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The elements from T. vaginalis are nested within the broad clade of eukaryotic Mutator elements.
This low degree of overlap is remarkable considering that the two species belong to the same broad clade of eukaryotes (opisthokonts).
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In the future, integrating broad clade-level comparative analyses of abiotic niche evolution with a more mechanistic understanding of the genetic basis of adaptive species differences (e.g. QTL mapping and functional studies) promises to provide substantial insights into the 'genetic architecture' of adaptation.
Based on their HVS-I motif we could group these samples into 6 broad clades, and resequenced complete mtDNA of 1-2 samples from each of those clades to assign them to a known or new haplogroups (Fig 4).
Molecular evolutionists have long recognized the prevalence of conservation of sequence via stabilizing ("purifying") selection across broad clades.
Through phylogenetic analysis of coding sequences, we found that these mtDNAs were organized into three broad clades that shared remarkable resemblance to clades constructed using the thousands of SNPs across nuclear sequences [ 4, 6], albeit at lower resolution.
Based on a total of 457 polymorphic positions across 6762 total aligned base pairs, mitochondrial sequences grouped into three broad clades.
The Arabidopsis GAUT family falls into three broad clades in which clade A is subdivided into clades A1-4, clade B into clades B 1-2, and clade C is undivided [ 46].
gambiae groups is closely related to An. bwambae, and the other is part of a broader clade that incorporates both the An.
Resolution of North American and Asian mtDNAs clades were more obscured, although each maintained distinct lineages within a broader clade.
The International Society of Genetic Genealogy [34] published a strictly cladistic Y-DNA haplogroup tree based on capital letters, in order to identify the broader clades, and a succession of numbers and letters for lower hierarchical levels, thus flexible enough to allow the unambiguous naming of haplogroups defined by newly discovered downstream markers.
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