Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire

To address these questions, we have investigated plant diversification in the Cerrado of South America by using a comparative phylogenetic approach. The Cerrado is a floristically diverse savanna that covers more than two million km² of Central Brazil and parts of Bolivia and Paraguay (Fig. 1). This region has been recognized as a global biodiversity hotspot with more than 10,000 plant species, of which 44% are endemic (1, 25, 26). Despite the floristic and global conservation importance of the Cerrado, little is known about the origins and diversification of its flora. Indeed, hypotheses about Cerrado origins range from the early Cretaceous (27), wherein Cerrado lineages were suggested to be possible precursors of the adjacent Amazonian and Atlantic rain forests, to the Holocene (28). Here we evaluate these alternatives, but we particularly focus on the hypothesis that the origin of the biome coincided with the rise to dominance of flammable C4 grasses within the past ten million years (6, 29).

In common with other tropical savannas, the Cerrado is dominated by C4 grasses which take advantage of high light and warm wet summers to rapidly accumulate biomass, which becomes flammable in the long dry winters, prompting fires, generally several times in a decade (30, 31). The synergy between fast (re)growth and flammability allows grasses to outcompete trees and shrubs, maintaining the open canopy typical of savannas in areas where, without fire, forests would dominate (31). Diverse fire adaptations are the hallmark of the endemic Cerrado flora (32). These adaptations include functionally herbaceous or woody geoxylic suffrutices with enlarged underground xylopodia or lignotubers, thick corky bark, pachycaul rosulate shrubs and trees with sparse branching, thick shoots and leaves concentrated at shoot tips, perennial herbs, and specialized flowering and fruiting phenologies (27, 32, 33). These adaptations are largely lacking in the flora of adjacent biomes where fire has been less important over evolutionary time scales (29). C4 grasses originated and started to diversify 32–25 Mya in several independent lineages (34). However, evidence from isotopic signatures of fossil mammal teeth (paleodiets) and paleosols, charcoal particles, and pollen from sites on different continents suggests that these lineages only became ecologically dominant 4–8 Mya (35–37). This near-synchronous expansion of grass-dominated vegetation in different parts of the world is regarded as marking the onset of the modern savanna biome (38).

To test the hypothesis that the evolution of the Cerrado flora followed the ecological expansion of flammable C4 grasses and to investigate the significance of fire adaptations as a selective advantage for Cerrado diversification, we assembled time-calibrated phylogenies for plant groups that include Cerrado elements. Our sample includes four datasets representing lineages rich in Cerrado endemics (Mimosa and Microlicieae, Melastomataceae) and lineages sparsely represented in the Cerrado (Lupinus and Andira), as well as diverse life forms including trees, shrubs, and perennial herbs. Two of the phylogenies (Mimosa and Andira) are published for the first time. Central to the study is a new phylogeny for the species-rich (>500 species) legume genus Mimosa, the second-largest plant genus in the Cerrado (26, 39). In addition, new analyses are presented of published data for the legume genus Lupinus (15) and the tribe Microlicieae (40). These phylogenies are used to infer divergence times and ancestral biomes for Cerrado lineages, investigate the evolution of fire adaptations, and ultimately to build an evolutionary picture of the historical assembly of species in the Cerrado.

Our analyses identified 15 Cerrado lineages, 11 in Mimosa, two in Andira and one each in Lupinus and Microlicieae (Fig. 2A). Most of these clades are robustly supported and represent groups where fire-adapted endemics make up the majority of species (see Table 1 and SI Appendix for descriptions of each lineage). In three of the study groups, Cerrado lineages form clades that are deeply nested within genera. In two, there are multiple independent Cerrado lineages. These findings are in line with floristic data showing the preponderance of species-level endemism and lack of endemic genera in the Cerrado (32, 33). Within Mimosa, Cerrado lineages originated independently at least 11 times (Fig. 2A). Two of these clades (Mimosa 3 and 8) are notably rich in fire-adapted species resulting from in situ Cerrado diversification and together represent ≈75% of all Cerrado species of Mimosa. Notably, both these species-rich Mimosa radiations are estimated to have arisen approximately 4 Mya. The diversity of life forms in these two clades (Fig. 2 B–G), including functionally herbaceous subshrubs, prostrate herbs, wand-like subshrubs and pachycaul rosette trees, reflects the diverse ways that species have evolved to tolerate fire disturbance. Similar multiple independent origins of Cerrado species are apparent in Andira, with two recent clades both having two species. The largest Cerrado clade sampled here, representing ≈200 Cerrado endemics (40), is nested within the tribe Microlicieae. However, it is clear that this was not the only incursion of Melastomataceae into the Cerrado, with several other fire-adapted Cerrado lineages in this family (e.g., in Miconia, Cambessedesia, and Tibouchina).

The estimated ages of Cerrado lineages span the late Miocene to Pliocene from 9.8 to 0.4 Mya, with the majority less than 4 Mya (Fig. 2J), broadly coinciding with the hypothesized expansion of C4 grass-dominated savanna biomes (38). Some Cerrado lineages apparently slightly predate hypothesized C4 grass dominance, but the majority are younger (Fig. 2J), and this is compatible with fire as a common underlying trigger prompting the evolution of endemic Cerrado species and lineages, although the precise dynamics of this are clearly complex (30, 31, 38). One factor influencing very recent (Quaternary) evolution of Cerrado lineages (e.g., in Andira) may have been dry glacial periods, when the Cerrado was likely to have been more extensive. The derived nature of Cerrado lineages found here is in line with analyses of the legume family as a whole that showed that savanna elements worldwide are in general recently derived from dry or wet forest ancestors (18).

The idea that the Cerrado lineages evolved in response to increased C4 grass dominance and fire frequency is reinforced by the occurrence of fire adaptations in these groups (Fig. 2, Table 1). Fire adaptations in Andira include thick corky bark and a geoxylic suffruticose growth form in Andira humilis, a subshrub with an extensive network of underground woody shoots (“underground tree”), a life form unique within this otherwise arborescent genus (41) (Fig. 2 H and I and SI Appendix). Within Mimosa, fire adaptations include: functionally herbaceous perennials with xylopodia (Fig. 2 B–E) that evolved multiple times independently from an ancestral shrubby habit; unusual pachycaul treelets with few branches, thick shoots and leaves clustered at shoot apices (Fig. 2 F and G and SI Appendix); and crowded, persistent stipules that protect shoot apices from fire. The evolution of fire-adapted life forms is strongly correlated with Cerrado occurrence in Mimosa (likelihood ratio statistic = 30.30, P < 0.01) but much rarer or absent in sister lineages growing in adjacent wet and seasonally dry tropical forest. Indeed, seasonally dry tropical forest (the “succulent biome” sensu in ref. 18), which is the ancestral biome for several Cerrado lineages (see below), although sharing a long dry season with the Cerrado, is characterized by sparse occurrence of grasses, abundant Cactaceae and other succulents, and lack of natural fires (18, 29, 37). The large, fire-adapted Microlicieae clade is also nested within a family that predominates in fire-free (rain forest and swamp) habitats (discussed in ref. 40). It is notable that similar fire adaptations are common across other plant families in the Cerrado. For example, of 301 plant species in a one-hectare plot in the southern Cerrado, 94 species across 64 genera and 37 families have xylopodia (32).

Adaptive shifts between ecological zones can play an important role in the generation of species diversity (4, 11). Our results alongside wider floristic data (32, 42) show that fire adaptation and Cerrado occurrence are phylogenetically labile with multiple independent lineages at shallow depths within species-level phylogenies and across genera in disparate plant families. These frequent adaptive shifts suggest that fire does not pose a significant adaptive barrier to shifts between biomes. In comparison, shifts from tropical into temperate biomes and mangrove vegetation have been infrequent (4, 8), suggesting that adaptations to high salt and substrate anoxia or frost are more complex to evolve. In the case of the Cerrado, the boundaries appear to have been porous to the ingress and recruitment of lineages from a range of fire-free wet and dry forest vegetation types. Of significance is the intermingling of open, fire-prone savanna with patches of closed, less fire-prone riverine gallery forest, which share few species in common but which can harbor both fire-adapted and fire-sensitive congeners and even sister species (43). Phenotypic plasticity in fire traits (e.g., the normally stunted A. humilis can sometimes form a shrub or treelet in the absence of fire; ref. 41) is a further indication of the potential ease of the evolutionary transitions associated with fire adaptation. We suggest that the ease of fire adaptation has been significant in generating high species diversity in the Cerrado, although the ingress of a lineage into this fire-prone habitat has not necessarily led to significant or rapid in situ diversification. The 10 largest genera (1,474 spp.) make up only 13% of the Cerrado flora (26), and many of the dominant Cerrado tree genera (e.g., Qualea and Caryocar) are represented by only few species.

Several authors have pointed to affinities between the woody flora of the Cerrado and the Atlantic and Amazon rain forests (32, 42–44). For example, of 121 woody species dominant in the Brazilian Cerrado, 99 belong to predominantly rain forest genera (6). These affinities are borne out by wet forest–Cerrado transitions implied by the phylogeny of Andira (SI Appendix) and undoubtedly many other groups not sampled here. However, the sister groups and putative ancestral areas and ecologies of Cerrado lineages identified in our phylogenies are diverse and include geographically adjacent seasonally dry tropical forests, subtropical grasslands, and wetlands, as well as wet forests (Table 1 and SI Appendix). In seven of 15 lineages, ancestral areas were recorded as equivocal, but even for these, the options with the highest probabilities frequently included dry and wet forest. These results agree with floristic data that suggest that neotropical savannas comprise a mixture of elements of various provenance and floristic affinities (42). The Cerrado is bordered by a diverse array of biomes (Fig. 1) including the Amazon and Atlantic wet forests, tropical and subtropical dry thorn scrub (Caatinga and Chaco), subtropical grasslands, and wetlands. The proximity of these diverse vegetation types that have all contributed to the recruitment of Cerrado lineages suggests that this privileged position in the heart of South America may have played a role in the Cerrado's striking species richness.

The in situ assembly of the endemic rich Cerrado flora via frequent recent adaptive shifts to resist fire stands in contrast to the widespread support for ideas that lineages tend to maintain their ancestral ecologies (8, 11, 13) and that dispersal of preadapted lineages has played an important role in the assembly of regional species pools (8). For example, the species-rich páramo biome in the Andes includes many northern, temperate plant lineages that were able to disperse and to take advantage of similar ecological conditions to diversify rapidly in the Andes (8, 15, 45). Similarly, many seasonally dry tropical forest clades show evidence of phylogenetic niche conservatism among disjunct areas across the tropics (16, 18). In these cases, it has apparently been easier to switch geography than ecology (8). However, this does not appear to be the case for the Cerrado, where niche evolution from adjacent closed, fire-free habitats to open, fire-prone habitats, cross-cutting other abiotic niche dimensions, has apparently been prevalent in the evolution of the Cerrado flora.

This study is an initial attempt to assemble a representative set of time-calibrated phylogenies for Cerrado plants. The lineages discovered represent just 3–4% of the Cerrado flora. Despite this sparse sampling, there are indications that our results are representative of the flora as a whole. First, the study groups include species-rich and species-poor lineages as well as diverse life forms. Second, the preponderance of species, as opposed to generic endemism and prevalence of fire adaptations amongst these endemics, support the idea that Cerrado lineages are derived and recent. Finally, preliminary phylogenies for other plant groups including Styrax (46), Viguiera (47), Ruellia (48), and Manihot (49), also show evidence of recently derived Cerrado lineages, multiple independent Cerrado lineages (in Ruellia, Manihot, and Styrax) and associated fire adaptations (e.g., xylopodia in Ruellia and Viguiera) (SI Appendix).

The emerging picture of Cerrado origins is of recent diversification of endemic plant lineages that took place during the late Miocene and early Pliocene, driven by the common trigger of fire adaptation and facilitated by ease of fire adaptation across plant groups from the diverse biomes immediately surrounding the Cerrado. This picture is very different from what is known about the origins and diversification of plants in one of the best-studied model hotspots, the Cape Floristic Province in South Africa, where plant lineages are estimated to range from less than 5–46 Mya, with no evidence for simultaneous initiation driven by a single trigger (20, 50). Linder (9) classified these older Cape lineages as mature radiations, in which stability over time has produced numerous endemic genera. In contrast, the Cerrado seems to be the product of more recent diversification with very few endemic genera. These contrasting scenarios suggest that the origins of species-rich biomes and underlying causes of high species diversity can be highly idiosyncratic, driven as much by unique features of regional- and continental-scale history and physiography as by any more universal ecological processes at more local scales (4, 9, 10). If species-rich biomes do indeed have very different histories, then understanding the differences between biomes, and hence the mechanisms responsible for the origin and maintenance of the variation in species richness over the globe, will be crucial for the interpretation of global biodiversity gradients across space (e.g., refs. 8 and 45) and time (e.g., refs. 51 and 52).

We thank Euan James, the Millenium Seed Bank Project, Sergio de Faria, Valquíria Dutra, Maria Schifino–Wittmann, Nair Dahmer, Ruth Eastwood, Joan Sutherland, Tiina Särkinen, Gwilym Lewis, Gerardo Vasconcelos, Carolyn Proença, Stephen Harris, Angélica Martínez, Sara Camargo, Janaína Nascimento, Terry Pennington, Melissa Luckow, John Wood, Carlos Reynel, Aniceto Daza, Rob Forrest, Margoth Atahuachi and Chris Fagg for help with field collections or provision of plant material, Anne Bruneau for part of the matK alignment, Tiina Särkinen and Greg Kenicer for unpublished matK sequences, David Spence and Neil Caithness, Oxford University E-Science Centre for help running BEAST on the National Computing Grid, Matt Lavin and two reviewers for comments on the manuscript, and the authorities in Peru, Bolivia, Mexico, and Brazil (IBAMA authorization project 02001.007621/2005) for permission to collect plant material. M.F.S. was supported by the Clarendon Fund, Wolfson College, and the Systematics Association during his PhD at the University of Oxford, C.S. was supported by the British Schools and Universities Foundation during her MSc at the Royal Botanic Garden Edinburgh, and C.E.H. was supported by the Royal Society.