MATERIALS AND METHODS A. Mitochondrial sequence data (MitoFish) The mitogenomes of 3,118 fish species were downloaded on September 8, 2022, from the MitoFish database, version 3.75 (Sato et al. 2018) at http://mitofish.aori.u-tokyo.ac.jp/download.html. The mitogenomes of several sets of species were selected from this dataset, and aligned with one another using the ClustalW software (Thompson et al. 1994). Table 1 shows a list of the selected taxonomic units as well as the number of species that have mitogenomes from the MitoFish dataset. The selected taxa (containing 29–167 species each) represent groups that are between the level of order and subclass, meaning that they are above the level generally accepted as the boundary of the kind. Three lamprey species were used as the outlier species in each analysis, Lampetra aepyptera, Lampetra appendix, and Lampetra fluviatilis. B. Ecological data (FishBase) The FishBase database (Froese and Pauly 2022) was used to help in determining the ecological status of a given fish species (freshwater, brackish water, or saltwater). Data analysis on the ecological status of a given fish species was done using the R package, ‘rfishbase’, version 2.0, using the fb_tbl(“species”) command. R version 4.1.0 was used. Heatmaps were created using the ‘heatmap’ function, and Silhouette plots with the ‘fviz_nbclust’ function. The sequence similarity matrix was calculated using the ‘seqinr’ package. C. Entropy calculation Shannon entropy was used to calculate the variety of freshwater, brackish water, and saltwater species in a given cluster. Entropy was calculated using the following equation: Figure 1. Depiction of differences between anadromous, catadromous, and amphidromous lifestyles. Taxonomic unit No. of genera No. of species Acipenseriformes 6 29 Anguilliformes 38 61 Beloniformes 12 32 Characiformes 38 54 Clupeiformes 47 96 Cyprinodontiformes 20 69 Elasmobranchii 84 167 Pleuronectiformes 45 72 Salmoniformes 11 75 Table 1. Number of genera and species with mitochondrial genomes from the Mitofish database. CSERHATI Molecular baraminology of fish 2023 ICC 183
RkJQdWJsaXNoZXIy MTM4ODY=