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SNP data: Comparison of molecular surveillance methods to assess changes in the population genetics of Plasmodium falciparum in high-transmission
<p>Genetic diversity and population structure of <em>Plasmodium falciparum</em> are assessed here using three established methods (i) SNP barcoding (panel of 24-biallelic loci), (ii) microsatellite genotyping (panel of 12-multiallelic loci), and (iii) varcoding (fingerprinting var gene diversity, akin to microhaplotyping) to identify changes in parasite population genetics in response to a short-term indoor residual spraying (IRS) intervention. Typical of high seasonal transmission in Africa, multiclonal infections were found in <span>82.3% (median 3; range 1–18) and 57.8% (median 2; range 1–12) of asymptomatic individuals pre- and post-IRS, respectively, in Bongo District, Ghana. </span>Since directly phasing multilocus haplotypes for population genetic analysis is not possible for biallelic SNPs and microsatellites, we chose 200 low-complexity infections for analysis. Each genotyping method presented a different pattern of change in population diversity and structure as a consequence of variability in usable data and the relative polymorphism of the molecular markers (<a>SNPs < microsatellites < var</a>). In terms of neutral variation, the 24-SNP barcode was the least informative, largely due to the bi-allelic nature of SNPs leading to a high proportion of double-allele calls (<a>DACs</a>), whereas multiallelic microsatellites showed high haplotype diversity with ten markers but no measurable change in population structure after IRS. Varcoding provided the most informative and nuanced description of changes in population structure, showing high diversity with a subtle but measurable change to less related var repertoires as a result of the IRS intervention. Relative performance, suitability, and cost-effectiveness of the methods relevant to local malaria elimination in high-transmission endemic areas are discussed. </p>
Figure 2 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Figure 2 Total number of shared haplotypes between populations of Usnea subfloridana in the south-eastern (SE), the western (W) and northern (N) regions of Estonia; the thickness of lines reflects the number of shared haplotypes between populations.
Figure 3 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Figure 3 Usnea subfloridana multilocus genotypes in the principal component analysis (PCA) ordination plot of the first and second axes. Samples are grouped according to the presence of lichen substance: samples containing thamnolic (square) or squamatic acid (circle).
Figure 1 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Figure 1 Distribution map of Usnea subfloridana in Estonia (light grey squares) and study populations (black circles) on Hiiumaa island in the western region (W), in the south-eastern region (SE) and in the northern region of Estonia; the map of Scandinavia was taken from free map resource http://d-maps.com/carte.php?num_car=5977&lang=en.
Figure 6 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Figure 6 Alleles of Usnea subfloridana and explanatory variables mean annual air temperature ('Temp') and geographical longitude of populations ('Long') in the bi-plot of the redundancy analysis (RDA) of the first and second axes. Labels of alleles prefixed by '8' or '9' indicate that these alleles belong to loci Us08 or Us09, respectively; for example, 8201 means that allele 201 is from Us08
Figure 4 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Figure 4 Usnea subfloridana multilocus genotypes (Us02, Us03, Us04, Us05, Us06, Us08, Us09) and explanatory variables mean annual air temperature ('Temp') and the presence of thamnolic acid ('Tham') in a lichen sample in the bi-plot of the redundancy analysis (RDA) of the first and second axes.
Figure 5 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Figure 5 Sample populations of Usnea subfloridana and explanatory variables mean annual air temperature ('Temp') and geographical longitude of populations ('Long') in the bi-plot of the redundancy analysis (RDA) of the first and second axes. The shape of symbols indicates the geographical location of studied populations (square – south-eastern region of mainland, circle - western island and diamond – north-eastern region) and the size of symbols indicates the number of different alleles found in the studied populations.
Figure 3A in Comparison of two morphometric methods for discriminating honey bee (Apis mellifera L.) populations in Turkey
Figure 3A. Scatter plot of principle component analysis of honey bee populations from different geographic regions based on TM (Thrace = ✳; Aegean = ×; Central Anatolia/Mediterranean = ◆; Southeastern Anatolia = △; Northeastern Anatolia = □).
TABLE 1. Comparison between Lepanthes cordillerana E. Restrepo, J. S in Lepanthes cordillerana (Orchidaceae) a new species and the landscape threats to its wild populations
<p><b>TABLE 1.</b> Comparison between <i>Lepanthes cordillerana</i> E.Restrepo, J.S.Moreno & Gal. -Tar. and related species (in alphabetic order).</p><table><tbody><tr><th><b>Character</b></th><th><i>L. cordillerana</i></th><th><i>L. intonsa</i></th><th><i>L. jubata</i></th><th><i>L. protuberans</i></th><th><i>L. teres</i></th></tr></tbody><tbody><tr><th><b>Leaves</b></th><td>Erect to horizontal,</td><td>Erect, thinly</td><td>Erect to suberect,</td><td>Erect, thickly</td><td>Erect, fleshy,</td></tr><tr><th></th><td>heavily coriaceous,</td><td>coriaceous, ovate,</td><td>coriaceous, ovate,</td><td>coriaceous, narrowly</td><td>narrowly ovoid,</td></tr><tr><th></th><td>lanceolate-acute,</td><td>acuminate, acute.</td><td>acuminate, margins</td><td>elliptical, acute.</td><td>terete, smooth</td></tr><tr><th></th><td>apex attenuate,</td><td></td><td>smooth or minutely</td><td></td><td>margined.</td></tr><tr><th></th><td>emarginate, margin</td><td></td><td>denticulate</td><td></td><td></td></tr><tr><th></th><td>ciliate.</td><td></td><td></td><td></td><td></td></tr><tr><th><b>Petals</b></th><td>Cream, suffused</td><td>Yellow, suffused</td><td>Whitish internally,</td><td>Greenish white,</td><td>Light yellow with red</td></tr><tr><th></th><td>with magenta-red,</td><td>with orange,</td><td>suffused with</td><td>with red border,</td><td>margins, transversely,</td></tr><tr><th></th><td>transversely bilobed,</td><td>microscopically</td><td>red externally,</td><td>microscopically</td><td>dolabriform,</td></tr><tr><th></th><td>microscopically</td><td>pubescent,</td><td>transversely oblong,</td><td>pubescent,</td><td>the upper lobe</td></tr><tr><th></th><td>pubescent, the upper</td><td>transversely oblong,</td><td>bilobed, both lobes</td><td>transversely</td><td>oblong with the</td></tr><tr><th></th><td>lobe oblong with the</td><td>the upper lobe</td><td>obtuse, the upper</td><td>bilobed, the lobes</td><td>apex rounded, the</td></tr><tr><th></th><td>apex rounded, the</td><td>oblong, apically</td><td>longer.</td><td>subtriangular, about</td><td>lower lobe smaller,</td></tr><tr><th></th><td>lower lobe oblong-</td><td>rounded and the</td><td></td><td>equally long, the</td><td>narrowly triangular,</td></tr><tr><th></th><td>acute, apex obtuse.</td><td>smaller, oblique,</td><td></td><td>apices rounded.</td><td>obtuse.</td></tr><tr><th></th><td></td><td>obtuse lower lobe.</td><td></td><td></td><td></td></tr><tr><th><b>Lip and</b></th><td>Cream-yellow, the</td><td>Reddish, the blades</td><td>Reddish, the blades</td><td>Rose, pubescent,</td><td>Yellow with red</td></tr><tr><th><b>appendix</b></th><td>blades marginally</td><td>oblong-obovate,</td><td>oblong, oblique, the</td><td>ciliate anteriorly,</td><td>margins, blades</td></tr><tr><th></th><td>suffused with red,</td><td>concave, the apical</td><td>margins with straight</td><td>the laminae oblong,</td><td>oblong, the</td></tr><tr><th></th><td>bilaminate, oblong,</td><td>margin long ciliated,</td><td>hairs, the connectives</td><td>with the apices and</td><td>apex ciliate, the</td></tr><tr><th></th><td>the apical margin</td><td>the connectives</td><td>rectangular,</td><td>bases rounded, the</td><td>connectives short,</td></tr><tr><th></th><td>abundantly long</td><td>oblong, elongated,</td><td>erect, lifting the</td><td>connectives broadly</td><td>cuneate, the appendix</td></tr><tr><th></th><td>ciliated at the apex,</td><td>lifting the appendix</td><td>blades above the</td><td>oblong, oblique,</td><td>a subspherical,</td></tr><tr><th></th><td>the connectives short,</td><td>straplike, sigmoid</td><td>column, the body</td><td>protuberant body,</td><td>bilobed body</td></tr><tr><th></th><td>cuneate, the body</td><td>in the lateral</td><td>broad, the sinus</td><td>the apex minimally</td><td>accommodated in a</td></tr><tr><th></th><td>broad, connate to the</td><td>view, pubescent,</td><td>broadly rounded</td><td>retuse without an</td><td>cavity in the sinus.</td></tr><tr><th></th><td>base of the column,</td><td>terminating in a small</td><td>and protruding</td><td>appendix.</td><td></td></tr><tr><th></th><td>the appendix capitate,</td><td>gland, hinged to the</td><td>with a minute,</td><td></td><td></td></tr><tr><th></th><td>cuneate basally,</td><td>sinus.</td><td>pedunculated,</td><td></td><td></td></tr><tr><th></th><td>apically caved,</td><td></td><td>bilobed appendix</td><td></td><td></td></tr><tr><th></th><td>villose.</td><td></td><td></td><td></td><td></td></tr></tbody></table>
Figure 2 from: Rao U, Rao S, Rathi A, Gothalwal R, Atkinson H (2011) A comparison of the variation in Indian populations of pigeonpea cyst nematode, Heterodera cajani revealed by morphometric and AFLP analysis. ZooKeys 135: 1-19. https://doi.org/10.3897/zookeys.135.1344
Figure 2 - AFLP Autoradiogram of pigeon pea cyst nematode Heterodera cajani with EcoRI (+AAG) + MseI, (+CAG) and EcoRI (+AAA) + MseI (CTA). Lane 1 to 11: Heterodera cajani populations from Andhra Pradesh, Allahabad, Bahadurgarh, Coimbatore, Kanpur-1, Ghaziabad, Gilberga, Hisar, Delhi, Kanpur-2, andMeja.
Figure 3 from: Rao U, Rao S, Rathi A, Gothalwal R, Atkinson H (2011) A comparison of the variation in Indian populations of pigeonpea cyst nematode, Heterodera cajani revealed by morphometric and AFLP analysis. ZooKeys 135: 1-19. https://doi.org/10.3897/zookeys.135.1344
Figure 3 - Dendograms from cluster analysis of Heterodera cajani a) for 1278 amplified restriction fragment digests using 24 primer pairs and b) the four primer pairs that suggest a similar dendogram to the full set. The using the upper tail rule the best cut procedure indicated the highest number of significant cluster partitions was 3 as in both cases with realised deviates and t statistics respectively of a) 1.47 and 4.66 and b) 1.59 and 5.04.
Figure 1 from: Rao U, Rao S, Rathi A, Gothalwal R, Atkinson H (2011) A comparison of the variation in Indian populations of pigeonpea cyst nematode, Heterodera cajani revealed by morphometric and AFLP analysis. ZooKeys 135: 1-19. https://doi.org/10.3897/zookeys.135.1344
Figure 1 - Dendograms from cluster analysis a) for the nine biometric measurements made on second stage juveniles of eleven populations of Heterodera cajani (see Table 2 for data) b) vulval cones of cysts of the same populations. (See Table 3 for data). The using the upper tail rule the best cut procedure indicated the highest number of significant cluster partitions was for a) 2 and for b) 3 with realized deviates and t- statistics respectively of a) 2.71 and 8.56 and b) 1.04 and 3.27.
Figure 4 from: Rao U, Rao S, Rathi A, Gothalwal R, Atkinson H (2011) A comparison of the variation in Indian populations of pigeonpea cyst nematode, Heterodera cajani revealed by morphometric and AFLP analysis. ZooKeys 135: 1-19. https://doi.org/10.3897/zookeys.135.1344
Figure 4 - India Map showing distances of collected 11 Heterodera cajani populations with distances in (Kilometres)
Efficacy Comparison Between Primary Care Physicians' Independent Auscultation and AI-assisted Auscultation for Congenital Heart Disease Screening in Patient-enriched Populations: a Randomized Controll
ClinicalTrials.gov study NCT06791096. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Comparison of Lens Fit and Lens Power of a New Contact Lens to Two Marketed Contact Lenses in a Population of Soft Contact Lens Wearers
ClinicalTrials.gov study NCT01244529. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Comparison of the Risk of Venous Thromboembolism (i.e., Blood Clots in the Veins) and Bleeding Events in a Population of Obese Patients Receiving Higher-Dose or Extended-Duration Versus Conventional-D
ClinicalTrials.gov study NCT05819125. IPD Sharing: YES. Countries: 1. Publications: 0.
SNP data: Comparison of molecular surveillance methods to assess changes in the population genetics of Plasmodium falciparum in high-transmission
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Data from: A comparison of single-sample estimators of effective population sizes from genetic marker data
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Data from: Inconsistent use of multiple comparison corrections in studies of population genetic structure: are some type I errors more tolerable than others?
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Behavior and welfare of an all-male band of captive Gelada monkeys (<em>Theropithecus gelada</em>): A comparison with other populations and implications for management
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