Convergent Adaptation in Mitochondria of Phylogenetically Distant Birds: Does it Exist?

Stronger evidence for relaxed selection than adaptive evolution in high-elevation animal mtDNA

Mitochondrial (mt) genes are the subject of many adaptive hypotheses due to the key role of mitochondria in energy production and metabolism. One widespread adaptive hypothesis is that selection imposed by life at high elevation leads to the rapid fixation of beneficial alleles in mtDNA, reflected in the increased rates of mtDNA evolution documented in many high-elevation species. However, the assumption that fast mtDNA evolution is caused by positive, rather than relaxed purifying selection has rarely been tested. Here, we calculated the dN/dS ratio, a metric of nonsynonymous substitution bias, and explicitly tested for relaxed selection in the mtDNA of over 700 species of terrestrial vertebrates, freshwater fishes, and arthropods, with information on elevation and latitudinal range limits, range sizes, and body sizes. We confirmed that mitochondrial genomes of high-elevation taxa have slightly higher dN/dS ratios compared to low-elevation relatives. High-elevation species tend to have smaller ranges, which predict higher dN/dS ratios and more relaxed selection across species and clades, while absolute elevation and latitude do not predict higher dN/dS. We also find a positive relationship between body mass and dN/dS, supporting a role for small effective population size leading to relaxed selection. We conclude that higher mt dN/dS among high-elevation species is more likely to reflect relaxed selection due to smaller ranges and reduced effective population size than adaptation to the environment. Our results highlight the importance of rigorously testing adaptive stories against non-adaptive alternative hypotheses, especially in mt genomes.

No Signs of Adaptations for High Flight Intensity in the Mitochondrial Genome of Birds

Mitochondrial genomes are expected to show adaptations for optimizing aerobic respiration in birds that make intense use of flight. However, there is limited empirical evidence of such a relationship. We here examine correlates of several mitochondrial genome characteristics and flight use across a diverse sample of 597 bird species. We developed an index of flight use intensity that ranged from 0 in flightless species to 9 in migratory hummingbirds and examined its association with nucleobase composition, amino acid class composition, and amino acid site allelic variation using phylogenetic comparative methods. We found no evidence of mitochondrial genome adaptations to flight intensity. Neither nucleotide composition nor amino acid properties showed consistent patterns related to flight use. While specific sites in mitochondrial genes exhibited variation associated with flight intensity, there was limited association between specific amino acid residues and flight intensity levels. Our findings suggest a complex genetic architecture for aerobic performance traits, where multiple genes in both mitochondria and the nucleus may contribute to overall performance. Other factors, such as gene expression regulation and anatomical adaptations, may play a more significant role in influencing flight performance than changes in mitochondrial genes. These findings highlight the need for comprehensive genomic analyses to unravel the intricate relationship between genetic variants and aerobic performance in birds.

Strategy of micro-environmental adaptation to cold seep among different brittle stars’ colonization

Diffusing fluid from methane seepage in cold seep field creates zones with physicochemical gradients and divergent ecosystems like the mussel beds and clam beds. Three species of brittle stars (Ophiuroidea) were discovered in the Haima cold seep fields, of which Ophiophthalmus serratus and Histampica haimaensis were found on top of or within mussel beds and clam beds, whereas Amphiura sp. was only collected from muds in the clam bed assemblage. Here, we evaluated the genetic signatures of micro-environmental adaptation of brittle stars to cold seep through the comparison of mitogenomes. This study provided two complete mitogenome sequences of O. serratus and Amphiura sp. and compared with those of H. haimaensis and other non-seep species. We found that the split events of the seep and non-seep species were as ancient as the Cretaceous period (∼148–98 Mya). O. serratus and H. haimaensis display rapid residue mutation and mitogenome rearrangements compared to their shallow or deep-sea relatives, in contrast, Amphiura sp. only show medium, regardless of nucleotide mutation rate or mitogenome rearrangement, which may correlate with their adaptation to one or two micro-ecosystems. Furthermore, we identified 10 positively selected residues in ND4 in the Amphiura sp. lineage, suggesting important roles of the dehydrogenase complex in Amphiura sp. adaptive to the cold seep environment. Our results shed light on the different evolutionary strategies during colonization in different micro-environments.