Helianthemum is the largest, most widely distributed and most taxonomically complex genus of the Cistaceae. To examine the intrageneric phylogenetic relationships in Helianthemum, we used sequence data from plastid DNA (ndhF, psbA-trnH, trnL-trnF) and the nuclear ITS region. The ingroup consisted of 95 species and subspecies (2 subgenera, 10 sections) from throughout the range of Helianthemum, while the outgroup was composed of 30 species representing all the genera in the Cistaceae (Cistus Crocanthemum, Fumana, Halimium, Hudsonia, Lechea, Tuberaria) plus Anisoptera thurifera subsp. polyandra (Dipterocarpaceae). To infer phylogenetic relationships, we analysed three different matrices (cpDNA, nrDNA, cpDNA + nrDNA concatenated) using maximum likelihood and Bayesian inference, and performed molecular dating to estimate the ages of origin of the main clades using a Bayesian approach. The cpDNA + nrDNA concatenated dataset provided the highest Bayesian posterior probabilities and bootstrap support values, and the results supported the monophyly of the genus Helianthemum and its sister relationship to a clade consisting of all species of Cistus, Crocanthemum, Halimium, Hudsonia and Tuberaria. This result means that we did not retrieve the sister relationship between Helianthemum and Crocanthemum (plus Hudsonia) that could be expected according to previous published studies. Despite their different statistical support, the topology of the inner branches of all the consensus trees showed that Helianthemum is characterized by the emergence of three major clades in agreement with above-species taxonomy, although unresolved polytomies still remain towards the tips of the trees (species and subspecies). Clade I (mainly distributed in Mediterranean and alpine environments in European and western Asiatic mountain chains) fully coincided with subg. Plectolobum, whereas subg. Helianthemum was retrieved in clade II (arid and semi-arid environments from Macaronesia, the Mediterranean, subtropical northern Africa, Anatolia and central Asia) and clade III (Mediterranean ecosystems around the Mediterranean Basin). The burst of diversification during the Plio-Pleistocene detected in the three main clades of Helianthemum is concomitant with the Messinian salinity crisis, the onset of Mediterranean climatic conditions, and Quaternary glaciations, as found in many other groups of Mediterranean plants. Thus, the general lack of resolution in the trees can be attributed to rapid species diversification and events of reticulate evolution. A series of further taxonomic and evolutionary inferences can be drawn from our analyses: (i) no species occupied an early-diverging position with regard the rest of the species; (ii) a close relationship between H. caput-felis and subg. Plectolobum; (iii) an unexpected close relationship between H. squamatum/ H. syriacum (and H. motae), H. lunulatum/ H. pomeridianum and among H. songaricum/ H. antitauricum/ H. germanicopolitanum; (iv) a close relationship between incertae sedis species and sect. Eri...

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.

Background and Aims Several biogeographical models have been proposed to explain the colonization and diversification patterns of Macaronesian lineages. In this study, we calculated the diversification rates and explored what model best explains the current distribution of the 15 species endemic to the Canary Islands belonging to Helianthemum sect. Helianthemum (Cistaceae). Methods We performed robust phylogenetic reconstructions based on genotyping-by-sequencing data and analysed the timing, biogeographical history and ecological niche conservatism of this endemic Canarian clade. Key Results Our phylogenetic analyses provided strong support for the monophyly of this clade, and retrieved five lineages not currently restricted to a single island. The pristine colonization event took place in the Pleistocene (~1.82 Ma) via dispersal to Tenerife by a Mediterranean ancestor. Conclusions The rapid and abundant diversification (0.75–1.85 species per million years) undergone by this Canarian clade seems the result of complex inter-island dispersal events followed by allopatric speciation driven mostly by niche conservatism, i.e. inter-island dispersal towards niches featuring similar environmental conditions. Nevertheless, significant instances of ecological niche shifts have also been observed in some lineages, making an important contribution to the overall diversification history of this clade.

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Background and Aims The Canary Islands have strong floristic affinities with the Mediterranean Basin. One of the most characteristic and diverse vegetation belt of the archipelago is the thermophilous woodland (between 200 and 900 m.a.s.l.). This thermophilous plant community consists of many non-endemic species shared with the Mediterranean Floristic Region together with Canarian endemic species. Consequently, phytogeographic studies have historically proposed the hypothesis of an origin of the Canarian thermophilous species following the establishment of the summer-dry mediterranean climate in the Mediterranean Basin around 2.8 million years ago. Methods Time-calibrated phylogenies for 39 plant groups including Canarian thermophilous species were primarily analysed to infer colonization times. In particular, we used 26 previously-published phylogenies together with 13 time-calibrated phylogenies (including newly generated plastid and nuclear DNA sequence data) to assess whether the time interval between stem and crown ages of Canarian thermophilous lineages postdates 2.8 Ma. For lineages postdating this time threshold, we additionally conducted ancestral area reconstructions to infer the potential source area for colonization. Key Results A total of 43 Canarian thermophilous lineages were identified from 39 plant groups. Both mediterranean (16) and pre-mediterranean (9) plant lineages were found. However, we failed to determine the temporal origin for 18 lineages because a stem-crown time interval overlaps with the 2.8 Ma threshold. The spatial origin of thermophilous lineages was also heterogeneous, including ancestral areas from the Mediterranean Basin (nine) and other regions (six). Conclusions Our findings reveal an unexpectedly heterogeneous origin of the Canarian thermophilous species in terms of colonization times and mainland source areas. A substantial proportion of the lineages arrived in the Canaries before the summer-dry climate was established on the Mediterranean Basin. The complex temporal and geographical origin of Canarian thermophilous species challenges the view of the Canary Islands (and Madeira) as a subregion within the Mediterranean Floristic Region.

Unraveling the relationships between ecological, functional traits and genetic diversity of narrow endemic plants provide opportunities for understanding how evolutionary processes operate over local spatial scales and ultimately how diversity is created and maintained. To explore these aspects in Sierra Nevada, the core of the Mediterranean Betic‐Rifean hotspot, we have analyzed nuclear DNA microsatellite diversity and a set of biological and environmental factors (physicochemical soil parameters, floral traits, and community composition) in two strictly endemic taxa from dolomite outcrops of Sierra Nevada (Helianthemum pannosum and H. apenninum subsp. estevei) and two congeneric widespread taxa (H. cinereum subsp. rotundifolium and H. apenninum subsp. apenninum) that further belong to two different lineages (subgenera) of Helianthemum. We obtained rather unexpected results contrasting with the theory: (a) The narrow endemic taxa showed higher values of genetic diversity as well as higher average values of pollen production per flower and pollen‐to‐ovule ratio than their widespread relatives; and (b) the two taxa of subg. Helianthemum, with larger corollas, approach herkogamy and higher pollen production than the two taxa of subg. Plectolobum, displayed lower genetic diversity and higher values of inbreeding. Altogether, these results disclose how genetic diversity may be affected simultaneously by a large number of intrinsic and extrinsic factors, especially in Pleistocene glacial refugia in mountains where the spatial context harbors a great ecological heterogeneity. On the other hand, differences in mating system and the significant effect of the substrate profile, both being highly diverse in the genus Helianthemum, in the genetic variability illustrate about the importance of these two factors in the diversification and species differentiation of this paradigmatic genus in the Mediterranean and open the field to formulate and test new hypotheses of local adaptation, trait evolution, and habitat diversification.

Helianthemum squamatum is a specialist gypsophile, the only species of a recently diverged lineage in subgenus Helianthemum characterized by having the lowest chromosome number in the genus (n = 5). With the hypothesis of great genome reorganization in the lineage of H. squamatum, we (1) modelled the evolution of the chromosome number in the genus Helianthemum, (2) analysed the karyotype and the nuclear DNA content of H. squamatum and its sister species H. syriacum (n = 10) and (3) studied in detail the meiotic process of H. squamatum. Our analyses show that: (1) the rate of chromosome losses in the lineage that gave rise to H. squamatum is 100 times higher than in the genus as a whole; (2) compared to its sister species, H. squamatum has a more symmetric karyotype composed of longer metacentric chromosomes and retains c. 80% of its nuclear DNA content and (3) achiasmatic behaviour of chromosomes occurs during microsporogenesis despite full synapsis. Our results are in agreement with previous knowledge showing that reduced chromosome numbers in determinate lineages are found in short-lived species adapted to stressful environments, and we suggest that a combination of fewer chromosomes, a smaller genome, a shorter life cycle and the suppression of meiotic recombination can together contribute to the maintenance of those advantageous allelic combinations that makes H. squamatum a true gypsophile, enabling the individual plants to cope with the harshness imposed by dry gypsum soils.

Molecular systematics requires the establishment of a robust phylogenetic framework including extensive geographical and taxonomic sampling. In this work, we proposed systematic changes in the genus Helianthemum based on phylogenetic trees obtained by both maximum likelihood and Bayesian analyses of GBS data. The implications of these phylogenetic results for the systematics of Helianthemum entail the establishment of a new subgenus and novel re-ascriptions of sections and species along with some nomenclatural novelties. The following new combinations are proposed: Helianthemum subg. Eriocarpum (Dunal) Martín-Hernanz, Velayos, Albaladejo & Aparicio; H. oelandicum subsp. conquense (Borja & Rivas Goday ex G.López) Martín-Hernanz, Velayos, Albaladejo & Aparicio; H. nummularium subsp. cantabricum (M.Laínz) Martín-Hernanz, Velayos, Albaladejo & Aparicio; H. nummularium subsp. tinetense (M.Mayor & Fern.Benito) Martín-Hernanz, Velayos, Albaladejo & Aparicio.