Genetically Depauperate in the Continent but Rich in Oceanic Islands: Cistus monspeliensis (Cistaceae) in the Canary Islands

BACKGROUND: Population genetic theory holds that oceanic island populations are expected to have lower levels of genetic variation than their mainland counterparts, due to founder effect after island colonization from the continent. Cistus monspeliensis (Cistaceae) is distributed in both the Canary Islands and the Mediterranean region. Numerous phylogenetic results obtained in the last years allow performing further phylogeographic analyses in Cistus. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed sequences from multiple plastid DNA regions in 47 populations of Cistus monspeliensis from the Canary Islands (21 populations) and the Mediterranean basin (26 populations). The time-calibrated phylogeny and phylogeographic analyses yielded the following results: (1) a single, ancestral haplotype is distributed across the Mediterranean, whereas 10 haplotypes in the Canary Islands; (2) four haplotype lineages are present in the Canarian Islands; (3) multiple colonization events across the archipelago are inferred; (4) the earliest split of intraspecific lineages occurred in the Early to Middle Pleistocene (<930,000 years BP). CONCLUSIONS/SIGNIFICANCE: The contrasting pattern of cpDNA variation is best explained by genetic bottlenecks in the Mediterranean during Quaternary glaciations, while the Canarian archipelago acted as a refugium of high levels of genetic diversity. Active colonization across the Canarian islands is supported not only by the distribution of C. monspeliensis in five of the seven islands, but also by our phylogeographic reconstruction in which unrelated haplotypes are present on the same island. Widespread distribution of thermophilous habitats on every island, as those found throughout the Mediterranean, has likely been responsible for the successful colonization of C. monspeliensis, despite the absence of a long-distance dispersal mechanism. This is the first example of a plant species with higher genetic variation among oceanic island populations than among those of the continent

The genomic basis of the plant island syndrome in Darwin’s giant daisies

Artículo escrito por un elevado número de autores. Solo se referencia el que aparece en primer lugar, el nombre del grupo de colaboración si hubiere y los autores pertenecientes a la UAMThe repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the ‘plant island syndrome’, include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin’s giant daisiesThis work was supported by the Norwegian Research Council via project number 287327 awarded to M.D.M., and a travel grant (project number 287327) granted to J.Ce. and M.D.M

Evolución en el género Linaria: biogeografía, cambio morfológico y sistemático de Linaria sect. Versicolores

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid. Facultad de Ciencias, Departamento de Biología. Fecha de lectura: 03-12-201

A western representative of an eastern clade: phylogeographic history of the gypsum-associated plant Nepeta Hispanica

The preference of certain plant species for gypsum soils with a patchy distribution leads to disjunct population structures that are thought to generate island-like dynamics potentially influencing biogeographic patterns at multiple evolutionary scales. Here, we study the evolutionary and biogeographic history of Nepeta hispanica, a western Mediterranean plant associated with gypsum soils and displaying a patchy distribution with populations very distant from each other. Three approaches were used: (a) interspecific phylogenetic analyses based on nuclear DNA sequences of the ITS region to unveil the relationships and times of divergence between N. hispanica and its closest relatives; (b) phylogeographic analyses using plastid DNA regions trnS-trnG and psbJ-petA to evaluate the degree of genetic isolation between populations of N. hispanica, their relationships and their genetic diversity; and (c) ecological niche modelling to evaluate historical distributional changes. Results reveal that N. hispanica belongs to an eastern Mediterranean and Asian (Irano-Turanian) clade diversified in arid environments since the Miocene-Pliocene. This species represents the only lineage of this clade that colonised the western Mediterranean, probably through the northern Mediterranean coast (southern Europe). Present Iberian populations display a high plastid genetic diversity and, even if geographically distant from each other, they are highly connected according to the distribution of plastid haplotypes and lineages. This can be explained by a scenario involving a complex history of back-and-forth colonisation events, facilitated by a relative stability of suitable conditions for the species across the western Mediterranean throughout the QuaternaryThis work would not have been possible without the support of Julian ´ García, Rub´en de Pablo, Jesús del Río, Leonardo Guti´errez, Javier Puente, Javier Pavon ´ and Luis M. Medrano, who helped us with field sample collection; Leopoldo Medina, Cyrille Chatelain, Jesús Riera and Javier Hernandez, ´ who granted us permission to use specimens from the MA, G, VAL and SALA herbaria respectively; and Emilio Cano, who provided his invaluable help in the RJB-CSIC molecular systematics laboratory. Fieldwork was financed by the Universidad Autonoma ´ de Madrid with a grant to IRG’s Master thesis. Laboratory work was funded by a Juan de la Cierva fellowship to MF-M (Spanish Ministry of Economy and Competitiveness, reference IJCI-2015–23459

Repeated asynchronous evolution of single-species endemics of ivies (Hedera L.) in Macaronesian archipelagos

Aim: Evolutionary studies of oceanic island endemics are usually focused on lineages that have experienced in situ radiation, while those that speciated once on the island or archipelago but have not further diversified (single-species endemics) remain understudied. The Macaronesian archipelagos, in the Atlantic Ocean, are home to significant numbers of single-species endemics. The genus Hedera L. (12 species) includes three single-species endemics from three Macaronesian archipelagos with putatively independent origins. Here, we tested the role of phylogenetic niche conservatism in their evolution. To that end, we (1) reconstructed the spatio-temporal origin of Macaronesian ivies using phylogenomics, and (2) assessed the role of climatic niche during their colonization and speciation. Location: Azores, Canary Islands, Madeira, western Mediterranean. Taxon: Hedera spp. Methods: We used 166 samples representing all Hedera species to generate genotyping-by-sequencing (GBS) libraries and performed time-calibrated phylogenomic and biogeographic analyses. Climatic preferences and climatic niche evolution were assessed using a geo-referenced database of the western ivy species (2,297 records). Results: Independent and asynchronous colonization and speciation were estimated for the three Macaronesian ivies, resulting in different degrees of phylogenetic and climatic niche differentiation: H. canariensis displayed an early divergence (7.5–12 Ma) and high phylogenetic and niche isolation; H. azorica had intermediate phylogenetic isolation and niche divergence from its closest relative H. helix (4.4–6.8 Ma) and H. maderensis was embedded within the climatically similar H. iberica (2.8–4.6 Ma). A strong phylogenetic signal was suggested for climatic niche in the western clade of Hedera, where the three Macaronesian ivies are placed. Main Conclusions: The three Macaronesian ivies represent the evolutionary stages leading to the emergence of single-species island endemics. Climatic niche conservatism appears to be involved in the evolution of single-species endemics, first by facilitating island colonization, and then by limiting in situ diversificationSpanish Ministry of Economy, Industry and Competitiveness, Grant/Award Number: CGL2017-87198-P and PID2019- 106840GA-C22; Universidad Autónoma de Madrid, Grant/Award Number: FPIUAM 201

Maximize Resolution or Minimize Error? Using Genotyping-By-Sequencing to Investigate the Recent Diversification of Helianthemum (Cistaceae)

A robust phylogenetic framework, in terms of extensive geographical and taxonomic sampling, well-resolved species relationships and high certainty of tree topologies and branch length estimations, is critical in the study of macroevolutionary patterns. Whereas Sanger sequencing-based methods usually recover insufficient phylogenetic signal, especially in recently diversified lineages, reduced-representation sequencing methods tend to provide well-supported phylogenetic relationships, but usually entail remarkable bioinformatic challenges due to the inherent trade-off between the number of SNPs and the magnitude of associated error rates. The genus Helianthemum (Cistaceae) is a species-rich and taxonomically complex Palearctic group of plants that diversified mainly since the Upper Miocene. It is a challenging case study since previous attempts using Sanger sequencing were unable to resolve the intrageneric phylogenetic relationships. Aiming to obtain a robust phylogenetic reconstruction based on genotyping-by-sequencing (GBS), we established a rigorous methodological workflow in which we i) explored how variable settings during dataset assembly have an impact on error rates and on the degree of resolution under concatenation and coalescent approaches, ii) assessed the effect of two extreme parameter configurations (minimizing error rates vs. maximizing phylogenetic resolution) on tree topology and branch lengths, and iii) evaluated the effects of these two configurations on estimates of divergence times and diversification rates. Our analyses produced highly supported topologically congruent phylogenetic trees for both configurations. However, minimizing error rates did produce more reliable branch lengths, critically affecting the accuracy of downstream analyses (i.e. divergence times and diversification rates). In addition to recommending a revision of intrageneric systematics, our results enabled us to identify three highly diversified lineages in Helianthemum in contrasting geographical areas and ecological conditions, which started radiating in the Upper Miocene.España, MINECO grants CGL2014- 52459-P and CGL2017-82465-PEspaña, Ministerio de Economía, Industria y Competitividad, reference IJCI-2015-2345

PAICE: A new R package to estimate the number of inter-island colonizations considering haplotype data and sample size

Aim: Colonization is a central topic in ecology and one of the cornerstones of island biogeography. Although the evolutionary history of island species is widely studied, the quantification of colonization is particularly challenging because the same area may be colonized multiple times by the same species, whereas initially successful colonization events may eventually be followed by extinction. Nevertheless, an estimation of the actual number of within-archipelago colonization events can be achieved when using adequate sample size and genetic data, which are essential parameters in the inference of colonization success of any species. Location: Canary Islands, Azores and Galápagos Islands. Taxon: Buteo galapagoensis, Croton scouleri, Setophaga petechia aureola and Xylocopa darwini (Galápagos); Canarina canariensis, Cistus monspeliensis, Juniperus cedrus and Olea europaea subsp. guanchica (Canary Islands); and Juniperus brevifolia and Picconia azorica (Azores). Methods: The new R package PAICE uses haplotype (from organelle DNA) sharing and haplotype relationships, and controls for sampling effort to estimate the number of within-archipelago colonization events in island-like systems. PAICE applies a sampling-effort correction based on rarefaction curves of field sampling (number of individuals or populations) and genetic sampling (number of DNA variable positions). The number of colonization events for the 10 insular species were estimated with PAICE and results compared with previous methods. Results: PAICE estimates a number of inter-island colonization events up to an order of magnitude greater than previous methods. Furthermore, PAICE can quantify the colonization events of any study species, in multiple biogeographic contexts and considering sampling size, thus providing a standardized estimate of colonization success. Main conclusions: The new package PAICE provides an estimation of the number of inter-island colonization events (regardless of dispersal routes or rates) based on haplotype data across islands. This new tool will allow gaining new insights on the intensity of long-distance-dispersal events, their drivers and consequences for the assembly of insular faunas and floras

The Pyrenees as a cradle of plant diversity: phylogeny, phylogeography and niche modeling of Saxifraga longifolia

The current distribution of most species results from ecological niche, past distribution, and migrations during glacial–interglacial periods and in situ evolution. Here, we disentangle the colonization history of Saxifraga longifolia Lapeyr., a limestone plant abundant in the Pyrenees and rare in other Iberian mountains and the African Atlas. Our working hypothesis is that the current distribution results from the shrinkage of a more extensive distribution in previous cold periods. We sampled 160 individuals of 32 populations across the whole distribution range and sequenced four DNA regions (rpl32-trnL, rps16-trnQ, trnS-trnG, and ITS). Ecological conditions were modeled to identify factors promoting high genetic diversity and long-term persistence areas for S. longifolia. In addition, we inferred phylogenetic relationships, phylogeographic divergence, genetic diversity, and migration routes. Seven plastid haplotypes were found, of which six occur in the Pyrenees and one in the High Atlas (Morocco). Discrete phylogeographic analysis (DPA) estimated migration routes predominantly from the Pyrenees to the other areas. Colonization events to those areas appear to have taken place recently given that the rest of the Iberian mountains do not harbor exclusive haplotypes. Iberian–Northern African distribution was inferred to be the result of long-distance dispersal because the split between Iberian and High Atlas haplotypes is estimated to have taken place in the last 4 million years ago when the Strait of Gibraltar was already open. Migrations from the Pyrenees to the south may have been favored by a corridor of predominant limestone rocks along Eastern Iberia, followed by successful overcoming the Strait of Gibraltar to reach northern Afric

Phylogenetic and phylogeographic evidence for the colonization success of the diplochorous Astydamia latifolia across the Canary Islands

Astydamia latifolia is the only species of the genus Astydamia, which forms an early-diverging lineage of Apiaceae, subfamily Apioideae. This species is subendemic to theCanary Islands and one of the most representative species of the coastal environ-ments of this archipelago. Astydamia displays diplochory, that is, diaspores with twolong-distance dispersal (LDD) syndromes. In particular, A. latifolia has both anemo-chorous and thalassochorous fruit traits (corky and winged mericarps). Although weexpect this species to have a high dispersal capacity, there is no genetic study ad-dressing it. The divergence time of this species from its sister taxon is also unknown.In this study, we aimed (i) to unveil the phylogenetic relationships and divergencetimes of A. latifolia; (ii) to reconstruct its phylogeographic structure across the CanaryIslands; and (iii) to estimate the number of inter-island colonization events. To theseends, we first sequenced the internal transcribed spacer (ITS) region for A. latifolia,reconstructed the phylogenetic relationships of Astydamia and Apiaceae relativesand estimated divergence times. Then, two plastid DNA regions (psaI-aacD and psbK-trnS) were sequenced for 158 individuals (from 36 Canarian population and one NWAfrican population) to reconstruct a haplotype network. The recently developedmethod Phylogeographic Analysis of Island Colonization Events (PAICE) was used toestimate the number of inter-island colonization events. Results show that A. latifolia isa phylogenetically isolated lineage that diverged from the most closely related genus(Molopospermum) in the Eocene–Miocene. It displays a low plastid DNA diversity (onlyfour haplotypes detected), which is accompanied by a high degree of haplotype shar-ing between islands and highly linear rarefaction curves of colonization obtained inPAICE. These findings suggest a high colonization ability for this species, most likelyrelated to the availability of two LDD syndromesCGL2015-67865-P, PGC2018-101650-B-I00, IJCI-2015-2345