Phylogeography of a widely distributed species reveals a cryptic assemblage of distinct genetic lineages needing separate conservation strategies

https://doi.org/10.1016/j.ppees.2018.10.003Get rights and content

Highlights

  • The widely spread Silene nutans is an assemblage of distinct genetic lineages.

  • Seven Evolutionary Significant Units were identified.

  • Genetic lineages differ in distribution and abundance, so in management strategies.

  • Genetic restoration not considering phylogeographic patterns risks failure.

  • Seed collection for ex situ conservation should mention the genetic lineage.

Abstract

Genetic structure in broadly distributed herbs may be shaped by past climate events, leading to distinct genetic lineages, and possibly to different Evolutionary Significant Units (ESUs). We identified the potential glacial refugia, postglacial (re)colonization routes, contact zones and ESUs in the widespread but locally rare Silene nutans to propose appropriate conservation strategies related to migration history-related genetic structure. We sequenced four plastid DNA markers from 136 populations covering S. nutans European distribution range. We built a network on concatenated sequences using statistical parsimony and performed Bayesian and Maximum Likelihood analyses to build a phylogenetic tree. Haplotype genetic diversity and between-population differentiation (GST, NST) were calculated. Based on 23 plastid haplotypes, populations were ascribed to seven strongly differentiated genetic lineages. Potential refugia were identified: in the Iberian and Italian Peninsulas, expanding to south-western France and the Alps, respectively; in south-central France, reaching England and Belgium; an eastern refugium, following a north-westward expansion; in the Balkans, expanding to north-eastern Italy, and in the Carpathians. Several contact zones were identified. Silene nutans consists of a cryptic assemblage of genetically distinct taxa, with at least seven ESUs. Evaluating the distribution range, the abundance, and the conservation status of each ESU is necessary for the preservation of the S. nutans species complex at European and regional levels. Ex situ conservation and genetic restoration involving plant translocations must consider the phylogeographic history and the distinct genetic lineages to avoid the introduction of poorly adapted plants and outbreeding depression leading to non-viable hybrid progeny, especially in contact zones.

Introduction

During the last decades, anthropogenic activities have profoundly affected the distribution and abundance of many plant species in Europe (Essl et al., 2013; Hautekèete et al., 2015). One of the major consequences of this is the fragmentation and degradation of wild habitats, resulting in strongly reduced areas of suitable habitats. Many plant species have (locally) declined and often remain as small and isolated populations. These small populations usually suffer from genetic erosion and inbreeding depression (Van Geert et al., 2008; Van Rossum, 2008; Maschinski et al., 2013; Ottewell et al., 2016). As a consequence, they may not hold the evolutionary resilience to persist in the current or restored habitat conditions and to adapt in response to environmental and climatic changes, leading to a high risk of extinction (Montalvo et al., 1997; Sgrò et al., 2011). Besides the traditional in situ ecological management aiming at restoring suitable habitats, genetic restoration measures need to be undertaken. In case it is not possible to restore the connectivity by gene flow and in the absence of seed rain and of a persistent seed bank in the soil, the restoration of the evolutionary potential of the populations requires assisted gene flow interventions such as artificial cross pollinations, hay transfer, seed sowing and plug plant transplantations (e.g., Weeks et al., 2011; Godefroid et al., 2016; Barmentlo et al., 2018). The conservation strategies that should be applied depend on the patterns of genetic variation and structure of the populations, which may differ across the distribution range of the species (Maurice et al., 2016; Ottewell et al., 2016; Duwe et al., 2017). For instance, if the remaining populations are too genetically depauperate and inbred, non-local pollen or seed source populations still retaining high genetic variation should be privileged (Maschinski et al., 2013; Mijangos et al., 2015; Zavodna et al., 2015). However, this implies an appropriate selection of the source populations in order to maximize evolutionary resilience while avoiding outbreeding depression in the progeny (Menges, 2008; Sgrò et al., 2011; Weeks et al., 2011). Therefore, a good knowledge of the genetic variation and structure throughout the distribution range of the species is needed to identify the Evolutionary Significant Units (ESUs) (Fraser and Bernatchez, 2001; Ottewell et al., 2016).

The current spatial structuring of genetic diversity within a species has not only been impacted by contemporary processes related to anthropogenic activities, but is often the result of past climate events. The glacial-interglacial repeated cycles during the Quaternary (ca. 2.4 million years ago to present) have played a significant role in shaping the present-day genetic structure. During glacial maxima, northern Europe was covered with ice, and Western, Central and Eastern Europe by permafrost and steppe-like habitats. The ranges of temperate plant species were usually restricted to southern Europe, only occurring in distant glacial western and eastern refugia, located in the Iberian and Italian peninsulas and in the Balkans, but also in the Pannonian Basin, the Carpathians and in the far east, e.g. in the Pontic steppe and the Russian plain (e.g., Taberlet et al., 1998; Heuertz et al., 2004; Tollefsrud et al., 2009; Hewitt, 2011; Tzedakis et al., 2013; Kajtoch et al., 2016; Kolář et al., 2016; Mráz and Ronikier, 2016; Volkova et al., 2016; Tóth et al., 2017). The populations that remained isolated from each other have evolved separately as a result of genetic drift and selective pressures. This has promoted allopatric genetic divergence, leading to distinct genetic lineages (Hewitt, 2011; Barnard-Kubow et al., 2015). Postglacial species range expansion has occurred northwards from these western and eastern refugia through different migration routes, allowing divergent lineages to meet, forming high genetically-diverse contact zones (e.g., Taberlet et al., 1998; Pamilo and Savolainen, 1999; Hewitt, 2000). In these contact zones, the differentiated lineages may hybridize (Barton and Hewitt, 1985; Hewitt, 2011; Havrdová et al., 2015; Soubani et al., 2015). Particular evolutionary processes, such as ecological specialization may also occur and/or the genetic lineages may have become so divergent that they are reproductively isolated. The populations of different lineages may then coexist without exchanging genes. Therefore, despite occurring in proximity, the lineages may correspond to different ESUs, or even to distinct species (Jiggins and Mallet, 2000; Barnard-Kubow et al., 2015; Martin et al., 2016, 2017).

In the present study, we used plastid DNA markers to investigate the phylogeographic pattern of the perennial herb Silene nutans L. (Caryophyllaceae) at a comprehensive scale in Europe. Silene nutans occupies a wide continental distributional range, extending from western and northern Europe to central Siberia and the South-Caucasus (Hegi, 1979; Jalas and Suominen, 1988). Throughout its distribution range, it shows a wide phenotypic variation, especially in reproductive traits, with the description of subspecies, varieties and edaphic ecotypes (Hepper, 1951; De Bilde, 1973; De Bilde et al., 1977; Jeanmonod and Bocquet, 1983; Van Rossum, 2000) and can vary in its abundance through its distribution range (Jalas and Suominen, 1988). In its north-western range margin, the species is locally rare, with disjunct populations, e.g. in UK, northern France, Belgium, The Netherlands, Denmark and Fennoscandia (Hultén, 1971; Fitter, 1978; Hegi, 1979; Hultén and Fries, 1986; Delvosalle, 2009). Several genetic lineages were identified, based on nuclear (microsatellites, allozymes) and plastid markers (Van Rossum et al., 1997, 1999, 2003; Van Rossum and Prentice, 2004; Martin et al., 2016; Van Rossum et al., 2016). The genetic structure in Western Europe appears to be mainly shaped by the climatic oscillations during the Quaternary past (postglacial) migration history (Martin et al., 2016; Van Rossum et al., 2016). In the present paper, we aim to identify the potential refugia during the glacial periods, the main postglacial (re)colonization routes, the contact zones between differentiated lineages, and the possible ESUs at the whole European scale. We discuss the implications of our findings for the conservation strategies to apply in relation to phylogeographic genetic patterns related to past migration history.

Section snippets

Species and plant material

Silene nutans (Caryophyllaceae) is a diploid (2n = 24), long-lived perennial rosette-forming herb. It typically occurs on calcareous and siliceous rock outcrops, in xero-thermophilous open grassland and forest edge habitats, up to elevations of 2500 m a.s.l. (Hepper, 1956; Van Rossum et al., 1999; Van Rossum, 2000). Flowers of S. nutans are protandrous, pollinated by insects, mainly by moths. The species shows a self-compatible reproductive system, but maternal discrimination against selfing

Plastid diversity

TrnG-trnS showed 11 haplotypes characterized by seven nucleotide substitutions and five indels (two of 2 bp and three of 19, 24 and 68 bp, respectively). For trnL-trnF we found 11 haplotypes, with six nucleotide substitutions and three indels of 2, 6 and 18 bp, and one mononucleotide repeat of poly T microsatellite. PsbA-trnH showed 11 haplotypes that were characterized by 14 nucleotide substitutions and one indel of 9 bp. For matK we found nine haplotypes and seven nucleotide substitutions.

A strong phylogeographic pattern with multiple refugia

Our study of the genetic patterns of S. nutans populations at a comprehensive scale in Europe, using plastid markers, reveals a clear phylogeographic structure. The populations can be ascribed to strongly differentiated genetic lineages (the seven branches of the network), and groups of related haplotypes are restricted to particular geographic regions. The phylogeographic pattern clearly shows that the current genetic structure of S. nutans has been shaped by past climatic events. Several

Conclusion

Many phylogeographic studies at a comprehensive European scale have focused on long-lived tree species (e.g. Petit et al., 2002; Heuertz et al., 2004; Tollefsrud et al., 2009; Havrdová et al., 2015; Mandák et al., 2016; Tóth et al., 2017). Only a few have investigated widely spread herbaceous species (Hathaway et al., 2009; Prentice et al., 2011; Sutkowska et al., 2014; Volkova et al., 2016). Our findings emphasize the importance of investigating widely distributed and morphologically variable

Acknowledgements

This work was supported by the National Fund for Research Luxembourg (AFR grant for S. Le Cadre). We thank all the collectors and Botanic Gardens cited in Appendix S1 in Supporting Information for their contribution to plant material sampling; the Conservatoire botanique national de Rennes, the BSBI (D.A. Pearman, R.E.N. Smith, M.J. Hawksford, S. Wild, W. McCarthy, A. Willmot, M.W. Rand, A. Knapp, J. Knight, Q. Groom), MNHN Luxemburg (G. Colling), Flo.Wer (W. Van Landuyt), Floron (W. van der

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    1

    Present address: Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada.

    2

    Present address: BIOGECO, INRA, Université de Bordeaux, F-33620 Cestas, France.

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