Incomplete lineage sorting
Incomplete lineage sorting is a characteristic of phylogenetic analysis where the tree produced by a single gene differs from the population or species level tree. As a result, species level tree may depend on the selected genes used for assessment. This is in contrast to complete lineage sorting, where the tree produced by the gene is the same as the population or species level tree. Both are common results in phylogenetic analysis, although it depends on the gene, organism, and sampling technique.
Incomplete lineage sorting commonly happens with sexual reproduction because the species cannot be traced back to a single person or breeding pair. When organism tribe populations are large (ie. thousands) each gene has some diversity and the gene tree consists of other pre-existing lineages. If the population is bigger these ancestral lineages are going to persist longer. When you get large ancestral populations together with closely timed speciation events these different pieces of DNA retain conflicting affiliations. This makes it hard to determine a common ancestor or points of branching.
Incomplete lineage sorting (ILS) occurs when a polymorphic ancestral species, with two or more alleles (haplotypes) at a given locus divides into two lineages. Both alleles can be retained in the descendant branches, and when one of those lineages divides again, the phylogenetic tree for that locus (the gene tree) may or may not match the branching order for the species-level evolutionary tree.
Incomplete lineage sorting is a common feature in viral phylodynamics, where the phylogeny represented by transmission of a disease from one person to the next, which is to say the population level tree, often doesn't correspond to the tree created from a genetic analysis due to the population bottlenecks that are an inherent feature of viral transmission of disease. Figure 1 illustrates how this can occur. This has relevance to criminal transmission of HIV where in some criminal cases, a phylogenetic analysis of one or two genes from the strains from the accused and the victim have been used to infer transmission; however, the commonality of incomplete lineage sorting means that transmission cannot be inferred solely on the basis of such a basic analysis.
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