Patterns and Processes in Plant Phylogeography in the Mediterranean Basin. A Review

Gonzalo Nieto Feliner

Real Jardín Botánico, CSIC

Plaza de Murillo 2

28014 Madrid

nieto@rjb.csic.es

Phone: +34 914203017

Mobile: +34 609446046

Running head: Plant phylogeography in the Mediterranean Basin

Key words: glacial refugia, hybridization, latitudinal patterns, Mediterranean Basin,

phylogeography, plants, spatio-temporal concordance, straits

1

12

1

2

3

4

34

ABSTRACT

Phylogeography, born to bridge population genetics and phylogenetics in an explicit geographic

context, has provided a successful platform for unveiling species evolutionary histories. The

Mediterranean Basin, one of the earth’s 25 biodiversity hotspots, is known for its complex

geological and palaeoclimatic history. Aiming to throw light on the causes and circumstances that

underlie such a rich biota, a review of the phylogeographic literature on plant lineages from the

Mediterranean Basin is presented focusing on two levels. First, phylogeographic patterns are

examined, arranged by potential driving forces such as longitude, latitude—and its interaction

with altitude—, straits or glacial refugia. Spatial coincidences in phylogeographic splits are found

but, in comparison to other regions such as the Alps or North America, no largely common

phylogeographic patterns across species are found in this region. Factors contributing to

phylogeographic complexity and scarcity of common patterns include less drastic effects of

Pleistocene glaciations than other temperate regions, environmental heterogeneity, the blurring

of genetic footprints via admixing over time and, for older lineages, possibly a greater

stochasticity due to the accumulation of responses to palaeoclimatic changes. At a second level,

processes inferred in phylogeographically-framed studies that are potential drivers of evolution

are examined. These include gradual range expansion, vicariance, long-distance dispersal,

radiations, hybridization and introgression, changes in reproductive system, and determinants of

successful colonization. Future phylogeographic studies have a great potential to help explaining

biodiversity patterns of plant groups and understanding why the Basin has come to be one of the

biodiversity hotspots on earth. This potential is based on the crucial questions that can be

addressed when geographic gaps are adequately filled (mainly northern Africa and the eastern

part of the region), on the important contribution of younger lineages—for which

phylogeographic approaches are most useful—to the whole diversity of the Basin, and on the

integration of new methods, particularly those that allow refining the search for spatio-temporal

concordance across genealogies.

2

56

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

29

30

78

CONTENTS

I. Introduction

II. Patterns

(1) Large-scale spatial patterns

(a) Longitudinal patterns

(b) Latitudinal patterns

(c) Glacial refugia

(d) Role of straits

(2) Spatio-temporal phylogeographic concordance

(3) Patterns and complexity

III. Processes

(a) Gradual range expansion

(b) Vicariance

(c) Long-distance dispersal

(d) Radiations

(e) Hybridization and introgression

(f) Changes in reproductive systems

(g) Ecology determining success of colonization

IV. Perspectives

V. Acknowledgements

VI. References

3

910

31

32

33

34

35

36

37

38

39

40

41

42

43

44

45

46

47

48

49

50

51

52

1112

I. INTRODUCTION

The Mediterranean Basin comprises a large territory around the Mediterranean Sea that is

characterized by a Mediterranean climate, that is to say, mild rainy winters and hot dry summers.

According to Quézel and Médail (2003) the Mediterranean region in a bioclimatic sense spans an

area of 2,300,000 km2, whose limits have sometimes been suggested as coinciding with the

natural distribution range of the olive tree (Olea europaea L.) (Fig. 1). It extends approx. 4000 km

along an east-west axis and approx. 1600 km along a north-south axis.

This region is of considerable biological interest because of its rich biota compared to the

surrounding areas and is considered one of the earth’s 25 biodiversity hot-spots (Myers et al.,

2000). At the plant species level, i.e., in floristic terms, the Mediterranean region contains a flora

that includes c. 24.000 species of which c. 60 % are endemics (Greuter 1991) whereas, for

instance, all of tropical Africa has a comparable plant richness (30,000 taxa) in a surface area four

times larger (Médail and Quezel, 1997). Compared to higher latitudes, 80% of all European plant

endemics are Mediterranean (Comes, 2004). This richness is attributed to a number of factors

including palaeogeologic and palaeoclimatic history, ecogeographical heterogeneity, human

influence (Blondel and Aronson, 1999; Blondel et al., 2010) and a high percentage of species with

narrow distribution ranges (Humphries et al., 1999; Thompson, 2005).

Geological and palaeoclimatic complexity is characteristic of the Mediterranean region. Its

geological evolution involves complicated interactions between orogenic processes and

widespread extensional tectonics (Rosenbaum et al., 2002). The area was formed during the

Cenozoic simultaneously with the convergence of the African and Eurasian Plates and three

associated smaller plates, Iberia, Apulia and Arabia (Dercourt et al., 1986; Krijgsman, 2002). The

western Mediterranean was particularly active tectonically and consisted during the Oligocene of

several small blocks that were remnants of a Paleozoic mountain chain, the Hercynian belt

(Rosenbaum et al., 2002). Rotation, migration and collision processes along more than 30 Mya

4

1314

53

54

55

56

57

58

59

60

61

62

63

64

65

66

67

68

69

70

71

72

73

74

75

76

77

1516

resulted in those small blocks located in the current territories of the Betic-Rif ranges, the Balearic

Islands, the Kabylies, Corsica, Sardinia, and Calabria. The eastern Mediterranean region (Hellenic

arc and Aegean basin) is more recent and its present configuration is the result of the collision of

the Arabian plate with stable Eurasia in middle Miocene, which closed the connection between

the Tethys Sea and the Indian Ocean (Krijgsman, 2002).

The palaeoclimatic history of the Mediterranean Basin included important long-term changes

such as the gradual global cooling since the Oligocene (Zachos et al., 2008) and an aridification

that started c. 9-8 Mya (Van Dam, 2006). During the Late Miocene, subduction processes in the

westernmost Mediterranean caused the closure of the marine gateways that existed between the

Atlantic Ocean and the Mediterranean Sea, leading to the desiccation of the Mediterranean Sea

that is known as the Messinian Salinity Crisis (MSC) 5.96-5.33 Mya (Hsü, 1972; Krijgsman, 2002).

This period was followed by the establishment of a Mediterranean type climate, around 3.2 Mya

(Suc, 1984). In addition, the Basin has been influenced by cyclical climatic changes, driven by the

Milankovitch oscillations, due to periodical shifts in the Earth's orbit and axial tilt that decreased

their periodicity to 100 Ky during the Pleistocene (Imbrie et al., 1993; Jansson and Dynesius,

2002).

Phylogeography has shed light on the evolutionary history of current plant species by

bridging population genetic approaches and phylogenetic focuses, or micro- and macroevolution,

as the father of the discipline put it (Avise et al., 1987). The geographic coverage of

phylogeographic investigations has been more intense in regions such as North America

(Brunsfeld et al., 2001; Soltis et al., 2006) and the Alps (Schönswetter et al., 2005), but has

reached most regions including the Arctic (Abbott and Comes, 2004), China (Qiu et al., 2011), the

Southern Hemisphere (Beheregaray, 2008) and also the Mediterranean region, where a

substantial increase in the number of studies has occurred over the last ten to twelve years.

5

1718

78

79

80

81

82

83

84

85

86

87

88

89

90

91

92

93

94

95

96

97

98

99

100

101

1920

The present paper reviews the topic of Mediterranean Plant Phylogeography aiming to throw

light on the evolutionary history of plants in the Basin, finding clues for its biodiversity richness

and complexity, and contributing to understand the whole puzzle of the history of European

plants during the last 2 - 3 My. The review has a double focus, on patterns and process, and has

been elaborated from studies published in over 130 papers.

A summary of the knowledge concerning a very significant part of the region, i.e., the three

southern European peninsulas (Iberia, Italy, Balkans), and the role they have played in European

biogeography during the last million years, has been recently published (Hewitt, 2011). The

Balkans represent the main biodiversity hotspot and the major source for postglacial colonization

of central and northern Europe and it was suggested that such richness could be related to

opportunities for dispersal and vicariance along a complex geological history that included several

land connections, disconnections and submergences, particularly during the Miocene and

Pliocene (Griffiths et al., 2004; Tzedakis, 2004). However, its geographic position closer to Asian

biotas probably also contributed to its richness (Mansion et al., 2008).

In the evolution of plant lineages in the Iberian Peninsula, on the other hand, determinant

factors are the mountain ranges allowing multiple refugia and producing “a pulsating patchwork

of allopatric to parapatric clades”, and the recurrent connections and disconnections with

Northern Africa starting even before the MSC between 7 and 14 Mya (Hewitt, 2011).

The Italian Peninsula is a younger conglomerate that contributed less to postglacial

colonization of central and northern Europe due to the strong geographic barrier represented by

the Alps. However, multiple refugia have been identified corresponding to major mountain blocks,

with a particular differentiation in the South both in animal (e.g., Joger et al., 2007; Canestrelli and

Nascetti, 2008) and in plant groups (Cozzolino et al., 2003; Vettori et al., 2004; Heuertz et al.,

2006; Španiel et al., 2011).

6

2122

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

123

124

125

2324

However, that work—one of the last by the late Godfrey Hewitt (Hewitt, 2011)—was almost

exclusively based on studies of mammals, reptiles, amphibians and insects. Despite the common

geological, climatic and environmental history for all organisms phylogeographic patterns might

vary. Mechanisms such as polyploidization and hybridization, and ecogeographical concepts such

as niche conservatism, are regarded as more significant in plants than in animal groups

(Sanmartín, 2007; Donoghue, 2008).

This review is focused on the species level, i.e., within species or closely-related species, as

was the original scope of Phylogeography (Avise et al., 1987). However, there is not a sharp

border line between species and closely-related species and thus some works going beyond the

species level that were important for the Mediterranean Basin have also been considered. On a

geographic side, despite being traditionally considered a part or an extension of the

Mediterranean region, the Macaronesian archipelagos have not been considered here because

oceanic island biogeography (and phylogeography) is a specific field that has received much

attention in recent years and a considerable part of the literature has been devoted to the

Macaronesian region (Juan et al., 2000; Sanmartín et al., 2008; Fernández-Palacios et al., 2011).

II. PATTERNS

In this section, the main phylogeographic patterns detected in plant groups across the

Mediterranean Basin are arranged following the inferred major driving forces or causal factors.

(1) Large-scale spatial patterns

Even if small scale factors and specific biological properties of the plant groups are important in

driving differentiation in an environmentally heterogeneous region like this, large scale factors

also have a role in contributing to gene flow interruption, and thus to phylogeographic splits. The

patterns listed below (longitudinal, latitudinal, sea straits, refugia) are associated to longitude and

7

2526

126

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

143

144

145

146

147

148

149

2728

latitude, spanning the size and shape of the region, and potentially contributed to create shared

patterns across plant groups.

(a) Longitudinal patterns

East-west phylogeographical breaks, i.e, occurring along the longest axis of the Mediterranean

Basin, have frequently been inferred, and sometimes dated, to have arisen as a consequence of

pre-Pleistocene diversification of lineages. The most apparent cases are those in which there is a

clear current geographical gap associated with a phylogeographic split, which might have resulted

from contraction of formerly continuous ranges. These disjunctions or highly scattered ranges are

seen in the lowland shrub Buxus balearica Lam. (Rosselló et al., 2007; Fig. 2), the salt-tolerant

succulent Microcnemum coralloides (Loscos & J. Pardo) Buen (Kadereit and Yaprak, 2008) or the

herbaceous legume Erophaca baetica (L.) Boiss. from evergreen oak forests (Casimiro-Soriguer et

al., 2010). In the coastal subshrub Cephalaria squamiflora (Sieber) Greuter such gap is emphasized

by its insular distribution ranging from the Balearics to the Aegean (Rosselló et al., 2009). When

there is no current geographic gap, the location of the phylogeographic break or the secondary

contact may still be detectable (e.g., in the perennial mountain herb Heliosperma pusillum

(Waldst. & Kit.) Rchb., Frajman and Oxelman, 2007), particularly when the distribution range is

linear as in the marsh sedge Carex extensa Gooden. (Escudero et al., 2010). It is however more

frequent that events subsequent to the initial gene flow interruption, such as partial westwards

colonization of genotypes originated in the East or vice versa, led to a more complex picture, as in

the case of the submediterranean herbaceous Anthyllis montana L. (Kropf et al., 2002), the laurel

trees Laurus nobilis L. and L. azorica (Seub.) Franco (Rodríguez-Sánchez et al., 2009) or the

thermophilous lowland shrub Myrtus communis L. (Migliore et al., 2012). Westward or eastward

waves of colonization, not only during the Pleistocene but at different times depending on the

climatic conditions and the ecological requirements of the species in question, have been decisive

in shaping the current species and genetic composition of the Mediterranean flora. Examples are

found in Araceae, Carex extensa, Erica arborea L. or Myrtus communis (Mansion et al., 2008;

8

2930

150

151

152

153

154

155

156

157

158

159

160

161

162

163

164

165

166

167

168

169

170

171

172

173

174

175

3132

Escudero et al., 2010; Désamoré et al., 2011; Migliore et al., 2012; respectively). Such expansions

have been reported to be important during the Oligocene–Miocene, when microplates located

between Paratethys and Tethys allowed land connections along the Mediterranean (Steininger

and Rögl, 1984; Meulenkamp and Sissingh, 2003). However, other organisms expanded through

the Southern rim of the Basin at different periods (North Africa – Arabia, Quézel, 1985) as the

steppic herbaceous perennial Ferula loscosii (Willk.) Lange (Pérez-Collazos et al., 2009) or some

thistles (Cardueae; Barres et al., 2013).

In addition to east-west phylogeographic splits, different levels in genetic diversity on a large

scale in eastern vs. western areas of the Mediterranean Basin have been found too, particularly in

trees. Some of those E-W differences have been related to the place of origin or major

diversification of the group in question (e.g., in Quercus suber L., Lumaret et al., 2005), while for

other groups decisive factors have occurred along their evolutionary history. For instance, among

gymnosperm tree species from the genus Abies, Cedrus, Cupressus and Pinus, a decreasing trend

in genetic diversity running east-west along the Basin has been detected and has been attributed

to an east (warm/wet) – west (cold/dry) trend during the last glacial maximum (LGM) (Fady, 2005;

Wu et al., 2007). Such a decreasing gradient of within-population genetic diversity from east to

west has also been found in a meta-analysis based on different groups of living organisms, but it is

stronger in the southern part (northern Africa) than in the northern Mediterranean, in low-land

plants than in plants at higher elevations, in trees that in other life-forms, and in bi-parentally and

paternally than in maternally inherited DNA markers (Conord et al., 2012). However, there is no

overall correlation between genetic diversity and species diversity across the Basin (Fady and

Conord, 2010) and different situations concerning richer eastern or western lineages are found at

the species level (e.g., in Cistus, Guzmán and Vargas, 2005; Hordeum, Jakob et al., 2007; or

Heliosperma, Frajman and Oxelman, 2007). Therefore, new evidence is necessary to understand

the extent and causes for the prevailing idea that the Eastern Mediterranean is a reservoir for

9

3334

176

177

178

179

180

181

182

183

184

185

186

187

188

189

190

191

192

193

194

195

196

197

198

199

200

3536

plant evolution or a cradle for lineages diversification (Mansion et al., 2009; Roquet et al., 2009;

Barres et al., 2013).

(b) Latitudinal patterns

As at the global scale from the poles to the Equator, diversity patterns associated with latitude are

also found in the Mediterranean region. The pattern that is most directly associated to latitude is

a north-south decreasing genetic diversity gradient occurring within lineages. This applies mainly

to the northern Mediterranean region and is even more explicit when territories north of the

Region are also considered. It resulted from the ways by which species responded to the climatic

oscillations during the Pleistocene searching for their climatic optimum, i.e., shifting their ranges

northwards or southwards. For cold-sensitive species this implied that a significant portion of

diversity lost in northern latitudes during glacial periods was preserved in southern regions and

also that only part of the genotypes, usually those occurring on the northern edge or closest to

the glaciated areas, recolonized the northern territories during the Interglacials (Hewitt, 2000).

Such south-north recolonization processes were rapid and resulted in a few genotypes occupying

much larger areas in northern latitudes in Europe compared to Mediterranean territories as well

as in a few alleles surfing on the front of the colonizing populations (Excoffier and Ray, 2008). This

—so called leading-edge expansion model—has been used to explain genetic diversity gradients

within lineages that are likely to have been due to sequential bottlenecks during colonization of

deglaciated areas. Contrasting roles in leading vs. trailing-edge populations led to differential

patterns in gene flow, differentiation and ultimately in shaping the genetic diversity of the species

(Hampe and Petit, 2005; Parisod and Joost, 2010).

The scenario of climatically-driven north-to-south range shifts took place in highly

mountainous terrain in many areas of the Basin particularly in Southern Europe, which

contributed to shape latitudinal patterns beyond a plain latitudinal diversity gradient. One of the

simplest approaches to focus on this latitude-altitude interaction was Kropf et al.’s (2006; 2008)

10

3738

201

202

203

204

205

206

207

208

209

210

211

212

213

214

215

216

217

218

219

220

221

222

223

224

225

3940

“successive vicariance” model regarding the postglacial retreat of cold-adapted species into high

elevations. They tested the implications of the assumption that the retreat should progress in

Europe from south to north as interglacial periods became warmer (De Beaulieu et al., 1994). On

the Iberian Peninsula, such a model would result in greater genetic distance between populations

from Sierra Nevada and the Pyrenees than between the Pyrenees and the Alps because the

southernmost populations had to retreat—and thus interrupt gene flow—earlier. They found

results consistent with this prediction in some, e.g., Silene rupestris L., Kernera saxatilis (L.) Rchb.,

Gentiana alpina Vill. and Saxifraga oppositifolia L., but not all species studied (Kropf et al., 2006;

2008).

(c) Glacial refugia

Mountains provided another dimension, altitude, to the latitudinal gradient and contributed

to compartmentalize the region creating climatically suitable enclaves, which allowed glacial

refugia to occur. According to Médail and Diadema (2009), refugia are areas “where distinct

genetic lineages have persisted through a series of Tertiary or Quaternary climate fluctuations

owing to special, buffering environmental characteristics”. Glacial refugia have important

biological implications, e.g., for conservation under a climate change scenario (Tzedakis, 2004).

The well-known general pattern of refugia in areas less affected by glaciations is strongly

supported by the fossil data (Bennet et al., 1991) and phylogeographic studies have made a major

contribution to identifying them (e.g., Taberlet et al., 1998; Hampe et al., 2003; Heuertz et al.,

2004; Provan and Bennett, 2008). But there have been different views on the number of refugia in

each species. Hewitt (2001) proposed the ‘paradigm postglacial colonization patterns’ model,

which considered each of the main sources of recolonization for northern European territories,

i.e., the three Mediterranean peninsulas (Iberian, Italian and Balkan), as a single refugium.

Although this scheme was useful for tree species in particular (Taberlet et al., 1998; Heuertz et al.,

2004), it was too simple to account for the evolutionary history of many groups due to the

importance of orography, among other factors. The ‘refugia-within-refugia’ model proposed by

11

4142

226

227

228

229

230

231

232

233

234

235

236

237

238

239

240

241

242

243

244

245

246

247

248

249

250

251

4344

Gómez and Lunt (2007) as a response to the latter advocates that phylogeographic breaks within

these peninsulas in a number of animal and plant groups demonstrate the preservation of various

lineages and thus the occurrence of multiple refugia. In fact, in those phylogeographic studies

that include Mediterranean populations together with populations from elsewhere, the

occurrence of multiple refugia in one or more of the three Peninsulas is the norm both for

herbaceous (Picó et al., 2008) and tree species such as Quercus spp. (Olalde et al., 2002; López de

Heredia et al., 2007), Populus spp. (Macaya-Sanz et al., 2012) or other groups (Carrión et al., 2003;

reviewed for Iberia in Rodríguez-Sánchez et al., 2010). Although there are more phylogeographic

examples from the Iberian Peninsula the refugia within refugia model clearly holds for the Italian

(Cozzolino et al., 2003; Ansell et al., 2008; Grassi et al., 2009; Španiel et al., 2011) and Balkan

peninsulas (Heuertz et al., 2001; Trewick et al., 2002; Kučera et al., 2010; Surina et al., 2011) (Fig.

3). This multiple refugia pattern has also been inferred in Southern Australia (Byrne, 2008),

probably because as in the Mediterranean Basin effects of climatic oscillations allowed survival

and resilience of different partly or totally isolated lineages within larger territories.

Spatial coincidence of refugia for different species greatly increases their interest as a sort of

sanctuaries for plant diversity (Tribsch and Schönswetter, 2003). There is coincidence at relatively

gross scales, e.g., the Andalusian ranges, Sicily or the Aegean region. However, factors related to

the biology or history of the group in question hinder fine matches for the location of refugia

across groups. For instance, there are scenarios that include also non-Mediterranean refugia, e.g.,

in Meconopsis cambrica (L.) Vig. (Valtueña et al., 2012) or specific traits associated with the

location of refugia, e.g., higher clonality in northern populations of Populus, more exposed to

glaciations (Macaya-Sanz et al., 2012). Another feature that has been found in Fagus and other

trees is the unexpectedly high degree of genetic diversity detected in non-Mediterranean

latitudes away from the glacial refugia even if allelic diversity was higher in the latter (Comps et

al., 2001; Widmer and Lexer, 2001; Petit et al., 2003). This pattern is due to the admixture of

divergent lineages recolonizing the continent from separate refugia.

12

4546

252

253

254

255

256

257

258

259

260

261

262

263

264

265

266

267

268

269

270

271

272

273

274

275

276

277

4748

In a previous paper I argued that evidencing refugia, even for refugia within refugia, was not an

ultimate goal but a first step in phylogeographic studies in the Mediterranean Basin (Nieto Feliner,

2011) because as sites where extinction has been minimized, the processes that underlie survival

in them seem to be of primary interest. Also, in the context of the scarcity of phylogeographic

patterns in the Mediterranean Basin (see patterns and complexity section), refugia represent an

exception and demand for explanatory processes. In the end—simple as it might sound—refugia

might be environmentally favorable enclaves in spatially convenient sites. This is consistent with a

long series of studies in the Alps (Schönswetter et al., 2005) and particularly with the finding of a

coincidental current genetic structure across numerous taxonomic plant groups that is correlated

with specific substrata (Alvarez et al., 2009). It seems that cases like this exemplify a meaningful

integration of historical and ecological components of biogeography that allows a better

understanding of current distribution patterns. Along this line, glacial refugia represent interesting

places from the community ecology perspective (Webb et al., 2002). As enclaves where

conservation is maximized and at the same time have a biogeographic dynamic nature, examining

phylogenetic community structure along with concepts such as habitat filtering vs. competitive

exclusion of closely related species can help understand the functioning of refugia.

(d) Role of straits

It is likely that straits have been an important modulator of phylogeography across the region (Fig.

4). This role is not unexpected in a region whose coastline stretches 46,000 km, making the sea a

barrier for biological exchange not only between islands but also between mainland and islands or

between mainland areas. The effectiveness of the sea as a barrier has varied over time due to

climatic and geological changes and depending on the plant group. For example, one of the most

significant sea barriers geographically, the Strait of Gibraltar, is considered to be a greater

biogeographic barrier than the Pyrenees or the Alps (Hewitt, 2011) and has acted as such for

species such as the continental juniper Juniperus thurifera L. (Terrab et al., 2008b), a sedge

growing in Quercus suber forests Carex helodes Link (Escudero et al., 2008), Abies spp. (Terrab et

13

4950

278

279

280

281

282

283

284

285

286

287

288

289

290

291

292

293

294

295

296

297

298

299

300

301

302

303

5152

al., 2007) or several Mediterranean conifers (Jaramillo-Correa et al., 2010), among others.

However, a number of studies found that it was not effective at interrupting gene flow between

African and European populations in both directions, e.g., in the bulbous monocot Androcymbium

gramineum (Cav.) McBride (Caujapé-Castells and Jansen, 2003), the coastal annual Hypochaeris

salzmanniana DC. (Ortiz et al., 2007), the legume shrub Calicotome villosa (Poir.) Link (Arroyo et

al., 2008), several mediterranean rockroses Cistus spp. (Guzmán and Vargas, 2009; Fernández-

Mazuecos and Vargas, 2010) or in Rosmarinus officinalis L. (Mateu et al., 2013). This variable role

of the strait of Gibraltar depending on the species is consistent with results from animal groups

(Hewitt, 2011). The lack of correlation between dispersal abilities and genetic exchange between

the two continents across this Strait is also noteworthy (Rodríguez-Sánchez et al., 2008; Guzmán

and Vargas, 2009).

The geographic position of straits, and not only their width, is a crucial factor in determining

their biogeographic role. For instance, besides filtering biological exchange between Africa and

Europe, the Strait of Gibraltar has been decisive in shaping diversity patterns in the area. The

concentration of plant diversity on both sides of the Strait, due to both the accumulation of relict

species and the high percentage of endemics, is likely to be strongly related to its geographic

location as a crossroad, which allows it to act as a melting-pot for lineages (Rodríguez-Sánchez et

al., 2008).

The depth of seafloor is another important factor since shallow waters maximized the effects

of eustatic sea-level shifts by narrowing the straits, modifying the shape and size of emerged lands

or even creating land corridors. Along the Mediterranean Basin, the MSC has been widely

classically invoked as the fundamental cause for land connections involving relatively shallow sea

floors (Bocquet et al., 1978) and, more moderately, after the advent of molecular data (e.g., in

Androcymbium gramineum for Gibraltar, Caujapé-Castells and Jansen, 2003; in the orchid

Anacamptis palustris (Jacq.) R.M. Bateman et al., for the Otranto Strait, Mussacchio et al., 2006).

14

5354

304

305

306

307

308

309

310

311

312

313

314

315

316

317

318

319

320

321

322

323

324

325

326

327

328

5556

In contrast to the MSC, the phylogeographic importance of Pleistocene land-bridges has not

been adequately considered until recently, when dated genealogical splits have been associated

to sea-level drops of up to 130 m that occurred during the LGM (Petit et al., 2002; Lambeck et al.,

2002). For instance, the current relationships between species across the Sicilian Channel were

shaped by eustatic sea-level shifts during the Pleistocene that facilitated biotic exchange between

Sicily and Tunisia and also between the islands in the region, Malta, Pantelleria, Lampedusa, and

the Aeolian and Aegadian archipelagos (Naciri et al., 2010; Zitari et al., 2011; Lo Presti and

Oberprieler, 2011; Fernández-Mazuecos and Vargas, 2011). In the Balearic Islands marine

transgressions during the interglacial periods divided the island of Majorca into two, whereas

during marine regressions sea-level drops united Majorca, Menorca and Cabrera into a single land

mass (Vesica et al., 2000; Gràcia et al., 2001). The latter regression during the Upper Pleistocene

at the end of the Mindel glaciation (c. 400,000 y BP) also connected Ibiza with the Dianic range in

Iberia which allowed biotic exchanges, e.g., in the perennial herb Cheirolophus intybaceus (Lam.)

Dostál (Garnatje et al., 2013). These eustatic sea-level shifts subsequently promoted or restricted

intraspecific gene flow, fragmenting populations and enhancing their divergence, e.g. in two

Asteraceae herbaceous Balearic endemics such as Senecio rodriguezii Willk. ex J.J. Rodr. (Molins et

al., 2009) and Crepis triasii (Cambess.) Nyman (Mayol et al., 2012). The impact of Pleistocene land-

bridges is also detectable in the Aegean sea (Bittkau and Comes, 2005) and is evident in narrow

and shallow straits like Bonifacio, between Corsica and Sardinia, which are not associated with

any phylogeographic break in a plastid haplotype network of the rockrose Cistus creticus L. (Falchi

et al., 2009).

The biology of the plants can result in opposite effects of the same strait on different species.

For instance, in the Eastern Mediterranean, phylogeographic breaks have been detected

coinciding with the straits of Bosporus for two species from sandy beaches such as Eryngium

maritimum L. and Cakile maritima Scop., and with the Dardanelles for Cakile maritima (Kadereit

and Westberg, 2007). However, because these two species occur in coastal habitats, Bosporus

15

5758

329

330

331

332

333

334

335

336

337

338

339

340

341

342

343

344

345

346

347

348

349

350

351

352

353

354

5960

and Dardanelles acted as geographic barriers in opposite periods compared to inland plants, and

along different geographic orientations (roughly east-west instead of north-south). Thus, unlike

for inland species, the closure of the two straits that resulted in the isolation of the Black Sea, the

Sea of Marmara and the Aegean Sea could represent an east-west barrier for a coastal expansion

of these species due to elimination of coastline. Yet, on the other end of the Basin, the fact that

the Strait of Gibraltar has remained open since the end of the MSC (c. 5.3 Mya) did not imply that

coastal land plants species could spread freely across it along an east-west direction; this was

probably due to sea-currents that precluded gene-flow via seeds in species with sea-dispersed

fruits (Kadereit and Westberg, 2007; Westberg and Kadereit, 2009). Sea-currents have been also

invoked to explain limitations to gene flow across the same strait for marine species (reviewed in

Patarnello et al., 2007). In all, the conclusion is that predicting the role of straits as

biogeographical barriers requires considering very diverse factors.

(2) Spatio-temporal phylogeographic concordance

Genealogical concordance is the most straightforward evidence for common historical factors

affecting the phylogeography of different groups in the Mediterranean region. Different types of

concordance are conceivable and Avise (1998; 2009) pointed out four: within-locus, multi-locus,

multi-species and among multiple lines of empirical evidence. The third of these—geographical

co-location of significant genealogical splits across multiple co-distributed species—has been

addressed using comparative phylogeographic approaches (Bermingham and Moritz, 1998) in the

Alps (e.g., Tribsch and Schönswetter, 2003; Schönswetter et al., 2004) or North America

(Brunsfeld et al., 2001; Soltis et al., 2006). In the Mediterranean Basin some comparative studies

have focused on taxonomic groups such as Cistus spp. (Fernández-Mazuecos and Vargas, 2010),

exemplifying how different phylogeographic patterns can arise in closely related species. Other

studies have focused on phylogenetically unrelated plants from similar habitats. In alpine

16

6162

355

356

357

358

359

360

361

362

363

364

365

366

367

368

369

370

371

372

373

374

375

376

377

378

379

6364

Mediterranean plants no common pattern was found (Vargas, 2003) whereas in coastal

communities there was some concordance in geographic clusters in the Eastern Mediterranean

but no strongly congruent patterns along their inferred evolutionary histories (e.g., Kadereit et al.,

2005; Kadereit and Westberg, 2007). The conclusion that species sharing habitats and even

showing co-located phylogeographic breaks might not share much of their overall

phylogeography is consistent with results from the early comparative study on the continental

scale by Taberlet et al. (1998).

In fact, co-location of phylogeographic breaks in different groups does not always imply time

or process coincidence, a phenomenon recognized as pseudocongruence at a deeper

biogeographic level (Donoghue and Moore, 2003). Pseudocongruence at the species level has

recently been shown by Jaramillo-Correa et al. (2010) in a study of five species of Mediterranean

conifers across the Strait of Gibraltar. And this concept is also applicable to the similarities in

ecological requirements of the species that coincide in Alpian refugia, commented above (Alvarez

et al., 2009). Also, evolutionary patterns need not be associated with important climatic events,

as illustrated by the diversification rates in the annual self-compatible Nigella arvensis L. group,

which were not affected by the onset of the Mediterranean climate (Bittkau and Comes, 2009).

Another commonly followed search for concordance examines matches between gene-tree

partitions (or historical patterns in general) of a given study group and dated historical abiotic

events (geographic or climatic changes). For instance, hybridization and introgression between

previously lineages can be associated to a breakdown of existing geographic barriers. Although

searches for this type of concordance are frequently hampered by too wide confidence intervals

for estimated dates of lineage events (Fromhage et al., 2004), a number of studies using dated

phylogeographies have proposed association between climatic or geographic factors and

evolutionary events in the Mediterranean (e.g., in Anthemis, Lo Presti and Oberprieler, 2009;

Dianthus, Valente et al., 2010; Erodium, Fiz-Palacios et al., 2010). Still, difference in coalescence

17

6566

380

381

382

383

384

385

386

387

388

389

390

391

392

393

394

395

396

397

398

399

400

401

402

403

404

6768

times should ideally be taken into account when examining matches of evolutionary patterns in

different species with the same abiotic event (see Perspectives section).

Lack of phylogeographic structure associated to rapid postglacial colonization also results in

some form of concordance. This seems to be the case in two tree species which, together with

long generation times, share the possession of edible fruits, which might have accelerated their

colonization of the Basin by humans: the stone pine, Pinus pinea L. (Vendramin et al., 2008) and

the chestnut tree, Castanea sativa Miller (Fineschi et al., 2000).

(3) Patterns and complexity

The main conclusion from the available evidence is that common phylogeographic patterns are

scarce in the Mediterranean Basin. In the Alps phylogeography has focused on postglacial

colonization, testing whether refugial areas could have existed in nunataks or at lower latitudes

(e.g., Tribsch and Schönswetter 2003; Schönswetter et al. 2005). The distinct patterns found in

this region seem to result from younger histories, whereas previous lineages disappeared due to

Pleistocene glaciations.

Compared to the Alps, scarcity of patterns in the Mediterranean Basin may partly derive from

blurring of genetic footprints via admixing over time. The successive contacts between

populations that have experienced some differentiation during glacial or interglacial periods, but

failed to develop complete reproductive barriers, lead to admixture and thus obscured genetic

footprints of whatever differentiation might have preceded those contacts. Scarcity of common

patterns may actually reflect a scarcity of simple patterns and thus be related to the idea of

complexity. In the Mediterranean Basin several phylogeographic studies have highlighted this

(Heuertz et al., 2004; Jiménez et al., 2004; López de Heredia et al., 2005, 2007; Médail and

Diadema, 2009; Lo Presti and Oberprieler, 2011; Fernández-Mazuecos and Vargas, 2011).

However, species of older, Tertiary, origin such as Erica arborea (Désamoré et al., 2011) or Myrtus

18

6970

405

406

407

408

409

410

411

412

413

414

415

416

417

418

419

420

421

422

423

424

425

426

427

428

429

7172

communis (Migliore et al., 2012) exemplify the idea of complexity resulting from survival and

partial admixture of lineages. These studies report a combination of extensive colonization waves

(frequently east-west or vice versa) and survival without great geographic displacement or, as

expressed in Migliore et al. (2012) “accumulation of the species’ responses to successive

palaeoenvironmental changes”. Also for older lineages, such accumulation of responses under

substantial climatic instability but without dramatic unifying climatic changes probably resulted in

greater stochasticity, which contributed to the scarcity of phylogeographic patterns in the Basin.

III. PROCESSES

Although comparative studies in the Basin have primarily looked for common patterns the

possibility of inferring common processes from different groups would be a great advantage albeit

a challenging one. The coincidence in space of the same processes in different species poses the

question of whether similar selection pressures lie behind them. Some of the processes can be

addressed within the frame of statistical phylogeography approaches that estimate population

parameters (Hickerson et al., 2010) but the focus here is wider. The following paragraphs highlight

a few processes that have been inferred, from phylogeographically-framed studies, to occur in

Mediterranean lineages and may be drivers, or at least important factors, in the evolutionary

history of plant groups. These are gradual range expansion, vicariance, long-distance dispersal

(LDD), radiations, hybridization and introgression, changes in reproductive systems, and ecological

determinants of colonization. The first three of those specifically refer to changes in species

distributions while the remaining are primarily involved in other aspects of evolutionary change,

such as shaping species genetic architecture, although ultimately affect their distributions too. All

of them have implications on phylogeography although in different ways and at different time

scales.

19

7374

430

431

432

433

434

435

436

437

438

439

440

441

442

443

444

445

446

447

448

449

450

451

452

453

454

7576

(a) Gradual range expansion

Following from the simplest way by which plants, as sessile organisms, track their climatic optima

during climate changes it is likely that gradual range expansion has played an important role, if

not the most, in distribution range changes over time. Such expansion has mainly occurred along

a north-south direction and along elevational gradients in the mountains and is currently

detectable, even at minimal time-scales, in alpine pioneer species as a response to global change

(Pauli et al., 2007). But other gradual range expansion scenarios not evidently driven by rapid

climate changes might have been also common in the Mediterranean. Gradual expansion should

have contributed substantially to westwards or eastwards colonization along the Basin either

across the northern (European) side or across Northern Africa and might account for small-scale

migration as reported in Anthyllis montana (Kropf et al., 2002).

(b) Vicariance

Mediterranean phylogeographic studies sometimes set as the null hypothesis the possibility that

current disjunct distributions of genotypes, species or closely related species are due to

vicariance, that is, the fragmentation of an ancient continuous range. The oldest tectonic events

invoked to explain currently recognizable patterns in this region date back to the geological

dynamism in the Oligocene that led to isolation of previously connected land-masses (Rosenbaum

et al., 2002). Thus, lineage splits in herbaceous lineages attributed to vicariance during that

period do not involve populations within species but closely related genera such as Helicodiceros

and its Eastern Mediterranean sister group Eminium (Mansion et al., 2008). However, in slowly

evolving tree species the idea that current genetic structures may reflect population divergence

pre-dating the onset of the Mediterranean climate (c. 3.2 Mya) is not perceived as odd (Petit et

al., 2005). Particularly striking is the interpretation of the partial matching found in Quercus suber

between current plastid intraspecific lineages and the western European Oligocene microplates,

20

7778

455

456

457

458

459

460

461

462

463

464

465

466

467

468

469

470

471

472

473

474

475

476

477

478

7980

which was attributed to tectonic-associated vicariance events produced at that time (Magri et al.,

2007).

The complex palaeogeology and palaeoclimatology of the Basin counteracted vicariance by

favoring contacts between previously isolated land-masses and the migration of island arcs. The

outcome is a reticulate biogeographical history in which ‘biotas repeatedly fragmented and

merged as dispersal barriers appeared and disappeared through time’ (Sanmartín, 2003; Salvo et

al., 2010). Therefore, finding whole matches between several areas and genetic groups is an

exception and the most frequent pattern is matches in single vicariant events separating two

lineages. Examples of this include both woody species such as Myrtus (Migliore et al., 2012) and

non-woody species such as Campanula (Cano-Maqueda et al., 2008), some of them associated

with well-dated raising of barriers, e.g., the opening of the Strait of Gibraltar, 5.3 Mya, in

Anthemis (Lo Presti and Oberprieler, 2009) or Linaria (Fernández-Mazuecos and Vargas, 2011).

A more recently reported model of vicariant relationship is associated with Pleistocene

climatic oscillations. During interglacial periods (including the current ‘postglacial’ one),

distribution areas of cold-adapted species were fragmented and restricted to higher elevations,

thus creating vicariance, which may have left genetic footprints. Current patterns attributed to

this type of vicariance have been reported in high elevation species, both herbaceous perennials

such as Pritzelago alpina (L.) Kuntze (Kropf et al., 2003), Silene rupestris, Gentiana alpina, Kernera

saxatilis, Saxifraga oppositifolia (Kropf et al., 2006; 2008), Androsace vitaliana (L.) Lapeyr. (Dixon

et al., 2009), Reseda sect. Glaucoreseda (Martín-Bravo et al., 2010) as well as trees such as Pinus

mugo Turra (Heuertz et al., 2010).

(c) Long-distance dispersal

LDD events inferred in the frame of phylogenetic studies of genera or species groups, using

analytical methods, have not been rare within the Mediterranean region (e.g., in Araceae,

Mansion et al., 2009; Erodium, Fiz-Palacios et al., 2010) and between this and other regions (e.g.

21

8182

479

480

481

482

483

484

485

486

487

488

489

490

491

492

493

494

495

496

497

498

499

500

501

502

503

8384

in Senecio, Coleman et al., 2003; Convolvulus, Carine et al., 2004; Hypochaeris, Tremetsberger et

al., 2005; Oligomeris, Martín-Bravo et al., 2009; Legousia, Roquet et al., 2009; and other groups,

Kadereit and Baldwin, 2012). At the phylogeographic level, the sharper the contrast between

genetic and geographic distance (specifically a low genetic distance combined with a high

geographic distance) the clearer the footprint of the LDD event is, which implies that older LDD

events are more difficult to document. LDD has been suggested to occur between mountain

ranges affecting cold-tolerant plants only recently, e.g., Alps and Iberian ranges (Androsace

vitaliana, Dixon et al., 2009), Pyrenees and Sierra Nevada (Papaver alpinum L., Kropf et al., 2006).

This is perhaps in contrast to those events mediated by marine bird flights involving coastal or low

elevation species, which have been considered classical examples of LDD. Of those LDD events

connecting areas isolated by sea, there are a number of reports between the Iberian Peninsula

and the Balearics (e.g., Cheirolophus intybaceus, Garnatje et al., 2013), the Iberian Peninsula and

Corsica-Sardinia (Armeria pungens (Link) Hoffmanns. & Link, Piñeiro et al., 2007; Juniperus

thurifera, Terrab et al., 2008b), as well as across the Strait of Sicily (Anthemis secundirramea Biv.,

Lo Presti and Oberprieler, 2011; Linaria Sect. Versicolores, Fernández-Mazuecos and Vargas, 2011)

(Fig. 5). For other coastal plants, marine long-distance dispersal has been important in some

species (e.g. Calystegia soldanella (L.) R. Br., Arafeh and Kadereit, 2006).

(d) Radiations

Although adaptive radiations are usually associated to islands (e.g., Aeonium in the Canary Islands,

Jorgensen and Ollesen, 2001), correlations between morphological traits and environmental

variables have revealed cases in the Mediterranean Basin, e.g., in Cistus (Guzmán et al., 2009).

Perhaps this is not unexpected given the environmental heterogeneity of the Basin and the

patchy landscape that offer a variety of niches in relatively close proximity. However, in some

cases there is no evidence for considering the radiations to be adaptive, e.g., in Dianthus broteri

Boiss. & Reuter (Balao et al., 2010) and Erodium spp. (Fiz-Palacios et al., 2010), while in others

radiations are explicitly considered non-adaptive. In fact, comparatively buffered climatic

22

8586

504

505

506

507

508

509

510

511

512

513

514

515

516

517

518

519

520

521

522

523

524

525

526

527

528

529

8788

oscillations and relatively uniform environments in the Aegean region have favored non-adaptive

radiation, driven instead by genetic drift and leading to allopatric speciation in this area, e.g., in

the Nigella arvensis group (Bittkau and Comes, 2005; Comes et al., 2008). Studies on other groups

are consistent with a scenario of random drift as the driver of plant diversification in the Aegean

region (e.g., Brassica cretica Lam., Edh et al., 2007). Altogether, these examples have stressed the

importance of non-adaptive radiation as compared to the most extended model of radiative

evolution (Gittenberger, 1991).

(e) Hybridization and introgression

The Mediterranean Basin gathers historical and ecological factors that render it a fertile arena for

hybridization and introgression (Thompson, 2005). Firstly, it is a biodiversity hotspot containing a

high degree of genetic and species diversity accumulated in a comparative small space over

extended time (Médail and Diadema, 2009). Secondly, adequate conditions have existed to

encourage contact between partially differentiated populations and closely related species.

Quaternary climate-driven shifts in species ranges involved shorter distances than in higher

latitudes (Hewitt, 2001) in part due to the fact that orography enabled species to track their

niches along altitude (Gutiérrez Larena et al., 2002; Naciri et al., 2010; Fuertes Aguilar et al., 2011;

Surina et al., 2011). This, together with the patchy nature of the landscape and the narrow ranges

of many species (Thompson, 2005) contributed to those contacts. There is evidence that contact

zones between close species of Antirrhinum that are able to hybridize can be finely defined by

niche modelling (Khimoun et al., 2012). This gives ground to the idea that maximizing ecotones in

a patchy landscape can favor hybridization in the Mediterranean and is also consistent with the

importance of ecological differentiation in the region (Thompson et al., 2005). Another favorable

environmental circumstance is habitat disturbance (Lamont et al., 2003; Seehausen et al., 2008)

and domestication, usually progressing from east to west (Besnard et al., 2007; 2013). In

comparison to central or northern European regions, humans have substantially altered the

Mediterranean Basin landscape over several thousand years, both through cultivation and

23

8990

530

531

532

533

534

535

536

537

538

539

540

541

542

543

544

545

546

547

548

549

550

551

552

553

554

555

9192

habitation, as well as by introducing non-native species. Disturbed habitats provide a suitable

ground for hybridization (Anderson, 1948; Levin et al., 1996) and the potential of alien species to

become invasive has been associated to hybridization too (Schierenbeck and Ellstrand, 2009).

These factors suggest that hybridization and introgression, which are common features in

plants throughout the world, might have been quantitatively important in the Mediterranean.

Testing if this is true is important because these processes can be main drivers of plant evolution

(Arnold, 1997; Mallet, 2005) but by no means easy because there are different possible

evolutionary outcomes of hybridization and introgression (Arnold, 1997; Soltis and Soltis, 2009)

that require specific pattern-detection strategies. Despite these difficulties, hybridization and

introgression have been detected in the Region based on different patterns. These include

incongruence between differently inherited markers (in Centaurium, Mansion et al., 2005;

Helliosperma, Frajman and Oxelman, 2007; Olea, Besnard et al., 2007; Anthemis, Lo Presti and

Oberprieler, 2011); sharing of haplotypes (e.g., in evergreen oaks, Belahbib et al., 2001; López de

Heredia et al., 2007; and Fraxinus, Heuertz et al., 2006) sometimes linked to altitudinal shifts (in

Armeria, Gutiérrez Larena et al., 2002); quantitative morphological variation, especially

intermediacy (in Cyclamen; Thompson et al., 2010); coalescent simulations to tell apart

hybridization from incomplete lineage sorting (in Linaria, Blanco-Pastor et al., 2012); or, more

rarely, species-independent geographic structure of variation for nuclear ribosomal DNA ITS (in

Armeria, Nieto Feliner et al., 2004).

Three aspects remain crucial to refine the assessment of the true incidence of

hybridization and introgression in the region. Understanding and documenting the ecological

factors, and in particular the adaptive significance of hybridization and introgression events, is

central to interpret and even predict the outcomes of these processes. Despite a few thoroughly

studied cases in other regions (Rieseberg et al., 2003), this is an elusive topic. Evidence in the

region is scanty but not lacking. For example, niche expansion associated with hybridization and

introgression is suggested in Armeria pungens (Piñeiro et al., 2011). Along with ecological

24

9394

556

557

558

559

560

561

562

563

564

565

566

567

568

569

570

571

572

573

574

575

576

577

578

579

580

581

9596

determinants of hybridization, a second crucial aspect is finely assessing reproductive barriers

between hybridizing species, which need not be constant across their ranges (e.g., in Narcissus,

Marques et al., 2012). The role of pollinators as premating barriers is very diverse. Examples of

week premating barriers involving pollinator sharing but leading to sterile hybrids due to post-

mating barriers include Mediterranean orchids (Cozzolino and Widmer, 2005). A third difficult

aspect is distinguishing introgression from lineage sorting (Albaladejo et al., 2005; Maureira-Butler

et al., 2008; Blanco-Pastor et al., 2012) and detecting old introgression. Next generation

sequencing techniques offer new possibilities for addressing those problems (Twyford and Ennos,

2012).

(f) Changes in reproductive systems

Intraspecific breeding system variation is a form of diversity. Thus, it is not unexpected that

it is well represented and, due to its lability and adaptive significance, to have changed several

times in a biodiversity hot-spot like the Mediterranean Basin. A number of phylogeographically

framed studies have identified changes in the reproductive system within this region, e.g., in

Mercurialis (Pannell et al., 2004), Ecbalium (Costich and Meagher, 1992), Hypochaeris (Ortíz et al.,

2007), Epipactis (Tranchida-Lombardo et al., 2011) or Erodium (Alarcón et al., 2011), among

others. In addition, it has long been known that annual life-forms are well represented in the

Mediterranean Basin (Raunkiaer, 1934). Since annuals are frequently associated with selfing

(Stebbins, 1970) and the shift from perennial outcrossing to annual selfing is considered to be

mostly irreversible (Barrett, 2013), the good representation of this life-cycle might be an indirect

indication of active breeding systems shifts.

There are a number of factors that are well represented in the Mediterranean region that

might be associated to breeding systems changes, e.g., human disturbance (Eckert et al., 2010),

environmental changes causing stress particularly in trailing edge populations (Levin, 2012),

threats of inbreeding in narrow habitats (Fiz-Palacios et al., 2010) or the occurrence of

25

9798

582

583

584

585

586

587

588

589

590

591

592

593

594

595

596

597

598

599

600

601

602

603

604

605

606

99100

biogeographic crossroads, such as the Strait of Gibraltar area, where populations of the same

species with different breeding systems accumulate following range shifts across this region

(Rodríguez-Sánchez et al., 2008). In contrast to these dynamic scenarios, breeding system shifts

are sometimes associated with relatively stable evolutionary scenarios in which differentiation has

been mainly due to genetic drift (e.g., Nigella in Bittkau and Comes, 2005; Comes et al., 2008).

Understanding the origin and maintenance of alternative reproductive systems is far from

simple and requires multiple approaches that go from the genetic basis to the ecological drivers

(Barrett, 1998; Charlesworth, 2006). However, breeding system variation revealed in a

phylogeographic context is a first step that can unveil possible associations between breeding

systems and haplotypes across space.

(g) Ecology determining success of colonization

Seedling establishment is a crucial stage in the colonization of new spots and, in general, in

species range expansion. When LDD events are involved, the success of colonization has been

traditionally been thought to depend primarily on the availability of dispersal vectors and other

factors related with the transport of the diaspores (Nathan, 2006) at least within historical

biogeography. This view somehow implies that once the most stochastic event is achieved, i.e.,

transporting a diaspore across a long distance, the rest of the elements for colonizing a new

territory are or comparatively minor importance. In recent years a view has emerged that gives a

bigger role in the colonization of new areas after LDD or surmounting narrow sea-barriers to

colonization abilities based on preadaptation of genotypes and availability of suitable habitats.

This view follows from research using different approaches including phylogeographically-

oriented studies from high latitudes (Alsos et al., 2007) and from Mediterranean groups. Among

the latter, some have stressed the lack of adaptations in seeds for transmarine transport

(Rodríguez-Sánchez et al., 2008; Fernández-Mazuecos and Vargas, 2010). Another study, using

species distribution modelling (SDM) and genetic data, has shown that the source of a successful

26

101102

607

608

609

610

611

612

613

614

615

616

617

618

619

620

621

622

623

624

625

626

627

628

629

630

631

103104

LDD of Armeria pungens from Iberia to Corsica-Sardinia were the populations occurring in the

most similar habitats, which happened to be geographically the most distant (Piñeiro et al., 2007).

If this pattern is frequent, it would be more correct to speak of long-distance colonization than of

long-distance dispersal, based on the idea that what we recognize as such are those events in

which colonization in the new territory has been achieved, whereas LDD events could be much

more frequent but many not resulting in successful colonization and therefore remaining

undetected.

IV. PERSPECTIVES

Plant phylogeography in the Mediterranean region will probably progress first by increasing the

number of markers sampled within genomes, as in any other discipline in evolutionary biology.

The main advantage of using genealogies from uniparentally inherited genes, i.e., discarding the

possibility of recombination and thus of mixed historical signals (Avise et al., 1987; Avise, 2009),

has been partly overridden years ago by the access to a range of multilocus markers such as

AFLPs, microsatellites, SNPs, and more recently by the availability of high throughput sequencing

techniques, even for non-model organisms (Emerson et al., 2010). This trend has been boosted by

the urge to sample larger parts of genomes when facing complex patterns and processes as we do

in the Mediterranean and also by the realization that relying on one or two gene genealogies to

infer past events at the species level, as done in classical phylogeography, entails risks. However,

inferring organism level evolution from that deluge of molecular data will continue to pose

problems that, conceptually, are not that different from those faced by molecular phylogenetics

in the nineties, i.e., homology/paralogy issues and the connections and disconnections between

gene tree and species tree.

A second aspect is the development and use of new approaches that seek to circumvent the

conceptual problems of more classical approaches. Knowles and Maddison (2002) introduced the

27

105106

632

633

634

635

636

637

638

639

640

641

642

643

644

645

646

647

648

649

650

651

652

653

654

655

656

107108

field of statistical phylogeography, which uses statistical approaches based on coalescent models

for parameter estimation and testing of alternative hypothesis. They focus on the processes that

generate the patterns of genetic variation and on assessing the confidence of phylogeographic

conclusions (Hickerson et al., 2010). The main argument is that if coalescent theory is not

considered, equating genealogical pattern with demographic and evolutionary processes may be

flawed (Arbogast et al., 2002). For example, genealogical splits caused by the same historical

abiotic event need not coincide exactly in time for two species showing disparate demographic

parameters (Knowles, 2009). Although several coalescent-based hypotheses testing methods

have been implemented, approximate Bayesian computation (ABC) is becoming increasingly used

since it bypasses the computational difficulties of calculating likelihood functions (Beaumont et

al., 2002). These methods are starting to be applied also in comparative phylogeographic studies

(Hierarchical Approximate Bayesian Computation methods, HABC). HABC methods estimate

‘hyper-parameters’, which inform degree of congruence among co-distributed species and ‘sub-

parameters’, which describe the demographic history of each species (Hickerson et al., 2006;

Beaumont, 2010). To the extent that statistical phylogeography minimizes the role of genealogies

(“a gene genealogy is a transitional variable for connecting data to demographic parameters

under an explicit statistical model” Hickerson et al., 2010), it is arguable whether it contributes to

narrowing the gap between phylogenetics and population genetics, as originally proposed by

Avise et al. (1987), and has led to hot debates (Beaumont et al., 2010). In any case, these

approaches should be tried in Mediterranean plant phylogeographic studies, where to date they

are virtually absent, unlike niche modelling approaches, which have been successfully used in

Mediterranean groups.

A third important component for the future of Mediterranean phylogeography is seeking for

congruence with independent data to improve the uncertainty and provide robustness to

phylogeographic hypotheses. Due to scantiness of the plant macrofossil record and the limited

utility of fossil pollen beyond non wind-pollinated species (Petit et al., 2002; Carrión et al., 2003;

28

109110

657

658

659

660

661

662

663

664

665

666

667

668

669

670

671

672

673

674

675

676

677

678

679

680

681

682

111112

López de Heredia et al., 2007; Terrab et al., 2008a), independent past evidence is expected to be

scarce for many plant groups. This is despite findings like those reported in Anderson et al. (2009)

in volcanic islands such as the Canaries, which remembers how fossil discovery is possible even in

places in which it was considered unlikely. Palaeoclimatic reconstructions in the Mediterranean

Basin and the projection of species distribution modelling into past scenarios (Waltari et al., 2007;

Benito-Garzón et al., 2007; Rodríguez-Sánchez and Arroyo, 2008; Rodríguez-Sánchez et al., 2010;

Fernández-Mazuecos and Vargas, 2013) are effective strategies to incorporate past evidence into

phylogeographic studies. But their usefulness will partly depend on filing gaps of palaeoclimatic

data for eastern and southern areas of the Basin and on refining them to be representative of the

environmental heterogeneity in the region (Jakob et al., 2007; Médail and Diadema, 2009).

Choosing simplified systems, e.g., with linear distribution ranges, may help in searching for

congruence too (Clausing et al., 2000; Piñeiro et al., 2007; Escudero et al., 2010).

Focusing on drivers of differentiation and thus beyond the neutral marker domain, another

interesting pursue is performing genome scans and searching for outlier loci showing a

significantly higher degree of differentiation, as this may be indicative of adaptive divergence

particularly when there is correlation with environmental variables (Herrera and Bazaga, 2008;

Excoffier et al., 2009; García et al., 2013). This exemplifies the tendency towards broadening the

scope of evolutionary questions addressed under a phylogeographic frame, which is likely to

increase as phylogeography becomes more inclusive. Combining efforts into integrative

hypothesis-based approaches is one of the keys to understand the complex picture of how the

Mediterranean biota have interacted and evolved along the Basin (Salvo et al., 2010).

Deepening comparative studies with the other four Mediterranean climate zones could also

throw light on plant evolution within the Basin (Cowling et al., 1996). Altogether the

Mediterranean biome covers 2% of the world’s surface, but is home to 20% of the total world’s

flora (Médail and Quézel, 1997). While some Mediterranean climate zones show common

features beyond the climate and the floristic richness, factors determining this richness and the

29

113114

683

684

685

686

687

688

689

690

691

692

693

694

695

696

697

698

699

700

701

702

703

704

705

706

707

708

115116

processes leading to it seem to differ substantially. For instance, the Mediterranean Basin seems

to share the high speciation and low extinction rates as well as the complex environmental

conditions with the Cape region and, maybe to some extent, the importance of soil types. Yet,

other factors that have apparently played a significant role in the diversity of the Cape region

were not crucial in the Mediterranean Basin. These are climatic stability (at least in comparable

terms), explosive radiation of a few clades that constitute most of the diversity, shifts in fire-

survival strategy, the timing of the onset of summer drought (Linder and Hardy, 2004; Linder,

2005; Schnitzler et al., 2011) and, underlying all these factors, lineage age (Valente and Vargas,

2013).

Large-scale comparative studies could also help to understand features of plant evolution in

time and space in this region. Large efforts like the IntraBiodiv Consortium that focused on the

Alps and Carpathians (e.g., Alvarez et al., 2009) would be useful in the Mediterranean but studies

focused on specific questions could give clues too. An example of the latter is Normand et al.

(2011), which assessed the relative importance of current climate vs. postglacial accessibility to

places with suitable conditions for explaining current plant species ranges in Europe. This study

found that accessibility was especially important for small-range species in southern Europe.

Another important question was addressed by the same team looking at the relationships

between Plio-Pleistocene climate changes, species richness and topographic heterogeneity. They

found a greater increase in species richness with increasing topographic heterogeneity in

southern Europe, than in northern Europe (Svenning et al., 2009).

In addition to the above exposed directions, some final remarks should be pointed out

regarding future phylogeographic studies in the Basin. There are substantial gaps in geographic

coverage for plant phylogeographic studies such as North Africa, the Balkans and the easternmost

part of the Basin. New evidence from the latter area is crucial to substantiate the idea that the

Eastern Mediterranean is a cradle for lineages diversification (Mansion et al., 2009; Barres et al.,

2013). Also, it is fortunate that recent rapid speciation events—associated with Pleistocene

30

117118

709

710

711

712

713

714

715

716

717

718

719

720

721

722

723

724

725

726

727

728

729

730

731

732

733

734

119120

climatic changes—have substantially contributed to the whole diversity of the area compared to

the Cape Flora (Valente and Vargas, 2013). Thus reconstructing the evolutionary history of a

growing number of younger lineages in the Mediterranean Basin, for which phylogeographic

approaches are particularly useful, will be insightful for the whole biota, including the possible

influence of humans. Because the location and dynamics of glacial refugia depend heavily on the

ecological requirements of each species, important questions regarding their role have to be

addressed using comparative approaches of species from the same habitats and with similar

biological characteristics.

All these things considered, the Mediterranean Basin continues to offer a highly

stimulating scientific ground which phylogeographic approaches can exploit with strong potential

to help explaining biodiversity patterns and understanding how the Basin has come to be one of

biodiversity hotspots on earth.

VI. ACKNOWLEDGEMENTS

I am grateful to Inés Álvarez, Elena Conti, Javier Fuertes, Myriam Heuertz, Joachim W. Kadereit,

Josep A. Rosselló, Isabel Sanmartín and two anonymous reviewers for providing very helpful

comments, and to Peter Linder for suggesting that I write this review, as well as for suggestions

and discussion. Support from the Spanish Ministerio de Ciencia e Innovación through the project

CGL2010-16138 is also acknowledged.

31

121122

735

736

737

738

739

740

741

742

743

744

745

746

747

748

749

750

751

752

753

123124

VII. REFERENCES

Abbott, R. J., Comes, H. P. 2004. Evolution in the Arctic: a phylogeographic analysis of the

circumarctic plant, Saxifraga oppositifolia (Purple saxifrage). New Phytol. 161, 211–224.

Alarcón, M. L., Roquet, C., Aldasoro, J. J. 2011. Evolution of pollen/ovule ratios and breeding

system in Erodium (Geraniaceae). Syst. Bot. 36, 661–676.

Albaladejo, R. G., Fuertes Aguilar, J., Aparicio, A., Nieto Feliner, G. 2005. Contrasting nuclear-

plastidial phylogenetic patterns in the recently diverged Iberian Phlomis crinita and P. lychnitis

lineages (Lamiaceae). Taxon 54, 987–998.

Alsos, I. G., Eidesen, P. B., Ehrich, D., Skrede, I., Westergaard, K., Jacobsen, G. H., Landvik, J. Y.,

Taberlet, P., Brochmann, C. 2007. Frequent long-distance plant colonization in the changing

Arctic. Science 316, 1606–1609.

Alvarez, N., Thiel-Egenter, C., Tribsch, A. et al. 2009. History or ecology? Substrate type as a major

driver of spatial genetic structure in Alpine plants. Ecol. Lett. 12, 632–640.

Anderson, C. L., Channing, A., Zamuner, A. B. 2009. Life, death and fossilization on Gran Canaria –

implications for Macaronesian biogeography and molecular dating. J. Biogeogr. 36, 2189-2201.

Anderson, E. 1948. Hybridization of the habitat. Evolution 2, 1–9.

Ansell, S. W., Grundmann, M., Russell, S. J., Schneider, H., Vogel, J. C. 2008. Genetic discontinuity,

breeding-system change and population history of Arabis alpina in the Italian Peninsula and

adjacent Alps. Mol. Ecol. 17, 2245–2257.

Arafeh, R., Kadereit, J. W. 2006. Long-distance seed dispersal, clone longevity and lack of

phylogeographical structure in the European distributional range of the coastal Calystegia

soldanella (L.) R. Br. (Convolvulaceae). J. Biogeogr. 33, 1461–1469.

Arbogast, B. S., Edwards, S. V., Wakeley, J., Beerli, P., Slowinski, J. B. 2002. Estimating divergence

times from molecular data on phylogenetic and population genetic timescales. Annu. Rev. Ecol.

Syst. 33, 707-740.

Arnold, M. L. 1997. Natural hybridization and evolution. Oxford University Press, New York.

32

125126

754

755

756

757

758

759

760

761

762

763

764

765

766

767

768

769

770

771

772

773

774

775

776

777

778

779

127128

Arroyo, J., Aparicio, A., Albaladejo, R. G., Muñoz, J., Braza, R. 2008. Genetic structure and

population differentiation of the Mediterranean pioneer spiny broom Calicotome villosa across

the Strait of Gibraltar. Biol. J. Linn. Soc. 93, 39–51.

Avise, J. C. 1998. The history and purview of phylogeography: a personal reflection. Mol. Ecol. 7,

371–379.

Avise, J. C. 2009. Phylogeography: retrospect and prospect. J. Biogeogr. 3, 3–15.

Avise, J. C., Arnold, J., Ball, R. M., Bermingham, E., Lamb, T., Neigel, J. E., Reeb, C. A., Saunders, N.

C. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population

genetics and systematics. Annu. Rev. Ecol. Syst. 18, 489–522.

Balao, F., Valente, L. M., Vargas, P., Herrera, J., Talavera, S. 2010. Radiative evolution of polyploid

races of the Iberian carnation Dianthus broteri (Caryophyllaceae). New Phytol. 187, 542–551.

Barres, L., Sanmartín, I., Anderson, C. L., Susanna, A., Buerki, S., Galbany-Casals, M., Vilatersana, R.

2013. Reconstructing the evolution and biogeographic history of tribe Cardueae (Compositae).

Am. J. Bot. 100, 867–882.

Barrett, S. C. 1998. The evolution of mating strategies in flowering plants. Trends Plants Sci. 3,

335–341.

Barrett, S. C. 2013. The evolution of plant reproductive systems: how often are transitions

irreversible?. Proc. R. Soc. B 280(1765), 20130913. doi: 10.1098/rspb.2013.0913

de Beaulieu, J.-L., Andrieu, V., Lowe, J. J., Ponel, P., Reille, M. 1994. The Weichselian late-glacial in

southwestern Europe (Iberian Peninsula, Pyrenees, Massif Central, northern Apennines). J.

Quat. Sci. 9, 101–107.

Beaumont, M. A., Zhang, W., Balding, D. J. 2002. Approximate Bayesian computation in

population genetics. Genetics 162, 2025-2035.

Beaumont, M.A. 2010. Approximate Bayesian computation in evolution and ecology. Annu. Rev.

Ecol. Evol. Syst. 41, 379–406.

33

129130

780

781

782

783

784

785

786

787

788

789

790

791

792

793

794

795

796

797

798

799

800

801

802

803

804

131132

Beaumont, M. A., Nielsen, R., Robert, C. et al. 2010. In defence of model based inference in ‐

phylogeography. Mol. Ecol. 19, 436–446.

Beheregaray, L. B. 2008. Twenty years of phylogeography: the state of the field and the challenges

for the Southern Hemisphere. Mol. Ecol. 17, 3754–3774.

Belahbib, N., Pemonge, M.-H., Ouassou, A., Sbay, H., Kremer, A., Petit, R. J. 2001. Frequent

cytoplasmic exchanges between oak species that are not closely related: Quercus suber and Q.

ilex in Morocco. Mol. Ecol. 10, 2003–2012.

Benito Garzón, M., Sánchez de Dios, R., Saínz Ollero, H. 2007. Predictive modelling of tree species

distributions on the Iberian Peninsula during the Last Glacial Maximum and Mid-Holocene.

Ecography 30, 120–134.

Bennett, K. D., Tzedakis, P., Willis, K. 1991. Quaternary refugia of north European trees. J.

Biogeogr. 18, 103–115.

Bermingham, E., Moritz, C. 1998. Comparative phylogeography: concepts and applications. Mol.

Ecol. 7, 367–369

Besnard, G., Rubio de Casas, R., Vargas, P. 2007. Plastid and nuclear DNA polymorphism reveals

historical processes of isolation and reticulation in the olive tree complex (Olea europaea). J.

Biogeogr. 34, 736–752.

Besnard, G., Khadari, B., Navascués, M., Fernández-Mazuecos, M., El Bakkali, A., Arrigo, N., Baali-

Cherif D., Brunini-Bronzini de Caraffa V., Santoni S., Vargas P., Savolainen, V. 2013. The

complex history of the olive tree: from Late Quaternary diversification of Mediterranean

lineages to primary domestication in the northern Levant. Proc. R. Soc. B 280(1756), 20122833.

Bittkau, C., Comes, H. P. 2005. Evolutionary processes in a continental island system: molecular

phylogeography of the Aegean Nigella arvensis alliance (Ranunculaceae) inferred from

chloroplast DNA. Mol. Ecol. 14, 4065–4083.

34

133134

805

806

807

808

809

810

811

812

813

814

815

816

817

818

819

820

821

822

823

824

825

826

827

828

135136

Bittkau, C., Comes, H. P. 2009. Molecular inference of a Late Pleistocene diversification shift in

Nigella s. lat. (Ranunculaceae) resulting from increased speciation in the Aegean archipelago. J.

Biogeogr. 36, 1346–1360.

Blanco-Pastor, J. L., Vargas, P., Pfeil, B. E. 2012. Coalescent simulations reveal hybridization and

incomplete lineage sorting in Mediterranean Linaria. PLoS ONE 7, e39089.

Blondel, J., Aronson, J. 1999. Biology and wildlife of the Mediterranean region. Oxford University

Press, New York.

Blondel, J., Aronson, J., Bodiou, J.-Y., Boeuf, G. 2010. The Mediterranean Basin - Biological

diversity in space and time. Oxford University Press, Oxford.

Bocquet, G., Widler, B., Kiefer, H. 1978. The Messinian Model, a new outlook for the floristics and

systematics of the Mediterranean area. Candollea 33, 269–287.

Brunsfeld, S. J., Sullivan, J., Soltis, D. E., Soltis, P. S. 2001. Comparative phylogeography of

northwestern North America, in: Silvertown, J., Antonovics, J. (Eds.), Integrating ecological and

evolutionary processes in a spatial context. Blackwell Science, Oxford, pp. 319–339.

Byrne, M. 2008. Evidence for multiple refugia at different time scales during Pleistocene climatic

oscillations in southern Australia inferred from phylogeography. Quat. Sci. Rev. 27, 2576–2585.

Canestrelli, D., Nascetti, G. 2008. Phylogeography of the pool frog Rana (Pelophylax) lessonae in

the Italian peninsula and Sicily: multiple refugia, glacial expansions and nuclear-mitochondrial

discordance. J. Biogeogr. 35, 1923–1936.

Cano-Maqueda, J., Talavera, S., Arista, M., Catalán, P. 2008. Speciation and biogeographical

history of the Campanula lusitanica complex (Campanulaceae) in the Western Mediterranean

region. Taxon 57, 1252–1266.

Carine, M. A., Russell, S. J., Santos-Guerra, A., Francisco-Ortega, J. 2004. Relationships of the

Macaronesian and Mediterranean floras: molecular evidence for multiple colonizations into

Macaronesia and back-colonization of the continent in Convolvulus (Convolvulaceae). Am. J.

Bot. 91, 1070–1085.

35

137138

829

830

831

832

833

834

835

836

837

838

839

840

841

842

843

844

845

846

847

848

849

850

851

852

853

854

139140

Carrión, J. S., Yll, E. I., Walker, M. J., Legaz, A. J., Chaín, C., López, A. 2003. Glacial refugia of

temperate, Mediterranean and Ibero-North African flora in south-eastern Spain: new evidence

from cave pollen at two Neanderthal man sites. Glob. Ecol. Biogeogr. 12, 119–129.

Casimiro-Soriguer, R., Talavera, M., Balao, F., Terrab, A., Herrera, J., Talavera, S. 2010. Phylogeny

and genetic structure of Erophaca (Leguminosae), a East–West Mediterranean disjunct genus

from the Tertiary. Mol. Phylogen. Evol. 56, 441–450.

Caujapé-Castells, J., Jansen, R. K. 2003. The influence of the Miocene Mediterranean desiccation

on the geographical expansion and genetic variation of Androcymbium gramineum (Cav.)

McBride (Colchicaceae). Mol. Ecol. 12, 1515–1525.

Charlesworth, D. 2006. Evolution of plant breeding systems. Current Biology 16, R726-R735.

Clausing, G., Vickers, K., Kadereit, J. W. 2000. Historical biogeography in a linear system: genetic

variation of sea rocket (Cakile maritima) and sea holly (Eryngium maritimum) along European

coasts. Mol. Ecol. 9, 1823–1833.

Coleman, M., Liston, A., Kadereit, J. W., Abbott, R. J. 2003. Repeat intercontinental dispersal and

Pleistocene speciation in disjunct Mediterranean and desert Senecio (Asteraceae). Am. J. Bot.

90, 1446–1454.

Comes, H. P. 2004. The Mediterranean region – a hotspot for plant biogeographic research. New

Phytol. 164, 11–14.

Comes, H. P., Tribsch, A., Bittkau, C. 2008. Plant speciation in continental island floras as

exemplified by Nigella in the Aegean Archipelago. Philos. Trans. R. Soc. B Biol. Sci. 363, 3083–

3096.

Comps, B., Gömöry, D., Letouzey, J., Thiébaut, B., Petit, R. J. 2001. Diverging trends between

heterozygosity and allelic richness during postglacial colonization in the European beech.

Genetics 157, 389–397.

Conord, C., Gurevitch, J., Fady, B. 2012. Large scale longitudinal gradients of genetic diversity: a ‐

meta analysis across six phyla in the Mediterranean basin. ‐ Ecol. Evol. 2, 2600–2614.

36

141142

855

856

857

858

859

860

861

862

863

864

865

866

867

868

869

870

871

872

873

874

875

876

877

878

879

880

143144

Costich, D. E., Meagher, T. R. 1992. Genetic variation in Ecballium elaterium (Cucurbitaceae):

breeding system and geographic distribution. J. Evol. Biol. 5, 589–601.

Cowling, R. M., Rundel, P. W., Lamont, B. B., Kalin Arroyo, M., Arianoutsou, M. 1996. Plant

diversity in Mediterranean-climate regions. Trends Ecol. Evol. 11, 362–366.

Cozzolino, S., Widmer, A. 2005. The evolutionary basis of reproductive isolation in Mediterranean

orchids. Taxon 54, 977–985.

Cozzolino, S., Cafasso, D., Pelegrino, G., Musacchio, A., Widmer, A. 2003. Fine-scale

phylogeographical analysis of Mediterranean Anacamptis palustris (Orchidaceae) populations

based on chloroplast minisatellite and microsatellite variation. Mol. Ecol. 12, 2783–2792.

van Dam, J. A. 2006. Geographic and temporal patterns in the late Neogene (12–3 Ma)

aridification of Europe: the use of small mammals as paleoprecipitation proxies. Palaeogeogr.

Palaeoclimatol. Palaeoecol. 238, 190–218.

Dercourt, J., Zonenshain, L. P., Ricou, L. E. et al. 1986. Geological evolution of the Tethys Belt from

the Atlantic to the Pamirs since the Lias. Tectonophysics 123, 241–315.

Désamoré, A., Laenen, B., Devos, N., Popp, M., González-Mancebo, J. M., Carine, M. A.,

Vanderpoorten, A. 2011. Out of Africa: north-westwards Pleistocene expansions of the heather

Erica arborea. J. Biogeogr. 38, 164–176.

Dixon, C. J., Schönswetter, P., Vargas, P., Ertl, S., Schneeweiss, G. M. 2009. Bayesian hypothesis

testing supports long-distance Pleistocene migrations in a European high mountain plant

(Androsace vitaliana, Primulaceae). Mol. Phylogen. Evol. 53, 580–591.

Donoghue, M. J. 2008. A phylogenetic perspective on the distribution of plant diversity. Proc.Natl.

Acad. Sci. USA 105, 11549–11555.

Donoghue, M. J., Moore, B. R. 2003. Toward an integrative historical biogeography. Integrat.

Comp. Biol. 43, 261–270.

37

145146

881

882

883

884

885

886

887

888

889

890

891

892

893

894

895

896

897

898

899

900

901

902

903

904

147148

Eckert, C. G., Kalisz, S., Geber, M. A., Sargent, R., Elle, E., Cheptou, P. O., Goodwillie, C., Johnston,

M. O., Kelly, J. K., Moeller, D. A., Porcher, E., Ree, R. H., Vallejo-Marín, M., Winn, A. A. 2010.

Plant mating systems in a changing world. Trends Ecol. Evol. 25, 35–43.

Edh, K., Widén, B., Ceplitis, A. 2007 Nuclear and chloroplast microsatellites reveal extreme

population differentiation and limited gene flow in the Aegean endemic Brassica cretica

(Brassicaceae). Mol. Ecol. 16, 4972–4983.

Emerson, K. J., Merz, C. R., Catchen, J. M., Hohenlohe, P. A., Cresko, W. A., Bradshaw, W. E.,

Holzapfel, C. M. 2010. Resolving postglacial phylogeography using high-throughput

sequencing. Proc. Natl. Acad. Sci. USA USA 107, 16196–16200.

Escudero, M., Vargas, P., Valcárcel, V., Luceño, M. 2008. Strait of Gibraltar: an effective gene-flow

barrier for wind-pollinated Carex helodes (Cyperaceae) as revealed by DNA sequences, AFLP,

and cytogenetic variation. Am. J. Bot. 95, 745–755.

Escudero, M., Vargas, P., Arens, P., Ouborg, N. J., Luceño, M. 2010. The east west north ‐ ‐

colonization history of the Mediterranean and Europe by the coastal plant Carex extensa

(Cyperaceae). Mol. Ecol. 19, 352–370.

Excoffier, L., Ray, N. 2008. Surfing during population expansions promotes genetic revolutions and

structuration. Trends Ecol. Evol. 23, 347–351.

Excoffier, L., Hofer, T., Foll, M. 2009. Detecting loci under selection in a hierarchically structured

population. Heredity 103, 285–298.

Fady, B. 2005. Is there really more biodiversity in Mediterranean forest ecosystems? Taxon 54,

905–910.

Fady, B., Conord, C. 2010. Macroecological patterns of species and genetic diversity in vascular

plants of the Mediterranean Basin. Divers. Distrib. 16, 53–64.

Falchi, A., Paolini, J., Desjobert, J. M., Melis, A., Costa, J., Varesi, L. 2009. Phylogeography of Cistus

creticus L. on Corsica and Sardinia inferred by the TRNL-F and RPL32-TRNL sequences of

cpDNA. Mol. Phylogen. Evol. 52, 538–543.

38

149150

905

906

907

908

909

910

911

912

913

914

915

916

917

918

919

920

921

922

923

924

925

926

927

928

929

930

151152

Fernández-Mazuecos, M., Vargas, P. 2010. Ecological rather than geographical isolation

dominates Quaternary formation of Mediterranean Cistus species. Mol. Ecol. 19, 1381–1395.

Fernández-Mazuecos, M., Vargas, P. 2011. Historical isolation versus recent long-distance

connections between Europe and Africa in bifid toadflaxes (Linaria sect.Versicolores). PLoS

ONE 6, e22234.

Fernández Mazuecos, M., Vargas, P. 2013. Congruence between distribution modelling and ‐

phylogeographical analyses reveals Quaternary survival of a toadflax species (Linaria elegans)

in oceanic climate areas of a mountain ring range. New Phytol. 198, 1274–1289.

Fernández Palacios, J. M., de Nascimento, L., Otto, R., Delgado, J. D., García del Rey, E., Arévalo, J.‐ ‐ ‐

R., Whittaker, R. J. 2011. A reconstruction of Palaeo Macaronesia, with particular reference to ‐

the long term biogeography of the Atlantic island laurel forests. ‐ J. Biogeogr. 38, 226–246.

Fineschi, S., Taurchini, D., Villani, F., Vendramin, G. G. 2000. Chloroplast DNA polymorphism

reveals little geographical structure in Castanea sativa Mill. (Fagaceae) throughout southern

European countries. Mol. Ecol. 9, 1495–1503.

Fiz-Palacios, O., Vargas, P., Vila, R., Papadopulos, A. S. T., Aldasoro, J. J. 2010. The uneven

phylogeny and biogeography of Erodium (Geraniaceae): radiations in the Mediterranean and

recent recurrent intercontinental colonization. Ann. Bot. 106, 871–884.

Frajman, B., Oxelman, B. 2007. Reticulate phylogenetics and phytogeographical structure of

Heliosperma (Sileneae, Caryophyllaceae) inferred from chloroplast and nuclear DNA

sequences. Mol. Phylogen. Evol. 3, 140–155.

Fromhage, L., Vences, M., Veith, M. 2004. Testing alternative vicariance scenarios in Western

Mediterranean discoglossid frogs. Mol. Phylogen. Evol. 31, 308–322.

Fuertes Aguilar, J., Gutiérrez Larena, B., Nieto Feliner, G. 2011. Genetic and morphological

diversity in Armeria (Plumbaginaceae) is shaped by glacial cycles in Mediterranean refugia. An.

Jard. Bot. Madr. 68, 175–197.

39

153154

931

932

933

934

935

936

937

938

939

940

941

942

943

944

945

946

947

948

949

950

951

952

953

954

955

155156

García, A., Iriondo, J. M., Escudero, A., Fuertes Aguilar, J., Nieto Feliner, G. 2013. Genetic patterns

of habitat fragmentation and past climate change effects in the Mediterranean high-mountain

plant Armeria caespitosa (Plumbaginaceae). Am. J. Bot. 100, 1641–1650.

Garnatje, T., Pérez Collazos, E., Pellicer, J., Catalán, P. 2013. ‐ Balearic insular isolation and large

continental spread framed the phylogeography of the western Mediterranean Cheirolophus

intybaceus s.l. (Asteraceae). Plant Biol. 15, 166–175.

Gittenberger, E. 1991. What about non-adaptive radiation? Biol. J. Linn. Soc. 43, 263–272.

Gómez, A., Lunt, D. H. 2007. Refugia within refugia: patterns of phylogeographic concordance in

the Iberian Peninsula, in: Weiss, S., Ferrand, N. (Eds.), Phylogeography of southern European

refugia. Springer, Berlin, pp. 155–188.

Gràcia, F., Clamor, B., Landreth, R., Vicens, D., Watkinson, P. 2001. Evidències geomorfológiques

dels canvis del nivell marí. Monogr. Soc. Hist. Nat. Balears 9, 91–119.

Grassi, F., Minuto, L., Casazza, G., Labra, M., Sala, F. 2009. Haplotype richness in refugial areas:

phylogeographical structure of Saxifraga callosa. J. Plant Res. 122, 377–387.

Greuter, W. 1991. Botanical diversity, endemism, rarity, and extinction in the Mediterranean area:

an analysis based on the published volumes of Med-Checklist. Bot. Chron. 10, 63–79.

Griffiths, H. I., Krystufek, B., Reed, J. M. (eds.) 2004. Balkan biodiversity: pattern and process in the

European hotspot. Kluwer, Dordrecht, Boston, London.

Gutiérrez Larena, B., Fuertes Aguilar, J., Nieto Feliner, G. 2002. Glacial-induced altitudinal

migrations in Armeria (Plumbaginaceae) inferred from patterns of chloroplast DNA haplotype

sharing. Mol. Ecol. 11, 1965–1974.

Guzmán, B., Vargas, P. 2005. Systematics, character evolution, and biogeography of Cistus L.

(Cistaceae) based on ITS, trnL–trnF, and matK sequences. Mol. Phylogen. Evol. 37, 644–660.

Guzmán, B., Vargas, P. 2009. Long distance colonization of the Western Mediterranean by ‐ Cistus

ladanifer (Cistaceae) despite the absence of special dispersal mechanisms. J. Biogeogr. 36,

954–968.

40

157158

956

957

958

959

960

961

962

963

964

965

966

967

968

969

970

971

972

973

974

975

976

977

978

979

980

981

159160

Guzmán, B. Lledó, M. D., Vargas, P. 2009. Adaptive radiation in Mediterranean Cistus (Cistaceae).

PLoS ONE 4, e6362.

Hampe, A., Petit, R. J. 2005. Conserving biodiversity under climate change: the rear edge matters.

Ecol. Lett. 8, 461–467.

Hampe, A., Arroyo, J., Jordano, P., Petit, R. J. 2003. Rangewide phylogeography of a bird-dispersed

Eurasian shrub: contrasting Mediterranean and temperate glacial refugia. Mol. Ecol. 12, 3415–

3426.

Herrera, C. M., Bazaga, P. 2008. Population genomic approach reveals adaptive floral divergence ‐

in discrete populations of a hawk moth pollinated violet. ‐ Mol. Ecol. 17, 5378–5390.

Heuertz, M., Hausman, J. F., Tsvetkov, I., Frascaria Lacoste, N., Vekemans, X. 2001. ‐ Assessment of

genetic structure within and among Bulgarian populations of the common ash (Fraxinus

excelsior L.). Mol. Ecol. 10, 1615–1623.

Heuertz, M., Fineschi, S., Anzidei, M., Pastorelli, R., Salvini, D., Paule, L., Frascaria-Lacoste, N.,

Hardy, O. J., Vekemans, X., Vendramin, G. G. 2004. Chloroplast DNA variation and postglacial

recolonization of common ash (Fraxinus excelsior L.) in Europe. Mol. Ecol. 13, 3437–3452.

Heuertz, M., Carnevale, S., Fineschi, S., Sebastiani, F., Hausman, J. F., Paule, L., Vendramin, G. G.

2006. Chloroplast DNA phylogeography of European ashes, Fraxinus sp.(Oleaceae): roles of

hybridization and life history traits. Mol. Ecol. 15, 2131–2140.

Heuertz, M., Teufel, J., González Martínez, S. C., Soto, A., Fady, B., Alía, R., Vendramin, G. G. 2010.‐

Geography determines genetic relationships between species of mountain pine (Pinus mugo

complex) in western Europe. J. Biogeogr. 37, 541–556.

Hewitt, G. M. 2000. The genetic legacy of Quaternary ice ages. Nature 405, 907–913.

Hewitt, G. M. 2001. Speciation, hybrid zones and phylogeography—or seeing genes in space and

time. Mol. Ecol. 10, 537–549.

Hewitt, G. M. 2011. Mediterranean peninsulas: the evolution of hotspots, in: Zachos, F. E., Habel,

J. C. (Eds.), Biodiversity hotspots. Springer, Berlin, Heidelberg, pp. 123–147.

41

161162

982

983

984

985

986

987

988

989

990

991

992

993

994

995

996

997

998

999

1000

1001

1002

1003

1004

1005

1006

1007

163164

Hickerson, M. J., Stahl, E. A., Lessios, H. A. 2006. Test for simultaneous divergence using

approximate Bayesian computation. Evolution 60, 2435–2453.

Hickerson, M. J., Carstens, B. C., Cavender-Bares, J., Crandall, K. A., Graham, C. H., Johnson, J. B.,

Rissler, L., Victoriano, P. F., Yoder, A. D. 2010. Phylogeography’s past, present, and future: 10

years after Avise, 2000. Mol. Phylogen. Evol. 54, 291–301.

Hsü, K. J. 1972. When the Mediterranean dried up. Sci. Am. 227, 27–36.

Humphries, C., Araújo, M., Williams, P., Lampinen, R., Lahti, T., Uotila, P. 1999. Plant diversity in

Europe: Atlas Florae Europaeae and WORLDMAP. Acta Bot. Fenn. 162, 11–21.

Imbrie J., Berger, A., Shackleton, N. J. 1993. Role of orbital forcing: a two-million-year perspective,

in: Eddy, J. A., Oeschger, H. (Eds.), Global changes in the perspective of the past. Wiley,

Chichester, pp. 263–277.

Jakob, S. S., Ihlow, A., Blattner, F. R. 2007. Combined ecological niche modelling and molecular

phylogeography revealed the evolutionary history of Hordeum marinum (Poaceae)—niche

differentiation, loss of genetic diversity, and speciation in Mediterranean Quaternary refugia.

Mol. Ecol. 16, 1713–1727.

Jansson, R., Dynesius, M. 2002. The fate of clades in a world of recurrent climatic change:

Milankovitch oscillations and evolution. Annu. Rev. Ecol. Syst. 33, 741–777.

Jaramillo-Correa, J. P., Grivet, D., Terrab, A., Kurt, Y., De-Lucas, A. I., Wahid, N., Vendramin, G. G.,

González-Martínez, S. C. 2010. The Strait of Gibraltar as a major biogeographic barrier in

Mediterranean conifers: a comparative phylogeographic survey. Mol. Ecol. 19, 5452–5468.

Jiménez, P., Lopez de Heredia, U., Collada, C., Lorenzo, Z., Gil, L. 2004. High variability of

chloroplast DNA in three Mediterranean evergreen oaks indicates complex evolutionary

history. Heredity 93, 510–515.

Joger, U., Fritz, U., Guicking, D., Kalyabina-Hauf, S., Nagy, Z. T., Wink, M. 2007. Phylogeography of

western Palaearctic reptiles – Spatial and temporal speciation patterns. Zool. Anz. 246, 293–

313.

42

165166

1008

1009

1010

1011

1012

1013

1014

1015

1016

1017

1018

1019

1020

1021

1022

1023

1024

1025

1026

1027

1028

1029

1030

1031

1032

1033

167168

Jorgensen, T. H., Olesen, J. M. 2001. Adaptive radiation of island plants: evidence from Aeonium

(Crassulaceae) of the Canary Islands. Perspect. Plant Ecol. Evol. Syst. 4, 29–42.

Juan, C., Emerson, B. C., Oromí, P., Hewitt, G. M. 2000. Colonization and diversification: towards a

phylogeographic synthesis for the Canary Islands. Trends Ecol. Evol. 15, 104–109.

Kadereit, J. W., Baldwin, B. G. 2012. Western Eurasian-western North American disjunct plant

taxa: the dry-adapted ends of formerly widespread north temperate mesic lineages and

examples of long-distance dispersal. Taxon 61, 3–17.

Kadereit, J. W., Westberg, E. 2007. Determinants of phylogeographic structure: a comparative

study of seven coastal flowering plant species across their European range. Watsonia 26, 229–

238.

Kadereit, G., Yaprak, A. E. 2008. Microcnemum coralloides (Chenopodiaceae-Salicornioideae): an

example of intraspecific East-West disjunctions in the Mediterranean region. An. Jard. Bot.

Madr. 65, 415–426.

Kadereit, J. W., Arafeh, R., Somogyi, G., Westberg, E. 2005. Terrestrial growth and marine

dispersal? Comparative phylogeography of five coastal plant species at a European scale.

Taxon 54, 861–876.

Khimoun, A., Cornuault, J., Burrus, M., Thebaud, C., Andalo, C. 2012. Ecology predicts parapatric

distributions in two closely related Antirrhinum majus subspecies. Evol. Ecol. 27, 51–64.

Knowles, L. L., Maddison, W. P. 2002. Statistical phylogeography. Mol. Ecol. 11, 2623–2635.

Knowles, L. L. 2009. Statistical phylogeography. Annu. Rev. Ecol. Evol. Syst. 40, 593–612.

Krijgsman, W. 2002. The Mediterranean: Mare Nostrum of earth sciences. Earth Planet. Sci. Lett.

205, 1–12.

Kropf, M., Kadereit, J. W., Comes, H. P. 2002. Late Quaternary distributional stasis in the

submediterranean mountain plant Anthyllis montana L.(Fabaceae) inferred from ITS sequences

and amplified fragment length polymorphism markers. Mol. Ecol. 11, 447–463.

43

169170

1034

1035

1036

1037

1038

1039

1040

1041

1042

1043

1044

1045

1046

1047

1048

1049

1050

1051

1052

1053

1054

1055

1056

1057

1058

171172

Kropf, M., Kadereit, J. W., Comes, H. P. 2003. Differential cycles of range contraction and

expansion in European high mountain plants during the Late Quaternary: insights from

Pritzelago alpina (L.) O. Kuntze (Brassicaceae). Mol. Ecol. 12, 931–949.

Kropf, M., Comes, H. P., Kadereit, J. W. 2006. Long-distance dispersal vs vicariance: the origin and

genetic diversity of alpine plants in the Spanish Sierra Nevada. New Phytol. 172, 169–184.

Kropf, M., Comes, H. P., Kadereit, J. W. 2008. Causes of the genetic architecture of south-west

European high mountain disjuncts. Plant Ecol. Divers. 1, 217–228.

Kučera, J., Marhold, K., Lihová, J. 2010. Cardamine maritima group (Brassicaceae) in the amphi-

Adriatic area: a hotspot of species diversity revealed by DNA sequences and morphological

variation. Taxon 59, 148–164.

Lambeck, K., Esat, T. M., Potter, E. K. 2002. Links between climate and sea levels for the past three

million years. Nature 419, 199–206.

Lamont, B. B., He, T., Enright, N. J., Krauss, S. L., Miller, B. P. 2003. Anthropogenic disturbance

promotes hybridization between Banksia species by altering their biology. J. Evol. Biol. 16,

551–557.

Levin, D. A. 2012. Mating system shifts on the trailing edge. Ann. Bot. 109, 613–620.

Levin, D. A., Francisco Ortega, J., Jansen, R. K. 1996. ‐ Hybridization and the extinction of rare plant

species. Conserv. Biol. 10, 10-16.

Linder, H. P. 2005. The evolution of diversity: the Cape flora. Trends Plants Sci. 10, 536–541.

Linder, H. P., Hardy, C. R. 2004. Evolution of the species-rich Cape flora. Philos. Trans. R. Soc. B

Biol. Sci. 359, 1623–1632.

Lo Presti, R. M., Oberprieler, C. 2009. Evolutionary history, biogeography, and eco-climatological

differentiation of the genus Anthemis L. (Compositae, Anthemideae) in the circum-

Mediterranean area. J. Biogeogr. 36, 1313–1332.

44

173174

1059

1060

1061

1062

1063

1064

1065

1066

1067

1068

1069

1070

1071

1072

1073

1074

1075

1076

1077

1078

1079

1080

1081

1082

175176

Lo Presti, R. M., Oberprieler, C. 2011. The central Mediterranean as a phytodiversity hotchpotch:

phylogeographical patterns of the Anthemis secundiramea group (Compositae, Anthemideae)

across the Sicilian Channel. J. Biogeogr. 38, 1109–1124.

López de Heredia, U., Jiménez, P., Díaz-Fernández, P., Gil, L. 2005. The Balearic Islands: a reservoir

of cpDNA genetic variation for evergreen oaks. J. Biogeogr. 32, 939–949.

López de Heredia, U., Carrión, J. S., Jiménez, P., Collada, C., Gil, L. 2007. Molecular and

palaeoecological evidence for multiple glacial refugia for evergreen oaks on the Iberian

Peninsula. J. Biogeogr. 34, 1505–1517.

Lumaret, R., Tryphon-Dionnet, M., Michaud, H., Sanuy, A., Ipotesi, E., Born, C., Mir, C. 2005.

Phylogeographical variation of chloroplast DNA in cork oak (Quercus suber). Ann. Bot. 96, 853–

861.

Macaya Sanz, D., Heuertz, M., López de Heredia, U., De Lucas, A. I., Hidalgo, E., Maestro, C., ‐

Prada, A., Alía, R., González Martínez, S. C. 2012. ‐ The Atlantic–Mediterranean watershed, river

basins and glacial history shape the genetic structure of Iberian poplars. Mol. Ecol. 21, 3593–

3609.

Magri, D., Fineschi, S., Bellarosa, R., Buonamici, A., Sebastiani, F., Schirone, B., Simeone, M. C.,

Vendramin, G. G. 2007. The distribution of Quercus suber chloroplast haplotypes matches the

palaeogeographical history of the western Mediterranean. Mol. Ecol. 16, 5259–5266.

Mallet, J. 2005. Hybridization as an invasion of the genome. Trends Ecol. Evol. 20, 229–237.

Mansion, G., Zeltner, L., Bretagnolle, F. 2005. Phylogenetic patterns and polyploid evolution

within the Mediterranean genus Centaurium (Gentianaceae – Chironieae). Taxon 54, 931–950.

Mansion, G., Rosenbaum, G., Schoenenberger, N., Bacchetta, G., Rosselló, J. A., Conti, E. 2008.

Phylogenetic analysis informed by geological history supports multiple, sequential invasions of

the Mediterranean Basin by the angiosperm family Araceae. Syst. Biol. 57, 269–285.

45

177178

1083

1084

1085

1086

1087

1088

1089

1090

1091

1092

1093

1094

1095

1096

1097

1098

1099

1100

1101

1102

1103

1104

1105

1106

179180

Mansion, G., Selvi, F., Guggisberg, A., Conti, E. 2009. Origin of Mediterranean insular endemics in

the Boraginales: integrative evidence from molecular dating and ancestral area reconstruction.

J. Biogeogr. 36, 1282–1296.

Marques, I., Fuertes Aguilar, J., Martins-Loução, M. A., Nieto Feliner, G. 2012. Spatial–temporal

patterns of flowering asynchrony and pollinator fidelity in hybridizing species of Narcissus.

Evol. Ecol. 26, 1433–1450.

Martín-Bravo, S., Vargas, P., Luceño, M. 2009. Is Oligomeris (Resedaceae) indigenous to North

America? Molecular evidence for a natural colonization from the Old World. Am. J. Bot. 96,

507–518.

Martín-Bravo, S., Valcárcel, V., Vargas, P., Luceño, M. 2010. Geographical speciation related to

Pleistocene range shifts in the western Mediterranean mountains (Reseda sect. Glaucoreseda,

Resedaceae).Taxon 59, 466–482.

Mateu-Andrés, I., Aguilella, A., Boisset. F., Currás, R., Guara, M., Laguna, E., Marzo, A., Puche, M.

F., Pedrola, J. 2013. Geographical patterns of genetic variation in rosemary (Rosmarinus

officinalis) in the Mediterranean basin. Bot. J. Linn. Soc. 171, 700–712.

Maureira-Butler I. J., Pfeil, B. E., Muangprom, A., Osborn, T. C., Doyle, J. J. 2008. The reticulate

history of Medicago (Fabaceae). Syst. Biol. 57, 466–482.

Mayol, M., Palau, C., Rosselló, J. A., González-Martínez, S. C., Molins, A., Riba, M. 2012. Patterns of

genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial

scales: insights on evolutionary processes leading to diversification in continental islands. Ann.

Bot. 109, 429–441.

Médail, F., Diadema, K. 2009. Glacial refugia influence plant diversity patterns in the

Mediterranean Basin. J. Biogeogr. 36, 1333–1345.

Médail, F., Quézel, P. 1997. Hot-spots analysis for conservation of plant biodiversity in the

Mediterranean Basin. Ann. Mo. Bot. Gard. 84, 112–127.

46

181182

1107

1108

1109

1110

1111

1112

1113

1114

1115

1116

1117

1118

1119

1120

1121

1122

1123

1124

1125

1126

1127

1128

1129

1130

1131

183184

Meulenkamp, J. E., Sissingh, W. 2003. Tertiary palaeogeography and tectonostratigraphic

evolution of the Northern and Southern Peri-Tethys platforms and the intermediate domains

of the African–Eurasian convergent plate boundary zone. Palaeogeogr. Palaeoclimatol.

Palaeoecol. 196, 209–228.

Migliore, J., Baumel, A., Juin, M., Médail, F. 2012. From Mediterranean shores to central Saharan

mountains: key phylogeographical insights from the genus Myrtus. J. Biogeogr. 39, 942–956.

Molins, A., Mayol, M., Rosselló, J. A. 2009. Phylogeographical structure in the coastal species

Senecio rodriguezii (Asteraceae), a narrowly distributed endemic Mediterranean plant. J.

Biogeogr. 36, 1372–1383.

Musacchio, A., Pellegrino, G., Cafasso, D., Widmer, A., Cozzolino, S. 2006. A unique A. palustris

lineage across the Otranto strait: botanical evidence for a past land-bridge? Plant Syst. Evol.

262, 103–111.

Myers, N., Mittermeier, R. A., Mittermeier, C. G., da Fonseca, G. A. B., Kent, J. 2000. Biodiversity

hotspots for conservation priorities. Nature 403, 853–858.

Naciri, Y., Cavat, F., Jeanmonod, D. 2010. Silene patula (Siphonomorpha, Caryophyllaceae) in

North Africa: a test of colonisation routes using chloroplast markers. Mol. Phylogen. Evol. 54,

922–932.

Nathan, R. 2006. Long-distance dispersal of plants. Science 313, 786–788.

Nieto Feliner, G. 2011. Southern European glacial refugia: a tale of tales. Taxon 65, 365–372.

Nieto Feliner, G., Gutiérrez Larena, B., Fuertes Aguilar, J. 2004. Fine scale geographical structure, ‐

intra individual polymorphism and recombination in nuclear ribosomal internal transcribed ‐

spacers in Armeria (Plumbaginaceae). Ann. Bot. 93, 189–200.

Normand, S., Ricklefs, R. E., Skov, F., Bladt, J., Tackenberg, O., Svenning, J. C. 2011. Postglacial

migration supplements climate in determining plant species ranges in Europe. Proc. R. Soc. B

278, 3644–3653.

47

185186

1132

1133

1134

1135

1136

1137

1138

1139

1140

1141

1142

1143

1144

1145

1146

1147

1148

1149

1150

1151

1152

1153

1154

1155

1156

187188

Olalde, M., Herrán, A., Espinel, S., Goicoechea, P. G. 2002. White oaks phylogeography in the

Iberian Peninsula. For. Ecol. Manag. 156, 89–102.

Ortiz, M. A., Tremetsberger, K., Talavera, S., Stuessy, T., García-Castaño, J. L. 2007. Population

structure of Hypochaeris salzmanniana DC. (Asteraceae), an endemic species to the Atlantic

coast on both sides of the Strait of Gibraltar, in relation to Quaternary sea level changes. Mol.

Ecol. 16, 541–552.

Pannell, J. R., Obbard, D. J., Buggs, R. J. A. 2004. Polyploidy and the sexual system: what can we

learn from Mercurialis annua? Biol. J. Linn. Soc. 82, 547–560.

Parisod, C., Joost, S. 2010. Divergent selection in trailing-versus leading-edge populations of

Biscutella laevigata. Ann. Bot. 105, 655–660.

Patarnello, T., Volckaert, F. A., Castilho, R. 2007. Pillars of Hercules: is the Atlantic–Mediterranean

transition a phylogeographical break? Mol. Ecol. 16, 4426–4444.

Pauli, H., Gottfried, M., Reiter, K., Klettner, C., Grabherr, G. 2007. Signals of range expansions and

contractions of vascular plants in the high Alps: observations (1994–2004) at the GLORIA*

master site Schrankogel, Tyrol, Austria. Glob. Change Biol. 13, 147-156.

Pérez Collazos, E., Sánchez Gómez, P., Jiménez, J. F., Catalán, P. 2009. ‐ ‐ The phylogeographical

history of the Iberian steppe plant Ferula loscosii (Apiaceae): a test of the abundant centre ‐

hypothesis. Mol. Ecol. 18, 848–861.

Petit, R. J., Hampe, A., Cheddadi, R. 2005. Climate changes and tree phylogeography in the

Mediterranean. Taxon 54, 877–885.

Petit, R. J., Brewer, S., Bordács, S. et al. 2002. Identification of refugia and post-glacial colonisation

routes of European white oaks based on chloroplast DNA and fossil pollen evidence. For. Ecol.

Manag. 156, 49–74.

Petit, R. J., Aguinagalde, I., de Beaulieu, J.-L., Bittkau, C., Brewer, S., Cheddadi, R., Ennos, R.,

Fineschi, S., Grivet, D., Lascoux, M., Mohanty, A., Müller-Starck, G., Demesure-Musch, B.,

48

189190

1157

1158

1159

1160

1161

1162

1163

1164

1165

1166

1167

1168

1169

1170

1171

1172

1173

1174

1175

1176

1177

1178

1179

1180

1181

191192

Palmé, A., Martín, J. P., Rendell, S., Vendramin, G. G. 2003. Glacial refugia: hotspots but not

melting pots of genetic diversity. Science 300, 1563–1565.

Picó, F. X., Méndez-Vigo, B., Martínez-Zapater, J. M., Alonso-Blanco, C. 2008. Natural genetic

variation of Arabidopsis thaliana is geographically structured in the Iberian Peninsula. Genetics

180, 1009–1021.

Piñeiro, R., Fuertes Aguilar, J., Draper, D., Nieto Feliner, G. 2007. Ecology matters: Atlantic–

Mediterranean disjunction in the sand-dune shrub Armeria pungens (Plumbaginaceae). Mol.

Ecol. 16, 2155–2171.

Piñeiro, R., Widmer, A., Fuertes Aguilar, J., Nieto Feliner, G. 2011. Introgression in peripheral

populations and colonization shape the genetic structure of the coastal shrub Armeria

pungens. Heredity 106, 228–240.

Provan, J., Bennett, K. D. 2008. Phylogeographic insights into cryptic glacial refugia. Trends Ecol.

Evol. 23, 564–571.

Quézel, P. 1985. Definition of the Mediterranean region and origin of its flora, in: Gómez-Campo,

C. (Ed.), Plant conservation in the Mediterranean area. Dr W. Junk Publishers, Dordrecht, pp.

9–24.

Quézel, P., Médail, F. 2003. Ecologie et biogéographie des forêts du bassin méditerranéen.

Elsevier (Collection Environnement), Paris.

Qiu, Y. X., Fu, C. X., Comes, H. P. 2011. Plant molecular phylogeography in China and adjacent

regions: tracing the genetic imprints of Quaternary climate and environmental change in the

world’s most diverse temperate flora. Mol. Phylogen. Evol. 59, 225–244.

Raunkiaer, C. 1934. Life forms of plants and statistical plant geography. Calderon Press, Oxford.

(English translation of collected papers by C. Raunkiaer 1903).

Rieseberg, L. H., Raymond, O., Rosenthal, D. M., Lai, Z., Livingstone, K., Nakazato, T., Durphy, J. L.,

Schwarzbach, A. E., Donovan, L. A., Lexer, C. 2003. Major ecological transitions in wild

sunflowers facilitated by hybridization. Science, 301(5637), 1211-1216.

49

193194

1182

1183

1184

1185

1186

1187

1188

1189

1190

1191

1192

1193

1194

1195

1196

1197

1198

1199

1200

1201

1202

1203

1204

1205

1206

1207

195196

Rodríguez-Sánchez, F., Arroyo, J. 2008. Reconstructing the demise of Tethyan plants: climate-

driven range dynamics of Laurus since the Pliocene. Glob. Ecol. Biogeogr. 17, 685–695.

Rodríguez-Sánchez, F., Pérez-Barrales, R., Ojeda, F., Vargas, P., Arroyo, J. 2008. The Strait of

Gibraltar as a melting pot for plant biodiversity. Quat. Sci. Rev. 27, 2100–2117.

Rodríguez-Sánchez, F., Guzmán, B., Valido, A., Vargas, P., Arroyo, J. 2009. Late Neogene history of

the laurel tree (Laurus L., Lauraceae) based on phylogeographical analyses of Mediterranean

and Macaronesian populations. J. Biogeogr. 36, 1270–1281.

Rodríguez-Sánchez, F., Hampe, A., Jordano, P., Arroyo, J. 2010. Past tree range dynamics in the

Iberian Peninsula inferred through phylogeography and palaeodistribution modelling: a

review. Rev. Palaeobot. Palynol. 162, 507–521.

Roquet, C., Sanmartín, I., Garcia-Jacas, N., Sáez, L., Susanna, A., Wikström, N., Aldasoro, J. J. 2009.

Reconstructing the history of Campanulaceae with a Bayesian approach to molecular dating

and dispersal–vicariance analyses. Mol. Phylogen. Evol. 52, 575–587.

Rosenbaum, G., Lister, G. S., Duboz, C. 2002. Reconstruction of the tectonic evolution of the

western Mediterranean since the Oligocene. J. Virtual Explor. 8, 107–130.

Rosselló, J. A., Lázaro, A., Cosín, R., Molins, A. 2007. A phylogeographic split in Buxus balearica

(Buxaceae) as evidenced by nuclear ribosomal markers: when ITS paralogues are welcome. J.

Mol. Evol. 64, 143–157.

Rosselló, J. A., Cosín, R., Bacchetta, G., Brullo, S., Mayol, M. 2009. Nuclear and chloroplast DNA

variation in Cephalaria squamiflora (Dipsacaceae), a disjunct Mediterranean species. Taxon 58,

1242–1253.

Salvo, G., Ho, S. Y. W., Rosenbaum, G., Ree, R., Conti, E. 2010. Tracing the temporal and spatial

origins of island endemics in the Mediterranean region: a case study from the Citrus family

(Ruta L., Rutaceae). Syst. Biol. 59, 705–722.

Sanmartín, I. 2003. Dispersal vs. vicariance in the Mediterranean: historical biogeography of the

Palearctic Pachydeminae (Coleoptera, Scarabaeoidea). J. Biogeogr. 30, 1883–1897.

50

197198

1208

1209

1210

1211

1212

1213

1214

1215

1216

1217

1218

1219

1220

1221

1222

1223

1224

1225

1226

1227

1228

1229

1230

1231

1232

1233

199200

Sanmartín, I. 2007. Event-based biogeography: integrating patterns, processes, and time, in:

Ebach, M.C., Tangney, R.S. (Eds.), Biogeography in a changing world, Systematics Association

Volume Series vol. 70. Taylor, Francis, London, pp. 135-156.

Sanmartin, I., van der Mark, P., Ronquist, F. 2008. Inferring dispersal: a Bayesian approach to

phylogeny-based island biogeography, with special reference to the Canary Islands. J.

Biogeogr. 35, 428–449.

Schierenbeck, K. A., Ellstrand, N. C. 2009. Hybridization and the evolution of invasiveness in plants

and other organisms. Biol. Invasions 11, 1093-1105.

Schnitzler, J., Barraclough, T. G., Boatwright, J. S., Goldblatt, P., Manning, J. C., Powell, M. P.,

Rebelo, T., Savolainen, V. 2011. Causes of plant diversification in the Cape biodiversity hotspot

of South Africa. Syst. Biol. 60, 343–57.

Schönswetter, P., Tribsch, A., Stehlik, I., Niklfeld, H. 2004. Glacial history of high alpine Ranunculus

glacialis (Ranunculaceae) in the European Alps in a comparative phylogeographical context.

Biol. J. Linn. Soc. 81, 183–195.

Schönswetter, P., Stehlik, I., Holderegger, R., Tribsch, A. 2005. Molecular evidence for glacial

refugia of mountain plants in the European Alps. Mol. Ecol. 14, 3547–3555.

Seehausen, O. L. E., Takimoto, G., Roy, D., Jokela, J. 2008. Speciation reversal and biodiversity

dynamics with hybridization in changing environments. Mol. Ecol. 17, 30–44.

Soltis, P. S., Soltis, D. E. 2009. The role of hybridization in plant speciation. Annu. Rev. Plant Biol.

60, 561–588.

Soltis, D. E., Morris, A. B., McLachlan, J. S., Manos, P. S., Soltis, P. S. 2006. Comparative

phylogeography of unglaciated eastern North America. Mol. Ecol. 15, 4261–4293.

Španiel, S., Marhold, K., Passalacqua, N. G., Zozomová-Lihová, J. 2011. Intricate variation patterns

in the diploid-polyploid complex of Alyssum montanum-A. repens (Brassicaceae) in the

Apennine Peninsula: evidence for long-term persistence and diversification. Am. J. Bot. 98,

1887–1904.

51

201202

1234

1235

1236

1237

1238

1239

1240

1241

1242

1243

1244

1245

1246

1247

1248

1249

1250

1251

1252

1253

1254

1255

1256

1257

1258

1259

203204

Stebbins, G. L. 1970. Adaptive radiation of reproductive characteristics in angiosperms, I:

pollination mechanisms. Annu. Rev. Ecol. Syst. 1, 307-326.

Steininger, F. F., Rögl, F. 1984. Paleogeography and palinspastic reconstruction of the Neogene of

the Mediterranean and Paratethys. Geol. Soc. Lond. Spec. Publ. 17, 659–668.

Suc, J. P. 1984. Origin and evolution of the Mediterranean vegetation and climate in Europe.

Nature 307, 429–432.

Surina, B., Schönswetter, P., Schneeweiss, G. M. 2011. Quaternary range dynamics of ecologically

divergent species (Edraianthus serpyllifolius and E. tenuifolius, Campanulaceae) within the

Balkan refugium. J. Biogeogr. 38, 1381–1393.

Svenning, J. C., Normand, S., Skov, F. 2009. Plio Pleistocene climate change and geographic ‐

heterogeneity in plant diversity–environment relationships. Ecography 32, 13–21.

Taberlet, P., Fumagalli, L., Wust-Saucy, A. G., Cosson, J.-F. 1998. Comparative phylogeography and

postglacial colonization routes in Europe. Mol. Ecol. 7, 453–464.

Terrab, A., Talavera, S., Arista, M., Paun, O., Stuessy, T. F., Tremetsberger, K. 2007. Genetic

diversity at chloroplast microsatellites (cpSSRs) and geographic structure in endangered West

Mediterranean firs (Abies spp., Pinaceae). Taxon 56, 409–416.

Terrab, A., Hampe, A., Lepais, O., Talavera, S., Vela, E., Stuessy, T. F. 2008a. Phylogeography of

North African Atlas cedar (Cedrus atlantica, Pinaceae): combined molecular and fossil data

reveal a complex Quaternary history. Am. J. Bot. 95, 1262–1269.

Terrab, A., Schönswetter, P., Talavera, S., Vela, E., Stuessy, T. F. 2008b. Range-wide

phylogeography of Juniperus thurifera L., a presumptive keystone species of western

Mediterranean vegetation during cold stages of the Pleistocene. Mol. Phylogen. Evol. 48, 94–

102.

Thompson, J. D. 2005. Plant evolution in the Mediterranean. Oxford University Press, Oxford.

Thompson, J. D., Gaudeul, M., Debussche, M. 2010. Conservation value of sites of hybridization in

peripheral populations of rare plant species. Conserv. Biol. 24, 236–245

52

205206

1260

1261

1262

1263

1264

1265

1266

1267

1268

1269

1270

1271

1272

1273

1274

1275

1276

1277

1278

1279

1280

1281

1282

1283

1284

1285

207208

Thompson, J. D., Lavergne, S., Affre, L., Gaudeul, M., Debussche, M. 2005. Ecological

differentiation of Mediterranean endemic plants. Taxon 54, 967–976.

Tranchida-Lombardo, V., Cafasso, D., Cristaudo, A., Cozzolino, S. 2011. Phylogeographic patterns,

genetic affinities and morphological differentiation between Epipactis helleborine and related

lineages in a Mediterranean glacial refugium. Ann. Bot. 107, 427–436.

Tremetsberger, K., Weiss-Schneeweiss, H., Stuessy, T. F., Samuel, R., Kadlec, G., Ortiz, M. Á.,

Talavera, S. 2005. Nuclear ribosomal DNA and karyotypes indicate a NW African origin of South

American Hypochaeris (Asteraceae, Cichorieae). Mol. Phylogen. Evol. 35, 102–116.

Trewick, S. A., Morgan Richards, M., Russell, S. J., Henderson, S., Rumsey, F. J., Pinter, I., Barrett, J.‐

A., Gibby, M., Vogel, J. C. 2002. Polyploidy, phylogeography and Pleistocene refugia of the

rockfern Asplenium ceterach: evidence from chloroplast DNA. Mol. Ecol. 11, 2003–2012.

Tribsch, A., Schönswetter, P. 2003. Patterns of endemism and comparative phylogeography

confirm palaeoenvironmental evidence for Pleistocene refugia in the Eastern Alps. Taxon 52,

477–497.

Twyford, A. D., Ennos, R. A. 2012. Next-generation hybridization and introgression. Heredity 108,

179–189.

Tzedakis, P. C. 2004. The Balkans as prime glacial refugial territory of European temperate trees,

in: Griffiths, H. I., Krystufek, B., Reed, J. M. (Eds.), Balkan biodiversity. Kluwer, Dordrecht,

Boston, London, pp. 49–68.

Valente, L. M., Vargas, P. 2013. Contrasting evolutionary hypotheses between two

mediterranean climate floristic hotspots: the Cape of southern Africa and the Mediterranean ‐

Basin. J. Biogeogr. 40, 2032–2046.

Valente, L. M., Savolainen, V., Vargas, P. 2010. Unparalleled rates of species diversification in

Europe. Proc. R. Soc. B 277, 1489–1496.

53

209210

1286

1287

1288

1289

1290

1291

1292

1293

1294

1295

1296

1297

1298

1299

1300

1301

1302

1303

1304

1305

1306

1307

1308

1309

211212

Valtueña, F. J., Preston, C. D., Kadereit, J. W. 2012. Phylogeography of a Tertiary relict plant,

Meconopsis cambrica (Papaveraceae), implies the existence of northern refugia for a

temperate herb. Mol. Ecol. 21, 1423–1437.

Vargas, P. 2003. Molecular evidence for multiple diversification patterns of alpine plants in

Mediterranean Europe. Taxon 52, 463–476.

Vendramin, G. G., Fady, B., González-Martínez, S. C., Hu, F. S., Scotti, I., Sebastiani, F., Soto, A.,

Petit, R. J. 2008. Genetically depauperate but widespread: the case of an emblematic

Mediterranean pine. Evolution 62, 680–688.

Vesica, P. L., Tuccimei, P., Turi, B., Fornós, J. J., Ginés, A., Ginés, J. 2000. Late Pleistocene

paleoclimates and sea-level change in the Mediterranean as inferred from stable isotope and

U-series studies of overgrowths on speleothems, Mallorca, Spain. Quat. Sci. Rev. 19, 865–879.

Vettori, C., Vendramin, G. G., Anzidei, M., Pastorelli, R., Paffetti, D., Giannini, R. 2004. Geographic

distribution of chloroplast variation in Italian populations of beech (Fagus sylvatica L.). Theor.

Appl. Genet. 109, 1–9.

Waltari, E., Hijmans, R. J., Peterson, A. T., Nyári, A. S., Perkins, S. L., Guralnick, R. P. 2007. Locating

Pleistocene refugia: comparing phylogeographic and ecological niche model predictions. PLoS

ONE 2, e563.

Webb, C. O., Ackerly, D. D., McPeek, M. A., & Donoghue, M. J. 2002. Phylogenies and community

ecology. Annu. Rev. Ecol. Syst. 33, 475-505.

Westberg, E., Kadereit, J. W. 2009. The influence of sea currents, past disruption of gene flow and

species biology on the phylogeographical structure of coastal flowering plants. J. Biogeogr. 36,

1398–1410.

Widmer, A., Lexer, C. 2001. Glacial refugia: sanctuaries for allelic richness, but not for gene

diversity. Trends Ecol. Evol. 16, 267–269.

Wiens, J. J., Graham, C. H. 2005. Niche conservatism: integrating evolution ecology and

conservation biology. Annu. Rev. Ecol. Syst. 36, 519–539.

54

213214

1310

1311

1312

1313

1314

1315

1316

1317

1318

1319

1320

1321

1322

1323

1324

1325

1326

1327

1328

1329

1330

1331

1332

1333

1334

1335

215216

Wu, H., Guiot, J., Brewer, S., Guo, Z. 2007. Climatic changes in Eurasia at the last glacial maximum

and mid-Holocene: reconstruction from pollen data using inverse vegetation modelling. Clim.

Dyn. 29, 211–229.

Zachos, J. C., Dickens, G. R., Zeeb, R. E. 2008. An early Cenozoic perspective on greenhouse

warming and carbon-cycle dynamics. Nature 451, 279–283.

Zitari, A., Tranchida-Lombardo, V., Cafasso, D., Helal, A. N., Scopece, G., Cozzolino, S. 2011. The

disjointed distribution of Anacamptis longicornu in the West-Mediterranean: the role of

vicariance versus long-distance seed dispersal. Taxon 60, 1041–1049.

55

217218

1336

1337

1338

1339

1340

1341

1342

1343

1344

219220

FIGURE LEGENDS:

Figure 1.- Delimitation of the Mediterranean region according to bioclimatic criteria (redrawn

from Quézel and Médail, 2003)

Figure 2.- Examples of east-west phylogeographic breaks associated with a distinct current

geographic gap. Distribution ranges of Buxus balearica (red), Erophaca baetica (grey) and

Cephalaria squamiflora (black) according to Rosselló et al. (2007), Casimiro-Soriguer et al., (2010)

and Rosselló et al. (2009), respectively.

Figure 3.- Examples of the refugia-within-refugia model advocating that each of the three

southern European peninsulas did not function as a single refugium during Pleistocene glacial

periods but each hosted different lineages in separate refugia as indicated by current genetic

structure (Gomez and Lunt, 2007). The map gathers information from a different plant group in

each of three peninsulas: hypothetic location of refugia during the LGM for Quercus spp. in the

Iberian peninsula according to Olalde et al. (2002); genetic groups in Arabis alpina in the Italian

peninsula (Ansell et al., 2008); taxonomic-genetic groups in the Cardamine maritima complex in

the Balkans (Kučera et al., 2010).

Figure 4.- Sea straits whose biogeographic role as barriers or corridors has been addressed in

phylogeographic studies around the Mediterranean Basin.

Figure 5.- Examples of inferred long-distance dispersal (LDD) events within the Mediterranean

Basin in Androsace vitaliana (dark blue), Papaver alpinum (yellow), Cheirolophus intybaceus (red),

Armeria pungens (lilac), Juniperus thurifera (light blue), Anthemis secundirramea (green), Linaria

Sect. Versicolores (orange), interpreted from Dixon et al. (2009), Kropf et al. (2006), Garnatje et al.

(2012), Piñeiro et al. (2007), Terrab et al. (2008b), Lo Presti and Oberprieler (2011) and

Fernández-Mazuecos and Vargas (2011), respectively.

56

221222

1345

1346

1347

1348

1349

1350

1351

1352

1353

1354

1355

1356

1357

1358

1359

1360

1361

1362

1363

1364

1365

1366

1367

223224