Comparative Mitogenomics Reveals Cryptic Species in Sillago ingenuua McKay, 1985 (Perciformes: Sillaginidae)

Abstract

It is unreliable to identify marine fishes only by external morphological features. Species misidentification brings great challenges to fishery research, resource monitoring and ecomanagement. Sillago ingenuua is an important part of commercial marine fishes, and in which, the morphological differences between different groups are not obvious. Here, we compared different geographical groups of S. ingenuua which were collected from Xiamen, Dongshan, Keelung, Songkhla and Java. The results showed that all samples of S. ingenuua were similar in external morphological characteristics and the shape of the swim bladder, but there were two distinctive lineages which were flagged as cryptic species based on DNA barcoding. The comparative mitogenomic results showed that S. ingenuua A and S. ingenuua B were identical in structural organization and gene arrangement. Their nucleotide composition and codon usage were also similar. A phylogenetic analysis was performed based on 13 concatenated PCGs from eight Sillago species. The results showed that the genetic distance between S. ingenuua A and S. ingenuua B was large (D = 0.069), and this genetic distance was large enough to reveal that S. ingenuua A and S. ingenuua B might be different species.

Keywords: Sillago ingenuua; cryptic species; genetic divergence; genome features; morphological consistency.

Figure 1

Sampling locations of S. ingenuua.

Figure 2

Swim bladders of S. ingenuua (collected from (A) Dongshan; (B) Java; (C) Keelung).

Figure 3

NJ tree for 32 COI sequences of S. ingenuua.

Figure 4

Gene organization for the mitogenomes of S. ingenuua A and S. ingenuua B. The structural organization and gene arrangement of S. ingenuua A and S. ingenuua B are identical; only the gene organization of S. ingenuua A is shown. Red regions represent tRNAs, yellow regions represent rRNAs, black regions represent PCGs and brown region represents CR.

Figure 5

Frequencies of codons ending with the same nucleotide in H-strand. Y-axis represents the percentage of relative synonymous codon usage (RSCU) values of codons ending with the same nucleotide, and the X-axis represents all codon families.

Figure 6

The main characteristics of mitochondrial control regions of S. ingenuua A (A) and S. ingenuua B (B). Termination-associated sequence (TAS), central conserved sequences (CSB-F, -E, -D, -C) and sequence blocks (CSB-1, -2, -3) were identified.

Figure 7

Inferred phylogenetic relationships among Sillago based on the concatenated nucleotide sequences of 13 mitochondrial protein-coding genes using maximum likelihood (ML) and Bayesian inference (BI). Numbers on branches are bootstrap percentages and Bayesian posterior probabilities. L. crocea (NC_011710) and T. jarbua (NC_027281) are outgroups.