DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria

Abstract

Within Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering at 100% bootstrap value including monophyletic ones were identified. The phylogenetic diversity (PD) ranged from 0.0397 (Synodontis obesus) to 0.2147 (Parachanna obscura). The highest percentage of genetic distance based on Kimura 2-parameter was 37.00 ± 0.0400. Intergeneric distances ranged from 15.8000 to 37.0000%. Congeneric distances were 6.9000 ± 0.0140–28.1000 ± 0.0380, with Synodontis as the existing synonymous genus. Confamilial distances in percentage were 16.0000 ± 0.0140 and 25.7000 ± 0.0300. Forty-two haplotypes and haplotype diversity of 0.9990 ± 0.0003 were detected. Nucleotide diversity was 0.7372, while Fu and Li’s D* test statistic was 2.1743 (P < 0.02). Tajima’s D was 0.2424 (P > 0.10) and nucleotide frequencies were C (17.70%), T (29.40%), A (24.82%), G (18.04%) and A + T (54.22%). Transitional mutations were more than transversions. Twenty species (99–100%) were identified with the e-value, maximum coverage and bit-score of 1e−43, 99–100 and 185–1194, respectively. Seventeen genera and 12 families were found and Clariidae (n = 14) was the most dominant among other families. The fish species resolution, diversity assessment and phylogenetic relationships were successfully obtained with the COI marker. Clariidae had the highest number of genera and families. Phylogenetic diversity analysis identified Parachanna obscura as the most evolutionarily divergent one. This study will contribute to fishery management, and conservation of freshwater fishes in Enugu and Anambra States, Nigeria.

Penentuan Jenis dan Status Konservasi Pari Layang-Layang yang Didaratkan Di TPI Gunung Lingkas Kota Tarakan Dengan Pendekatan Molekuler

“…Konsistensi hasil pohon filogenetik diukur dengan tiga metode analisis yaitu Neighbor-Joining (NJ) [14,18,19,20], Maximum Likelihood (ML) [14,20], dan Minimum Evolution (ME) [14,[18][19][20][21][22] dengan boostrap test masing-masing 1000 kali pengulangan dan jarak evolusi dihitung dengan metode Kimura-2-parameter (K2P). Jarak diversitas genetik juga dihitung dengan metode K2P yang telah terintegrasi dalam aplikasi MEGA versi X [23]. Informasi dari database BOLD dilaporkan terdapat 26 data sekuen G. zonura yang tersimpan di dalam sistem, 15 di antaranya bersifat publik dan sisanya bersifat pribadi (unpublished).…”

Advancing traceability using DNA sequence on seafood product: fraudulence in shrimp crackers

“…Meanwhile, the genetic distances of KU XIV and other DNA samples are large due to inter-species variability. This inter-species variability is responsible for large genetic distance values as shown by Ude et al (2020).…”

Molecular characterization of Malapterurus minjiriyaSagua, 1987 and phylogenetic relationships within the genus Malapterurus (Silurifomes, Malapteruridae) from Nigerian inland water bodies

“…Correct identification of morphologically similar species is essential for fisheries management and biodiversity documentation (Amanda & Luciane, 2010). Recent studies on Nigerian freshwater fishes showed that genetic data, in combination with morphological data, could aid accurate and unambiguous identification of the fish species (Nneji et al ., 2020; Oladipo et al ., 2020; Uden et al ., 2020). The application of molecular tools, involving mitochondrial cytochrome c oxidase subunit I ( COI ), has contributed significantly to fish systematics (Iyiola et al ., 2018; Nwani et al ., 2011; Oladipo et al ., 2020).…”

“…Currently, DNA barcoding has been advocated as a useful tool for the species identification of various life stages and identification of hidden diversity (Iyiola et al ., 2018; Nneji et al ., 2020; Ward et al ., 2005). Further, the mitochondrial COI gene has been used in elucidating phylogenetic relationships between and within fish species (Iyiola et al ., 2018; Nneji et al ., 2020; Uden et al ., 2020).…”