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

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.