DOI: 10.5061/dryad.05qfttdzp
title: Excessive parallelism in protein evolution of Lake Baikal amphipod species flock

description: Repeated emergence of similar adaptations is often explained by parallel
 evolution of underlying genes. However, evidence of parallel evolution at
 amino acid level is limited. When the analyzed species are highly
 divergent, this can be due to epistasic interactions underlying the
 dynamic nature of the amino acid preferences: the same amino acid
 substitution may have different phenotypic effects on different genetic
 backgrounds. Distantly related species also often inhabit radically
 different environments, which makes the emergence of parallel adaptations
 less likely. Here, we hypothesize that parallel molecular adaptations are
 more prevalent between closely related species. We analyze the rate of
 parallel evolution in genome-size sets of orthologous genes in three
 groups of species with widely ranging levels of divergence: 47 species of
 the relatively recent lake Baikal amphipod radiation, a species flock of
 very closely related cichlids, and a set of significantly more divergent
 vertebrates. In genes of amphipods, the rate of parallel substitutions at
 nonsynonymous sites exceeded that at synonymous sites, suggesting rampant
 selection driving parallel adaptation. By contrast, in cichlids, the rate
 of nonsynonymous parallel evolution nearly equalled that at synonymous
 sites, while in vertebrates, this rate was lower than that at synonymous
 sites, indicating the role of drift in fixation of parallel substitutions.
 Further data is needed to clarify the cause of the excessive parallelism
 observed in gammarids.
description: <strong>Transcriptomic analysis:</strong>
 We used the transcriptomic sequences of closely related gammarid
 species from Lake Baikal (Naumenko et al. 2017). Of the 67 species
 analyzed in that work, we picked the 47 species for which the sequenced
 sample was based on exactly one individual. Orthologous groups of genes
 were calculated with OrthoMCL 2.0.9 with the inflation parameter set to
 1.5 (Li 2003). If a particular species carried multiple paralogous
 sequences of a gene, this species was excluded from the analysis of this
 gene. Codon-aware alignments for orthogroups were obtained with
 TranslatorX (Abascal et al. 2010) using the Muscle method (Edgar 2004).
 Poorly aligned sequences were detected and removed from the alignments
 using the following rule: 1) A column in an alignment
 was considered "good" if it carried the same nucleotide in at
 least 50% of species; 2) Sequences for which fewer than
 50% positions were "good" were removed from the
 alignment. This exclusion process was performed using
 TrimAl 1.4 (Capella-Gutierrez et al. 2009). Finally we obtained 4366
 orthologous groups of genes. Alignments for all genes were concatenated,
 and a phylogenetic tree was reconstructed using RAxML 8.1.20 (Stamatakis
 2014) with GTR+Gamma model, 20 starting maximum parsimony trees and 100
 bootstrap analysis pseudoreplicates. As mutations in the third positions
 of codons are often synonymous, the third positions of codons accumulate
 substitutions quicker than the first two. Therefore, we used partitioning,
 with separate substitution models for the first two and for the third
 codon positions. The obtained tree was similar to that obtained
 previously. <strong>Sanger
 sequencing:</strong> Purified PCR products were
 bidirectionally sequenced on an ABI 3500 Genetic Analyzer (Applied
 Biosystems) using the BigDye Terminator v 3.1 Cycle Sequencing Kit
 (Applied Biosystems) and the same primers as for PCR.
description: In README.txt file the is description of provided data.