Chapter 4. COELACANTH-SPECIFIC ADAPTIVE GENES GIVE
4.2 Introduction
Coelacanth, the name derived from its characteristic hollow caudal fin, was first described in 1839 from the fossil records (Agassiz, 1844). Abundance of the fossils from the Early Devonian to the Late Cretaceous sediments implied that the fish flourished during the period. However, drastic disappearance of the post-Devonian coelacanth fossils implies that its population rapidly declined with Cretaceous–
Paleogene (K–Pg) mass extinction. Therefore, scientific community was shocked at unexpected report of living coelacanth Latimeria chalumnae in east coast of South Africa in 1938, and Latimeria menadoensis in Indonesia (Erdmann et al., 1998, Smith, n.d). Coelacanth initially gained the title ‘living fossil’ after this first observation due to its morphological similarity to its ancient form in fossil record, and the fact that it is sole survivor in Actinistia, a group mostly consisted of fossil lobe-finned fishes in Sarcopterygii. The term was considered appropriate for decades, but controversy over appropriateness of the term recently have been aroused. The morphological similarity between extant coelacanth and the fossil record had been one of the reason why coelacanth was called ‘living fossil,’ but as the diverse shape of coelacanth was reported (Friedman and Coates, 2006, Wendruff and Wilson, 2012), coelacanth's morphological conservation has become questionable. In addition, with coelacanth being observed in the diverse shape among the actinistians, it was suggested that coelacanth-specific evolution has been accumulated after the divergence from the most recent common ancestor (MRCA) of Sarcopterygii (Bockmann et al., 2013).
For all the dispute, coelacanth gives essential information to trace back the origin of tetrapod limbs, which is one of the key events influenced landing of vertebrates. Coelacanth forms a clade with lungfish and tetrapods which are classified into the sarcopterygians, sharing conserved skeletons in fleshy fins or derivative, vertebrate limbs. Coelacanth possesses a muscular lobed-fins composed with cartilages, including one homologous to humerus and femur which articulates fins to pectoral or pelvic girdle, which is an intermediate form of actinopterygians
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and tetrapods (Francillon et al., 1973). The phenotype related to water-to-land transition originates from the genetic factors shared among the sarcopterygian clade, which makes it important to analyze its genomic sequence. As lungfish turned out to be closer relative of tetrapods than coelacanth, it became more meaningful to analyze coelacanth genome to investigate the first emergence of landing-related traits different from Actinopterygii.
Comparative genomics serves as a valuable tool to find out genomic features related to common or specific traits between different species. In coelacanth, comparing common sequence shared with other vertebrates revealed genetic factors that may have adaptively evolved while the landing-related traits emerged in their MRCA. For example, island I region of the HoxD gene cluster is conserved within Sarcopterygii but not in Actinopterygii, which has indispensable role in developing autopod of mouse (Fromental-Ramain et al., 1996). Not only the island I region, but also several conserved noncoding elements (CNEs) which are located in regulatory regions of key genes for limb development such as bmp7, grem1, shh, and gli3 were reported (Nikaido et al., 2013, Zuniga et al., 2012). Especially, based on the first construction of coelacanth reference genome, the adaptation of vertebrates to land environment were determined by comparing it with other bony vertebrate genomes, such as, conserved limb enhancers in HoxD locus, amino acid differences in homeobox genes related to organism's basic body plan between coelacanth, ray- finned fishes, and tetrapods (Amemiya et al., 2013). In addition, one of the genes related to nitrogen waste metabolism which may be necessary in non-aquatic habitats, Carbamoyl phosphate synthase I (CPS1), was subjected to positive selection on branches leading to tetrapods and to amniotes, respectively (Amemiya et al., 2013).
By sorting out the type of point mutation whether synonymous or nonsynonymous, ratio between the frequency of each mutation can be calculated (dN/dS) to deduce type of selection that a gene went through (Yang and Bielawski, 2000). Synonymous substitution does not affect the phenotype, so it is free from the selective pressure and occurs at constant rate. On contrary, frequency of nonsynonymous mutation (dN) rises when the diversifying evolution takes place for
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example, by exposure to the new environment. In dolphin, positively selected genes (PSGs) enriched based on branch-site model, provided better understanding for its aquatic adaptation, like echolocation and fat storage (McGowen et al., 2012).
However, dN/dS analysis in coelacanth has been applied only to small sets of genes, such as a gene cluster or coelacanth specific retrocopies (Du and He, 2015, Zapilko and Korsching, 2016). In this study, I describe the result of genome-wide search of PSGs in coelacanth associated with this species specific adaptation to the aquatic habitat nearby the ocean floor or primordial changes of the most common ancestor of Sarcopterygii to affect landing of tetrapods. Hierarchical clustering of the discovered genes according to their biological function elucidated the group function of PSGs specific to coelacanth. In particular, I observed the genes significantly clustered into nitrogen-metabolism process which involves conversion of ammonia into urea. Moreover, through analyzing specific amino acid substitution within genes crucial to the limb development that is shared by coelacanth and tetrapods but absent in ray-finned fish lineage, this study implies the importance of these genetic features for vertebrate landing.
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