Editing Convergent evolution (section)

== Methods of inference ==

[[File:Phenotypic-landscape-inference-reveals-multiple-evolutionary-paths-toC4-photosynthesis-elife00961fs002.jpg|thumb|upright=1.5|[[Angiosperm]] phylogeny of orders based on classification by the Angiosperm Phylogeny Group. The figure shows the number of inferred independent origins of C<sub>3</sub>-C<sub>4</sub> photosynthesis and [[C4 photosynthesis|C<sub>4</sub> photosynthesis]] in parentheses.]]

Phylogenetic reconstruction and [[Ancestral reconstruction|ancestral state reconstruction]] proceed by assuming that evolution has occurred without convergence. Convergent patterns may, however, appear at higher levels in a phylogenetic reconstruction, and are sometimes explicitly sought by investigators. The methods applied to infer convergent evolution depend on whether pattern-based or process-based convergence is expected. Pattern-based convergence is the broader term, for when two or more lineages independently evolve patterns of similar traits. Process-based convergence is when the convergence is due to similar forces of [[natural selection]].<ref name="Stayton2">{{Cite journal |last=Stayton |first=C. Tristan |date=2015 |title=The definition, recognition, and interpretation of convergent evolution, and two new measures for quantifying and assessing the significance of convergence |journal=Evolution |volume=69 |issue=8 |pages=2140–2153 |doi=10.1111/evo.12729|pmid=26177938 |s2cid=3161530 }}</ref>

=== Pattern-based measures ===

Earlier methods for measuring convergence incorporate ratios of phenotypic and [[phylogenetic]] distance by simulating evolution with a [[Brownian motion]] model of trait evolution along a phylogeny.<ref>{{cite journal |last=Stayton |first=C. Tristan|title=Is convergence surprising? An examination of the frequency of convergence in simulated datasets |journal=Journal of Theoretical Biology |volume=252 |issue=1 |pages=1–14 |doi=10.1016/j.jtbi.2008.01.008 |pmid=18321532|year=2008|bibcode=2008JThBi.252....1S}}</ref><ref>{{cite journal |last1=Muschick |first1=Moritz |last2=Indermaur |first2=Adrian |last3=Salzburger |first3=Walter |title=Convergent Evolution within an Adaptive Radiation of Cichlid Fishes |journal=Current Biology |volume=22 |issue=24 |pages=2362–2368 |doi=10.1016/j.cub.2012.10.048 |pmid=23159601 |year=2012|doi-access=free |bibcode=2012CBio...22.2362M }}</ref> More recent methods also quantify the strength of convergence.<ref>{{Cite journal |last1=Arbuckle |first1=Kevin |last2=Bennett |first2=Cheryl M. |last3=Speed |first3=Michael P. |date=July 2014 |title=A simple measure of the strength of convergent evolution |journal=Methods in Ecology and Evolution |volume=5 |issue=7 |pages=685–693 |doi=10.1111/2041-210X.12195|bibcode=2014MEcEv...5..685A |doi-access=free }}</ref> One drawback to keep in mind is that these methods can confuse long-term stasis with convergence due to phenotypic similarities. Stasis occurs when there is little evolutionary change among taxa.<ref name="Stayton2" />

Distance-based measures assess the degree of similarity between lineages over time. Frequency-based measures assess the number of lineages that have evolved in a particular trait space.<ref name="Stayton2" />

=== Process-based measures ===

Methods to infer process-based convergence fit models of selection to a phylogeny and continuous trait data to determine whether the same selective forces have acted upon lineages. This uses the [[Ornstein–Uhlenbeck process]] to test different scenarios of selection. Other methods rely on an ''[[A priori knowledge|a priori]]'' specification of where shifts in selection have occurred.<ref>{{Cite journal |last1=Ingram |first1=Travis |last2=Mahler |first2=D. Luke |date=2013-05-01 |title=SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise Akaike Information Criterion |journal=Methods in Ecology and Evolution |volume=4 |issue=5 |pages=416–425 |doi=10.1111/2041-210X.12034 |bibcode=2013MEcEv...4..416I |s2cid=86382470 |doi-access=free }}</ref>