Genomic islands of divergence infer a phenotypic landscape in Pacific lamprey

Abstract

High rates of dispersal can breakdown coadapted gene complexes. However, concentrated genomic architecture (i.e., genomic islands of divergence) can suppress recombination to allow evolution of local adaptations despite high gene flow. Pacific lamprey (Entosphenus tridentatus) is a highly dispersive anadromous fish. Observed trait diversity and evidence for genetic basis of traits suggests it may be locally adapted. We addressed whether concentrated genomic architecture could influence local adaptation for Pacific lamprey. Using two new whole genome assemblies and genotypes from 7,716 single nucleotide polymorphism (SNP) loci in 518 individuals from across the species range, we identified four genomic islands of divergence (on chromosomes 01, 02, 04, and 22). We determined robust phenotype-by-genotype relationships by testing multiple traits across geographic sites. These trait associations probably explain genomic divergence across the species' range. We genotyped a subset of 302 broadly distributed SNPs in 2,145 individuals for association testing for adult body size, sexual maturity, migration distance and timing, adult swimming ability, and larval growth. Body size traits were strongly associated with SNPs on chromosomes 02 and 04. Moderate associations also implicated SNPs on chromosome 01 as being associated with variation in female maturity. Finally, we used candidate SNPs to extrapolate a heterogeneous spatiotemporal distribution of these predicted phenotypes based on independent data sets of larval and adult collections. These maturity and body size results guide future elucidation of factors driving regional optimization of these traits for fitness. Pacific lamprey is culturally important and imperiled. This research addresses biological uncertainties that challenge restoration efforts.

Supergene origin and maintenance in Atlantic cod

“…The presence of four long (4–17 Mbp) and old (0.40–1.66 Ma) inversion-based supergenes in Atlantic cod adds to recent findings of inversions of similar size and/or age in butterflies[12], ants[2], birds[4], lampreys[88], and Drosophila [75]. For non-model organisms, these findings are largely owed to improvements in sequencing technology within the last decade, including long-read sequencing and chromosome conformation capture techniques, and may become more common as these techniques are applied to an increasing number of species.…”

The Evolution of Oxytocin and Vasotocin Receptor Genes in Jawed Vertebrates: A Clear Case for Gene Duplications Through Ancestral Whole-Genome Duplications

“…In particular, we benefited from the recent advancements in the sequencing of cartilaginous fish genomes (32-35) as well as the advancement of the Vertebrate Genomes Project (36). This study includes two additional mammalian species, including platypus (Ornithorhynchus anatinus), nine additional avian species representing a wide segment of the extant avian diversity, nine additional reptilian species, four additional amphibian species, the gray bichir, reedfish, American paddlefish (18) and sterlet (17), which occupy key positions at the base of ray-finned fish evolution, ten additional teleost species, seven additional cartilaginous fish species representing all three major lineages, as well as the cyclostomes inshore hagfish (Eptatretus burgeri) (37), Pacific lamprey (Entosphenus tridentatus) (38) and sea lamprey (Petromyzon marinus). The full list of species, including genome assembly and database information has been deposited in Figshare (see Supplementary Material section), and a subset is shown in Table 1.…”

Whole-Genome Duplications and the Diversification of the Globin-X Genes of Vertebrates

“…Such taxa include the sterlet ( Du et al 2020 ), salmonids ( Berthelot et al 2014 ; Lien et al 2016 ), members of the subfamily Cyprininae ( Xu et al 2014 ; Chen et al 2019 ; Xu et al 2019 ), and the African clawed frog ( Xenopus laevis ) ( Session et al 2016 ). In the case of the pacific lamprey, Entosphenus tridentatus ( Hess et al 2020 ), the pouched lamprey, Geotria australis , and the southern lamprey, Mordacia mordax , we annotated GbX genes by pairwise comparisons with the GbX genes of the sea lamprey, Petromyzon marinus , using BLAST ( Altschul et al 1990 ) and the “Blast 2 sequences” tool ( Tatusova and Madden 1999 ). Similarly, we used the GbX genes from elephant fish to search for unannotated GbX paralogs in additional genomes from other cartilaginous fishes.…”