Round and pointed-head grenadier fishes (Actinopterygii: Gadiformes) represent a single sister group: Evidence from the complete mitochondrial genome sequences

Abstract

The gene order of mitochondrial genomes (mitogenomes) has been employed as a useful phylogenetic marker in various metazoan animals, because it may represent uniquely derived characters shared by members of monophyletic groups. During the course of molecular phylogenetic studies of the order Gadiformes (cods and their relatives) based on whole mitogenome sequences, we found that two deep-sea grenadiers (Squalogadus modificatus and Trachyrincus murrayi: family Macrouridae) revealed a unusually identical gene order (translocation of the tRNA^{Leu (UUR)}). Both are members of the same family, although their external morphologies differed so greatly (e.g., round vs. pointed head) that they have been placed in different subfamilies Macrouroidinae and Trachyrincinae, respectively. Additionally, we determined the whole mitogenome sequences of two other species, Bathygadus antrodes and Ventrifossa garmani, representing a total of four subfamilies currently recognized within Macrouridae. The latter two species also exhibited gene rearrangements, resulting in a total of three different patterns of unique gene order being observed in the four subfamilies. Partitioned Bayesian analysis was conducted using available whole mitogenome sequences from five macrourids plus five outgroups. The resultant trees clearly indicated that S. modificatus and T. murrayi formed a monophyletic group, having a sister relationship to other macrourids. Thus, monophyly of the two species with disparate head morphologies was corroborated by two different lines of evidence (nucleotide sequences and gene order). The overall topology of the present tree differed from any of the previously proposed, morphology-based phylogenetic hypotheses.

Introduction

Since publication of the whole human mitochondrial genome (mitogenome) sequence (Anderson et al., 1981), such sequences have been determined for many vertebrates (477 species as of July 2005; National Center for Biotechnology Information [NCBI]: www.ncbi.nlm.nih.gov/genomes/ORGANELLES/7742.html). Most of these vertebrates share an identical mitochondrial gene order, although deviations from such have been reported for all major vertebrate lineages, such as amphibians (Macey et al., 1997, Sumida et al., 2001, Yoneyama, 1987), reptiles (Kumazawa and Nishida, 1995, Macey et al., 1997, Quinn and Mindell, 1996), birds (Bensch and Harlid, 2000, Desjardins and Morais, 1990, Desjardins and Morais, 1991, Mindell et al., 1998), marsupials (Janke et al., 1994, Pääbo et al., 1991), and fishes (Inoue et al., 2001c, Inoue et al., 2003, Lee and Kocher, 1995, Mabuchi et al., 2004, Miya and Nishida, 1999, Miya et al., 2001, Miya et al., 2003, Miya et al., 2005).

Much attention has been paid to processes and mechanisms that generate such a unique gene order (Boore, 1999), many systematists emphasizing the potential utility of such in phylogenetic inferences (Bensch and Harlid, 2000, Boore, 1999, Dowton et al., 2002, Inoue et al., 2001c, Kumazawa and Nishida, 1995, Kurabayashi and Ueshima, 2000, Macey et al., 1997, Morrison et al., 2002). Based on the duplication-random loss model (Macey et al., 1997, Moritz and Brown, 1987), which assumes the occurrence of tandem duplication of gene regions by a slipped-strand mispairing mechanism and subsequent deletion of genes, parallel evolution of identical gene orders in distantly related organisms is less likely because of supposed random deletion of genes from the duplicated region. Thus, along with the apparently greater conservation of the mitochondrial gene order in vertebrates, it has been suggested that the unique gene order has potential phylogenetic utility as a phylogenetic marker for the resolution of higher-level relationships among vertebrate taxa (Boore, 1999, Boore and Brown, 1998, Inoue et al., 2001c, Kumazawa and Nishida, 1995, Macey et al., 1997; but see Mindell et al., 1998).

During the course of molecular phylogenetic studies of the order Gadiformes (cods and their relatives) using mitogenomic data, we found that mitogenomes from two deep-sea grenadiers (Squalogadus modificatus and Trachyrincus murrayi) exhibited a uniquely identical gene order. Both are members of the family Macrouridae, although their external morphologies are so distinct from each other (e.g., round vs. pointed head; Figs. 1A and B) that they have been placed in different subfamilies (Macrouroidinae and Trachyrincinae; Nelson, 1994). Although recent morphological studies (Endo, 2002, Iwamoto, 1989, Nolf and Steurbaut, 1989) have suggested a closer affinity on the basis of morphological characters (Fig. 2), no additional evidence has been presented since then.

The Macrouridae also known as grenadiers or rattails are common deep demersal fishes occurring in mainly >200 m depths. They are the most diverse and best-represented of the 12 families included in Gadiformes (Nelson, 1994), with some 30 genera and about 384 species currently recognized (FishBase August 2005: www.fishbase.org). They have very unique morphologies, typified by large eyes and bodies that gradually taper from the first dorsal fin to form a long, sharp, pointed tail (Fig. 1). The family is currently classified into four subfamilies (Nelson, 1994), Bathygadinae, Macrouroidinae, Trachyrincinae, and Macrourinae, each with a characteristic body form (Fig. 1). Several morphology-based subfamilial classifications and phylogenetic hypotheses having been proposed (Fig. 2; Endo, 2002, Howes, 1989, Iwamoto, 1989, Nolf and Steurbaut, 1989, Okamura, 1989). These hypotheses differ greatly as to whether or not Macrourinae and Trachyrincinae form a sister-group relationship, and to the phylogenetic position of Bathygadinae (Figs. 2A–C). Prior to the present study, no molecular phylogenetic study had been conducted above the generic level for the macrourids (see Katsarou and Nævdal, 2001, Morita, 1999, Wilson and Attia, 2003).

This study describes the shared unique gene order in the mitogenomes of S. modificatus and T. murrayi. In addition, we sequenced the entire mitogenomes of two other species, representing a total of four macrourid subfamilies, and conducted partitioned Bayesian phylogenetic analysis to verify the phylogenetic utility of the unique gene order within the macrourids.