Interpretation of patterns of genetic variation in endemic plant species of oceanic islands

Preliminary insights of the genetic diversity and invasion pathways of Cedrela odorata in the Galapagos Islands, Ecuador

Cedrela odorata is considered the second most invasive tree species of the Galapagos Islands. Although it is listed in CITES Appendix II and there are population losses in mainland Ecuador, in Galapagos it is paradoxically a species of concern due to its invasive potential. Genetic studies can shed light on the invasion history of introduced species causing effects on unique ecosystems like the Galapagos. We analyzed nine microsatellite markers in C. odorata individuals from Galapagos and mainland Ecuador to describe the genetic diversity and population structure of C. odorata in the Galapagos and to explore the origin and invasion history of this species. The genetic diversity found for C. odorata in Galapagos (H e = 0.55) was lower than reported in the mainland (H e = 0.81), but higher than other invasive insular plant species, which could indicate multiple introductions. Our results suggest that Ecuador's northern Coastal region is the most likely origin of the Galapagos C. odorata, although further genomic studies, like Whole Genome Sequencing, Rad-Seq, and/or Whole Genome SNP analyses, are needed to confirm this finding. Moreover, according to our proposed pathway scenarios, C. odorata was first introduced to San Cristobal and/or Santa Cruz from mainland Ecuador. After these initial introductions, C. odorata appears to have arrived to Isabela and Floreana from either San Cristobal or Santa Cruz. Here, we report the first genetic study of C. odorata in the Galapagos and the first attempt to unravel the invasion history of this species. The information obtained in this research could support management and control strategies to lessen the impact that C. odorata has on the islands' local flora and fauna.

A historical stepping-stone path for an island-colonizing cactus across a submerged "bridge" archipelago

Here we use population genomic data (ddRAD-Seq) and ecological niche modeling to test biogeographic hypotheses for the divergence of the island-endemic cactus species Cereus insularis Hemsl. (Cereeae; Cactaceae) from its sister species C. fernambucensis Lem. The Cereus insularis grows in the Fernando de Noronha Islands (FNI), a Neotropical archipelago located 350 km off the Brazilian Atlantic Forest (BAF) coast. Phylogeographic reconstructions support a northward expansion by the common ancestor of C. insularis and C. fernambucensis along the mainland BAF coast, with C. insularis diverging from the widespread mainland taxon C. fernambucensis after colonizing FNI in the late Pleistocene. The morphologically distinct C. insularis is monophyletic and nested within C. fernambucensis, as expected from a progenitor-derivative speciation model. We tested alternative biogeographic and demographic hypotheses for the colonization of the FNI using Approximate Bayesian Computation. We found the greatest support for a stepping-stone path that emerged during periods of decreased sea level (the "bridge" hypothesis), in congruence with historical ecological niche modeling that shows highly suitable habitats on stepping-stone islands during glacial periods. The outlier analyses reveal signatures of selection in C. insularis, suggesting a putative role of adaptation driving rapid anagenic differentiation of this species in FNI.

Phylogenomic and population genomic analyses reveal the spatial-temporal dynamics of diversification of the Nigella arvensis complex (Ranunculaceae) in the Aegean archipelago

The continental-shelf islands of the Aegean Sea provide an ideal geographical setting for evolutionary-biogeographical studies but disentangling the relationships between palaeogeographical history and the times, orders of modes of taxon divergence is not straightforward. Here, we used phylogenomic and population genomic approaches, based on orthologous gene sequences and transcriptome-derived SNP data, to reconstruct the spatial-temporal evolution of the Aegean Nigella arvensis complex (Ranunculaceae; 11 out of 12 taxa). The group's early diversification in the Early/Mid-Pliocene (c. 3.77 Mya) resulted in three main lineages (Greek mainland vs. central Aegean + Turkish mainland/eastern Aegean islands), while all extant taxa are of Late Plio-/Early Pleistocene origin (c. 3.30-1.59 Mya). Demographic modelling of the outcrossing taxa uncovered disparate modes of (sub)speciation, including divergence with gene flow on the Greek mainland, para- or peripatric diversification across eastern Aegean islands, and a 'mixing-isolation-mixing (MIM)' mode of subspeciation in the Cyclades. The two selfing species (N. stricta, N. doerfleri) evolved independently from the outcrossers. Present-day island configurations are clearly insufficient to explain the spatial-temporal history of lineage diversification and modes of (sub)speciation in Aegean Nigella. Moreover, our identification of positively selected genes in almost all taxa calls into question that this plant group represents a case of 'non-adaptive' radiation. Our study revealed an episodic diversification history of the N. arvensis complex, giving new insight into the modes and drivers of island speciation and adaption across multiple spatiotemporal scales.

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.

Plastomes of Sonchus (Asteraceae) endemic to the Atlantic Madeira archipelago: Genome structure, comparative analysis, and phylogenetic relationships

The woody Sonchus alliance, a spectacular example of adaptive radiation with six genera and approximately 31 species, is found exclusively on three Macaronesian Islands (Madeira, Canaries, and Cape Verdes) in the Atlantic Ocean. Four of the Sonchus taxa are restricted to Madeira, including shrubs and small trees at higher elevations (S. fruticosus and S. pinnatus), and caudex perennials in the lower coastal areas (S. ustulatus subsp. maderensis and S. ustulatus subsp. ustulatus). The Madeiran Sonchus stemmed from a single colonization event that originated from the Canaries < 3 million years ago. However, the plastome evolution and species relationships remains insufficiently explored. We therefore assembled and characterized the plastomes of four Sonchus taxa from Madeira and conducted a phylogenomic analysis. We found highly conserved plastome sequences among the taxa, further supporting a single and recent origin. We also found highly conserved plastomes among the cosmopolitan weedy Sonchus, Macaronesian Sonchus in the Atlantic, and Juan Fernández Islands Dendroseris in the Pacific. Furthermore, we identified four mutation hotspot regions (trnK-rps16, petN-psbM, ndhF-Ψycf1, and ycf1) and simple sequence repeat motifs. This study strongly supports the monophyly of Madeiran Sonchus. However, its relationship with the remaining woody Sonchus alliance from the Canary Islands requires further investigation.

Integrative Taxonomy of Armeria Taxa (Plumbaginaceae) Endemic to Sardinia and Corsica

Sardinia and Corsica are two Mediterranean islands where the genus Armeria is represented by 11 taxa, 10 out of which are endemic. An integrative approach, using molecular phylogeny, karyology, and seed and plant morphometry was used to resolve the complex taxonomy and systematics in this group. We found that several taxa are no longer supported by newly produced data. Accordingly, we describe a new taxonomic hypothesis that only considers five species: Armeria leucocephala and A. soleirolii, endemic to Corsica, and A. morisii, A. sardoa, and A. sulcitana, endemic to Sardinia.

Phylogenomics of the Olea europaea complex using 15 whole genomes supports recurrent genetic admixture together with differentiation into seven subspecies

BACKGROUND

The last taxonomic account of Olea recognises six subspecies within Olea europaea L., including the Mediterranean olive tree (subsp. europaea) and five other subspecies (laperrinei, guanchica, maroccana, cerasiformis, and cuspidata) distributed across the Old World, including Macaronesian islands. The evolutionary history of this monophyletic group (O. europaea complex) has revealed a reticulated scenario involving hybridization and polyploidization events, leading to the presence of a polyploid series associated with the subspecies. However, how the polyploids originated, and how the different subspecies contributed to the domestication of the cultivated olive are questions still debated. Tracing the recent evolution and genetic diversification of the species is key for the management and preservation of its genetic resources. To study the recent history of the O. europaea complex, we compared newly sequenced and available genomes for 27 individuals representing the six subspecies.

RESULTS

Our results show discordance between current subspecies distributions and phylogenomic patterns, which support intricate biogeographic patterns. The subspecies guanchica, restricted to the Canary Islands, is closely related to subsp. europaea, and shows a high genetic diversity. The subsp. laperrinei, restricted now to high mountains of the Sahara desert, and the Canarian subsp. guanchica contributed to the formation of the allotetraploid subsp. cerasiformis (Madeira islands) and the allohexaploid subsp. maroccana (western Sahara region). Our phylogenomic data support the recognition of one more taxon (subsp. ferruginea) for the Asian populations, which is clearly segregated from the African subsp. cuspidata.

CONCLUSIONS

In sum, the O. europaea complex underwent several processes of hybridization, polyploidy, and geographical isolation resulting in seven independent lineages with certain morphological traits recognised into subspecies.

Evolutionary genomics of oceanic island radiations

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.

Spatiotemporal process of long-distance seed dispersal in a pantropically distributed sea hibiscus group

Long-distance dispersal (LDD) of seeds plays an essential role in the migration of plants to a new habitat and maintaining gene flow among geographically isolated populations. Pantropical plants with sea-drifted seeds, which have one of the largest distributions in all flowering plants, have achieved their global distribution by LDD. However, the spatiotemporal processes to achieve the wide distribution and the role of LDD in it have not yet been elucidated. In this study, we conducted phylogenomic analyses on the plastome, genome-wide nuclear SNP, and low-copy gene data of Hibiscus tiliaceus and its relatives. The dated phylogeny suggested that global expansion started approximately 4 million years ago (Ma), and species diversification occurred 1 Ma. Plastome phylogeny confirmed the nonmonophyly of the haplotypes in the two widely distributed coastal species, H. tiliaceus and H. pernambucensis. In contrast, genome-wide nuclear SNP phylogenies demonstrated clear genetic segregation among species and/or geographical regions. Ancestral polymorphisms in chloroplast genomes shared among widely distributed species have remained below the range of rapid expansion and speciation of marginal populations. This study demonstrated that the LDD of sea-drifted seeds contributed to the rapid expansion and pantropical distribution of sea hibiscus in the last few million years, and adaptation to local environment or isolation by regional effect after LDD promoted speciation, suppressing gene flow.

Possible northern persistence of Siebold's beech, Fagus crenata, at its northernmost distribution limit on an island in Japan Sea: Okushiri Island, Hokkaido

Siebold's beech, Fagus crenata, is widely distributed across the Japanese Archipelago and islands in Japan Sea. Similar to the northern limit of the geographical distribution of F. crenata on the mainland of Hokkaido, the northern limit of the distribution of F. crenata on islands in the Japan Sea is observed on Okushiri Island (ca 42°N). To understand the genetic relationships of F. crenata on Okushiri Island, we examined chloroplast (cp) DNA haplotypes and 11 nuclear microsatellite (SSR) loci among 1,838 individuals from 44 populations from Okushiri Island, mainland Hokkaido, and the northern part of the Tohoku region on Honshu Island. We identified 2 cpDNA haplotypes, which represent not only populations on the Japan Sea coast but also those on the Pacific coast and this suggested the Okushiri Island populations might not be formed by single colonization. Genetic diversity of the Okushiri Island populations of nuclear SSR was not lower than the mainland and the STRUCTURE analysis revealed the Okushiri Island individuals were admixed between Hokkaido and Tohoku clusters. Approximate Bayesian computation inferred that divergence between Tohoku and Hokkaido, and admixture between two populations which generated Okushiri populations occurred before the last glacial maximum (LGM), that is, 7,890 (95% hyper probability density (HPD): 3,420 - 9,910) and 3,870 (95% HPD: 431- 8,540) generations ago, respectively. These inferences were well supported by a geological history which suggested an isolation of Okushiri Island from Hokkaido started prior to the Middle Pleistocene. We discuss the possible persistence of F. crenata during the last glacial maximum on northern islands in the Japan Sea such as Okushiri Island.

Contrasting genetic diversity between Planchonella obovata sensu lato (Sapotaceae) on old continental and young oceanic island populations in Japan

Genetic diversity of plant populations on islands is likely to be influenced by characteristics such as island origin (oceanic or continental) and their age, size, and distance to continental landmasses. In Japan, Planchonella obovata sensu lato which is found on both continental and oceanic islands of varying age, size, and distance to East Asian continental areas—is an ideal system in which to investigate the factors influencing genetic diversity of island plant species. In this study, we examined the genetic diversity of P. obovata s.l. populations, in the context of the species population genetic structure, demography, and between island migration, from 668 individuals, 28 populations and 14 islands including both continental (the Yaeyama Islands) and oceanic islands (the Daito, Bonin, and Volcano Islands) using 11 microsatellite markers. The Yaeyama and Volcano Islands respectively had the highest and lowest genetic diversity, and island origin and age significantly affected genetic diversity. Clustering analysis revealed that populations were grouped into Bonin, Volcano, and Yaeyama + Daito groups. However, Bonin and Volcano groups were distinct despite the relatively short geographical distance between them. Approximate Bayesian Computation analysis suggested that the population size was stable in Bonin and Yaeyama + Daito groups, whereas population reduction occurred in Volcano group, and migration between groups were very limited. Younger oceanic islands showed lower genetic diversity, probably due to limited gene flow and a lack of time to accumulate unique alleles. Genetic structure was generally consistent with the geographic pattern of the islands, but in Volcano, a limited number of founders and limited gene flow among islands are likely to have caused the large genetic divergence observed.

Interspecific hybridization and island colonization history, not rarity, most strongly affect the genetic diversity in a clade of Mascarene-endemic trees

Many factors shape the genetic diversity of island-endemic trees, with important implications for conservation. Oceanic island-endemic lineages undergo an initial founding bottleneck during the colonization process and subsequently accumulate diversity following colonization. Moreover, many island endemics occur in small populations and are further threatened by anthropogenic factors that cause population declines, making them susceptible to losses in genetic diversity through genetic drift, inbreeding, and bottlenecks. However, life-history traits commonly found in trees, such as outcrossing mechanisms, long lifespans, and a propensity for interspecific hybridization, may help buffer against losses of genetic variation. To assess the relative importance of colonization history, rarity, and distribution in shaping genetic diversity of island-endemic trees, we conducted a comparative population genomic analysis of 13 species of Diospyros (Ebenaceae) endemic to the Mascarene Islands that differ in island colonization history, distribution, population size, and IUCN threat status. We genotyped 328 individuals across the islands using 2b-RADseq, compared genetic diversity both among and within species, and assessed patterns of genetic structure. Genetic diversity did not vary significantly by IUCN status, but we found that species that co-occur with others on the same intermediate-aged island (Mauritius) had much greater genetic diversity than those that occur solitarily on an island (Réunion and Rodrigues), likely because of greater interspecific hybridization among species with overlapping distributions and processes related to time since island colonization. Results presented here were used to determine priority localities for in situ and ex situ conservation efforts to maximize the genetic diversity of each Mascarene Diospyros species.

Origin and dispersion pathways of guava in the Galapagos Islands inferred through genetics and historical records

Guava (Psidium guajava) is an aggressive invasive plant in the Galapagos Islands. Determining its provenance and genetic diversity could explain its adaptability and spread, and how this relates to past human activities. With this purpose, we analyzed 11 SSR markers in guava individuals from Isabela, Santa Cruz, San Cristobal, and Floreana islands in the Galapagos, as well as from mainland Ecuador. The mainland guava population appeared genetically differentiated from the Galapagos populations, with higher genetic diversity levels found in the former. We consistently found that the Central Highlands region of mainland Ecuador is one of the most likely origins of the Galapagos populations. Moreover, the guavas from Isabela and Floreana show a potential genetic input from southern mainland Ecuador, while the population from San Cristobal would be linked to the coastal mainland regions. Interestingly, the proposed origins for the Galapagos guava coincide with the first human settlings of the archipelago. Through approximate Bayesian computation, we propose a model where San Cristobal was the first island to be colonized by guava from the mainland, and then, it would have spread to Floreana and finally to Santa Cruz; Isabela would have been seeded from Floreana. An independent trajectory could also have contributed to the invasion of Floreana and Isabela. The pathway shown in our model agrees with the human colonization history of the different islands in the Galapagos. Our model, in conjunction with the clustering patterns of the individuals (based on genetic distances), suggests that guava introduction history in the Galapagos archipelago was driven by either a single event or a series of introduction events in rapid succession. We thus show that genetic analyses supported by historical sources can be used to track the arrival and spread of invasive species in novel habitats and the potential role of human activities in such processes.

Genome-Wide Single Nucleotide Polymorphism Analysis Elucidates the Evolution of Prunus takesimensis in Ulleung Island: The Genetic Consequences of Anagenetic Speciation

Of the two major speciation modes of endemic plants on oceanic islands, cladogenesis and anagenesis, the latter has been recently emphasized as an effective mechanism for increasing plant diversity in isolated, ecologically homogeneous insular settings. As the only flowering cherry occurring on Ulleung Island in the East Sea (concurrently known as Sea of Japan), Prunus takesimensis Nakai has been presumed to be derived through anagenetic speciation on the island. Based on morphological similarities, P. sargentii Rehder distributed in adjacent continental areas and islands has been suggested as a purported continental progenitor. However, the overall genetic complexity and resultant non-monophyly of closely related flowering cherries have hindered the determination of their phylogenetic relationships as well as the establishment of concrete continental progenitors and insular derivative relationships. Based on extensive sampling of wild flowering cherries, including P. takesimensis and P. sargentii from Ulleung Island and its adjacent areas, the current study revealed the origin and evolution of P. takesimensis using multiple molecular markers. The results of phylogenetic reconstruction and population genetic structure analyses based on single nucleotide polymorphisms detected by multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) and complementary cpDNA haplotypes provided evidence for (1) the monophyly of P. takesimensis; (2) clear genetic differentiation between P. takesimensis (insular derivative) and P. sargentii (continental progenitor); (3) uncertain geographic origin of P. takesimensis, but highly likely via single colonization from the source population of P. sargentii in the Korean Peninsula; (4) no significant reduction in genetic diversity in anagenetically derived insular species, i.e., P. takesimensis, compared to its continental progenitor P. sargentii; (5) no strong population genetic structuring or geographical patterns in the insular derivative species; and (6) MIG-seq method as an effective tool to elucidate the complex evolutionary history of plant groups.

Genome-wide SNP analysis to assess the genetic population structure and diversity of Acrocomia species

Acrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm (Elaeis guineenses) even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of Acrocomia genus, including 172 samples from seven species, with a focus on A. aculeata with 117 samples covering a wide geographical area of occurrence of the species, using Single Nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS).The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.

Evolutionary effects of geographic and climatic isolation between Rhododendron tsusiophyllum populations on the Izu Islands and mainland Honshu of Japan

Geographic and environmental isolations of islands and the mainland offer excellent opportunity to investigate colonization and survival dynamics of island populations. We inferred and compared evolutionary processes and the demographic history of Rhododendron tsusiophyllum, in the Izu Islands and the much larger island Honshu, treated here as the mainland, using thousands of nuclear SNPs obtained by ddRAD-seq from eight populations of R. tsusiophyllum and three populations of R. tschonoskii as an outgroup. Phylogenetic relationships and their habitats suggest that R. tsusiophyllum had evolved and migrated from cold north to warm south regions. We detected clear genetic divergence among populations in three regions of Honshu and the Izu Islands, suggesting restricted migration between them due to isolated habitats on mountains even in the mainland. The three regions have different changes in effective population size, especially, genetic diversity and population size of the Izu Islands are small compared to the others. Further, habitats of populations in the Izu Islands are warmer than those in Honshu, suggesting that they have undergone adaptive evolution. Our study provides evidences of montane rather than insular isolation on genetic divergence, survival of populations and significance of adaptive evolution for island populations with small population size and low genetic diversity, despite close proximity to mainland populations.

Polyploidy on Islands: Its Emergence and Importance for Diversification

Whole genome duplication or polyploidy is widespread among floras globally, but traditionally has been thought to have played a minor role in the evolution of island biodiversity, based on the low proportion of polyploid taxa present. We investigate five island systems (Juan Fernández, Galápagos, Canary Islands, Hawaiian Islands, and New Zealand) to test whether polyploidy (i) enhances or hinders diversification on islands and (ii) is an intrinsic feature of a lineage or an attribute that emerges in island environments. These island systems are diverse in their origins, geographic and latitudinal distributions, levels of plant species endemism (37% in the Galapagos to 88% in the Hawaiian Islands), and ploidy levels, and taken together are representative of islands more generally. We compiled data for vascular plants and summarized information for each genus on each island system, including the total number of species (native and endemic), generic endemicity, chromosome numbers, genome size, and ploidy levels. Dated phylogenies were used to infer lineage age, number of colonization events, and change in ploidy level relative to the non-island sister lineage. Using phylogenetic path analysis, we then tested how the diversification of endemic lineages varied with the direct and indirect effects of polyploidy (presence of polyploidy, time on island, polyploidization near colonization, colonizer pool size) and other lineage traits not associated with polyploidy (time on island, colonizer pool size, repeat colonization). Diploid and tetraploid were the most common ploidy levels across all islands, with the highest ploidy levels (>8x) recorded for the Canary Islands (12x) and New Zealand (20x). Overall, we found that endemic diversification of our focal island floras was shaped by polyploidy in many cases and certainly others still to be detected considering the lack of data in many lineages. Polyploid speciation on the islands was enhanced by a larger source of potential congeneric colonists and a change in ploidy level compared to overseas sister taxa.

Generation of Chloroplast Molecular Markers to Differentiate Sophora toromiro and Its Hybrids as a First Approach to Its Reintroduction in Rapa Nui (Easter Island)

Sophora toromiro is an endemic tree of Rapa Nui with religious and cultural relevance that despite being extinct in the wild, still persists in botanical gardens and private collections around the world. The authenticity of some toromiro trees has been questioned because the similarities among hybrid lines leads to misclassification of the species. The conservation program of toromiro has the objective of its reinsertion into Rapa Nui, but it requires the exact genotyping and certification of the selected plants in order to efficiently reintroduce the species. In this study, we present for the first time the complete chloroplast genome of S. toromiro and four other Sophora specimens, which were sequenced de-novo and assembled after mapping the raw reads to a chloroplast database. The length of the chloroplast genomes ranges from 154,239 to 154,473 bp. A total of 130-143 simple sequence repeats (SSR) loci and 577 single nucleotide polymorphisms (SNPs) were identified.

Projected climate change threatens significant range contraction of Cochemiea halei (Cactaceae), an island endemic, serpentine-adapted plant species at risk of extinction

AIM

Threats faced by narrowly distributed endemic plant species in the face of the Earth's sixth mass extinction and climate change exposure are especially severe for taxa on islands. We investigated the current and projected distribution and range changes of Cochemiea halei, an endemic island cactus. This taxon is of conservation concern, currently listed as vulnerable on the International Union for the Conservation of Nature Red List and as a species of special concern under Mexican federal law. The goals of this study are to (a) identify the correlations between climate variables and current suitable habitat for C. halei; (b) determine whether the species is a serpentine endemic or has a facultative relationship with ultramafic soils; and (c) predict range changes of the species based on climate change scenarios.

LOCATION

The island archipelago in Bahía Magdalena on the Pacific coast, Baja California Sur, Mexico.

METHODS

We used temperature and precipitation variables at 30-arc second resolution and soil type, employing multiple species distribution modeling methods, to identify important climate and soil conditions driving current habitat suitability. The best model of current suitability is used to predict possible effects of four climate change scenarios based on best-case to worst-case representative concentration pathways, with projected climate data from two general circulation models, over two time periods.

MAIN CONCLUSIONS

The occurrence of the species is found to be strongly correlated with ultramafic soils. The most important climate predictor for habitat suitability is annual temperature range. The species is predicted to undergo range contractions from 21% to 53%, depending on the severity and duration of exposure to climate change. The broader implications for a wide range of narrowly adapted, threatened, and endemic plant species indicate an urgent need for threat assessment based on habitat suitability and climate change modeling.

Chloroplast DNA insights into the phylogenetic position and anagenetic speciation of Phedimus takesimensis (Crassulaceae) on Ulleung and Dokdo Islands, Korea

Phedimus takesimensis (Ulleungdo flat-leaved stonecrop) is endemic to Ulleung and Dokdo Islands off the east coast of the Korean Peninsula. It was suggested that P. takesimensis originated via anagenetic speciation from the continental progenitor species P. kamtchaticus or P. aizoon. However, little is known of the phylogenetic relationships and population genetic structure among species of Phedimus in the Korean Peninsula and Ulleung/Dokdo Islands. We inferred the phylogenetic relationships among congeneric species in Korea based on nuclear ribosomal DNA internal transcribed spacer and chloroplast noncoding regions. We also sampled extensively for P. takesimensis on Ulleung Island and the continental species, P. kamtschaticus and P. aizoon, to assess the genetic consequences of anagenetic speciation. We found (1) the monophyly of P. takesimensis, (2) no apparent reduction in genetic diversity in anagenetically derived P. takesimensis compared to the continental progenitor species, (3) apparent population genetic structuring of P. takesimensis, and (4) two separate colonization events for the origin of the Dokdo Island population. This study contributes to our understanding of the genetic consequences of anagenetic speciation on Ulleung Island.

Comparative genetic and epigenetic diversity in pairs of sympatric, closely related plants with contrasting distribution ranges in south-eastern Iberian mountains

Genetic diversity defines the evolutionary potential of a species, yet mounting evidence suggests that epigenetic diversity could also contribute to adaptation. Elucidating the complex interplay between genetic and epigenetic variation in wild populations remains a challenge for evolutionary biologists, and the intriguing possibility that epigenetic diversity could compensate for the loss of genetic diversity is one aspect that remains basically unexplored in wild plants. This hypothesis is addressed in this paper by comparing the extent and patterns of genetic and epigenetic diversity of phylogenetically closely related but ecologically disparate species. Seven pairs of congeneric species from Cazorla mountains in south-eastern Spain were studied, each pair consisting of one endemic, restricted-range species associated to stressful environments, and one widespread species occupying more favourable habitats. The prediction was tested that endemic species should have lower genetic diversity due to population fragmentation, and higher epigenetic diversity induced by environmental stress, than their widespread congeners. Genetic (DNA sequence variants) and epigenetic (DNA cytosine methylation variants) diversities and their possible co-variation were assessed in three populations of each focal species using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MSAP). All species and populations exhibited moderate to high levels of genetic polymorphism irrespective of their ecological characteristics. Epigenetic diversity was greater than genetic diversity in all cases. Only in endemic species were the two variables positively related, but the difference between epigenetic and genetic diversity was greater at populations with low genetic polymorphism. Results revealed that the relationship between genetic and epigenetic diversity can be more complex than envisaged by the simple hypothesis addressed in this study, and highlight the need of additional research on the actual role of epigenetic variation as a source of phenotypic diversity before a realistic understanding of the evolutionary relevance of epigenetic phenomena in plant adaptation can be achieved.

Genome skimming and microsatellite analysis reveal contrasting patterns of genetic diversity in a rare sandhill endemic (Erysimum teretifolium, Brassicaceae)

Barriers between islands often inhibit gene flow creating patterns of isolation by distance. In island species, the majority of genetic diversity should be distributed among isolated populations. However, a self-incompatible mating system leads to higher genetic variation within populations and very little between-population subdivision. We examine these two contrasting predictions in Erysimum teretifolium, a rare self-incompatible plant endemic to island-like sandhill habitats in Santa Cruz County, California. We used genome skimming and nuclear microsatellites to assess the distribution of genetic diversity within and among eight of the 13 remaining populations. Phylogenetic analyses of the chloroplast genomes revealed a deep separation of three of the eight populations. The nuclear ribosomal DNA cistron showed no genetic subdivision. Nuclear microsatellites suggest 83% of genetic variation resides within populations. Despite this, 18 of 28 between-population comparisons exhibited significant population structure (mean F_ST = 0.153). No isolation by distance existed among all populations, however when one outlier population was removed from the analysis due to uncertain provenance, significant isolation by distance emerged (r² = 0.5611, p = 0.005). Population census size did not correlate with allelic richness as predicted on islands. Bayesian population assignment detected six genetic groupings with substantial admixture. Unique genetic clusters were concentrated at the periphery of the species’ range. Since the overall distribution of nuclear genetic diversity reflects E. tereifolium’s self-incompatible mating system, the vast majority of genetic variation could be sampled within any individual population. Yet, the chloroplast genome results suggest a deep split and some of the nuclear microsatellite analyses indicate some island-like patterns of genetic diversity. Restoration efforts intending to maximize genetic variation should include representatives from both lineages of the chloroplast genome and, for maximum nuclear genetic diversity, should include representatives of the smaller, peripheral populations.

Genetic diversity, structure, and demography of Pandanus boninensis (Pandanaceae) with sea drifted seeds, endemic to the Ogasawara Islands of Japan: Comparison between young and old islands

Pandanus boninensis, endemic to the Ogasawara Islands, Japan, is distributed on both the older Bonin and younger Volcano Islands. In this study, we conducted population genetic analyses of P. boninensis on these islands to examine the population diversity and structure across old and young islands, to assess potential differences in population demography with island age, and to collect any evidence of migration between old and young islands. We found that the genetic diversity of expressed sequence tag (EST)-based microsatellite (SSR) markers, the nucleotide diversity of nuclear DNA sequences, and the haplotype diversity of chloroplast DNA on young islands were lower than those on old islands. Clustering analyses of EST-SSR indicated that populations on old islands were strongly diverged from those on young islands. Approximate Bayesian computation analysis of EST-SSR suggested that population expansion occurred on old islands while population reduction occurred on young islands. We also found evidence of migration among old islands (mostly from south to north), while it appears that there have been very few migration events between old and young islands. These differences could be due to the fact that young islands tend to be geographically isolated and support smaller populations that began a shorter time ago from limited founders. The P. boninensis populations on the Volcano Islands are interesting from an evolutionary perspective as they constitute a classic example of the early stages of progressive colonization on oceanic islands with small effective population sizes and low genetic diversity.

Whole Plastome Sequencing Within Silene Section Psammophilae Reveals Mainland Hybridization and Divergence With the Balearic Island Populations

Reconstructing the phylogenetic relationships within Caryophyllaceae tribe Sileneae has been obscured by hybridization and incomplete lineage sorting. Silene is the largest genus in the Caryophyllaceae, and unraveling its evolutionary history has been particularly challenging. In order to infer the phylogenetic relationships among the five species in Silene section Psammophilae, we have performed a genome skimming approach to acquire the complete plastid genome (cpDNA), nuclear ribosomal cistron (nrDNA), and partial mitochondrial genome (mtDNA). We have included 26 populations, representing the range of each species' distribution. This section includes five morphologically similar species endemic to the Iberian Peninsula and Balearic Islands (Ibiza and Formentera), yet some of them occupy distinct edaphic habitats (e.g. maritime sands, calcareous sandstones). In addition to phylogeographic analyses, genetic structuring using the chloroplast data set was inferred with Discriminant Analysis of Principal Components (DAPC), analyses of molecular variance (AMOVA), and a partial Mantel test. Reference-guided assembly of 50 bp single-end and 250 bp paired-end Illumina reads produced the nearly complete cpDNA genome (154 kbp), partial mtDNA genome (from 81 to 114 kbp), and the nrDNA cistron (6.4 kbp). Selected variable regions of the cpDNA and mtDNA assemblies were confirmed by Sanger sequencing. Phylogenetic analyses of the mainland populations reveal incongruence among the three genomes. None of the three data sets produced relationships consistent with taxonomy or geography. In contrast, Silene cambessedesii, present in the Balearic Islands, is the only species that forms a strongly supported monophyletic clade in the cpDNA genome and is strongly differentiated with respect to the remaining taxa of the Iberian Peninsula. These results contrast with those obtained for mainland populations. Across the entire analysis, only one well-supported mainland clade of Silene littorea and Silene stockenii emerges from the southern region of the Iberian Peninsula. DAPC and AMOVA results suggest the absence of genetic structure among mainland populations of Silene section Psammophilae, whereas partial Mantel test discarded spatial correlation of genetic differentiation. The widespread incongruence between morphology-based taxonomic boundaries and phylogeography suggests a history of interspecific hybridization, in which only a substantial geographic barrier, like isolation by the Mediterranean Sea, was sufficient to create and maintain species boundaries in Silene section Psammophilae.

Multiple origins and the population genetic structure of Rubus takesimensis (Rosaceae) on Ulleung Island: Implications for the genetic consequences of anagenetic speciation

To determine the origin and genetic consequences of anagenesis in Rubus takesimensis on Ulleung Island, Korea, we compared the genetic diversity and population structure of R. takesimensis with those of its continental progenitor R. crataegifolius. We broadly sampled a total of 315 accessions in 35 populations and sequenced five noncoding regions of chloroplast DNA. Rubus takesimensis emerged as nonmonophyletic and several geographically diverse continental populations were likely responsible for the origin of R. takesimensis; the majority of R. takesimensis accessions were sisters to the clade containing accessions of R. crataegifolius, primarily from the Korean peninsula, while rare accessions from three populations shared common ancestors with the ones from the southern part of the Korean peninsula, Jeju Island, and Japan. A few accessions from the Chusan population originated independently from the Korean peninsula. Of 129 haplotypes, 81 and 48 were found exclusively in R. crataegifolius and R. takesimensis, respectively. We found unusually high genetic diversity in two regions on Ulleung Island and no geographic population structure. For R. crataegifolius, two major haplotype groups were found; one for the northern mainland Korean peninsula, and the other for the southern Korean peninsula and the Japanese archipelago. Compared with populations of R. crataegifolius sampled from Japan, much higher haplotype diversity was found in populations from the Korean peninsula. The patterns of genetic consequences in R. takesimensis need to be verified for other endemic species based on chloroplast DNA and independent nuclear markers to synthesize emerging patterns of anagenetic speciation on Ulleung Island.

Phylogeny of Hawaiian Melicope (Rutaceae): RAD-seq Resolves Species Relationships and Reveals Ancient Introgression

Hawaiian Melicope are one of the major adaptive radiations of the Hawaiian Islands comprising 54 endemic species. The lineage is monophyletic with an estimated crown age predating the rise of the current high islands. Phylogenetic inference based on Sanger sequencing has not been sufficient to resolve species or deeper level relationships. Here, we apply restriction site-associated DNA sequencing (RAD-seq) to the lineage to infer phylogenetic relationships. We employ Quartet Sampling to assess information content and statistical support, and to quantify discordance as well as partitioned ABBA-BABA tests to uncover evidence of introgression. Our new results drastically improved resolution of relationships within Hawaiian Melicope. The lineage is divided into five fully supported main clades, two of which correspond to morphologically circumscribed infrageneric groups. We provide evidence for both ancestral and current hybridization events. We confirm the necessity for a taxonomic revision of the Melicope section Pelea, as well as a re-evaluation of several species complexes by combining genomic and morphological data.

Estimated six per cent loss of genetic variation in wild populations since the industrial revolution

Genetic variation is fundamental to population fitness and adaptation to environmental change. Human activities are driving declines in many wild populations and could have similar effects on genetic variation. Despite the importance of estimating such declines, no global estimate of the magnitude of ongoing genetic variation loss has been conducted across species. By combining studies that quantified recent changes in genetic variation across a mean of 27 generations for 91 species, we conservatively estimate a 5.4%-6.5% decline in within-population genetic diversity of wild organisms since the industrial revolution. This loss has been most severe for island species, which show a 27.6% average decline. We identified taxonomic and geographical gaps in temporal studies that must be urgently addressed. Our results are consistent with single time-point meta-analyses, which indicated that genetic variation is likely declining. However, our results represent the first confirmation of a global decline and provide an estimate of the magnitude of the genetic variation lost from wild populations.

Genetic diversity and population divergences of an indigenous tree (Coffea mauritiana) in Reunion Island: role of climatic and geographical factors

Oceanic islands are commonly considered as natural laboratories for studies on evolution and speciation. The evolutionary specificities of islands associated with species biology provide unique scenarios to study the role of geography and climate in driving population divergence. However, few studies have addressed this subject in small oceanic islands with heterogeneous climates. Being widely distributed in Reunion Island forest, Coffea mauritiana represents an interesting model case for investigating patterns of within-island differentiation at small spatial scale. In this study, we examined the genetic diversity and population divergences of C. mauritiana using SNP markers obtained from 323 individuals across 34 locations in Reunion Island. Using redundancy analysis, we further evaluated the contribution of geographic and climatic factors to shaping genetic divergence among populations. Genetic diversity analyses revealed that accessions clustered according to the source population, with further grouping in regional clusters. Genetic relationships among the regional clusters underlined a recent process of expansion in the form of step-by-step colonization on both sides of the island. Divergence among source populations was mostly driven by the joint effect of geographic distance and climatic heterogeneity. The pattern of isolation-by-geography was in accordance with the dispersal characteristics of the species, while isolation-by-environment was mostly explained by the heterogeneous rainfall patterns, probably associated with an asynchronous flowering among populations. These findings advance our knowledge on the patterns of genetic diversity and factors of population differentiation of species native to Reunion Island, and will also usefully guide forest management for conservation.

Psidium guajava in the Galapagos Islands: Population genetics and history of an invasive species

The threat of invasive plant species in island populations prompts the need to better understand their population genetics and dynamics. In the Galapagos islands, this is exemplified by the introduced guava (Psidium guajava), considered one of the greatest threats to the local biodiversity due to its effective spread in the archipelago and its ability to outcompete endemic species. To better understand its history and genetics, we analyzed individuals from three inhabited islands in the Galapagos archipelago with 11 SSR markers. Our results reveal similar genetic diversity between islands, and the populations appear to be distinct: the islands of San Cristobal and Isabela are genetically different while the population of Santa Cruz is a mixture from both. Additional evidence for genetic bottlenecks and the inference of introduction events suggests an original introduction of the species in San Cristobal, from where it was later introduced to Isabela, and finally into Santa Cruz. Alternatively, a second introduction in Isabela might have occurred. These results are contrasted with the historical record, providing a first overview of the history of P. guajava in the Galapagos islands and its current population dynamics.

The complete plastome sequence of Rubus takesimensis endemic to Ulleung Island, Korea: Insights into molecular evolution of anagenetically derived species in Rubus (Rosaceae)

Previous phylogenetic studies have suggested that Rubus takesimensis (Rosaceae), which is endemic to Ulleung Island, Korea, is closely related to R. crataegifolius, which is broadly distributed across East Asia. A recent phylogeographic study also suggested the possible polyphyletic origins of R. takesimensis from multiple source populations of its continental progenitor R. crataegifolius in China, Japan, Korea, and the Russian Far East. However, even though the progenitor-derivative relationship between R. crataegifolius and R. takesimensis has been established, little is known about the chloroplast genome (i.e., plastome) evolution of anagenetically derived species on oceanic islands and their continental progenitor species. In the present study, we characterized the complete plastome of R. takesimensis and compared it to those of R. crataegifolius and four other Rubus species. The R. takesimensis plastome was 155,760 base pairs (bp) long, a total of 46 bp longer than the plastome of R. crataegifolius (28 from LSC and 18 from SSC). No structural or content rearrangements were found between the species pairs. Four highly variable intergenic regions (rpl32/trnL, rps4/trnT, trnT/trnL, and psbZ/trnG) were identified between R. takesimensis and R. crataegifolius. Compared to the plastomes of other congeneric species (R. corchorifolius, R. fockeanus, and R. niveus), six highly variable intergenic regions (ndhC/psaC, rps16/trnQ, trnK/rps16, trnL/trnF, trnM/atpE, and trnQ/psbK) were also identified. A total of 116 simple sequence repeats (SSRs), including 48 mononucleotide, 64 dinucleotide, and four trinucleotide repeat motifs were characterized in R. takesimensis. The plastome resources generated by the present study will help to elucidate plastome evolution within the genus and to resolve phylogenetic relationships within highly complex and reticulated lineages. Phylogenetic analysis supported both the monophyly of Rubus and the sister relationship between R. crataegifolius and R. takesimensis.

Development of 26 microsatellite markers in Bupleurum latissimum (Apiaceae), an endangered plant endemic to Ulleung Island, Korea

PREMISE OF THE STUDY

To enhance our understanding of evolutionary consequences and to establish a suitable conservation strategy, we isolated microsatellite markers for the endangered Bupleurum latissimum (Apiaceae), which is endemic to the oceanic Ulleung Island. We also attempted cross-amplification in B. euphorbioides and B. longeradiatum to investigate its continental progenitors.

METHODS AND RESULTS

Using high-throughput sequencing data, we developed 26 polymorphic microsatellite loci in three multiplexes, of which 13 loci were polymorphic in the two related species. For B. latissimum, alleles numbered two to four and the observed and expected heterozygosity ranged from 0.000 to 0.500 and 0.061 to 0.529, respectively.

CONCLUSIONS

These developed markers will be useful for understanding evolutionary patterns of B. latissimum in an oceanic island system and for establishing suitable conservation strategies at the genetic level.

Diversification in continental island archipelagos: new evidence on the roles of fragmentation, colonization and gene flow on the genetic divergence of Aegean Nigella (Ranunculaceae)

Background and Aims

Disentangling the relative roles of past fragmentation (vicariance), colonization (dispersal) and post-divergence gene flow in the genetic divergence of continental island organisms remains a formidable challenge. Amplified fragment length polymorphisms (AFLPs) were used to (1) gain further insights into the biogeographical processes underlying the Pleistocene diversification of the Aegean Nigella arvensis complex; (2) evaluate the role of potential key factors driving patterns of population genetic variability (mating system, geographical isolation and historical contingencies); and (3) test the robustness of conclusions previously drawn from chloroplast (cp) DNA.

Methods

Genetic diversity was analysed for 235 AFLP markers from 48 populations (497 individuals) representing 11 taxa of the complex using population genetic methods and Bayesian assignment tests.

Key Results

Most designated taxa are identifiable as genetically distinct units. Both fragmentation and dispersal-driven diversification processes occurred at different geological time scales, from Early to Late Pleistocene, specifically (1) sea barrier-induced vicariant speciation in the Cyclades, the Western Cretan Strait and Ikaria; and (2) bi-regional colonizations of the 'Southern Aegean Island Arc' from the Western vs. Eastern Aegean mainland, followed by allopatric divergences in Crete vs. Rhodos and Karpathos/Kasos. Outcrossing island taxa experienced drift-related demographic processes that are magnified in the two insular selfing species. Population genetic differentiation on the mainland seems largely driven by dispersal limitation, while in the Central Aegean it may still be influenced by historical events (island fragmentation and sporadic long-distance colonization).

Conclusions

The biogeographical history of Aegean Nigella is more complex than expected for a strictly allopatric vicariant model of divergence. Nonetheless, the major phylogeographical boundaries of this radiation are largely congruent with the geography and history of islands, with little evidence for ongoing gene exchange between divergent taxa. The present results emphasize the need to investigate further biological and landscape features and contemporary vs. historical processes in driving population divergence and taxon diversification in Aegean plant radiations.

Genetic implications of bottleneck effects of differing severities on genetic diversity in naturally recovering populations: An example from Hawaiian coot and Hawaiian gallinule

The evolutionary trajectory of populations through time is influenced by the interplay of forces (biological, evolutionary, and anthropogenic) acting on the standing genetic variation. We used microsatellite and mitochondrial loci to examine the influence of population declines, of varying severity, on genetic diversity within two Hawaiian endemic waterbirds, the Hawaiian coot and Hawaiian gallinule, by comparing historical (samples collected in the late 1800s and early 1900s) and modern (collected in 2012–2013) populations. Population declines simultaneously experienced by Hawaiian coots and Hawaiian gallinules differentially shaped the evolutionary trajectory of these two populations. Within Hawaiian coot, large reductions (between −38.4% and −51.4%) in mitochondrial diversity were observed, although minimal differences were observed in the distribution of allelic and haplotypic frequencies between sampled time periods. Conversely, for Hawaiian gallinule, allelic frequencies were strongly differentiated between time periods, signatures of a genetic bottleneck were detected, and biases in means of the effective population size were observed at microsatellite loci. The strength of the decline appears to have had a greater influence on genetic diversity within Hawaiian gallinule than Hawaiian coot, coincident with the reduction in census size. These species exhibit similar life history characteristics and generation times; therefore, we hypothesize that differences in behavior and colonization history are likely playing a large role in how allelic and haplotypic frequencies are being shaped through time. Furthermore, differences in patterns of genetic diversity within Hawaiian coot and Hawaiian gallinule highlight the influence of demographic and evolutionary processes in shaping how species respond genetically to ecological stressors.

Molecular genetic analysis of two native desert palm genera, Washingtonia and Brahea, from the Baja California Peninsula and Guadalupe Island

The complex geological and ecological processes that have generated high levels of biodiversity and endemism in the Baja California Peninsula have been the subject of intensive study. However, relatively little is known about phylogeography of the iconic endemic palm species of this region. We therefore analyzed a total of 2,294 bp of chloroplast and 738 bp of nuclear sequence data in 169 samples of five native palm species from Baja California, Sonora and Guadalupe Island. We found that Washingtonia and Brahea palms had low levels of genetic diversity and were highly structured, with the majority of species and major geographic regions being characterized by distinct haplotypes. We also found strong support for currently recognized species in Washingtonia, but our results were less clear cut for Brahea due to haplotype sharing. Furthermore, patterns of population structure were broadly consistent with historical vicariant events such as the inundation of the Isthmus of La Paz, the formation of the Sea of Cortez, and the more recent colonization and isolation of Guadalupe Island's palms. Our findings contribute toward a growing appreciation of the complexity of plant responses to past geological changes and also provide valuable baseline genetic data on relict American palm species.

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.

Viola woosanensis, a recurrent spontaneous hybrid between V. ulleungdoensis and V. chaerophylloides (Violaceae) endemic to Ulleung Island, Korea

Ulleung Island is an oceanic volcanic island in Korea, which has never been connected to the adjacent continent. Previous studies highlighted Ulleung Island as an excellent system to study the pattern and process of early stages of flowering plant evolutions on oceanic island. The predominant mode of speciation in flowering plants on Ulleung Island appears to be anagenesis. However, the potentially important role of hybrid speciation among incompletely reproductively isolated lineages cannot be ruled out. Viola woosanensis (Violaceae) is of purportedly hybrid origin between V. ulleungdoensis (i.e., formerly recognized as V. selkirkii in Ulleung Island) and V. chaerophylloides, based on morphology. To examine the origin of V. woosanensis, we sampled a total of 80 accessions, including V. woosanensis and its putative parental species and sequenced nrDNA ITS, and four highly variable chloroplast noncoding regions (trnL-trnF, rpl16 intron, atpF-atpH, and psbA-trnH). Representative species of Viola from Korea were also included in the phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference). Additive polymorphic sites in the nrDNA ITS regions were confirmed by cloning amplicons from representative species. The molecular data strongly supported the hybrid origin of V. woosanensis, and the maternal and paternal parent were determined to be V. ulleungdoensis and V. chaerophylloides, respectively. The presence of two parental ribotypes in V. woosanensis (with the exception in one population) was confirmed by cloning, suggesting V. woosanensis is primarily the F1 generation. No trace of backcrossing and introgression with its parents was detected due to low fertility of hybrid species. We found a multiple and unidirectional hybrid origin of V. woosanensis. Additional studies are required to determine which factors contribute to asymmetric gene flow of Viola species in Ulleung Island.

Determinants of genetic diversity

Genetic polymorphism varies among species and within genomes, and has important implications for the evolution and conservation of species. The determinants of this variation have been poorly understood, but population genomic data from a wide range of organisms now make it possible to delineate the underlying evolutionary processes, notably how variation in the effective population size (Ne) governs genetic diversity. Comparative population genomics is on its way to providing a solution to 'Lewontin's paradox' - the discrepancy between the many orders of magnitude of variation in population size and the much narrower distribution of diversity levels. It seems that linked selection plays an important part both in the overall genetic diversity of a species and in the variation in diversity within the genome. Genetic diversity also seems to be predictable from the life history of a species.

Scrophularia arguta, a widespread annual plant in the Canary Islands: a single recent colonization event or a more complex phylogeographic pattern?

Many studies have addressed evolution and phylogeography of plant taxa in oceanic islands, but have primarily focused on endemics because of the assumption that in widespread taxa the absence of morphological differentiation between island and mainland populations is due to recent colonization. In this paper, we studied the phylogeography of Scrophularia arguta, a widespread annual species, in an attempt to determine the number and spatiotemporal origins of dispersal events to Canary Islands. Four different regions, ITS and ETS from nDNA and psbA-trnH and psbJ-petA from cpDNA, were used to date divergence events within S. arguta lineages and determine the phylogenetic relationships among populations. A haplotype network was obtained to elucidate the phylogenetic relationships among haplotypes. Our results support an ancient origin of S. arguta (Miocene) with expansion and genetic differentiation in the Pliocene coinciding with the aridification of northern Africa and the formation of the Mediterranean climate. Indeed, results indicate for Canary Islands three different events of colonization, including two ancient events that probably happened in the Pliocene and have originated the genetically most divergent populations into this species and, interestingly, a recent third event of colonization of Gran Canaria from mainland instead from the closest islands (Tenerife or Fuerteventura). In spite of the great genetic divergence among populations, it has not implied any morphological variation. Our work highlights the importance of nonendemic species to the genetic richness and conservation of island flora and the significance of the island populations of widespread taxa in the global biodiversity.

Evolutionary and Biogeographic Insights on the Macaronesian Beta-Patellifolia Species (Amaranthaceae) from a Time-Scaled Molecular Phylogeny

The Western Mediterranean Region and Macaronesian Islands are one of the top biodiversity hotspots of Europe, containing a significant native genetic diversity of global value among the Crop Wild Relatives (CWR). Sugar beet is the primary crop of the genus Beta (subfamily Betoideae, Amaranthaceae) and despite the great economic importance of this genus, and of the close relative Patellifolia species, a reconstruction of their evolutionary history is still lacking. We analyzed nrDNA (ITS) and cpDNA gene (matK, trnH-psbA, trnL intron, rbcL) sequences to: (i) investigate the phylogenetic relationships within the Betoideae subfamily, and (ii) elucidate the historical biogeography of wild beet species in the Western Mediterranean Region, including the Macaronesian Islands. The results support the Betoideae as a monophyletic group (excluding the Acroglochin genus) and provide a detailed inference of relationships within this subfamily, revealing: (i) a deep genetic differentiation between Beta and Patellifolia species, which may have occurred in Late Oligocene; and (ii) the occurrence of a West-East genetic divergence within Beta, indicating that the Mediterranean species probably differentiated by the end of the Miocene. This was interpreted as a signature of species radiation induced by dramatic habitat changes during the Messinian Salinity Crisis (MSC, 5.96-5.33 Mya). Moreover, colonization events during the Pleistocene also played a role in shaping the current diversity patterns among and within the Macaronesian Islands. The origin and number of these events could not be revealed due to insufficient phylogenetic resolution, suggesting that the diversification was quite recent in these archipelagos, and unravelling potential complex biogeographic patterns with hybridization and gene flow playing an important role. Finally, three evolutionary lineages were identified corresponding to major gene pools of sugar beet wild relatives, which provide useful information for establishing in situ and ex situ conservation priorities in the hotspot area of the Macaronesian Islands.

Oceanic island biogeography through the lens of the general dynamic model: assessment and prospect

The general dynamic model of oceanic island biogeography (GDM) has added a new dimension to theoretical island biogeography in recognizing that geological processes are key drivers of the evolutionary processes of diversification and extinction within remote islands. It provides a dynamic and essentially non-equilibrium framework generating novel predictions for emergent diversity properties of oceanic islands and archipelagos. Its publication in 2008 coincided with, and spurred on, renewed attention to the dynamics of remote islands. We review progress, both in testing the GDM's predictions and in developing and enhancing ecological-evolutionary understanding of oceanic island systems through the lens of the GDM. In particular, we focus on four main themes: (i) macroecological tests using a space-for-time rationale; (ii) extensions of theory to islands following different patterns of ontogeny; (iii) the implications of GDM dynamics for lineage diversification and trait evolution; and (iv) the potential for downscaling GDM dynamics to local-scale ecological patterns and processes within islands. We also consider the implications of the GDM for understanding patterns of non-native species diversity. We demonstrate the vitality of the field of island biogeography by identifying a range of potentially productive lines for future research.

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.

Genetic consequences of cladogenetic vs. anagenetic speciation in endemic plants of oceanic islands

Adaptive radiation is a common mode of speciation among plants endemic to oceanic islands. This pattern is one of cladogenesis, or splitting of the founder population, into diverse lineages in divergent habitats. In contrast, endemic species have also evolved primarily by simple transformations from progenitors in source regions. This is anagenesis, whereby the founding population changes genetically and morphologically over time primarily through mutation and recombination. Gene flow among populations is maintained in a homogeneous environment with no splitting events. Genetic consequences of these modes of speciation have been examined in the Juan Fernández Archipelago, which contains two principal islands of differing geological ages. This article summarizes population genetic results (nearly 4000 analyses) from examination of 15 endemic species, involving 1716 and 1870 individuals in 162 and 163 populations (with amplified fragment length polymorphisms and simple sequence repeats, respectively) in the following genera: Drimys (Winteraceae), Myrceugenia (Myrtaceae), Rhaphithamnus (Verbenaceae), Robinsonia (Asteraceae, Senecioneae) and Erigeron (Asteraceae, Astereae). The results indicate that species originating anagenetically show high levels of genetic variation within the island population and no geographic genetic partitioning. This contrasts with cladogenetic species that show less genetic diversity within and among populations. Species that have been derived anagenetically on the younger island (1-2 Ma) contain less genetic variation than those that have anagenetically speciated on the older island (4 Ma). Genetic distinctness among cladogenetically derived species on the older island is greater than among similarly derived species on the younger island. An important point is that the total genetic variation within each genus analysed is comparable, regardless of whether adaptive divergence occurs.

Do island plant populations really have lower genetic variation than mainland populations? Effects of selection and distribution range on genetic diversity estimates

Ecological and evolutionary studies largely assume that island populations display low levels of neutral genetic variation. However, this notion has only been formally tested in a few cases involving plant taxa, and the confounding effect of selection on genetic diversity (GD) estimates based on putatively neutral markers has typically been overlooked. Here, we generated nuclear microsatellite and plastid DNA sequence data in Periploca laevigata, a plant taxon with an island-mainland distribution area, to (i) investigate whether selection affects GD estimates of populations across contrasting habitats; and (ii) test the long-standing idea that island populations have lower GD than their mainland counterparts. Plastid data showed that colonization of the Canary Islands promoted strong lineage divergence within P. laevigata, which was accompanied by selective sweeps at several nuclear microsatellite loci. Inclusion of loci affected by strong divergent selection produced a significant downward bias in the GD estimates of the mainland lineage, but such underestimates were substantial (>14%) only when more than one loci under selection were included in the computations. When loci affected by selection were removed, we did not find evidence that insular Periploca populations have less GD than their mainland counterparts. The analysis of data obtained from a comprehensive literature survey reinforced this result, as overall comparisons of GD estimates between island and mainland populations were not significant across plant taxa (N = 66), with the only exception of island endemics with narrow distributions. This study suggests that identification and removal of markers potentially affected by selection should be routinely implemented in estimates of GD, particularly if different lineages are compared. Furthermore, it provides compelling evidence that the expectation of low GD cannot be generalized to island plant populations.