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.

The Southern Hemisphere has traditionally been considered as having a fundamentally vicariant history. The common trans-Pacific disjunctions are usually explained by the sequential breakup of the supercontinent Gondwana during the last 165 million years, causing successive division of an ancestral biota. However, recent biogeographic studies, based on molecular estimates and more accurate paleogeographic reconstructions, indicate that dispersal may have been more important than traditionally assumed. We examined the relative roles played by vicariance and dispersal in shaping Southern Hemisphere biotas by analyzing a large data set of 54 animal and 19 plant phylogenies, including marsupials, ratites, and southern beeches (1,393 terminals). Parsimony-based tree fitting in conjunction with permutation tests was used to examine to what extent Southern Hemisphere biogeographic patterns fit the breakup sequence of Gondwana and to identify concordant dispersal patterns. Consistent with other studies, the animal data are congruent with the geological sequence of Gondwana breakup: (Africa(New Zealand(southern South America, Australia))). Trans-Antarctic dispersal (Australia <--> southern South America) is also significantly more frequent than any other dispersal event in animals, which may be explained by the long period of geological contact between Australia and South America via Antarctica. In contrast, the dominant pattern in plants, (southern South America(Australia, New Zealand)), is better explained by dispersal, particularly the prevalence of trans-Tasman dispersal between New Zealand and Australia. Our results also confirm the hybrid origin of the South American biota: there has been surprisingly little biotic exchange between the northern tropical and the southern temperate regions of South America, especially for animals.

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

We analysed patterns of animal dispersal, vicariance and diversification in the Holarctic based on complete phylogenies of 57 extant non-marine taxa, together comprising 770 species, documenting biogeographic events from the Late Mesozoic to the present. Four major areas, each corresponding to a historically persistent landmass, were used in the analyses: eastern Nearctic (EN), western Nearctic (WN), eastern Palaeoarctic (EP) and western Palaeoarctic (WP). Parsimony-based tree fitting showed that there is no significantly supported general area cladogram for the dataset. Yet, distributions are strongly phylogenetically conserved, as revealed by dispersalvicariance analysis (DIVA). DIVA-based permutation tests were used to pinpoint phylogenetically determined biogeographic patterns. Consistent with expectations, continental dispersals (WP-EP and WN-EN) are significantly more common than palaeocontinental dispersals (WN-EP and EN-WP), which in turn are more common than disjunct dispersals (EN-EP and WN-WP). There is significant dispersal asymmetry both within the Nearctic (WN+EN more common than EN+WN) and the Palaeoarctic (EP+WP more common than WP-tEP). Cross-Beringian faunal connections have traditionally been emphasized but are not more important than cross-Atlantic connections in our data set. To analyse changes over time, we sorted biogeographic events into four major time periods using fossil, biogeographic and molecular evidence combined with a 'branching clock. These analyses show that trans-Atlantic distributions (EN-WP) were common in the Early-Mid Tertiary (70-20 Myr), whereas trans-Beringian distributions (WN-EP) were rare in that period. Most EN-EP disjunctions date back to the Early Tertiary (7045 Myr), suggesting that they resulted from division of cross-Atlantic rather than cross-Beringian distributions. Diversification in WN and W P increased in the Quaternary (< 3 Myr), whereas in E P and EN it decreased from a maximum in the Early-Mid Tertiary. 0 2001 The Linnean Society of London ADDITIONAL KEY WORDS: historical biogeographytrans-Atlantictrans-Beringiandisjunct.This incongruence is measured in abstract terms, such as items of error or amount of homoplasy. The incongruence can then be interpreted a posteriori in terms of biogeographic events, such as dispersal and extinction. The exact procedure for this a posteriori translation remains elusive. Furthermore, because no model is specified, it is difficult to predict the analytical behaviour of pattern-based methods and counter-intuitive results often occur (e.g. Ronquist, 1995Ronquist, , 1996.In contrast, event-based methods are explicitly derived from models of biogeographic processes. The relevant events are identified and associated with costs that are inversely related to the likelihood of t h e events. The analysis consists of a search for the reconstruction, which minimizes the total cost. This optimal reconstruction explicitly specifies the biogeographic events of interest, unlike pattern-based