Positive selection and precipitation effects on the mitochondrial NADH dehydrogenase subunit 6 gene in brown hares (Lepus europaeus) under a phylogeographic perspective.
Previous studies in hares and jackrabbits have indicated that positive selection has shaped the genetic diversity of mitochondrial genes involved in oxidative phosphorylation, which may affect cellular energy production and cause regional adaptation to different environmental (climatic) pressures. I...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2019-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0224902 |
| _version_ | 1818916659231981568 |
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| author | Milomir Stefanović Mihajla Djan Nevena Veličković Dejan Beuković Vukan Lavadinović Chavdar Dinev Zhelev Yasin Demirbaş Ladislav Paule Csongor István Gedeon Zissis Mamuris Annika Posautz Christoph Beiglböck Anna Kübber-Heiss Franz Suchentrunk |
| author_facet | Milomir Stefanović Mihajla Djan Nevena Veličković Dejan Beuković Vukan Lavadinović Chavdar Dinev Zhelev Yasin Demirbaş Ladislav Paule Csongor István Gedeon Zissis Mamuris Annika Posautz Christoph Beiglböck Anna Kübber-Heiss Franz Suchentrunk |
| author_sort | Milomir Stefanović |
| collection | DOAJ |
| description | Previous studies in hares and jackrabbits have indicated that positive selection has shaped the genetic diversity of mitochondrial genes involved in oxidative phosphorylation, which may affect cellular energy production and cause regional adaptation to different environmental (climatic) pressures. In the present study, we sequenced the NADH dehydrogenase subunit 6 (MT-ND6) gene of 267 brown hares (L. europaeus) from Europe and Asia Minor and tested for positive selection and adaptations acting on amino acid sequences (protein variants). Molecular diversity indices and spatial clustering were assessed by DnaSP, Network, and Geneland, while the presence of selection signals was tested by codeml in PAML, and by using the Datamonkey Adaptive Evolution web server. The SPSS software was used to run multinomial regression models to test for possible effects of climate parameters on the currently obtained protein variants. Fifty-eight haplotypes were revealed with a haplotype diversity of 0.817, coding for 17 different protein variants. The MT-ND6 phylogeographic pattern as determined by the nucleotide sequences followed the earlier found model based on the neutrally evolving D-loop sequences, and reflected the earlier found phylogeographic Late Pleistocene scenario. Based on several selection tests, only one codon position consistently proved to be under positive selection. It did occur exclusively in the evolutionarily younger hares from Europe and it gave rise to several protein variants from the southeastern and south-central Balkans. The occurrence of several of those variants was significantly favored under certain precipitation conditions, as proved by our multinomial regression models. Possibly, the great altitudinal variation in the Balkans may have lead to bigger changes in precipitation across that region and this may have imposed an evolutionarily novel selective pressure on the protein variants and could have led to regional adaptation. |
| first_indexed | 2024-12-20T00:21:41Z |
| format | Article |
| id | doaj.art-fa65c21187e2445fb5f6500fdf47c043 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-20T00:21:41Z |
| publishDate | 2019-01-01 |
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| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-fa65c21187e2445fb5f6500fdf47c0432022-12-21T20:00:11ZengPublic Library of Science (PLoS)PLoS ONE1932-62032019-01-011411e022490210.1371/journal.pone.0224902Positive selection and precipitation effects on the mitochondrial NADH dehydrogenase subunit 6 gene in brown hares (Lepus europaeus) under a phylogeographic perspective.Milomir StefanovićMihajla DjanNevena VeličkovićDejan BeukovićVukan LavadinovićChavdar Dinev ZhelevYasin DemirbaşLadislav PauleCsongor István GedeonZissis MamurisAnnika PosautzChristoph BeiglböckAnna Kübber-HeissFranz SuchentrunkPrevious studies in hares and jackrabbits have indicated that positive selection has shaped the genetic diversity of mitochondrial genes involved in oxidative phosphorylation, which may affect cellular energy production and cause regional adaptation to different environmental (climatic) pressures. In the present study, we sequenced the NADH dehydrogenase subunit 6 (MT-ND6) gene of 267 brown hares (L. europaeus) from Europe and Asia Minor and tested for positive selection and adaptations acting on amino acid sequences (protein variants). Molecular diversity indices and spatial clustering were assessed by DnaSP, Network, and Geneland, while the presence of selection signals was tested by codeml in PAML, and by using the Datamonkey Adaptive Evolution web server. The SPSS software was used to run multinomial regression models to test for possible effects of climate parameters on the currently obtained protein variants. Fifty-eight haplotypes were revealed with a haplotype diversity of 0.817, coding for 17 different protein variants. The MT-ND6 phylogeographic pattern as determined by the nucleotide sequences followed the earlier found model based on the neutrally evolving D-loop sequences, and reflected the earlier found phylogeographic Late Pleistocene scenario. Based on several selection tests, only one codon position consistently proved to be under positive selection. It did occur exclusively in the evolutionarily younger hares from Europe and it gave rise to several protein variants from the southeastern and south-central Balkans. The occurrence of several of those variants was significantly favored under certain precipitation conditions, as proved by our multinomial regression models. Possibly, the great altitudinal variation in the Balkans may have lead to bigger changes in precipitation across that region and this may have imposed an evolutionarily novel selective pressure on the protein variants and could have led to regional adaptation.https://doi.org/10.1371/journal.pone.0224902 |
| spellingShingle | Milomir Stefanović Mihajla Djan Nevena Veličković Dejan Beuković Vukan Lavadinović Chavdar Dinev Zhelev Yasin Demirbaş Ladislav Paule Csongor István Gedeon Zissis Mamuris Annika Posautz Christoph Beiglböck Anna Kübber-Heiss Franz Suchentrunk Positive selection and precipitation effects on the mitochondrial NADH dehydrogenase subunit 6 gene in brown hares (Lepus europaeus) under a phylogeographic perspective. PLoS ONE |
| title | Positive selection and precipitation effects on the mitochondrial NADH dehydrogenase subunit 6 gene in brown hares (Lepus europaeus) under a phylogeographic perspective. |
| title_full | Positive selection and precipitation effects on the mitochondrial NADH dehydrogenase subunit 6 gene in brown hares (Lepus europaeus) under a phylogeographic perspective. |
| title_fullStr | Positive selection and precipitation effects on the mitochondrial NADH dehydrogenase subunit 6 gene in brown hares (Lepus europaeus) under a phylogeographic perspective. |
| title_full_unstemmed | Positive selection and precipitation effects on the mitochondrial NADH dehydrogenase subunit 6 gene in brown hares (Lepus europaeus) under a phylogeographic perspective. |
| title_short | Positive selection and precipitation effects on the mitochondrial NADH dehydrogenase subunit 6 gene in brown hares (Lepus europaeus) under a phylogeographic perspective. |
| title_sort | positive selection and precipitation effects on the mitochondrial nadh dehydrogenase subunit 6 gene in brown hares lepus europaeus under a phylogeographic perspective |
| url | https://doi.org/10.1371/journal.pone.0224902 |
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