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Caucasian treasure: genomics sheds light on the evolution of half-extinct Sevan trout, Salmo ischchan, species flock

Citation

Levin, Boris et al. (2021), Caucasian treasure: genomics sheds light on the evolution of half-extinct Sevan trout, Salmo ischchan, species flock, Dryad, Dataset, https://doi.org/10.5061/dryad.qfttdz0h8

Abstract

Five ecologically and phenotypically divergent ecomorphs/young species of the genus Salmo are known from a landlocked alpine lake in the Caucasus, Lake Sevan, that was isolated ca. 20 000 years ago by a waterfall. It is an unprecedented example of sympatric diversification within a species-rich lineage with the predominant mode of speciation being allopatric. The main driver of diversification within Sevan trout was spawning resource partitioning. Four lacustrine ecomorphs with different temporal-spatial spawning strategies and divergent phenotypes evolved along with a fifth ecomorph, brook trout, inhabiting the tributaries. Unfortunately, the Sevan trout diversity was almost destroyed by human activity, with two ecomorphs becoming extinct in the 1980s. We performed reconstruction of the evolutionary history of Sevan trouts based on NGS sequencing of both contemporary and aDNA (∼ 50 y.o. dried scales) of all Sevan trout ecomorphs. Our study of complete mitogenomes along with nuclear SNPs data revealed the monophyly of four lacustrine ecomorphs and local brook trout, all derived from the anadromous form Caspian salmon, S. caspius. The species tree suggests a scenario of stepping evolution from riverine to lacustrine spawning. Two genomic clusters of the riverine and lacustrine spawners were revealed within the flock of Sevan trouts. The Holocene climatic oscillations and the desiccation of tributaries could have played an important role in the origin of lacustrine spawning. The relationships between lacustrine ecomorphs were not yet fully resolved, suggesting recent incipient speciation. These ecomorphs warrant further investigation.

Methods

Shot gun Illumina sequencing 150 bp PE.

Full mitochondrial genomes.

Genome-wide SNP sets for various analyses - phylogeny (ML, BI, SVDQ), population genomics (PCA, STRUCTURE), population history and hybridization (DIYABC, ABBA-BABA).

Funding

Russian Foundation for Basic Research, Award: 19-04-00719