Origins of Biodiversity—Response

Competing paradigms of Amazonian diversification and the Pleistocene refugium hypothesis

“…If many (or most, cf. Hoorn et al ., ) speciation events giving rise to the extant biota took place in the Pleistocene, as our butterfly data (as well as a recent meta‐analysis of birds by Smith et al ., ) suggest, then the argument that ‘diversification of most animals and plants occurred well before the onset of climate oscillations in the late Neogene’ (Antonelli et al ., , p. 389) is false: regardless of when their clades evolved or how diverse they may have been in the past, the diversity of species that live in Amazonia today is mostly of Pleistocene origin.…”

“…There are two different ways to pose the question of when this diversity arose. From a proximate perspective, most extant species are thought to be only a few hundred thousand to a few million years old (Hoorn et al ., ), an estimate corroborated by evidence from Neotropical butterflies and birds (Garzón‐Orduña et al ., ; Smith et al ., ), and so one may enquire about processes and mechanisms acting during that time period to account for the origins of living species. From the perspective of deeper time, one can also ask questions about the ages of origin and temporal patterns of diversification (or impoverishment) of various clades through evolutionary history, noting of course, that ‘diversification’ of more inclusive taxa is a process that takes place through time, not an event to which a single date can be attached.…”

“…(), and, indeed, the general assumption of Hoorn et al . (), suggest that any paradigm that rejects Pleistocene speciation as a significant component of Amazonian diversification is incomplete. It is our opinion, based on the evidence reviewed above, that: (1) shared patterns of biotic distribution exist in Amazonia that can be parsimoniously interpreted as the results of vicariance; (2) speciation of many of the taxa involved occurred in the Pleistocene; and (3) Pleistocene climatic fluctuations and resultant shifts in biotic distributions provide a parsimonious causal explanation for those events – particularly in the absence of other general explanatory hypotheses.…”

Species-specific phylogeographical patterns and Pleistocene east-west divergence inAnnona(Annonaceae) in the Brazilian Cerrado

“…1). Increased evidence has recently pointed to lineage divergence in the Amazonian biome mainly in the Miocene/Pliocene (Hoorn et al, 2010(Hoorn et al, , 2011. S1), where the dry season is longer and more severe than in the central and southern Cerrado.…”

Phylogenetic insights into Andean plant diversification

“…Moreover, current lineage diversity is always overestimated in phylogenetic studies compared to historical diversity, because newer lineages have had less time to go extinct than ancient lineages (Harvey et al, 1994). In this line, Hoorn et al (2011) argued that crown node ages of clades "lead to more robust age estimation of deeper nodes even when many species are missing." However, disentangling the relative effects of different events that overlap in time may prove impossible using dated phylogenies (Pennington and Dick, 2010).…”