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Dataset for paper 'McAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks'
<p>The .zip file includes four datasets for testing the performance of McAN (doi: https://doi.org/10.1093/bib/bbad174).</p>
Fig. 13 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 13. Distribution map of Ngirhaphium in Southeast Asia
Fig. 9 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 9. Distribution map of Ngirhaphium meieri, new species and Ngirhaphium thaicum, new species.
Fig. 7 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 7. Ngirhaphium meieri, new species, female habitus. Scale = 1 mm.
Fig. 6 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 6. Ngirhaphium meieri, new species, male habitus (photo: Abdulloh Samoh). Scale = 1 mm.
Fig. 3 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 3. Ngirhaphium thaicum, new species male habitus. Scale = 1 mm.
Fig. 4 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 4. Ngirhaphium thaicum, new species habitus female. Scale = 1 mm.
FIGURE 4. Combined haplotype networks from CytB data for Laminatubus paulbrooksi n in Laminatubus (Serpulidae, Annelida) from eastern Pacific hydrothermal vents and methane seeps, with description of two new species
FIGURE 4. Combined haplotype networks from CytB data for Laminatubus paulbrooksi n. sp. (top) from Pacific Costa Rica margin and Gulf of California (Mexico) localities and L. joycebrooksae n. sp. (bottom) from Costa Rica. There was little variability among the L. joycebrooksae n. sp. sequences and a distinct break to L. paulbrooksi n. sp. This corresponds to a minimum 6.4% uncorrected distance. Laminatubus paulbrooksi n. sp. showed marked intraspecific variability with distinct breaks among the three main sites; Costa Rica (9°N), Pescadero (23°N) and Guaymas Basin (27°N). * indicates the holotypes for L. paulbrooksi n. sp. and L. joycebrooksae n. sp. respectively.
Data from: PopART: full-feature software for haplotype network construction
1. Haplotype networks are an intuitive method for visualising relationships between individual genotypes at the population level. 2. Here, we present popart, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication-ready figure production. 3. popart also provides a platform for the implementation and distribution of new network-based methods – we describe one such new method, integer neighbour-joining. 4. The software is open source and freely available for all major operating systems.
FIGURE 7. Haplotype parsimony networks for ITS1 in A comparative study of populations of Ectopleura crocea and Ectopleura ralphi (Hydrozoa, Tubulariidae) from the Southwestern Atlantic Ocean
FIGURE 7. Haplotype parsimony networks for ITS1+5.8S (A) and COI (B) for the different populations of Ectopleura crocea and Ectopleura ralphi of the Southwestern Atlantic Ocean. Black circles for the Argentine haplotypes, white ones for Brazilian localities; the sizes of the circles are proportional to the number of localities sharing the haplotype; small black circles represent hypothetical or unsampled haplotypes. Lines connecting circles represent one substitution step. Note that A BO/MP samples differ from JU/PA/BO only by an indel of three base pairs (AAT/– – –). Locality codes are represented inside the circles as MA: Macaé, JU: Juréia, PA: Paraná, BO: Bombas, MP: Mar del Plata.
FIGURE 3. Haplotype network for P in Phylogeny and genetic variation within the widely distributed Bluntnose Minnow, Pimephales notatus (Cyprinidae), in North America
FIGURE 3. Haplotype network for P. notatus. Median-joining haplotype network for the mitochondrial (cytb) gene examined for P. notatus. Each circle represents a different haplotype; circle sizes are proportional to the number of individuals possessing a particular haplotype. Major drainages are represented by different colors. Small red dots represent missing (unsampled or extinct) haplotypes. Lines between circles represent one mutational step, and numbers presented are the number of mutations between haplotypes. Dotted-square-lines depict two major lineages resolved in mtDNA phylogenetic analyses. Dotted-circle depicts a subclade represented in detail (inset). One specimen from P. tenellus was included for comparisons.
Fig. 3. Haplotype network for 419 in Across mountains and ocean: species delimitation and historical connectivity in Holarctic and Arctic-Alpine wolf spiders (Lycosidae, Pardosa)
Fig. 3. Haplotype network for 419 specimens of P. saltuaria species group based on mitochondrial COI data. Haplotypes are colored based on morphological identification. Each line is 1 mutation step.
FIGURE 4. COI haplotype networks. A in Three New Species of Deep-Sea Wood-Associated Sea Stars (Asteroidea: Caymanostellidae) from the Eastern Pacific
FIGURE 4. COI haplotype networks. A—Caymanostella scrippscognaticausa sp. nov. locality network; B—Caymanostella davidalani sp. nov. locality network; C—Caymanostella davidalani sp. nov. depth network.
Figure 2. Geographic distribution and haplotype networks for 12S in Effects of Quaternary climatic oscillations over the Chacoan fauna: phylogeographic patterns in the southern three-banded armadillo Tolypeutes matacus (Cingulata: Chlamyphoridae)
Figure 2. Geographic distribution and haplotype networks for 12S (top panels) and control region (bottom panels). The panels on the left plot the geographical distribution and frequency of haplotypes in the different localities analysed. Localities were labelled according to their ID (see Table 1). The right panels show the haplotype networks, where the dashes on the lines represent mutations, and the black circles represent intermediate variants not found. Principal Chacoan rivers are shown in light-blue labels. Capitalized labels indicate names of Argentinean provinces, and labels with all letters in uppercase refer to neighbouring countries.
Fig. 5 Haplotype networks for datasets IV in Dugesia hepta and Dugesia benazzii (Platyhelminthes: Tricladida): two sympatric species with occasional sex?
Fig. 5 Haplotype networks for datasets IV (a Dunuc12) and III (b Cox1). Haplotypes are depicted as individual circles which are proportional to their abundancy (number of sequences), highlighted in a white square. Mutations are either depicted with black bars or black triangles when the number of mutations between linked haplotypes is equal to or exceeds a certain
Fig. 3 Median-joining haplotype network obtained for 867 in Diversification and evolutionary history of brush-tailed mice, Calomyscidae (Rodentia), in southwestern Asia
Fig. 3 Median-joining haplotype network obtained for 867 bp of mitochondrial Cyt b of the genus Calomyscus. Circle size is relative to haplotype frequency; black circles represent extinct or unsampled
FIGURE 2. Haplotype network calculated from a 360 in A new species of Uroplatus (Gekkonidae) from Ankarana National Park Madagascar, of remarkably high genetic divergence
FIGURE 2. Haplotype network calculated from a 360 bp segment of the nuclear gene CMOS for the species in the Uroplatus ebenaui group.
Fig. 2 Mitochondrial haplotype network using the 590 in Differentiation of North African foxes and population genetic dynamics in the desert-insights into the evolutionary history of two sister taxa, Vulpes rueppellii and Vulpes vulpes
Fig. 2 Mitochondrial haplotype network using the 590-bp concatenated sequences from Cyt-b and D-loop and a total of 46 sequences (same as in Fig. 1, except for C. lupus not being used as an outgroup in the TCS network). a Neighbour-Net network based on uncorrected patristic distances as implemented in SPLITSTREE. Canis lupus (DQ480504) was used as an outgroup. Numbers indicate bootstrap values. Scale bar represents 0.01 sequence divergence. Highlighoed are the four species, the three V. vulpes clades and the location within the network of the V. vulpes sample from Egypt. Colour patterns are concordant with Fig. 1 and b. b Statistical parsimony network assuming a 95 % parsimony threshold, as constructed by TCS. Symbol size and branch lengths are proportional to the number of shared individuals per haplotype and the number of mutational steps amongst haplotypes, respectively. Numbers in black background also refer to the number of mutation steps between species and V. vulpes clades. Symbols and colours are concordant with Fig. 1 and a. Haplotype codes, sample origin and corresponding accession numbers are available in Online Resource Table S1
Fig. 3 Haplotype-networks for a in Species status and population structure of mussels (Mollusca: Bivalvia: Mytilus spp.) in the Wadden Sea of Lower Saxony (Germany)
Fig. 3 Haplotype-networks for a COI (n haplotypes 0 15; n sequences 0 111), b VD1 (n haplotypes 0 17; n sequences 0 81), and c the combined data set (n haplotypes 0 16; n sequences 0 64). The sizes of the symbols are proportional to the number of individuals sharing that haplotypes (unique haplotypes are not included), with the rectangular haplotype having had the largest outgroup weight. Each node corresponds to one mutation step. The patterns used for the symbols match those used in the geographical distribution maps (Fig. 2)
Fig. 2 in Using haplotype networks, estimation of gene flow and phenotypic characters to understand species delimitation in fungi of a predominantly Antarctic Usnea group (Ascomycota, Parmeliaceae)
Fig. 2 Enlargement of the Usnea aurantiaco-atra group of the Bayesian inference (Fig. 1) depicting 101 taxa. Posterior probabilities ≥ 0.95 are visualized by bold branches. Colors match the sampling site colours in Fig. 4a. A! fertile specimen with apothecia, S! vegetative reproduction via soralia. Most important clades of the nested clade analysis (Fig. 4a,b) are plotted on the phylogenetic tree
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International Brain Laboratory public data
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OpenNeuro
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