Lists of species and codes: Gammaridae_sample_list.txt, Cichlidae_sample_list.txt, Vertebrata_sample_list.txt files contain list of species we used in analysis. For Gammarids and Vertebrates there are provided short code names, which are used in tables and phylogenetic trees. Data used for P test and main results: Gammaridae_cds_alignments.tar.gz folder contains 4366 cds alignments of baikalian gammarids, which were used in "P-test" for parallel evolution estimation. Gammaridae_tree.newick file contains phylogenetic tree of Gammarids. 900_groups_of_4_species_P_test_raw_data.csv file provides groups of 4 species, which were used in P-test analysis. 300 groups of Gammarids, 300 groups of Cichlids and 300 groups of vertebrates are listed. The table also contains phylogenetic distances between path1 and path 2, as well as number of parallel synonymous and nonsynonymous substitutions of different types. 900_groups_of_4_species_P_test_results.csv table contains dSP, dNP and dP calculation results for 900 above listed groups of 4 species. Polymorphism data analysis: 300_groups_of_4_species_with_Eulimnogammarus_verrucosus_P_test_raw_data.csv file provides groups of 4 species, which were used for polymorphism estimation in parallel sites. Each group necessarily contains Eulimnogammarus verrucosus, as this species is used for polymorphism analysis. Phylogenetic distances and raw calculations for P test analysis are also included. 300_groups_of_4_species_with_Eulimnogammarus_verrucosus_P_test_results.csv table contains dSP, dNP and dP calculation results for 300 above listed groups of 4 species (all groups contain Eulimnogammarus verrucosus). Sanger resequencing: Sanger_sequences.zip folder contains sanger sequences of 3 genes (proteasome subunit alpha type-3-like, polyadenylate-binding protein 4-like, peptidyl-prolyl cis-trans isomerase FKBP4-like) for two species (Ommatogammarus albinus and Eulimnogammarus marituji). These sanger sequences are aligned with transcriptomic sequences of same species’ homologous genes. Miyata distance frequencies: Miyata_distance_freqs_for_parall_and_nonparall_sites.csv file contains frequencies of amino acid substitutions with different Miyata distances. Parallel and non-parallel substitutions are counted independently.