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This latter scenario, the "naked coral" hypothesis, is strongly supported by analyses based on mitochondrial (mt) protein sequences, whereas the former is equally strongly supported by analyses of mt nucleotide sequences.
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Dr. Wallace's tree is based on mitochondrial DNA, tiny rings of genetic material that are bequeathed only by the egg cell and thus through the maternal line.
Such trees were drawn up by Dr. Wallace and others, based on mitochondrial DNA, and more recently by Dr. Underhill and his colleagues, based on mutations they found in the Y chromosome.
The two alleles from the European D. pulex isolate are the sister group to all the other members of the pulex species complex, which is concordant with the phylogeny based on mitochondrial (mt DNA ([ 25], Figure 2).
We thus present data based on mitochondrial DNA alone.
We performed the first phylogeographic study of the genus Orcula based on comprehensive mitochondrial (mt) and nuclear (nc) data sets including material of all 13 species.
Finally, Van Buren et al. [16] used simulations of MT growth to estimate Elong based on measured MT growth speeds.
The study was based on both mt data and directly PCR amplified introns of nuclear genes.
Despite its popularity, phylogenetic inference based on complete mt genomes has important analytical challenges.
One is the attachment of astral MTs to bivalent kinetochores, called the search-and-capture model and is based on the MT dynamic instability (Section 2.1.2).
Phylogenetic analyses based on complete mt genome data resolved a higher number of internal branches of the caenogastropod tree than individual mt genes.
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