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These results are hence contrary to the expectation that C. miliaris would exhibit more structure at the mitochondrial locus than the nuclear ones and suggest that the isolation of the Easter Island population (i.e., genetic drift) alone cannot explain the observed level of divergence at MIL2 or MIL3.
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Current barcoding methods are usually based on a single mitochondrial locus, such as cytochrome c oxidase subunit I (COI).
We used Amplified Fragment Length Polymorphisms (AFLP), and sequences of two nuclear loci and one mitochondrial locus to reconstruct phylogenetic relationships.
Partial gene sequences were generated for 2 nuclear loci and 1 mitochondrial locus; Internal Transcribed Spacer 1 and 2 (ITS1 & ITS2), the protein coding Histone 3 (H3) and mitochondrial Cytochrome Oxidase I (COI).
We sequenced one mitochondrial locus and five nuclear loci in 63 specimens and obtained a robust phylogeny.
For each cell, we amplified by PCR and analyzed by gel electrophoresis the ND3 mitochondrial locus.
This phenomenon affects nuclear loci more commonly than faster evolving mitochondrial loci, but mitochondrial genes can be equally affected, particularly in closely related taxa where hardly any diversification in nuclear genes is found [ 19].
Since multiple mitochondria are present in individual organisms but display the same haplotype, mitochondrial loci are more easily detected by PCR than single-copy nuclear genes, which results in generally higher PCR sensitivities.
In combination with previously published nuclear and mitochondrial loci, this yields a data set of more than 16 kb and adds approximately 275 kb of DNA sequence to current databases.
Rather than being driven by a subset of mitochondrial loci, this correlation is significant (at P < 0.05) in 36/37 genes and is significant in 35/37 genes after correcting for DssH (table 1).
With their broader distribution and larger population sizes, Swainson's hawks are more variable than Galápagos hawks at minisatellite [ 26] and mitochondrial loci [ 22, 27].
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