Editing Salmonidae (section)

=== Genetics ===
[[File:Winthrop National Fish Hatchery 22 - how Steelhead grow from eggs (cropped).jpg|thumb|[[Oncorhynchus mykiss]] maturing from eggs.]]
Based on the most current evidence, salmonids diverged from the rest of [[Teleost|teleost fish]] no later than 88 million years ago, during the late [[Cretaceous]]. This divergence was marked by a [[Gene duplication|whole-genome duplication event]] in the ancestral salmonid, where the diploid ancestor became [[Polyploid|tetraploid]].<ref>{{cite book|doi=10.1007/978-1-4684-4652-4_1|chapter=Tetraploidy and the Evolution of Salmonid Fishes|title=Evolutionary Genetics of Fishes|pages=1–53|year=1984|last1=Allendorf|first1=Fred W.|last2=Thorgaard|first2=Gary H.|isbn=978-1-4684-4654-8}}</ref><ref name=":0">{{cite journal|doi=10.1098/rspb.2013.2881|pmid=24452024|pmc=3906940|title=A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification|journal=Proceedings of the Royal Society B: Biological Sciences|volume=281|issue=1778|pages=20132881|year=2014|last1=MacQueen|first1=D. J.|last2=Johnston|first2=I. A.}}</ref> This duplication is the fourth of its kind to happen in the evolutionary lineage of the salmonids, with two having occurred commonly to all bony vertebrates, and another specifically in the teleost fishes.<ref name=":0"/>

Extant salmonids all show evidence of partial tetraploidy, as studies show the genome has undergone selection to regain a diploid state. Work done in the [[rainbow trout]] (''Onchorhynchus mykiss'') has shown that the genome is still partially-tetraploid. Around half of the duplicated protein-coding genes have been deleted, but all apparent [[MicroRNA|miRNA sequences]] still show full duplication, with potential to influence regulation of the rainbow trout's genome. This pattern of partial tetraploidy is thought to be reflected in the rest of extant salmonids.<ref name=":2">{{cite journal|doi=10.1038/ncomms4657|pmid=24755649|pmc=4071752|bibcode=2014NatCo...5.3657B|title=The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates|journal=Nature Communications|volume=5|pages=3657|last1=Berthelot|first1=Camille|last2=Brunet|first2=Frédéric|last3=Chalopin|first3=Domitille|last4=Juanchich|first4=Amélie|last5=Bernard|first5=Maria|last6=Noël|first6=Benjamin|last7=Bento|first7=Pascal|last8=Da Silva|first8=Corinne|last9=Labadie|first9=Karine|last10=Alberti|first10=Adriana|last11=Aury|first11=Jean-Marc|last12=Louis|first12=Alexandra|last13=Dehais|first13=Patrice|last14=Bardou|first14=Philippe|last15=Montfort|first15=Jérôme|last16=Klopp|first16=Christophe|last17=Cabau|first17=Cédric|last18=Gaspin|first18=Christine|last19=Thorgaard|first19=Gary H.|last20=Boussaha|first20=Mekki|last21=Quillet|first21=Edwige|last22=Guyomard|first22=René|last23=Galiana|first23=Delphine|last24=Bobe|first24=Julien|last25=Volff|first25=Jean-Nicolas|last26=Genêt|first26=Carine|last27=Wincker|first27=Patrick|last28=Jaillon|first28=Olivier|last29=Crollius|first29=Hugues Roest|last30=Guiguen|first30=Yann|year=2014}}</ref>

The earliest presumed [[Crown group|crown-group]] salmonid fish (''[[Eosalmo|E. driftwoodensis]]'') does not appear until the middle Eocene.<ref>{{cite journal|doi=10.1134/s1022795415050105|title=Genetic history of salmonid fishes of the genus Oncorhynchus|journal=Russian Journal of Genetics|volume=51|issue=5|pages=491–505|year=2015|last1=Zhivotovsky|first1=L. A.|pmid=26137638|s2cid=13487086}}</ref> This fossil already displays traits associated with extant salmonids, but as the genome of E. ''driftwoodensis'' cannot be sequenced, it cannot be confirmed if polyploidy was present in this animal at this point in time.

Given a lack of earlier transition fossils, and the inability to extract genomic data from specimens other than extant species, the dating of the whole-genome duplication event in salmonids was historically a very broad categorization of times, ranging from 25 to 100 million years in age.<ref name=":2" /> New advances in [[Molecular clock|calibrated relaxed molecular clock analyses]] have allowed for a closer examination of the salmonid genome, and has allowed for a more precise dating of the whole-genome duplication of the group, that places the latest possible date for the event at 88 million years ago.<ref name=":0" />

This more precise dating and examination of the salmonid whole-genome duplication event has allowed more speculation on the radiation of species within the group. Historically, the whole-genome duplication event was thought to be the reason for the variation within Salmonidae. Current evidence done with molecular clock analyses revealed that much of the speciation of the group occurred during periods of intense climate change associated with the last ice ages, with especially high speciation rates being observed in salmonids that developed an anadromous lifestyle.<ref name=":0" />