DNA barcodes of Saudi Arabian birds: Implications for species identification and diversity analysis

Abstract

Objectives: DNA barcoding using cytochrome c oxidase I (COI) gene is an effective tool for species identification with additional power of measuring molecular diversity and phylogenetic inference. In this study, we evaluated the performance of COI gene sequences for species identification and molecular diversity analysis of some Saudi Arabian birds. Methods: We sequenced the 694 base pair segment of COI gene from 5 samples of white cheeked bulbul (Pycnonotus leucogenys), 4 samples of black scrub robin (Cercotrichas podobe), and 2 samples of crested lark (Galerida cristata), all belonged to the same Order. We also included all the COI sequences available in the GenBank for these birds with the aim of studying molecular diversity across geographies. For species identification, we enriched our dataset by including COI barcodes of other Saudi Arabian bird species, including Arabian partridge (Alectoris melanocephala), houbara bustard (Chlamydotis undulata macqueenii), green bee-eater (Merops orientalis), laughing dove (Streptopelia senegalensis), namaqua dove (Oena capensis) and collared dove (Streptopelia decaocto), representing different genera. Results: White-cheeked bulbul from Saudi Arabia showed more diversity than the same birds from Iraq. The mean nucleotide difference and nucleotide diversity were 5.20 and 0.009 respectively with as Tajima’s D score of 1.6549 indicating the scarcity of rare alleles. The specimens of black scrub robin from Saudi Arabia and Djibouti showed mixed phylogeny with only two segregating sties and a near zero Tajima’s D score indicating no major selection. Out of 18 samples of crested lark, 13 birds from 4 different geographical regions showed identical sequences, while 3 birds from Russia and 1 from Cyprus grouped in a separate cluster and 1 crusted lark from Djibouti differed from all. The mean nucleotide difference and nucleotide diversity were 0.6993 and 0.0014, while a negative Tajima’s D of −1.1956 indicated the presence of rare alleles. Phylogenetic analysis of 9 different species of Saudi Arabian birds showed the discriminatory power of COI barcodes as all the different species grouped separately in specific clusters. Conclusions: COI barcodes are not only indispensable tools for species identification but can also be used for analyzing molecular diversity and phylogenetic inference.

Keywords

• COI barcoding
• Saudi Arabian birds
• Species identification
• Molecular diversity