Salmonidae

Salmonidae is a family of ray-finned fish, the only living family currently placed in the order Salmoniformes. It includes salmon, trout, chars, freshwater whitefishes, and graylings, which collectively are known as the salmonids. The Atlantic salmon and trout of the genus Salmo give the family and order their names.

Salmonidae Temporal range: Upper Cretaceous–Recent[1] PreꞒ Ꞓ O S D C P T J K Pg N
Chinook salmon (Oncorhynchus tschawytscha)
Scientific classification
Kingdom:	Animalia
Phylum:	Chordata
Class:	Actinopterygii
Superorder:	Protacanthopterygii
Order:	Salmoniformes Bleeker, 1859
Family:	Salmonidae G. Cuvier, 1816
Type species
Salmo Linnaeus, 1758
Genera
(see text)

Salmonids have a relatively primitive appearance among the teleost fish, with the pelvic fins being placed far back, and an adipose fin towards the rear of the back. They are slender fish, with rounded scales and forked tails. Their mouths contain a single row of sharp teeth.[2] Although the smallest species is just 13 cm (5.1 in) long as an adult, most are much larger, with the largest reaching 2 m (6.6 ft).[1]

All salmonids spawn in fresh water, but in many cases, the fish spend most of their lives at sea, returning to the rivers only to reproduce. This lifecycle is described as anadromous. They are predators, feeding on small crustaceans, aquatic insects, and smaller fish.[2]

Evolution

Current salmonids comprise three lineages, taxonomically treated as subfamilies: whitefish (Coregoninae), graylings (Thymallinae), and the char, trout, and salmons (Salmoninae). Generally, all three lineages are accepted to allocate a suite of derived traits indicating a monophyletic group.[3]

The Salmonidae first appear in the fossil record in the middle Eocene with the fossil Eosalmo driftwoodensis, which was first described from fossils found at Driftwood Creek, central British Columbia. These genus shares traits found in the Salmoninae, whitefish, and grayling lineages. Hence, E. driftwoodensis is an archaic salmonid, representing an important stage in salmonid evolution.[3]

A gap appears in the salmonine fossil record after E. driftwoodensis until about seven million years ago (mya), in the late Miocene, when trout-like fossils appear in Idaho, in the Clarkia Lake beds.[4] Several of these species appear to be Oncorhynchus—the current genus for Pacific salmon and some 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 and cutthroat trout, and Pacific salmon lineages had diverged before the beginning of the Pliocene. Consequently, the split between Oncorhynchus and Salmo (Atlantic salmon) must have occurred well before the Pliocene. Suggestions have gone back as far as the early Miocene (about 20 mya).[3][5]

Genetics

Based on the most current evidence, salmonids diverged from the rest of teleost fish no later than 88 million years ago, during the late Cretaceous. This divergence was marked by a whole-genome duplication event in the ancestral salmonid, where the diploid ancestor became tetraploid.[6][7] 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.[7]

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 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.[8]

The first fossil species representing a true salmonid fish (E. driftwoodensis) does not appear until the middle Eocene.[9] 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. This fossil is also significantly younger than the proposed salmonid divergence from the rest of the teleost fishes, and is the earliest confirmed salmonid currently known. This means that the salmonids have a ghost lineage of approximately 33 million years.

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 25-100 million years in age.[8] New advances in 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.[7]

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.[7]

Classification

Together with the closely related Esociformes (the pikes and related fishes), Osmeriformes (e.g. smelts), and Argentiniformes, the Salmoniformes comprise the superorder Protacanthopterygii.

The Salmonidae are divided into three subfamilies and around 10 genera. The concepts of the number of species recognised vary among researchers and authorities; the numbers presented below represent the higher estimates of diversity:[1]

Phylogeny of Salmonidae[10][11]

Coregoninae   Prosopium       Stenodus     Coregonus         Thymallinae Thymallus   Salmoninae     Brachymystax     Hucho         Salmo       Oncorhynchus       Parahucho     Salvelinus (incl. Salvethymus)

Order Salmoniformes

• Family: Salmonidae
  • Subfamily: Coregoninae
    • Coregonus - whitefishes (78 species)
    • Prosopium - round whitefishes (six species)
    • Stenodus - beloribitsa and nelma (one or two species)
  • Subfamily: Thymallinae
    • Thymallus - graylings (14 species)
  • Subfamily: Salmoninae
    • Brachymystax - lenoks (four species)
    • † Eosalmo (one species, Eocene)
    • Hucho (four species)
    • Oncorhynchus - Pacific salmon and trout (12 species)
    • Parahucho - Sakhalin taimen (one species)
    • Salmo - Atlantic salmon and trout (47 species)
    • Salvelinus - Char and trout (e.g. brook trout, lake trout) (51 species)
    • Salvethymus - Long-finned char (one species)

Hybrid crossbreeding

The following table shows results of hybrid crossbreeding combination in Salmonidae.[12]

Crossbreeding
			male
			Salvelinus		Oncorhynchus								Salmo
			leucomaenis (white-spotted char)	fontinalis (Brook trout)	mykiss (Rainbow trout)	masou masou (masu salmon)	masou ishikawae (Amago Salmon)	gorbuscha (pink salmon)	nerka (Sockeye salmon)	keta (chum salmon)	kisutsh (coho salmon)	tshawytscha (chinook salmon)	trutta (Brown trout)	salar (Atlantic Salmon)
female
	(Salvelinus)	leucomaenis (white-spotted char)	-	O	X	O	O		X	X			O
		fontinalis (Brook trout)	O	-	X	O	O		X	X	O		X	X
	(Oncorhynchus)	mykiss (Rainbow trout)	O	O	-	O	O	O	X	X	X		X	X
		masou masou (masu salmon)	O	X	X	-	O		X	X	O	O	X
		masou ishikawae (Amago Salmon)	O	O	X	O	-		X				O
		gorbuscha (pink salmon)	X					-	O	O		O
		nerka (Sockeye salmon)	X	X	X	X	X	O	-	O	O	O	X
		keta (chum salmon)	X	X	X	X		O	O	-	O	X		X
		kisutsh (coho salmon)		X	X			O	O	X	-	O	X	X
		tshawytscha (chinook salmon)				O		O	O	X	O	-
	Salmo	trutta (Brown trout)	O	O	X	O	O		X		X		-	O
		salar (Atlantic Salmon)		O	X					X	X		O	-

note :- : The identical kind, O : (survivability), X : (Fatality)

References

1. Froese, Rainer, and Daniel Pauly, eds. (2008). "Salmonidae" in FishBase. December 2008 version.
2. McDowell, Robert M. (1998). Paxton, J.R.; Eschmeyer, W.N. (eds.). Encyclopedia of Fishes. San Diego: Academic Press. pp. 114–116. ISBN 978-0-12-547665-2.
3. McPhail, J.D.; Strouder, D.J. (1997). "Pacific Salmon and Their Ecosystems: Status and Future Options". The Origin and Speciation of Oncorhynchus. New York, New York: Chapman & Hall.
4. Smiley, Charles J. "Late Cenozoic History of the Pacific Northwest" (PDF). Association for the Advancement of Science: Pacific Division. Archived from the original (PDF) on August 4, 2004. Retrieved August 8, 2006.
5. Montgomery, David R. (2000). "Coevolution of the Pacific Salmon and Pacific Rim Topography" (PDF). Department of Geological Sciences, University of Washington. Archived from the original (PDF) on September 1, 2006. Retrieved August 8, 2006.
6. Allendorf, Fred W.; Thorgaard, Gary H. (1984). "Tetraploidy and the Evolution of Salmonid Fishes". Evolutionary Genetics of Fishes. pp. 1–53. doi:10.1007/978-1-4684-4652-4_1. ISBN 978-1-4684-4654-8.
7. MacQueen, D. J.; Johnston, I. A. (2014). "A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification". Proceedings of the Royal Society B: Biological Sciences. 281 (1778): 20132881. doi:10.1098/rspb.2013.2881. PMC 3906940. PMID 24452024.
8. Berthelot, Camille; Brunet, Frédéric; Chalopin, Domitille; Juanchich, Amélie; Bernard, Maria; Noël, Benjamin; Bento, Pascal; Da Silva, Corinne; Labadie, Karine; Alberti, Adriana; Aury, Jean-Marc; Louis, Alexandra; Dehais, Patrice; Bardou, Philippe; Montfort, Jérôme; Klopp, Christophe; Cabau, Cédric; Gaspin, Christine; Thorgaard, Gary H.; Boussaha, Mekki; Quillet, Edwige; Guyomard, René; Galiana, Delphine; Bobe, Julien; Volff, Jean-Nicolas; Genêt, Carine; Wincker, Patrick; Jaillon, Olivier; Crollius, Hugues Roest; Guiguen, Yann (2014). "The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates". Nature Communications. 5: 3657. Bibcode:2014NatCo...5.3657B. doi:10.1038/ncomms4657. PMC 4071752. PMID 24755649.
9. Zhivotovsky, L. A. (2015). "Genetic history of salmonid fishes of the genus Oncorhynchus". Russian Journal of Genetics. 51 (5): 491–505. doi:10.1134/s1022795415050105.
10. Crête-Lafrenière, Alexis; Weir, Laura K.; Bernatchez, Louis (2012). "Framing the Salmonidae Family Phylogenetic Portrait: A More Complete Picture from Increased Taxon Sampling". PLOS ONE. 7 (10): e46662. Bibcode:2012PLoSO...746662C. doi:10.1371/journal.pone.0046662. PMC 3465342. PMID 23071608.
11. Shedko, S. V.; Miroshnichenko, I. L.; Nemkova, G. A. (2013). "Phylogeny of salmonids (salmoniformes: Salmonidae) and its molecular dating: Analysis of mtDNA data". Russian Journal of Genetics. 49 (6): 623–637. doi:10.1134/S1022795413060112.
12. Ito, Daisuke; Fujiwara, Atushi; Abe, Syuiti (2006). "Hybrid Inviability and Chromosome Abnormality in Salmonid Fish". The Journal of Animal Genetics. 34: 65–70. doi:10.5924/abgri2000.34.65.

Further reading

• Behnke, Robert J. Trout and Salmon of North America, Illustrated by Joseph R. Tomelleri. 1st Chanticleer Press ed. New York: The Free Press, 2002. ISBN 0-7432-2220-2
• Dushkina, L.A. (January 1994). "Farming of Salmonids in Russia". Aquaculture & Fisheries Management. 25 (1): 121–126. doi:10.1111/j.1365-2109.1994.tb00672.x.
• Froese, Rainer, and Daniel Pauly, eds. (2004). "Salmonidae" in FishBase. October 2004 version.
• "Salmonidae". Integrated Taxonomic Information System. Retrieved December 12, 2004.
• Froese, Rainer, and Daniel Pauly, eds. (2004). "Salmoniformes" in FishBase. October 2004 version.
• Sepkoski, Jack (2002). "A compendium of fossil marine animal genera". Bulletins of American Paleontology. 364: 560. Retrieved May 17, 2011.