Karami, M. | Search bioRxiv

bioRxiv2024

DNA barcoding of passerine birds at an ornithological crossroad reveals significant East-West genetic lineage divergence

Exploring genetic diversity is essential for precise species delimitation, especially within taxonomically complex groups like passerine birds. Traditional morphological methods often fail to resolve species boundaries; however, DNA barcoding, particularly through the mitochondrial cytochrome c oxidase subunit I (COI) gene, provides a powerful alternative method for accurate species identification. This study establishes a comprehensive DNA barcode library for Iranian passerine birds, analyzing 537 COI sequences from 94 species across 23 families and 53 genera. We observed a pronounced barcode gap, with average intraspecific divergence at 0.4% and interspecific divergence at 18.6%. Notable intraspecific variation emerged in the Persian nuthatch (Sitta tephronota) and the Lesser whitethroat (Curruca curruca), while the goldfinch (Carduelis carduelis) showed limited genetic differentiation despite marked morphological distinctions. Phylogenetic analysis revealed significant east-west genetic splits in C. curruca and S. tephronota, reflecting geographic and zoogeographic boundaries of Iran. These findings demonstrate the effectiveness of DNA barcoding in elucidating biogeographic patterns, emphasizing the key role of Iran as an ornithological crossroads for avian biodiversity. Moreover, our results suggest that much of the genetic variation in the COI gene arises from synonymous mutations, highlighting the role of purifying selection in shaping mtDNA diversity across species.

zoology↗

bioRxiv2023

Designing efficient randstrobes for sequence similarity analyses

Substrings of length k, commonly referred to as k-mers, play a vital role in sequence analysis, reducing the search space by providing anchors between queries and references. However, k-mers are limited to exact matches between sequences. This has led to alternative constructs, such as spaced k-mers, that can match across substitutions. We recently introduced a class of new constructs, strobemers, that can match across substitutions and smaller insertions and deletions. Randstrobes, the most sensitive strobemer proposed in [18], has been incorporated into several bioinformatics applications such as read classification, short read mapping, and read overlap detection. Randstrobes are constructed by linking together k-mers in a pseudo-random fashion and depend on a hash function, a link function, and a comparator for their construction. Recently, we showed that the more random this linking appears (measured in entropy), the more efficient the seeds for sequence similarity analysis. The level of pseudo-randomness will depend on the hashing, linking, and comparison operators. However, no study has investigated the efficacy of the underlying operators to produce randstrobes. In this study, we propose several new construction methods. One of our proposed methods is based on a Binary Search Tree (BST), which lowers the time complexity and practical runtime to other methods for some parametrizations. To our knowledge, we are also the first to describe and study the types of biases that occur during construction. We designed three metrics to measure the bias. Using these new evaluation metrics, we uncovered biases and limitations in previous methods and showed that our proposed methods have favorable speed and sampling uniformity to previously proposed methods. Lastly, guided by our results, we change the seed construction in strobealign, a short-read mapper, and find that the results change substantially. Also, we suggest combining the two versions to improve accuracy for the shortest reads in our evaluated datasets. Our evaluation highlights sampling biases that can occur and provides guidance on which operators to use when implementing randstrobes.

bioinformatics↗