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

Abstract 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 char...

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Autores principales:	Lin Zhang, Keping Sun, Gábor Csorba, Alice Catherine Hughes, Longru Jin, Yanhong Xiao, Jiang Feng
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Mitogenome Rhinolophus Comparative analysis Positive selection Ecology QH540-549.5 Evolution QH359-425
Acceso en línea:	https://doaj.org/article/acb3101cb7664ad282c3ae0bcde4792a
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spelling	oai:doaj.org-article:acb3101cb7664ad282c3ae0bcde4792a2021-11-07T12:04:14ZComplete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats10.1186/s12862-021-01926-22730-7182https://doaj.org/article/acb3101cb7664ad282c3ae0bcde4792a2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12862-021-01926-2https://doaj.org/toc/2730-7182Abstract 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.Lin ZhangKeping SunGábor CsorbaAlice Catherine HughesLongru JinYanhong XiaoJiang FengBMCarticleMitogenomeRhinolophusComparative analysisPositive selectionEcologyQH540-549.5EvolutionQH359-425ENBMC Ecology and Evolution, Vol 21, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Mitogenome Rhinolophus Comparative analysis Positive selection Ecology QH540-549.5 Evolution QH359-425
spellingShingle	Mitogenome Rhinolophus Comparative analysis Positive selection Ecology QH540-549.5 Evolution QH359-425 Lin Zhang Keping Sun Gábor Csorba Alice Catherine Hughes Longru Jin Yanhong Xiao Jiang Feng Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats
description	Abstract 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.
format	article
author	Lin Zhang Keping Sun Gábor Csorba Alice Catherine Hughes Longru Jin Yanhong Xiao Jiang Feng
author_facet	Lin Zhang Keping Sun Gábor Csorba Alice Catherine Hughes Longru Jin Yanhong Xiao Jiang Feng
author_sort	Lin Zhang
title	Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats
title_short	Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats
title_full	Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats
title_fullStr	Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats
title_full_unstemmed	Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats
title_sort	complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats
publisher	BMC
publishDate	2021
url	https://doaj.org/article/acb3101cb7664ad282c3ae0bcde4792a
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Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats

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