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
asexualmicrobes or
somatic cells,
cell lineages exactly match genetic lineages, and can be
traced.[1]
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
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]
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]