Mitogenomic analysis in European brown hare (
            <i>Lepus europaeus</i>
            ) proposes genetic and functional differentiation between the distinct lineages

Giannoulis, Themistoklis; Stamatis, Costas; Tsipourlianos, Andreas; Mamuris, Zissis

doi:10.1080/24701394.2016.1278540

Cited by 12 publications

(19 citation statements)

References 49 publications

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“…Given that the oxidative phosphorylation process produces 95% of cellular energy, it is not surprising that genes encoding for OXPHOS subunits are under adaptive selection. Giannoulis et al [5] suggested that variations in these genes would directly in uence the metabolic performance which may in turn affect the tness of an organism. Generally, variation in mitochondrial OXPHOS genes may convey a signal of adaptation to environmental, particularly climatic, conditions (e.g., 6, 8-10, 25, 45, 46].…”

Section: Discussionmentioning

confidence: 99%

“…However, the assumption of non-neutral evolution of mtDNA can interfere with historical inferences in population and evolutionary biology [4]. Indeed, mitochondrial genes encoding for OXPHOS subunits are expected to be under selection, because variations in these genes may affect the organism tness by directly in uencing the metabolic performance with potential effects on the immunity [5,6]. Therefore, mtDNA-encoded OXPHOS genes present very good study systems for understanding the evolution of adaptive traits in species.…”

Section: Introductionmentioning

confidence: 99%

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Positive Selection on Two Mitochondrial Coding Genes and Adaptation Signals in Hares (Genus Lepus) from China

Awadi

Slimen

Schaschl

et al. 2020

Preprint

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Background: Animal mitochondria play a central role in energy production in the cells through the oxidative phosphorylation (OXPHOS) pathway. Recent studies of selection on different mitochondrial OXPHOS genes have revealed the adaptive implications of amino acid changes in these subunits. In hares, climatic variation and/or introgression were suggested to be at the origin of such adaptation. Here we looked for evidence of positive selection in three mitochondrial OXPHOS genes, using tests of selection, protein structure modelling and effects of amino acid substitutions on the protein function and stability. We also used statistical models to test for climate and introgression effects on sites under positive selection. Results: Our results revealed seven sites under positive selection in ND4 and three sites in Cytb. However, no sites under positive selection were observed in the COX1 gene. All three subunits presented a high number of codons under negative selection. Sites under positive selection were mapped on the tridimensional structure of the predicted models for the respective mitochondrial subunit. Of the ten amino acid replacements inferred to have evolved under positive selection for both subunits, six were located in the transmembrane domain. On the other hand, three codons were identified as sites lining proton translocation channels. Furthermore, four codons were identified as destabilizing with a significant variation of Δ vibrational entropy energy between wild and mutant type. Moreover, the PROVEAN analysis suggested that among all positively selected sites two fixed amino acid replacements altered the protein functioning. The statistical model runs indicated significant effects of climate on the presence of ND4 and Cytb protein variants, but no effect by trans-specific mitochondrial DNA introgresson.Conclusions: Positive selection was observed in several codons in two OXPHOS genes. We found that substitutions in the positively selected codons have structural and functional impacts on the encoded proteins. Our results are concordantly suggesting that adaptations have strongly affected the evolution of mtDNA of hare species with potential effects on the protein function. Environmental/climatic changes appear to be a major trigger of this adaptation, whereas trans-specific introgressive hybridization seems to play no major role for the occurrence of protein variants.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Positive Selection on Two Mitochondrial Coding Genes and Adaptation Signals in Hares (Genus Lepus) from China

Awadi

Slimen

Schaschl

et al. 2020

Preprint

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“…This information gap has prevented the delineation of a comprehensive picture of genetic diversity and phylogeographic structure of the species. European brown hares have been classified to two major lineages, European (EUR) and Anatolian/Middle Eastern (AME) [ 6 , 15 , 17 – 18 ] that co-exist in Republic of Northern Macedonia, North-Eastern Greece and Bulgaria [ 6 , 10 , 15 ]. In this study, we presented a relatively comprehensive dataset on mtDNA cytochrome b , tRNA-Thr, tRNA-Pro and control region fragments (a total of 916 bp) of brown hares in Central-Eastern Europe, where two datasets were used in the genetic analyses; the first dataset included a 358-bp control region sequence, whereas the second dataset covered a concatenated sequence of mtDNA fragments (the 916-bp sequence).…”

Section: Discussionmentioning

confidence: 99%

“…Thus, based on our data, extending the contact zone to Georgia and the Middle East, as speculated by others [ 6 , 15 ] is not justified. It is interesting that among the sequences previously reported from Cyprus [ 15 , 17 ], one brown hare (CYP4, listed in S1 and S2 Tables; published by [ 17 ]) shared a common haplotype (CR40 that distributes across Northern Europe; see Fig 3 and S1 Table for detailed information) of European lineage origin (subclade CE). However, the haplotype was found outside the range of Northern Europe only in Cyprus.…”

Section: Discussionmentioning

confidence: 99%

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Large-scale mitochondrial DNA analysis reveals new light on the phylogeography of Central and Eastern-European Brown hare (Lepus europaeus Pallas, 1778)

et al. 2018

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European brown hare, Lepus europaeus, from Central and Eastern European countries (Hungary, Poland, Serbia, Lithuania, Romania, Georgia and Italy) were sampled, and phylogenetic analyses were carried out on two datasets: 1.) 137 sequences (358 bp) of control region mtDNA; and 2.) 105 sequences of a concatenated fragment (916 bp), including the cytochrome b, tRNA-Thr, tRNA-Pro and control region mitochondrial DNA. Our sequences were aligned with additional brown hare sequences from GenBank. A total of 52 and 51 haplotypes were detected within the two datasets, respectively, and assigned to two previously described major lineages: Anatolian/Middle Eastern (AME) and European (EUR). Furthermore, the European lineage was divided into two subclades including South Eastern European (SEE) and Central European (CE). Sympatric distribution of the lineages of the brown hare in South-Eastern and Eastern Europe revealed contact zones there. BAPS analysis assigned sequences from L. europaeus to five genetic clusters, whereas CE individuals were assigned to only one cluster, and AME and SEE sequences were each assigned to two clusters. Our findings uncover numerous novel haplotypes of Anatolian/Middle Eastern brown hare outside their main range, as evidence for the combined influence of Late Pleistocene climatic fluctuations and anthropogenic activities in shaping the phylogeographic structure of the species. Our results support the hypothesis of a postglacial brown hare expansion from Anatolia and the Balkan Peninsula to Central and Eastern Europe, and suggest some slight introgression of individual haplotypes from L. timidus to L. europaeus.

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Hares from the Late Pleistocene of Ukraine: a phylogenetic analysis and the status of Lepus tanaiticus (Mammalia, Lagomorpha)

Rabiniak,

Rekovets,

Kovalchuk

et al. 2023

Biologia

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Hares (genus Lepus) are widely distributed in Europe, and they are adapted to various types of habitats. Many species are known to hybridise, and previous molecular genetic studies have revealed recurrent introgressions between species at all stages of the genus’s radiation. The Don hare (Lepus tanaiticus) was described from the Late Pleistocene of the Southern Urals and subsequently reported from coeval deposits of various regions of northern Eurasia. It is morphologically close to the mountain hare (Lepus timidus) and recent studies of mitochondrial DNA questioned its status as an independent species. Here we compare cytochrome b and control-region sequences of mtDNA of arctic Lepus, including, for the first time, eight specimens from Late Pleistocene localities of Ukraine, in order to analyse the phylogenetic relationships between representatives of different taxa. The phylogenetic tree and haplotype network analyses do not support the taxonomic distinctness of the Don hare, and only specimens of Lepus arcticus and Lepus othus form monophyletic groups based on the control-region sequences. Instead, L. tanaiticus are scattered among specimens of L. timidus. The obtained results support the hypothesis that the Don hare is an ancient morphotype of L. timidus, and its distinctive morphological traits are the result of increased geographical variation of the latter due to range expansion and adaptation to the specific conditions of the periglacial biome, similarly to other Late Pleistocene small-mammal species.

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Mitogenomic analysis in European brown hare ( Lepus europaeus ) proposes genetic and functional differentiation between the distinct lineages

Cited by 12 publications

References 49 publications

Positive Selection on Two Mitochondrial Coding Genes and Adaptation Signals in Hares (Genus Lepus) from China

Positive Selection on Two Mitochondrial Coding Genes and Adaptation Signals in Hares (Genus Lepus) from China

Large-scale mitochondrial DNA analysis reveals new light on the phylogeography of Central and Eastern-European Brown hare (Lepus europaeus Pallas, 1778)

Hares from the Late Pleistocene of Ukraine: a phylogenetic analysis and the status of Lepus tanaiticus (Mammalia, Lagomorpha)

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