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Figure 1. The pretransmission interval and incomplete lineage sorting in the phylogeny of a human-transmissible virus. The shaded tree represents a transmission chain where each region represents the pathogen population in each of three patients. The width of the shaded regions corresponds to the genetic diversity. In this scenario, A infects B with an imperfect transmission bottleneck, and then B infects C. The genealogy at the bottom is reconstructed from a sample of a single lineage from each patient at three distinct time points. When diversity exists in donor A, a pre-transmission interval will occur at each inferred transmission event (MRCA(A,B) precedes transmission from A to B), and the order of transmission events may become randomized in the virus genealogy. Note that the pre-transmission interval also is a random variable defined by the donor’s diversity at time of each transmission. Terminal branch lengths are also elongated due to these processes.

Incomplete lineage sorting[1][2][3] 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.[4][5] 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.


In diploid organismsEdit

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.[4]

In virusesEdit

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.[6]

See alsoEdit


  1. ^ Simpson, Michael G (2010-07-19). Plant Systematics. ISBN 9780080922089.
  2. ^ Kuritzin, A; Kischka, T; Schmitz, J; Churakov, G (2016). "Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data". PLOS Computational Biology. 12 (3): e1004812. Bibcode:2016PLSCB..12E4812K. doi:10.1371/journal.pcbi.1004812. PMC 4788455. PMID 26967525.
  3. ^ Suh, A; Smeds, L; Ellegren, H (2015). "The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds". PLOS Biology. 13 (8): e1002224. doi:10.1371/journal.pbio.1002224. PMC 4540587. PMID 26284513.
  4. ^ a b Rogers, Jeffrey; Gibbs, Richard A. (2014-05-01). "Comparative primate genomics: emerging patterns of genome content and dynamics". Nature Reviews Genetics. 15 (5): 347–359. doi:10.1038/nrg3707. PMC 4113315. PMID 24709753.
  5. ^ Shen, Xing-Xing; Hittinger, Chris Todd; Rokas, Antonis (2017). "Contentious relationships in phylogenomic studies can be driven by a handful of genes". Nature Ecology & Evolution. 1 (5). doi:10.1038/s41559-017-0126. ISSN 2397-334X. PMC 5560076. PMID 28812701.
  6. ^ Leitner, Thomas (May 2019). "Phylogenetics in HIV transmission: taking within-host diversity into account". Current Opinion in HIV and AIDS. 14 (3): 181. doi:10.1097/COH.0000000000000536. ISSN 1746-630X.

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