Introduction and synthesis: plant phylogeny and the origin of major biomes

Abstract

Phylogenetic trees based upon DNA sequence data, when calibrated with a dimension of time, allow inference of: (i) the pattern of accumulation of lineages through time; (ii) the time of origin of monophyletic groups; (iii) when lineages arrived in different geographical areas; (iv) the time of origin of biome-specific morphologies. This gives a powerful new view of the history of biomes that in many cases is not provided by the incomplete plant fossil record. Dated plant phylogenies for angiosperm families such as Leguminosae (Fabaceae), Melastomataceae sensu stricto, Annonaceae and Rhamnaceae indicate that long-distance, transoceanic dispersal has played an important role in shaping their distributions, and that this can obscure any effect of tectonic history, previously assumed to have been the major cause of their biogeographic patterns. Dispersal from other continents has also been i mportant in the assembly of the Amazonian rainforest flora and the Australian flora. Comparison of dated biogeographic patterns of plants and animals suggests that recent long-distance dispersal might be more prevalent in plants, which has major implications for community assembly and coevolution. Dated plant phylogenies also reveal the role of past environmental changes on the evolution of lineages in species-rich biomes, and show that recent Plio-Pleistocene diversification has contributed substantially to their current species richness. Because of the critical role of fossils and morphological characters in assigning ages to nodes in phylogenetic trees, future studies must include careful morphological consideration of fossils and their extant relatives in a phylogenetic context. Ideal study systems will be based upon DNA sequence data from multiple loci and multiple fossil calibrations. This allows cross-validation both of age estimates from different loci, and from different fossil calibrations. For a more complete view of biome history, future studies should emphasize full taxon sampling in ecologically important groups, and should focus on geographical areas for which few species-level phylogenies are available, such as tropical Africa and Asia. These studies are urgent because understanding the history of biomes can both inform conservation decisions, and help predict the effects of future environmental changes at a time when biodiversity is being impacted on an unprecedented scale.

The evolutionary reality of higher taxa in mammals

“…The simulation model results apply equally to ecological specialization within the same geographical region. If shifts between niches are rare relative to the rate of species turnover, distinct ecological guilds of closely related species should emerge over time [28,64,65]. Note that strict neutrality is assumed for simplicity but is not required for hESUs to emerge, as long as limits are present that cause species turnover across the entire clade.…”

Tropical mountain cradles of dry forest diversity

“…Becerra's study (4) is an exciting contribution to historical biogeography, which, in the absence of adequate fossils, turns increasingly to plant phylogeny to infer biome histories (5). The dry forest study raises challenging methodological questions.…”

Relaxed molecular clocks for dating historical plant dispersal events

“…This raises questions about how and when they acquired their disjunct habitats. When lineages arrive in new habitats they will usually diverge and sometimes speciate, therefore, dating dispersal and lineage splits has broad implications for understanding rates of diversification [1], the evolution of biota [2,3] and associated faunas [4][5][6], and the time taken for species to adapt to novel environments [7][8][9][10]. Recent biogeographic studies that have included time estimates have revealed strikingly fast diversification rates in some floras, such as the Cape Region of South Africa, the recency of species accumulation even in ancient lineages, such as ferns [1], and the persistence of precarious mutualisms over many millions of years, such as the interactions between figs and fig wasps and between yucca and yucca moths [4,6].…”