Phylogenetic relationships in two African Cedreloideae tree genera (Meliaceae) reveal multiple rain/dry forest transitions

Abstract

Resolving phylogenetic relationships allows the investigation of how species diversity has evolved in various ecosystems. The genera Entandrophragma and Khaya consist of tree species distributed in different African biomes (lowland rain forest, dry forest and savanna, montane forest), and are suitable to examine how (single or multiple events) and when the processes of diversification led to biome transitions. Based on the sequencing of plastome (pDNA: c. 160,000 bp), ribosomal DNA (rDNA: c. 5,300 bp), and habitat characteristic data for each species, we have: (i) reconstructed phylogenetic relationships between species and estimated the divergence period between the main lineages, and (ii) reconstructed ancestral states regarding biome preferences. The phylogenetic trees obtained with both markers support monophyly of the five sections of Entandrophragma previously defined based on fruit and floral characters. Nevertheless, the position of some species from the pDNA and rDNA tree topologies varied within sections. In Khaya, pDNA and rDNA show very divergent topologies, possibly due to a more recent diversification involving incomplete lineage sorting and/or recurrent hybridization events. Khaya diversified during the Pliocene and Pleistocene according to both markers; whereas, according to rDNA data, the Entandrophragma sections diverged during the early Miocene and species within sections diverged from the late Miocene to the Pleistocene. Divergence date estimates tended to be more recent using pDNA data. Biome transitions could not be reconstructed in Khaya as the species tree remains unresolved. Contrarily, three independent biome transitions were inferred in Entandrophragma. The first transition from rain to dry forests occurred during the Miocene and two other transitions were inferred during the Pleistocene, one from rain forest to dry forest and another from rain forest to mountain forest. Overall, we demonstrate that multiple biome transitions occurred, starting from a rain forest biome, possibly reflecting the global trend of aridification of Africa throughout the Cenozoic.

Biogeography and ecology in a pantropical family, the Meliaceae

“…Notes. A molecular study (Monthe et al, 2019) showed five clades in the genus, and these are mapped here (Fig. 8).…”

“…14A). A molecular phylogeny (Monthe et al, 2019) arranged the species in two main clades, and these display a high level of allopatry ( Fig. 14A).…”

“…In Entandrophragma, Monthe et al (2019) wrote that the phylogenetic relationships "reveal multiple rain/dry forest transitions" (italics added). However, this is an inference, not an observation, and is based on the questionable assumption that paraphyletic basal grades occupy ecological centres of origin.…”

“…Distribution of Entandrophragma C.DC. (Data fromMonthe et al, 2019, and African Plant Database, 2019). The five maps (continued on the next page) show the five clades; these have the phylogeny: 1 (2 (3 (4 + 5))).…”

Transitions between biomes are common and directional in Bombacoideae (Malvaceae)

“…Morley, ), and dry climate is an important phylogenetic constraint to plant evolution for many lineages (Cássia‐Silva, Freitas, Alves, Bacon, & Collevatti, ; Olmstead, ; Qian, Jin, & Ricklefs, ). However, transitions from evergreen rain forest to seasonally dry biomes, especially savanna, are known from plant lineages in the Neotropics (Bacon, Moraes R., Jaramillo, & Antonelli, ; Lohmann, Bell, Calió, & Winkworth, ), Africa (Estrella, Forest, Wieringa, Fougère‐Danezan, & Bruneau, ; Monthe et al, ; Veranso‐Libalah, Kadereit, Stone, & Couvreur, ), and Australia (Crisp et al, ) and the floristic study of Dexter et al () suggests permeability of lowland tropical biomes globally.…”