Codon-based analysis of selection pressure and genetic structure in the Psammobates tentorius (Bell, 1828) species complex, and phylogeny inferred from both codons and amino acid sequences
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Date
2021
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Publisher
John Wiley & Sons
Abstract
This study used codon analysis (dN/dS and Tv/Ti) to investigate selection pressure
and genetic structure in the highly polymorphic Psammobates tentorius species
complex, and amino acid sequences to construct a phylogeny tree for it. Our results
revealed a strong selection signal at node ‘C2 + C3’, possibly driven by aridity intensification resulting from the development of the Benguela Current. A similar signal was noticed at C3, possibly due to the same driving force. These findings suggest that
environmental selection pressure favoured those groups and that further cladogenic
events were possible. Selection pressure was also found to be high at C1, C4 and C7,
which may indicate that they are also favoured by the current selection pressure.
The codon-based phylogeny did not retrieve any potentially undescribed species, but
nonetheless provided support for the validity of the seven distinct clades retrieved
with the DNA sequence data. The amino acid sequence-based phylogeny generally
supported the seven lineages as valid putative species. Investigation at the genomic
scale could, however, help to solve the issue. In general, we found the codon, dN,
dS, Tv, Ti and amino acid sequence-based phylogenetic inferences useful in species
delimitation and recommend their use in species delimitation studies.
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Keywords
amino acid sequences, nonsynonymous and synonymous substitution, southern Africa, transition, transversion
Citation
Zhao, Z., Heideman, N., & Hofmeyr, M. D. (2021). Codon-based analysis of selection pressure and genetic structure in the Psammobates tentorius (Bell, 1828) species complex, and phylogeny inferred from both codons and amino acid sequences. African Journal of Ecology, 59(2), 497–509. https://doi.org/10.1111/aje.12840