Abstract
To understand the phylogenetic position of Larimichthys polyactis within the family Sciaenidae and the phylogeny of this family, the organization of the mitochondrial genome of small yellow croaker was determined herein. The complete, 16,470 bp long, mitochondrial genome contains 37 mitochondrial genes (13 protein-coding, 2 ribosomal RNA and 22 transfer RNA genes), as well as a control region (CR), as in other bony fishes. Comparative analysis of initiation/termination codon usage in mitochondrial protein-coding genes of Percoidei species, indicated that COI in Sciaenidae entails an ATG/AGA codon usage different from other Percoidei fishes, where absence of a typical conserved domain or motif in the control regions is common. Partitioned Bayesian analysis of 618 bp of COI sequences data were used to infer the phylogenetic relationships within the family Sciaenidae. An improvement in harmonic mean -lnL was observed when specific models and parameter estimates were assumed for partitions of the total data. The phylogenetic analyses did not support the monophyly of Otolithes, Argyrosomus, and Argyrosominae. L. polyactis was found to be most closely related to Collichthys niveatus, whereby, according to molecular systematics studies, the relationships within the subfamily Pseudosciaenidae should be reconsidered.
Highlights
Animal mitochondrial DNA, a 16-19 kb long circular molecule, comprises 37 genes encoding 22 transfer RNAs, 13 proteins, 2 ribosomal RNAs, and a putative control region (CR) (Brown, 1985; Boore, 1999)
Over recent years, the genetic characteristics of the small yellow croaker have come under investigation by means of molecular markers (Meng et al, 2003; Lin et al, 2009; Xiao et al, 2009), information is still limited, and the complete mitochondrial genome sequence, critical in studies of genome evolution and species phylogeny, continues unavailable
Pre-defined complete mitochondrial genome sequences of the small yellow croaker were compared with those reported for Percoidei species, whereupon partitioned Bayesian analysis was applied to infer the phylogeny of Sciaenidae fishes
Summary
Animal mitochondrial DNA, a 16-19 kb long circular molecule, comprises 37 genes encoding 22 transfer RNAs (tRNAs), 13 proteins, 2 ribosomal RNAs, and a putative control region (CR) (Brown, 1985; Boore, 1999). Mismodeling itself commonly occurs when a single model, inappropriate for multiple-gene regions involving several models of evolution, as stem and loop in RNA, or codon positions in protein genes, is employed for those multiple data partitions best explained by separate models of DNA evolution. Pre-defined complete mitochondrial genome sequences of the small yellow croaker were compared with those reported for Percoidei species, whereupon partitioned Bayesian analysis was applied to infer the phylogeny of Sciaenidae fishes.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
