Palaeo-islands as refugia and sources of genetic diversity within volcanic archipelagos: the case of the widespread endemicCanarina canariensis(Campanulaceae)

Inter and intra-island genetic structure and differentiation of the endemic Bolle's Laurel Pigeon (Columba bollii) in the Canary archipelago

Islands provide excellent settings for studying the evolutionary history of species, since their geographic isolation and relatively small size limit gene flow between populations, and promote divergence and speciation. The endemic Bolle's Laurel Pigeon Columba bollii is an arboreal frugivorous bird species distributed on laurel forests in four islands of the Canary archipelago. To elucidate the population genetics, we genotyped ten microsatellite loci using DNA obtained from non-invasive samples collected across practically all laurel forest remnants, and subsequently grouped into eight sampling sites. Analyses including F-statistics, Bayesian clustering approaches, isolation by distance tests and population graph topologies, were used to infer the genetic diversity and the population differentiation within and among insular populations. Additionally, we evaluated the effect of null alleles on data analysis. Low genetic diversity was found in all populations of Bolle's Laurel Pigeon, with no significant differences in diversity among them. However, significant genetic differentiation was detected among all populations, with pigeons from La Palma and El Hierro exhibiting the closest affinity. Bayesian clustering supported population separation between islands, and also detected fine-scale structure within the Tenerife and La Gomera populations. Our results suggest that, despite columbids have a high movement ability, they can show signature of genetic divergence among populations, particularly on oceanic islands. Geological history of the islands and distribution range of habitats could have close influence on the evolutionary trajectories of these birds. This approach can provide practical tools to implement appropriate conservation measures for range-restricted species and their habitat.

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

Astydamia latifolia is the only species of the genus Astydamia, which forms an early-diverging lineage of Apiaceae, subfamily Apioideae. This species is subendemic to the Canary Islands and one of the most representative species of the coastal environments of this archipelago. Astydamia displays diplochory, that is, diaspores with two long-distance dispersal (LDD) syndromes. In particular, A. latifolia has both anemochorous and thalassochorous fruit traits (corky and winged mericarps). Although we expect this species to have a high dispersal capacity, there is no genetic study addressing it. The divergence time of this species from its sister taxon is also unknown. In this study, we aimed (i) to unveil the phylogenetic relationships and divergence times of A. latifolia; (ii) to reconstruct its phylogeographic structure across the Canary Islands; and (iii) to estimate the number of inter-island colonization events. To these ends, we first sequenced the internal transcribed spacer (ITS) region for A. latifolia, reconstructed the phylogenetic relationships of Astydamia and Apiaceae relatives and estimated divergence times. Then, two plastid DNA regions (psaI-aacD and psbK-trnS) were sequenced for 158 individuals (from 36 Canarian population and one NW African population) to reconstruct a haplotype network. The recently developed method Phylogeographic Analysis of Island Colonization Events (PAICE) was used to estimate the number of inter-island colonization events. Results show that A. latifolia is a phylogenetically isolated lineage that diverged from the most closely related genus (Molopospermum) in the Eocene-Miocene. It displays a low plastid DNA diversity (only four haplotypes detected), which is accompanied by a high degree of haplotype sharing between islands and highly linear rarefaction curves of colonization obtained in PAICE. These findings suggest a high colonization ability for this species, most likely related to the availability of two LDD syndromes.

Molecular analyses of the Kalotermes dispar-complex (Blattodea: Kalotermitidae) from the Canary Islands reveal cryptic intraspecific divergence and a connection to a lone Nearctic congener

The Canary Islands is a Macaronesian volcanic archipelago with a depauperate community of three species of Kalotermitidae, including Kalotermes dispar. A total of 54 Kalotermes colonies were collected from Gran Canaria, Tenerife, La Gomera, La Palma, and El Hierro islands. Soldiers and imagos were morphologically examined and sequenced for four mitochondrial markers. Although morphological differences could not be detected, phylogenetic analysis of both cox1/tRNA/cox2 and rrnL markers revealed two distinct clades of K. dispar, suggesting cryptic diversity. The diversification within the Canary Kalotermes lineage most likely occurred around 7.5 Mya, while the divergence within the two clades was reconstructed at about 3.6 Mya and 1.9 Mya. Kalotermes approximatus from the southeastern Nearctic constitutes a sister to the Canary Kalotermes, while the Palearctic K. flavicollis, K. italicus, and K. phoenicae form a separate clade. It is hypothesized that a faunal exchange of Kalotermes from the Nearctic to the Canary Islands occurred via transoceanic rafting during the mid-Miocene.

The sweet tabaiba or there and back again: phylogeographical history of the Macaronesian Euphorbia balsamifera

BACKGROUND AND AIMS

Biogeographical relationships between the Canary Islands and north-west Africa are often explained by oceanic dispersal and geographical proximity. Sister-group relationships between Canarian and eastern African/Arabian taxa, the 'Rand Flora' pattern, are rare among plants and have been attributed to the extinction of north-western African populations. Euphorbia balsamifera is the only representative species of this pattern that is distributed in the Canary Islands and north-west Africa; it is also one of few species present in all seven islands. Previous studies placed African populations of E. balsamifera as sister to the Canarian populations, but this relationship was based on herbarium samples with highly degraded DNA. Here, we test the extinction hypothesis by sampling new continental populations; we also expand the Canarian sampling to examine the dynamics of island colonization and diversification.

METHODS

Using target enrichment with genome skimming, we reconstructed phylogenetic relationships within E. balsamifera and between this species and its disjunct relatives. A single nucleotide polymorphism dataset obtained from the target sequences was used to infer population genetic diversity patterns. We used convolutional neural networks to discriminate among alternative Canary Islands colonization scenarios.

KEY RESULTS

The results confirmed the Rand Flora sister-group relationship between western E. balsamifera and Euphorbia adenensis in the Eritreo-Arabian region and recovered an eastern-western geographical structure among E. balsamifera Canarian populations. Convolutional neural networks supported a scenario of east-to-west island colonization, followed by population extinctions in Lanzarote and Fuerteventura and recolonization from Tenerife and Gran Canaria; a signal of admixture between the eastern island and north-west African populations was recovered.

CONCLUSIONS

Our findings support the Surfing Syngameon Hypothesis for the colonization of the Canary Islands by E. balsamifera, but also a recent back-colonization to the continent. Populations of E. balsamifera from northwest Africa are not the remnants of an ancestral continental stock, but originated from migration events from Lanzarote and Fuerteventura. This is further evidence that oceanic archipelagos are not a sink for biodiversity, but may be a source of new genetic variability.

Phylogenetics and phylogeography of Euphorbia canariensis reveal an extreme Canarian-Asian disjunction but limited inter-island colonization

Euphorbia canariensis is an iconic endemic species representative of the lowland xerophytic communities of the Canary Islands. It is widely distributed in the archipelago despite having diasporas unspecialized for long-distance dispersal. Here, we reconstructed the evolutionary history of E. canariensis at two levels: a time-calibrated phylogenetic analysis aimed at clarifying interspecific relationships and large-scale biogeographic patterns; and a phylogeographic study focused on the history of colonization across the Canary Islands. For the phylogenetic study, we sequenced the ITS region for E. canariensis and related species of Euphorbia sect. Euphorbia. For the phylogeographic study, we sequenced two cpDNA regions for 28 populations representing the distribution range of E. canariensis. The number of inter-island colonization events was explored using PAICE, a recently developed method that includes a sample size correction. Additionally, we used species distribution modelling (SDM) to evaluate environmental suitability for E. canariensis through time. Phylogenetic results supported a close relationship between E. canariensis and certain Southeast Asian species (E. epiphylloides, E. lacei, E. sessiliflora). In the Canaries, E. canariensis displayed a west-to-east colonization pattern, not conforming to the "progression rule", i.e. the concordance between phylogeographic patterns and island emergence times. We estimated between 20 and 50 inter-island colonization events, all of them in the Quaternary, and SDM suggested a late Quaternary increase in environmental suitability for E. canariensis. The extreme biogeographic disjunction between Macaronesia and Southeast Asia (ca. 11,000 km) parallels that found in a few other genera (Pinus, Dracaena). We hypothesize that these disjunctions are better explained by extinction across north Africa and southwest Asia rather than long-distance dispersal. The relatively low number of inter-island colonization events across the Canaries is congruent with the low dispersal capabilities of E. canariensis.

Parallel anagenetic patterns in endemic Artemisia species from three Macaronesian archipelagos

Anagenetic speciation is an important mode of evolution in oceanic islands, yet relatively understudied compared to adaptive radiation. In the Macaronesian region, three closely related species of Artemisia (i.e. A. argentea, A. thuscula and A. gorgonum) are each endemic from a single archipelago (i.e. Madeira, Canary Islands and Cape Verde, respectively), representing a perfect opportunity to study three similar but independent anagenetic speciation processes. By analysing plastid and nuclear DNA sequences, as well as nuclear DNA amount data, generated from a comprehensive sampling in all the islands and archipelagos where these species are currently distributed, we intend to find common evolutionary patterns that help us explain the limited taxonomic diversification experienced by endemic Macaronesian Artemisia. Our time-calibrated phylogenetic reconstruction suggested that divergence among the three lineages occurred in a coincidental short period of time during the Pleistocene. Haplotype and genetic differentiation analyses showed similar diversity values among A. argentea, A. thuscula and A. gorgonum. Clear phylogeographic patterns-showing comparable genetic structuring among groups of islands-were also found within the three archipelagos. Even from the cytogenetic point of view, the three species presented similarly lower genome size values compared to the mainland closely related species A. arborescens. We hypothesize that the limited speciation experienced by the endemic Artemisia in Madeira, Canary Islands and Cape Verde archipelagos could be related to their recent parallel evolutionary histories as independent lineages, combined with certain shared characteristics of seed dispersal, pollen transport and type of habitat.

Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos

Biological invasions in remote areas that experience low human activity provide unique opportunities to elucidate processes responsible for invasion success. Here we study the most widespread invasive plant species across the isolated islands of the Southern Ocean, the annual bluegrass, Poa annua. To analyse geographical variation in genome size, genetic diversity and reproductive strategies, we sampled all major sub-Antarctic archipelagos in this region and generated microsatellite data for 470 individual plants representing 31 populations. We also estimated genome sizes for a subset of individuals using flow cytometry. Occasional events of island colonization are expected to result in high genetic structure among islands, overall low genetic diversity and increased self-fertilization, but we show that this is not the case for P. annua. Microsatellite data indicated low population genetic structure and lack of isolation by distance among the sub-Antarctic archipelagos we sampled, but high population structure within each archipelago. We identified high levels of genetic diversity, low clonality and low selfing rates in sub-Antarctic P. annua populations (contrary to rates typical of continental populations). In turn, estimates of selfing declined in populations as genetic diversity increased. Additionally, we found that most P. annua individuals are probably tetraploid and that only slight variation exists in genome size across the Southern Ocean. Our findings suggest multiple independent introductions of P. annua into the sub-Antarctic, which promoted the establishment of genetically diverse populations. Despite multiple introductions, the adoption of convergent reproductive strategies (outcrossing) happened independently in each major archipelago. The combination of polyploidy and a mixed reproductive strategy probably benefited P. annua in the Southern Ocean by increasing genetic diversity and its ability to cope with the novel environmental conditions.

Are Cenozoic relict species also climatic relicts? Insights from the macroecological evolution of the giant sedges of Carex sect. Rhynchocystis (Cyperaceae)

PREMISE

Most of the Paleotropical flora widely distributed in the Western Palearctic became extinct during the Mio-Pliocene as a result of global geoclimatic changes. A few elements from this Cenozoic flora are believed to remain as relicts in Macaronesia, forming part of the laurel forests. Although the origins of the present species assembly are known to be heterogeneous, it is unclear whether some species should be considered climatic relicts with conserved niches. An ideal group for studying such relict characteristics is a Miocene lineage of Carex sect. Rhynchocystis (Cyperaceae), which comprises four species distributed in mainland Palearctic and Macaronesia.

METHODS

We reconstructed the current and past environmental spaces for extant mainland and Macaronesian species, as well as for Pliocene fossils. We also studied the bioclimatic niche evolution. Species distribution modeling and ensemble small modeling were performed to assess the potential distribution over time.

RESULTS

Climatic niche analyses and distribution modeling revealed that the ecological requirements of Macaronesian species did not overlap with those of either mainland species or with the Pliocene fossils. Conversely, the niches of mainland species displayed significant similarity and equivalence.

CONCLUSIONS

Macaronesian species are not climatic relicts from the Paleotropical flora, but instead seem to have changed the ecological niche of their ancestors. By contrast, despite their ancient divergence (Late Miocene), mainland C. pendula and C. agastachys show conserved niches, with competitive exclusion likely shaping their mostly allopatric ranges.

Pleistocene expansion, anthropogenic pressure and ocean currents: Disentangling the past and ongoing evolutionary history of Patella aspera Röding, 1798 in the archipelago of Madeira

AIMS

Rising sea-level following the Last Glacial Maximum lead to fragmentation of coastal limpet populations between islands of the Archipelago of Madeira. This fragmentation is reinforced by recent heavy exploitation reducing effective population size on Madeira Island. We use the limpet P. aspera to understand how the role of processes at different time scales (i.e. changes in the sea level and overexploitation) can influence the genetic composition of an extant species, relating these processes to reproductive phenology and seasonal shifts in ocean currents.

LOCATION

Madeira Island, Porto Santo and Desertas (Archipelago of Madeira, NE Atlantic Ocean).

TAXON

The limpet Patella aspera.

METHODS

Twelve microsatellite genetic markers were used. A power analysis was used to evaluate the power of the microsatellite markers to detect a signal of population differentiation. Long-term past migrations were assessed using a Bayesian Markov Montecarlo approach in the software MIGRATE-n to estimate mutation-scaled migration rates (M = m/μ; m, probability of a lineage immigrating per generation; μ, mutation rate). Two scenarios were evaluated using an Approximate Bayesian Computation (ABC) in the software DIYABC 2.1 (i) Scenario 1: considered a population scenario from a reduced Ne at time t₃ to a higher Ne at time t₂; and (ii) Scenario 2 considering a reduction of Ne from a time t₃ to a time t₂.

RESULTS

Colonization of the archipelago by Portuguese settlers six centuries ago probably led to an important decrease in the genetic diversity of the species (N_e). Contemporary gene flow strongly support a pattern of high asymmetric connectivity explained by the reproductive phenology of the species and spatio-temporal seasonal changes in the ocean currents. Spatio-temporal reconstructions using Bayesian methods, including coalescent and Approximate Bayesian Computation (ABC) approaches, suggest changes in the migration patterns from highly symmetric to highly asymmetric connectivity with subtle population differentiation as consequence of post-glacial maximum sea level rise during the Holocene.

MAIN CONCLUSIONS

Our results suggest that anthropogenic activity could have had serious effects on the genetic diversity of heavily exploited littoral species since the end of the Pleistocene, probably accelerating in recent years.

Rare and widespread: integrating Bayesian MCMC approaches, Sanger sequencing and Hyb-Seq phylogenomics to reconstruct the origin of the enigmatic Rand Flora genus Camptoloma

PREMISE

Genera that are widespread, with geographically discontinuous distributions and represented by few species, are intriguing. Is their achieved disjunct distribution recent or ancient in origin? Why are they species-poor? The Rand Flora is a continental-scale pattern in which closely related species appear codistributed in isolated regions over the continental margins of Africa. Genus Camptoloma (Scrophulariaceae) is the most notable example, comprising three species isolated from each other on the northwest, eastern, and southwest Africa.

METHODS

We employed Sanger sequencing of nuclear and plastid markers, together with genomic target sequencing of 2190 low-copy nuclear genes, to infer interspecies relationships and the position of Camptoloma within Scrophulariaceae by using supermatrix and multispecies-coalescent approaches. Lineage divergence times and ancestral ranges were inferred with Bayesian Markov chain Monte Carlo (MCMC) approaches. The population history was estimated with phylogeographic coalescent methods.

RESULTS

Camptoloma rotundifolium, restricted to Southern Africa, was shown to be a sister species to the disjunct clade formed by C. canariense, endemic to the Canary Islands, and C. lyperiiflorum, distributed in the Horn of Africa-Southern Arabia. Camptoloma was inferred to be sister to the mostly South African tribes Teedieae and Buddlejeae. Stem divergence was dated in the Late Miocene, while the origin of the extant disjunction was inferred as Early Pliocene.

CONCLUSIONS

The current disjunct distribution of Camptoloma across Africa was likely the result of fragmentation and extinction and/or population bottlenecking events associated with historical aridification cycles during the Neogene; the pattern of species divergence, from south to north, is consistent with the "climatic refugia" Rand Flora hypothesis.

Molecular phylogenetics of Lotus (Leguminosae) with emphasis in the tempo and patterns of colonization in the Macaronesian region

With a wide distribution range including Europe and Asia, Lotus (Leguminosae) represents the largest genus within Loteae. It is particularly diverse in the Mediterreanean region and in the five archipelagos of Macaronesia (Atlantic Ocean). However, little is known about the relationships among the 14 sections currently recognized within Lotus and about the timing and patterns of its colonization in the Macaronesian region. In this investigation, we use four DNA regions (nuclear ribosomal ITS plus three plastid regions) in the most comprehensive sampling of Lotus species to date (some endemic species within the Canary Islands were poorly represented in previous phylogenetic analyses) to infer relationships within this genus and to establish patterns of colonization in Macaronesia. Divergence time estimates and habitat reconstruction analyses indicate that Lotus likely diverged about 7.86 Ma from its sister group, but all colonization events to Macaronesia occurred more recently (ranging from the last 0.23 to 2.70 Ma). The diversification of Lotus in Macaronesia involved between four and six independent colonization events from four sections currently distributed in Africa and Europe. A major aspect shaping the current distribution of taxa involved intra-island colonization of mainly new habitats and inter-island colonization of mostly similar habitats, with Gran Canaria and Tenerife as the major sources of diversification and of further colonization events. Section Pedrosia is the most diverse in terms of colonization events, number of species, and habitat heterogeneity, including a back-colonization event to the continent. Subsections within Pedrosia radiated into diverse habitat types recently (late Pleistocene, ca 0.23-0.29 Ma) and additional molecular markers and sampling would be necessary to understand the most recent dispersal events of this group within the Canary Islands and Cape Verde.

Fostering Conservation via an Integrated Use of Conventional Approaches and High-Throughput SPET Genotyping: A Case Study Using the Endangered Canarian Endemics Solanum lidii and S. vespertilio (Solanaceae)

Islands provide unique opportunities to integrated research approaches to study evolution and conservation because boundaries are circumscribed, geological ages are often precise, and many taxa are greatly imperiled. We combined morphological and hybridization studies with high-throughput genotyping platforms to streamline relationships in the endangered monophyletic and highly diverse lineage of Solanum in the Canarian archipelago, where three endemic taxa are currently recognized. Inter-taxa hybridizations were performed, and morphological expression was assessed with a common-garden approach. Using the eggplant Single Primer Enrichment Technology (SPET) platform with 5,093 probes, 74 individuals of three endemic taxa (Solanum lidii, S. vespertilio subsp. vespertilio, and S. vespertilio subsp. doramae) were sampled for SNPs. While morphological and breeding studies showed clear distinctions and some continuous variation, inter-taxon hybrids were fertile and heterotic for vigor traits. SPET genotyping revealed 1,421 high-quality SNPs and supported four, not three, distinct taxonomic entities associated with post-emergence geological, ecological and geographic factors of the islands. Given the lack of barriers to hybridization among all the taxa and their molecular differences, great care must be taken in population management. Conservation strategies must take account of the sexual and breeding systems and genotypic distribution among populations to successfully conserve and restore threatened/endangered island taxa, as exemplified by Solanum on the Canary Islands.

Genetic structure of the Canarian palm tree (Phoenix canariensis) at the island scale: does the 'island within islands' concept apply to species with high colonisation ability?

Oceanic islands are dynamic settings that often promote within-island patterns of strong population differentiation. Species with high colonisation abilities, however, are less likely to be affected by genetic barriers, but island size may impact on species genetic structure regardless of dispersal ability. The aim of the present study was to identify the patterns and factors responsible for the structure of genetic diversity at the island scale in Phoenix canariensis, a palm species with high dispersal potential. To this end, we conducted extensive population sampling on the three Canary Islands where the species is more abundant and assessed patterns of genetic variation at eight microsatellite loci, considering different within-island scales. Our analyses revealed significant genetic structure on each of the three islands analysed, but the patterns and level of structure differed greatly among islands. Thus, genetic differentiation fitted an isolation-by-distance pattern on islands with high population densities (La Gomera and Gran Canaria), but such a pattern was not found on Tenerife due to strong isolation between colonised areas. In addition, we found a positive correlation between population geographic isolation and fine-scale genetic structure. This study highlights that island size is not necessarily a factor causing strong population differentiation on large islands, whereas high colonisation ability does not always promote genetic connectivity among neighbouring populations. The spatial distribution of populations (i.e. landscape occupancy) can thus be a more important driver of plant genetic structure than other island, or species' life-history attributes.

Unmasking cryptic biodiversity in polyploids: origin and diversification of Aster amellus aggregate

BACKGROUND AND AIMS

The origin of different cytotypes by autopolyploidy may be an important mechanism in plant diversification. Although cryptic autopolyploids probably comprise the largest fraction of overlooked plant diversity, our knowledge of their origin and evolution is still rather limited. Here we study the presumed autopolyploid aggregate of Aster amellus, which encompasses diploid and hexaploid cytotypes. Although the cytotypes of A. amellus are not morphologically distinguishable, previous studies showed spatial segregation and limited gene flow between them, which could result in different evolutionary trajectories for each cytotype.

METHODS

We combine macroevolutionary, microevolutionary and niche modelling tools to disentangle the origin and the demographic history of the cytotypes, using chloroplast and nuclear markers in a dense population sampling in central Europe.

KEY RESULTS

Our results revealed a segregation between diploid and hexaploid cytotypes in the nuclear genome, where each cytotype represents a monophyletic lineage probably homogenized by concerted evolution. In contrast, the chloroplast genome showed intermixed connections between the cytotypes, which may correspond to shared ancestral relationships. Phylogeny, demographic analyses and ecological niche modelling supported an ongoing differentiation of the cytotypes, where the hexaploid cytotype is experiencing a demographic expansion and niche differentiation with respect to its diploid relative.

CONCLUSIONS

The two cytotypes may be considered as two different lineages at the onset of their evolutionary diversification. Polyploidization led to the occurrence of hexaploids, which expanded and changed their ecological niche.

A tale of two forests: ongoing aridification drives population decline and genetic diversity loss at continental scale in Afro-Macaronesian evergreen-forest archipelago endemics

BACKGROUND AND AIMS

Various studies and conservationist reports have warned about the contraction of the last subtropical Afro-Macaronesian forests. These relict vegetation zones have been restricted to a few oceanic and continental islands around the edges of Africa, due to aridification. Previous studies on relict species have generally focused on glacial effects on narrow endemics; however, little is known about the effects of aridification on the fates of previously widespread subtropical lineages.

METHODS

Nuclear microsatellites and ecological niche modelling were used to understand observed patterns of genetic diversity in two emblematic species, widely distributed in these ecosystems: Canarina eminii (a palaeoendemic of the eastern Afromontane forests) and Canarina canariensis (a palaeoendemic of the Canarian laurel forests). The software DIYABC was used to test alternative demographic scenarios and an ensemble method was employed to model potential distributions of the selected plants from the end of the deglaciation to the present.

KEY RESULTS

All the populations assessed experienced a strong and recent population decline, revealing that locally widespread endemisms may also be alarmingly threatened.

CONCLUSIONS

The detected extinction debt, as well as the extinction spiral to which these populations are subjected, demands urgent conservation measures for the unique, biodiversity-rich ecosystems that they inhabit.

Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above

Reconstructing phylogenetic relationships at the micro- and macroevoutionary levels within the same tree is problematic because of the need to use different data types and analytical frameworks. We test the power of target enrichment to provide phylogenetic resolution based on DNA sequences from above species to within populations, using a large herbarium sampling and Euphorbia balsamifera (Euphorbiaceae) as a case study. Target enrichment with custom probes was combined with genome skimming (Hyb-Seq) to sequence 431 low-copy nuclear genes and partial plastome DNA. We used supermatrix, multispecies-coalescent approaches, and Bayesian dating to estimate phylogenetic relationships and divergence times. Euphorbia balsamifera, with a disjunct Rand Flora-type distribution at opposite sides of Africa, comprises three well-supported subspecies: western Sahelian sepium is sister to eastern African-southern Arabian adenensis and Macaronesian-southwest Moroccan balsamifera. Lineage divergence times support Late Miocene to Pleistocene diversification and climate-driven vicariance to explain the Rand Flora pattern. We show that probes designed using genomic resources from taxa not directly related to the focal group are effective in providing phylogenetic resolution at deep and shallow evolutionary levels. Low capture efficiency in herbarium samples increased the proportion of missing data but did not bias estimation of phylogenetic relationships or branch lengths.

Phylogeography of the Macaronesian Lettuce Species Lactuca watsoniana and L. palmensis (Asteraceae)

The phylogenetic relationships and phylogeography of two relatively rare Macaronesian Lactuca species, Lactuca watsoniana (Azores) and L. palmensis (Canary Islands), were, until this date, unclear. Karyological information of the Azorean species was also unknown. For this study, a chromosome count was performed and L. watsoniana showed 2n = 34. A phylogenetic approach was used to clarify the relationships of the Azorean endemic L. watsoniana and the La Palma endemic L. palmensis within the subtribe Lactucinae. Maximum parsimony, Maximum likelihood and Bayesian analysis of a combined molecular dataset (ITS and four chloroplast DNA regions) and molecular clock analyses were performed with the Macaronesian Lactuca species, as well as a TCS haplotype network. The analyses revealed that L. watsoniana and L. palmensis belong to different subclades of the Lactuca clade. Lactuca watsoniana showed a strongly supported phylogenetic relationship with North American species, while L. palmensis was closely related to L. tenerrima and L. inermis, from Europe and Africa. Lactuca watsoniana showed four single-island haplotypes. A divergence time estimation of the Macaronesian lineages was used to examine island colonization pathways. Results obtained with BEAST suggest a divergence of L. palmensis and L. watsoniana clades c. 11 million years ago, L. watsoniana diverged from its North American sister species c. 3.8 million years ago and L. palmensis diverged from its sister L. tenerrima, c. 1.3 million years ago, probably originating from an African ancestral lineage which colonized the Canary Islands. Divergence analyses with *BEAST indicate a more recent divergence of the L. watsoniana crown, c. 0.9 million years ago. In the Azores colonization, in a stepping stone, east-to-west dispersal pattern, associated with geological events might explain the current distribution range of L. watsoniana.

Species delimitation and conservation genetics of the Canarian endemic Bethencourtia (Asteraceae)

Bethencourtia Choisy ex Link is an endemic genus of the Canary Islands and comprises three species. Bethencourtia hermosae and Bethencourtia rupicola are restricted to La Gomera, while Bethencourtia palmensis is present in Tenerife and La Palma. Despite the morphological differences previously found between the species, there are still taxonomic incongruities in the group, with evident consequences for its monitoring and conservation. The objectives of this study were to define the species differentiation, perform population genetic analysis and propose conservation strategies for Bethencourtia. To achieve these objectives, we characterized 10 polymorphic SSR markers. Eleven natural populations (276 individuals) were analyzed (three for B. hermosae, five for B. rupicola and three for B. palmensis). The results obtained by AMOVA, PCoA and Bayesian analysis on STRUCTURE confirmed the evidence of well-structured groups corresponding to the three species. At the intra-specific level, B. hermosae and B. rupicola did not show a clear population structure, while B. palmensis was aggregated according to island of origin. This is consistent with self-incompatibility in the group and high gene flow within species. Overall, the genetic diversity of the three species was low, with expected heterozygosity values of 0.302 (B. hermosae), 0.382 (B. rupicola) and 0.454 (B. palmensis). Recent bottleneck events and a low number of individuals per population are probably the causes of the low genetic diversity. We consider that they are naturally rare species associated with specific habitats. The results given in this article will provide useful information to assist in conservation genetics programs for this endemic genus.

Phylogenetic relationships and phylogeography of relevant lineages within the complex Campanulaceae family in Macaronesia

Macaronesia has long been recognized as a natural model for studying evolutionary processes in plant diversification. Several studies have attempted to focus on single lineages, and few have covered the diversification of a family across all the archipelagos. We used a comprehensive sample to clarify the phylogenetic relationships and the biogeographic history of the Macaronesian Campanulaceae. Hypotheses related to the colonization of these archipelagos will be used to examine the diversification patterns of different lineages. We sequenced the ITS region and six cpDNA markers (atpB, matK, petD, rbcL, trnL-F, and psbA-trnH) from 10 Campanulaceae species, including seven endemic species in Macaronesia. The phylogeny of these taxa was reconstructed using maximum parsimony, maximum likelihood, and Bayesian inference. To study the relationships within each lineage, haplotype networks were calculated using NeighborNet and TCS algorithms. Moreover, data were combined with fossil information to construct time-calibrated trees for the Macaronesian Campanulaceae species. The phylogenetic analyses are largely congruent with current taxon circumscriptions, and all the endemic genera formed monophyletic clades, namely Azorina in Azores; Musschia in Madeira; and Campanula in Cape Verde. The Azorina clade and the Cape Verde endemic Campanula may share a common ancestor in North Africa, and the divergence was dated ca. 12.3 million years ago (Mya). The divergence of the Musschia clade began in the Pliocene ca. 3.4 Mya. Moreover, several examples of intraspecific variation were revealed among the native species with a clear geographic structured patterns, suggesting that cryptic diversity might exist within the native Macaronesian Campanulaceae when compared to the close mainland taxa (e.g., Campanula erinus, Trachelium caeruleum), but additional studies are needed to support the molecular data. This study highlights the power of combining data (e.g., phylogeny and divergence times, with species distribution data) for testing diversification hypotheses within the unique Macaronesian flora, providing useful information for future conservation efforts.

Opposite trends in the genus Monsonia (Geraniaceae): specialization in the African deserts and range expansions throughout eastern Africa

The African Austro-temperate Flora stands out by its important species richness. A distinctive element of this flora is Monsonia (Geraniaceae), mostly found in the Namib-Karoo but also in the Natal-Drakensberg, the Somalian Zambezian and the Saharo-Arabian regions. Here, we reconstruct the evolution and biogeographic history of Monsonia based on nuclear and plastid markers, and examine the role of morphological and niche evolution in its diversification using species distribution modeling and macroevolutionary models. Our results indicate that Monsonia first diversified in the Early Miocene c.21 Ma, coinciding with the start of desertification in southwestern Africa. An important diversification occurred c. 4-6 Ma, after a general cooling trend in western South Africa and the rising of the Eastern African Mountains. The resulting two main lineages of Monsonia are constituted by: (1) Namib-Karoo succulents, and (2) herbs of the Natal-Drakensberg plus three species that further colonised steppes in north and eastern Africa. The highest diversity of Monsonia is found in the Namib-Karoo coastal belt, within a mosaic-like habitat structure. Diversification was likely driven by biome shifts and key innovations such as water-storing succulent stems and anemochorous fruits. In contrast, and unlike other arid-adapted taxa, all species of Monsonia share a C₃ metabolism.

Genetic diversity and differentiation patterns in Micromeria from the Canary Islands are congruent with multiple colonization dynamics and the establishment of species syngameons

Background

Especially on islands closer to the mainland, such as the Canary Islands, different lineages that originated by multiple colonization events could have merged by hybridization, which then could have promoted radiation events (Herben et al., J Ecol 93: 572–575, 2005; Saunders and Gibson, J Ecol 93: 649–652, 2005; Caujapé-Castells, Jesters, red queens, boomerangs and surfers: a molecular outlook on the diversity of the Canarian endemic flora, 2011). This is an alternative to the scenario where evolution is mostly driven by drift (Silvertown, J Ecol 92: 168–173, 2004; Silvertown et al., J Ecol 93: 653–657, 2005). In the former case hybridization should be reflected in the genetic structure and diversity patterns of island species. In the present work we investigate Micromeria from the Canary Islands by extensively studying their phylogeographic pattern based on 15 microsatellite loci and 945 samples. These results are interpreted according to the hypotheses outlined above.

Results

Genetic structure assessment allowed us to genetically differentiate most Micromeria species and supported their current classification. We found that populations on younger islands were significantly more genetically diverse and less differentiated than those on older islands. Moreover, we found that genetic distance on younger islands was in accordance with an isolation-by-distance pattern, while on the older islands this was not the case. We also found evidence of introgression among species and islands.

Conclusions

These results are congruent with a scenario of multiple colonizations during the expansion onto new islands. Hybridization contributes to the grouping of multiple lineages into highly diverse populations. Thus, in our case, islands receive several colonization events from different sources, which are combined into sink populations. This mechanism is in accordance with the surfing syngameon hypothesis. Contrary to the surfing syngameon current form, our results may reflect a slightly different effect: hybridization might always be related to colonization within the archipelago as well, making initial genetic diversity to be high to begin with. Thus the emergence of new islands promotes multiple colonization events, contributing to the establishment of hybrid swarms that may enhance adaptive ability and radiation events. With time, population sizes grow and niches start to fill. Consequently, gene-flow is not as effective at maintaining the species syngameon, which allows genetic differentiation and reproductive isolation to be established between species. This process contributes to an even further decrease in gene-flow between species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-1031-y) contains supplementary material, which is available to authorized users.

Panmixia and dispersal from the Mediterranean Basin to Macaronesian Islands of a macrolichen species

The Mediterranean region, comprising the Mediterranean Basin and the Macaronesian Islands, represents a center of diversification for many organisms. The genetic structure and connectivity of mainland and island microbial populations has been poorly explored, in particular in the case of symbiotic fungi. Here we investigated genetic diversity and spatial structure of the obligate outcrossing lichen-forming fungus Parmelina carporrhizans in the Mediterranean region. Using eight microsatellite and mating-type markers we showed that fungal populations are highly diverse but lack spatial structure. This is likely due to high connectivity and long distance dispersal of fungal spores. Consistent with low levels of linkage disequilibrium and lack of clonality, we detected both mating-type idiomorphs in all populations. Furthermore we showed that the Macaronesian Islands are the result of colonization from the Mediterranean Basin. The unidirectional gene flow, though, seemed not to be sufficient to counterbalance the effects of drift, resulting in comparatively allelic poor peripheral populations. Our study is the first to shed light on the high connectivity and lack of population structure in natural populations of a strictly sexual lichen fungus. Our data further support the view of the Macaronesian Islands as the end of the colonization road for this symbiotic ascomycete.

Geographical distance and barriers explain population genetic patterns in an endangered island perennial

Island plants are frequently used as model systems in evolutionary biology to understand factors that might explain genetic diversity and population differentiation levels. Theory suggests that island plants should have lower levels of genetic diversity than their continental relatives, but this hypothesis has been rejected in several recent studies. In the Azores, the population level genetic diversity is generally low. However, like in most island systems, there are high levels of genetic differentiation between different islands. The Azores lettuce, Lactuca watsoniana, is an endangered Asteraceae with small population sizes. Therefore, we expect to find a lower level of genetic diversity than in the other more common endemic Asteraceae. The intra- and interpopulation genetic structure and diversity of L. watsoniana was assessed using eight newly developed microsatellite markers. We included 135 individuals, from all 13 known populations in the study. Because our microsatellite results suggested that the species is tetraploid, we analysed the microsatellite data (i) in codominant format using PolySat (Principal Coordinate Analysis, PCoA) and SPAgedi (genetic diversity indexes) and (ii) in dominant format using Arlequin (AMOVA) and STRUCTURE (Bayesian genetic cluster analysis). A total of 129 alleles were found for all L. watsoniana populations. In contrast to our expectations, we found a high level of intrapopulation genetic diversity (total heterozigosity = 0.85; total multilocus average proportion of private alleles per population = 26.5 %, Fis = -0.19). Our results show the existence of five well-defined genetic groups, one for each of the three islands São Miguel, Terceira and Faial, plus two groups for the East and West side of Pico Island (Fst = 0.45). The study revealed the existence of high levels of genetic diversity, which should be interpreted taking into consideration the ploidy level of this rare taxon.

Colonization and diversification of the Euphorbia species (sect. Aphyllis subsect. Macaronesicae) on the Canary Islands

Diversification between islands and ecological radiation within islands are postulated to have occurred in the Euphorbia species (sect. Aphyllis subsect. Macaronesicae) on the Canary Islands. In this study, the biogeographical pattern of 11 species of subsect. Macaronesicae and the genetic differentiation among five species were investigated to distinguish the potential mode and mechanism of diversification and speciation. The biogeographical patterns and genetic structure were examined using statistical dispersal-vicariance analysis, Bayesian phylogenetic analysis, reduced median-joining haplotype network analysis, and discriminant analysis of principal components. The gene flow between related species was evaluated with an isolation-with-migration model. The ancestral range of the species of subsect. Macaronesicae was inferred to be Tenerife and the Cape Verde Islands, and Tenerife-La Gomera acted as sources of diversity to other islands of the Canary Islands. Inter-island colonization of E. lamarckii among the western islands and a colonization of E. regis-jubae from Gran Canaria to northern Africa were revealed. Both diversification between islands and radiation within islands have been revealed in the Euphorbia species (sect. Aphyllis subsect. Macaronesicae) of the Canary Islands. It was clear that this group began the speciation process in Tenerife-La Gomera, and this process occurred with gene flow between some related species.

Diversity hotspots of the laurel forest on Tenerife, Canary Islands: a phylogeographic study of Laurus and Ixanthus

BACKGROUND AND AIMS

Macaronesian laurel forest is among the worldwide hotspots of threatened biodiversity. With increasing evidence that woodland composition on the Canary Islands changed dramatically during the last few thousand years, the aim of this study was to find evidence for substantial recent population dynamics of two representative species from laurel forest.

METHODS

Amplified fragment length polymorphism (AFLP) was used to evaluate fine-scaled genetic variation of the paradigmatic tree Laurus novocanariensis (Lauraceae) and a long-lived herbaceous gentian from core laurel forest, Ixanthus viscosus (Gentianaceae), on Tenerife. Bioclimatic variables were analysed to study the respective climate niches. A chloroplast DNA screening was performed to evaluate additional genetic variation.

KEY RESULTS

Genetic diversity of the laurel tree showed severe geographic partitioning. On Tenerife, fine-scaled Bayesian clustering of genetic variation revealed a western and an eastern gene pool, separated by a zone of high admixture and with a third major gene pool. Compared with genetic clusters found on the other Canary Islands, the East-West differentiation on Tenerife seems to be more recent than differentiation between islands. This is substantiated by the finding of extremly low levels of chloroplast DNA-based polymorphisms. Ixanthus showed no geographic structuring of genetic variation.

CONCLUSIONS

Genetic data from Tenerife indicate contemporary gene flow and dispersal on a micro/local scale rather than reflecting an old and relic woodland history. In particular for Laurus, it is shown that this species occupies a broad bioclimatic niche. This is not correlated with its respective distribution of genetic variation, therefore indicating its large potential for contemporary rapid and effective colonization. Ixanthus is more specialized to humid conditions and is mostly found in the natural Monteverde húmedo vegetation types, but even for this species indications for long-term persistence in the respective bioclimatically differentiated regions was not find.

Genetic structure of Micromeria (Lamiaceae) in Tenerife, the imprint of geological history and hybridization on within-island diversification

Geological history of oceanic islands can have a profound effect on the evolutionary history of insular flora, especially in complex islands such as Tenerife in the Canary Islands. Tenerife results from the secondary connection of three paleo‐islands by a central volcano, and other geological events that further shaped it. This geological history has been shown to influence the phylogenetic history of several taxa, including genus Micromeria (Lamiaceae). Screening 15 microsatellite markers in 289 individuals representing the eight species of Micromeria present in Tenerife, this study aims to assess the genetic diversity and structure of these species and its relation with the geological events on the island. In addition, we evaluate the extent of hybridization among species and discuss its influence on the speciation process. We found that the species restricted to the paleo‐islands present lower levels of genetic diversity but the highest levels of genetic differentiation suggesting that their ranges might have contracted over time. The two most widespread species in the island, M. hyssopifolia and M. varia, present the highest genetic diversity levels and a genetic structure that seems correlated with the geological composition of the island. Samples from M. hyssopifolia from the oldest paleo‐island, Adeje, appear as distinct while samples from M. varia segregate into two main clusters corresponding to the paleo‐islands of Anaga and Teno. Evidence of hybridization and intraspecific migration between species was found. We argue that species boundaries would be retained despite hybridization in response to the habitat's specific conditions causing postzygotic isolation and preserving morphological differentiation.

Spatial and ecological population genetic structures within two island-endemic Aeonium species of different niche width

The Crassulacean genus Aeonium is a well-known example for plant species radiation on oceanic archipelagos. However, while allopatric speciation among islands is documented for this genus, the role of intra-island speciation due to population divergence by topographical isolation or ecological heterogeneity has not yet been addressed. The aim of this study was to investigate intraspecific genetic structures and to identify spatial and ecological drivers of genetic population differentiation on the island scale. We analyzed inter simple sequence repeat variation within two island-endemic Aeonium species of La Palma: one widespread generalist that covers a large variety of different habitat types (Ae. davidbramwellii) and one narrow ecological specialist (Ae. nobile), in order to assess evolutionary potentials on this island. Gene pool differentiation and genetic diversity patterns were associated with major landscape structures in both species, with phylogeographic implications. However, overall levels of genetic differentiation were low. For the generalist species, outlier loci detection and loci-environment correlation approaches indicated moderate signatures of divergent selection pressures linked to temperature and precipitation variables, while the specialist species missed such patterns. Our data point to incipient differentiation among populations, emphasizing that ecological heterogeneity and topographical structuring within the small scales of an island can foster evolutionary processes. Very likely, such processes have contributed to the radiation of Aeonium on the Canary Islands. There is also support for different evolutionary mechanisms between generalist and specialist species.