Spatial genetics of brown hares (Lepus europaeus Pallas, 1778) from Turkey: Different gene pool architecture on either side of the Bosphorus?

Demirbaş, Yasin; Albayrak, İrfan; Koca, Ayça Özkan; Stefanović, Milomir; Knauer, Felix; Suchentrunk, Franz

doi:10.1016/j.mambio.2018.09.005

Cited by 6 publications

(4 citation statements)

References 41 publications

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“…In spite of the presence of both Anatolian and typical “European”lineages in the southeastern and southern Balkans, D-loop sequence diversity of brown hares from the Anatolian Peninsula is still higher than in the Balkans. This pattern of diversity is also reflected by the nuclear gene pool as evidenced by both allozyme and microsatellite data [28, 32].…”

Section: Discussionmentioning

confidence: 98%

Positive selection and precipitation effects on the mitochondrial NADH dehydrogenase subunit 6 gene in brown hares (Lepus europaeus) under a phylogeographic perspective

et al. 2019

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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.

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Section: Discussionmentioning

confidence: 98%

Positive selection and precipitation effects on the mitochondrial NADH dehydrogenase subunit 6 gene in brown hares (Lepus europaeus) under a phylogeographic perspective

et al. 2019

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“…To test for statistically significant differences of genetic diversity between the demographic groups, we performed linear mixed effects models (e.g.,[76, 77]) using lme4 [78] and lmerTest [79] implemented in R platform (R Core Team, 2018). We used number of alleles, allelic richness, observed and expected heterozygosities as dependent variables, demographic group and locus type (MHC and microsatellites) as explanatory factors, and locus as random variable.…”

Section: Methodsmentioning

confidence: 99%

Alternated selection mechanisms maintain adaptive diversity in different demographic scenarios of a large carnivore

et al. 2019

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Background Different population trajectories are expected to impact the signature of neutral and adaptive processes at multiple levels, challenging the assessment of the relative roles of different microevolutionary forces. Here, we integrate adaptive and neutral variability patterns to disentangle how adaptive diversity is driven under different demographic scenarios within the Iberian wolf ( Canis lupus ) range. We studied the persistent, the expanding and a small, isolated group within the Iberian wolf population, using 3 MHC class II genes (DRB1, DQA1, and DQB1), which diversity was compared with 39 microsatellite loci. Results Both the persistent and the expanding groups show evidence of balancing selection, revealed by a significant departure from neutrality at MHC loci, significant higher observed and expected heterozygosity and lower differentiation at MHC than at neutral loci, and signs of positive selection. However, despite exhibiting a significantly higher genetic diversity than the isolated group, the persistent group did not show significant excess of MHC heterozygotes. The expanding group, while showing a similar level of genetic diversity than the persistent group, displays by contrast a significant excess of MHC heterozygotes, which is compatible with the heterozygote advantage mechanism. Results are not clear regarding the role of drift and selection in the isolated group due to the small size of this population. Although diversity indices of MHC loci correspond to neutral expectations in the isolated group, accelerated MHC divergence, revealed by a higher differentiation at MHC than neutral loci, may indicate diversifying selection. Conclusion Different selective pressures were observed in the three different demographic scenarios, which are possibly driven by different selection mechanisms to maintain adaptive diversity. Electronic supplementary material The online version of this article (10.1186/s12862-019-1420-5) contains supplementary material, which is available to authorized users.

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“…The differences between the Thracian and Anatolian mainland populations indicate that the Marmara waterway (also called the Turkish Straits System) is a barrier that prevents gene flow between A. chukar populations. Recent genetic studies also support the claim that the Marmara waterway limits the dispersal capability of many terrestrial organisms, including mammals, insects, and plants, between Anatolia and Thrace/the Balkans [ 40 , 51 , 135 , 136 , 137 ]. Because of differences in tectonic evolution and the complex climatic conditions of the Çanakkale and İstanbul Strait, the barrier effects and permeability of the two straits have also changed over time.…”

Section: Discussionmentioning

confidence: 81%

“…Depending on their permeability, altitudinal barriers (mountains) have played an important role in shaping Anatolian biodiversity during the Quaternary climatic fluctuations [ 46 , 47 ]. Evidence for this is the presence of many closely related species in Türkiye near high altitudinal (hard) barriers [ 42 , 48 , 49 , 50 , 51 , 52 , 53 ]. The role of an altitudinal barrier as a contact zone or phylogenetic breaking area is closely related to its hard or soft barrier effect during climatic fluctuations [ 54 , 55 ].…”

Section: Introductionmentioning

confidence: 99%

Geographic Genetic Structure of Alectoris chukar in Türkiye: Post-LGM-Induced Hybridization and Human-Mediated Contaminations

Kaya

Kabasakal

Erdoğan

2023

Biology

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Türkiye is considered an important evolutionary area for Chukar partridge (Alectoris chukar), since it is both a potential ancestral area and a diversification center for the species. Using 2 mitochondrial (Cty-b and D-loop) and 13 polymorphic microsatellite markers, we investigated the geographic genetic structure of A. chukar populations to determine how past climatic fluctuations and human activities have shaped the gene pool of this species in Türkiye. Our results indicate, firstly, that only A. chukar of the genus Alectoris is present in Türkiye (Anatolia and Thrace), with no natural or artificial gene flow from congenerics. Secondly, the geographic genetic structure of the species in Türkiye has been shaped by topographic heterogeneity, Pleistocene climatic fluctuations, and artificial transport by humans. Third, there appears to be three genetic clusters: Thracian, Eastern, and Western. Fourth, the post-LGM demographic expansion of the Eastern and Western populations has formed a hybrid zone in Central Anatolia (~8 kyBP). Fifth, the rate of China clade-B contamination in Türkiye is about 8% in mtDNA and about 12% in nuDNA, with the Southeastern Anatolian population having the highest contamination. Sixth, the Thracian population was the most genetically distinct, with the lowest genetic diversity and highest level of inbreeding and no China clad-B contamination. These results can contribute to the conservation regarding A. chukar populations, especially the Thracian population.

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Spatial genetics of brown hares (Lepus europaeus Pallas, 1778) from Turkey: Different gene pool architecture on either side of the Bosphorus?

Cited by 6 publications

References 41 publications

Positive selection and precipitation effects on the mitochondrial NADH dehydrogenase subunit 6 gene in brown hares (Lepus europaeus) under a phylogeographic perspective

Positive selection and precipitation effects on the mitochondrial NADH dehydrogenase subunit 6 gene in brown hares (Lepus europaeus) under a phylogeographic perspective

Alternated selection mechanisms maintain adaptive diversity in different demographic scenarios of a large carnivore

Geographic Genetic Structure of Alectoris chukar in Türkiye: Post-LGM-Induced Hybridization and Human-Mediated Contaminations

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