Extent of mitochondrial DNA sequence variation in Atlantic cod from the Faroe Islands: a resolution of gene genealogy

Abstract

Variation in a 250 base pair (bp) fragment of the mitochondrial cytochrome b (cyt b) has been used extensively for population studies in Atlantic cod Gadus morhua. To study the shape of the gene genealogy and the nature of the polymorphism, sequences of another region of the cyt b gene and the TP intergenic spacer were added, making a total of 566 bp from 74 cod from the Faroe Islands. A total of 44 segregating sites defined 41 haplotypes, many at frequencies greater than 5%. Haplotype diversity was 0.97 and nucleotide diversity 0.73% per base. A topology referred to as a constellation gene genealogy was observed with four major haplotypes at high frequencies, from each of which a number of rare variants were derived. A young relative age of the haplotypes was gauged from the structure of the genealogy. The variation was mostly at synonymous sites within the coding region and thus likely to be neutral or under weak purifying selection. By comparative analysis this also applies to the TP spacer. Applying the locus to study population variation in the Faroe Islands by AMOVA revealed that the overall areas and localities within areas accounted for none of the variation, and all the variation was due to differences among individuals.

The complete mitochondrial genome of the whiting, Merlangius merlangus and the haddock, Melanogrammus aeglefinus: A detailed genomic comparison among closely related species of the Gadidae family

“…However, the recent alignment of ten gadiform mt ribosomal and cytochrome b genes has clarified some of the unresolved phylogenetic relationships, corroborating that the Gadidae is the most derived group, with the most recent genus being Gadus, Boreogadus, Merlangius, Melanogrammus and Pollachius (Bakke and Johansen, 2005). Although at the intra-specific level mtDNA genetic variation has been extensively studied in Atlantic cod (G. morhua) (Carr and Marshall, 1991;Carr et al, 1995;Arnason and Palsson, 1996;Arnason et al, 1998Arnason et al, , 2000Sigurgislason and Arnason, 2003;Arnason, 2004) very little is known on most other commercial gadoid species.…”

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

“…Early studies of hemoglobin protein markers found significant frequency differences among geographic locations (Cross & Payne, 1978; Frydenberg, Møller, Nævdal, & Sick, 1965; Gjøsæter, Jørstad, Nævdal, & Thorkildsen, 1992; Møller, 1968; Sick, 1965a,b), although selection and temperature differences have since explained many of these results (Jamieson & Birley, 1989; Mork & Sundnes, 1985). Trans‐Atlantic differences are evident in protein loci (Jamieson, 1967; Mork, Ryman, Ståhl, Utter, & Sundnes, 1985), mitochondrial cytochrome b (Carr & Marshall, 1991a; Sigurgíslason & Árnason, 2003), and nuclear DNA markers (Pogson, Mesa, & Boutilier, 1995), although results at local scales remain ambiguous. Extensive mtDNA analyses have found little or no structure in waters off the coasts of eastern North America (Carr, Snellen, Howse, & Wroblewski, 1995), Iceland (Árnason, Pálsson, & Arason, 1992; Árnason, Petersen, Kristinsson, Sigurgíslason, & Pálsson, 2000), the Faroe Islands (Sigurgíslason & Árnason, 2003), Norway (Árnason & Pálsson, 1996), and the Baltic Sea (Árnason, Petersen, & Pálsson, 1998).…”

“…Trans‐Atlantic differences are evident in protein loci (Jamieson, 1967; Mork, Ryman, Ståhl, Utter, & Sundnes, 1985), mitochondrial cytochrome b (Carr & Marshall, 1991a; Sigurgíslason & Árnason, 2003), and nuclear DNA markers (Pogson, Mesa, & Boutilier, 1995), although results at local scales remain ambiguous. Extensive mtDNA analyses have found little or no structure in waters off the coasts of eastern North America (Carr, Snellen, Howse, & Wroblewski, 1995), Iceland (Árnason, Pálsson, & Arason, 1992; Árnason, Petersen, Kristinsson, Sigurgíslason, & Pálsson, 2000), the Faroe Islands (Sigurgíslason & Árnason, 2003), Norway (Árnason & Pálsson, 1996), and the Baltic Sea (Árnason, Petersen, & Pálsson, 1998). In contrast, microsatellite studies suggest range‐wide isolation by distance (O'Leary, Coughlan, Dillane, McCarthy, & Cross, 2007), and significant structure in waters off North America (e.g., Flemish cap, Bentzen, Taggart, Ruzzante, & Cook, 1996; inshore vs. offshore, Ruzzante, Taggart, Cook, & Goddard, 1996; Arctic populations, Hardie, Gillett, & Hutchings, 2006), Norway (Knutsen, Jorde, André, & Stenseth, 2003), and the North Sea (Hutchinson, Carvalho, & Rogers, 2001).…”

Complete mitochondrial genome sequences of the Arctic Ocean codfishes Arctogadus glacialis and Boreogadus saida reveal oriL and tRNA gene duplications

“…In addition, extensive partial mtDNA sequences were reported recently by Carr and coworkers for an additional Wve Gadidae species (Coulson et al 2006). Several of the Gadidae species have been investigated in phylogenetic (Carr et al 1999;Møller et al 2002;Johansen 2002, 2005;Coulson et al 2006;Teletchea et al 2006;Ursvik et al 2007) or population studies (Shields and Gust 1995;Sigurgislason and Arnason 2003;Arnason 2004;Yanagimoto et al 2004) based on mtDNA sequences. These reports show that the Gadidae Wshes are typically characterized by a monophyletic evolutionary origin and a low-level geographic structuring of mitochondrial genotypes.…”