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Analysis of Chloroplast DNA Variability Confirms the Existence of Several Pleistocene Lime Refugia in Southern Siberia

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Abstract

The periodicity of the range expansions of representatives of broad-leaved (nemoral) forests in the south of Siberia in the Quaternary and the presence of glacial refugia of broad-leaved species remain poorly studied. In this work, we investigate the variability of five fragments of chloroplast DNA in two known populations of the Nasczokin’s lime (T. nasczokinii Stepanov) located near the city of Krasnoyarsk and in five populations of the Far Eastern species, Amur lime (T. amurensis Rupr.), in comparison with the variability data of the small-leaved lime (T. cordata Mill.) and Siberian lime (T. sibirica Bayer). The results of the study of chloroplast DNA were compared with the polymorphism of nuclear microsatellite loci and with floristic and paleogeographic data. It was found that the two studied Siberian taxa, T. sibirica and T. nasczokinii, have an independent origin, since they carry two significantly different haplotypes of chloroplast DNA. The t3a haplotype, fixed in Nasczokin’s lime, was found only in Europe, while the t2 haplotype, fixed in Siberian lime (Kuznetsk Alatau Mts.), dominates in the eastern populations of small-leaved lime—in Western Siberia, the Urals, and the Russian Plain. Both haplotypes differ from those found in the Amur lime, which excludes the contribution of the Far Eastern species to the Siberian populations. The obtained data on the variability of chloroplast DNA in endemic Siberian taxa of Tilia are consistent with the results of the variability of nuclear markers and confirm the species status of T. nasczokinii. Taken together, these data suggest that Nasczokin’s lime, independently and earlier than Siberian lime, separated from small-leaved lime and, later, like T. sibirica, survived several glacial maxima in the south of Siberia.

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ACKNOWLEDGMENTS

We are grateful to M.I. Sedaeva, N.A. Kochunova, T.N. Veklich, E.A. Andysheva, L.A. Kameneva, A.I. Izmailov, I.Yu. Isakov, A.G. Bystrushkin, T.V. Semerikova, Yu.Ya. Khrunyk, L.I. Agafonov, and V.L. Semerikov for participation in the collection of lime samples; K.A. Panikovskaya and A.N. Kravchenko for help in laboratory analyses; E.V. Zinoviev for paleontological consultations; and an anonymous reviewer for constructive comments.

Funding

This study was carried out with financial support from the Russian Foundation for Basic Research, the Government of the Krasnoyarsk Krai, and the Krasnoyarsk Regional Science Foundation, project no. 19-44-240006 p_a; the collection of part of the material was carried out within the framework of state contracts of the Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, no. 122021000090-5 and the Sukachev Institute of Forest, Siberian Branch, Russian Academy of Sciences, no. 0287-2021-0009.

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  1. Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, 620144, Yekaterinburg, Russia

    S. A. Semerikova

  2. Sukachev Institute of Forest, Siberian Branch, Russian Academy of Sciences, 660036, Krasnoyarsk, Russia

    A. K. Ekart

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  1. S. A. Semerikova
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Correspondence to S. A. Semerikova or A. K. Ekart.

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The authors declare that they have no conflicts of interest. This article does not contain any studies involving animals or human participants performed by any of the authors.

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Translated by V. Mittova

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Semerikova, S.A., Ekart, A.K. Analysis of Chloroplast DNA Variability Confirms the Existence of Several Pleistocene Lime Refugia in Southern Siberia. Russ J Genet 58, 393–403 (2022). https://doi.org/10.1134/S1022795422030127

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