The role of selection in the evolution of marine turtles mitogenomes

Ramos, Elisa; Freitas, Lucas; Nery, Mariana F.

doi:10.1038/s41598-020-73874-8

Cited by 21 publications

(18 citation statements)

References 93 publications

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“…We found that each mtDNA PCG in the 21 species was generally lower than 1, indicating that mtDNA PCGs were subjected to purifying selection in different environments. Similar results were obtained by previous studies on marine turtles [ 36 ], horseshoe bats [ 48 ], and birds [ 49 ]. In addition, different dN/dS values for each of the 13 mtDNA PCGs indicate differing functional constraints among the genes [ 50 ].…”

Section: Discussionsupporting

confidence: 92%

“…A common question in the field of evolutionary biology is how different environmental conditions shape mitogenomic evolution. Studies have revealed that organisms possess more patterns of adaptation to ecological change than expected [ 36 ]. In this comprehensive study, we presented a comparative analysis of the mitogenomes of Gobiidae species and examined natural selection at the molecular genetic level.…”

Section: Discussionmentioning

confidence: 99%

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Adaptability and Evolution of Gobiidae: A Genetic Exploration

Shang

Wang

Liu

et al. 2022

Animals

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The Gobiidae family occupy one of the most diverse habitat ranges of all fishes. One key reason for their successful colonization of different habitats is their ability to adapt to different energy demands. This energy requirement is related to the ability of mitochondria in cells to generate energy via oxidative phosphorylation (OXPHOS). Here, we assembled three complete mitochondrial genomes of Rhinogobius shennongensis, Rhinogobius wuyanlingensis, and Chaenogobius annularis. These mitogenomes are circular and include 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and one non-coding control region (CR). We used comparative mitochondrial DNA (mtDNA) genome and selection pressure analyses to explore the structure and evolutionary rates of Gobiidae mitogenomics in different environments. The CmC model showed that the ω ratios of all mtDNA PCGs were <1, and that the evolutionary rate of adenosine triphosphate 8 (atp8) was faster in Gobiidae than in other mitochondrial DNA PCGs. We also found evidence of positive selection for several sites of NADH dehydrogenase (nd) 6 and atp8 genes. Thus, divergent mechanisms appear to underlie the evolution of mtDNA PCGs, which might explain the ability of Gobiidae to adapt to diverse environments. Our study provides new insights on the adaptive evolution of Gobiidae mtDNA genome and molecular mechanisms of OXPHOS.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Adaptability and Evolution of Gobiidae: A Genetic Exploration

Shang

Wang

Liu

et al. 2022

Animals

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“…However, the mitochondrial genomes can conflict with a phylogeny estimated from the nuclear genome due to the replacement of organelle genomes from one species or populations with those of another mediated by hybridization and introgression [41][42][43][44]. The use of mitochondrial genome datasets may also provide evidences of adaptive radiations, as signatures of selection were detected during reconstructing mitochondrial genome phylogenies for the number of vertebrate taxa including deep-sea fishes [45,46], marine turtles [47,48], and mammals [49][50][51][52][53][54]. Yet, mitochondrial genomes remain an important tool both for phylogenies resolution and for the species identification by barcoding using individual mitochondrial genes or complete genomes.…”

Section: Introductionmentioning

confidence: 99%

A mitochondrial genome phylogeny of voles and lemmings (Rodentia: Arvicolinae): Evolutionary and taxonomic implications

et al. 2021

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Arvicolinae is one of the most impressive placental radiations with over 150 extant and numerous extinct species that emerged since the Miocene in the Northern Hemisphere. The phylogeny of Arvicolinae has been studied intensively for several decades using morphological and genetic methods. Here, we sequenced 30 new mitochondrial genomes to better understand the evolutionary relationships among the major tribes and genera within the subfamily. The phylogenetic and molecular dating analyses based on 11,391 bp concatenated alignment of protein-coding mitochondrial genes confirmed the monophyly of the subfamily. While Bayesian analysis provided a high resolution across the entire tree, Maximum Likelihood tree reconstruction showed weak support for the ordering of divergence and interrelationships of tribal level taxa within the most ancient radiation. Both the interrelationships among tribes Lagurini, Ellobiusini and Arvicolini, comprising the largest radiation and the position of the genus Dinaromys within it also remained unresolved. For the first time complex relationships between genus level taxa within the species-rich tribe Arvicolini received full resolution. Particularly Lemmiscus was robustly placed as sister to the snow voles Chionomys in the tribe Arvicolini in contrast with a long-held belief of its affinity with Lagurini. Molecular dating of the origin of Arvicolinae and early divergences obtained from the mitogenome data were consistent with fossil records. The mtDNA estimates for putative ancestors of the most genera within Arvicolini appeared to be much older than it was previously proposed in paleontological studies.

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“…The role of selection in the evolution of mitochondrial DNA (mtDNA) attracted little attention until recently [ 3 , 9 , 23 , 24 ]. Mitochondrial OXPHOS genes have been shown to display evidence of adaptive evolution in, for example, dogs, bats, birds and fishes [ 21 , 22 , 25 , 26 ], and numerous studies have detected signals of positive selection in mitochondrial genes [ 21 – 23 , 27 ], suggesting positive selection plays a strong potential role in adaptation [ 28 , 29 ].…”

Section: Introductionmentioning

confidence: 99%

Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats

et al. 2021

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Background In genus Rhinolophus, species in the Rhinolophus philippinensis and R. macrotis groups are unique because the horseshoe bats in these group have relatively low echolocation frequencies and flight speeds compared with other horseshoe bats with similar body size. The different characteristics among bat species suggest particular evolutionary processes may have occurred in this genus. To study the adaptive evidence in the mitochondrial genomes (mitogenomes) of rhinolophids, especially the mitogenomes of the species with low echolocation frequencies, we sequenced eight mitogenomes and used them for comparative studies of molecular phylogeny and adaptive evolution. Results Phylogenetic analysis using whole mitogenome sequences produced robust results and provided phylogenetic signals that were better than those obtained using single genes. The results supported the recent establishment of the separate macrotis group. The signals of adaptive evolution discovered in the Rhinolophus species were tested for some of the codons in two genes (ND2 and ND6) that encode NADH dehydrogenases in oxidative phosphorylation system complex I. These genes have a background of widespread purifying selection. Signals of relaxed purifying selection and positive selection were found in ND2 and ND6, respectively, based on codon models and physicochemical profiles of amino acid replacements. However, no pronounced overlap was found for non-synonymous sites in the mitogenomes of all the species with low echolocation frequencies. A signal of positive selection for ND5 was found in the branch-site model when R. philippinensis was set as the foreground branch. Conclusions The mitogenomes provided robust phylogenetic signals that were much more informative than the signals obtained using single mitochondrial genes. Two mitochondrial genes that encoding proteins in the oxidative phosphorylation system showed some evidence of adaptive evolution in genus Rhinolophus and the positive selection signals were tested for ND5 in R. philippinensis. These results indicate that mitochondrial protein-coding genes were targets of adaptive evolution during the evolution of Rhinolophus species, which might have contributed to a diverse range of acoustic adaptations in this genus.

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The role of selection in the evolution of marine turtles mitogenomes

Cited by 21 publications

References 93 publications

Adaptability and Evolution of Gobiidae: A Genetic Exploration

Adaptability and Evolution of Gobiidae: A Genetic Exploration

A mitochondrial genome phylogeny of voles and lemmings (Rodentia: Arvicolinae): Evolutionary and taxonomic implications

Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats

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