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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 sequencingbased 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, Depto. de Biodiversidad, Ecología y Evolución, Fac. de Ciencias Biológicas, TRUE, pub

Background and Aims The Canary Islands have strong floristic affinities with the Mediterranean Basin. One of the most characteristic and diverse vegetation belts 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 new 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 in

A recurring feature of oceanic archipelagos is the presence of adaptive radiations that generate endemic, species-rich clades that can offer outstanding insight into the links between ecology and evolution. Recent developments in evolutionary genomics have contributed towards solving long-standing questions at this interface. Using a comprehensive literature search, we identify studies spanning 19 oceanic archipelagos and 110 putative adaptive radiations, but find that most of these radiations have not yet been investigated from an evolutionary genomics perspective. Our review reveals different gaps in knowledge related to the lack of implementation of genomic approaches, as well as undersampled taxonomic and geographic areas. Filling those gaps with the required data will help to deepen our understanding of adaptation, speciation, and other evolutionary processes.

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 Africa.

The 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 daisies.

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.

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 Quaternary.

The path followed by species in the colonization of remote oceanic islands ultimately depends on their phylogenetic constraints and ecological responses. In this study, we aim to evaluate the relative role of geographical and ecological forces in the origin and evolution of the Madeiran ivy (Hedera maderensis), a single-species endemic belonging to the western polyploid clade of Hedera. To determine the phylogenetic placement of H. maderensis within the western polyploid clade, we analyzed 40 populations (92 individuals) using genotyping-by-sequencing and including Hedera helix as outgroup. Climatic niche differences among the study species were evaluated using a database with 867 records representing the entire species ranges. To test species responses to climate, 13 vegetative and reproductive functional traits were examined for 70 populations (335 individuals). Phylogenomic results revealed a nested pattern with H. maderensis embedded within the south-western Iberian H. iberica. Gradual niche differentiation from the coldest and most continental populations of H. iberica to the warm and stable coastal population sister to H. maderensis parallels the geographical pattern observed in the phylogeny. Similarity in functional traits is observed for H. maderensis and H. iberica. The two species show leaves with higher specific leaf area (SLA), lower leaf dry matter content (LDMC) and thickness and fruits with lower pulp fraction than the other western polyploid species H. hibernica. Acquisition of a Macaronesian climatic niche and the associated functional syndrome in mainland European ivies (leaves with high SLA, and low LDMC and thickness, and fruits with less pulp content) was a key step in the colonization of Madeira by the H. iberica/H. maderensis lineage, which points to climatic pre-adaptation as key in the success of island colonization (dispersal and establishment). Once in Madeira, budding speciation was driven by geographical isolation, while ecological proc

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 rout

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.

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 Africa.

Researchers in phylogenetic systematics typically choose a few individual representatives of every species for sequencing based on convenience (neighboring populations, herbarium specimens, samples provided by experts, garden plants). However, few studies are based on original material, type material or topotypic material (living specimens from the locality where the type material was collected). The use of type or topotypic material in phylogenetic studies is paramount particularly when taxonomy is complex, such as that of Antirrhinum (Plantaginaceae). In this paper, we used topotypic materials of Antirrhinum at the species level (34 species proposed by previous authors), 87 specimens representing the species distributions and >50,000 informative nucleotide characters (from ∼4,000 loci) generated by the genotyping-by-sequencing (GBS) technique: (i) to test two explicit taxonomic hypotheses widely followed by local taxonomic treatments; (ii) to robustly estimate phylogenetic relationships; (iii) to investigate the evolution of key morphological characters and biogeographic centers of differentiation. Two GBS phylogenies based on two datasets (87 localities and 34 topotypic specimens) revealed that: (1) Sutton’s (1988) taxonomic account is the most congruent with phylogenetic results, whereas division of Antirrhinum into three major clades disagrees with Rothmaler’s (1956) infrageneric classification; (2) monophyly of populations currently included in the same species is primarily supported; (3) the historically recognized Antirrhinum majus group is not monophyletic; (4) sister-group relationships are robust for eight species pairs; (5) the evolutionary radiation of 26 species since the Pliocene is underpinned given a high rate of diversification (0.54 spp. Myr); (6) a geographic pattern of speciation is reconstructed, with northern Iberia as the center of early diversification followed by more recent speciation in southeastern Iberia; and (7) multiple acquisitions o

The high diversification rates of plant lineages in the Mediterranean Basin hotspot have been linked to a complex interaction of climatic stressors, geographic isolation and soil type, but the question remains as to which of these factors has been the most significant environmental driver of recent speciation. Here, we draw on distributional data for the entire endemic flora of the Iberian Peninsula, together with DNA-based phylogenies and spatial phylogenetic methods, to explore the patterns of relative phylogenetic endemism at different spatial resolutions and phylogenetic scales (superclades) and assess how environmental factors contribute to explain these patterns. We found that recent diversification of angiosperms as a whole, and particularly of eudicots, has been boosted by environmental stressors including high values of soil pH and dry-seasonal climatic conditions, while diversification of monocots has not been associated with soil conditions but with high elevation and less seasonal climate. Synthesis. These results provide robust insights into the environmental factors driving recent plant diversification in the Mediterranean Basin, including a role of soil properties that had not been quantified before. The contrasting environmental drivers of diversification in eudicots and monocots highlight the importance of analysing spatial phylogenetic patterns at multiple phylogenetic scales to get a better understanding of the processes that shape biodiversity.

Accurate inference in phylogeography requires appropriate sampling strategies. Complex questions demand a large sample size at both the population and genetic levels to obtain precise reconstructions. This is the case of the phylogeographic history of Cistus monspeliensis, a plant that displays low plastid (cpDNA) diversity in the Mediterranean Basin but high diversity in the Canary Islands. Here, we aimed to identify Mediterranean refugial areas and to accurately quantify inter-island colonization events in the Canaries. Using a previous study as starting point, we increased sample size in two ways: (i) additional sampling of plastid genetic markers (from 1041 to 1899 bp); and (ii) additional sampling of populations (from 47 to 69) in long-term persistence areas suggested by species distribution modeling (SDM). The synergy between SDM and extended population sampling helped find higher genetic diversity. Our deeper phylogeographic sampling of C. monspeliensis revealed the following: (i) potential refugia in long-term persistence areas with high cpDNA diversity in western Europe and the Canary Islands; and (ii) a significant increase (from 7 to 12) in the number of inferred inter-island colonization events across the archipelago. Our results stress the usefulness of SDM to identify the genetic signature associated with potential refugial areas. We herein propose a field sampling approach based on SDM that, in combination with a larger cpDNA sampling, can help answer a wide array of phylogeographic questions, such as the location of Quaternary refugia and number of colonizations across archipelagos.