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38 results for “haplotype diversity”
Fig. 3 in Haplotype variation in the Physa acuta group (Basommatophora): genetic diversity and distribution in Serbia Abstract
Fig. 3: Haplotype networks from 43 Physa acuta group specimens, obtained using statistical parsimony (TCS). Circles represent specific haplotypes; the size of the circles reflects the number of individuals with a particular haplotype (not to scale); the dots between the circles represent mutational steps.
Fig. 2 in Haplotype variation in the Physa acuta group (Basommatophora): genetic diversity and distribution in Serbia Abstract
Fig. 2: Phylogenetic trees based on mt16S rDNA, obtained using the Maximum Likelihood (ML) method. Bootstrap values are indicated below the branches. Scale bar indicates the number of substitutions per site.
Fig. 3 Phylogenetic relationships among the 16 mtDNA haplotypes observed. a in Unveiling cryptic diversity among Müllerian co-mimics: insights from the Western Palaearctic Syntomis moths (Lepidoptera: Erebidae: Arctiinae)
Fig. 3 Phylogenetic relationships among the 16 mtDNA haplotypes observed. a Maximum likelihood tree retrieved by the analysis in IQTREE; support values at the relevant nodes are SH-aLRT support (%) and standard bootstrap support (%) based on 1000 replicates. b Maximum clade credibility tree recovered by the Bayesian analysis in BEAST, showing the divergence time from the most recent common
Figures 4–5. Mitochondrial D-loop 474 in Molecular confirmation of the occurrence of Anguilla interioris (Actinopterygii: Anguilliformes) in North Maluku of Indonesia and mitochondrial DNA haplotype diversity among existing specimens
Figures 4–5. Mitochondrial D-loop 474 bp sequence analyses. (4) Phylogenetic analysis based on maximum likelihood algorithm with the sample codes, GenBank accession numbers and sample sites shown. Bootstrap percentages are shown at the tree nodes. (5) Haplotype network with the haplotypes labelled as H1 to H9. The circle size is proportional to the number of samples, and different sample sites are represented by different colours. Small white circle represents median vector which is the hypothesized or missing haplotype. Each dash on the line symbolizes one mutational step.
Figure 1 in Molecular confirmation of the occurrence of Anguilla interioris (Actinopterygii: Anguilliformes) in North Maluku of Indonesia and mitochondrial DNA haplotype diversity among existing specimens
Figure 1. Sampling locations of Anguilla interioris in North Maluku of East Indonesia. Sampling locations are shown in red (circle: COI, triangle: D-loop). Locations of Bougainville of Papua New Guinea, Papua New Guinea mainland, Negros Oriental and Sibutad of Philippines, and Ambon and Bengkulu of Indonesia, which were used in molecular phylogenetic and haplotype network analyses, are shown in purple (circle: COI, triangle: D-loop). Specimen records are shown in square with growth stages; L [larval (leptocephalus); Kuroki et al. 2006, Wouthuyzen et al. 2009, Aoyama et al. 2018], J [juvenile (glass eel); Sugeha et al. 2008, Fahmi et al. 2012, Wibowo et al. 2021] and A (adult; Watanabe et al. 2004, Fahmi et al. 2012, Wibowo et al. 2021, this study). Base maps were downloaded from http://viewer. nationalmap.gov/viewer (USGS 2022) and from the OpenStreetMap at https://www.openstreetmap.org.
Figure 1 in Haplotype diversity of brown trout Salmo trutta (L.) in the broader Iron Gate area
Figure 1. Sampling sites on the streams Brnjica (1), Dobrinjska reka (2), Kožica (3), Mala Boljetinska reka (4), Zlatica (5), Porečka reka (6), Rečka reka (7), Vratna (8), and Zamna (9) in the broader Iron Gate area with the position in the Balkan region given in small figure in lower left.
Figure 2 in Haplotype diversity of brown trout Salmo trutta (L.) in the broader Iron Gate area
Figure 2. Relationships between CR haplotypes of brown trout populations in the broader Iron Gate area constructed using maximum likelihood (A) and maximum parsimony (B) methods (numbers at particular branches represent bootstrap probabilities; bootstrap values under 40% are not represented).
Figure 1. A in Increased haplotype diversity of Emys orbicularis (Linnaeus, 1758) (Reptilia: Emydidae) in northern Iran
Figure 1. A) Map of Eurasia and the samples used for this study. Shaded area at lower right indicates the study area and the colors of the occurrence points correspond to the lineage numbers in the phylogenetic tree. B) Map of Iran, Armenia and Azerbaijan and samples for lineage VII. Red circles indicate samples from Genbank (Fitz et al., 2009), red stars are our new samples.
Figure 2 in Increased haplotype diversity of Emys orbicularis (Linnaeus, 1758) (Reptilia: Emydidae) in northern Iran
Figure 2. Bayesian inference tree (MrBayes) based on the cytochrome b gene fragment. Colors of the branches correspond to the lineage colors in Figure 1. Posterior probabilities and divergence time estimation (n parentheses) are next to the nodes.
Fig. 2. Statistical parsimony cladogram network representing relationships among the 45 haplotypes for a 615 in Genetic diversity of Halyomorpha halys (Hemiptera, Pentatomidae) in Korea and comparison with COI sequence datasets from East Asia, Europe, and North America
Fig. 2. Statistical parsimony cladogram network representing relationships among the 45 haplotypes for a 615 bp fragment of the COI gene of Halyomorpha halys. Each circle is labeled with haplotype number, and the size of each circle is proportional to the frequency of each haplotype [H3 (n = 353); H1 (n = 285); H22 (n = 43); H8 (n = 34); H33 (n = 23); H2 (n = 16); H32 (n = 8); H7, H9–H13, and H43 (n = 3); H6, H14, H34, H39, and H40 (n = 2); H4–H5, H12, H15–H21, H23, H30–H31, H35–H38, H41, H42, and H44–H51 (n = 1)]. Differing colors indicate countries in which samples were collected.
Figure 3 in Increased haplotype diversity of Emys orbicularis (Linnaeus, 1758) (Reptilia: Emydidae) in northern Iran
Figure 3. Haplotype network of all studied samples based on the Cytochrome b gene fragment.
Data from: Non-random association of MHC-I alleles in favor of high diversity haplotypes in wild songbirds revealed by computer-assisted MHC haplotype inference using the R package MHCtools
<p><strong>Data set from:</strong></p> <p>Roved J., Hansson B., Stervander, M., Hasselquist D., & Westerdahl H. (2020). Non-random association of MHC-I alleles in favor of high diversity haplotypes in wild songbirds revealed by computer-assisted MHC haplotype inference using the R package MHCtools.</p>
Data from: Intraspecific haplotype diversity in Cherleria sedoides L. (Caryophyllaceae) is best explained by chloroplast capture from an extinct species
Cherleria sedoides, a plant species widespread in alpine areas of the major European mountain ranges and in Scotland, contains two highly divergent chloroplast haplotype groups, one widespread (WH) and one present only in some populations in the Alps (AH). We investigated whether this haplotype diversity is the result of (1) intraspecific differentiation, (2) retention of an ancestral polymorphism or (3) hybridisation. For this purpose, 106 matK sequences from throughout the Caryophyllaceae and 80 trnQ-rps16 and psbD-trnT sequences of C. sedoides (51) and other species of Cherleria (29) were used for the construction of phylogenies and haplotype networks. As the two haplotype groups were never each other's closest relatives, haplotype diversity as a result of intraspecific differentiation is unlikely. Patterns of genetic differentiation within the WH and AH groups are very different. Whereas WH shows a radial pattern typical of rapid expansion, AH is divided into two divergent subgroups each containing more variation than the WH group. This suggests that the two haplotype groups have dissimilar histories and are therefore unlikely to represent an ancestral polymorphism. Instead, we conclude that the polymorphism is best interpreted as the result of hybridisation. As the WH and AH haplotype groups fall into Cherleria, but do not group with any extant species, we conclude that the rare AH group represents the original C. sedoides, and that the WH group was captured from another, now extinct, species of Cherleria.
Data from: Testing the species–genetic diversity correlation in the Aegean archipelago: towards a haplotype-based macroecology?
A positive correlation between species and genetic diversity (SGDC) has been proposed, consistent with neutral predictions in macroecology. We assessed the SGDC in tenebrionid beetle communities of the Aegean archipelago on fifteen islands of different sizes, distances to mainland, and ages of isolation. Alpha- and beta-diversity of species and haplotypes were assessed using sequences of >1000 individuals (mitochondrial Cytochrome Oxidase I and nuclear Muscular Protein 20) to test the SGDC. We show that: (i) there is a strong species-area and haplotype-area relationship; (ii) species richness in island communities is correlated with intraspecific genetic diversity in the constituent species except when island size or distance to mainland are factored out in partial correlations; (iii) community similarity declines exponentially at an increasing rate when calculated based on species, nuclear and mtDNA haplotypes; and (iv) distance decay of community similarity is slower in dispersive sand-dwelling lineages compared to less dispersive lineages that are not sand-obligate. Taken together, these correlated patterns at the species and haplotype level are consistent with individual-based stochastic dispersal proposed by neutral theories of biodiversity. The results also demonstrate the utility of haplotype data for exploring macroecological patterns in poorly known biota and predicting large-scale biodiversity patterns based on genetic inventories of local samples.
Figure 1. Haplotype network derived from 704 in Repeated sampling adds to the genetic diversity of Lepidochelys olivacea (Eschscholtz 1829) olive ridley sea turtle
Figure 1. Haplotype network derived from 704 bp mitochondrial D-loop fragment. Circle sizes are proportional to the frequency of each haplotype. The black circles are hypothetical haplotypes not sampled. Each colour represents the ocean basin where the sample was taken: blue is Pacific Ocean, yellow is Indian Ocean, red is Atlantic Ocean, and green is Indo-Pacific Ocean.
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.
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).
Data from: Testing the species–genetic diversity correlation in the Aegean archipelago: towards a haplotype-based macroecology?
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Data from: Intraspecific haplotype diversity in Cherleria sedoides L. (Caryophyllaceae) is best explained by chloroplast capture from an extinct species
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