Editing Directional selection (section)

=== Detection methods ===
Directional selection most often occurs during environmental changes or population migrations to new areas with different environmental pressures. Directional selection allows for swift changes in [[allele frequency]] that can accompany rapidly changing environmental factors and plays a major role in speciation.<ref name=":1" /> Analysis on quantitative trait locus ([[QTL]]) effects has been used to examine the impact of directional selection in phenotypic diversification. QTL is a region of a gene that corresponds to a specific phenotypic trait, and the measuring the statistical frequencies of the traits can be helpful in analyzing phenotypic trends.<ref>{{Cite book |last=Powder |first=Kara E. |chapter=Quantitative Trait Loci (QTL) Mapping |date=March 2024 |title=EQTL Analysis |url=https://pubmed.ncbi.nlm.nih.gov/31849018/ |series=Methods in Molecular Biology|volume=2082 |pages=211–229 |doi=10.1007/978-1-0716-0026-9_15 |pmid=31849018 |isbn=978-1-0716-0025-2 }}</ref> In one study, the analysis showed that directional changes in QTLs affecting various traits were more common than expected by chance among diverse species. This was an indication that directional selection is a primary cause of the phenotypic diversification that can eventually result in speciation.<ref>{{cite journal | last1=Rieseberg | first1=Loren H. | last2=Widmer | first2=Alex | last3=Arntz | first3=A. Michele | last4=Burke | first4=John M. | title=Directional selection is the primary cause of phenotypic diversification | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=99 | issue=19 | pages=12242–5 | date=2002-09-17 | pmid=12221290 | doi=10.1073/pnas.192360899 |pmc=129429 | bibcode=2002PNAS...9912242R | doi-access=free }}</ref>

There are different statistical tests that can be run to test for the presence of directional selection in a population.  A highly indicative test of changes in allele frequencies is the QTL sign test, and other tests include the Ka/Ks ratio test and the relative rate test. The QTL sign test compares the number of antagonistic QTL to a neutral model, and allows for testing of directional selection against [[genetic drift]].<ref>{{cite journal | last1 = Orr | first1 = H.A. | year = 1998 | title = Testing Natural Selection vs. Genetic Drift in Phenotypic Evolution Using Quantitative Trait Locus Data | journal = Genetics | volume = 149 | issue = 4| pages = 2099–2104 | doi = 10.1093/genetics/149.4.2099 | pmid=9691061 | pmc=1460271}}</ref>  The [[Ka/Ks ratio]] test compares the number of non-synonymous to synonymous substitutions, and a ratio that is greater than 1 indicates directional selection.<ref>{{cite journal | last=Hurst | first=Laurence D | title=The Ka/Ks ratio: diagnosing the form of sequence evolution | journal=Trends in Genetics | publisher=Elsevier BV | volume=18 | issue=9 | year=2002 | issn=0168-9525 | doi=10.1016/s0168-9525(02)02722-1 | pmid=12175810 | pages=486–487}}</ref>  The relative ratio test looks at the accumulation of advantageous traits against a neutral model, but needs a phylogenetic tree for comparison. This can prove difficult if the full phylogenic history is not known or is not specific enough for the test comparison.<ref>{{cite journal | last1=Creevey | first1=Christopher J. | last2=McInerney | first2=James O. | title=An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences | journal=Gene | publisher=Elsevier BV | volume=300 | issue=1–2 | year=2002 | issn=0378-1119 | doi=10.1016/s0378-1119(02)01039-9 | pmid=12468084 | pages=43–51}}</ref>