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How do the authors account for potential inconsistencies in mitochondrial genome evolution across different red algal lineages? Were any alternative phylogenetic models tested to assess the robustness of the tree topology? The study highlights the absence of rpl5 and rpl20 in C. tenellus. Could the authors elaborate on whether these gene losses are specific to C. tenellus or a broader pattern in Gigartinales?
The authors provide a well-structured phylogenetic analysis of Chondracanthus tenellus within the Gigartinales using complete mitochondrial genome sequences. However, addressing potential inconsistencies in mitochondrial genome evolution across different red algal lineages is indeed a crucial aspect. The study employs maximum likelihood (ML) analysis with the Tamura-Nei model, but it does not specify whether alternative phylogenetic models (e.g., Bayesian inference or other substitution models) were tested to assess the robustness of the tree topology. Exploring multiple models and conducting model selection tests (e.g., AIC, BIC) could strengthen the reliability of the inferred phylogeny.
Regarding the reported absence of rpl5 and rpl20 in C. tenellus, the authors mention that similar losses have been observed in other Gigartinales, including Chondrus crispus and Sarcopeltis skottsbergii. This suggests a broader evolutionary pattern within the family rather than a lineage-specific event in C. tenellus. However, additional comparative genomic studies incorporating more species within Gigartinales could help confirm whether these gene losses represent a conserved evolutionary trend or independent loss events. Clarification on whether synteny analyses were performed to identify potential compensatory mechanisms for these missing genes would also be valuable.