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2,315 results for “Comparative analysis”
Data from: De novo assembly and comparative analysis of the Ceratodon purpureus transcriptome
The bryophytes are a morphologically and ecologically diverse group of plants that have recently emerged as major model systems for a variety of biological processes. In particular, the genome sequence of the moss, Physcomitrella patens, has significantly enhanced our understanding of the evolution of developmental processes in land plants. However, to fully explore the diversity within bryophytes, we need additional genomic resources. Here we describe analyses of the transcriptomes of a male and a female isolate of the moss, C. purpureus, generated using the 454 FLX technology. Comparative analyses between C. purpureus and P. patens indicated that this strategy generated nearly complete coverage of the protonemal transcriptome. An analysis of the overlap in gene sets between C. purpureus and P. patens provides new insights into the evolution of gene family composition across the land plants. In spite of the overall transcriptomic similarity between the two species, Ka/Ks analysis of P. patens and C. purpureus suggest considerable physiological and developmental divergence. Additionally, while the codon usage was very similar between these two mosses, C. purpureus genes showed a slightly greater codon usage bias than P. patens genes potentially because of the contrasting mating system of the two species. Finally, we found evidence of a genome doubling ~65-76 MYA that likely coincided with the contemporaneous polyploidy event inferred for P. patens but postdates the divergence of P. patens and C. purpureus. The powerful laboratory tools now available for C. purpureus will enable the research community to fully exploit these genomic resources.
Data from: Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae)
Background: Domestication has played an important role in shaping characteristics of the inflorescence and plant height in cultivated cereals. Taking advantage of meta-analysis of QTLs, phylogenetic analyses in 502 diverse sorghum accessions, GWAS in a sorghum association panel (n = 354) and comparative data, we provide insight into the genetic basis of the domestication traits in sorghum and rice. Results: We performed genome-wide association studies (GWAS) on 6 traits related to inflorescence morphology and 6 traits related to plant height in sorghum, comparing the genomic regions implicated in these traits by GWAS and QTL mapping, respectively. In a search for signatures of selection, we identify genomic regions that may contribute to sorghum domestication regarding plant height, flowering time and pericarp color. Comparative studies across taxa show functionally conserved 'hotspots' in sorghum and rice for awn presence and pericarp color that do not appear to reflect corresponding single genes but may indicate co-regulated clusters of genes. We also reveal homoeologous regions retaining similar functions for plant height and flowering time since genome duplication an estimated 70 million years ago or more in a common ancestor of cereals. In most such homoeologous QTL pairs, only one QTL interval exhibits strong selection signals in modern sorghum. Conclusions: Intersections among QTL, GWAS and comparative data advance knowledge of genetic determinants of inflorescence and plant height components in sorghum, and add new dimensions to comparisons between sorghum and rice.
Data from: Comparative analysis of encephalization in mammals reveals relaxed constraints on anthropoid primate and cetacean brain scaling
There is a well-established allometric relationship between brain and body mass in mammals. Deviation of relatively increased brain size from this pattern appears to coincide with enhanced cognitive abilities. To examine whether there is a phylogenetic structure to such episodes of changes in encephalization across mammals, we used phylogenetic techniques to analyse brain mass, body mass and encephalization quotient (EQ) among 630 extant mammalian species. Among all mammals, anthropoid primates and odontocete cetaceans have significantly greater variance in EQ, suggesting that evolutionary constraints that result in a strict correlation between brain and body mass have independently become relaxed. Moreover, ancestral state reconstructions of absolute brain mass, body mass and EQ revealed patterns of increase and decrease in EQ within anthropoid primates and cetaceans. We propose both neutral drift and selective factors may have played a role in the evolution of brain–body allometry.
Data from: Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales
The research field of comparative genomics is moving from a focus on genes to a more holistic view including the repetitive complement. This study aimed to characterize relative proportions of the repetitive fraction of large, complex genomes in a non-model system. The monocotyledonous plant order Asparagales (onion, asparagus, agave) comprises some of the largest angiosperm genomes and represents variation in both genome size and structure (karyotype). Anonymous, low coverage, single-end Illumina data from eleven exemplar Asparagales taxa were assembled using a de novo method. Resulting contigs were annotated using a reference library of available monocot repetitive sequences. Mapping reads to contigs provided rough estimates of relative proportions of each type of transposon in the nuclear genome. The results were parsed into general repeat types and synthesized with genome size estimates and a phylogenetic context to describe the pattern of transposable element evolution among these lineages. The major finding is that while some lineages in Asparagales exhibit conservation in repeat proportions, there is generally wide variation in types and frequency of repeats. This approach is an appropriate first step in characterizing repeats in evolutionary lineages with a paucity of genomic resources.
Data from: Detecting adaptive evolution in phylogenetic comparative analysis using the Ornstein-Uhlenbeck model
Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and more detailed evolutionary hypotheses, including adaptive hypotheses with multiple selective optima and hypotheses with rate variation within and across lineages. The statistical performance of these sophisticated models has received relatively little systematic attention, however. We conducted an extensive simulation study to quantify the statistical properties of a class of models toward the simpler end of the spectrum that model phenotypic evolution using Ornstein–Uhlenbeck processes. We focused on identifying where, how, and why these methods break down so that users can apply them with greater understanding of their strengths and weaknesses. Our analysis identifies three key determinants of performance: a discriminability ratio, a signal-to-noise ratio, and the number of taxa sampled. Interestingly, we find that model-selection power can be high even in regions that were previously thought to be difficult, such as when tree size is small. On the other hand, we find that model parameters are in many circumstances difficult to estimate accurately, indicating a relative paucity of information in the data relative to these parameters. Nevertheless, we note that accurate model selection is often possible when parameters are only weakly identified. Our results have implications for more sophisticated methods inasmuch as the latter are generalizations of the case we study.
Comparative genomic analysis reveals cellulase plays an important role in the pathogenicity of Setosphaeria turcica f. sp. Zeae
<p><i><span>Setosphaeria turcica</span></i><span> f. sp. <i>sorghi</i> and <i>S. turcica</i> f. sp. <i>zeae</i>, the two formae speciales of <i>S. turcica</i>, cause northern leaf blight disease of sorghum and corn, respectively, and often cause serious economic losses. They show obvious host specialization and have a close evolutionary relationship. Genomic sequencing can provide more information for understanding the virulence mechanisms of pathogens. However, the complete genomic sequence of <i>S. turcica</i> f. sp. <i>sorghi</i> has not yet been reported, and no comparative genomic information is available for the two formae speciales. In this study, based on the analysis of genomic structure, there were more protein-coding genes in <i>S. turcica</i> f. sp. <i>sorghi</i> than <i>S. turcica</i> f. sp. <i>zeae</i></span><span>, </span><span>showing positive selection in the evolution of <i>S. turcica</i>. The results of genomic functional analysis showed that the two formae speciales had a large number of identical protein-coding genes, while there were also specific protein families, including metabolic pathway proteins, transport proteins, </span><span>CAZy</span><span>s, pathogen and host interaction proteins. We also investigated the expression of specific effector-coding genes in <i>S. turcica</i> f. sp. <i>zeae</i>, and found that the endo-1, 4-β-D-glucanase coding gene </span><i><span>CEL</span><span>2</span></i><span>, an important component of cellulase, was significantly up-regulated during the interaction process. Finally, gluconolactone inhibited cellulase activity and decreased infection rate and pathogenicity, which indicates that cellulase is essential for maintaining virulence. These findings demonstrate that cellulase plays an important role in the pathogenicity of <i>S. turcica</i> f. sp. <i>zeae</i>. </span></p>
Data from: Convergence analysis of a finite element skull model of Herpestes javanicus (Carnivora, Mammalia): implications for robust comparative inferences of biomechanical function
Predictions of skull biomechanical capability based on virtual models constitute a valuable data source for testing hypotheses about craniodental form and feeding behavior. Such comparative analyses also inform dietary reconstruction in extinct species. 3D modeling using Finite Element (FE) methods is a common technique applied to the comparative analysis of craniodental function in extinct and extant vertebrates. However, taxonomically diverse skull models in the literature often are not directly comparable to each other, in part because of distinctions in how boundary conditions are defined, but also because of substantial differences in the number of FEs composing the models. In this study, we test whether a conventional convergence test is adequate in identifying the minimum number of FEs needed to achieve internally stable results for a single species. We constructed a series of skull models of Herpestes javanicus, and simulated unilateral biting across the dentition; the models differed in the number of FEs, degrees of freedom at the joint and bite point constraints, and type of tetrahedral FEs used. We found that convergence patterns differed across constraint types, FE quantities, and bite position simulated. Four-noded tetrahedral (tet-4) FE models with relaxed constraints produced the most stable measurements compared to over-constrained tet-4 models and to relaxed tet-10 models. In absence of an optimal FE quantity from convergence testing, we propose a broadly applicable sub-sampling protocol, whereby average measurement values across multiple models per specimen are used for among-species comparisons. A regime of sampling three low FE quantity models produced the closest estimates of mean measurement values relative to larger model sets, being within the 95% bootstrap estimated confidence intervals. Future studies should focus on identifying sources of variation associated with other FE modeling protocols, so that they can be accounted for before biomechanical attributes from these simulations are used to infer form–function linkage.
Data from: Comparative analysis of vestibular ecomorphology in birds
The bony labyrinth of vertebrates houses the semicircular canals. These sense rotational accelerations of the head and play an essential role in gaze stabilisation during locomotion. The sizes and shapes of the semicircular canals have hypothesised relationships to agility and locomotory modes in many groups, including birds, and a burgeoning palaeontological literature seeks to make ecological interpretations from the morphology of the labyrinth in extinct species. Rigorous tests of form–function relationships for the vestibular system are required to support these interpretations. We test the hypothesis that the lengths, streamlines and angles between the semicircular canals are related to body size, wing kinematics and flying style in birds. To do this, we applied geometric morphometrics and multivariate phylogenetic comparative methods to a dataset of 64 three-dimensional reconstructions of the endosseous labyrinth obtained using micro-computed tomography scanning of bird crania. A strong relationship between centroid size of the semicircular canals and body size indicates that larger birds have longer semicircular canals compared with their evolutionary relatives. Wing kinematics related to manoeuvrability (and quantified using the brachial index) explain a small additional portion of the variance in labyrinth size. We also find strong evidence for allometric shape change in the semicircular canals of birds, indicating that major aspects of the shape of the avian labyrinth are determined by spatial constraints. The avian braincase accommodates a large brain, a large eye and large semicircular canals compared with other tetrapods. Negative allometry of these structures means that the restriction of space within the braincase is intense in small birds. This may explain our observation that the angles between planes of the semicircular canals of birds deviate more strongly from orthogonality than those of mammals, and especially from agile, gliding and flying mammals. Furthermore, we find little support for relationships between labyrinth shape and flying style or wing kinematics. Overall, our results suggest that the topological problem of fitting long semicircular canals into a spatially constrained braincase is more important in determining the shape of the avian labyrinth than the specifics of locomotory style or agility. Our results tentatively indicate a link between visual acuity and proportional size of the labyrinth among birds. This suggests that the large labyrinths of birds compared with other tetrapods may result from their generally high visual acuities, and not directly from their ability to fly. The endosseous labyrinths of extinct birds and their close dinosaurian relatives may allow broad inferences about flight or vision, but so far provide few specific insights into detailed aspects of locomotion.
Data from: Investigation of the effect of cochlear implant electrode length on speech comprehension in quiet and noise compared with the results with users of electro-acoustic-stimulation, a retrospective analysis
Objectives: This investigation evaluated the effect of cochlear implant (CI) electrode length on speech comprehension in quiet and noise and compare the results with those of EAS users. Methods: 91 adults with some degree of residual hearing were implanted with a FLEX20, FLEX24, or FLEX28 electrode. Some subjects were postoperative electric-acoustic-stimulation (EAS) users; the other subjects were in the groups of electric stimulation-only (ES-only). Speech perception was tested in quiet and noise at 3 and 6 months of ES or EAS use. Speech comprehension results were analyzed and correlated to electrode length. Results: While the FLEX20 ES and FLEX24 ES groups were still in their learning phase between the 3 to 6 months interval, the FLEX28 ES group was already reaching a performance plateau at the three months appointment yielding remarkably high test scores. EAS subjects using FLEX20 or FLEX24 electrodes outscored ES-only subjects with the same short electrodes on all 3 tests at each interval, reaching significance with FLEX20 ES and FLEX24 ES subjects on all 3 tests at the 3-months interval and on 2 tests at the 6- months interval. Amongst ES-only subjects at the 3- months interval, FLEX28 ES subjects significantly outscored FLEX20 ES subjects on all 3 tests and the FLEX24 ES subjects on 2 tests. At the-6 months interval, FLEX28 ES subjects still exceeded the other ES-only subjects although the difference did not reach significance. Conclusions: Among ES-only users, the FLEX28 ES users had the best speech comprehension scores, at the 3- months appointment and tendentially at the 6 months appointment. EAS users showed significantly better speech comprehension results compared to ES-only users with the same short electrodes.
Data from: Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes
Background: Chlamydia pecorum is the causative agent of a number of acute diseases, but most often causes persistent, subclinical infection in ruminants, swine and birds. In this study, the genome sequences of three C. pecorum strains isolated from the faeces of a sheep with inapparent enteric infection (strain W73), from the synovial fluid of a sheep with polyarthritis (strain P787) and from a cervical swab taken from a cow with metritis (strain PV3056/3) were determined using Illumina/Solexa and Roche 454 genome sequencing. Results: Gene order and synteny was almost identical between C. pecorum strains and C. psittaci. Differences between C. pecorum and other chlamydiae occurred at a number of loci, including the plasticity zone, which contained a MAC/perforin domain protein, two copies of a >3400 amino acid putative cytotoxin gene and four (PV3056/3) or five (P787 and W73) genes encoding phospholipase D. Chlamydia pecorum contains an almost intact tryptophan biosynthesis operon encoding trpABCDFR and has the ability to sequester kynurenine from its host, however it lacks the genes folA, folKP and folB required for folate metabolism found in other chlamydiae. A total of 15 polymorphic membrane proteins were identified, belonging to six pmp families. Strains possess an intact type III secretion system composed of 18 structural genes and accessory proteins, however a number of putative inc effector proteins widely distributed in chlamydiae are absent from C. pecorum. Two genes encoding the hypothetical protein ORF663 and IncA contain variable numbers of repeat sequences that could be associated with persistence of infection. Conclusions: Genome sequencing of three C. pecorum strains, originating from animals with different disease manifestations, has identified differences in ORF663 and pseudogene content between strains and has identified genes and metabolic traits that may influence intracellular survival, pathogenicity and evasion of the host immune system.
Data from: Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): comparative analysis of global accessions and Senegalese landraces
Background: Pearl millet is a staple food for people in arid and semi-arid regions of Africa and South Asia due to its high drought tolerance and nutritional qualities. A better understanding of the genomic diversity and population structure of pearl millet germplasm is needed to support germplasm conservation and genetic improvement of this crop. Here we characterized two pearl millet diversity panels, (i) a set of global accessions from Africa, Asia, and the America, and (ii) a collection of landraces from multiple agro-ecological zones in Senegal. Results: We identified 83,875 single nucleotide polymorphisms (SNPs) in 500 pearl millet accessions, comprised of 252 global accessions and 248 Senegalese landraces, using genotyping by sequencing (GBS) of PstI-MspI reduced representation libraries. We used these SNPs to characterize genomic diversity and population structure among the accessions. The Senegalese landraces had the highest levels of genetic diversity (π), while accessions from southern Africa and Asia showed lower diversity levels. Principal component analyses and ancestry estimation indicated clear population structure between the Senegalese landraces and the global accessions, and among countries in the global accessions. In contrast, little population structure was observed across in the Senegalese landraces collections. We ordered SNPs on the pearl millet genetic map and observed much faster linkage disequilibrium (LD) decay in Senegalese landraces compared to global accessions. A comparison of pearl millet GBS linkage map with the foxtail millet (Setaria italica) and sorghum (Sorghum bicolor) genomes indicated extensive regions of synteny, as well as some large-scale rearrangements in the pearl millet lineage. Conclusions: We identified 83,875 SNPs as a genomic resource for pearl millet improvement. The high genetic diversity in Senegal relative to other regions of Africa and Asia supports a West African origin of this crop, followed by wide diffusion. The rapid LD decay and lack of confounding population structure along agro-ecological zones in Senegalese pearl millet will facilitate future association mapping studies. Comparative population genomics will provide insights into panicoid crop evolution and support improvement of these climate-resilient crops.
FIGURE 3 in Mitochondrial genome of Abraxas suspecta (Lepidoptera: Geometridae) and comparative analysis with other Lepidopterans
FIGURE 3. Codon distribution in members of the Lepidoptera. CDspT = codons per thousand codons.
FIGURE 5 in Mitochondrial genome of Abraxas suspecta (Lepidoptera: Geometridae) and comparative analysis with other Lepidopterans
FIGURE 5. Putative secondary structures of the 23 tRNA genes of the A. suspecta mitogenome.
Figure 80 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 80. Bemisia afer complex, Madeira, Levada above Ribeiro Bonito, nr. Sao Jorge, 550 m, 01 Apr. 1996, ex. Chamaespartium sp.?, Leguminosae, Martin and Aguiar, colls., JHM #6583.
Figure 72 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 72. Bemisia lauracea Martin et al., Madeira, Seixal, 6-iii-1992, ex. Ocotea foetens, F. Aguiar, coll., #C125.
Figure 62 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 62. Bemisia afer complex, Canary Islands, Tenerife, Barranco, de las Moradas, at 7-900m, 18 May 1997, ex. Hypericum grandifolium, J. Martin, coll., JHM # 7041.
Figure 17 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 17. Bemisia guieriae Bink-Moenen, Sudan: Kordofan, 18-iv-81, ex: Guiera senegalensis, J. Martin coll. (Reprinted by permission from Springer Science+Business Media B.V.).
Figure 18 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 18. Bemisia tuberculata Bondar, Specimen TB2 #3, Araras P.C. Brasil, 6/69 ex. Manihot ultissima, A.S. Costa, Det. L.M. Russell.
Figure 47 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 47. Bemisia pongamiae Takahashi, Taiwan, Taipei, 6-IX-1985, ex. Pongamia pinnata, C.C. Ko, coll.
Figure 12 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 12. Bemisia miniscula Danzig, Adzharia, Keda, Caucasus, USSR, 3-IX-60, ex: Cistus salvifolius, E. Danzig, coll. (Synonym of B. tabaci).
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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.