Editing Effective population size (section)

== Empirical measurements ==

In a rare experiment that directly measured genetic drift one generation at a time, in ''Drosophila'' populations of census size 16, the effective population size was 11.5.<ref>{{cite journal|last=Buri|first=P|journal=Evolution|year=1956|volume=10|issue=4|pages=367–402|title=Gene frequency in small populations of mutant Drosophila|doi=10.2307/2406998|jstor=2406998}}</ref> This measurement was achieved through studying changes in the frequency of a neutral allele from one generation to another in over 100 replicate populations.

More commonly, effective population size is estimated indirectly by comparing data on current within-species [[nucleotide diversity|genetic diversity]] to theoretical expectations. According to the [[neutral theory of molecular evolution]], an idealised diploid population will have a pairwise [[nucleotide diversity]] equal to 4<math>\mu</math>''N''<sub>''e''</sub>, where <math>\mu</math> is the [[mutation rate]]. The effective population size can therefore be estimated empirically by dividing the nucleotide diversity by 4<math>\mu</math>.<ref name="Lynch 2003" /> This captures the cumulative effects of genetic drift, genetic hitchhiking, and background selection over longer timescales. More advanced methods, permitting a changing effective population size over time, have also been developed.<ref name="Weinreich 2023">{{cite book |last1=Weinreich |first1=Daniel M. |title=The foundations of population genetics |date=2023 |publisher=The MIT Press |location=Cambridge, Massachusetts |isbn=978-0262047579}}</ref>

The effective size measured to reflect these longer timescales may have little relationship to the number of individuals physically present in a population.<ref>
{{cite journal
|title=Is the population size of a species relevant to its evolution?
|journal=Evolution
|year=2001
|volume=55
|pages=2161–2169
|doi=10.1111/j.0014-3820.2001.tb00732.x 
|author=Gillespie, JH
|pmid=11794777
|issue=11|doi-access=free
}}
</ref> Measured effective population sizes vary between genes in the same population, being low in genome areas of low recombination and high in genome areas of high recombination.<ref>{{cite journal |title=Toward a selection theory of molecular evolution|journal=Evolution|year=2008|volume=62|pages=255–265|doi=10.1111/j.1558-5646.2007.00308.x |author=Hahn, Matthew W.
|pmid=18302709|issue=2|doi-access=free}}</ref><ref>{{cite journal|title=Rethinking Hardy–Weinberg and genetic drift in undergraduate biology|journal=BioEssays|year=2012|doi=10.1002/bies.201100178|author=Masel, Joanna|author-link=Joanna Masel|pmid=22576789 |volume=34|issue=8|pages=701–10|s2cid=28513167}}</ref> Sojourn times are proportional to N in neutral theory, but for alleles under selection, sojourn times are proportional to log(N). [[Genetic hitchhiking]] can cause neutral mutations to have sojourn times proportional to log(N): this may explain the relationship between measured effective population size and the local recombination rate.<ref>{{cite journal |last1=Neher |first1=Richard A. |title=Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation |journal=Annual Review of Ecology, Evolution, and Systematics |date=23 November 2013 |volume=44 |issue=1 |pages=195–215 |doi=10.1146/annurev-ecolsys-110512-135920|arxiv=1302.1148 }}</ref>

If the [[Genetic linkage#Linkage map|recombination map]] of [[Genetic linkage#Recombination frequency|recombination frequencies]] along [[chromosome]]s is known, ''N''<sub>''e''</sub> can be inferred from ''r''<sub>P</sub><sup>2</sup> = 1 / (1+4''N''<sub>''e''</sub> ''r''), where ''r''<sub>P</sub> is the [[Pearson correlation coefficient]] between loci.<ref>{{cite journal |last1=Tenesa |first1=Albert |last2=Navarro |first2=Pau |last3=Hayes |first3=Ben J. |last4=Duffy |first4=David L. |last5=Clarke |first5=Geraldine M. |last6=Goddard |first6=Mike E. |last7=Visscher |first7=Peter M. |title=Recent human effective population size estimated from linkage disequilibrium |journal=Genome Research |date=April 2007 |volume=17 |issue=4 |pages=520–526 |doi=10.1101/gr.6023607|pmid=17351134 |pmc=1832099 |hdl=20.500.11820/b0ffcebe-9ce4-4efe-8bd9-70327945df8b |hdl-access=free }}</ref> This expression can be interpreted as the probability that two [[Lineage (genetic)|lineages]] coalesce before one allele on either lineage recombines onto some third lineage.<ref name="Weinreich 2023"></ref>

A survey of publications on 102 mostly wildlife animal and plant species yielded 192 ''N''<sub>''e''</sub>/''N'' ratios. Seven different estimation methods were used in the surveyed studies. Accordingly, the ratios ranged widely from 10<sup>''-6''</sup> for Pacific oysters to 0.994 for humans, with an average of 0.34 across the examined species. Based on these data they subsequently estimated more comprehensive ratios, accounting for fluctuations in population size, variance in family size and unequal sex-ratio. These ratios average to only 0.10-0.11.<ref name="Frankham 1995">{{Cite journal| volume = 66| pages = 95–107|author1=R. Frankham | title = Effective population size/adult population size ratios in wildlife: a review| journal = Genetics Research | year = 1995| doi = 10.1017/S0016672300034455 | issue = 2| doi-access = free}}</ref>

A genealogical analysis of human hunter-gatherers ([[Eskimo]]s) determined the effective-to-census population size ratio for haploid (mitochondrial DNA, Y chromosomal DNA), and diploid (autosomal DNA) loci separately: the ratio of the effective to the census population size was estimated as 0.6–0.7 for autosomal and X-chromosomal DNA, 0.7–0.9 for mitochondrial DNA and 0.5 for Y-chromosomal DNA.<ref name="Matsumura 2008">{{Cite journal| volume = 275| pages = 1501–1508|author1=S. Matsumura|author2=P. Forster| title = Generation time and effective population size in Polar Eskimos.| journal = Proc Biol Sci| year = 2008| doi = 10.1098/rspb.2007.1724| issue = 1642| pmid = 18364314| pmc = 2602656}}</ref>