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423 results for “Haplotypes”
Figure 5. Minimum spanning haplotype network derived from a 658 base-pair cytochrome c oxidase subunit I in Six degrees of separation in barnacles? Assessing genetic variability in the sea-turtle epibiont Stomatolepas elegans (Costa) among turtles, beaches and oceans
Figure 5. Minimum spanning haplotype network derived from a 658 base-pair cytochrome c oxidase subunit I (COI) fragment from 57 Stomatolepas elegans collected from nine different Lepidochelys olivacea nesting on Playa Teopa, Jalisco, Mexico, six S. elegans from Caretta caretta from the western Atlantic, and six S. praegustator from C. caretta from the western Atlantic. Circle sizes are proportional to the frequency of each haplotype, with haplotype 1 being most common. Coloured pie slices are also proportional, and represent the number of S. elegans from each turtle characterized by the respective haplotype. Colours represent the nine Mexican turtles randomly sampled for S. elegans populations. Open circles with numbers indicate Atlantic haplotypes. Solid black circles designate hypothetical missing haplotypes. The network includes S. elegans haplotypes 1–21, and S. praegustator haplotypes 19, 26–30. Haplotypes 1–17, shown in colour, represent Jalisco, Mexico specimens collected from nine different turtles in the Pacific, and haplotypes 18–21 and 26–30, shown as unshaded circles, represent southeastern United States Atlantic specimens collected from six different C. caretta (see Table 1).
Figure 3. Haplotype networks for cytochrome oxidase I in Bythinella Moquin-Tandon, 1856 (Gastropoda: Rissooidea: Bythinellidae) in Romania: species richness in a glacial refugium
Figure 3. Haplotype networks for cytochrome oxidase I (COI), computed with TCS 1.21; square and ellipse size reflects haplotype frequency; connection limit excluding homoplastic changes was set to 95% (hence excluding some haplotypes from network); haplotypes in squares have biggest outgroup weights.
FIGURE 3. Haplotype network for the 800 in Genetic evaluation of the Baja California rock squirrel Otospermophilus atricapillus (Rodentia: Sciuridae)
FIGURE 3. Haplotype network for the 800-bp Cyt b data set includes populations from California and the Baja California Peninsula. Each perpendicular hash mark across the line between adjacent haplotypes in the network represents a single-base substitution. The circle size is directly proportional to the number of specimens per haplotype; the key to the haplotype (Table 1) is adjacent to each circle; some haplotypes are present in more than one population. The clades are in boxes; Clade A (Southern Clade, lowlands across California and Baja California Peninsula); Clade B (Northern Clade, El Dorado Natural Forest); and Clade C (Central Clade, California highlands in Yosemite). Color for the haplotype circles are based on subspecies designation (see material and methods from subspecies allocation. Solid circle = O. b. atricapillus, dark gray circle O. b. beecheyi, light gray circle O. b. douglasii, open circle = O. b. fisheri, solid ellipse = O. b. nudipes, dark gray ellipse = O. b. parvulus, light gray ellipse = O. b. rupinarum, and open ellipse = O. b. sierrae.
FIGURE 2. Minimum spanning haplotype networks for all S in Review of the systematic status of Sceloporus arenicolus Degenhardt and Jones, 1972 with an estimate of divergence time
FIGURE 2. Minimum spanning haplotype networks for all S. graciosus group samples sequenced at each of three nuclear loci. Size of each circle corresponds to the frequency of that haplotype. Shading corresponds to clade membership in Figure 3.
FIGURE 3 in High haplotype diversity in a microendemic Malagasy gecko species, Lygodactylus mirabilis (Pasteur, 1962)
FIGURE 3: Haplotype network of L. mirabilis using all the 31 sampled individuals (1251 bp, cytochrome b and 16S rRNA genes). Circle size indicates the frequency of the haplotype, as indicated by the circles on the left side of the figure. Black dots indicate missing haplotypes. Straight lines between two haplotypes indicate that they differ by one mutation.
FIGURE 1. A in High haplotype diversity in a microendemic Malagasy gecko species, Lygodactylus mirabilis (Pasteur, 1962)
FIGURE 1. A) Map of Madagascar with indicated the location of the Ankaratra Massif. B) Distribution map of the surveyed area along the mountain peaks of the Ankaratra Massif in Madagascar (see Material and Methods for further explanations). White points indicate where Lygodactylus mirabilis specimens have been found; grey points indicate the locations of the individuals sampled and used for the genetic analysis. C) Altitudinal range of the recorded individuals of L. mirabilis found. Grey areas are proportional to the number of L. mirabilis eggs found at specific altitudes.
Haplotype-based genome-wide association increases the predictability of leaf rust (Puccinia triticina) resistance in wheat
<p></p><p>Resistance breeding is crucial for a sustainable control of wheat leaf rust and SNP-based genome-wide association studies (GWAS) are widely used to dissect leaf rust resistance. Unfortunately, GWAS based on SNPs explained often only a small proportion of the genetic variation. We compared SNP-based GWAS with a method based on functional haplotypes (FH) considering epistasis in a comprehensive hybrid wheat mapping population composed of 133 parents plus their 1,574 hybrids and characterized with 626,245 high-quality SNPs. In total, 2,408 and 1,139,828 significant associations were detected in the mapping population by using SNP-based and FH-GWAS, respectively. These associations mapped to 25 and 69 candidate regions, correspondingly. SNP-based GWAS highlighted two already-known resistance genes, i.e. Lr22a and Lr34-B, while FH-GWAS not only detected associations on these genes but also on two additional genes, i.e. Lr10 and Lr1. As revealed by a second hybrid wheat population for independent validation, using detected associations from SNP-based and FH-GWAS reached predictabilities of 11.72% and 22.86%, respectively. Therefore, FH-GWAS is not only more powerful to detect associations, but also improves the accuracy of marker-assisted selection as compared to the SNP-based approach.</p><p></p>
Figure 10. Haplotype parsimonious networks constructed from cytochrome c oxidase subunit I in A new genus of large hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae)
Figure 10. Haplotype parsimonious networks constructed from cytochrome c oxidase subunit I sequences of 30 specimens of: A, Gigantopelta chessoia sp. nov.; B, Gigantopelta aegis sp. nov. Open circles are represented haplotypes, number inside the circles and sizes of the circles correspond to number of individuals sharing the haplotype. Filled circles are hypothesized intermediate haplotypes that are not represented by sequences.
Life‐stage‐dependent supergene haplotype frequencies and metapopulation neutral genetic patterns of Atlantic cod, Gadus morhua, from Canada's Northern cod stock region and adjacent areas
<p class="BodyA">Among highly migratory fish species, nursery areas occupied by juveniles often differ from adult habitats. To better understand the spatial dynamics of Canada's Northern cod stock, juveniles caught off the east coast of Newfoundland and Labrador were compared to adults from the same region as well as individuals from other areas in Atlantic Canada using ddRAD-derived SNPs. A reduced proportion of homozygotes with a chromosomal inversion located in LG1 was detected between juvenile and adult samples in the Northern cod stock region, potentially indicating age-dependent habitat use or ontogenetic selection for attributes associated with the many genes located in LG1. No neutral genetic differences were found between samples from the Northern cod stock; however, significant differences were found between some of these samples and cod collected from St. Pierre Bank, Bay of Fundy, Browns Bank and the southern Scotian Shelf. Clustering analysis of variants at neutral loci provided evidence for three major genetic units: 1) the Newfoundland Atlantic Coast, 2) eastern and southern Gulf of St. Lawrence and Burgeo Bank, and 3) the Bay of Fundy, Browns Bank and southern Scotian Shelf. Both adaptive and neutral population structure within the Northern cod stock should be considered by managers to promote rebuilding.</p>
Data from: Dispersal limitations and long-term persistence drive differentiation from haplotypes to communities within a tropical sky-island: evidence from community metabarcoding
<p>Neutral theory proposes that dispersal stochasticity is one of the main drivers of local diversity. Haplotypes-level genetic variation can now be efficiently sampled from across whole communities, thus making it possible to test neutral predictions from the genetic to species-level diversity, and higher. However, empirical data is still limited, with the few studies to date coming from temperate latitudes. Here, we focus on a tropical mountain within the Transmexican Volcanic Belt to evaluate spatially fine-scale patterns of arthropod community assembly to understand the role of dispersal limitation and landscape features as drivers of diversity. We sampled whole-communities of arthropods for eight orders at a spatial scale ranging from 50 m to 19 km, using <span>whole community metabarcoding. We explored multiple hierarchical levels, from individual haplotypes to lineages at 0.5, 1.5, 3, 5, 7.5% similarity thresholds, to evaluate patterns of richness, turnover,</span><span> and distance decay of similarity </span><span>with isolation-by-distance and isolation-by-resistance (</span><span>costs to dispersal given by landscape features</span><span>) approaches. </span><span>Our results showed that distance and altitude influence distance decay of similarity at all hierarchical levels. This holds for arthropod groups of contrasting dispersal abilities, but with different strength depending on the spatial scale. Our results support a model where local-scale differentiation mediated by dispersal constraints, combined with long-term persistence of lineages, is an important driver of diversity within tropical sky islands.</span></p>
Figure 5. The haplotype minimum spanning network using 612 in Phylogeny of the order Phoenicopteriformes and population genetics of the Caribbean flamingo (Phoenicopterus ruber: Aves)
Figure 5. The haplotype minimum spanning network using 612 bp of the cytochrome b gene to compare colonies of Caribbean flamingos from Cuba (N = 49), Bonaire (N = 38) and Galápagos (N = 35).
Chloroplast haplotypes and main haplotypes of nrITS clones of Gentiana crassicaulis
<p>The Himalaya-Hengduan Mountain region is one of the hotspots of biodiversity research. The uplift of the Qinghai-Tibetan Plateau (QTP) and the Quaternary glaciation caused great environmental changes in this region, and the responses of many species in the QTP to the Quaternary climate are still largely unknown. The genetic structure and phylogeographical history of Gentiana crassicaulis Duthie ex Burk, an endemic Chinese alpine species in this area, were investigated based on four chloroplast fragments and internal transcribed spacer region of the nuclear ribosomal DNA (nrITS) sequences of 11 populations. The populations with highly diverse chloroplast haplotypes were mainly found at the edge of the QTP. There were two main haplotypes of nrITS clones, one shared by the Yunnan and Guizhou populations, and the other by the remaining populations. The population with the highest diversity was the Gansu population, located at the edge of the plateau. Based on molecular dating, the diversification of G. crassicaulis at the edge of the plateau occurred before the Last Glacial Maximum (LGM), and the species may have completed its expansion from the edge to the platform. Ecological Niche Models were conducted to predict the distributional ranges of G. crassicaulis at present, during the LGM, and during the last interglacial (LIG) period. The results demonstrated that G. crassicaulis survived on the QTP platform and at the edge during the LGM but afterward retreated from the platform to the southern edge, followed by expansion to the platform.</p>
Alternanthera philoxeroides haplotypes growth response to N and P
<p class="MsoNormal"><span><span>Interactions between invaders and resource availability may explain variation in their success or management efficacy. For widespread invaders, regional variation in plant response to nutrients can reflect phenotypic plasticity of the invader, genetic structure of invading populations, or a combination of the two. The wetland weed </span><span>Alternanthera philoxeroides</span><span> (alligatorweed) is established throughout the southeastern USA and California, and has high genetic diversity despite primarily spreading clonally. Despite its history in the USA, the role of genetic variation for invasion and management success is only now being uncovered. To better understand how nutrients and genotype may influence </span><span>A. philoxeroides</span><span> invasion, we measured the response of plants from 26 </span><span>A. philoxeroides</span><span> populations (three cp haplotypes) to combinations of nitrogen (</span><span>4 or 200 mg/L N) </span><span>and phosphorus </span><span>(0.4 or 40 mg/L P)</span><span>. We measured productivity (biomass accumulation and allocation), plant architecture (stem diameter and thickness, branching intensity) and foliar traits (toughness, dry matter content, percent N, percent P). A short-term developmental assay was also conducted by feeding a subset of plants from the nutrient experiment to the biological control agent </span><span>Agasicles hygrophila,</span><span> to determine whether increased availability of N or P to its host influenced agent performance, as has been previously suggested. </span><span>A. philoxeroides</span><span> haplotype Ap1 was more plastic than other haplotypes in response to nutrient amendments, producing more than double the biomass from low to high N and 50-68% higher shoot:root ratio than other haplotypes in the high N treatment. </span><span>A. philoxeroides</span><span> haplotypes differed in 7 of 10 variables in response to increased N. We found no differences in short-term </span><span>A. hygrophila</span><span> development between haplotypes but mass was 23% greater in high than low N treatments. This study is the first to explore the interplay between nutrient availability, genetic variation, and phenotypic plasticity in invasive characteristics of the global invader, </span><span>A. philoxeroides</span><span>.</span></span></p>
Fig. 2.—Bayesian maximum clade credibility tree showing 37 mitochondrial genome haplotypes from 60 in Phylogeography of moose in western North America
Fig. 2.—Bayesian maximum clade credibility tree showing 37 mitochondrial genome haplotypes from 60 moose and an inset of sample locations according to haplotype number, sampled in western North America, 2004–2016, and including a Eurasian moose mitogenome from Kazakhstan (Hassanin et al. 2012—GenBank accession NC_020677). In the tree, each haplotype is followed by a sequence of highlighted (by subspecies) and labeled (by state or provincial abbreviation) squares signifying the location where each sample was collected. In the inset, haplotypes unique to a single individual are colored white, while the seven haplotypes found in multiple moose are colored by haplotype number.
FIG. 4. Haplotype network for the mitochondrial genes cytochrome b in Phylogeography of the Chocó Endemic Rainbow Characin (Teleostei: Rhoadsia)
FIG. 4. Haplotype network for the mitochondrial genes cytochrome b (Cyt-b, top) and cytochrome oxidase I (COI, bottom) color coded by site. The size of the circles is proportional to the haplotype frequency. The number of mutations between the haplotypes are represented by hatch marks. The populations within drainages are represented by different color shades (see legend). Haplotypes fall into two groups: the northern (N, enclosed by blue dashed line) and the southern group (S, enclosed by red dashed line).
Figure 2. Haplotype median joining network estimated from dataset 1, comprising 76 in Phylogeography and evolutionary lineage diversity in the small-eared greater galago, Otolemur garnettii (Primates: Galagidae)
Figure 2. Haplotype median joining network estimated from dataset 1, comprising 76 samples of partial cytochrome b (402 bp).
FIGURE 5. Haplotype network for Austroniscus brandtae n in Combining morphological and mitochondrial DNA data to describe a new species of Austroniscus Vanhöffen, 1914 (Isopoda, Janiroidea, Nannoniscidae) linking abyssal and hadal depths of the Puerto Rico Trench
FIGURE 5. Haplotype network for Austroniscus brandtae n. sp. for the mitochondrial ribosomal large subunit 16S. Sampled haplotypes are shown as solid circles with circle area proportional to the number of individuals possessing that haplotype; black circles represent unsampled haplotypes required to connect the network. The number of mutational steps between haplotypes are shown along connecting lines. The colours represent sampling locations as indicated in the legend.
FIGURE 4. Haplotype network for Austroniscus brandtae n in Combining morphological and mitochondrial DNA data to describe a new species of Austroniscus Vanhöffen, 1914 (Isopoda, Janiroidea, Nannoniscidae) linking abyssal and hadal depths of the Puerto Rico Trench
FIGURE 4. Haplotype network for Austroniscus brandtae n. sp. for COI (cytochrome c oxidase subunit I). Sampled haplotypes are shown as solid circles with circle area proportional to the number of individuals possessing that haplotype; black circles represent unsampled haplotypes required to connect the network. The number of mutational steps between haplotypes are shown along connecting lines. The colours represent sampling locations as indicated in the legend.
Haplotype variations data for the complete 5.3 Mbp region
<p><em>Variations </em>data for the complete chromosome 2A 5.3 Mbp region +/- 1 Mbp of the whole dataset.</p>
Modified LRphase and Simulated Dataset for "LRphase: an efficient algorithm for assigning haplotypic identity to long reads"
<p><strong>A modified version of LRphase was used to simulate reads for a single hypothetical human genome with maternal and paternal phasing information. Briefly, haplotype-specific reference sequences were generated with `bcftools consensus` <a href="https://paperpile.com/c/VO12CC/SIk9">(Li 2011)</a> based on the rescued GIAB VCF and hg38 human reference sequence. Each haplotype-specific fasta was fed separately into pbsim2 <a href="https://paperpile.com/c/VO12CC/NMmE">(Ono, Asai, and Hamada 2021)</a> as the reference from which simulated reads were randomly drawn, up to 1X coverage. Parameters controlling the read length distribution, sequencing, and base calling error rates were set to emulate typical performance of the MinIon sequencing platform with flow cell version R10.4.1 (https://nanoporetech.com/products/minion). These are as follows: `--depth 1 –hmm_model R103.model --difference-ratio '23:31:46' --length-mean 25000 --length-min 100 --length-max 1000000 –length-sd 20000 --accuracy-mean 0.98 --accuracy-min 0.01 --accuracy-max 1.00`. Simulated reads were aligned to the hg38 reference genome with minimap2 <a href="https://paperpile.com/c/VO12CC/Y2HP">(Li 2018)</a> and correct phasing and alignment coordinates were encoded in the read names. Finally, samtools <a href="https://paperpile.com/c/VO12CC/YLss">(Li et al. 2009)</a> was used to remove duplicated and supplementary reads, and concatenate, sort, and index reads into a single combined bam file. Of 258,539 total reads, 246,210 were mappable, and 178,504 overlapped at least one heterozygous variant in HG001.</strong></p>
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Allen Brain Atlas
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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.
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