DNA barcoding and phylogeny of Calidris and Tringa (Aves: Scolopacidae)

Abstract

The avian genera Calidris and Tringa are the largest of the widespread family of Scolopacidae. The phylogeny of members of the two genera is still a matter of controversial. Mitochondrial cytochrome c oxidase subunit I (COI) can serve as a fast and accurate marker for the identification and phylogeny of animal species. In this study, we analyzed the COI barcodes of thirty-one species of the two genera. All the species had distinct COI sequences. Two hundred and twenty-one variable sites were identified. Kimura two-parameter distances were calculated between barcodes. Neighbor-joining and maximum likelihood methods were used to construct phylogenetic trees. All the species could be discriminated by their distinct clades in the phylogenetic trees. The phylogenetic trees grouped all the species of Calidris and Tringa into different monophyletic clade, respectively. COI data showed a well-supported phylogeny for Calidris and Tringa species.

DNA Barcode of Seven Indonesian Hornbills Species (Aves: Bucerotidae) Based on Mitochondrial DNA Cytochrome Oxidase Subunit I

“…Average genetic distance within species was ranged from 0.002 (0.2%) to 0.008 (0.8%), within genus 0.045 (4.5%), and within family 0.046 (4.6%) (Table 5). Genetic distance distinguishing within species were lower than those learnt from previous studies (Yoo et al 2006;Astuti and Sulandari 2010;Huang and Tu 2016); yet, it remains the same on genus and 184 Jarulis et al et al (2004), Kerr et al (2007), Astuti and Sulandari (2010), and Huang and Tu (2016). Genetic distance within species is usually less than 1% and infrequently reaching more than 2% (Waugh 2007), as seen in average genetic distance within species of Korean birds and Phasianidae as much as 0.3% (Yoo et al 2006;Cai et al 2010), in Neotropical birds which ranged between 0 to 13.7% (Tavares et al 2011) and in parrots that ranged from 0.1 to 0.7% (Gonçalves et al 2015).…”

“…In our research, the COI gene was successfully amplified into the length of 746 bp. It is longer than the one suggested for DNA barcode purpose (Hebert et al 2004;Hajibabaei et al 2006;Prehadi et al 2015;Huang and Tu 2016 We presented similarity scores of 31 hornbill individuals examined with BoLD System in Table 3 where each individual paired with the three hornbills in out-group and ranked according to the degree of its similarity. Five hornbill species fell within those ranges, they are Penelopides panini, Aceros waldeni, A. coronatus, Rhabdotorrhinus (Aceros) corrugatus, and R. leucocephalus.…”

“…The genetic distance to accurately identify species should be above 5% (Waugh 2007). Huang and Tu (2016) reported the mean divergence of the COI gene within genus in Ardeidae was 13.08%; 8.2% within genera of Korean birds (Yoo et al 2006); 4.8-15.6% within Thamnophilidae (Passeriformes) (Vilaça et al 2006); 5.35% on Phasianidae (Cai et al 2010); 7.95% on Scandinavian birds (Johnsen et al 2010); and 9.52% on Green Bee-eater (Merops orientalis) (Arif et al 2011). Genetic distance within Bucerotidae family 0.046 (4.6%), which is lower than what found in previous studies (Table 6).…”

“…Sequence diversity of COI genes (648 bp) retains potential use for identification on species level, as well as having function as DNA barcode (Hebert et al 2003a, b;Hebert and Gregory 2005). DNA barcoding based on COI has been successful in species determination and phylogeny across animal species (Huang and Tu 2016), as well proven satisfied on animal identification (Hajibabaei et al 2006).…”

DNA Barcode of Mountain White-Eye Zosterops montanus (Aves: Zosteropidae) Based on Mitochondrial DNA Cytochrome Oxidase Sub Unit I

“…The minimum genetic distance between (Zosterops and Yuhina) of the Zosteropidae family is 0.117 (11.7%), the maximum is 0.140 (14%) and the average is 0.125 (12.5%). This study is in line with the research of Huang and Tu, which found that the average difference in the COI gene in the genus Ardeidae was 13.08% [28] and Yoo et al in the Korean bird genera 8.2% [29]. Based on genetic distance, Z. montanus from Bengkulu has different species from 6 other Zosterops and 5 Yuhina.…”