Robinson Crusoe Island of the Juan Fernández Archipelago, as is the case with many oceanic islands, has experienced strong human disturbances through exploitation of resources and introduction of alien biota. To understand these impacts and for purposes of diversity and resource management, an accurate assessment of the composition and structure of plant communities was made. We analyzed the vegetation with 106 relevés (vegetation records) and subsequent Twinspan ordination and produced a detailed colored map at 1:30,000. The resultant map units are (1) endemic upper montane forest, (2) endemic lower montane forest, (3) Ugni molinae shrubland, (4) Rubus ulmifolius-Aristotelia chilensis shrubland, (5) fern assemblages, (6) Libertia chilensis assemblage, (7) Acaena argentea assemblage, (8) native grassland, (9) weed assemblages, (10) tall ruderals, and (11) cultivated Eucalyptus, Cupressus, and Pinus. Mosaic patterns consisting of several communities are recognized as mixed units: (12) combined upper and lower montane endemic forest with aliens, (13) scattered native vegetation among rocks at higher elevations, (14) scattered grassland and weeds among rocks at lower elevations, and (15) grassland with Acaena argentea. Two categories are included that are not vegetation units: (16) rocks and eroded areas, and (17) settlement and airfield. Endemic forests at lower elevations and in drier zones of the island are under strong pressure from three woody species, Aristotelia chilensis, Rubus ulmifolius, and Ugni molinae. The latter invades native forests by ascending dry slopes and ridges. It successfully outcompetes endemic taxa, including its congener Ugni selkirkii. The aggressive herb Acaena argentea severely threatens to overtake native grassland.

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.

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.