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An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes
- Source :
- PLoS Computational Biology, Vol 17, Iss 9, p e1008949 (2021), PLoS Computational Biology
- Publication Year :
- 2021
- Publisher :
- Public Library of Science (PLoS), 2021.
-
Abstract
- A current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new method to recover the phylogeny of haplotypes from short-read sequences obtained using pooled amplicons from a mixture of individuals, without barcoding. The method, AFPhyloMix, accepts an alignment of the mixture of reads against a reference sequence, obtains the single-nucleotide-polymorphisms (SNP) patterns along the alignment, and constructs the phylogenetic tree according to the SNP patterns. AFPhyloMix adopts a Bayesian inference model to estimate the phylogeny of the haplotypes and their relative abundances, given that the number of haplotypes is known. In our simulations, AFPhyloMix achieved at least 80% accuracy at recovering the phylogenies and relative abundances of the constituent haplotypes, for mixtures with up to 15 haplotypes. AFPhyloMix also worked well on a real data set of kangaroo mitochondrial DNA sequences.<br />Author summary In evolutionary studies, it is customary to obtain homologous sequences from different individuals in a population or a species to construct a phylogeny. Frequently, sequences from different individuals will be identical; we refer to a set of identical sequences as a haplotype. If short-read sequencing technologies are used to obtain sequences from many individuals, the sequence from each individual is tagged with a unique barcode, and a mixed sample of tagged sequences is subsequently sequenced. The tagged sequences can be identified using the appropriate bioinformatics tools, for further downstream analyses. We have developed a novel method, AFPhyloMix, to reconstruct the phylogeny of a mixed sample of homologous sequences, and the relative abundance of different haplotypes, from different individuals without the need for barcoding. AFPhyloMix aligns the short reads obtained to a reference alignment, and identifies the variable sites along the alignment. On the basis of the patterns of nucleotide frequencies at these and neighbouring sites, AFPhyloMix uses a Bayesian inference model to compute the phylogenetic tree and the haplotype relative abundances. Our results show that AFPhyloMix works well on both the simulated data set and the real data set.
- Subjects :
- 0106 biological sciences
Heredity
Single Nucleotide Polymorphisms
Biochemistry
01 natural sciences
DNA barcoding
Database and Informatics Methods
Biology (General)
Phylogeny
Data Management
0303 health sciences
Ecology
Phylogenetic tree
Nucleotides
Simulation and Modeling
Phylogenetic Analysis
Markov Chains
Phylogenetics
Genetic Mapping
Computational Theory and Mathematics
Modeling and Simulation
Sequence Analysis
Monte Carlo Method
Algorithms
Research Article
Computer and Information Sciences
Mitochondrial DNA
Bioinformatics
QH301-705.5
Nucleotide Sequencing
Genomics
Sequence alignment
Computational biology
Biology
Research and Analysis Methods
DNA, Mitochondrial
Polymorphism, Single Nucleotide
010603 evolutionary biology
03 medical and health sciences
Cellular and Molecular Neuroscience
Genetics
DNA Barcoding, Taxonomic
Humans
Evolutionary Systematics
Molecular Biology Techniques
Sequencing Techniques
Molecular Biology
Ecology, Evolution, Behavior and Systematics
Taxonomy
030304 developmental biology
Evolutionary Biology
Haplotype
Biology and Life Sciences
Bayes Theorem
Haplotypes
Mutation
Sequence Alignment
Reference genome
Subjects
Details
- ISSN :
- 15537358
- Volume :
- 17
- Database :
- OpenAIRE
- Journal :
- PLOS Computational Biology
- Accession number :
- edsair.doi.dedup.....a9ef80a6a9bd892a95c09d244ea69963