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Strains of Mycobacterium tuberculosis complex (MTBC) can be classified into major lineages based on their genotype.
The divergence dating program BEAST was used to estimated origins and radiations of major lineages based on 31 fossil calibrations (Table 2).
In this study, we develop a tensor clustering framework to find the sublineage structure of MTBC strains labeled by major lineages based on multiple biomarkers.
Traditionally, the genus Xiphophorus has been suggested to consist of four major lineages based on their geographical distributions and other phenotypic traits (i.e., northern platyfish, northern swordtails, southern platyfish and southern swordtails; Figure 1a) [ 2, 11, 21, 22].
Given that the most severe cases of convergent evolution occur in the dominant subtype (VIII), the use of a typing scheme that first defines major lineages based on SNPs followed by VNTR and/or additional typing methods, as has been proposed for other organisms [ 5, 9], will not substantially clarify transmission dynamics at this limited spatial scale.
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We used BEAST v.1.6.1 [ 70] to estimate divergence times among major frog lineages based on molecular data.
Our results reveal the differentiation of two major evolutionary lineages based on H2A.Z promoter sequences, one encompassing the H2A.Z-1 promoter sequences and the other including H2A.Z-2 promoter sequences.
The taxa included in the TUB analyses represented all species and major lineages found in the phylogenetic analyses based on the combined, five-locus dataset (Figure 2).
We identified three major clusters of evolutionary lineages based on how genes in various functional categories changed via gene duplication on these lineages (supplementary fig. S13 C, Supplementary Material online).
Sturmbauer et al. [ 27] defined 12 mitochondrial lineages based on a phylogenetic reconstruction using a parsimony method implemented in TCS [ 31], which have evolved in the course of two major radiations about 700 945 Ka and 399 540 Ka.
Phylogenies of major lineages of insects based on morphological and/or molecular data have sometimes been contentious, often lacking the data to distinguish between alternative evolutionary relationships [ 11- 15].
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