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Lineage (genetic)

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A genetic lineage includes all descendants of a given genetic sequence, typically following a new mutation. It is not the same as an allele because it excludes cases where different mutations give rise to the same allele, and includes descendants that differ from the ancestor by one or more mutations. The genetic sequence can be of different sizes, e.g. a single gene or a haplotype containing multiple adjacent genes along a chromosome. Given recombination, each gene can have a separate genetic lineages, even as the population shares a single organismal lineage. In asexual microbes or somatic cells, cell lineages exactly match genetic lineages, and can be traced.[1]

Incomplete lineage sorting

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Main article: Incomplete lineage sorting
Figure 1. Incomplete lineage sorting. The gene G has two versions (alleles), G0 and G1. The ancestor of A, B and C originally had only one version of gene G, G0. At some point, a mutation occurred and the ancestral population became polymorphic, with some individuals having G0 and others G1. When species A split off, it retained only G1, while the ancestor of B and C remained polymorphic. When B and C diverged, B retained only G1 and C only G0; neither were now polymorphic in G. The tree for gene G shows A and B as sisters, whereas the species tree shows B and C as sisters.

Incomplete lineage sorting describes when the phylogenetic tree for a gene does not match that of the species. For example, while most human gene lineages coalesce first with chimpanzee lineages, and then with gorilla lineages, other configurations also occur.[2]

Lineage selection

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Lineage selection occurs when the frequency of members of one lineage changes relative to another lineage. It is useful for studying alleles with complex effects that play out over multiple generations, e.g. alleles that affect recombination, evolvability, or altruism.[3][4] Lineage selection is also useful in determining the effects of mutations in highly structured environments such as tumors.[5]

Long-term stochastic outcomes of competition among lineages can be quantified within mathematical models as the ratio of fixation probability : counterfixation probability.[6] Inclusive fitness is equal to the average organismal fitness of individuals across the probability distribution of possible lineages.[7]

Tree sequence recording

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Tree sequence recording describes efficient methods to record surviving lineages while conducting computer simulations of population genetics.[8] Resulting 'forward time' computer simulations offer an alternative to 'backward time' coalescent theory. Tree sequence recording has been incorporated into the population simulation software SLiM.[9]

References

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  1. ^ Levy, Sasha F.; Blundell, Jamie R.; Venkataram, Sandeep; Petrov, Dmitri A.; Fisher, Daniel S.; Sherlock, Gavin (March 2015). "Quantitative evolutionary dynamics using high-resolution lineage tracking". Nature. 519 (7542): 181–186. Bibcode:2015Natur.519..181L. doi:10.1038/nature14279. PMC 4426284. PMID 25731169.
  2. ^ Rivas-González, Iker; Rousselle, Marjolaine; Li, Fang; Zhou, Long; Dutheil, Julien Y.; Munch, Kasper; Shao, Yong; Wu, Dongdong; Schierup, Mikkel H.; Zhang, Guojie (2 June 2023). "Pervasive incomplete lineage sorting illuminates speciation and selection in primates". Science. 380 (6648). doi:10.1126/science.abn4409. PMID 37262154.
  3. ^ Graves, Christopher J.; Weinreich, Daniel M. (2 November 2017). "Variability in Fitness Effects Can Preclude Selection of the Fittest". Annual Review of Ecology, Evolution, and Systematics. 48 (1): 399–417. doi:10.1146/annurev-ecolsys-110316-022722. PMC 6768565. PMID 31572069.
  4. ^ De Vienne, Damien M.; Giraud, Tatiana; Gouyon, Pierre-Henri (2013). "Lineage Selection and the Maintenance of Sex". PLOS ONE. 8 (6e66906): e66906. Bibcode:2013PLoSO...866906D. doi:10.1371/journal.pone.0066906. PMC 3688966. PMID 23825582.
  5. ^ Nunney, Leonard (1999-03-07). "Lineage selection and the evolution of multistage carcinogenesis". Proceedings of the Royal Society of London B: Biological Sciences. 266 (1418): 493–498. doi:10.1098/rspb.1999.0664. ISSN 0962-8452. PMC 1689794. PMID 10189713.
  6. ^ King, Oliver D.; Masel, Joanna (December 2007). "The evolution of bet-hedging adaptations to rare scenarios". Theoretical Population Biology. 72 (4): 560–575. doi:10.1016/j.tpb.2007.08.006. PMC 2118055. PMID 17915273.
  7. ^ Akçay, Erol; Van Cleve, Jeremy (2016-02-05). "There is no fitness but fitness, and the lineage is its bearer". Phil. Trans. R. Soc. B. 371 (1687): 20150085. doi:10.1098/rstb.2015.0085. ISSN 0962-8436. PMC 4760187. PMID 26729925.
  8. ^ Kelleher, Jerome; Thornton, Kevin R.; Ashander, Jaime; Ralph, Peter L. (1 November 2018). "Efficient pedigree recording for fast population genetics simulation". PLOS Computational Biology. 14 (11): e1006581. Bibcode:2018PLSCB..14E6581K. doi:10.1371/journal.pcbi.1006581. PMC 6233923. PMID 30383757.
  9. ^ Haller, Benjamin C.; Galloway, Jared; Kelleher, Jerome; Messer, Philipp W.; Ralph, Peter L. (March 2019). "Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes". Molecular Ecology Resources. 19 (2): 552–566. doi:10.1111/1755-0998.12968. PMC 6393187.
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