The reason is geographical isolation and the effect of stabilizing selection.
1) Baikal for a long time (about 20 million years) has no connection with other water bodies, therefore organisms from other water bodies cannot get into Lake Baikal.
2) In Baikal, species that could have survived in all other (interconnected) water bodies could have survived.
3) As a result of mutations and natural selection, the gene pool of the original organisms has changed, which led to the emergence of new species. Baikal populations that do not have a connection with populations of other water bodies evolved independently of other populations of their species and turned into separate endemic species.
4) In Lake Baikal, unique conditions (for example, high oxygen content) and its own unique ecosystem, therefore, the direction of evolution of organisms in Lake Baikal differs from the direction of evolution of organisms in other bodies of water.
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