Assessing signals of selection and historical demography to develop conservation strategies in the Chilean emblematic Araucaria araucana.

Loss of genetic diversity reduces the ability of species to evolve and respond to environmental change. Araucaria araucana is an emblematic conifer species from southern South America, with important ethnic value for the Mapuche people (Pehuenche); the Chilean Government has catalogued its conservation status as vulnerable. Climatic fluctuations were potentially a major impact in the genetic variation within many tree species. In this context, the restricted geographic distribution of A. araucana in Chile appears to be a consequence of the Last Glacial Maximum (LGM). During the past two centuries, strong human intervention has also affected the geographical distribution and population sizes of A. araucana. Reduction of population size may cause loss of genetic diversity, which could affect frequency of adaptive loci. The aims of this study were to know the existence of potential loci under selection and populations with genetic, demographic disequilibrium in the Chilean distribution of A. araucana. Based on 268 polymorphic AFLP loci, we have investigated potential loci under selection and genetic, demographic disequilibrium within seven Chilean populations of Araucaria araucana. Correlation of 41 outlier loci with the environmental variables of precipitation and temperature reveals signatures of selection, whereas 227 neutral loci provide estimates of demographic equilibrium and genetic population structure. Three populations are recommended as priorities for conservation.

Plastid Phylogenomics of Dendroseris (Cichorieae; Asteraceae): Insights Into Structural Organization and Molecular Evolution of an Endemic Lineage From the Juan Fernández Islands.

Dendroseris D. Don comprises 11 species endemic to the Juan Fernández islands in Chile. They demonstrate spectacular and unusual growth forms of rosette trees with extremely variable morphology and occupy wide ecological ranges on the islands. These unique plants are now highly threatened with extinction with very small population sizes, typically consisting of 10 or fewer individuals in wild. Despite morphological and ecological divergence among species of Dendroseris, their monophyly has been supported in previous studies, but with little resolution among subgeneric groups. We assembled seven complete plastome sequences from seven species of Dendroseris, including representatives from three subgenera, and carried out comparative phylogenomic analyses. The plastomes are highly conserved in gene content and order, with size ranging from 152,199 to 152,619 bp and containing 130 genes (87 coding genes, 6 rRNA genes, and 37 tRNA genes). Plastid phylogenomic analyses based on both the complete plastome sequences and 81 concatenated coding genes only show Dendroseris nested within Sonchus sensu lato, and also that inter-subgeneric relationships are fully resolved. Subg. Phoenicoseris is resolved as sister to the remaining species of the genus and a sister relationship between the two subgenera Dendroseris and Rea. Ten mutation hotspots from LSC and SSC regions and variable SSRs are identified as potential chloroplast markers for future phylogenetic and phylogeographic studies of Sonchus and related groups.

Correction to: Factors driving adaptive radiation in plants of oceanic islands: a case study from the Juan Fernández Archipelago.

The article Factors driving adaptive radiation in plants of oceanic islands: a case study from the Juan Fernández Archipelago, written by Koji Takayama, Daniel J. Crawford, Patricio López­Sepúlveda, Josef Greimler, Tod F. Stuessy was originally published electronically on the publisher's internet portal (currently SpringerLink) on 13 March 2018 without open access.

Strong indication of an extinction-based saturation of the flora on the Pacific Robinson Crusoe Islands.

Oceanic islands are vulnerable ecosystems and their flora has been under pressure since the arrival of the first humans. Human activities and both deliberately and inadvertently introduced biota have had and continue to have a severe impact on island endemic plants. The number of alien plants has increased nearly linearly on many islands, perhaps resulting in extinction-based saturation of island floras. Here, we provide evidence for such a scenario in Alejandro Selkirk, Robinson Crusoe Islands (Archipelago Juan Fernández, Chile). We compared species richness and species composition of historical vegetation samples from 1917 with recent ones from 2011. Changes in species' relative occurrence frequency were related to their taxonomic affiliation, dispersal mode, distribution status, and humidity and temperature preferences. While total species richness of vascular plants remained relatively similar, species composition changed significantly. Plants endemic to the Robinson Crusoe Islands declined, exotic species increased substantially within the period of ca. 100 years. Further, the relative occurrence frequency of plants with preferences for very warm and humid climate decreased, while the opposite was found for plants preferring drier and colder environments. Potential drivers responsible for this dramatic shift in the vegetation within only one century might have been the large goat population affecting especially small populations of endemic plants and climatic changes. Taking into account a substantial extinction debt, we expect further shifts in the vegetation of this small oceanic island toward alien plants. This would have significant negative consequences on global biodiversity, considering that island floras contribute substantially to global plant species richness due to their high proportion of endemics.

Factors driving adaptive radiation in plants of oceanic islands: a case study from the Juan Fernández Archipelago.

Adaptive radiation is a common evolutionary phenomenon in oceanic islands. From one successful immigrant population, dispersal into different island environments and directional selection can rapidly yield a series of morphologically distinct species, each adapted to its own particular environment. Not all island immigrants, however, follow this evolutionary pathway. Others successfully arrive and establish viable populations, but they remain in the same ecological zone and only slowly diverge over millions of years. This transformational speciation, or anagenesis, is also common in oceanic archipelagos. The critical question is why do some groups radiate adaptively and others not? The Juan Fernández Islands contain 105 endemic taxa of angiosperms, 49% of which have originated by adaptive radiation (cladogenesis) and 51% by anagenesis, hence providing an opportunity to examine characteristics of taxa that have undergone both types of speciation in the same general island environment. Life form, dispersal mode, and total number of species in progenitors (genera) of endemic angiosperms in the archipelago were investigated from literature sources and compared with modes of speciation (cladogenesis vs. anagenesis). It is suggested that immigrants tending to undergo adaptive radiation are herbaceous perennial herbs, with leaky self-incompatible breeding systems, good intra-island dispersal capabilities, and flexible structural and physiological systems. Perhaps more importantly, the progenitors of adaptively radiated groups in islands are those that have already been successful in adaptations to different environments in source areas, and which have also undergone eco-geographic speciation. Evolutionary success via adaptive radiation in oceanic islands, therefore, is less a novel feature of island lineages but rather a continuation of tendency for successful adaptive speciation in lineages of continental source regions.

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.

Progressive migration and anagenesis in Drimys confertifolia of the Juan Fernández Archipelago, Chile.

A common mode of speciation in oceanic islands is by anagenesis, wherein an immigrant arrives and through time transforms by mutation, recombination, and drift into a morphologically and genetically distinct species, with the new species accumulating a high level of genetic diversity. We investigate speciation in Drimys confertifolia, endemic to the two major islands of the Juan Fernández Archipelago, Chile, to determine genetic consequences of anagenesis, to examine relationships among populations of D. confertifolia and the continental species D. winteri and D. andina, and to test probable migration routes between the major islands. Population genetic analyses were conducted using AFLPs and nuclear microsatellites of 421 individuals from 42 populations from the Juan Fernández islands and the continent. Drimys confertifolia shows a wide genetic variation within populations on both islands, and values of genetic diversity within populations are similar to those found within populations of the continental progenitor. The genetic results are compatible with the hypothesis of high levels of genetic variation accumulating within anagenetically derived species in oceanic islands, and with the concept of little or no geographical partitioning of this variation over the landscape. Analysis of the probability of migration within the archipelago confirms colonization from the older island, Robinson Crusoe, to the younger island Alejandro Selkirk.

Relationships and genetic consequences of contrasting modes of speciation among endemic species of Robinsonia (Asteraceae, Senecioneae) of the Juan Fernández Archipelago, Chile, based on AFLPs and SSRs.

This study analyses and compares the genetic signatures of anagenetic and cladogenetic speciation in six species of the genus Robinsonia (Asteraceae, Senecioneae), endemic to the Juan Fernández Islands, Chile. Population genetic structure was analyzed by amplified fragment length polymorphism (AFLP) and microsatellite (simple sequence repeat, SSR) markers from 286 and 320 individuals, respectively, in 28 populations. Each species is genetically distinct. Previous hypotheses of classification among these species into subgenera and sections, via morphological, phytochemical, isozymic and internal transcribed spacer (ITS) data, have been confirmed, except that R. saxatilis appears to be related to R. gayana rather than R. evenia. Analysis of phylogenetic results and biogeographic context suggests that five of these species have originated by cladogenesis and adaptive radiation on the older Robinson Crusoe Island. The sixth species, R. masafuerae, restricted to the younger Alejandro Selkirk Island, is closely related to and an anagenetic derivative of R. evenia from Robinson Crusoe. Microsatellite and AFLP data reveal considerable genetic variation among the cladogenetically derived species of Robinsonia, but within each the genetic variation is lower, highlighting presumptive genetic isolation and rapid radiation. The anagenetically derived R. masafuerae harbors a level of genetic variation similar to that of its progenitor, R. evenia. This is the first direct comparison of the genetic consequences of anagenetic and cladogenetic speciation in plants of an oceanic archipelago.

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

Oceanic islands offer special opportunities for understanding the patterns and processes of evolution. The availability of molecular markers in recent decades has enhanced these opportunities, facilitating the use of population genetics to reveal divergence and speciation in island systems. A common pattern seen in taxa on oceanic islands is a decreased level of genetic variation within and among populations, and the founder effect has often been invoked to explain this observation. Founder effects have a major impact on immigrant populations, but, over millions of years, the original genetic signature will normally be erased as a result of mutation, recombination, drift and selection. Therefore, the types and degrees of genetic modifications that occur must often be caused by other factors, which should be considered when explaining the patterns of genetic variation. The age of the island is extremely important because oceanic islands subside on their submarine plates over time. Erosion caused by wind, rain and wave action combine to grind down soft volcanic substrates. These geomorphological events can have a dramatic impact on population number and size, and hence levels of genetic diversity. The mode of speciation is also of significance. With anagenesis, genetic variation accumulates through time, whereas, with cladogenenesis, the gene pool splits into populations of adaptively radiating species. Breeding systems, population sizes and generation times are also important, as is hybridization between closely related taxa. Human disturbance has affected plant population number and size through the harvesting of forests and the introduction of invasive plants and animals. Therefore, the explanation of the observed levels of genetic variation in species of oceanic islands requires the consideration of many interconnected physical, biological and anthropomorphic factors.

Development of microsatellite markers in Robinsonia (Asteraceae) an endemic genus of the Juan Fernández Archipelago, Chile.

Ten microsatellite markers were developed for Robinsonia (Asteraceae), a genus endemic to the Juan Fernández Archipelago, Chile. Polymorphisms of these markers were tested using one population each of R. evenia, R. gayana, and R. gracilis. The number of alleles for these markers ranged from 2 to 17 per locus, and expected heterozygosity ranged from 0 to 0.847 by population. A significant deviation from Hardy-Weinberg equilibrium was observed in zero to two markers in each population, and no significant linkage disequilibrium between markers was detected. The markers reported here would be useful for evolutionary studies and conservation strategies in Robinsonia.

Genetic variation (AFLPs and nuclear microsatellites) in two anagenetically derived endemic species of Myrceugenia (Myrtaceae) on the Juan Fernández Islands, Chile.

PREMISE OF THE STUDY: Anagenesis (or phyletic evolution) is one mode of speciation that occurs in the evolution of plants on oceanic islands. Of two endemic species on the Juan Fernández Islands (Chile), Myrceugenia fernandeziana and M. schulzei (Myrtaceae), believed to have originated anagenetically from different continental progenitors, the first is endemic to Robinson Crusoe Island and has no clear tie to continental relatives; the last is endemic to the younger island, Alejandro Selkirk Island, and has close affinity to M. colchaguensis in mainland Chile. METHODS: Using AFLPs and six nuclear microsatellites from 381 individuals representing 33 populations, we determined patterns of genetic variation within and among populations on both islands and between those of the islands and mainland. KEY RESULTS: Considerable genetic variation was found within populations on both islands. The level of gene diversity within M. schulzei was equivalent to that of its close continental relative M. colchaguensis. Genetic diversity was not partitioned geographically in M. fernandeziana and was weakly so and nonsignificantly in M. schulzei. CONCLUSIONS: The high genetic variation in both taxa is most likely due to anagenetic speciation. Subsidence of the older island Robinson Crusoe, landscape erosion, and restructuring of communities have severely reduced the overall island population to a single panmictic system. On the younger and less modified Alejandro Selkirk Island, slightly stronger patterns of genetic divergence are seen in M. schulzei. Because both species are genetically diverse and number in the thousands of individuals, neither is presently endangered in the archipelago.

Development of microsatellite markers in species of Erigeron (Asteraceae) endemic to the Juan Fernández Archipelago, Chile.

PREMISE OF THE STUDY: Microsatellite markers were developed in Erigeron rupicola and tested by amplification in six Erigeron species endemic to the Juan Fernández Archipelago, Chile, to investigate genetic diversity and population structure. • METHODS AND RESULTS: Using 454 pyrosequencing, 24 primer pairs were developed in E. rupicola, 12 of which amplified and presented polymorphism among endemic species of Erigeron in the Archipelago. Two populations from E. rupicola and E. fernandezianus were genotyped, and one to eight alleles per locus per population were detected. The expected heterozygosity ranged from 0.000 to 0.812. • CONCLUSIONS: These results indicate the utility of primers for cross-species populational studies in all endemic species of Erigeron in the Archipelago.