Nélida Padilla-García

Evolutionary, phylogenetic, and biogeographical studies within the diploid-polyploid complex Veronica subsect. Pentasepalae (Veronica L., Plantaginaceae): Cette thèse vise à déterminer la contribution des processus de polyploïdisation et d'hybridation dans l'histoire évolutive des espèces compris dans le groupe taxonomique Veronica sous-sect. Pentasepalae. La thèse est liée à trois disciplines principales : évolution, phylogénétique, et phylogéographie. D'abord, nous avons reconstruit une phylogénie moléculaire pour Veronica sous-sect. Pentasepalae à l'aide de méthodes de distance en utilisant marqueurs AFLPs (Amplified Fragment Length Polymorphisms) incluant tous les taxons reconnus dans la sous-section, afin de comprendre les relations phylogénétiques entre espèces et d'évaluer si elles sont monophylétiques. En outre, une révision de la taxonomie du groupe a été effectuée en utilisant une approche intégrative. Cette thèse tente également d'améliorer notre compréhension des implications de la polyploïdie dans la répartition géographique des populations végétales naturelles. C'est dans ce but que nous avons effectué la première estimation approfondie des niveaux de ploïdie dans V. sous-sect. Pentasepalae à l'échelle mondiale. La relation entre les niveaux de ploïdie et les variables environnementales a été évaluée, ainsi que le rôle de l'histoire biogéographique des espèces dans la distribution géographique des cytotypes. Notre dernier objectif est de détecter les processus biologiques et historiques qui ont façonné l'histoire évolutive de Veronica aragonensis, une espèce endémique des montagnes de la Péninsule Ibérique. Séquençage de nouvelle génération et analyses HRM (high-resolution melting) ont été utilisées pour caractériser un nouvel ensemble de microsatellites spécifiques, qui ont servi à évaluer la diversité et la structure génétiques de l’espèce, ainsi que les niveaux de flux génétique au sein des populations et entre elles. Les patrons génétiques ont été étudiés dans les trois zones de répartition de V. aragonensis (les Pyrénées, les Pré-Pyrénées et le Système Bétique) afin de vérifier si la répartition actuelle de la plante correspond à un processus de fragmentation ou à un événement de dispersion à longue distance. De plus, nous avons essayé d'identifier des populations qui auraient pu servir de refuge glaciaire à V. aragonensis pendant les glaciations du Quaternaire. Finalement, nous proposons des stratégies pour la conservation de la diversité génétique de ce taxon rare et endémique.

The Balkan Peninsula is a biodiversity hotspot where topographic and habitat heterogeneity have shaped genetic differentiation. Polyploidization significantly contributes to diversification within plant lineages, including the allopolyploid complex of the Austrian speedwell, which comprises diploid, tetraploid and hexaploid lineages. We sampled 751 individuals from 50 populations belonging to this complex across the Balkan Peninsula and Central Europe. Diversity patterns were investigated through microsatellite markers (SSRs), plastid DNA sequences, ploidy estimations, morphological data and climatic niche differentiation analysis. Five lineages were detected within the complex according to nuclear DNA data. The plastid DNA haplotypes form two main groups that overall match those detected by SSR data and could suggest that the hexaploid lineage resulted from two different allopolyploid events. The hexaploid shows higher nuclear genetic diversity and morphological variation than its lower-ploidy relatives, which might allow the species to respond to a wider range of environmental conditions and be responsible for its success (i.e., a broader geographic range and ecological niche). Style length is a crucial character to distinguish diploids from polyploids, which may affect pollination biology within the complex.

The Balkan Peninsula is a biodiversity hotspot where topographic and habitat heterogeneity have shaped genetic differentiation. Polyploidization significantly contributes to diversification within plant lineages, including the allopolyploid Veronica austriaca complex. We sampled 751 individuals from 50 Balkan and Central European populations belonging to the hexaploid V. austriaca and its putative diploid (V. dalmatica) and tetraploid progenitors. Diversity patterns were investigated through microsatellite markers (SSRs), plastid DNA sequences, ploidy estimations, morphological data and climatic niche differentiation analysis. Five lineages were detected within the complex according to nuclear DNA data. The plastid DNA haplotypes form two main groups that overall match those detected by SSRs data and could suggest that the hexaploid V. austriaca resulted from two different allopolyploid events. Our analyses evidence rapid and recent colonization of diverse mesic grassy habitats by an allopolyploid perennial herb across a large European scale. The enhanced dispersal abilities of the hexaploid V. austriaca (compared to its lower ploidy relatives) seem to result from higher genetic diversity and ecological niche differentiation, which may also be related to slight morphological differences of potential functional significance. Style length is a crucial character to distinguish diploids from polyploids, which may affect pollination biology within the complex.

Purifying selection is expected to prevent the accumulation of transposable elements (TEs) within their host, especially when located in and around genes and if affected by epigenetic silencing. However, positive selection may favor the spread of TEs, causing genomic imprinting under parental conflict, as genomic imprinting allows parent-specific influence over resource accumulation to the progeny. Concomitantly, the number and frequency of TE insertions in natural populations are conditioned by demographic events. In this study, we aimed to test how demography and selective forces interact to affect the accumulation of TEs around genes, depending on their epigenetic silencing, with a particular focus on imprinted genes. To this aim, we compared the frequency and distribution of TEs in Arabidopsis lyrata from Europe and North America. Generally, we found that TE insertions showed a lower frequency when they were inserted in or near genes, especially TEs targeted by epigenetic silencing, suggesting purifying selection at work. We also found that many TEs were lost or got fixed in North American populations during the colonization and the postglacial range expansion from refugia of the species in North America, as well as during the transition to selfing, suggesting a potential “TE load.” Finally, we found that silenced TEs increased in frequency and even tended to reach fixation when they were linked to imprinted genes. We conclude that in A. lyrata, genomic imprinting has spread in natural populations through demographic events and positive selection acting on silenced TEs, potentially under a parental conflict scenario.

Summary: Polyploidisation is a significant reproductive barrier, yet genetic evidence indicates that interploidy admixture is more common than previously thought. Theoretical models and controlled crosses support the ‘triploid bridge’ hypothesis supposing that hybrids of intermediate ploidy facilitate gene flow. However, comprehensive evidence combining experimental and genetic data is missing. In this study, we investigated the rates and directions of gene flow within a diploid– autotetraploid contact zone of Cardamine amara , a species with abundant natural triploids. We cytotyped over 400 wild individuals, conducted reciprocal interploidy crosses and inferred gene flow based on genome-wide sequencing of 84 individuals. Triploids represent a conspicuous entity in mixed-ploidy populations (5%), yet only part of them arose through interploidy hybridisation. Despite being rarely formed, triploid hybrids can backcross with their parental cytotypes, producing viable offspring that are often euploid (in 42% of cases). In correspondence, we found a significant genome-wide signal of gene flow for sympatric, but not allopatric, diploids and tetraploids. Coalescent simulations demonstrated significant bidirectional introgression which is stronger in the direction towards the tetraploid cytotype. Triploids, though rare, play a key role in overcoming polyploidy-related reproductive barriers. We present integrative evidence for bidirectional interploidy gene flow mediated by a triploid bridge in natural populations.

Aim: Although whole‐genome duplication (WGD) is an important speciation force, we still lack a consensus on the role of niche differentiation in polyploid evolution. In addition, the role of genome doubling per se vs. later divergence on polyploid niche evolution remains obscure. One reason for this might be that the intraspecific genetic structure of polyploid complexes and interploidy gene flow is often neglected in ecological studies. Here, we aim to investigate to which extent these evolutionary processes impact our inference on niche differentiation of autopolyploids.Location: Europe.Taxon: Arabidopsis arenosa (Brassicaceae).Methods: Leveraging a total of 352 cytotyped populations of diploid‐autotetraploid A. arenosa, we examined differences among climatic niches of diploid and tetraploid lineages both globally, and independently for each tetraploid lineage with respect to the niche of its evolutionary closest relative. Then, we tested whether there was an effect of additional interploidy introgression from other sympatric but ancestrally divergent diploid lineages of A. arenosa on climatic niches of tetraploids.Results: Ecological niche shift of tetraploids is only detected when the assignment of populations to intraspecific genetic lineages is considered. We found different patterns of climatic niche evolution (i.e. niche conservatism, contraction or expansion) in each tetraploid lineage when compared to its evolutionary closest relatives. We observed an effect of interploidy gene flow in patterns of climatic niche evolution of the tetraploid ruderal lineage of A. arenosa.Main conclusions: The niche shift of tetraploids in A. arenosa is not driven by WGD per se but rather reflects dynamic post‐WGD evolution in the species, involving tetraploid migration out of their ancestral area and interploidy introgression with other diploid lineages. Our study supports that evolutionary processes following WGD—which usually remain undetected by studies neglecting evolutionary history of polyploids—may play a key role in the adaptation of polyploids to challenging environments.

Aim: Although whole genome duplication (WGD) is an important speciation force, we still lack a consensus on the role of niche differentiation in polyploid evolution. In addition, the role of genome doubling per se vs. later divergence on polyploid’s niche evolution remains obscure. One reason for this might be that the intraspecific genetic structure of polyploid complexes and interploidy gene flow is often neglected in ecological studies. Here, we aim to investigate to which extent these evolutionary processes impact our inference on niche differentiation of autopolyploids. Location: Europe Taxon: Arabidopsis arenosa (Brassicaceae) Methods: Leveraging a total of 352 cytotyped populations of diploid-autotetraploid A. arenosa , we examined differences among climatic niches of diploid and tetraploid lineages both globally, and independently for each tetraploid lineage with respect to the niche of its evolutionary closest relative. Then, we tested if there was an effect of additional interploidy introgression from other sympatric but more ancestral diploid lineages of A. arenosa on climatic niches of tetraploids. Results: Ecological niche shift of tetraploids is only detected when the assignment of populations to intraspecific genetic lineages is considered. We found different patterns of climatic niche evolution (i.e. niche conservatism, contraction or expansion) in each tetraploid lineage when compared to its evolutionary closest relatives. We observed an effect of interploidy gene flow in patterns of climatic niche evolution of tetraploid ruderal plants of A. arenosa . Main conclusions: The niche shift of tetraploids in A. arenosa is not driven by WGD per se but rather reflects dynamic post-WGD evolution in the species, involving tetraploid migration out of their ancestral area and interploidy introgression with other diploid lineages. Our study supports that evolutionary processes following WGD - which usually remain undetected by studies neglecting evolutionary history of polyploids - may play a key role in the adaptation of polyploids to challenging environments.

Phylogeographic and evolutionary studies are necessary to establish solid taxonomic treatments and to implement effective conservation programs. Unfortunately, a well‐argued and well‐founded taxonomic framework is still lacking for some Mediterranean taxa. This is the case of Arenaria section Pseudomoehringia, a group that currently comprises three species endemic to the Iberian Peninsula (A. funiculata, A. suffruticosa, and A. tejedensis) and A. glochidisperma, which is restricted to the Rif mountains, North Africa. However, the taxonomic boundaries and phylogenetic relationships among these species are still uncertain. To explore the evolutionary history and phylogeographic patterns within this section, analyses based on nuclear (amplified fragment length polymorphism and internal transcribed spacer) and plastid DNA markers (psbA‐3’ trnK‐matK and rps16) were performed. Our study has confirmed the monophyly of the section, in which two species are clearly identified (A. funiculata and A. glochidisperma) and an additional species complex (“A. suffruticosa + A. tejedensis complex”) is also supported as a monophyletic clade. The phylogeographic results point toward a dispersal event of a common ancestor of the group from the Iberian Peninsula, giving rise to A. glochidisperma in North Africa. Moreover, A. funiculata and A. glochidisperma are identified as closely related species edaphically differentiated across the Strait of Gibraltar. Our study indicates low levels of a recent gene flow among populations of the “A. suffruticosa + A. tejedensis complex,” which are genetically highly structured and suggest an isolation by distance pattern, probably due to a combination of ecological and geographic barriers. Furthermore, the taxonomic and conservation status of taxa included in Arenaria section Pseudomoehringia has been reviewed.

Background and Aims: The distribution of cytotypes and its potential correlation with environmental variables represent a cornerstone to understanding the origin and maintenance of polyploid lineages. Although many studies have addressed this question in single species at a regional scale, only a few have attempted to decipher this enigma in groups of closely related species at a broad intercontinental geographical scale. Here, we consider ca. 20 species of a diploid-polyploid complex (Veronica subsect. Pentasepalae) of recent and rapid diversification represented in Europe and North Africa to study the frequency and distribution of cytotypes and its relationship with environmental variables. Methods: A total of 680 individuals (207 populations) were sampled. Ploidy levels were determined using flow cytometry. Ecological differentiation among cytotypes was tested using climatic and environmental variables related to temperature, precipitation, vegetation and biogeographical region, among others, and by performing univariate and multivariate (constrained PCoA) analyses. Key Results: Four ploidy levels (2x, 4x, 6x, 8x) were found and genome downsizing was observed to occur within the group. Plants of different ploidy level are ecologically differentiated, with hexaploids and octoploids occurring in wetter and colder habitats with a higher seasonality than diploids. A south-to-north distribution pattern was found, with diploids occupying southern refugial areas and octoploids being more frequent in northern regions of Europe above the permafrost boundary. Conclusions: The distribution of cytotypes can be explained by ecological differentiation, the geographical position of refuge areas during the Quaternary climatic oscillations, as well as by ice and permafrost retreat patterns. The Balkan Peninsula constitutes the most important contact zone between cytotypes. This work provides the first comprehensive ploidy screening within V. subsect. Pentasepalae at a broad scale and indicates that polyploidy and genome downsizing might have contributed to the colonization of new habitats in a recently diverged polyploid complex.