of either high or low introgression tended to be in terminal chromosomal regions that are generally rich in both genes and crossover events, with long stretches around the centromere having limited crossover activity resulting in relatively constant low introgression frequencies. Constraints on fixation and selection of donor alleles highlights the challenges of utilizing introgression breeding in crop improvement.</p>
Population genetics and comparative morphology of two serpentine Phlox species
<p>Hybridization between rare and widespread species can result in loss of genetic integrity for the rarer species, which can have management and conservation implications. One rare species, <em>Phlox hirsuta</em>, is a serpentine endemic in northern California, and it frequently co-occurs with a widespread congener, <em>P. speciosa</em>. Putative hybrids were recognized based on intermediate morphology, so the possibility of hybridization was explored using floral morphological and molecular data. Ninety-eight individuals of <em>P. hirsuta</em> and <em>P. speciosa</em> were collected from each of three populations, and floral features were measured and compared. Eleven microsatellite loci were amplified for species and putative hybrids, and inter- and intraspecific genetic diversity and relationships were investigated with multiple methods. Variation in morphological and molecular data was recognized. Floral variation was greater for <em>P. hirsuta</em> than <em>P. speciosa</em>. Putative hybrids were genetically allied with <em>P. speciosa</em>, but two individuals of <em>P. hirsuta</em> were resolved to have genetic similarity with <em>P. speciosa</em>. While hybridization is possible between the species, it is uncommon and appears to be primarily unidirectional, with <em>P. speciosa</em> as the hypothesized male parent and <em>P. hirsuta</em> as the hypothesized female parent. The small number of recognized hybrids may be due to ineffective interspecific pollination, early acting inbreeding depression, hybrids being less fit than parents, and/or small sample sizes. Reinforcement does not appear to play a role in secondary contact between species. Both microsatellite loci and floral morphology varied across the small geographic range of <em>P. hirsuta</em>, suggesting local differentiation and adaptation are possible over short distances.</p>
Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes
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Data from: Comparative phylogeography, genetic differentiation, and contrasting reproductive modes in three fungal symbionts of a multipartite bark beetle symbiosis
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Population genetics and comparative morphology of two serpentine Phlox species
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Data from: genetic evidence of differential dispersal pattern in Asiatic wild dog: comparing populations with different pack size and tiger densities
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Data from: Comparing microsatellites and single nucleotide polymorphisms to evaluate genetic structure and diversity in wolverines (Gulo gulo) across Alaska and western Canada
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Comparative studies on genetic differentiation between two closely related species of <em>Drosophila,</em> <em>D. bipectinata</em> and <em>D. malerkotliana</em>
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Genomic tools for comparative conservation genetics among three recently diverged stag beetles (Lucanus, Lucanidae)
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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.