Search

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 the Mediterranean Basin. The complex temporal and geographic origin of Canarian thermophilous species challenges the view of the Canary Islands (and Madeira) as a subregion within the Mediterranean Floristic Region.

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., D.D.C. was supported by a Humboldt postdoctoral fellowship. J.C. was supported by a Research Council of Norway travel grant (project 287327). J.C. thanks Andy Foote for early input and ideas on what a review encompasses. The authors are extremely grateful to four anonymous reviewers and the editor whose thoughtful criticism led to a significant improvement of this manuscript. This publication is contribution number 2488 of the Charles Darwin Foundation for the Galapagos Islands.

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., This research was partially financed by the “Ministerio de Economía, Industria y Competitividad (Spain),” project VULBIMON (CGL2017‐90040‐R). FP‐G. was supported by the Youth Employment Initiative (European Social Fund and Community of Madrid; reference PEJ‐2018‐AI/ AMB‐10790).

Euphorbia canariensisis an iconic endemic species of the Canary Islands and one of the most characteristic species of lowland xerophytic communities known, in Spanish, as ‘cardonal-tabaibal’. This species is widely distributed in the archipelago, which contrasts with the theoretically low dispersal abilities suggested by its unspecialized diasporas. Furthermore, the phylogenetic relationships of this species are unclear, although it is thought to be related to the IndianE. epiphylloidesand not to other cactus-likeEuphorbiaof the Canary Islands (E. handiensis) and Africa. Here we aimed to reconstruct the evolutionary history ofE. canariensisat two levels: (i) a phylogenetic approach aimed at unravelling relationships of this species and large-scale biogeographic patterns, and (ii) a phylogeographic approach focused on the history of colonization between islands of the Canarian archipelago in relation to habitat availability for this species through time. Based on previous phylogenetic studies ofEuphorbia, we sequenced the ITS region forE. canariensisand several potentially related species to build a phylogenetic framework. We also sequenced two cpDNA regions for 92 individuals from 29 populations ofE. canariensisrepresenting its distribution range. We estimated the number of inter-island colonization events using PAICE, a recently developed method that includes a sampling effort correction. Additionally, we used species distribution modelling (SDM) to project current habitat availability forE. canariensisto past periods. Phylogenetic results supported the CanarianE. canariensisas closely related to the Southeast AsianE. epiphylloidesandE. sessiliflora. In the Canarian archipelago,E. canariensisdisplayed a surprising west-to-east colonization pattern. The estimated number of inter-island colonization events was c. 20 – 50, and SDM suggested an increase in habitat availability in recent times. In summary, in this study we confirmed an extreme biogeographic disjunction between Macaronesia and Southeast Asia, described only for a small number of plant species, and estimated relatively low dispersal capabilities forE. canariensis, with a west-to-east colonization pattern in the Canary Islands.HighlightsThe CanarianEuphorbia canariensisis sister to Southeast Asian species.This lineage shows one of the widest disjunctions affecting Macaronesian plants.The lack of intermediate relatives could be the result of extinction events.E. canariensisdisplays low colonization ability in the Canarian archipelago.

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, This study is part of projects CGL2015-67865-P and PGC2018-101650-B-I00, funded by the Spanish Ministry of Economy, Industry and Competitiveness. A.J.C. was supported by the Spanish Ministry of Education, Culture and Sport through an FPU fellow-ship (FPU16/05681) and a FPU mobility fellowship (EST18/00383). M.F.-M. was supported by a Juan de la Cierva fellowship (Spanish Ministry of Economy and Competitiveness; reference IJCI-2015-23459) and by a Special Intramural Project of the Spanish National Research Council (CSIC; reference 201930E078). R.H.H. was funded by the Portuguese Foundation for Science and Technology (grant: UID/BIA/04004/2021). No permits were needed for this study

The preference of certain plant species for gypsum soils 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 clade diversified in arid environments since the Miocene-Pliocene. This species represents the only extant lineage of this clade that colonized 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 Iberian Peninsula throughout the Quaternary.

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.

Una especie nueva de Linaria sect. Supinae en la Sierra de Gredos (Sistema Central, Península Ibérica)Linaria vettonica Luceño, Mazuecos & P. Vargas, a new species of Linaria sect. Supinae, is described. It is a narrow endemic inhabiting the southern hills of the western and central massifs of Sierra de Gredos (Sistema Central mountains, Iberian Peninsula). The five populations found occur on siliceous, sandy soils of Quercus pyrenaica woodland clearings and slopes. L. vettonica can be distinguished from Linaria caesia by the densely glandular-pubescent inflorescence, dark purple corolla and brown seeds with tuberculate disc, and from L. aeruginea by its erect fertile stems and dark purple -never blackishcorolla.Key words: Linaria, Sierra de Gredos, narrow endemic, taxonomy, seed micromorphology. ResumenSe describe Linaria vettonica Luceño, Mazuecos & P. Vargas, una nueva especie de Linaria sect. Supinae. Se trata de un endemismo restringido que se distribuye por las vertientes meridionales de los macizos occidental y central de la Sierra de Gredos (Sistema Central, Península Ibérica). Las cinco poblaciones encontradas aparecieron sobre suelos arenosos silíceos en claros y laderas de bosques de Quercus pyrenaica. L. vettonica se distingue de L. caesia por sus inflorescencias densamente glandular-pubescentes, corolas de color púrpura oscuro y semillas marrones con disco ornamentado con numerosos tubérculos. De L. aeruginea se distingue por sus tallos fértiles erectos y sus flores de color púrpura oscuro, nunca negruzcas.Palabras clave: Linaria, sierra de Gredos, endemismo restringido, taxonomía, micromorfología de semillas.

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–1); (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 of key taxonomic characters in the course of Antirrhinum diversification are strongly supported, with no evidence of hybridization between major clades. Our results also suggest incipient speciation in some geographic areas and point to future avenues of research in evolution and systematics of Antirrhinum.

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.

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.

Geography and climate have been the main drivers of evolution in recent geological epochs. While new lineages of species have been formed in the last millions of years (speciation) and others have vanished as a result of historical climate changes (extinction), some ancient lineages appear to have persisted to the present day without net diversification. In this paper, evolution of ancient lineages is addressed by combining phylogenetic and conservation approaches to test the concept of ‘endangered living fossil’ (ELF). Using endangered, monospecific genera as starting point, we propose three criteria to identify ELFs (in order): (1) scarcity and narrow distribution of populations, i.e. the species (and thus the genus) is categorised as either ‘endangered’ or ‘critically endangered’ using IUCN criteria; (2) evolutionary distinctiveness, i.e. phylogenetic singularity of a single-species lineage as a result of a null net diversification rate; (iii) ancient divergence, i.e. split from the closest extant relatives predating the dramatic climate changes of particular geological epochs (specifically changes since the Miocene-Pliocene boundary). The vascular flora of the Iberian Peninsula offers a suitable study system to reliably test the ELF concept. Indeed, time-calibrated phylogenies revealed that five of the six critically endangered, monospecific genera endemic to the Iberian Peninsula are ELFs. These five genera appear to have diverged from their closest relatives in the Oligocene (Gyrocaryum), Miocene (Avellara, Castrilanthemum, Gadoria) and around the Miocene-Pliocene boundary (Naufraga). This result entails long-term survival (with no net diversification) through at least three dramatic climate changes: the Messinian Salinity Crisis (late Miocene), the establishment of the mediterranean climate (Pliocene), and the glacial-interglacial cycles (Pleistocene). Using results from the literature, we found examples of ELFs for the mediterranean floras of California (Dodecahema), Chile (Avellanita, Gomortega, Legrandia) and other Mediterranean areas of Europe (Petagnaea, Phitosia). ELFs are unique and threatened lineages representing an exceptional evolutionary heritage, and therefore they should be prioritised in biodiversity research and conservation programs.

Peripheral populations (i.e., those occurring on the edge of a species’ distribution range) can have different origins and genetic characteristics, and they may be critical for the conservation of genetic diversity. We investigated European peripheral populations of Scrophularia arguta, a widespread, annual plant distributed from Arabia to Northwest Africa and Macaronesia. Only two small disjunct population groups of this species occur in Europe, specifically in West-Central and Southeast Iberia. To disclose the origin of these populations and determine their importance for the conservation of S. arguta genetic diversity, we analyzed DNA sequences from two nuclear and two plastid regions and amplified fragment length polymorphism markers in populations sampled mainly across the western distribution range of the species, and modeled the species distribution under present and late Quaternary conditions. The analyses revealed the presence of three distinct lineages of S. arguta in Europe, as a result of multiple colonization waves at different times in the Quaternary. Two of these lineages, occurring in Southeast Iberia, are the result of more or less recent dispersal from Northwest Africa. In contrast, West-Central Iberian populations are strongly differentiated from the remaining range of S. arguta and can be considered as peripheral relict populations. Our study is the first to demonstrate the occurrence of at least three colonizations of the European continent from Africa by a native plant species. The diverse histories and genetic makeup of the resulting populations confirm the importance of peripheral populations, and particularly of ancient relict populations, for the conservation of global genetic diversity in widespread species.

AimThe tribe Antirrhineae, including snapdragons, toadflaxes and relatives, is a model group for plant evolutionary research. It is widely distributed across the Northern Hemisphere and the Neotropics, but displays an uneven distribution of diversity, with more than 50% of species and subspecies in the Mediterranean Region. Here we conducted the first detailed, worldwide biogeographic analysis of the Antirrhineae and tested two alternative hypotheses (time-for-speciation vs. diversification rate differences) to explain the uneven distribution of diversity.LocationWorldwide, with a focus on the Mediterranean Region.Taxontribe Antirrhineae (Plantaginaceae).MethodsA phylogenetic biogeographic approach was taken, accounting for area connections through time. Ancestral ranges, dispersal events, speciation and lineage accumulation within areas were estimated. Diversification rates for taxa present and absent in the Mediterranean Region were compared, accounting for the effect of a floral key innovation (nectar spur).ResultsA proto-Mediterranean origin in the Late Eocene was estimated, and the Mediterranean Region stood out as the main centre for speciation and dispersal. Congruent patterns of long-distance dispersal from the Mediterranean Region to North America were recovered for at least two amphiatlantic clades. A significant floristic exchange between the Mediterranean and south-western Asia was detected. We found no evidence of different diversification rates between lineages inside and outside the Mediterranean Region.Main conclusionsThe Mediterranean Region played a key role in the origin of the current distribution of the Antirrhineae. However, the higher species richness found in this region appears to be the result of a time-for-speciation effect rather than of increased diversification rates. The establishment of current mediterranean climates in the Northern Hemisphere appears to have contributed to the recent diversification of the group, in combination with colonisation of adjacent regions with arid and semi-arid climates.

Poor morphological and molecular differentiation in recently diversified lineages is a widespread phenomenon in plants. Phylogenetic relationships within such species complexes are often difficult to resolve because of the low variability in traditional molecular loci. Furthermore, biological phenomena responsible for topological incongruence such as Incomplete Lineage Sorting (ILS) and hybridisation complicate the resolution of phylogenetic relationships among closely related taxa. In this study, we employ a Genotyping-by-sequencing (GBS) approach to disentangle evolutionary relationships within a species complex belonging to the Neotropical orchid genus Cycnoches. This complex includes seven taxa distributed through Central America and the Colombian Chocó, and is nested within a clade estimated to have first diversified in the early Quaternary. Previous phylogenies inferred from few loci failed to provide support for internal relationships within the complex. Our Neighbour-net and coalescent-based analyses inferred from ca. 13,000 GBS loci obtained from 31 individuals belonging to six of the seven traditionally accepted Cycnoches taxa provided a robust phylogeny for this group. The genus Cycnoches includes three main clades that are further supported by morphological traits and geographic distributions. Similarly, a topology reconstructed through maximum likelihood (ML) inference of concatenated GBS loci produced results that are comparable with those reconstructed through coalescence and network-based methods. Our comparative phylogenetic informativeness analyses suggest that the low support evident in the ML phylogeny might be attributed to the abundance of uninformative GBS loci, which can account for up to 50% of the total number of loci recovered. The phylogenomic framework provided here, as well as morphological evidence and geographical patterns, suggest that the six entities previously thought to be different species or subspecies might actually represent only three distinct segregates. We further discuss the limited phylogenetic informativeness found in our GBS approach and its utility to disentangle relationships within recent and rapidly evolving species complexes. Our study is the first to demonstrate the utility of GBS data to reconstruct relationships within young (~2 Ma) Neotropical plant clades, opening new avenues for studies of species complexes that populate the species-rich orchid family UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL)

Drosophyllaceae is the only plant family endemic to the Mediterranean Floristic Region. It includes a single species, the carnivorous Drosophyllum lusitanicum, which is hypothesised to be a relict plant. Our aim here is to reconstruct the evolutionary history of Drosophyllum to evaluate whether the African-European disjunction across the Strait of Gibraltar is the result of vicariance or long-distance dispersal, and to assess the role of the Strait of Gibraltar area in the long-term persistence of this species. A time-calibrated phylogeny based on nuclear ITS sequences estimated a mid-Eocene to mid-Miocene age (19–44 Mya) for the common ancestor of Drosophyllaceae and its sister clade (Ancistrocladaceae-Dioncophyllaceae). In contrast, differentiation of ITS lineages of Drosophyllum occurred in the Pleistocene, after the opening of the Strait of Gibraltar (ca. 5 Mya). A haplotype network built using two plastid DNA regions revealed six haplotypes in Drosophyllum, five of which occur in the Strait of Gibraltar area. Four of the six haplotypes were present in both European and African populations. Therefore, although Drosophyllaceae diverged from the closest relatives in ancient times, the current distribution of Drosophyllum is relatively recent (Pleistocene). Given that the Strait of Gibraltar was already open in the Pliocene, the disjunct distribution of this species between Europe and Africa appears to be the result of multiple events of long-distance dispersal. Species distribution modelling (SDM) was used to reconstruct the potential distribution of Drosophyllum throughout the late Quaternary (last interglacial, Last Glacial Maximum, mid-Holocene and present), which revealed long-term persistence around the Strait of Gibraltar and in the south-western Iberian Peninsula. The Strait of Gibraltar area and the south-western Iberian Peninsula may have shared similar climatic conditions, and thus acted as refugia for Drosophyllum throughout the late Quaternary.

Iberodes M. Serrano, R. Carbajal & S. Ortiz es un genero de Boraginaceas subendemico de la peninsula Iberica, con poblaciones disyuntas en Francia (region sureste y costa oeste en el Golfo de Vizcaya). Este genero comprende cinco especies de plantas anuales (una de ellas con dos subespecies), originalmente consideradas dentro del genero Omphalodes (Serrano et al., 2016). Si tenemos en cuenta la especializacion ecologica de las cinco especies, el genero se puede dividir en dos grupos: por un lado, tres especies de ambientes continentales del interior; y por otro, dos especies litorales que viven sobre dunas costeras. Otra peculiaridad anadida de este genero es que cuatro de las cinco especies estan catalogadas dentro de las categorias de riesgo y amenaza de la UICN, y tres de ellas cuentan con proteccion legal de acuerdo con los catalogos regionales de Castilla y Leon y Galicia, el Catalogo Espanol, la Directiva de Habitats y el Convenio de Berna

SUMMARYTraditional classification of speciation modes has focused on physical barriers to gene flow. While allopatry has been viewed as the most common mechanism of speciation, parapatry and sympatry, both entail speciation in the face of ongoing gene flow and thus both are far more difficult to detect and demonstrate.Iberodes(Boraginaceae, NW Europe) with a small number of recently derived species (five) and contrasting morphological traits, habitats and distribution patterns constitutes an ideal system in which to study drivers of lineage divergence and differentiation.To reconstruct the evolutionary history of the genus, we undertook an integrative study entailing: (i) phylogenomics based on restriction-site associated DNA sequencing (RAD-seq), (ii) morphometrics, and (iii) climatic niche modelling.Key results revealed a history of repeated progenitor-derivative speciation, manifesting in paraphyletic pattern withinIberodes. Climatic niche analyses, together with the morphometric data and species distributions, suggest that ecological and geographical differentiation have interacted to shape the diversity of allopatric and parapatric distributions observed inIberodes.Our integrative study has enabled to overcome previous barriers to understanding parapatric speciation by demonstrating the recurrence of progenitor-derivative speciation in plants with gene flow and ecological differentiation, explaining observed parapatry and paraphyly.

Critically endangered species representing ancient, evolutionarily isolated lineages must be given priority when allocating resources for conservation projects. Sound phylogenetic analyses and divergence time estimations are required to detect them, and studies on their population genetics, ecological requirements and breeding system are needed to understand their evolutionary history and to design efficient conservation strategies. Here we present the paradigmatic case of Avellara, a critically endangered monotypic genus of Compositae inhabiting a few swamps in the west-southwest Iberian coastal plains. Our phylogenetic and dating analyses based on nuclear (ITS) and plastid (matK) DNA sequences support a Miocene (>8.6 Ma) divergence between Avellara and closely related genera, resulting in marked morphological and ecological differentiation. We found alarmingly low levels of genetic diversity, based on AFLPs and plastid DNA sequences, and confirmed the prevalence of clonal reproduction. Species distribution modelling suggested a large macroclimatically suitable area for Avellara in the western Iberian Peninsula, but its apparently narrow microecological requirements restrict its distribution to peatlands with low-mineralised waters. Although five populations have been recorded from Spain and Portugal in the past, its current distribution may be reduced to only one population, recurrently found in the last decade but threatened by herbivory and habitat degradation. All this confirms the consideration of Avellara as a threatened species with high phylogenetic singularity, and makes it a flagship species for plant conservation in both Spain and Portugal that should be given priority in the design of in situ and ex situ conservation programmes.

Floral nectar spurs are widely considered a key innovation promoting diversification in angiosperms by means of pollinator shifts. We investigated the macroevolutionary dynamics of nectar spurs in the tribe Antirrhineae (Plantaginaceae), which contains 29 genera and 300–400 species (70–80% spurred). The effect of nectar spurs on diversification was tested, with special focus on Linaria, the genus with the highest number of species. We generated the most comprehensive phylogeny of Antirrhineae to date and reconstructed the evolution of nectar spurs. Diversification rate heterogeneity was investigated using trait-dependent and trait-independent methods, and accounting for taxonomic uncertainty. The association between changes in spur length and speciation was examined within Linaria using model testing and ancestral state reconstructions. We inferred four independent acquisitions of nectar spurs. Diversification analyses revealed that nectar spurs are loosely associated with increased diversification rates. Detected rate shifts were delayed by 5–15 Myr with respect to the acquisition of the trait. Active evolution of spur length, fitting a speciational model, was inferred in Linaria, which is consistent with a scenario of pollinator shifts driving diversification. Nectar spurs played a role in diversification of the Antirrhineae, but diversification dynamics can only be fully explained by the complex interaction of multiple biotic and abiotic factors., This work was supported by the Marie Curie Intra‐European Fellowship LINARIA‐SPECIATION (FP7‐PEOPLE‐2013‐IEF, reference 624396), an Isaac Newton Trust Research Grant (Trinity College, Cambridge), a Juan de la Cierva fellowship to MF‐M (Spanish Ministry of Economy and Competitivity, reference IJCI‐2015‐23459) and a Generalitat Valenciana postdoctoral grant to AJ (Ministry of Education, Culture and Sport, reference BEST/2014/264).

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., This research was funded by grants CGL2014-52459-P and CGL2017-82465-P from the Spanish Ministerio de Economía y Competitividad to AA. SM-H is currently funded by the Spanish Secretaría de Estado de Investigación, Desarrollo e Innovación (FPI fellowship, 2015). MF-M was supported by a Juan de la Cierva fellowship (Spanish Ministerio de Economía, Industria y Competitividad, reference IJCI-2015-23459

Poor morphological and molecular differentiation in recently diversified lineages is a widespread phenomenon in plants. Phylogenetic relationships within such species complexes are often difficult to resolve because of the low variability in traditional molecular loci, as well as various other biological phenomena responsible for topological incongruence such as ILS and hybridization. In this study, we employ a Genotyping-by-sequencing (GBS) approach to disentangle evolutionary relationships within a species complex belonging to the Neotropical orchid genus Cycnoches. The complex includes seven taxa distributed in Central America and the adjacent Chocó biogeographic region, nested within a clade estimated to have first diversified in the early Quaternary. Previous phylogenies inferred from a handful of loci failed to provide support for internal relationships within the complex. Our Neighbor-net and coalescent-based analyses inferred from ca. 13,000 GBS loci obtained from 31 individuals belonging to six of the seven traditionally accepted Cycnoches species provided a robustly supported network. The resulting three main clades are corroborated by morphological traits and geographical distributions. Similarly, Maximum Likelihood (ML) inferences of concatenated GBS-loci produced results comparable with those derived from coalescence and network-based methods, albeit always with poor statistical support. The low support evident in the ML phylogeny might be attributed to the abundance of uninformative GBS loci, which can account for up to 50% of the total number of loci recovered. The phylogenomic framework provided here, as well as morphological evidence and geographical patterns, suggest that the six entities previously thought to be different species might actually represent only three distinct segregates. Our study is the first to demonstrate the utility of GBS data in phylogenomic research of a very young Neotropical plant clade (~2 Ma), and it paves the way for the study of the many other species complexes that populate the species-rich orchid family.

Disentangling species boundaries and phylogenetic relationships within recent evolutionary radiations is a challenge due to the poor morphological differentiation and low genetic divergence between species, frequently accompanied by phenotypic convergence, interspecific gene flow and incomplete lineage sorting. Here we employed a genotyping-by-sequencing (GBS) approach, in combination with morphometric analyses, to investigate a small western Mediterranean clade in the flowering plant genus Linaria that radiated in theQuaternary.After confirming the morphological and genetic distinctness of eight species, we evaluated the relative performances of concatenation and coalescent methods to resolve phylogenetic relationships. Specifically, we focused on assessing the robustness of both approaches to variations in the parameter used to estimate sequence homology (clustering threshold). Concatenation analyses suffered from strong systematic bias, as revealed by the high statistical support for multiple alternative topologies depending on clustering threshold values. By contrast, topologies produced by two coalescent-based methods (NJst, SVDquartets) were robust to variations in the clustering threshold. Reticulate evolution may partly explain incongruences between NJst, SVDquartets and concatenated trees. Integration of morphometric and coalescent-based phylogenetic results revealed (i) extensive morphological divergence associated with recent splits between geographically close or sympatric sister species and (ii) morphological convergence in geographically disjunct species. These patterns are particularly true for floral traits related to pollinator specialization, including nectar spur length, tube width and corolla color, suggesting pollinatordriven diversification. Given its relatively simple and inexpensive implementation, GBS is a promising technique for the phylogenetic and systematic study of recent radiations, but care must be taken to evaluate the robustness of results to variation of data assembly parameters., This work was supported by the Marie Curie Intra-European Fellowship LINARIA-SPECIATION (FP7-PEOPLE-2013-IEF, project reference 624396) and an Isaac Newton Trust Research Grant (Trinity College, Cambridge)

Biogeographic hypotheses for the flora of Macaronesia have been subject of numerous studies given the singularity of a complex system of Atlantic volcanic islands. Phylogenetic analyses, divergence time estimates and biogeographic reconstructions of 10 Scrophularia species and subspecies distributed in Macaronesia and adjacent regions have been conducted in order to investigate the spatio-temporal patterns of island colonization. The Colonization Window Hypothesis (CWH) and the Relictual Series Hypothesis (RSH) proposed by previous authors were tested. Species and lineages relationships were analyzed based on one nuclear (ITS) and three plastid ( trn L- trn F, psb A- trn H, trn Q- rps 16) DNA regions, and using Bayesian inference and maximum likelihood methods. Biogeographic reconstructions were performed using specific maximum-likelihood (DEC) and parsimony-based (S-DIVA) methods. Our results supported at least five independent colonization events from the W Mediterranean to Macaronesian archipelagos by Scrophularia lineages. These events were the result of long-distance dispersal over sea barriers despite the unspecialized diaspores of Scrophularia . In addition, the colonization history of Macaronesian lineages of Scrophularia is better explained by the Colonization Window Hypothesis based on the geographical proximity of Macaronesian–W Mediterranean sister groups and the wide range of colonization times.

Linaria incarnata has been treated as a widely distributed Ibero-North African species in the latest taxonomic reviews. Morphological and phylogenetic disparity between populations of this species has been previously reported. Here we present new morphological and phylogenetic evidence for the disintegration of L. incarnata into three distinct species: L. incarnata from the western Iberian Peninsula; L. mamorensis sp. nov. from north-western Morocco; and L. onubensis from south-western Spain. The relatively poor morphological differentiation between these taxa (which can be regarded as cryptic species) and their distinct phylogenetic positions indicate that characters of the L. incarnata morphotype have been acquired multiple times in the evolution of Linaria section Versicolores. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 00, 000–000.

Integrative taxonomy, based on the combination of multiple lines of evidence, provides the foundations for a robust species delimitation. Here we provide a taxonomic synopsis of the Iberian clade of Linaria subsect. Versicolores based on recently published morphometric and phylogenomic data. This clade radiated in the Iberian Peninsula (western Mediterranean) during the Quaternary and is being intensively studied from phylogenetic, evolutionary, biogeographic, ecological and developmental standpoints. Eight morphologically and genetically distinct species are recognised in the clade: L. algarviana, L. becerrae, L. clementei, L. incarnata, L. onubensis, L. salzmannii, L. spartea and L. viscosa. For each accepted species, the type material and notes on diagnostic characters, distribution, habitat and intraspecific variability are provided. Five names are typified (four neotypes and one lectotype are designated), and references to previous typifications are also presented. A distribution map and an identification key are presented. This synopsis will provide the basis for future research on speciation and evolution of the clade.

A review of 27 angiosperm clades (26 genera) of species-rich and species-poor plant groups of the Mediterranean floristic region was performed with phylogenetic and biological trait data. The emergent pattern is that a majority of Mediterranean plant clades split from their sister groups between the Miocene (23-5 Ma) and the Oligocene (34-23 Ma), far earlier than the onset of the Mediterranean climate (ca. 3.2 Ma). In addition, 12 of 14 clades of the species-poor group have stem ages inferred for each clade in the Miocene or older, and six of 13 clades within the species-rich group show divergence of each stem clade within the Oligocene and/or Miocene. High levels of species diversity are related to an ancient (Paleocene-Miocene) origin and also to recent origin (Pliocene-Pleistocene) followed by active speciation and even explosive radiations: some species and lineages diversified over a short period (Aquilegia, Cistus, Dianthus, Linaria sect. Supinae, Reseda). In the species-rich group, key reproductive characters were found to be significantly more important for species recognition than key vegetative characters in eight clades, but no difference was found in four clades, and vegetative characters were predominant in one clade (Saxifraga). Geographical differentiation is proposed as predominant over divergence driven by pollination ecology. We hypothesise an evolutionary process in which lineages adapted to pre-Mediterranean (pre-Pliocene) conditions in relatively small, xeric areas became strongly competitive and expanded as the Mediterranean climate became dominant (Pliocene-Quaternary) across the Mediterranean Basin.

Background and Aims Nectar spurs (tubular outgrowths of a floral organ which contain, or give the appearance of containing, nectar) are hypothesized to be a ‘key innovation’ which can lead to rapid speciation within a lineage, because they are involved in pollinator specificity. Despite the ecological importance of nectar spurs, relatively little is known about their development. We used a comparative approach to investigate variation in nectar spur length in a clade of eight Iberian toadflaxes. Methods Spur growth was measured at the macroscopic level over time in all eight species, and growth rate and growth duration compared. Evolution of growth rate was reconstructed across the phylogeny. Within the clade we then focused on Linaria becerrae and Linaria clementei, a pair of sister species which have extremely long and short spurs, respectively. Characterization at a micromorphological level was performed across a range of key developmental stages to determine whether the difference in spur length is due to differential cell expansion or cell division. Key Results We detected a significant difference in the evolved growth rates, while developmental timing of both the initiation and the end of spur growth remained similar. Cell number is three times higher in the long spurred L. becerrae compared with L. clementei, whereas cell length is only 1.3 times greater. In addition, overall anisotropy of mature cells is not significantly different between the two species. Conclusions We found that changes in cell number and therefore in cell division largely explain evolution of spur length. This contrasts with previous studies in Aquilegia which have found that variation in nectar spur length is due to directed cell expansion (anisotropy) over variable time frames. Our study adds to knowledge about nectar spur development in a comparative context and indicates that different systems may have evolved nectar spurs using disparate mechanisms.

Castrilanthemum debeauxii is a critically endangered annual plant narrowly distributed in mountains of SE Iberia. It occurs in spiny scrublands on limestone soils dominated by Erinacea anthyllis at medium altitudes. Phylogenetic results indicate that the monotypic Castrilanthemum constitutes a paleoendemic lineage that diverged from its closest extant relatives in the Miocene. To achieve a better understanding of its recent evolution and conservation status, we performed an analysis of genetic variation and structure of four subpopulations using plastid haplotypes and AFLPs. We also investigated additional characteristics (ecological requirements, reproductive biology, pre-dispersal seed predation) that are relevant to evaluate the conservation status of the species. Castrilanthemum was found to be a facultative selfer with no major germination limitations. We detected moderate levels of genetic diversity based on AFLPs and plastid DNA sequences. The low genetic structure found for both nuclear and plastid markers, together with species distribution modeling results, pointed to high gene flow, which might counteract processes of genetic erosion caused by the low number of individuals. We found significant levels of pre-dispersal seed predation by the burrowing larvae of a tephritid fly, which may have contributed to the decline of the populations. Based on our results, we suggest directions for the management of Castrilanthemum. In particular, we recommend seeding and collection of seeds for banks, and discuss the possibilities of population reinforcement and reintroduction in localities where the species is currently extinct., This research was funded by Banco Santander, the Spanish National Research Council (CSIC) and Fundación General CSIC (FGCSIC) through a Proyecto Cero on endangered species 2010 (“Do all endangered species hold the same value?: origin and conservation of living fossils of flowering plants endemic to Spain”).

Plants growing in high-mountain environments may share common morphological features through convergent evolution resulting from an adaptative response to similar ecological conditions. The Carex flava species complex (sect. Ceratocystis, Cyperaceae) includes four dwarf morphotypes from Circum-Mediterranean mountains whose taxonomic status has remained obscure due to their apparent morphological resemblance. In this study we investigate whether these dwarf mountain morphotypes result from convergent evolution or common ancestry, and whether there are ecological differences promoting differentiation between the dwarf morphotypes and their taxonomically related large, well-developed counterparts. We used phylogenetic analyses of nrDNA (ITS) and ptDNA (rps16 and 5'trnK) sequences, ancestral state reconstruction, multivariate analyses of macro- and micromorphological data, and species distribution modeling. Dwarf morphotype populations were found to belong to three different genetic lineages, and several morphotype shifts from well-developed to dwarf were suggested by ancestral state reconstructions. Distribution modeling supported differences in climatic niche at regional scale between the large forms, mainly from lowland, and the dwarf mountain morphotypes. Our results suggest that dwarf mountain morphotypes within this sedge group are small forms of different lineages that have recurrently adapted to mountain habitats through convergent evolution.

Speciation research bridges the realms of macro- and microevolution. Evolutionary developmental biology (evo-devo) has classically dealt with macroevolutionary questions through a comparative approach to distantly related organisms, but the field later broadened in focus to address recent speciation and microevolution. Here we review available evidence of the power of evo-devo approaches to understand speciation in plants at multiple scales. At a macroevolutionary scale, evidence is accumulating for evolutionary developmental mechanisms giving rise to key innovations promoting speciation. At the macro microevolution transition, we review instances of evo-devo change underlying both the origin of reproductive barriers and phenotypic changes distinguishing closely related species. At the microevolutionary scale, the study of developmental variation within species provides insight into the processes that generate the raw material for evolution and speciation. We conclude by advocating a strong interaction between developmental biology and evolutionary biology at multiple scales to gain a deeper understanding of plant speciation.