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--- curation_of_phylogenomic_datasets [2023/09/19 12:21] – [Identifying xenologs] 134.190.232.90
+++ curation_of_phylogenomic_datasets [2025/03/06 11:50] (current) – 134.190.145.228
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-====== Construction and Curation of phylogenomic datasets ======
+Joran Martijn
+====== Curation of phylogenomic datasets ======
 Phylogenomic analyses attempt to use genomic data to answer phylogenetic questions. Often we're asking about the shape of a species tree. How did modern day taxa diverge over their evolutionary history? What is the deepest divergence (i.e. the root) of these taxa?
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   * if one of the pair had underwent horizontal gene transfer at some point in its evolutionary history since its divergence with the other of the pair, and the pair's common ancestor gene was present in the LCA or one of its descendants, it constitutes an **in-xenolog**. *
-Typically when we construct new phylogenomic datasets, we use similarity searches such as BLAST and DIAMOND and HMMER to generate sets of genes.
+Typically when we construct new phylogenomic datasets, we use similarity searches such as BLAST and DIAMOND and HMMER (sometimes in combination with Markov Clustering, or MCL, algorithms) to generate sets of genes.
 This is an extremly practical approach, but can be fairly rough. Genes that are truely orthologs relative to genes that were found with BLAST may be missed if similarity searches are too stringent. On the other hand, genes that are NOT true orthologs (i.e. their divergence with the genes found with BLAST //predates// the LCA) may be falsely included if similarity searches are too loose. Such false positives are typically **out-paralogs**, i.e. they diverged by a duplication in an ancestor that //predates// the LCA, or **out-xenologs** *, i.e. they were introduced into the species tree via horizontal-gene transfer from some external donor and they diverged from the other genes in a common ancestor that //predates// the LCA.
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 Be on the lookout for phylogenetic artefacts though. A gene that is in fact a regular ortholog may branch with strong support with an unrelated taxon, for example because they have similar taxonomic compositions, or they both have (independently) undergone accelerated rates of evolution. Phylogenetic artefacts can also occurr in single gene trees. We do NOT want to remove such genes. Alleviation of artefacts should be done after the phylogenomics dataset has been curated.
-  * Are situated on a long, well supported branch, that, if used for rooting the gene tree, yields an ingroup with a species tree like topology. This may indicate genes that were introduced into these taxa via horizontal gene transfer from a donor //outside// the species tree, i.e. **out-xenologs**. This pattern is pretty much identical to that of **out-paralogs** (see above). In either case, you would want to remove these genes from the phylogenomics dataset
+  * Are situated on a long, well supported branch, that, if used for rooting the gene tree, yields an ingroup with a species tree like topology. This may indicate genes that were introduced into these taxa via horizontal gene transfer from a donor //outside// the species tree, i.e. **out-xenologs**.
+This pattern is pretty much identical to that of **out-paralogs** (see above). In either case, you would want to remove these genes from the phylogenomics dataset
 * NOTE: I made the terms 'in-xenolog' and 'out-xenolog' up, but I think it makes sense.