The Making of Amazonian Diversity The biodiversity of the Amazon Basin is legendary, but the processes by which it has been generated have been debated. In the late 20th century the prevalent view was that the engine of diversity was repeated contraction and expansion of forest refugia during the past 3 million years or so. Hoorn et al. (p. 927 ) analyze findings from a diverse range of disciplines, including molecular phylogeny, ecology, sedimentology, structural geology, and palaeontology, to offer an overview of the entire history of this region during the Cenozoic era (66 million years ago). The uplift of the Andes was a pivotal event in the evolution of Amazonian landscapes because it continually altered river drainage patterns, which in turn put a variety of pressures on organisms to adapt to changing conditions in a multiplicity of ways. Hence, the diversity of the modern biota of the Amazon has more ancient origins than previously thought.

Recent phylogenetic studies have revealed the major role played by the uplift of the Andes in the extraordinary diversification of the Neotropical flora. These studies, however, have typically considered the Andean uplift as a single, time-limited event fostering the evolution of highland elements. This contrasts with geological reconstructions indicating that the uplift occurred in discrete periods from west to east and that it affected different regions at different times. We introduce an approach for integrating Andean tectonics with biogeographic reconstructions of Neotropical plants, using the coffee family (Rubiaceae) as a model group. The distribution of this family spans highland and montane habitats as well as tropical lowlands of Central and South America, thus offering a unique opportunity to study the influence of the Andean uplift on the entire Neotropical flora. Our results suggest that the Rubiaceae originated in the Paleotropics and used the boreotropical connection to reach South America. The biogeographic patterns found corroborate the existence of a long-lasting dispersal barrier between the Northern and Central Andes, the ''Western Andean Portal.'' The uplift of the Eastern Cordillera ended this barrier, allowing dispersal of boreotropical lineages to the South, but gave rise to a huge wetland system (''Lake Pebas'') in western Amazonia that prevented in situ speciation and floristic dispersal between the Andes and Amazonia for at least 6 million years. Here, we provide evidence of these events in plants.biogeography ͉ Neotropical biodiversity ͉ Rubiaceae

SignificanceThe formation of the Isthmus of Panama, which linked North and South America, is key to understanding the biodiversity, oceanography, atmosphere, and climate in the region. Despite its importance across multiple disciplines, the timing of formation and emergence of the Isthmus and the biological patterns it created have been controversial. Here, we analyze molecular and fossil data, including terrestrial and marine organisms, to show that biotic migrations across the Isthmus of Panama began several million years earlier than commonly assumed. An earlier evolution of the Isthmus has broad implications for the mechanisms driving global climate (e.g., Pleistocene glaciations, thermohaline circulation) as well as the rich biodiversity of the Americas.

1. Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo-referencing or dating, can diminish their usefulness. Manual cleaning is time-consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records.2. Here, we present CoordinateCleaner, an r-package to scan datasets of species occurrence records for geo-referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo-referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio-temporal tests for fossils.3. We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90 million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.