Padrões geográficos e correlações ambientais da variação morfológica e genética em CARYOPHYLLACEAE endémicas do ocidente da Península Ibérica

(1)

D

and environmental

correlations

of morphological

and genetic variation

in endemic

Caryophyllaceae

in Western Iberian

Peninsula

João Filipe Figueiredo da Rocha

Doutoramento em Biologia

Departamento de Biologia 2014

Orientador

Doutor Rubim Manuel Almeida da Silva, Professor Auxiliar, Faculdade de Ciências da Universidade do Porto

Coorientador

Doutor António Maria Luís Crespí, Professor Auxiliar, Universidade de Trás-os-Montes e Alto Douro

Doutor Francisco Amich García, Professor Catedrático, Faculdade de Biologia da Universidade de Salamanca

(2)

(3)

Foreword

According to the number 3 of the 7th Article of regulation of the Doctoral Program in Biology from Faculdade de Ciências da Universidade do Porto (and in agreement with the Portuguese Law Decree Nº 74/2006), the present thesis integrates the articles listed below, written in collaboration with co-authors. The candidate declares that he contributed to conceiving the ideas, compiling and producing the databases and analysing the data, and also declares that he led the writing of all chapters.

List of papers:

Chapter 3 – Rocha J, Castro I, Ferreira V, Carnide V, Pinto-Carnide O, Amich F,

Almeida R, Crespí A (Submitted) Phylogeography of Silene section Cordifolia in the Mountain ranges of North Iberian Peninsula and Alps. Botanical Journal of the

Linnean Society.

Chapter 4 – Rocha J, Ferreira V, Castro I, Carnide V, Amich F, Almeida R, Crespí

A (Submitted) Phylogeography of Silene scabriflora in Iberian Peninsula. American

Journal of Botany.

Chapter 5 – Rocha J, Almeida R, Amich F, Crespí A (Submitted)

Morpho-environmental behaviour of Silene scabriflora in Iberian Peninsula: Atlantic versus Mediterranean climate. Botanical Studies.

Chapter 6 – Rocha J, Amich F, Crespí A, Almeida R (Submitted) Silene section

Cordifolia in Iberian Peninsula: Phenotypic traits variation versus environmental

variation. Botanical Studies.

Chapter 7 – Rocha J, Crespí A, Almeida R, Amich F (2012) Status and

conservation of Silene section Cordifolia in the Iberian Peninsula: a menaced group under global environmental change. Plant Ecology & Diversity.

Chapter 8 – Rocha J, Almeida R, Amich F, Crespí A (Submitted) Bordering

species under climate change: Where to go? The case of two Silene scabriflora subspecies in Iberian Peninsula. Environmental Conservation.

(4)

4 FCUP

Geographic patterns and environmental correlations of morphological and genetic variation in endemic Caryophyllaceae in Western Iberian Peninsula

This thesis was supported by the Portuguese Science Foundation through the PhD grant SFRH / BD / 43167 / 2008 (QREN-POPH, typology 4.1).

Este trabalho foi realizado com o apoio da Fundação para a Ciência e Tecnologia, através da bolsa de doutoramento com a referência SFRH / BD / 43167 / 2008 (QREN-POPH, tipologia 4.1).

(5)

Acknowledgments

I would like to thank all the people and institutions that, in some way, contributed, directly or indirectly, for the proper conduct of this work:

Firstly, I wish to express my deepest and sincere gratitude to Professor Rubim Almeida, this dissertation advisor, whose support was very important. During the most complicated work is essential not only scientific, but also a broad vision that is transmitted to us by more experienced researchers. I thank the motivation that gave me, and also the fact that I do not recall the objectives leaving disperse.

To Professor António Luís Crespí, my co-supervisor, for his tireless scientific monitoring, indispensable for teaching, support and incentives constantly demonstrated, and also because it was always present and available not only academically, but also with his friendship over all this work.

Thanks also to Professor Francisco Amich, my co-supervisor, who always showed additional support available for guidance, for valuable scientific discussions, the support given, the sympathy and friendship always manifested, by the willingness and practicality that has always shown.

To Professor João Honrado, my sincere appreciation for the valuable scientific discussions and support provided, indispensable to the progress of this work.

To the Curators of all Herbaria consulted for their cooperation.

Among the various contributors to the experimental realization of this work, which is to extend my appreciation, I note:

• The Fundação para a Ciência e Tecnologia (FCT), by funding provided through a PhD scholarship (SFRH / BD / 43167 / 2008).

• The Faculty of Science, University of Porto and in particular the Department of Biology, for having accepted me as a PhD student, and the various logistical supports granted.

To Adriano, Álvaro, Claúdia, Cristina and Senhor Alberto.

To my friends, for the several moments and unforgettable experiences, with direct impact on my personal and professional life.

(6)

6 FCUP

To the one and only, Carla. The true “Special One”.

Finally, thank you to those who I am most proud of ... my family.

My Grandparents, thank you for having taught me the value of simple things. Who I am today, I owe it all to you.

My Mother ... Thank you for giving me the best of examples to chart my path.

Thanks bro!

To everyone in my family.

Without you, none of this would make sense ... I dedicate it to you all.

(7)

Resumo

A Península Ibérica foi um dos mais importantes refúgios glaciais do Pleistoceno no subcontinente europeu. A complexidade fisiográfica e posição geográfica favoreceram a sobrevivência de espécies de plantas e animais na Península Ibérica durante o Pleistoceno. As oscilações climáticas durante os períodos glaciais tiveram um impacto profundo sobre a distribuição de espécies de plantas e sobre a sua diversidade genética.

A filogeografia examina os arranjos espaciais de linhagens genéticas e é uma poderosa ferramenta para inferir sobre os processos que determinam a composição genética das espécies ou grupos de espécies. Os estudos filogeográficos podem desvendar as mudanças históricas nos padrões de fluxo genético, isolamento e contacto secundário entre populações divergentes, em diferentes escalas espaciais e temporais.

As respostas de cada indivíduo, população ou taxon às condições ambientais são mediadas pelos seus caracteres, e geralmente são agrupados sob formas estratégia de vida. Portanto, a análise de padrões geográficos e ambientais da distribuição de caracteres e síndromes adaptativos num determinado grupo taxonómico pode ajudar a inferir sobre os prováveis determinantes ambientais da evolução desse grupo num contexto geográfico restrito.

Acumulam-se evidências de alterações climáticas que alteram a distribuição de muitas espécies, e de que mais alterações no futuro serão inevitáveis. Uma rápida alteração climática deixa uma clara impressão digital sobre a biodiversidade global, e a nível local é um grande desafio para os conservacionistas. O conhecimento detalhado da auto-ecologia de uma espécie, bem como as informações sobre a disponibilidade de habitats adequados e os impactos das alterações climáticas sobre a espécie, e o seu habitat, são requisitos para um planeamento adequado de conservação. Para este efeito, a modelação da distribuição de espécies tem sido sugerida como uma ferramenta eficaz para avaliar o potencial de distribuição geográfica de espécies em diferentes cenários climáticos.

Os principais objectivos deste estudo passam por perceber a história passada dos

taxa estudados, explicar a sua distribuição actual e entender como estes podem

comportar-se no futuro sob cenários de alterações climáticas. Para esse efeito, foram utilizadas ferramentas genéticas, morfológicas e de modelação:

(8)

8 FCUP

- Cinco pares de primers cpSSR (chloroplast Simple Sequence Repeat), foram utilizados na análise à Silene secção Cordifolia, para abordar as hipóteses sobre as relações filogeográficas entre os Alpes e as cadeias montanhosas do norte da Península Ibérica;

- A técnica de ISSR foi utilizada para analisar a diversidade genética entre as subespécies de Silene scabriflora, e estudar as hipóteses sobre as relações filogeográficas no oeste da Península Ibérica;

- Uma abordagem morfo-ambiental é utilizada para caracterizar os taxa estudados;

- O software Maxent foi usado para modelar a distribuição actual e prever a distribuição dos taxa estudados, com base em variáveis ambientais e em cenários de alterações climáticas, e identificar as áreas com o maior valor para conservação.

A análise de fragmentos cloroplastidiais de cpSSR revelou uma clara diferenciação genética, reflectindo a existência no germoplasma estudado de quatro linhagens genéticas distintas na Silene secção Cordifolia. Com base na árvore do mínimo haplótipo, uma origem da Silene secção Cordifolia nos Alpes é sugerida a partir da posição terminal da Silene cordifolia.

Os resultados sugerem que os marcadores ISSR são úteis para distinguir as populações de subespécies de Silene scabriflora, de acordo com a origem geográfica, e confirmam a importância destes estudos genéticos para a concepção de estratégias de conservação de germoplasma. A análise de ISSR em subespécies de Silene

scabriflora indica uma grande variação genética entre as amostras examinadas. A

análise de componentes principais (PCA) mostrou uma clara correlação entre a semelhança genética e as localizações geográficas de cada subespécie analisada, mostrando que cada amostra é geneticamente estruturada e pode ser considerada uma população distinta. Com base nestes resultados, a hipótese de colonização do norte da Península Ibérica a partir do Sul da Península Ibérica é formulada.

Uma alta correlação entre a variação morfológica e ambiental é observada em todos os taxa estudados. Os taxa endémicos do norte da Península Ibérica de Silene

scabriflora (Silene scabriflora subsp. gallaecica e Silene scabriflora subsp. megacalycina) apresentam a menor variação morfo-ambiental. Os indivíduos de Silene foetida apresentam também uma menor variação em relação a Silene acutifolia.

(9)

Os resultados indicam que os modelos previram com uma elevada precisão as distribuições actuais dos taxa estudados. Em dois cenários de aumento de CO2, previu-se que estes serão susceptíveis a uma grande redução do habitat potencial. Um deslocamento em direcção a norte para a maioria dos modelos é observado. Os

taxa Silene foetida subsp. foetida, Silene foetida subsp. gayana, e Silene scabriflora

subsp. gallaecica mostraram-se em risco de extinção.

O Noroeste da Península Ibérica apresenta-se como a área de ligação entre Silene secção Cordifolia e Silene scabriflora com dinâmicas de fluxo genéticas diferentes, e como um centro de diferenciação genética.

A inclusão de Silene foetida subsp. foetida, Silene foetida subsp. gayana e Silene

scabriflora subsp. gallaecica em programas de conservação nacionais, e programas

de monitorização a longo prazo, deve ser considerada.

Palavras-chave: Silene, espécies endémicas, filogeografia, morfologia, modelação, ambiente, biogeografia, cpDNA, cpSSR, ISSR, haplótipo, genótipo refúgio, previsão habitat potencial, alterações climáticas, Pleistoceno.

(10)

(11)

Abstract

Iberian Peninsula was one of the most important Pleistocene glacial refugia in the European subcontinent. Physiographic complexity and geographical position favoured plant and animal species survival in the Iberian Peninsula throughout the Pleistocene. Climatic oscillations during glacial periods had a profound impact on plant species distribution and in its genetic diversity.

Phylogeography examines the spatial arrangements of genetic lineages and is a powerful tool for inferring the processes that determine the genetic composition of species or species groups. Phylogeographic studies can disentangle historical changes in patterns of gene flow, isolation and secondary contact among divergent populations at various spatial and temporal scales.

The responses of each individual, population or taxon to environmental conditions are mediated by their characters, and are usually grouped under life strategy forms. Therefore the analysis of geographic and environmental patterns of character distribution and adaptive syndromes in a certain taxonomic group context may support inferences about the probable environmental determinants of the evolution from that group in a restricted geographic context.

Evidence of climatic change altering the distribution of many species is accumulating and more change in the future is inevitable. Rapid climate change leaves a clear ﬁngerprint on global biodiversity and locally is a major challenge for conservationists. Detailed knowledge of a species’ autecology, as well as information on the availability of suitable habitats, and the impacts of climate change on the species and its habitat are requirements for adequate conservation planning. For this purpose, species distribution modelling has been suggested as an effective tool to assess the potential geographic distributions of species under different climate scenarios.

The main objectives for this study were to disentangle the past history of the studied

taxa, explain its current distribution, and understand how they could behave in the

future under scenarios of climate change. For that purpose, phylogeographic, morphological and modelling tools were used:

- Five pairs of cpSSR (chloroplast Simple Sequence Repeat) primers were used to analyse Silene section Cordifolia, to address the hypotheses on the phylogeographical relationships between Alps and the north Iberian Peninsula mountain ranges;

(12)

12 FCUP

- The ISSR technique was employed to study genetic diversity among Silene

scabriflora subspecies, and study the hypotheses on the phylogeographic

relationships in western Iberian Peninsula;

- A morpho-environmental approach is used to characterize the studied taxa; - Maxent software was used to model the current distribution, predict the

distribution of the studied taxa based on environmental variables under climate change scenarios, and identify areas with the most value for conservation.

Chloroplast cpSSR data revealed a clear specific and intra-specific genetic differentiation reflecting the existence in the studied germplasm of four distinct genetic lineages in Silene section Cordifolia. Based in the haplotype minimum spanning tree, an origin of Silene section Cordifolia in the Alps is suggested from the terminal position of Silene cordifolia.

The results suggest that ISSR markers are useful in distinguishing the populations of

Silene scabriflora subspecies according to geographical origin, and confirm the

importance of genetic studies for designing germplasm conservation strategies. The ISSR analysis in Silene scabriflora subspecies indicates a wide genetic variation among the samples examined. The PCA analysis showed a clearly correlation between genetic similarity and geographic locations of each Silene scabriflora subspecies analysed, showing that each sample is genetically structured and can be considered a distinct population. Based on these results, a northwards colonization hypothesis of Iberian Peninsula from South Iberian Peninsula is formulated.

A high correlation between morphological and environmental variation is observed in all the studied taxa. Northern subspecies of Silene scabriflora present the lowest environmental variation. Silene foetida also present a lower morpho-environmental variation than Silene acutifolia.

The results indicated that the models performed well, predicting with high accuracy the current distributions of the studied taxa. Under two scenarios of increasing CO2, the studied taxa were predicted to be susceptible to a major reduction of suitable habitat. A northwards displacement for most models is observed. Both Silene foetida subspecies were shown to be at risk of extinction, as also Silene scabriflora subsp. gallaecica.

Northwest Iberian Peninsula presents itself as the connecting area between Silene section Cordifolia and Silene scabriflora, with different genetic flow dynamics, and a centre for genetic differentiation.

(13)

The inclusion of Silene foetida subsp. foetida, Silene foetida subsp. gayana, Silene

scabriflora subsp. tuberculata and Silene scabriflora subsp. gallaecica in national

conservation programmes, and long-term monitoring programmes must be considered.

Key-words: Silene, endemic species, phylogeography, morphology, environmental, biogeography, cpDNA, cpSSR, ISSR, haplotypes, genotypes, refugia, suitable habitat prediction, climate change, species distribution modelling, Pleistocene.

(14)

(15)

LIST OF CONTENTS

FOREWORD 3 ACKNOWLEDGMENTS 5 RESUMO 7 ABSTRACT 11 LIST OF CONTENTS 15 LIST OF TABLES 23 LIST OF FIGURES 27 SECTION A Chapter 1. Introduction 35 1.1. Analysis and modelling of geographic patterns of diversity 35

1.2. Silene 36

1.3. Iberian Peninsula 38

1.4. Objectives 40

1.5. Structure of the thesis 41

1.6. References 42

Chapter 2. Research Parameters 51

2.1. Study area 51

2.2. Phylogeography 54

2.2.1. Objectives 54

2.2.2. Methodological description 55

(16)

16 FCUP

2.31. Objectives 56

2.3.3. Botanical criteria 57

2.4. Geographic patterns analysis 57

2.4.1. Objectives 57

2.5. References 58

SECTION B

Chapter 3. Phylogeography of Silene section Cordifolia in the

Mountain ranges of North Iberian Peninsula and Alps 65

Abstract 65

3.1. Introduction 66

3.2. Material and methods 69

3.2.1. Plant material and sampling 69

3.2.2. DNA extraction and cpSSRs amplification 70

3.2.3. Data analysis 71

3.3. Results 72

3.3.1. Polymorphisms at chloroplast microsatellite loci 72

3.3.2. Distribution of haplotypes 73

3.4. Discussion 74

3.4.1. Distribution of cpDNA haplotypes 74

(17)

3.4.3. Vicariant haplotype differentiation and subsequent

long-distance dispersal 76

3.5. Conclusions 78

3.6. References 79

Chapter 4. Phylogeography of Silene scabriflora in Iberian Peninsula 87

Abstract 87

4.2. Material and methods 91

4.2.1. Plant material and sampling 91

4.2.2. DNA isolation 93

4.2.3. ISSR amplification 93

4.2.4. Data analysis 94

4.3. Results 95

4.3.1. Genetic diversity and differentiation 95

4.3.2. Relationships among subspecies 98

4.4. Discussion 100

4.5. References 103

Chapter 5. Morpho-environmental behaviour of Silene scabriflora in

Iberian Peninsula: Atlantic versus Mediterranean climate 109

Abstract 109

5.2. Methods 111

(18)

18 FCUP

5.2.2. Occurrence data 112

5.2.3. Morphometric analysis 112

5.2.4. Environmental analysis 113

5.2.5. Variation analysis 115

5.2.6. Statistical analysis 115

5.2.7. Modelling of species distribution 115

5.3. Results 117

5.3.4. Distribution and Potential habitat area 121

5.4. Discussion 123

5.5. References 126

Chapter 6. Silene section Cordifolia in Iberian Peninsula: Phenotypic

traits variation versus environmental variation 133

Abstract 133

6.2. Materials and methods 135

6.2.1. Target species and study area 135

6.2.3. Morphometric analysis 137

6.2.5. Statistical analysis 139

(19)

6.4. Discussion 145

6.5. References 148

Chapter 7. Status and conservation of Silene section Cordifolia in the Iberian Peninsula: a menaced group under global environmental

change 153 Abstract 153 7.1. Introduction 154 7.2. Methods 155 7.2.1. Occurrence data 155 7.2.2. Study area 156 7.2.3. Environmental data 156

7.3. Results 161

7.3.1. Potential distribution area 161

7.3.3. Potential effects of climate change 165

7.4. Discussion 168

7.4.1. Model evaluation 168

7.4.3. Conservation and management implications 172

(20)

20 FCUP

Chapter 8. Bordering species under climate change: Where to go?

The case of two Silene scabriflora subspecies in Iberian Peninsula 185

Abstract 185 8.1. Introduction 186 8.2. Methods 187 8.2.1. Occurrence data 187 8.2.2. Study area 187 8.2.3. Environmental data 188

8.3. Results 191

8.3.1. Potential distribution area 191

8.4. Discussion 197

8.4.1. Model evaluation 197

8.4.3. Conservation and management implications 201

8.5. References 202

SECTION C

Chapter 9. Discussion 215

9.1. Phylogeography 215

9.1.1. Silene section Cordifolia 215

(21)

9.2. Morphology 220

9.3. Modelling 222

9.4. General Discussion 224

9.5. References 229

SECTION D

Chapter 10. General Conclusions and Future Directions 241

Chapter 11. Additional Lines of Work 243

Appendix I. List of morphological characters 245

Appendix II. List of environmental variables 249

Appendix III. Species data 253

(22)

(23)

LIST OF TABLES

Table 3.1. List of the studied taxa, location of sampling and number of

individuals analysed 70

Table 3.2. Composition of the haplotypes obtained from analysis of five

chloroplast microsatellites 72

Table 4.1. List of all accessions by subspecies with the respective

geographical location of each collection site 92

Table 4.2. ISSR patterns obtained using the ten selected primers among the four Silene scabriflora subspecies; TB – Total bands; PB – Polymorphic bands; MB – Monomorphyc bands; EB – Exclusive bands; %P – Percentage of polymorphism; (B = C, G, T; D= A,

G, T; R= A, G; V= A, C, G; Y= C, T) 96

Table 4.3. Genetic diversity parameters of studied taxa: na-number of alleles; ne-effective number of alleles; h – Nei’s gene diversity; I – Shannon’s Information index; Ht - Total genetic diversity within subspecies as a whole ; Hs - Genetic diversity within subspecies; Gst - Coefficient of genetic differentiation among

species; Nm - Gene flow 97

Table 4.4. Nei’s original measures of genetic identity and genetic distance. Nei’s genetic identity (above diagonal) and genetic

distance (below diagonal) 99

Table 5.1. Relation of the morphological characteristics analysed (and

their respective trait codes) 113

Table 5.2. Environmental variables considered as potential predictors for

Silene scabriflora habitat distribution 114

Table 5.3. Numerical values for the CDA upon the morphological matrix

classified on the basis of the subspecies classification 118

Table 5.4. Numerical values for the CDA upon the environmental matrix

(24)

24 FCUP

Table 5.5. Total variation of morphological characters and environmental

variables per taxon 120

Table 6.1. Environmental variables considered as potential predictors for

Silene acutifolia, Silene foetida subsp. foetida and Silene

foetida subsp. gayana habitat distribution 137

Table 6.2. Relation of the morphological characteristics analysed (and

their respective trait codes) 138

Table 6.3. Numerical values for the CDA upon the morphological matrix

classified on the basis of the taxa classification 141

Table 6.4. Numerical values for the CDA upon the environmental matrix

classified on the basis of the taxa classification 142

Table 6.5. Total variation of morphological characters and environmental

variables per taxon 143

Table 6.6. Values of correlations between the variation of discriminant morphological characters and the variation of discriminant

environmental variables (p-value < 0,05 marked in bold) 144

Table 6.7. Statistical significant correlations (p-level < 0,05), found between the variation of discriminant morphological characters

and the variation of environmental variables 145

Table 7.1. Environmental variables considered as potential predictors of the current habitat distribution of Silene acutifolia, Silene foetida

subsp. foetida and Silene foetida subsp. gayana 158

Table 7.2. The ranges of values per taxon of the most important

environmental variables in model development. Elev, elevation; AMT, annual mean temperature; MDR, mean diurnal range; TS, temperature seasonality; TAR, temperature annual range; MTWtQ, mean temperature wettest quarter; MTCQ, mean temperature coldest quarter; AP, annual precipitation; PWtM, precipitation wettest month; PS, precipitation seasonality; PCQ,

(25)

Table 7.3. Probability values of habitat suitability (PHS) and remaining percentage of current area (RPCA; %) for Silene sect.

Cordifolia using two scenarios (A2a and B2a) for four-time

slices (2000, 2020, 2050 and 2080) 167

Table 8.1. Environmental variables chosen as potential predictors for

Silene scabriflora current habitat distribution 189

Table 8.2. The ranges of values per taxon of the most important

environmental variables in model development. Elev, elevation; AMT, annual mean temperature; MDR, mean diurnal range; TS, temperature seasonality; TAR, temperature annual range; MTWtQ, mean temperature wettest quarter; MTCQ, mean temperature coldest quarter; AP, annual precipitation; PWtM, precipitation wettest month; PS, precipitation seasonality; PCQ,

precipitation coldest quarter 195

Table 8.3. Probability values of habitat suitability (PHS) and remaining percentage of current area (RPCA; %) for Silene scabriflora subsp. gallaecica, and for Silene scabriflora subsp. tuberculata using two scenarios (A2a and B2a) for four-time slices (2000,

(26)

(27)

LIST OF FIGURES

Figure 2.1. Study area and its main geographical characteristics 51

Figure 2.2. Annual precipitation (AP) 52

Figure 2.3. Annual average temperature (AAT) 53

Figure 3.1. Current distribution of the studied taxa 68

Figure 3.2. Sampling locations 70

Figure 3.3. Chloroplast haplotype network showing stepwise differences in allele size. Numbers on the lines connecting haplotypes

indicate the number of nucleotide difference accumulated 73

Figure 3.4. Minimum-length spanning tree of the cpSSRs haplotypes of

Silene acutifolia (haplotype A), S. cordifolia (haplotype D), S. foetida subsp. foetida (haplotype B) and S. foetida subsp. gayana (haplotype C). Each asterisk represents one allele

difference between haplotypes 74

Figure 3.5. Putative dispersion of the germplasm analysed 76

Figure 4.1. Distribution of the studied taxa in Iberian Peninsula. White triangles – S.scabriflora subsp. gallaecica; White squares -

S.scabriflora subsp. megacalycina; Black circles -

S.scabriflora subsp. scabriflora; White circles - S.scabriflora

subsp. tuberculata 90

Figure 4.2. Geographical location of each collection site. White triangles –

S.scabriflora subsp. gallaecica; White squares - S.scabriflora

subsp. megacalycina; Black circles - S.scabriflora subsp.

scabriflora; White circles - S.scabriflora subsp. tuberculata 93

Figure 4.3. Dendrogram of 24 genotypes from Silene scabriflora

subspecies showing genetic similarity, based on ISSRs data,

(28)

28 FCUP

Figure 4.4. Principal Components Analysis (PCA) based on genetic

similarity of Silene scabriflora subspecies 99

Figure 4.5. Silene scabriflora hypothetic colonisation routes of west Iberian Peninsula. White triangles – S.scabriflora subsp.

gallaecica; White squares - S.scabriflora subsp.

megacalycina; Black circles - S.scabriflora subsp. scabriflora;

White circles - S.scabriflora subsp. tuberculata 101

Figure 5.1. Main geographical characteristics of the study area 111

Figure 5.2. Dendrogram of the Pearson’s correlation matrix for the

morphological matrix, based on the cluster analysis 117

Figure 5.3. CDA for Silene scabriflora based on the morphological matrix 118

Figure 5.4. CDA for Silene scabriflora based on the environmental matrix. Three major and distinct tendencies are observed: S.

scabriflora subsp. megacalycina in the top left corner, S. scabriflora subsp. gallaecica in the bottom left corner and S.

scabriflora subsp. tuberculata in the right 119

Figure 5.5. Box-plots for the variation matrices of morphological characters (left), and environmental variables (right) for S.

scabriflora subsp. scabriflora (a), S. scabriflora subsp.

tuberculata (b), S. scabriflora subsp. megacalycina (c) and S.

scabriflora subsp. gallaecica (d) 121

Figure 5.6. Distribution of: Silene scabriflora subsp. gallaecica (white triangles); Silene scabriflora subsp. megacalycina (white squares); Silene scabriflora subsp. tuberculata (white circles); and Silene scabriflora subsp. scabriflora (black circles), in the

study area 122

Figure 5.7. Potential distribution areas for Silene scabriflora subsp.

scabriflora (a), Silene scabriflora subsp. tuberculata (b), Silene scabriflora subsp. megacalycina (c) and Silene scabriflora

(29)

Figure 6.1. Distribution range of Silene section Cordifolia in Iberian Peninsula. Black squares for Silene foetida subsp. foetida; Black triangles for Silene foetida subsp. gayana; White circles for Silene acutifolia. Study area (a; Background gradient indicates elevation. Lighter colours correspond to areas with

higher elevation) and its location in Iberian Peninsula (b) 136

Figure 6.2. Dendrogram of the Pearson’s correlation matrix for the

morphological matrix, based on the cluster analysis 140

Figure 6.3. CDA for Silene acutifolia and Silene foetida based on the morphological matrix. Three major and distinct tendencies are observed: S. foetida subsp. gayana in the top left corner, S.

foetida subsp. foetida in the bottom left corner and S. acutifolia

in the right 141

Figure 6.4. CDA for Silene acutifolia and Silene foetida subspecies based on the environmental matrix. Three major and distinct

tendencies are observed: S. foetida subsp. gayana in the top left corner (grey triangles), S. foetida subsp. foetida in the right (black circles) and S. acutifolia in the bottom left corner (black

crosses) 142

Figure 6.5. Box-plots for the variation matrices of morphological

characters (left), and environmental variables (right) 143

Figure 7.1. The distribution range of Silene sect. Cordifolia in northern Spain and northern and central Portugal (a), Iberian Peninsula (b). Black square, Silene foetida subsp. foetida; black triangle, S. foetida subsp. gayana; white circle, S. acutifolia in northern Spain and northern and central Portugal (a). In (a) background gradient indicates elevation; lighter colours correspond to

areas with higher altitude 159

Figure 7.2. Current predicted suitable habitat maps for (a) Silene acutifolia (white circles indicate occurrence points used for model evaluation); (b) Silene foetida subsp. foetida (black squares indicate occurrence points used for model evaluation); (c)

(30)

30 FCUP

Silene foetida subsp. gayana (black triangles indicate

occurrence points used for model evaluation) 162

Figure 7.3. Accuracy assessment of the Maxent model through the receiver operating characteristic (ROC) curve. Sensitivity equals the proportion of test localities correctly predicted as presence. The quantity equals the proportion of all map pixels predicted to have suitable conditions for Silene acutifolia (a),

Silene foetida subsp. foetida (b) and Silene foetida subsp.

gayana (c) 163

Figure 7.4. Jack-knife analysis of individual environmental predictor importance for each species, applied to the Maxent modelling, and its relation to overall model quality or ‘total gain’ (grid bar). Medium grey bars indicate the gain achieved when including that predictor only and excluding remaining predictors; light grey bars show how the total gain is diminished without the given predictor. Silene acutifolia (a); Silene foetida subsp.

foetida (b); Silene foetida subsp. gayana (c) 164

Figure 7.5. Predicted suitable habitat for (a) Silene acutifolia; (b) Silene

foetida subsp. foetida; (c) Silene foetida subsp. gayana;

obtained with an ensemble-forecast approach across the general circulation models CCCMA for three time slices (2020

(1), 2050 (2) and 2080 (3)) and one storyline (A2a) 166

Figure 7.6. Predicted suitable habitat for (a) Silene acutifolia; (b) Silene

foetida subsp. foetida; (c) Silene foetida subsp. gayana;

obtained by an ensemble-forecast approach across the general circulation models CCCMA for three time slices (2020

(1), 2050 (2) and 2080 (3)) and one storyline (B2a) 168

Figure 8.1. Study area and its location in South-Western Europe 188

Figure 8.2. Current predicted suitable habitat maps for (a) Silene

scabriflora subsp. gallaecica; (b) Silene scabriflora subsp. tuberculata; (c) Known occurrence locations for Silene scabriflora subsp. gallaecica (white circles) and for Silene

(31)

Figure 8.3. Accuracy assessment of the Maxent model through the receiver operating characteristic (ROC) curve. Sensitivity equals the proportion of test localities correctly predicted as presence. The quantity equals the proportion of all map pixels predicted to have suitable conditions for Silene scabriflora subsp. gallaecica (a) and Silene scabriflora subsp. tuberculata

(b) 193

Figure 8.4. Jack-knife analysis of individual environmental predictor importance for each species, applied to the Maxent modelling, and its relation to overall model quality or ‘total gain’ (grid bar). Medium grey bars indicate the gain achieved when including that predictor only and excluding remaining predictors; light grey bars show how the total gain is diminished without the given predictor. Silene scabriflora subsp. gallaecica (a); Silene

scabriflora subsp. tuberculata 194

Figure 8.5. Predicted suitable habitat for Silene scabriflora subsp.

gallaecica (a) and Silene scabriflora subsp. tuberculata (b)

(1), 2050 (2), 2080 (3)), and one storyline (A2a) 196 Figure 8.6. Predicted suitable habitat for Silene scabriflora subsp.

gallaecica (a) and Silene scabriflora subsp. tuberculata (b)

(32)

(33)

(34)

(35)

1. Introduction

1.1. Analysis and modelling of geographic patterns of diversity

The patterns of current geographic distribution of biological diversity are closely tied to historical factors and results from its response to a set of ecological and biogeographical processes that work at distinct spatial and temporal scales. The study of biological diversity geographic patterns can be made considering its several levels, since the specific diversity till genetic diversity, and several methodologies and specific tools exist for this purpose (Guisan and Zimmermann 2000; Guisan and Thuiller 2005; Elith et al. 2006; Thuiller et al. 2008).

The analysis of morphological, karyological, reproductive or chorological characteristics in a taxonomic and ecological context, allows the identification of evolutionary and biogeographic tendencies (Pillar and Sosinski Jr. 2003; Cousins and Lindborg 2004; Endels et al. 2007; Bello et al. 2010), while along the study of the ecological features of an endemic flora reveals general patterns, but also peculiarities and differences of the endemic part of a flora when compared with the whole flora of the area (Melendo et al. 2003). The responses of each individual, population or taxon to environmental conditions are mediated by their characters, and are usually grouped under life strategy forms (Grime 2001). Therefore the analysis of geographic and environmental patterns of character distribution and adaptive syndromes in a certain taxonomic group context may support inferences about the probable environmental determinants of the evolution from that group in a restricted geographic context (Pillar and Sosinski Jr. 2003; Cousins and Lindborg 2004; Endels et al. 2007; Bello et al. 2010).

The study of phenotypic plasticity has had a significant evolution in the last decades. The concept that plasticity variation is considered “background noise” in evolutionary studies has altered to become the main objective to several investigations that use a set of methods, including molecular and quantitative genetic as well as the several approaches that model the plastic responses evolution (Pigliucci 2005).

There is strong co-variation between climatic factors and broad-scale diversity gradients, and a majority of the broad-scale hypotheses are related to climatic variables or factors related to climate (Richerson and Lum 1980; Currie 1991; Rohde 1992; O’Brien 1998; Hawkins et al. 2003; Currie et al. 2004). The patterns of current

(36)

36 FCUP

distribution of species are partially driven by climatic shifts that causes migrations to latitudes where higher range of life-supporting environments are available (Hewitt 2000).

When combined with other sources of information (namely the resource to genetic tools), the identification of factors that determine the taxa current distribution and that could have influenced its morphological diversification, may have an important contribution in predicting future dynamics (Thuiller et al. 2008), in establishing conservation strategies (Araújo et al. 2011), or even to plan diversity studies at genetic level. Indeed, the available molecular tools potentiate new approaches to many of these non-resolved classical problems and new advances are being made combining genomic, molecular and phylogenetic evolutionary studies with phenotypic and ecological information (Bernasconi et al. 2009).

1.2. Silene

The family Caryophyllaceae Juss., has a cosmopolitan distribution and includes a number of common ornamental plants, such as carnations (Dianthus L.) and baby’s breath (Gypsophila L.). The family is primarily Holarctic in its distribution, with two important hotspots of diversity in the Mediterranean and Irano-Turanian regions (Bittrich 1993), and includes about 3000 species distributed among 88 genera (Rabeler and Hartman 2005), with a distribution ranging from the Artic to the Antarctic. The number of genera declines to 82 if one accepts a broad concept of Silene (Greuter 1995; Morton 2005) or could increase to more than 120 if one accepts all the segregates of several of the large genera that have been proposed (Oxelman et al. 2001; Tzvelev 2001). The most common classifications (Pax and Hoffman 1934; Bittrich 1993) of Caryophyllaceae are based on characters of the stipules, petals, sepals, and fruits. Understanding the relationships within the Caryophyllaceae has been difficult, in part because many of the genera are not well defined morphologically and are difficult to distinguish (Bittrich 1993). At the same time, the definition of monophyletic groups within the family has been problematic because of difficulty in determining phylogenetically useful characters and the possibility of widespread convergence of characters used in formal classifications, including embryogeny, leaf morphology, chromosome numbers, number of floral parts, and the presence and nature of nectaries (Harbaugh et al. 2010).

(37)

Most of its research was based on several aspects of group biology, but relationships between genus and species are still not very clear, due to the high level of homoplasy or due to the focus of studies in the interfamily relationships of Caryophyllales. Understanding the relationships within the Caryophyllaceae has been difficult, in part because of arbitrarily and poorly defined genera and difficulty in determining phylogenetically useful morphological characters (Harbaugh et al. 2010). Possible morphological homoplasy and difficulty in determining morphological synapomorphies make the use of molecular phylogenetic data critical in understanding the relationships within the Caryophyllaceae (Smissen et al. 2002; Fior et al. 2006). At the same time most of the molecular studies that have included members of the Caryophyllaceae have been focused on the relationships of the families within the order Caryophyllales rather than on relationships within the family (Rettig et al. 1992; Downie and Palmer 1994; Downie et al. 1997; Cuénoud et al. 2002).

Nevertheless, it is well known and several ecological, physiological and biochemical aspects have been studied from many species (Bernasconi et al. 2009, Valente et al. 2010). Indeed one of the most studied genera is Silene L., which has been used as model to several genetic and ecological studies (Desfeux and Lejeune 1996). Because species vary widely in their breeding system, sex determination and ecology, the genus has historically played an important role in genetic and ecological studies dating back to Mendel and Darwin (Blavet et al. 2011).

The genus Silene, studied by Darwin, Mendel and other early scientists, is re-emerging as a system for studying interrelated questions in ecology, evolution and developmental biology (Bernasconi et al. 2009). It is a genus with high plasticity, and its species have a wide variation in its reproductive systems and ecology. In fact, there are many cases that require profound biosystematic studies since the diagnose characters are in low number and based mostly in morphology and habit (Chowdhuri 1957; Melzheimer 1977; Oxelman et al. 2001).

The detailed knowledge that has been obtained about Silene genus and its interacting organisms over more than a century provides a rich source of interesting unresolved questions in plant ecology and evolution. With increasing availability of genetic tools, further progress in Silene genus should be possible on the range of fundamental questions outlined here (Bernasconi et al. 2009).

The ecological knowledge available in species of this genus will prove to be an important advantage in comparison with many other systems that were developed as

(38)

38 FCUP

models because of molecular tractability alone, but without valuable information about natural populations. In the age of PCR and genome-wide sequencing of DNA and mRNA, as also illustrated by Mimulus (Wu et al. 2008), molecular non-model species in which interesting biological questions are waiting to be solved attract renewed interest and allow new advances (Bernasconi et al. 2009).

1.3. Iberian Peninsula

The Iberian Peninsula is one of the richest Mediterranean areas in vascular plant species (Groombridge 1992). Looking through a global hotspot view, one of these biodiversity hotspots lies in the south of the Iberian Peninsula and the north of Morocco (Médail and Quézel 1997; Myers et al. 2000). A past analysis of species richness distribution in this region (Castro Parga et al. 1996) shows that mountain areas score highest in species richness (Lobo et al. 2001).

The high level of endemism in both Iberian plants and animals (Gómez-Campo and Malato-Beliz 1985; Doadrio 1988; Moreno Saiz et al. 1998; Ribera 2000; García-Barros

et al. 2002) indirectly suggests in situ long-term survival, differentiation and speciation.

Its highly original flora and high level of endemism are related to their considerable orographic and climatic diversity, geomorphological and soils complexity, its extreme south-western European location, and its marked isolation produced by insularity (Domínguez-Lozano et al. 2000). This diversity is caused by a high local diversity, i.e., by the simultaneous occurrence of a large number of species in the same areas, but also by a high regional diversity, since ecological conditions and landscapes change dramatically even between neighbouring zones (Blondel and Aronson 1995).

The main pattern at an European scale and throughout the late Quaternary is the individual response of all species with expansions/contractions in their distribution due to climatic oscillations and the persistence in southern peninsulas (Iberian, Italy and Balkan), acting as refugia during the most aggressive conditions of the Last Glacial Maximum (Taberlet et al. 1998). Palaeoclimatic high resolution studies in the Mediterranean region suggest that this region was strongly affected by the climatic and hydrological changes of the North Atlantic basin during the Last Glacial Period, i.e. the Heinrich events and the Dansgaard-Oeschger oscillations (Cacho et al. 1999). There were local glaciers in most of the mountain ranges of Iberian Peninsula (Messerli 1967). Models of atmospheric conditions in the northern hemisphere at the Last Glacial

(39)

Maximum show that all of southern Europe was influenced by this climatic phenomena, also during the summer months (Lamb 1971). Accordingly, humid winter conditions were widespread at low lying coastal locations of southern Portugal. Winters were warm and dry only along the southeastern coast of the Iberian Peninsula (Schütt 2005). The glacial epochs caused an increase in the extent of the ice sheet, mostly in northern latitudes, inducing adverse conditions with the decrease of life sustainability (Davis and Shaw 2001; Hewitt 2000, 2004). These climatic changes must have had an impact on terrestrial environments (Sanchez-Goñi et al. 2000), leading for example to the displacement of plant species, both in terms of altitude and latitude (Davis 1994). Whereas some species responded to past climatic shifts with southward migrations, others remained at the same latitude with altitudinal shifts in their distribution (Davis and Shaw 2001; Hewitt 2004). The changing climate and the need to colonize new areas challenges species to survive in refugia and adapt to face new climate conditions (Davis and Shaw 2001; Hewitt 2000; Taberlet and Cheddadi 2002)

Therefore, Iberian Peninsula is pointed as one of the most important Pleistocene glacial refugia in the European subcontinent (Hewitt 1999, 2001; Pignatii 1978; Willis 1996). Several characteristics favoured survival in the Iberian Peninsula throughout the Pleistocene. First, the Iberian Peninsula possesses high physiographic complexity, with several large mountain ranges primarily oriented east-west. This mountain range orientation offers the highest microclimatic scope, and allows survival of populations by altitudinal shifts, tracking suitable microclimates up or down mountains as the general climate worsens or ameliorates (Hewitt 1996; Willis 1996). Second, due to its geographical position, the Iberian Peninsula is under the influence of both the North Atlantic and the Mediterranean, and enjoys a wide range of climates, including desert, Mediterranean, Alpine, and Atlantic. Its low latitude location, when compared to remaining Europe, allowed a more tolerant climate although was affected by the same instability processes, resulting in a dynamic environment throughout the late Quaternary. Interestingly, these very same characteristics, together with its large area (580 000 km2_{), make it unlikely that Iberia offered a single homogeneous and}

continuous refugial area throughout the Pleistocene. Instead, the differential distribution and fragmented nature of suitable habitats favour the occurrence of multiple glacial refugia isolated from one another by the harsh climate of the high central Iberian plateau (Gómez and Lunt 2007).

Additionally, an increasing number of phylogeographic studies of European flora and fauna depict the Iberian Peninsula not only as a cradle for genetic differentiation, but

(40)

40 FCUP

also a species repository for the northern latitudes of Europe after the Pleistocene Ice Ages (Gómez and Lunt 2007). Thus, since the last reviews on European phylogeography (Comes and Kadereit 1998; Taberlet et al. 1998; Hewitt 1999), many species have been added to the wide array of organisms known to have colonized western and northern Europe from the Iberian Peninsula after the Ice Ages.

1.4. Objectives

The present investigation is based in the following assumptions:

a. The current taxa distribution results from its response to environmental and recent paleoenvironmental characteristics.

b. Taxa responses to environmental conditions are mediated by its characters.

c. The knowledge of current taxa distribution allows to document genetic diversity patterns.

d. The analysis of geographic and environmental patterns of characters distribution, life strategies and genetic diversity allows inferring about the probable environmental determinants in the study groups evolution.

And it is intended to respond to the following general questions:

1. Which factors most contribute to the taxa current geographic distribution?

2. Can these factores be used to accurately predict the current geographic distribution of taxa?

3. In what way are characters current geographic distribution and genetic diversity determined by the same factors?

4. Which infers could be made about the studied group’s evolution (phylogeny and phylogeography) in the Iberian Peninsula from the results?

5. Which infers could be made about predictions of future distributions under scenarios of climate change?

(41)

1.5. Structure of the thesis

The thesis was organized in 4 sections:

Section A – The first section consists on: Chapter 1. Introduction

A general introduction which contextualizes the work done in this thesis, a brief

history of Iberian Peninsula and Silene studies are presented. The main objectives

of the thesis are also exposed.

Chapter 2. Research Parameters

The main geographic and methodological tools used to achieve the objectives are

presented. The detailed methodological tools can be found from the individual

chapters.

Section B – The second section presents the articles developed for this thesis, as previous listed, according to the following chapters:

Chapter 3 – Phylogeography of Silene section Cordifolia in the Mountain ranges of North Iberian Peninsula and Alps.

Chapter 4 – Phylogeography of Silene scabriflora in Iberian Peninsula.

Chapter 5 – Morpho-environmental behaviour of Silene scabriflora in Iberian Peninsula: Atlantic versus Mediterranean climate.

Chapter 6 – Silene section Cordifolia in Iberian Peninsula: Phenotypic traits variation versus environmental variation.

Chapter 7 – Status and conservation of Silene section Cordifolia in the Iberian Peninsula: a menaced group under global environmental change.

(42)

42 FCUP

Chapter 8 – Bordering species under climate change: Where to go? The case of two

Silene scabriflora subspecies in Iberian Peninsula.

Section C – In the third section, the results of the phylogeographical, morphological and modelling studies are discussed.

Chapter 9. Discussion

This chapter has been separated in 4 parts: one for each of the previous main

themes, and a fourth where they are discussed together in a timeline perspective.

Section D – This last section presents the main conclusions of this thesis. Chapter 10. Conclusions and Future Directions

A broad perspective synthesizing the main achievements is presented. Possible

future lines of work are presented.

Chapter 11. Additional Lines of work

In this last chapter some parallel lines of work resulting from the thesis are listed.

1.6. References

Araújo MB, Alagador D, Cabeza M, Nogués-Bravo D, Thuiller W (2011) Climate change threatens European conservation áreas. Ecology Letters 14: 484–492. Bello F, Lavorel S, Díaz S, Harrington R, Cornelissen JHC, Bardgett RD, Berg MP,

Cipriotti P, Feld CK, Hering D, da Silva PM, Potts SG, Sandin L, Sousa JP, Storkey J, Wardle DA, Harrison PA (2010) Towards an assessment of multiple ecosystem processes and services via functional traits. Biodiversity Conservation 19: 2873–2893.

Bernasconi G, Antonovics J, Biere A, Charlesworth D, Delph LF, Filatov D, Giraud T, Hood ME, Marais GAB, McCauley D, Pannell JR, Shykoff JA, Vyskot B, Wolfe

(43)

LM, Widmer A (2009) Silene as a model system in ecology and evolution. Heredity 103: 5–14.

Bittrich V (1993) Caryophyllaceae. In Kubitzki K, Rohwer J, Bittrich V [eds.], The families and genera of vascular plants, vol. 2. Magnoliid, Hamamelid, and Caryophyllid families, 206–236. Springer Verlag. Berlin, Germany.

Blavet N, Charif D, Oger-Desfeux C, Marais GAB, Widmer A (2011) Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database. BioMed Central Genomics 12: 376.

Blondel J, Aronson J (1995) Biodiversity and ecosystem function in mediterranean basin: human and non-human determinants In: Davis GW, Richardson DM (eds.) Mediterranean-Type ecosystems: The function of Biodiversity. Ecological studies 109, Springer-Verlag, Berlin-Heidelberg. New York, USA.

Cacho I, Grimalt JO, Pelejero C, Canals M, Sierro FJ, Flores JA, Shackleton N (1999) Dansgaard-Oeschger and Heinrich event imprints in Alboran Sea paleotempera tures. Paleoceanography 14: 698–705.

Castro Parga I, Moreno Saíz JC, Humphries CJ, Williams P (1996) Strengthening the Natural and National Park System of Iberia to conserve vascular plants? Botanical Journal of the Linnean Society 121: 189–206.

Chowdhuri PK (1957) Studies in the genus Silene. Notes Royal Botanic Garden Edinburgh, 22: 221–278.

Comes HP, Kadereit JW (1998) The effect of Quaternary climatic changes on plant distribution and evolution. Trends in Plant Science 3: 432–438.

Cousins SAO, Lindborg R (2004) Assessing changes in plant distribution patterns – indicator species vs. plant functional types. Ecological indicators 4: 17–27. Cuénoud P, Savolainen V, Chatrou LW, Powell M, Grayer RJ, Chase MW (2002)

Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences. American Journal of Botany 89: 132–144.

Currie DJ (1991) Energy and large-scale patterns of animal and plant-species richness. The American Naturalist 137: 27–49.

(44)

44 FCUP

Currie DJ, Mittelbach GG, Cornell HV, Field R, Guégan JF, Hawkins BA, Kaufman DM, Kerr JT, Oberdorff T, O’Brien E, Turner JRG (2004) Predictions and tests of climate-based hypotheses of broad-scale variation in taxonomic richness. Ecology Letters 7: 1121–1134.

Davis MB (1994) Ecology and palaeoecology begin to merge. Trends in Ecology and Evolution. 9: 357–358.

Davis MB, Shaw RG (2001) Range Shifts and Adaptive Responses to Quaternary Climate Change. Science 292: 673–679.

Desfeux C, Lejeune B (1996) Systematics of Euromediterranean Silene (Caryophyllaceae): evidence from a phylogenetic analysis using ITS sequences. Comptes Rendus de l’Academie des Sciences. Serie III, Sciences de la Vie 319: 351–358.

Doadrio I (1988) Delimitation of areas in the Iberian Peninsula on the basis of freshwater fishes. Bonn zoological Bulletin 39: 113–128.

Domínguez-Lozano F, Galicia-Herbada D, Rivero LM, Saiz JMM, Ollero HS (2000) Areas of high floristic endemism in Iberia and the Balearic islands: an approach to biodiversity conservation using narrow endemics. Belgian Journal of Entomology 2: 171–185.

Downie D, Katz-Downie S, Cho K (1997) Relationships in the Caryophyllales as suggested by phylogenetic analysis of partial chloroplast DNA ORF2280 homolog sequences. American Journal of Botany 84: 252–273.

Downie SR, Palmer JD (1994) A chloroplast DNA phylogeny of the Caryophyllales based on structural and inverted repeat restriction site variation. Systematic Botany 19: 236–252.

Elith J, Graham CH, Anderson RP, Dudík M, Ferrier S, Guisan A, Hijmans RJ, Huettmann F, Leathwick JR, Lehmann A, Li J, Lohmann LG, Loiselle BA, Manion G, Moritz C, Nakamura M, Nakazawa Y, Overton JMM, Peterson AT, Phillips SJ, Richardson K, Scachetti-Pereira R, Schapire RE, Soberón J, Williams S, Wisz MS, Zimmermann NE (2006) Novel methods improve prediction of species’ distributions from occurrence data. Ecography 29: 129– 151.

(45)

Endels P, Adriaens D, Bekker RM, Knevel IC, Decocq G, Hermy M (2007) Groupings of life-history traits are associated with distribution of forest plant species in a fragmented landscape. Journal of Vegetation Science 18: 499–508.

Fior S, Karis PO, Casazza G, Minuto L, Sala F (2006) Molecular phylogeny of the Caryophyllaceae (Caryophyllales) inferred from chloroplast matK and nuclear rDNA ITS sequences. American Journal of Botany 93: 399–411.

García-Barros E, Gurrea P, Luciañez MJ, Cano JM, Munguira ML, Moreno JC, Sainz H, Sanz MJ, Simón JC (2002) Parsimony analysis of endemicity and its application to animal and plant geographical distributions in the Ibero-Balearic region (western Mediterranean). Journal of Biogeography 29: 109–124.

Gómez A, Lunt DH (2007) Refugia within refugia: patterns of phylogeographic concordance in the Iberian Peninsula in: Weiss S, Ferrand N (eds.) Phylogeography of Southern European Refugia. Springer, Netherlands.

Gómez-Campo C, Malato-Beliz J (1985) The Iberian Peninsula in: Gomez-Campo C (ed.) Plant Conservation in the Mediterranean Area. Junk Publishers. Dordrecht, Netherlands.

Greuter W (1995) Silene (Caryophyllaceae) in Greece: a subgeneric and sectional classification. Taxon 44: 543–581.

Grime JP (2001) Plant strategies, vegetation processes, and ecosystem properties. Second edition. Wiley. Chichester, UK.

Groombridge B (1992) Global biodiversity. Status of the earth's living resources. First edition. Chapman and Hall. London, UK.

Guisan A, Thuiller W (2005) Predicting species distribution: offering more than simple habitat models. Ecological Letters 8: 993–1009.

Guisan A, Zimmermann NE (2000) Predictive habitat distribution models in ecology. Ecological Modelling 135: 147–186.

Harbaugh DT, Nepokroeff M, Rabeler RK, McNeill J, Zimmer EA, Wagner W (2010) A new lineage-based tribal classification of the family Caryophyllaceae. International Journal of Plant Sciences 171: 185–198.

(46)

46 FCUP

Hawkins BA, Field R, Cornell HV, Currie DJ, Guégan JF, Kaufman DM, Kerr JT, Mittelbach GG, Oberdorff T, O’Brien EM, Porter EE, Turner JRG (2003) Energy, water, and broad-scale geographic patterns of species richness. Ecology 84: 3105–3117.

Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society 58: 247– 276.

Hewitt GM (1999) Post-glacial re-colonization of European biota. Biological Journal of the Linnean Society 68: 87–112.

Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature 405: 907– 913.

Hewitt GM (2001) Speciation, hybrid zones and phylogeography - or seeing genes in space and time. Molecular Ecology 10: 537–549.

Hewitt GM (2004) Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences 359: 183–195.

Lamb HH (1971) Climates and Circulation Regimes Developed over the Northern Hemisphere during and since the Last Ice Age. Palaeogeography, Palaeoclimatology, Palaeoecology 10: 125–162.

Lobo JM, Castro I, Moreno JC (2001) Spatial and environmental determinants of vascular plant species richness distribution in the Iberian Peninsula and Balearic Islands. Biological Journal of the Linnean Society, 73: 233–253.

Médail F, Quézel P (1997) Hot-spots analysis for conservation of plant biodiversity in the Mediterranean Basin. Annals of the Missouri Botanical Garden 84: 112–127. Melendo M, Gimenez E, Cano E, Gomez-Mercado F, Valle F (2003) The endemic flora in the South of the Iberian Peninsula: Taxonomic composition, biological spectrum, pollination, reproductive mode and dispersal. Flora - Morphology, Distribution, Functional Ecology of Plants 198: 260–276.

Melzheimer V (1977) Biosystematiche Revision einiger Silene-Arten (Caryophyllaceae) der Balkaninsel (Griechenland). Botanische Jahrbücher für Systematik 98: 1–92.

(47)

Messerli B (1967) Die eiszeitliche und gegenwärtige Vergletscherung im Mittelmeerraum. Geographica Helvetica 22: 105–228.

Moreno Saiz JC, Castro Parga I, Sainz Ollero H (1998) Numerical analyses of distribution of Iberian and Balearic endemic monocotyledons. Journal of Biogeography 25: 179–194.

Morton JK (2005) Silene. Pages 168–216 in Flora of North America Editorial Committee, eds. Flora of North America North of Mexico. Vol 5. Oxford University Press. New York, USA.

Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403: 853–858.

O’Brien EM (1998) Water–energy dynamics, climate, and prediction of woody plant species richness: an interim general model. Journal of Biogeography 25: 379– 398.

Oxelman B, Lidén M, Rabeler RK, Popp M (2001) A revised generic classification of the tribe Sileneae (Caryophyllaceae). Nordic Journal of Botany 20: 743–748. Pax F, Hoffmann K (1934) Caryophyllaceae. Pages 275–364 in Engler A, Harms H

eds. Die natürlichen Pflanzenfamilien. 2d ed. Engelmann. Leipzig, Germany.

Pigliucci M (2005) Evolution of phenotypic plasticity: where are we going now? Trends in Ecology and Evolution 20: 481–486.

Pignatti S (1978) Evolutionary trends in Mediterranean flora and vegetation. Vegetatio 37: 175–185.

Pillar VD, Sosinski Jr EE (2003) An improved method for searching plant functional types by numerical analysis. Journal of Vegetation Science 14: 323–332.

Rabeler RK, Hartman RL (2005) 43. CARYOPHYLLACEAE Jussieu - Pink Family [description of Caryophyllaceae, generic key, 4 subfamilies, and 37 generic descriptions, parts of pages 45 pp. camera ready pages from page7-214.] Flora of North America, vol. 5. Oxford University Press. Oxford, UK.

Rettig JH, Wilson HD, Manhart JR (1992) Phylogeny of the Caryophyllales: gene sequence data. Taxon 41: 201–209.