Inferring speciation and extinction processes from extant species data
Institut für Integrative Biologie, Eidgenössiche Technische Hochschule Zürich, 8092 Zürich, Switzerland
Querying the past is hard. Speciation and extinction processes are on a scale of thousands to millions of years. Thus, they are most often studied by reconstructing the evolutionary past. This past is reconstructed using phylogenetic methods either on the basis of data from living species or by directly examining the fossil record. Robust methods for inferring the evolutionary past purely on the basis of living species would allow us to understand speciation and extinction processes for the large number of groups without a good fossil record.
Generally, studies using living species infer lower extinction rates than the rates suggested by the fossil record ( 1, 2). A new study in PNAS ( 3) suggests that this mismatch is due to our use of oversimplified models of speciation and extinction.
Fifteen years ago, Nee et al. ( 4) presented the first method to infer speciation and extinction rates on the basis of “reconstructed” phylogenies, i.e., phylogenies inferred on only extant species ( Fig. 1 A and B ). This first likelihood method relied on the idea that lineages in a reconstructed phylogeny accumulate through time with rate λ − μ (where λ is the speciation rate and μ is the extinction rate) and accumulate in the very recent past with rate λ. The change in rate of lineage accumulation from λ − μ to λ, called the “pull-of-the-present” (5), allows us to estimate both λ and μ given only data from living species.
( A and B) Complete phylogeny ( A) with associated reconstructed phylogeny ( B), which is obtained by suppressing all extinct lineages. ( C– G)Models for speciation and extinction. Red denotes a fast rate, purple an intermediate rate, and blue a slow rate of speciation. C–E indicate the three models accounting for rate heterogeneity through time and across subclades: ( C) Morlon …