Genetic diversity is an important measure for biodiversity in alpine plants

Intraspecific, genetic diversity is rarely used as a measure for biodiversity, although it may reflect the adaptive potential of species in changing environments. The international project IntraBioDiv examined whether intraspecific diversity coincides with other measures of biodiversity. Furthermore, it evaluated if protection measures for alpine plants may be improved if intraspecific diversity were considered.

Species richness is the most widely used measure for biodiversity assessment. However, it is intraspecific diversity (genetic polymorphism) that represents the evolutionary and adaptive potential of each species in changing environments. To evaluate how the different measures of biodiversity may serve as surrogates for each other, the IntraBioDiv consortium studied possible correlations between intraspecific diversity and species richness or habitat diversity.
The EC-supported project combined the efforts of 17 institutions from 10 European countries, studying the entire ranges of the Alps and the Carpathians. The project was initiated and coordinated by Pierre Taberlet (University of Grenoble).

Our objectives were:

• to find and explain possible relationships among inter- and intraspecific plant diversity and habitat variation
• to evaluate the existing network of protected areas for its coverage of biodiversity, including genetic diversity.
  
  

We asked the following specific questions, using the Alps and the Carpathians as model systems:

• Is there statistical congruence between intra-/interspecific biodiversity?
• Do areas of high endemism, often coinciding with glacial refugia, harbour a great degree of intraspecific diversity, and what is the relationship between rare gene variants and species?
• Is habitat variation, characterised by environmental parameters, a good surrogate for intra- and interspecific diversity?

Results

Most investigations are now completed. We already published some of the results in scientific articles and further articles will appear soon. The relevant data will be made available for researchers and conservation managers through public data bases. Two PhD thesis that were completed at WSL comprise important results of the project:

Thiel-Egenter, C. (2007). Inter- and intraspecific differentiation and genetic diversity in alpine plants: when phylogeography meets biogeography. WSL Birmensdorf, University of Zurich.
The fundaments of biogeography were laid by the early biologists by their recognition of the underlying factors that influence species distribution patterns, namely history, dispersal and ecology. However, biogeographic questions related with these factors are still actively discussed and far from being answered. In this thesis, patterns in the distribution of both species and alleles are inferred from extensive data on alpine plant taxa and related with factors concerning the Quaternary history, barriers for dispersal and species ecological traits. Besides distribution patterns, also levels of genetic diversity were investigated and shed light on historical population processes and on the relative influence of mountain system (Alps and Carpathians), elevation and species- specific traits.

Steinmann, K. (2008): Testing basic assumptions of species richness hypotheses using plant species distribution data. WSL Birmensdorf, University of Zurich.
The Earth’s species richness is the result of biological evolution over the last billions of years. Manifold processes interact together and influence the spatial distribution of species richness. Trying to answer the question of “why are there so many kinds of species”, researchers developed countless species richness hypotheses over the last two centuries. Different mechanisms influencing species richness patterns act on different spatial and temporal scales. As in natural systems space and diversity are correlated, it is difficult to disentangle the manifold factors, which are correlated either as a consequence of mechanistic relationships or as a matter of stochasticity. In this thesis we tested the following aspects of plant species diversity:

1. Climate gradients and species richness of functional groups
2. Habitat diversity and area effect on species richness
3. Climate gradients and historical effects on species richness

Study area

The study on the relationship of diversity at all three levels of biodiversity encompassed the entire ranges of the European Alps and the Carpathians. While species and habitat diversity were assessed on areas above 1000m a.s.l., the genetic analysis were restricted to the range above 1500m a.s.l.

Grid system
Grid system adopted for assessing ecosystem, species and genetic diversity of alpine vascular plants. Each grid cell that comprised a minimal area above a defined threshold represents approximately 563km². The sampling for the genetically analyzed species was restricted to areas of higher altitude and comprised only every second grid cell in the Alps.

Methods

WSL staff

• Schoville SD, Dalongeville A, Viennois G, et al. (2018) Preserving genetic connectivity in the European Alps protected area network. Biological Conservation 218, 99–109.

• Rogivue A, Graf R, Parisod C, Holderegger R, Gugerli F (2018) The phylogeographic structure of Arabis alpina in the Alps shows consistent patterns across different types of molecular markers and of geographic scales. Alpine Botany 128, 35–45.

• Alvarez N, Thiel-Egenter C, Tribsch A, Manel S, Taberlet P, Küpfer P, Holderegger R, Brodbeck S, Gaudeul M, Gielly L, Mansion G, Negrini R, Paun O, Pellecchia M, Rioux D, Schönswetter P, Schüpfer F, Van Loo M, Winkler M, Gugerli F, IntraBioDiv consortium 2009. Biogeographic history of alpine plants: substrate ecology drives genetic structures. Ecology Letters 12: 632–640.

• Gugerli F, Englisch T, Niklfeld H, Tribsch A, Mirek Z, Ronikier M, Zimmermann NE, Holderegger R, Taberlet P, IntraBioDiv Consortium 2008. Relationships among levels of biodiversity and the relevance of intraspecific diversity in conservation – a project synopsis. Perspectives in Plant Ecology, Evolution and Systematics 10: 259–281.

• Jay F, Manel S, Alvarez N, Durand E, Thuiller W, Holderegger R, Taberlet P, François O 2012. Forecasting changes in population genetic structure of Alpine plants in response to global warming. Molecular Ecology 21: 2354–2368.

• Manel S, Gugerli F, Thuiller W, Alvarez N, Legendre P, Holderegger R, Gielly L, Taberlet P, IntraBioDiv Consortium 2012. Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation. Molecular Ecology 21: 3729–3738.
• Taberlet P, Zimmermann NE, Englisch T, Tribsch A, Holderegger R, Alvarez N, Niklfeld H, Mirek Z, Moilanen A, Ahlmer RW, Ajmone-Marsan P, Bona E, Bovio M, Choler P, Cieślak E, Coldea G, Colli L, Cristea V, Dalmas J-P, Frajman B, Garraud L, Gaudeul M, Gielly L, Gutermann W, Jogan N, Kagalo AA, Korbecka G, Küpfer P, Lequette B, Letz RD, Manel S, Mansion G, Marhold K, Martini F, Negrini R, Niño F, Paun O, Pellecchia M, Perico G, Piekos-Mirkowa H, Prosser F, Puscas M, Ronikier M, Scheuerer M, Schneeweiss GM, Schönswetter P, Schratt-Ehrendorfer L, Schüpfer F, Selvaggi A, Steinmann K, Thiel-Egenter C, van Loo M, Winkler M, Wohlgemuth T, Wraber T, Gugerli F, IntraBioDiv Consortium 2012. Genetic diversity in widespread species is not congruent with species richness in alpine plant communities. Ecology Letters 15: 1439–1448.

• Thiel-Egenter C, Alvarez N, Holderegger R, Tribsch A, Englisch T, Wohlgemuth T, Colli L, Gaudeul M, Gielly L, Jogan N, Linder HP, Negrini R, Niklfeld H, Pellecchia M, Rioux D, Schönswetter P, Taberlet P, van Loo M, Winkler M, IntraBioDiv Consortium, Gugerli F 2011. Break zones in the distributions of alleles and species in alpine plants. Journal of Biogeography 37: 772–782.

• Thiel-Egenter C, Gugerli F, Alvarez N, Brodbeck S, Cieslak E, Colli L, Englisch T, Gaudeul M, Gielly L, Korbecka G, Negrini R, Patrini M, Paun O, Pellecchia M, Rioux D, Ronikier M, Schönswetter P, Schüpfer F, Taberlet P, Tribsch A, Van Loo M, Winkler M, Holderegger R, IntraBioDiv Consortium 2009. Effects of life history traits on high-mountain plant genetic diversity: a multi-species, large-scale study across the Alps and the Carpathians. Global Ecology & Biogeography 18: 78–87.

• Thiel-Egenter C, Holderegger R, Brodbeck S, IntraBioDiv Consortium, Gugerli F 2009. Concordant genetic breaks, identified by combining clustering and tessellation methods, in two co-distributed alpine plant species. Molecular Ecology 18: 4495–4507.

• Tribsch A, Englisch T, Gugerli F, Holderegger R, Niklfeld H, Steinmann K, Thiel-Egenter C, Zimmermann NE, Taberlet P, IntraBioDiv Consortium 2010. Integrating data across biodiversity levels; the project IntraBioDiv. In: Körner C, Spehn EM (eds.), Data Mining for Global Trends in Mountain Biodiversity, 89–105. CRC/Taylor & Francis, Boca Raton.

IntraBioDiv consortium

• Alvarez, N., Arrigo, N., IntraBioDiv Consortium 2008. An R (CRAN) scripts collection for computing genetic structure similarities based on STRUCTURE 2 outputs. Molecular Ecology Resources 8: 757–762.

• Alvarez N, Manel S, Schmitt T, IntraBioDiv Consortium 2012. Contrasting diffusion of Quaternary gene pools across Europe: the case of the arctic-alpine Gentiana nivalis L. (Gentianaceae). Flora 207: 408–413.

• Coldea G, Stoică I-A, Puşcaş M, Ursu T, Oprea A, IntraBioDiv Consortium 2009. Alpine–subalpine species richness of the Romanian Carpathians and the current conservation status of rare species. Biodiversity and Conservation 18: 1441–1458.

• Ehrich D, Gaudeul M, Assefa A, Koch M, Mummenhoff K, Nemomissa S, IntraBioDiv Consortium, Brochmann C 2007. Genetic consequences of Pleistocene range shifts: contrast between the Arctic, the Alps and the East African mountains. Molecular Ecology 16: 2542–2559.

• Manel S, Berthoud F, Bellemain E, Gaudeul M, Luikart G, Swenson JE, Waits LP, Taberlet P, IntraBioDiv Consortium 2007. A new individual-based spatial approach for identifying genetic discontinuities in natural populations. Molecular Ecology 16: 2031–2043.

• Meirmans PG, Goudet J, IntraBioDiv Consortium, Gaggiotti OE 2011. Ecology and life history affect different aspects of the population structure of 27 high-alpine plants. Molecular Ecology 20: 3144–3155.

• Mraz P, Gaudeul M, Gielly L, Choler P, Taberlet P, IntraBioDiv Consortium 2007. Genetic structure of Hypochaeris uniflora (Asteraceae) suggests vicariance in the Carpathians and rapid post-glacial colonization of the Alps from an eastern Alpine refugium. Journal of Biogeography 34: 2100–2114.

• Paun O, Schönswetter P, Winkler M, IntraBioDiv Consortium, Tribsch A 2008. Historical divergence versus contemporary gene flow: evolutionary history of the calcicole Ranunculus alpestris group (Ranunculaceae) in the European Alps and the Carpathians. Molecular Ecology 17: 4263–4275.

• Ronikier M, Cieślak E, Korbecka G 2008. High genetic differentiation in the alpine plant Campanula alpina Jacq. (Campanulaceae): evidence for glacial survival in several Carpathian regions and long isolation between the Carpathians and the Eastern Alps. Molecular Ecology 17: 1763–1775.

• Tribsch A, Taberlet P, IntraBioDiv Consortium 2006. The EU-Project IntraBioDiv – Tracking surrogates for intraspecific biodiversity: towards efficient selection strategies for the conservation of natural genetic resources using comparative mapping and modelling approaches. In: Price MA (ed.), Global Change in Mountain Regions, 148–150. Sapiens Publishing, Duncow, Kirkmahoe, Dumfrieshire.

• Winkler M, Tribsch A, Paun O, Englisch T, IntraBioDiv Consortium, Schönswetter P 2010. Pleistocene distribution range shifts were accompanied by breeding system divergence within Hornungia alpina (Brassicaceae) in the Alps. Molecular Phylogenetics and Evolution 54: 571–582.