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In general, there is little phylogenetic divergence detected in this clade.
We believe that, as more fish β2M sequences become available, reanalysis of the data may be able to better resolve the evolutionary history of the seeming ecological divergence detected among fish sequences and that of the L. calcarifer β2M gene from the rest of the β2M gene tree.
The high level of divergence detected here in the dendritic transcriptome of rats and mice might suggest the existence of species-specific RNA subcellular localization mechanisms.
Colonization of Mesoamerica by Astyanax before the final closure of the Isthmus of Panama (3.3 Mya) explains the deep level of divergence detected in Lower Central America.
High rates of sequence divergence detected in genes located at, or near, chromosomal rearrangements have often been interpreted as indirect evidence of chromosomal speciation through suppressed recombination [ 9– 16].
The conspecificity of S. coriacea, S. cichorioides, S. sachalinensis, and S. yendoana was suggested on the basis of low genetic divergence detected with ITS-1, ITS-2, RubispacerandrbcLnd rbcL sequences [ 8, 9, 11- 13, 60].
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The sequence divergences detected among these phytoseiids were much higher at the mitochondrial 12S rRNA gene locus (9.5 45%) than the nuclear rRNA internal transcribed spacer region (ITS-1, 5.8S, and ITS-2) (1.2 23%) (Navajas et al., 1999; Jeyaprakash and Hoy, unpublished).
Because of the molecular divergences detected by phylogenetic and AMOVA analyses, Migrate was run on each geographical region separately.
Both the range and the average of genetic divergences detected will vary according to the taxonomic group selected and be influenced by the phylogenetic relatedness of selected species, as well as by the number and geographical distribution of species and specimens in a data set [ 19, 28, 29, 93, 94].
Functional divergence analyses detect divergence of two proteins at particular sites and evolutionary time points but do not provide a measure of the amount of decoupled evolution between the proteins after gene duplication.
Type I functional divergence detects changes in evolutionary rates between clusters indicative of changes in constraint or selective pressure, while both the SDP algorithm and Type II functional divergence aim to identify residues that are conserved within a cluster but show a change in amino acid properties between clusters.
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