DNA barcoding
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https://www.allgenetics.eu/services/genomics-for-researchers/dna-metabarcoding
这个文章里面提到了一个 the generation of rarefaction curves. 曲线 要研究下这个曲线是怎么来的 -
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https://www.mdpi.com/2076-0817/11/5/486/htm
DNA Barcoding of Potential Mosquito Disease Vectors (Diptera, Culicidae) in Jazan Region, Saudi Arabia
提到了CO1标识物种 也有一些限制 某些物种准确度比较低
The COI DNA barcoding method, however, does come with its own limitations. The approach has had limited success in identifying plant and fungi species [20,21,22]. It also failed to distinguish certain mosquito species, namely Anopheles (such as Anopheles dacia and Anopheles messeae), Aedes (Aedes sticticus, Aedes cantans, Aedes geminus, Aedes cinereus, and Aedes nigrinus) Culex (Culex pipiens s.l.; pipiens, molestus and quinquefasciatus), Culiseta (Culiseta fumipennis, Culiseta litorea, and Culiseta morsitans), and two closely related species of Ochlerotatus [1,14,15,16,19,23,24]. In addition, the approach requires a comprehensive reference database for barcode comparison and matching for it to succeed [10]. Moreover, Duran et al. (2020) [25] found that tiger beetle species were frequently misidentified (24.5% of the time) when using COI barcodes, apparently due to mtDNA introgression amongst closely related species. It is worth noting that in animal mitochondrial gene trees, polyphyly is common and a taxonomically detected phenomenon [26]. The authors have significantly reviewed the major causes of mtDNA non-monophyly. Hence, an integrated approach for characterizing mosquitoes using both molecular and morphological identification is thought to be the most ideal for species identification [16].All raw sequences were manually inspected and edited using Geneious v. 9.1.3 (Biomatters, Auckland, New Zealand). Multiple sequence alignment for PCR products was performed using the BioEdit program.
Phylogenetic Analysis
ll sequences were aligned using MAFFT software with the default parameters [37]. Estimates of evolutionary divergence between sequences, and the number of base substitutions per site from between sequences were performed using the maximum composite likelihood model [38].To ensure the accuracy of the phylogenetic reconstruction, preliminary optimization steps were performed, including estimating both the pairwise distance matrix and the best-fit substitution model using the MEGAX software
The optimal substitution model was identified as the general time reversible model with gamma distribution rates (GTR + G), based on the lowest Bayesian information criterion (BIC) and Akaike information criterion (AIC) scores. The output of these optimization steps was used as input for reconstructing Bayesian phylogenetic trees using version 1.10.4 of BEAST software
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