Editing Salmonidae (section)

== Evolution ==
Current salmonids comprise three main [[clade]]s taxonomically treated as [[subfamilies]]: [[Coregoninae]] ([[freshwater whitefish]]es), [[Thymallinae]] ([[Thymallus|grayling]]s), and [[Salmoninae]] ([[trout]], [[salmon]], [[Salvelinus|char]], [[Hucho|taimens]] and [[lenok]]s). Generally, all three [[lineage (evolution)|lineage]]s are accepted to allocate a suite of derived traits indicating a [[clade|monophyletic]] group.<ref name=":1322" /><ref name="McPhail">{{cite book |last=McPhail |first=J.D. |title=The Origin and Speciation of ''Oncorhynchus'' |author2=Strouder, D.J. |publisher=[[Chapman & Hall]] |year=1997 |location=New York, New York |chapter=Pacific Salmon and Their Ecosystems: Status and Future Options}}</ref>

The suborder Salmonoidei, containing only Salmonidae, is one of two extant clades within the order Salmoniformes, which first appeared during the [[Santonian]] and [[Campanian]] stages of the [[Late Cretaceous]].<ref>{{Cite journal |last1=Szabó |first1=Márton |last2=Ősi |first2=Attila |date=September 2017 |title=The continental fish fauna of the Late Cretaceous (Santonian) Iharkút locality (Bakony Mountains, Hungary) |journal=Central European Geology |volume=60 |issue=2 |pages=230–287 |bibcode=2017CEJGl..60..230S |doi=10.1556/24.60.2017.009 |issn=1788-2281 |doi-access=free |hdl-access=free |hdl=10831/67493}}</ref><ref>{{Cite book |last1=Brinkman |first1=Donald B. |title=At the Top of the Grand Staircase: The Late Cretaceous of Southern Utah |last2=Newbrey |first2=Michael G. |last3=Neuman |first3=Andrew G. |last4=Eaton |first4=Jeffrey G. |publisher=Indiana University Press |year=2013 |isbn=9780253008961 |editor-last=Titus |editor-first=Alan L. |location=Bloomington |pages=195–236 |chapter=Freshwater Osteichthyes from the Cenomanian to Late Campanian of Grand Staircase–Escalante National Monument, Utah |editor-last2=Loewen |editor-first2=Mark A. |chapter-url=https://www.researchgate.net/publication/289813917}}</ref> The other is the [[Esocoidei]], which contains the [[Pike (fish)|pikes]] and [[Umbridae|mudminnows]].<ref name=":1322" /> Formerly, many more families were included within this group, but all have since been reclassified into their own orders. During the early 21st century, Salmoniformes was redefined to include only Salmonidae as a [[Monotypic taxon|monotypic]] order.<ref name="Nelson5">{{cite book |author1=J. S. Nelson |url=https://sites.google.com/site/fotw5th/ |title=Fishes of the World |author2=T. C. Grande |author3=M. V. H. Wilson |publisher=Wiley |year=2016 |isbn=978-1-118-34233-6 |edition=5th |pages=348 |access-date=2019-02-23 |archive-url=https://web.archive.org/web/20190408194051/https://sites.google.com/site/fotw5th/ |archive-date=2019-04-08 |url-status=dead}}</ref> However, as recent phylogenetic studies have affirmed the relationship between the Salmonoidei and Esocoidei, the latter have returned to being considered a suborder of Salmoniformes.<ref name=":1322" /><ref>{{cite journal |last1=Near |first1=Thomas J |last2=Thacker |first2=Christine E |date=18 April 2024 |title=Phylogenetic classification of living and fossil ray-finned fishes (Actinopterygii) |journal=Bulletin of the Peabody Museum of Natural History |volume=65 |page=101 |bibcode=2024BPMNH..65..101N |doi=10.3374/014.065.0101 |doi-access=free}}</ref>[[File:Eosalmo driftwoodensis 02.jpg|thumb|right|''[[Eosalmo driftwoodensis]]'' fossil<br/>[[Klondike Mountain Formation]]]]It is thought that salmon and pike diverged from one another during the [[Cretaceous]], but until 2025, there was no [[fossil]] evidence of salmonids occurring during this time period. In 2025, the earliest known fossil salmonid, ''[[Sivulliusalmo|Sivulliusalmo alaskensis]]'', was described from the early [[Maastrichtian]]-aged [[Prince Creek Formation]] of [[Alaska]], with indeterminate remains of this genus also being identified from the older [[Campanian]]-aged [[Dinosaur Park Formation]] of [[Alberta]]. The occurrence of ''Sivulliusalmo'' in these northern habitats suggests that the modern salmonid preference for cool, high-latitude waters is an ancient, conserved trait.<ref name=Brinkman2025>{{Cite journal |last=Brinkman |first=Donald B. |last2=López |first2=J. Andrés |last3=Erickson |first3=Gregory M. |last4=Eberle |first4=Jaelyn J. |last5=Muñoz |first5=Xochitl |last6=Wilson |first6=Lauren N. |last7=Perry |first7=Zackary R. |last8=Murray |first8=Alison M. |last9=Van Loon |first9=Lisa |last10=Banerjee |first10=Neil R. |last11=Druckenmiller |first11=Patrick S. |date=2025 |title=Fishes from the Upper Cretaceous Prince Creek Formation, North Slope of Alaska, and their palaeobiogeographical significance |url=https://onlinelibrary.wiley.com/doi/full/10.1002/spp2.70014 |journal=Papers in Palaeontology |language=en |volume=11 |issue=3 |pages=e70014 |doi=10.1002/spp2.70014 |issn=2056-2802}}</ref>

Prior to the description of ''Sivulliusalmo'', the earliest record of salmonids was the [[Ypresian|Early Eocene]]-aged<ref>{{Cite journal |last1=Eberle |first1=Jaelyn J. |last2=Rybczynski |first2=Natalia |last3=Greenwood |first3=David R. |date=2014-06-07 |title=Early Eocene mammals from the Driftwood Creek beds, Driftwood Canyon Provincial Park, northern British Columbia |url=http://www.tandfonline.com/doi/abs/10.1080/02724634.2014.838175 |journal=Journal of Vertebrate Paleontology |language=en |volume=34 |issue=4 |pages=739–746 |bibcode=2014JVPal..34..739E |doi=10.1080/02724634.2014.838175 |issn=0272-4634}}</ref> [[Eosalmo|''Eosalmo driftwoodensis'']], a <!--presumed--> stem-[[salmonine]], which was first described from fossils found at [[Driftwood Canyon Provincial Park|Driftwood Creek]], central [[British Columbia]],<ref name=":1">{{Cite journal |last1=Campbell |first1=Matthew A. |last2=López |first2=J. Andrés |last3=Sado |first3=Tetsuya |last4=Miya |first4=Masaki |date=2013 |title=Pike and salmon as sister taxa: Detailed intraclade resolution and divergence time estimation of Esociformes + Salmoniformes based on whole mitochondrial genome sequences |url=https://doi.org/10.1016/j.gene.2013.07.068 |journal=Gene |volume=530 |issue=1 |pages=57–65 |doi=10.1016/j.gene.2013.07.068 |issn=0378-1119 |pmid=23954876}}</ref> and has been recovered from most sites in the [[Eocene Okanagan Highlands]].<ref name="Wilson1977">{{cite journal |last1=Wilson |first1=M.V. |year=1977 |title=Middle Eocene freshwater fishes from British Columbia |journal=Life Sciences Contributions, Royal Ontario Museum |volume=113 |pages=1–66}}</ref><ref name="Wilson1999">{{cite journal |last= Wilson |first= M.V.H. |author2=Li, Guo-Qing |title=  Osteology and systematic position of the Eocene salmonid †''Eosalmo driftwoodensis'' Wilson from western North America |journal= Zoological Journal of the Linnean Society |volume= 99 |issue= 125 |pages= 279–311 |year= 1999 |url= http://www.lifesci.ucsb.edu/eemb/labs/oakley/research/WilsonLi.pdf |access-date= 2010-01-01 |doi=10.1111/j.1096-3642.1999.tb00594.x|doi-access= free }}</ref><ref name="WilsonAsmt09">Wilson, M.V.H. 2009. McAbee Fossil Site Assessment Report. 60 pp.[https://www2.gov.bc.ca/assets/gov/farming-natural-resources-and-industry/natural-resource-use/land-water-use/crown-land/fossil-management/mcabee_fossil_site_assessment_report.pdf Online PDF]. Accessed 17 May 2021.</ref> This genus shares traits found in all three subfamily lineages. Hence, ''E. driftwoodensis'' is an archaic salmonid, representing an important stage in salmonid evolution.<ref name="McPhail" /> Fossil scales of [[Freshwater whitefish|coregonines]] are known from the Late Eocene or Early Oligocene of California.<ref name=":3">{{Cite journal |last=David |first=Lorre R. |date=1946 |title=Some Typical Upper Eogene Fish Scales from California |url=https://authors.library.caltech.edu/records/v03cm-86s21 |journal=Contributions to Paleontology |volume=IV}}</ref>

A gap appears in the salmonine fossil record after ''E. driftwoodensis'' until about 7 million years ago ([[megaannum|mya]]), in the [[Late Miocene]], when trout-like fossils appear in [[Idaho]], in the [[Clarkia fossil beds|Clarkia Lake beds]].<ref>{{cite web|url=http://www.sou.edu/aaaspd/TableContents/LateCenHist.pdf/ |title=Late Cenozoic History of the Pacific Northwest |last=Smiley |first=Charles J |publisher=Association for the Advancement of Science: Pacific Division |access-date=August 8, 2006 |format=[[Portable Document Format|PDF]] |url-status=dead |archive-url=https://web.archive.org/web/20040804035723/http://www.sou.edu/aaaspd/TableContents/LateCenHist.pdf |archive-date=August 4, 2004 }}</ref> Several of these species appear to be ''[[Oncorhynchus]]'' — the current genus for Pacific salmon and Pacific trout. The presence of these species so far inland established that ''Oncorhynchus'' was not only present in the Pacific drainages before the beginning of the [[Pliocene]] (~5–6 mya), but also that [[rainbow trout|rainbow]] and [[cutthroat trout]], and Pacific salmon lineages had diverged before the beginning of the Pliocene. Consequently, the split between ''Oncorhynchus'' and ''[[Salmo]]'' (Atlantic salmon and European trout) must have occurred well before the Pliocene. Suggestions have gone back as far as the [[Early Miocene]] (about 20 mya).<ref name="McPhail" /><ref name="Montgomery">{{cite news |url=http://duff.ess.washington.edu/grg/publications/pdfs/salmonevolution.pdf/ |title=Coevolution of the Pacific Salmon and Pacific Rim Topography |last=Montgomery |first=David R. |year=2000 |publisher=Department of Geological Sciences, [[University of Washington]] |access-date=August 8, 2006 |format=PDF |url-status=dead |archive-url=https://web.archive.org/web/20060901100943/http://duff.ess.washington.edu/grg/publications/pdfs/salmonevolution.pdf |archive-date=September 1, 2006}}</ref>

=== 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" />