title: Paralogous mitochondrial control region in the giant tiger shrimp, Penaeus monodon (F.) affects population genetics inference: A cautionary tale.
abstract: The mitochondrial control region (mtCR) is a widely used genetic marker for phylogenetic, phylogeographic and population genetic inference. The analysis of mtCR in 115 Indonesian specimens of the giant tiger shrimp, Penaeus monodon, revealed 26 individuals yielding a second - apparently paralogous - sequence in addition to the putatively authentic mitochondrial haplotype. The paralogous haplotypes fell into two major haplogroups that are highly diverged with respect to the authentic mitochondrial haplotypes (average pairwise sequence divergence of 12.5% and 5.0%, respectively). A comparison with published mtCR sequences of P. monodon showed that the paralogous contaminant sequences were inadvertently included in a series of recent population genetic studies, leading to seriously compromised conclusions about genetic diversity and differentiation. The prevalence of the paralogous haplotypes throughout the sampled Indo-Pacific populations is highly skewed: From African and Indian individuals only paralogs have been sequenced, while they are completely absent from Australian individuals. This suggests that geographically unequally distributed allelic variants at binding sites of the primer pair ordinarily used to amplify mtCR in P. monodon suppressed the amplification of authentic mtCR in a wide range of samples.
authors.affiliation: Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Walther
authors.forename: Gerhard
authors.initials: G
authors.lastname: Schöfl
authors.forename: Grit
authors.initials: G
authors.lastname: Mrotzek
authors.lastname: Haryanti
authors.forename: Ketut
authors.initials: K
authors.lastname: Sugama
authors.forename: Hans Peter
authors.initials: HP
authors.lastname: Saluz
mesh_terms: D000818:Animals; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000235:genetics*; D014644:Genetic Variation; D005828:Genetics, Population; D006239:Haplotypes; D007214:Indonesia; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D033561:Penaeidae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial