lineage (genetic)#Basal lineage
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.{{cite journal |last1=Levy |first1=Sasha F. |last2=Blundell |first2=Jamie R. |last3=Venkataram |first3=Sandeep |last4=Petrov |first4=Dmitri A. |last5=Fisher |first5=Daniel S. |last6=Sherlock |first6=Gavin |title=Quantitative evolutionary dynamics using high-resolution lineage tracking |journal=Nature |date=March 2015 |volume=519 |issue=7542 |pages=181–186 |doi=10.1038/nature14279|pmid=25731169 |pmc=4426284 |bibcode=2015Natur.519..181L }}
Incomplete lineage sorting
{{main|Incomplete lineage sorting}}
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.{{cite journal |last1=Rivas-González |first1=Iker |last2=Rousselle |first2=Marjolaine |last3=Li |first3=Fang |last4=Zhou |first4=Long |last5=Dutheil |first5=Julien Y. |last6=Munch |first6=Kasper |last7=Shao |first7=Yong |last8=Wu |first8=Dongdong |last9=Schierup |first9=Mikkel H. |last10=Zhang |first10=Guojie |title=Pervasive incomplete lineage sorting illuminates speciation and selection in primates |journal=Science |date=2 June 2023 |volume=380 |issue=6648 |doi=10.1126/science.abn4409|pmid=37262154 }}
Lineage selection
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.{{cite journal |last1=Graves |first1=Christopher J. |last2=Weinreich |first2=Daniel M. |title=Variability in Fitness Effects Can Preclude Selection of the Fittest |journal=Annual Review of Ecology, Evolution, and Systematics |date=2 November 2017 |volume=48 |issue=1 |pages=399–417 |doi=10.1146/annurev-ecolsys-110316-022722|pmid=31572069 |pmc=6768565 }}{{Cite journal|title=Lineage Selection and the Maintenance of Sex|journal=PLOS ONE|volume=8 |issue=6e66906|doi=10.1371/journal.pone.0066906|pmid=23825582|pages=e66906|year = 2013|last1 = De Vienne|first1 = Damien M.|last2 = Giraud|first2 = Tatiana|last3 = Gouyon|first3 = Pierre-Henri|pmc = 3688966|bibcode=2013PLoSO...866906D|doi-access=free}} Lineage selection is also useful in determining the effects of mutations in highly structured environments such as tumors.{{Cite journal|last=Nunney|first=Leonard|date=1999-03-07|title=Lineage selection and the evolution of multistage carcinogenesis|journal=Proceedings of the Royal Society of London B: Biological Sciences|language=en|volume=266|issue=1418|pages=493–498|doi=10.1098/rspb.1999.0664|issn=0962-8452|pmc=1689794|pmid=10189713}}
Long-term stochastic outcomes of competition among lineages can be quantified within mathematical models as the ratio of fixation probability : counterfixation probability.{{cite journal |last1=King |first1=Oliver D. |last2=Masel |first2=Joanna |title=The evolution of bet-hedging adaptations to rare scenarios |journal=Theoretical Population Biology |date=December 2007 |volume=72 |issue=4 |pages=560–575 |doi=10.1016/j.tpb.2007.08.006|pmid=17915273 |pmc=2118055 }} Inclusive fitness is equal to the average organismal fitness of individuals across the probability distribution of possible lineages.{{Cite journal|last1=Akçay|first1=Erol|last2=Van Cleve|first2=Jeremy|date=2016-02-05|title=There is no fitness but fitness, and the lineage is its bearer|journal=Phil. Trans. R. Soc. B|language=en|volume=371|issue=1687|pages=20150085|doi=10.1098/rstb.2015.0085|issn=0962-8436|pmc=4760187|pmid=26729925}}
Tree sequence recording
Tree sequence recording describes efficient methods to record surviving lineages while conducting computer simulations of population genetics.{{cite journal |last1=Kelleher |first1=Jerome |last2=Thornton |first2=Kevin R. |last3=Ashander |first3=Jaime |last4=Ralph |first4=Peter L. |title=Efficient pedigree recording for fast population genetics simulation |journal=PLOS Computational Biology |date=1 November 2018 |volume=14 |issue=11 |pages=e1006581 |doi=10.1371/journal.pcbi.1006581|doi-access=free |pmid=30383757 |pmc=6233923 |bibcode=2018PLSCB..14E6581K }} 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.{{cite journal |last1=Haller |first1=Benjamin C. |last2=Galloway |first2=Jared |last3=Kelleher |first3=Jerome |last4=Messer |first4=Philipp W. |last5=Ralph |first5=Peter L. |title=Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes |journal=Molecular Ecology Resources |date=March 2019 |volume=19 |issue=2 |pages=552–566 |doi=10.1111/1755-0998.12968|pmc=6393187 }}
Sexual lineages compared to asexual lineages
Sexual reproduction is the most common form of reproduction in the genetic lineages of multicellular organisms, and a complete lack of sexual reproduction is relatively rare among such organisms, particularly animals. Sexual reproduction appears to have emerged very early in the evolution of eukaryotes implying that the essential features of meiosis were already present in the earliest eukaryotic genetic lineage.{{cite journal | last=Dacks | first=Joel | last2=Roger | first2=Andrew J. | title=The First Sexual Lineage and the Relevance of Facultative Sex | journal=Journal of Molecular Evolution | volume=48 | issue=6 | date=1999 | issn=0022-2844 | doi=10.1007/PL00013156 | pages=779–783 | PMID = 10229582 | s2cid = 9441768 | bibcode=1999JMolE..48..779D}}{{cite journal | last=Bernstein | first=Harris | last2=Bernstein | first2=Carol | title=Evolutionary Origin of Recombination during Meiosis | journal=BioScience | volume=60 | issue=7 | date=2010-08-01 | issn=1525-3244 | doi=10.1525/bio.2010.60.7.5 | pages=498–505 | s2cid = 86663600}}
Among eukaryotes, almost all lineages with asexual modes of reproduction maintain meiosis either in a modified form or as an alternative pathway.Hörandl, Elvira; Hadacek, Franz (2013). "The oxidative damage initiation hypothesis for meiosis". Plant Reproduction. 26 (4): 351–367. {{doi|10.1007/s00497-013-0234-7}}, {{PMC|3825497}}, {{PMID|23995700}} A constraint on a meiotic sexual lineage undergoing switching to an ameiotic, asexual form of reproduction appears to be the concomitant loss of the protective recombinational repair of DNA damage that is a key function of meiosis.Bernstein, H.; Hopf, F.A.; Michod, R.E. (1987). "The Molecular Basis of the Evolution of Sex". Molecular Genetics of Development. Advances in Genetics. Vol. 24. pp. 323–70. {{doi|10.1016/s0065-2660(08)60012-7}}, {{ISBN|9780120176243}}, {{PMID|3324702}}Avise, J. (2008) Clonality: The Genetics, Ecology and Evolution of Sexual Abstinence in Vertebrate Animals. See pp. 22-25. Oxford University Press. {{ISBN|978-0-19-536967-0}}