Andean South America, including the adjacent lowland environments, can be evaluated in reference to the patterns and processes that characterize plant diversity, evolution, and distribution. Although its ecological complexity is bewildering and the evolutionary and geological history is convoluted and poorly understood, progress can be made by testing the relationship of known processes and paleoevents to patterns of diversification and distribution.

Plant diversity patterns can be quantified and mapped in order to permit the study of linkages to environmental parameters and to past speciation and extinction processes. Such studies show the importance of dispersal barriers and long altitudinal gradients for the evolution of Andean plants. Phylogenetic studies allow for the tying of these processes to the timing of connections from the Andes to adjacent tropical forests, grasslands, and deserts, to other highlands in South America, or to other continents. They can also reveal temporal relationships among a variety of plant lineages, allowing for the identification of basal groups, of paleoendemics, and of the recently derived neoendemics. The special places in South America that have high representation of these restricted-range taxa can be better understood as a result. In the Andean context, these are often located in isolated habitat islands, with moisture regimes ranging from arid to perhumid.

These patterns allow the development of conservation actions that respond to the presence of special places for plant diversification and of special species that require immediate attention. Further research will include the documentation of patterns at ever-finer spatial resolutions, to better match our biodiversity databases with the topographical and ecological features found in South America. The phylogenetics of plant molecular and morphological characters provide a necessary evolutionary framework that can then be compared to processes identified as important among animal and fungi lineages. For Andean South America, coevolution of plant and animal species is an important source of additional complexity, while trends of evolution to occupy drier and/or higher environments appear in numerous lineages. Anthropogenic influences on these patterns and processes are little understood, but humans have affected and will continue to shape the composition, diversity, and geography of South American biota.

Conservation of biodiversity will necessitate choices among areas, taxa, and land-use patterns. Lack of data on distribution and pattern in biodiversity makes these difficult decisions even more problematic for those charged with the conservation and sustainable use of the diversity of life. Quantitative methods have promise in helping with this task in that they allow people to make their values explicit, and they also allow representation and comparison of many different types of data.

In this article I examine patterns of species richness and range-size rarity, or endemism, in the Neotropics with a data set from the genus Solanum (Solanaceae). Distribution data for 180 species of forest-dwelling solanums were analyzed. Patterns of species richness, range-size rarity (endemism), and several area-selection methods were examined. Montane areas are relatively rich both in all species and in endemic species, with maximal peaks in the Andes. The peak of species richness coincides with the domain (i.e., continental) midpoint (9°30′ S latitude), suggesting that the pattern observed may be partly due to the geometry of species ranges. The Solanum results are compared with those obtained for other taxonomic groups in the Neotropics, and problems with quantitative data sets in conservation are discussed. Collecting deficit, parochial taxonomy, and habitat destruction, both historical and current, are all factors that will affect the utility of such analyses. It is clear that if conservation is to work on the ground, we need to know more about what occurs in the montane Neotropics and that continued work at a basic taxonomic level is essential to our ultimate ability to conserve biological diversity.

Some scientists have suggested that the Huancabamba Depression in northern Peru—i.e., the partial interruption of the Andean chain by the Río Chamaya drainage system—represents a major biogeographical barrier to montane taxa. Others have suggested that the Amotape-Huancabamba Zone in the Andes of northern Peru and the extreme south of Ecuador is an area of particular biological diversity and possibly a phytogeographical zone in its own right.

The phytogeography of this area is investigated here with data mainly from the Loasaceae, supplemented by data on other plant and animal groups and by some new data from Passiflora L. (Passifloraceae) and Ribes L. (Grossulariaceae). The Huancabamba Depression itself does not seem to have been a major dispersal barrier for these groups. However, a phytogeographical zone—the Amotape-Huancabamba Zone—between the Río Jubones system in Ecuador and the Río Chamaya system in Peru can be recognized from the available data. This zone seems to be home to numerous endemic species and species groups and has a high level of diversity (6–8 times as high as adjacent areas to the north and to the south in the groups studied). The species of this area show narrow endemicity and often strikingly aberrant morphological characters, compared with representatives of the same groups from other areas.

The overlap between northern and southern groups in the area, the mosaic nature of its habitats (geology, geography, and climate), and a varied geological history (habitat fragmentation, secondary contact) seem to be the three most important factors contributing to these patterns of diversification. At least some phylogenetically old taxa appear to have survived in the Amotape-Huancabamba Zone. The region thus seems to be home to a high number of both neoendemics and paleoendemics.

In the Neotropics, the Ericaceae are an Andean-centered family, adapted to moist, open, cool montane environments. Overall species richness increases nearer the Equator, with the highest species numbers concentrated in Colombia and Ecuador between 1000 m and 3000 m. There are 46 genera (70% endemic) and about 800 species (ca. 94% endemic) of Ericaceae native to the Neotropics. Five biogeographical regions are recognized for the neotropical Ericaceae, with the greatest species diversity found in the Andes of northwestern South America. Following Pliocene/Pleistocene mountain-building and climatic events, neotropical Ericaceae underwent dynamic speciation and extensive adaptive radiation due to their ecological and life-form plasticity, colonization abilities, adaptation to epiphytic habits, and coevolution with hummingbirds. Given high diversity and singularity within neotropical Ericaceae, along with high levels of habitat alteration, protection of Andean montane ecosystems should become a priority for the conservation of Ericaceae in the Neotropics.

Evaluation of the lichen flora of the Northern Andes must be based on a restricted number of better-known groups, probably less than 25% of the flora. This is because our knowledge of the taxonomy and distribution of lichens in the Tropics is still very incomplete.

In the Andes, the groups with foliose and fruticose growth forms are particularly well represented; the crustose group seems less important. This is in contrast with the surrounding lowlands, where crustose is the dominant growth form. At higher taxonomic levels there is a resemblance in taxonomic composition with the cooler zones of the world, which disappears at the generic or sectional levels. A conspicuous morphological feature is the frequency of foliose lichens with linear, rhizinate, or ciliate lobes, probably an adaptation to very humid conditions.

More than half of the species have a wide distribution throughout the Tropics or at least in the Neotropics. Among the more restricted taxa is a humid montane element. At the highest elevations a temperate element is apparent, usually with bicentric distribution in both hemispheres. Perhaps 10% of the species are known only from the region; local endemism is probably very scarce. A few taxa appear to be restricted to Ecuador and southern Colombia or Venezuela; so far, only a single species is known with certainty to be restricted to the humid páramos of Colombia. There are distinct affinities with the lichen flora of southeastern Brazil and the Caribbean–Central American area but not with the adjacent Guayana Highland.

The abiotic, historical, and autecological factors determining the range sizes of tropical plant species and the distribution of endemism are still poorly understood. In this study, the variation of range-size rarity was analyzed among the bromeliad communities of 74 forest sites in the Bolivian Andes and adjacent lowlands with respect to 14 environmental factors reflecting mostly climatic conditions and to species attributes such as life-form, ecophysiological type, pollination mode, and fruit type. The global ranges of all 192 recorded bromeliad species were mapped on a 1° grid, quantified as the number of 1° grids occupied by a species, and range-size rarity indices were calculated as the mean inverse range size of all species at a given study site.

At the community level, range-size rarity increased with elevation, most notably among epiphytic taxa. Range-size rarity of terrestrial forest species increased with decreasing habitat area, presumably reflecting the agglomeration of endemic species in isolated dry forest valleys with restricted area. Epiphytes showed higher range-size rarity in the most humid areas, which are also geographically isolated. At the species level, range size revealed a limited relationship to pollination mode or ecophysiological type but differed significantly between epiphytic species (large ranges) and terrestrial and saxicolous taxa (small ranges). However, this pattern was outweighed by differences among fruit types, with berries corresponding to large ranges, winddispersed seeds with flight appendages to intermediate ranges, and wind-dispersed seeds without appendages to small ranges. It is hypothesized that the tendency toward larger ranges among epiphytes (of any plant group) is due at least partly to the prevalence of taxa with adaptations to long-distance dispersal, ensuring efficient colonization of canopy habitats while preventing the differentiation of populations.

The Oxalis tuberosa alliance is a group of morphologically similar Oxalis species allied to the Andean tuber crop oca, O. tuberosa. Originally described by cytologists as a dozen species sharing a base chromosome number rare in Oxalis (x = 8), the alliance as defined here includes additional species for which cytological information is not yet available but which are supported as members on molecular and/or morphological grounds. The alliance includes members found in the Andean region from Venezuela to northern Argentina, with one species at high elevations in Central America. They occur from the high Andean steppes (páramo and puna) to the cloud forests of middle elevations and include both restricted endemics and variable widespread species complexes.

Geographical and altitudinal distributions of members of the alliance and selected Oxalis species outside the alliance were compared with a combined phylogenetic analysis of DNA sequence data of ITS and ncpGS (chloroplast-expressed glutamine synthetase). Groups within the alliance (i.e., major clades on the molecular trees) occur across widespread, overlapping regions in the Andes, with only partial ecological separation. The hypothesis that the O. tuberosa alliance may have developed in the Andes of southern Peru and northwestern Bolivia and radiated southward and, especially, northward along the Andean axis is suggested by patterns of distributions of members of the alliance and outgroups. In spite of uncertain species delimitations, it is clear that the alliance includes many endemic species and ecotypes that have very restricted distributions. As relatives of the Andean tuber crop Oxalis tuberosa, the genetic diversity represented by this geographical variability should be a high priority for conservation.

Chuquiraga is a genus of 23 species of evergreen shrubs endemic to South America. It is distributed principally along the Andes from Colombia to Chile and Argentina, and it is especially diversified in the Central Andes and in the deserts and semideserts of southern South America. The genus exhibits a wide array of leaf-morphology types and two different head and floral types apparently related to hummingbird and insect pollination.

In this study, phylogenetic relationships among Chuquiraga species were resolved by parsimony cladistic analysis using morphological characters. The resulting cladogram was used to interpret morphological, ecological, and biogeographical patterns in a historical context. Biotic and abiotic environmental factors hypothesized to have exerted selective pressure on morphological traits of its species were optimized onto the phylogeny to suggest how and when these factors may have affected the evolution and diversification of the genus.

Results suggest an origin of the genus in southern South America, with two major evolutionary radiations, one more northern in the Central and Northern Andes, and the other in the Southern Andes and the North Chilean, Patagonia and Monte Deserts. Pollination by hummingbirds seems to have been an important factor in the origin of the northern clade, affecting floral morphology. Herbivory by vertebrates and increased aridity seem to have been important selective forces in the evolution and diversification of the southern clade, especially affecting leaf morphology. These changes were probably associated with the major elevation of the Andes in late Tertiary and with the hyperaridization and climatic fluctuations of Pleistocene and Holocene times.

Malesherbiaceae are xerophytic plants of Chile, Peru, and Argentina. The 24 species of the only genus, Malesherbia, live in a variety of arid habitats in the Pacific coastal desert and adjacent Andes of Peru, Chile, and neighboring Argentina. Taxa with distributions in both Peru and Chile are rare; for this reason the family provides an excellent case study for the biogeography of this region of western South America.

Phylogenetic analysis of ITS sequence data using Turneraceae as an outgroup shows a correlation between the phylogeny and the distribution of Malesherbiaceae. The origin of the family is placed in the late Miocene to early Pliocene, when the region became permanently arid. The five major clades of the family likely diverged during the Pliocene. A single clade consisting of species native to Peru and the Atacama Desert indicates that the family was introduced to Peru once. Most modern species appear to have evolved in response to Pleistocene climatic fluctuations.