Abstract Eight whole mitochondrial genomes from the barnacle Notochthamalus scabrosus, with one from the northern lineage and seven from the divergent southern lineage, are presented. The annotated and aligned data were analyzed for signals of non-neutral evolution. Overall, these data are consistent with purifying selection operating on the protein-coding regions of the mitochondrion. However, a notable region of nonsynonymous substitution at the 3' end of the ND2 gene region, along with unusual site frequency spectra in two other gene regions, was identified.
"The lengths of srRNA and lrRNA are 825 and 1306 bp, respectively, which are similar to values in the other barnacle mitochondrial genomes (Shen et al., 2014a; Tsang et al., 2014c; Wares, 2015). The two rRNAs, located between trnL 1 and the control region, are separated by one tRNA gene (trnV) (Fig. 1; Table 2). "
"To identify potential regions on the easily-sequenced mitochondrial locus, a single individual of A. fragilis (AS1943, collected in the Upper Florida Keys and detailed in Meyers, Porter & Wares (2013)) was shotgun sequenced with a single Illumina MiSeq library preparation as in Wares (2013). Resultant single-end 250nt reads were trimmed and mapped to the A. humilis mitochondrial genome (GenBank DQ643831) using Geneious 7.1.4 "
[Show abstract][Hide abstract] ABSTRACT: There are well-known difficulties in using the cytochrome oxidase I (COI) mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promising gene regions for species delineation. I assembled the whole mitochondrial genome for Agaricia fragilis from Illumina single-end 250 bp reads and compared this sequence to that of the congener A. humilis. Although these data suggest that the cytochrome b (CYB) gene region is more promising, comparison of available CYB sequence data from scleractinian and other reef-building corals indicates that multilocus approaches are still probably necessary for phylogenetic and population genetic analysis of recently-diverged coral taxa.
"With the data here representing a much larger number of markers from the nuclear genome, it is clear that either the mitochondrial cline represents selection on divergent mitotypes, which has been observed in other marine systems (Schizas et al. 2001, 2002), or the phylogeographic diversity of the nuclear genome will be clarified with sampling of individuals further to the south than in this study, or both. We have recently discovered that the southern mitochondrial lineage is fixed for the B mitotype in populations at the southern end of Argentina (Wares 2013; J. P. Wares, unpublished data). It is likely that the region between the southernmost samples represented in the current data set and our collection from southern Argentina will identify further diversity, and perhaps divergence, in the nuclear genome . "
[Show abstract][Hide abstract] ABSTRACT: A mitochondrial cline along the Chilean coast in the barnacle Notochthamalus scabrosus suggests a species history of transient allopatry and secondary contact. However, previous studies of nuclear sequence divergence suggested population genetic homogeneity across northern and central Chile. Here we collect SNP data from pooled population samples sequenced with RAD-seq procedures, confirm these data using a GoldenGate array, and identify a discordance between population genetic patterns in the nuclear and mitochondrial genomes. This discordance was noted in previous work on this species, but here it is confirmed that the nuclear genome exhibits only slight phylogeographic variation across 3000km of coastline, in the presence of a strong and statistically significant mitochondrial cline. There are nevertheless markers (approximately 5% of nuclear SNPs) exhibiting cytonuclear disequilibrium relative to mitotype. Although these data confirm our previous explorations of this species, it is likely that some of the nuclear genomic diversity of this species has yet to be explored, as comparison with other barnacle phylogeography studies suggest that a divergence of similar magnitude should be found in the nuclear genome somewhere else in the species range.
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