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

Abstract

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.

An atypical mating system in a neotropical manakin

“…Among other possible mechanisms, we consider that population bottlenecks in the recent past of the Araripe manakin may have led to genetic drift in some traits. We also speculate that the historical changes in proportions of savannah and rainforest in the Amazonian basin (reviewed in [70]) may have led to disjoint distributions and isolation of some taxa in exceptionally small fragments, which may have been the case for both the Araripe and helmeted manakins. In addition to the historical constriction of forested areas occupied by the Araripe manakin, anthropogenic disturbances leading to further fragmentation in the region may also have led to changes in the species' mating system [71].…”

The onset of grasses in the Amazon drainage basin, evidence from the fossil record

“…Haffer's (1969) hypothesis, however, wasn't based on basin-wide palynological records or climatic reconstructions, but on his observations of modern bird distributions. It claims rapid allopatric speciation originating as recently as the Pleistocene as a key mechanism applying for a wide range of forest taxa (Rocha and Kaefer 2019).…”

Contrasting Trends of Population Size Change for Two Eurasian Owlet Species—Athene brama and Glaucidium radiatum From South Asia Over the Late Quaternary

“…In the tropics, there is considerable empirical support for the impact of forest fragmentation and open habitat expansion during the glacial periods on the population history of many species (Schneider and Moritz, 1999;Cabanne et al, 2007;Wurster et al, 2010;Piñeiro et al, 2017;Song et al, 2020). However, data contradicting this general pattern (Batalha-Filho et al, 2012;Rocha and Kaefer, 2019) underscore the importance of understanding regional patterns across taxonomic groups. Among tropical regions, South Asia remains poorly represented in studies that include genetic data (Reddy, 2014), even fewer that examine historical climatic oscillation-induced species range dynamics.…”