ArticleBMC genomics2013
Unsupervised genome-wide recognition of local relationship patterns.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
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- High genomic differentiation and limited gene flow indicate recent cryptic speciation within the genusFrontiers in microbiology · 2022Article
- Different Sources of Allelic Variation Drove Repeated Color Pattern Divergence in Cichlid Fishes.Molecular biology and evolution · 2021Article
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- Convergent evolution of conserved mitochondrial pathways underlies repeated adaptation to extreme environments.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Genomic evidence for gene flow between monarchs with divergent migratory phenotypes and flight performance.Molecular ecology · 2020Article
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- Local ancestry analysis reveals genomic convergence in extremophile fishes.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods.Journal of psychiatric research · 2019Article
- Genomic analysis on pygmy hog reveals extensive interbreeding during wild boar expansion.Nature communications · 2019Article
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- ACES: a machine learning toolbox for clustering analysis and visualization.BMC genomics · 2018Article
- Functional and evolutionary genomic inferences inProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Speciation in sympatry with ongoing secondary gene flow and a potential olfactory trigger in a radiation of Cameroon cichlids.Molecular ecology · 2018Article
- Article
- IntroMap: a signal analysis based method for the detection of genomic introgressions.BMC genetics · 2017Article
- PiiL: visualization of DNA methylation and gene expression data in gene pathways.BMC genomics · 2017Article
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11 authors.
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Abstract
backgroundPhenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, they must first be identified and characterised, preferably on a large scale and in an automated fashion.
resultsWe developed Saguaro, a combination of a Hidden Markov Model (HMM) and a Self Organising Map (SOM), to characterise local phylogenetic relationships among aligned sequences using cacti, matrices of pair-wise distance measures. While the HMM determines the genomic boundaries from aligned sequences, the SOM hypothesises new cacti in an unsupervised and iterative fashion based on the regions that were modelled least well by existing cacti. After testing the software on simulated data, we demonstrate the utility of Saguaro by testing two different data sets: (i) 181 Dengue virus strains, and (ii) 5 primate genomes. Saguaro identifies regions under lineage-specific constraint for the first set, and genomic segments that we attribute to incomplete lineage sorting in the second dataset. Intriguingly for the primate data, Saguaro also classified an additional ~3% of the genome as most incompatible with the expected species phylogeny. A substantial fraction of these regions was found to overlap genes associated with both the innate and adaptive immune systems.
conclusionsSaguaro detects distinct cacti describing local phylogenetic relationships without requiring any a priori hypotheses. We have successfully demonstrated Saguaro's utility with two contrasting data sets, one containing many members with short sequences (Dengue viral strains: n = 181, genome size = 10,700 nt), and the other with few members but complex genomes (related primate species: n = 5, genome size = 3 Gb), suggesting that the software is applicable to a wide variety of experimental populations. Saguaro is written in C++, runs on the Linux operating system, and can be downloaded from http://saguarogw.sourceforge.net/.
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