Filogeografía, evolución de nicho y especiación en un linaje mediterráneo-macaronésico: Lavatera maritima-Lavatera acerifolia (Malvaceae)

Tesis Doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología. Fecha de lectura: 08-09-2017Esta tesis tiene embargado el acceso al texto completo hasta el 08-09-201

Expanding the southern range margin at the cost of massive asymmetric introgression: Armeria pungens (Plumbaginaceae)

Armeria (Plumbaginaceae) is a primarily Mediterranean angiosperm genus with low pre- and postzygotic reproductive isolation, in which a number of taxa have been proposed to be of hybrid origin. The southernmost population of a coastal sand-dune Iberian-Corsica-Sardinian species (A. pungens) was reported to be introgressed by a sympatric congener (A. macrophylla) based on nrDNA ITS and plastid DNA Sanger sequences, morphometric data, genome size variation and ecological niche. A genotyping-by-sequencing (GBS) genomic study reveals that such introgression is markedly asymmetric towards A. pungens both for the nuclear and plastid genomes. For the latter, a plastid capture has occurred in the study site, which can be considered a hybrid zone. By contrast, genetic clustering analyses hardly reveal any introgression in its congener A. macrophylla. The introgression scenario is consistent with Currat et al.¿s (2008) model in which a species invading an occupied territory becomes massively introgressed with local genes. This is due to demographic imbalance between the two species, with reduced population densities of the invader at the colonization front. This scenario is facilitated by factors such as low interspecific reproductive isolation and remoteness of the source of the invasion, which are met in the Armeria hybrid zone. Although the recent origin of the introgressed population -and the hybrid zone- is so far based on circumstantial evidence, our results may provide clues for understanding how complex genetic admixture patterns are shaped in their early stages

Demography‐driven and adaptive introgression in a hybrid zone of the Armeria syngameon

Syngameons represent networks of otherwise distinct species connected by limited gene exchange. Although most studies have focused on how species maintain their cohesiveness despite gene flow, there are additional relevant questions regarding the evolutionary dynamics of syngameons and their drivers, as well as the success of their members and the network as a whole. Using a ddRADseq approach, we analysed the genetic structure, genomic clines and demographic history of a coastal hybrid zone involving two species of the Armeria (Plumbaginaceae) syngameon in southern Spain. We inferred that a peripheral population of the sand dune‐adapted A. pungens diverged from the rest of the conspecific populations and subsequently hybridized with a locally more abundant pinewood congener, A. macrophylla . Both species display extensive plastid DNA haplotype sharing. Genomic cline analysis identified bidirectional introgression, but more outlier loci with excess A. pungens than A. macrophylla ancestry, suggesting the possibility of selection for A. pungens alleles. This is consistent with the finding that the A. pungens phenotype is selected for in open habitats, and with the strong correlation found between ancestry and phenotype. Taken together, our analyses suggest an intriguing scenario in which bidirectional introgression may, on the one hand, help to avoid reduced levels of genetic diversity due to the small size and isolated location of the A. pungens range‐edge population, thereby minimizing demographic risks of stochastic extinction. On the other hand, the data also suggest that introgression into A. macrophylla may allow individuals to grow in open, highly irradiated, deep sandy, salt‐exposed habitats.CEnter of the study of Biodiversity in Amazoni

Hybridization and cryptic speciation in the Iberian endemic plant genus Phalacrocarpum (Asteraceae-Anthemideae)

Understanding the role and impact of reticulation in phylogenetic inquiry has improved with extended use of high throughput sequencing data. Yet, due to the dynamism of genomes over evolutionary time, disentangling old hybridization events remains a serious challenge. Phalacrocarpum is one of the 27 Iberian endemic plant genera, currently considered monotypic but including three subspecies. Its uncertain phylogenetic relationships within tribe Anthemideae (Asteraceae) point to an Early Miocene divergence from its sister group, and its persistent taxonomic instability has been proposed to be due to hybridization. We aim at understanding the evolutionary history of this genus using SNPs called from a genotyping-by-sequencing (GBS) analysis, Sanger sequences —from three plastid DNA regions (psbJ-petA, petB-petD, trnH-psbA) and the nuclear ribosomal ITS regions (cloned)— as well as leaf morphometric multivariate analysis. SNP data and Sanger sequences strongly support the unforeseen existence of a cryptic species in the eastern populations of P. oppositifolium subsp. anomalum. Broad molecular and morphometric patterns of variation found in conflictive populations from the Sanabria Valley region convincingly identify a recent previously undocumented hybrid zone. By contrast, evidence is less conclusive on relationships between subspecies hoffmannseggii, oppositifolium and a second conflictive group along the border of Galicia and Portugal (Orense massifs). Although genetic clustering analysis of SNP data suggests that the former subspecies was the mother progenitor in hybridization events that gave rise to the other two groups, we found considerable uniqueness of ITS ribotypes and plastid haplotypes in them. This result, in the context of Pleistocene climatically-driven range shifts in NW Iberian Peninsula, can be due to periods of isolation, genetic bottlenecks and drift superimposed on old hybridization events. Our study confirms the idea that unraveling old hybridization events may be compromised by the suite of evolutionary processes accumulated subsequently, particularly in areas with a history of climatic instability.Peer reviewe

Colonization history of the Canary Islands endemic Lavatera acerifolia, (Malvaceae) unveiled with Genotyping-by-Sequencing data and niche modeling

[Usage Notes] Dataset consists of genomic data generated in vcf format.[Aim] Differentiation of island lineages from mainland relatives and radiation after initial colonization are two important processes generating island diversity. Both of these processes are influenced by colonization dynamics and contemporary connections between island species and their source populations. The classic island progression rule model, i.e., dispersal from mainland to older islands and subsequently to younger islands, can be considered a null hypothesis, particularly for islands that are geographically aligned perpendicular to the mainland coast with ages inversely proportional to distance from the mainland. Alterations to this pattern have been reported, particularly in archipelagoes that are geographically closely adjacent to mainland source populations. Here we aim to integrate genomic and environmental niche data to infer the colonization history of a Canary endemic species and to understand its current diversity patterns.[Location] Canary Islands.[Taxon] Lavatera acerifolia (Malvaceae).[Methods] We used high-throughput genotyping-by-sequencing (GBS) combined with species distribution modelling (SDM) projected onto past conditions. Genetic structure (clustering methods), relatedness (coalescent and ML trees), nucleotide diversity and differentiation (population genetics) were assessed based on SNPs obtained from three alternative bioinformatics pipelines. The influence of environmental variables over time was assessed with a GLM in which the response variable was amount of heterozygous sites per individual.[Results] Four genetic groups were identified arranged along a longitudinal gradient, and the earliest diverging coincides with the older, and easternmost, islands (Lanzarote and Fuerteventura). Genetic diversity is reduced in the westernmost islands, which are more distant from the mainland, host few populations and yet apparently offer more suitable habitats.[Main conclusions] The inferred colonization scenario generally fits the progression rule model, but suggests a more complex pattern for the central islands. For the westernmost islands, the contrast between high availability of suitable habitats and reduced genetic diversity and number of populations suggests a colonization front moving at a slow pace, rather than local extinctions, as an explanation for the scarcity of populations in those islands. Historical projections of SDM lend support to this interpretation.Spanish Ministry of Science, Technology and Innovation, Award: CGL2010-16138. Spanish Ministry of Economy and Competitivity, Award: CGL2013-49097-C2-1-P, CGL2017-88500-P (AEI/FEDER, UE). FPI fellowship, Award: BES-2011-049852.Peer reviewe

Colonization history of the Canary Islands endemic Lavatera acerifolia, (Malvaceae) unveiled with genotyping-by-sequencing data and niche modelling

Aim: Differentiation of island lineages from mainland relatives and radiation after initial colonization are two important processes generating island diversity. Both of these processes are influenced by colonization dynamics and contemporary connections between island species and their source populations. The classic island progression rule model, that is dispersal from mainland to older islands and subsequently to younger islands, can be considered a null hypothesis, particularly for islands that are geographically aligned perpendicular to the mainland coast with ages inversely proportional to distance from the mainland. Alterations to this pattern have been reported, particularly in archipelagos that are geographically closely adjacent to mainland source populations. Here we aim to integrate genomic and environmental niche data to infer the colonization history of a Canary endemic species and to understand its current diversity patterns. Location: Canary Islands. Taxon: Lavatera acerifolia (Malvaceae). Methods: We used high-throughput genotyping-by-sequencing (GBS) combined with species distribution modelling (SDM) projected onto past conditions. Genetic structure (clustering methods), relatedness (coalescent and ML trees), nucleotide diversity and differentiation (population genetics) were assessed based on SNPs obtained from three alternative bioinformatics pipelines. The influence of environmental variables over time was assessed with a generalized linear model in which the response variable was amount of heterozygous sites per individual. Results: Four genetic groups were identified arranged along a longitudinal gradient, and the earliest diverging coincides with the older, and easternmost, islands (Lanzarote and Fuerteventura). Genetic diversity is reduced in the westernmost islands, which are more distant from the mainland, host few populations and yet apparently offer more suitable habitats. Main conclusions: The inferred colonization scenario generally fits the progression rule model, but suggests a more complex pattern for the central islands. For the westernmost islands, the contrast between high availability of suitable habitats and reduced genetic diversity and number of populations suggests a colonization front moving at a slow pace, rather than local extinctions, as an explanation for the scarcity of populations in those islands. Historical projections of SDM lend support to this interpretation

A snapshot of progenitor–derivative speciation in Iberodes (Boraginaceae)

Traditional classification of speciation modes has focused on physical barriers to gene flow. Allopatric speciation with complete reproductive isolation is viewed as the most common mechanism of speciation. Parapatry and sympatry, by contrast, entail speciation in the face of ongoing gene flow, making them more difficult to detect. The genus Iberodes (Boraginaceae, NW Europe) comprises five species with contrasting morphological traits, habitats and species distributions. Based on the predominance of narrow and geographically distant endemic species, we hypothesized that geographical barriers were responsible for most speciation events in Iberodes. We undertook an integrative study including: (i) phylogenomics through restriction-site-associated DNA sequencing (RAD-seq), (ii) genetic structure analyses, (iii) demographic modelling, (iv) morphometrics, and (v) climatic niche modelling and niche overlap analysis. The results revealed a history of recurrent progenitor–derivative speciation manifested by a paraphyletic pattern of nested species differentiation. Budding speciation mediated by ecological differentiation is suggested for the coastal lineage, deriving from the inland widespread Iberodes linifolia during the Late Pliocene. Meanwhile, geographical isolation followed by niche shifts are suggested for the more recent differentiation of the coastland taxa. Our work provides a model for distinguishing speciation via ecological differentiation of peripheral, narrowly endemic I. kuzinskyanae and I. littoralis from a widespread extant ancestor, I. linifolia. Ultimately, our results illustrate a case of Pliocene speciation in the probable absence of geographical barriers and get away from the traditional cladistic perspective of speciation as producing two species from an extinct ancestor, thus reminding us that phylogenetic trees tell only part of the story

Insect pollination in temperate sedges? A case study in Rhynchospora alba (Cyperaceae)

Sedges (Cyperaceae) are commonly pollinated by wind, but some transitions from wind to insect pollination have been reported in tropical sedges. Despite being a temperate sedge, the pollination strategy of Rhynchospora alba may partly depend on insects, as suggested by its white-colored inflorescences. Here we quantify the contribution of insects to the reproductive fitness of R. alba as an exploration of the success of entomophily in temperate sedges. Honeybees and hoverflies seem to be the primary visitors of R. alba in the study site, and pollen of R. alba was recovered from the mouthparts and legs of the insects. Treatments excluding insects led to a lower reproductive fitness (regarding fruit weight and fruit viability) than those not excluding them. Therefore, insects seem to contribute significantly to the pollination of R. alba despite moderate morphological adaptation. We highlight the role of entomophily as an overlooked reproductive mechanism in cold-temperate sedges

Phylogeographical and cytogeographical history of Artemisia herba-alba (Asteraceae) in the Iberian Peninsula and North Africa: mirrored intricate patterns on both sides of the Mediterranean Sea

Artículo de 18 páginas con mapas de especificación geográfica, tablas de datos y figuras de distribución.Artemisia herba-alba is an important component of Mediterranean dry steppe floras, being widely distributed in arid areas of the Iberian Peninsula and North-West Africa. In this study, we use genetic, cytogenetic and niche modelling tools to investigate the natural history of the species, focusing particularly on the role played by polyploidization to explain current diversity patterns throughout the main distribution range of the plant. Our sequencing data indicate a complex phylogeographical structure showing similar haplotype diversity patterns on both sides of the Strait of Gibraltar and no clear signals of genetic refugia. According to our cytogeographical results, we inferred multiple polyploidization events, which probably took place on the Iberian Peninsula and in North Africa independently. Environmental niche modelling suggested stable potential distributions of A. herba-alba on both sides of the Mediterranean Sea under present and past Last Glacial Maximum conditions, which could be related to the intricate spatial genetic and cytogenetic patterns shown by the species. Finally, environmental modelling comparison among cytotypes revealed that the niche of tetraploids is narrower and nested in that of diploids, a result that could indicate environmental specialization and could potentially explain recurrent establishment success of tetraploids.This work was supported by the Catalan government (grant number 2017SGR1116); by the Spanish government [grant numbers CGL2010-18039, CGL2013-49097-C2-2-P, CGL2017-84297-R (AEI/FEDER, UE)] and by the Algerian Ministry of Higher Education and Scientific Research.Abstract INTRODUCTION MATERIAL AND METHODS RESULTS DISCUSSION CONCLUSIONS SUPPORTING INFORMATION ACKNOWLEDGEMENTS REFERENCES Supplementary dat