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146 results for “pattern sequence”
A codon model for associating phenotypic traits with altered selective patterns of sequence evolution
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Four new genome sequences of the Pallas's cat (Otocolobus manul): an insight into the patterns of within-species variability
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Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes
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Molecular sequencing and morphological identification reveal similar patterns in native bee communities across public and private grasslands of eastern North Dakota
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Data from: Genomic footprint of cladogenesis revealed through RADseq and Sanger sequencing demonstrates congruent patterns in the velvet worm Peripatopsis sedgwicki species complex (Onychophora: Peripatopsidae)
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Sequences of the nuclear gene ADH for thirteen species of willows and two poplars: Investigating patterns of habitat specialization in fifteen co-occurring willow and poplar species.
Thirteen willow (Salix) species occur in southeastern Minnesota and often co-occur within the same wetlands. This high local diversity is challenging to explain since closely related species are often functionally similar and density-dependent interactions such as competition and susceptibility to pests and pathogens should limit their co-occurrence. However, if willow species are partitioning resources, or if they are phylogenetically structured so that closely related species rarely co-occur, then the impact of these density-dependent processes could be reduced. In this study, I examined the role of niche partitioning in maintaining local willow diversity by documenting species distributions in plots across a water availability gradient and comparing species physiology in the field and greenhouse. By taking a phylogenetic approach, I also investigated whether willow communities exhibit phylogenetic community structure and whether there is evidence for environmental filtering.
Data from: Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches
Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in a genotyping-by-sequencing (GBS) protocol. We focus on data from two species of Populus, because this genus has a relatively small genome and is emerging as a target for population genomic studies. We estimate the proportions and patterns of genomic sampling by examining the Populus trichocarpa genome (Nisqually-1), and demonstrate a pronounced bias towards coding regions when using the methylation-sensitive ApeKI restriction enzyme in this species. Using population-level data from a closely related species (P. tremuloides), we also investigate various approaches for filtering GBS data to retain high-depth, informative SNPs that can be used for population genetic analyses. We find a data filter that includes the designation of ambiguous alleles resulted in metrics of population structure and Hardy-Weinberg equilibrium that were most consistent with previous studies of the same populations based on other genetic markers. Analyses of the filtered data (27,910 SNPs) also resulted in patterns of heterozygosity and population structure similar to a previous study using microsatellites. Our application demonstrates that technically and analytically simple approaches can readily be developed for population genomics of natural populations.
Data from: Genotyping by sequencing reveals contrasting patterns of population structure, ecologically mediated divergence and long-distance dispersal in North American palms
Comparative studies can provide powerful insights into processes that affect population divergence and thereby help to elucidate the mechanisms by which contemporary populations may respond to environmental change. Furthermore, approaches such as genotyping by sequencing (GBS) provide unprecedented power for resolving genetic differences among species and populations. We therefore used GBS to provide a genome-wide perspective on the comparative population structure of two palm genera, Washingtonia and Brahea, on the Baja California peninsula, a region of high landscape and ecological complexity. First, we used phylogenetic analysis to address taxonomic uncertainties among five currently recognised species. We resolved three main clades, the first corresponding to W. robusta and W. filifera, the second to B. brandegeei and B. armata, and the third to B. edulis from Guadalupe Island. Focusing on the first two clades, we then delved deeper by investigating the underlying population structure. Striking differences were found, with GBS uncovering four distinct Washingtonia populations and identifying a suite of loci associated with temperature, consistent with ecologically mediated divergence. By contrast, individual mountain ranges could be resolved in Brahea and few loci were associated with environmental variables, implying a more prominent role of neutral divergence. Finally, evidence was found for long-distance dispersal events in Washingtonia but not Brahea, in line with knowledge of the dispersal mechanisms of these palms including the possibility of human-mediated dispersal. Overall, our study demonstrates the power of GBS together with a comparative approach to elucidate markedly different patterns of genome-wide divergence mediated by multiple effectors.
Data from: Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations
Understanding the genetic basis of local adaptation has long been the focus of evolutionary biology. Recently there has been increased interest in deciphering the evolutionary role of Daphnia's plasticity and the molecular mechanisms of local adaptation. Using transcriptome data, we assessed the differences in gene expression profiles and sequences within and between four European Daphnia galeata populations. To distinguish neutral from adaptive differentiation, we corrected for phylogenetic differentiation of Daphnia populations. We also applied a "transcriptome scan" approach to investigate the role of natural selection in shaping divergent expression profiles among populations. Furthermore, a SNP analysis allowed inferring population structure and the distribution of genetic variation. Using sequence information, the transcripts were annotated using a comparative genomics approach. In total, ~33% of 32903 transcripts were differentially expressed between populations. Among 10280 differentially expressed transcripts, 5209 transcripts deviated from neutral expectations and were likely involved in local adaptation. The population divergence at the sequence level was higher than at the gene expression level by several orders of magnitude and revealed very distinct clusters according to population origin. Our analysis revealed the respective roles of genetic drift and selection in the four Daphnia populations. This study is a first attempt to understand the genetic background of adaptation to environmental changes in a key species of aquatic ecosystems in absence of any laboratory induced stressor.
Data from: Insights into the genetic relationships and breeding patterns of the African tea germplasm based on nSSR markers and cpDNA sequences
Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (HS) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed "mosaic" group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection during geographic differentiation or local breeding preferences. This study represents the first step toward effective utilization of differently inherited molecular markers for exploring the breeding status of African tea. The findings here will be important for planning the exploration, utilization, and conservation of tea germplasm for future breeding efforts in Africa.
Spatial transcriptome mapping of the desmoplastic growth pattern of colorectal liver metastases by in situ sequencing - Image and In SItu Sequencing data
<p>Image and ISS data for Spatial transcriptome mapping of the desmoplastic growth pattern of colorectal liver metastases by in situ sequencing reveals a biologically relevant zonation of the desmoplastic rim.</p><p>Image data consists of:</p><ul><li>Nucler stain (DAPI)</li><li>Masks for liver, rim and tumor regions</li><li>H&E images of parallel tissue sections</li></ul><p>Gene and cluster marker data is collected in the <i>markers.h5ad</i> file which can be read using AnnData (<a href="https://anndata.readthedocs.io/en/latest/">https://anndata.readthedocs.io/en/latest/)</a>. </p><p> </p>
Integrative taxonomic analysis to reveal the species status of Bombus flavidus, combining COI and nuclear sequencing, wing morphometrics and secretions used for mate attraction as well as patterns of color polymorphism
<p>Bumble bees, due to their morphological monotony and color diversity, have presented difficulties with species delimitation. Recent bumble bee declines have made it ever more imperative to resolve the status of species to address conservation concerns. Some of the taxa found to be most threatened are the often-rare socially parasitic bumble bees, which have additional trophic requirements. Among the socially parasitic bumble bees,<i> Bombus flavidus</i> Eversmann has contentious species status. While multiple separate species allied with <i>Bombus flavidus</i> have been suggested, until recently, recognition of two species, a Nearctic <i>Bombus fernaldae</i> (Franklin) and Palearctic <i>B. flavidus,</i> was favoured. Limited genetic data, however, suggested that even these could be a single widespread species, <i>B. flavidus</i>. We addressed the species status of this lineage using an integrative taxonomic approach, combining <i>COI</i> and nuclear sequencing, wing morphometrics and secretions used for mate attraction. We also explore patterns of color polymorphism that have previously confounded taxonomy in this lineage. Our results support the conspecific status of <i>Bombus fernaldae</i> and <i>Bombus flavidus,</i> however, sampling specimens from across the range of these two taxa revealed a distinct population within this broader species confined to eastern North America. This makes the distribution of the social parasite <i>B. flavidus</i> the broadest of any bumble bee, broader than the known distribution of any non-parasitic bumble bee species. Analysis of color phenotypes revealed that color polymorphisms are retained across the range of the species, but may be influenced by local mimicry complexes. Following these results, <i>Bombus flavidus</i> Eversmann, 1852<i> </i>is synonymized with <i>Bombus fernaldae </i>(Franklin, 1911) <b>syn. nov.</b> and a subspecific status, <i>Bombus flavidus </i><i>appalachiensis</i> <b>ssp. nov.</b>, is assigned to the distinct lineage ranging from the Appalachians to the eastern boreal regions of the United States and far southeastern Canada.</p>
The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding the origin of domestic goat
<p>The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated <i>in silico</i> strategy for identifying and assembling the goat Y-linked scaffolds <span>using existing data</span>. A total of 11.5 Mb Y-linked sequences were clustered into 33 scaffolds, and 187 protein-coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat Radiation-Hybrid map (RH map). The existing whole-genome re-sequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2,000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10,000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post-Neolithic period.</p>
FIGURE 12 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 12. Ranges of the species based on existing information. A—H. spatzi, B—H. nitidulus, C—H. dintelmanni, D—H. sp. 1, E—H. tuberculatus, F—H. bangwae, G—H. parallelus, H—H. marmoratus, I—H. marginatus, J—H. noblei, K—H. goetzei, L—H. glandicolor, M—H. mariae, N—H. viridiflavus.
FIGURE 11 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 11. Illustrations of typical colour patterns in the Hyperolius viridiflavus complex: A—H. viridiflavus, from an illustration of 1845 by J. Vignaud; B—H. marmoratus, Storms River, South Africa, photo A. Channing; C—H. marginatus, North Luangwa National Park, Zambia, photo A. Channing; D—H. parallelus, PEM A12451, Cuanavale Source, Angola, photo W. Conradie; E—H. nitidulus, Lamto, Côte d'Ivoire, photo M.-O. Rödel; F—H. glandicolor, Kinangop, Kenya, photo A. Channing; G—H. tuberculatus, ZMB 91677, Dja Reserve, Cameroon, photo M.-O. Rödel; H—H. mariae, Kiloza, Tanzania, photo A. Channing; I—H. noblei, PEM A10608, Quinonga, Mozambique, photo W. Conradie; J—H. goetzei, Iringa, Tanzania, photo A. Channing; K—H. spatzi, Senegal, photo A. Hillers; L—H. dintelmanni, CAS 254137, Edib Hills, Cameroon, photo D. Portik.
FIGURE 10 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 10. Localities of sequences (black circles), type localities (stars) and location of junior synonyms of Hyperolius noblei (A), H. goetzei (B), H. spatzi (C) and H. dintelmanni (D). Locality codes are explained in Table 3.
FIGURE 8 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 8. Localities of sequences (black circles), type localities (stars) and location of junior synonyms of Hyperolius nitidulus (A), H. mariae (B) and H. sp 1 (C). Locality codes are explained in Table 3.
FIGURE 9 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 9. Localities of sequences (black circles), type localities (stars) and location of junior synonyms of Hyperolius bangwae (A), H. tuberculatus (B), and H. glandicolor (C). Locality codes are explained in Table 3.
FIGURE 6 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 6. Localities of sequences (black circles), type locality (star) and location of junior synonyms of Hyperolius marginatus. Locality codes are explained in Table 3.
FIGURE 7 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA
FIGURE 7. Localities of sequences (black circles), type locality (star) and location of junior synonyms of Hyperolius parallelus. Locality codes are explained in Table 3.
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.