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Downloaded From2 Biogeographical network analysis of plant species distribution in the Mediterranean region Maxime Lenormand,1, ∗ Guillaume Papuga,2, 3, ∗ Olivier Argagnon,2 Maxence Soubeyrand,1 Guilhem De Barros,2 Samuel Alleaume,1 and Sandra Luque1 1Irstea, UMR TETIS, 500 rue JF Breton, 34093 Montpellier, France 2Conservatoire botanique national m´editerran´eende Porquerolles, Parc scientifique Agropolis, 2214 boulevard de la Lironde, 34980 Montferrier sur Lez, France 3UMR 5175 CEFE, CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France The delimitation of bioregions helps to understand historical and ecological drivers of species distribution. In this work, we performed a network analysis of the spatial distribution patterns of plants in south of France (Languedoc-Roussillon and Provence-Alpes-C^oted'Azur) to analyze the biogeographical structure of the French Mediterranean flora at different scales. We used a network approach to identify and characterize biogeographical regions, based on a large database containing 2.5 million of geolocalized plant records corresponding to more than 3,500 plant species. This methodology is performed following five steps, from the biogeographical bipartite network construction, to the identification of biogeographical regions under the form of spatial network communities, the analysis of their interactions and the identification of clusters of plant species based on the species contribution to the biogeographical regions. First, we identified two sub-networks that distinguish Mediterranean and temperate biota. Then, we separated eight statistically significant bioregions that present a complex spatial structure. Some of them are spatially well delimited, and match with particular geological entities. On the other hand fuzzy transitions arise between adjacent bioregions that share a common geological setting, but are spread along a climatic gradient. The proposed network approach illustrates the biogeographical structure of the flora in southern France, and provides precise insights into the relationships between bioregions. This approach sheds light on ecological drivers shaping the distribution of Mediterranean biota: the interplay between a climatic gradient and geological substrate shapes biodiversity patterns. Finally this work exemplifies why fragmented distributions are common in the Mediterranean region, isolating groups of species that share a similar eco-evolutionary history. INTRODUCTION logical advances have allowed for the development of more rigorous frameworks (Kreft & Jetz, 2010). Mul- The delimitation of biogeographical regions or tivariate methods, such as hierarchical clustering algo- bioregions based on the analysis of their biota has been rithms, have thus been successfully applied in a wide a founding theme in biogeography, from the pioneer range of studies focused on a variety of organisms, un- work of Wallace(1876), Murray(1866) or Wahlen- der very different spatial scale (from regional to world- berg(1812) to the most recent advances of Cheruvelil wide perspective). Yet, the production of detailed et al. (2017); Ficetola et al. (2017). Describing spatial cartographic outputs portraying the differentiation of patterns of biodiversity has appeared fundamental to vegetation into distinct homogeneous bioregions re- understand the historical diversification of biota, and mains difficult, especially where spatial heterogeneity gain a better understanding of ecological factors that of assemblages is associated with complex environ- imprint spatial patterns of biodiversity (Graham & mental gradients (Mikolajczak et al., 2015). Besides, Hijmans, 2006; Ricklefs, 2004). Additionally, it has the identification of meaningful and coherent biore- become a key element in the identification of spatial gions represents only one step of the biogeographical conservation strategies (Funk et al., 2002; Mikolajczak regionalizations (Morrone, 2018). It is also crucial to propose new metrics to quantify the relationship be- arXiv:1803.05275v3 [q-bio.PE] 7 Jan 2019 et al., 2015; Rushton et al., 2004). To divide a given territory into meaningful and coherent bioregions, the tween bioregions and to analyze species and spatial overall aim is to minimize the heterogeneity in taxo- relationships. nomic composition within regions, while maximizing Some regions of the world oppose inherent diffi- differences between them (Kreft & Jetz, 2010; Stod- culties due to their highly diversified biota, reflect- dart, 1992). Although such delineation of bioregions ing complex eco-evolutionary processes. The Mediter- has been based for a long time on expert knowledge of ranean basin is one of the largest and most impor- qualitative data collection the increasing availability tant biodiversity hotspots in the world (Blondel et al., of species-level distribution data and recent techno- 2010; Myers et al., 2000). This region hosts about 25,000 plant species representing 10% of the world's total floristic richness concentrated on only 1% of the ∗ Corresponding authors: [email protected] & guil- world's surface (Greuter, 1991). Additionally, a high [email protected] who contributed equally to this level of narrow endemism is a major feature of this work. biome (Thompson, 2005). Endemism and richness re- 2 sult in a very heterogeneous region, whose compre- plant species revealed by botanical inventories (Tison hension of spatial patterns of plant distribution is & Foucault, 2014; Tison et al., 2014) and the detailed clue to get better insights into past and actual pro- databases compiled by the French National Botanic cesses shaping biodiversity (Qu´ezel, 1999). The onset Conservatory of Porquerolles and the Alpine National of the Mediterranean climate during the Pliocene and Botanic Conservatory. The objective of this work is the diverse glacial periods of the Pleistocene (Qu´ezel to delineate bioregions, identify groups of species and & M´edail, 2004) have shaped the most important analyse the relationships between the two entities. phases of plant evolution since the Tertiary (Thomp- son, 2005). Additionally, due to a long history of hu- man presence, contemporary flora has been widely in- MATERIALS AND METHODS fluenced by human-mediated dispersal, land-use and other pressures (Dahlin et al., 2014; Fenu et al., 2014). Dataset and study area The French Mediterranean area stretches from the Pyrenees in the south-west to the slopes of the Mar- The study area, situated in southern France, itime and Ligurian Alps in the east. It encompasses encompasses the former Languedoc-Roussillon re- three zones highlighted as glacial refugia (M´edail& gion (five departments of the current Occitanie re- Diadema, 2009), and the eastern sector represents one gion: Pyr´en´ees-Orientales, Aude, H´erault,Gard and of the ten main biodiversity hotspots in the Mediter- Loz`ere)and the whole Provence-Alpes-C^oted'Azur ranean area (M´edail& Qu´ezel, 1997). This area rep- region. It extends around the entire Mediterranean resents the northern limit of the Mediterranean cli- coastline of mainland France and inland, compris- mate in the western basin, and thus constitutes a cli- ing almost all the Mediterranean hinterland, totalling matic transition from a Mediterranean zone that has 558; 776 km2 (Figure1). The topography is struc- a summer drought to a temperate zone less prone to tured by three major mountain ranges, the Pyrenees summer drought (Walter & Breckle, 1991 1994). On in the southwest, the Massif central in the north- a finer scale, the climate is more complex with sev- west and the Maritime Alps in the north-east. In- eral subtypes and intricated boundaries (Joly et al., between, the landscape is mostly hilly with some low- 2010; Tassin, 2017). Several works have tried to map lands around rivers that flow into lagoons or marshy the distribution of biogeographical entities. To date, deltas such as the Camargue. The Rh^oneis the main no statistical analysis had been ran to tackle those structuring river and delimitates western and eastern expert-based maps with up-to-date plant records, in subregions. Acidic substrates and silicate soils are order to test their reliability. mainly found in the aforementioned mountain ranges In order to depict spatial structure in such a com- and in the smaller Maures-Est´erelrange in southern plex regional flora, a large dataset is required. While Provence. The remaining part of the territory is dom- the level of diversity and complexity of such dataset inated by calcareous or marly substrates (principally may appear overwhelming at first glance, the emer- Cretaceous and Jurassic), with some significant allu- gence of network-based approaches has opened new vial zones and small volcanic areas. paths for identifying and delimiting bioregions where The SILENE database1, has been created in 2006, the presence-absence matrix is represented by a bi- and is the reference botanical database in the study partite network. For example, Kougioumoutzis et al. area. It contains historical data gathered from the sci- (2014) applied the NetCarto algorithm (Guimer`a& entific literature and herbaria along with more recent Nunes Amaral, 2005) in order to identify biogeograph- data coming from public studies, partnerships, local ical modules within the phytogeographical area of the amateur botanist networks and professional botanists Cyclades. Similarly, Vilhena & Antonelli(2015) pro- of the Botanical Conservatory. Our analysis is based 2 posed a network approach for delimiting biogeograph- on a 5 × 5 km grid cells. We decided to only
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