What has become of the refugia hypothesis to explain biological diversity in Amazonia?

The spatial distribution of biodiversity and related processes is the core of Biogeography. Amazonia is the world's most diverse rainforest and the primary source of diversity to several Neotropical regions. The origins of such diversity continue to be an unresolved question in evolutionary biology. Among many competing hypotheses to explain the evolution of the Amazonian biodiversity, one stands out as the most influential: the refugia hypothesis by Jürgen Haffer. Here, we provide a chronological overview on how the refugia hypothesis evolved over the decades and how the criticism from different fields affected its acceptance. We conclude that the refugia hypothesis alone cannot explain the diversification of the complex Amazonian diversity, and perhaps it was not the most important diversification mechanism. However, the debate provoked by refugia has produced a great amount of knowledge on Amazonian climatic, geological, and evolutionary processes, as well as on species distributions, movements, and history.     

If hippopotamuses cannot swim,how did they colonize islands?

Owing to their aquatic lifestyle, hippopotamuses are normally believed to have reached islands by swimming. Yet, some studies suggest they cannot swim due to their relatively high density. If so, this raises the question of how hippopotamuses would have reached some islands. Their immigration into the British Isles, Sicily, Malta, Zanzibar and Mafia can be accounted for, because these islands sit on continental shelves and were often linked to the mainland during the Pleistocene glacio‐eustatic sea‐level falls. In contrast, their occurrence in Crete, Cyprus and Madagascar would be more difficult to explain. Available geological evidence does not seem to rule out that the latter islands might have been connected with the nearest mainland areas in very recent times. This study intends to consider possibilities about how hippopotamuses reached islands and to show that more effective collaboration is required among specialists involved with the study of insular evolution, colonization and speciation.     

Evidence of Sundaland’s subsidence requires revisiting its biogeography

It is widely accepted that sea level changes intermittently inundated the Sunda Shelf throughout the Pleistocene, separating Java, Sumatra and Borneo from the Malay Peninsula and from each other. On this basis, the dynamics of the biodiversity hotspot of Sundaland is consistently regarded as solely contingent on glacial sea level oscillations, with interglacial highstands creating intermittent dispersal barriers between disjunct landmasses. However, recent findings on the geomorphology of the currently submerged Sunda shelf suggest that it subsided during the Pleistocene and that, over the Late Pliocene and Quaternary, is was never submerged prior to Marine Isotope Stage 11 (MIS 11, 400 ka). This would have enabled the dispersal of terrestrial organisms regardless of sea level variations until 400 ka and hampered movements thereafter, at least during interglacial periods. Existing phylogeographic data for terrestrial organisms conform to this scenario: available divergence time estimates reveal an 8- to 9-fold increase in the rate of vicariance between landmasses of Sundaland after 400 ka, corresponding to the onset of episodic flooding of the Sunda shelf. These results highlight how reconsidering the paleogeographic setting of Sundaland challenges understanding the mechanisms generating Southeast Asian biodiversity.     

Biogeography of Southeast Asia and the West Pacific

The biogeography of Southeast Asia and the West Pacific is complicated by the fact that these are regions on the border of two palaeocontinents that have been separated for a considerable period of time. Thus, apart from any patterns of vicariance, two general patterns relating to dispersal can be expected: a pattern of Southeast Asian elements, perhaps of Laurasian origin, expanding into Australian areas, and a reverse pattern for Australian elements, perhaps of Gondwanan origin. On top of this, both Australian and Southeast Asian elements occur in the Pacific. They dispersed there as the Pacific plate moved westward, bringing the different islands within reach of Southeast Asia and Australia. In order to reconstruct the biotic history of these areas, two large data sets consisting of both plants and animals were generated, one for each pattern, which were analysed using cladistic methods. The general patterns that emerged were weakly supported and do not allow general conclusions.     

Historical biogeography of the Brazilian Atlantic forest and the Carnaval–Moritz model of Pleistocene refugia: what do phylogeographical studies tell us?

The present study uses published phylogeographical studies to test the Carnaval–Moritz (CM) model of forest dynamics in the Atlantic forest of Brazil. The model predicts that a large forested area in the north–central region of this biome has remained stable during the last glacial maximum, and only relicts in its current southernmost distributions. All available sequences for phylogeographical studies on vertebrates on the Atlantic forest were obtained from GenBank. All datasets consisted of mitochondrial sequences and were submitted to the same analyses, including time of divergence and migration rates between phylogeographical lineages, as well as historical demography analyses, including neutrality tests and N_e estimates. The species studied showed different degrees of phylogeographical structure. Two contact zones are defined: one very heterogeneous in south‐east Brazil that was largely congruent with the CM model and one around the Doce river further north. Population genetics analyses showed a smaller effective number on southern population, and most of these southern populations showed evidence for recent demographic expansion. These features are also in agreement with the CM model. Additionally, divergence/expansion events dated back to the Pleistocene epoch in all but one organism. According to hierarchical approximate Bayesian computation analysis, most of the data can be attributed to a single event. The results highlight the need for more finescale studies in the Atlantic forest. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 499–509.     

Neotropical seasonally dry forests and Quaternary vegetation changes

Seasonally dry tropical forests have been largely ignored in discussions of vegetation changes during the Quaternary. We distinguish dry forests, which are essentially tree‐dominated ecosystems, from open savannas that have a xeromorphic fire‐tolerant, grass layer and grow on dystrophic, acid soils. Seasonally dry tropical forests grow on fertile soils, usually have a closed canopy, have woody floras dominated by the Leguminosae and Bignoniaceae and a sparse ground flora with few grasses. They occur in disjunct areas throughout the Neotropics. The Chaco forests of central South America experience regular annual frosts, and are considered a subtropical extension of temperate vegetation formations. At least 104 plant species from a wide range of families are each found in two or more of the isolated areas of seasonally dry tropical forest scattered across the Neotropics, and these repeated patterns of distribution suggest a more widespread expanse of this vegetation, presumably in drier and cooler periods of the Pleistocene. We propose a new vegetation model for some areas of the Ice‐Age Amazon: a type of seasonally dry tropical forest, with rain forest and montane taxa largely confined to gallery forest. This model is consistent with the distributions of contemporary seasonally dry tropical forest species in Amazonia and existing palynological data. The hypothesis of vicariance of a wider historical area of seasonally dry tropical forests could be tested using a cladistic biogeographic approach focusing on plant genera that have species showing high levels of endemicity in the different areas of these forests.