The unstable coexistence of lineages within a large community for extended periods of time has been hypothesized as a cause of Neotropical diversity [7
]. However, our results suggest that such a model is incomplete; rather, the complex pattern of diversification is strongly intertwined with paleogeographic events. Our inferences about the past history of the poison frogs using ancestral area reconstructions and diversification analyses provide new insights on speciation and extinction patterns in the Neotropics. Three species richness patterns are potential explanations for the extant diversity differences among regions of the Neotropics: (1) high immigration into one region after suitable geoclimatic conditions are established; (2) gradual in situ diversification of old endemic clades, regardless of the geoclimatic conditions, promoting species accumulation; or (3) rapid in situ diversification of endemic clades after favorable geoclimatic conditions are established. We found that all three patterns might apply to different areas depending on historical context.
All extant Amazonian species descended from 14 lineages that dispersed into the Amazon Basin, mostly after the Miocene floodbasin system receded. The recurrent immigrations that originated mostly in the adjacent Andes (species-richness pattern 1), combined with an increased rate of diversification, explain the high α–diversity of Amazonia. Later, from the Miocene-Pliocene boundary to the present, a rapid in situ diversification (pattern 3) gave rise to the extant Amazonian endemic biota. Therefore, most species in Amazonia originated in the last 10 MY. Moreover, lineages immigrating into Amazonia at <8.0 MYA radiated rapidly, resulting in widespread species and young clades (e.g., Ameerega, Allobates trilineatus, A. femoralis, and Dendrobates ventrimaculatus groups).
The diversity in the Chocoan-Central American super-region derived from scattered immigrations (pattern 1) from Andes to the early Chocoan rainforest during the late Miocene. However, starting at the Miocene-Pliocene boundary, significant orogenic events gave rise to the Central American archipelago [11
] followed by sea level fluctuations [38
], which provided the conditions for repeated dispersal and vicariance events in pre-PLB islands. Evidence of rapid in situ diversification (pattern 3) is supported by the high genetic diversity observed among poison frogs and other lineages especially between Western and Eastern Panamá [12
]. Interestingly, our results might explain the high β–diversity of other endemic clades within the Chocó-Central America super-region [8
] as originating initially from long-distance dispersals between disconnected islands, with diversification later during isolation by high sea levels.
The Andes have undergone extended in situ diversification (pattern 2) since the late Eocene. However, our analyses also provided evidence of decline in the diversification rate since the middle Oligocene, which has important implications for history and conservation of the endemic Andean fauna. First, the Andes uplift at the Miocene–Pliocene boundary caused significant changes in the rate of diversification in the lowland transition zone. We found that several poison frog lineages distributed on one or both sides of the Andes had dispersed repeatedly before the Miocene uplift (i.e., five cross-Andean and five Northern to Central Andes migrations). Paleogeological evidence supports introgression of shallow seas across the northern Andes during the Miocene [14
], suggesting a historical connection between the Amazon Basin and the Chocó. Second, the Pliocene Andean uplift (>2,000 m above sea level) [27
] formed a significant barrier to dispersal, because no other cross-Andean dispersals were found. The uplift also was associated with dramatic ecological changes [27
] and a decrease in diversification rates. These results suggest a role for niche conservatism [41
], in that some lineages may have gone extinct because of failure to adapt. Alternatively, despite greater sampling effort in the Andes region than in other areas, we failed to find some previously common Andean species (e.g., Hyloxalus jacobuspetersi
and the Ecuadorian H. lehmanni
). Consequently, it is difficult to separate a natural decrease in diversification rates from the current trend of amphibian species extinctions at high altitudes due to anthropogenic habitat alteration [43
], increased UV radiation [44
], climate change [45
], or pandemic infection [46
]. In contrast, the montane transition zones of the Andes and adjacent lowlands (Chocó and Amazonia) have become centers of rapid cladogenesis (pattern 3), and species richness in these transition zones might be underestimated because many Neotropical lineages have been shown to contain several cryptic species [47
]. Therefore, dispersals within or across the Andes diminished during the Pliocene, but diversification has intensified in the Andes-lowlands interface.
Although some of the oldest lineages of poison frogs originated in the Guiana Shield and the Venezuelan Highlands (>30 species), our results suggest extended in situ diversification (pattern 2) followed by a decline in the rate of diversification of endemic clades in both areas since the early Miocene. Along the same lines, the Guiana Shield has high poison frog endemism, which is mostly restricted to the summits of the sandstone tepuis [48
], while recent Amazonian poison frog immigrants occupy lowlands adjacent to the tepuis. Our results suggest that the decline of endemic Guianan diversity might be associated with ecological changes in habitat due to the collapse of the ancient tepuis [4
] and repeated dispersals from Amazonian lineages since the Pliocene. However, the diversity of poison frogs in the Guiana Shield is only beginning to be revealed [48
]. In contrast, diversification in the Venezuelan region most likely reflects the oldest vicariant event in Dendrobatidae, at 40.9 MYA. The costal ranges of Mérida, Cordillera de la Costa, and Paria peninsula are species rich but their total area is less than 5% of that of the Amazon Basin. No lineage of this endemic fauna has dispersed out to other regions since the early radiation of the poison frog family in the late Eocene. However, Eocene floristic paleoecological reconstruction of the Venezuelan Highlands area showed that it was more diverse than at present [49
], suggesting that the ancestral habitat of the first poison frogs might have been lowland. The depauperate dendrobatid fauna of the Venezuelan llanos and Brazilian Shield plateau is puzzling, but might be related to Holocene aridity [50
The recurring dispersals to Amazonia suggests that a large part of dendrobatid diversity results from repeated immigration waves at <10.0 MYA, followed by a rapid in situ diversification after geoclimatic conditions suitable for a rainforest ecosystem were present. The biota of Amazonia was not isolated during the process of diversification, but finely intertwined with the development and export of biodiversity across the entire Neotropical realm. Poison frog diversity in the Chocoan-Central American super-region was significantly associated with formation of the PLB in the Pliocene. Repeated dispersals between disconnected islands followed vicariance by cyclic high sea-level periods, promoted rapid in situ diversification and endemism of poison frog lineages. The extant Andean, Guianan, and Venezuelan Highlands fauna most likely originated after prolongated in situ diversification since the origin of the poison frog clade, but the pace of species formation within these areas has slowed down. Phylogenetic analyses on tropical biota such as birds [51
] and the species-rich genus Inga
] as well as models of diversification [3
], have argued that the Amazon might accumulate older lineages; however, the origin of those lineages is not clear. Our results are the first to provide evidence, to our knowledge, of the major involvement of the Andes as a source of diversity of both the Amazon and the Chocó–Central America region. Because 23.5% of endemic Amazonian amphibian species are dendrobatids (i.e., ~70 of 298) [53
], our results may generalize to other Neotropical terrestrial biota with similar distribution. Moreover, these results provide a crucial broad spatiotemporal framework that, coupled with realistic phylogeny-based explanations of the current richness in Neotropics, explains why species occur where they do and how they came to get there. Thus, the major patterns of dispersals and radiations in the Neotropics were already set by the Miocene–Pliocene boundary, but the ongoing process of Neotropical radiation is occurring now, in the Chocó–Central America region and especially in the Amazonian rainforest.