title: Effects of crossovers between homeologs on inheritance and population genomics in polyploid-derived salmonid fishes.
abstract: A whole genome duplication occurred in the ancestor of all salmonid fishes some 50-100 million years ago. Early inheritance studies with allozymes indicated that loci in the salmonid genome are inherited disomically in females. However, some pairs of duplicated loci showed patterns of inheritance in males indicating pairing and recombination between homeologous chromosomes. Nearly 20% of loci in the salmonid genome are duplicated and share the same alleles (isoloci), apparently due to homeologous recombination. Half-tetrad analysis revealed that isoloci tend to be telomeric. These results suggested that residual tetrasomic inheritance of isoloci results from homeologous recombination near chromosome ends and that continued disomic inheritance resulted from homologous pairing of centromeric regions. Many current genetic maps of salmonids are based on single nucleotide polymorphisms and microsatellites that are no longer duplicated. Therefore, long sections of chromosomes on these maps are poorly represented, especially telomeric regions. In addition, preferential multivalent pairing of homeologs from the same species in F1 hybrids results in an excess of nonparental gametes (so-called pseudolinkage). We consider how not including duplicated loci has affected our understanding of population and evolutionary genetics of salmonids, and we discuss how incorporating these loci will benefit our understanding of population genomics.
authors.affiliation: From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb). fred.allendorf@gmail.com.
authors.forename: Fred W
authors.initials: FW
authors.lastname: Allendorf
authors.affiliation: From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb).
authors.forename: Susan
authors.initials: S
authors.lastname: Bassham
authors.affiliation: From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb).
authors.forename: William A
authors.initials: WA
authors.lastname: Cresko
authors.affiliation: From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb).
authors.forename: Morten T
authors.initials: MT
authors.lastname: Limborg
authors.affiliation: From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb).
authors.forename: Lisa W
authors.initials: LW
authors.lastname: Seeb
authors.affiliation: From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb).
authors.forename: James E
authors.initials: JE
authors.lastname: Seeb
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D023902:Chromosome Pairing; D019143:Evolution, Molecular; D005260:Female; D020440:Gene Duplication; D008040:Genetic Linkage; D005819:Genetic Markers; D005828:Genetics, Population; D059765:Homologous Recombination; D008297:Male; D011123:Polyploidy; D012487:Salmonidae / Q000235:genetics*
chemical_list: D005819:Genetic Markers
keywords: Salmonidae; homeologs; interference; ohnologs; pseudolinkage; residual tetrasomy