Geological events of biological importance in the history of the Andes include their impact on global climates through an influence on atmospheric circulation, rainfall patterns, and the atmospheric concentration of CO₂; habitat diversification from lowlands through páramo to glaciated peaks; and migratory pathways ranging from discontinuous (mesic elements), highly discontinuous (páramo elements), barriers (to east-west migrations), to selective pathways (via the dry Andean valleys). The timing of these effects is a function of the uplift history of three (to nine) morphotectonic segments of the Andes resulting in (1) mostly lowland swamp and fluvial environments in the Cretaceous and Paleocene, (2) moderate uplands beginning in the Late Eocene (ca. 40 million years ago [Ma]), (3) appression of an offshore volcanic chain (the proto–Cordillera Occidental) in the Oligocene (ca. 30 Ma), (4) uplift of the proto–Cordillera Oriental and the Altiplano to about half their present altitude by the Middle Miocene (ca. 15 Ma), and (5) uplift of the remaining half within approximately the past 10 million years. The early appearance of a biological community recognizable as the Atacama Desert is estimated at ca. 15 Ma, and the beginnings of a páramo at ca. 3.5 Ma. Longer-term (Milankovitch) and shorter-term (Younger Dryas, Medieval warm/dry period, Little Ice Age, Heinrich, and Dansgaard-Oeschger [D-O]) climatic events, known initially from the high latitudes, are now widely recognized throughout Latin America, including the Andes. They document a dynamic physical environment from the Cretaceous through the Holocene and on all timescales.

Over the last eight years, we have developed several paleoenvironmental records from a broad geographic region spanning the Altiplano in Bolivia (18°S–22°S) and continuing south along the western Andean flank to ca. 26°S. These records include: cosmogenic nuclide concentrations in surface deposits, dated nitrate paleosoils, lake levels, groundwater levels from wetland deposits, and plant macrofossils from urine-encrusted rodent middens. Arid environments are often uniquely sensitive to climate perturbations, and there is evidence of significant changes in precipitation on the western flank of the central Andes and the adjacent Altiplano. In contrast, the Atacama Desert of northern Chile is hyperarid over many millions of years. This uniquely prolonged arid climate requires the isolation of the Atacama from the Amazon Basin, a situation that has existed for more than 10 million years and that resulted from the uplift of the Andes and/or formation of the Altiplano plateau. New evidence from multiple terrestrial cosmogenic nuclides, however, suggests that overall aridity is occasionally punctuated by rare rainfall events that likely originate from the Pacific. East of the hyperarid zone, climate history from multiple proxies reveals alternating wet and dry intervals where changes in precipitation originating from the Atlantic may exceed 50%. An analysis of Pleistocene climate records across the region allows reconstruction of the spatial and temporal components of climate change. These Pleistocene wet events span the modern transition between two modes of interannual precipitation variability, and regional climate history for the Central Andean Pluvial Event (CAPE; ca. 18–8 ka) points toward similar drivers of modern interannual and past millennial-scale climate variability. The north-northeast mode of climate variability is linked to El Niño–Southern Oscillation (ENSO) variability, and the southeast mode is linked to aridity in the Chaco region of Argentina.

By combining distributions and phylogenies for large groups of birds, it is now possible to disentangle the relative roles of contemporary ecology and history in explaining the distribution of biodiversity on earth. In South America, avian lineages, which represent radiations during the warm parts of the Tertiary, are best represented in the tropical lowlands and Andean forelands. During the upper Tertiary, diversification was most intense in the tropical Andes region, with recruitment back into the tropical lowlands and into South America's open biomes. Within the tropical Andes, endemism (mean inverse range size) and mean branch length (number of phylogenetic nodes on lineages) increase from the foothills up to the tree line and then decline again in the barren highlands, suggesting that the tree-line zone plays a special role in the diversification process. The resulting endemism is locally aggregated, often with marked peaks in areas immediately adjacent to ancient population centers. Thus, the process of evolution of new species is linked with local factors that, over a shorter time perspective, were also favorable for people. If we want to maintain the process of diversification, it becomes essential to supplement the traditional approach of preserving biodiversity in wilderness areas with few people with efforts to support sustainable development in populated areas.

The complex geography of the Neotropical montane system is a natural laboratory for population divergence. Understanding which geographic barriers (lowland barriers, arid river valleys, and montane barriers above the tree line separate these regions of endemism) are instrumental in promoting and maintaining population divergence is an important step in preserving genetic diversity and endemism within the region. Here, I analyze patterns of genetic differentiation between 16 predefined regions of endemism for 43 co-distributed zoogeographic species complexes of Neotropical montane forest birds. The analysis shows that lowland barriers generate the highest levels of genetic differentiation, while barriers above the tree line in the Andes show the least. Within the Andes, arid river valleys promote population divergence to varying degrees. The Río Marañón shows the greatest effect, but the Río Apurímac and Río Quinimari are also associated with extensive genetic differentiation, while genetic divergence across other river valleys is generally weak. Most barriers are associated with a wide span of divergence times, supporting a protracted history of dispersal postdating barrier formation. If the goal is to maintain genetic diversity, preservation of populations within each region of endemism would help to ensure the continued survival of evolutionarily distinct lineages within species. Considering the alarming rate of deforestation in Neotropical montane regions, preservation of suitable tracts of montane forest is needed within each region of endemism, with special emphasis placed on endemism regions separated by lowland barriers and by deep intermontane river valleys.

The mosses of the tropical Andes are examined to determine a conservative estimate of diversity, excluding a significant number of unconfirmed names and dubious reports that have distorted estimates in the past. In this analysis, 1376 species represented by 327 genera and 69 families are recognized. Within this cohort, species endemism for the tropical Andes is estimated at 31%. Regionally, the number of mosses restricted to the northern Andes (321 species) is higher than the number restricted to the central Andes (241 species). Regional endemism exhibits a similar pattern: more endemics in the northern Andes (155 species) than in the central Andes (129 species).

The genus Macrocarpaea (Griseb.) Gilg (Gentianaceae, Helieae) is among the largest woody genera of tropical gentians, with most of its species occurring in the wet mountainous forests of the Andes. Phylogenetic and dispersal-vicariance analyses (DIVA) of 57 of the 105 currently recognized species in the genus, using two data sets from nuclear DNA (ITS and 5S-NTS sequences) and morphology, show a single origin of the Andean species from an ancestral distribution that includes southeastern Brazil. Within the Andes, species divide into two major clades: (1) northern species from the cordilleras of northern Ecuador, Colombia, and Venezuela; and (2) southern species of the Andean Amotape–Huancabamba Zone in Ecuador and Peru, as well as the Andes of central and southern Peru and Bolivia. The Amotape–Huancabamba Zone is supported as the ancestral area for Macrocarpaea within the Andes. There are repeated speciation patterns within the Andes, and three Mesoamerican species derive from the northern clade, as is the single sampled species from the Guayana Shield. The position of the subclade of the three Caribbean species is less certain, but it currently nests among Andean species. An Atlantic coastal Brazilian clade is placed as sister group to all other Macrocarpaea, providing further support for an ancestral refuge in southeastern Brazil for the Helieae. The biogeographic analysis showed that local speciation is more common than long-distance dispersal, and allopatric speciation is more common than sympatric speciation. Using detailed, georeferenced herbarium collection data, patterns in environmental characteristics between clades and sister species were analyzed with Spatial Evolutionary and Ecological Vicariance Analysis (SEEVA), utilizing geographic information system (GIS) and statistical methods. Sister clades and taxa were evaluated for statistical significance in variables such as annual rainfall and temperature, elevation, temperature and rainfall seasonality, geological bedrock age, and soil type to evaluate ecological vicariance between sister groups. The results indicate that there are no general patterns for each variable, but that there are many significant divergences in ecological niches between both larger sister groups and sister species, and ecological niche conservation was also observed when subsequent nodes in the phylogeny were compared.

Patterns of broad-scale plant species richness are thought to be largely determined by (1) variation in energy and water availability among sampling units (species energy hypothesis), (2) habitat and topographic heterogeneity within sampling units (spatial heterogeneity hypothesis), and (3) regional differences in geographic configuration and history (regional effects hypothesis). However, lack of taxonomic and distribution data, particularly for tropical regions, has impeded assessments of the relative importance of these three hypotheses. We used a large botanical database to estimate the pattern of relative vascular plant richness across the western Neotropics and regression models to measure the extent to which this estimated pattern supported predictions from each of the above three hypotheses. Variation in plant richness across three major paleophysiographic regions (northwest South America, southern Central America, and northern Central America) was primarily predicted by the spatial heterogeneity hypothesis, with secondary contributions from the species energy hypothesis and, to a lesser extent, the regional effects hypothesis. Regression models that incorporated the relative contributions of all three hypotheses predicted peaks of relative species richness mostly in topographically complex areas (e.g., Sierra Madre de Chiapas, Cordillera de Tilarán, Cordillera de Talamanca, Panama's Cordillera Central, the Andes, and the Venezuelan Guayana); relatively low richness in central Mexico and Yucatán, Los Llanos of Venezuela, and in the Gran Chaco region of Bolivia, Paraguay, and Argentina; and a richness trough in lowland Amazonia relative to southern Central America, the Andes, and the Venezuelan Guayana. We discussed the contrast between our results and previous assessments that found plant richness to be primarily determined by the species energy hypothesis and predicted different patterns of plant richness across the western Neotropics.

Some landscapes cannot be understood without references to the kinds, degrees, and history of human-caused modifications to the Earth's surface. The tropical latitudes of the Andes represent one such place, with agricultural land-use systems appearing in the Early Holocene. Current land use includes both intensive and extensive grazing and crop- or tree-based agricultural systems found across virtually the entire range of possible elevations and humidity regimes. Biodiversity found in or adjacent to such humanized landscapes will have been altered in abundance, composition, and distribution in relation to the resiliency of the native species to harvest, land cover modifications, and other deliberate or inadvertent human land uses. In addition, the geometries of land cover, resulting from differences among the shapes, sizes, connectivities, and physical structures of the patches, corridors, and matrices that compose landscape mosaics, will constrain biodiversity, often in predictable ways. This article proposes a conceptual model that implies that the continued persistence of native species may depend as much on the shifting of Andean landscape mosaics as on species characteristics themselves. Furthermore, mountains such as the Andes display long gradients of environmental conditions that alter in relation to latitude, soil moisture, aspect, and elevation. Global environmental change will shift these, especially temperature and humidity regimes along elevational gradients, causing changes outside the historical range of variation for some species. Both land-use systems and conservation efforts will need to respond spatially to these shifts in the future, at both landscape and regional scales.

No other line of practice requires application of science more urgently than conservation. Here we explore several elements that must be put in place to establish lines of communication between scientists and managers of protected areas. First, it is necessary that scientists are aware of the information needs of managers, that they produce the relevant information, and that this information is available to managers. Second, it is necessary that managers not only know how to access, process, and incorporate the information, but that they also internalize their need for that science and the clear advantages of incorporating it into their practice. We propose several mechanisms to ensure an adequate flow of information between the two groups: active dialogue between the parties, translators of science located both in academia and government and nongovernmental organizations (NGOs), and execution of joint projects. In particular, we argue that science-oriented NGOs can play a major role in bridging the gap between basic science and on-the-ground conservation. We finish by describing three case studies in which some of these models have been explored in Colombia and how science has been applied to address conservation and management concerns.