Tempo and mode of evolution revealed from molecular phylogenies.

Abstract

The analysis of the tempo and mode of evolution has a strong tradition in paleontology. Recent advances in molecular phylogenetic reconstruction make it possible to complement this work by using data from extant species.Cladogenesis is the division of one evolutionary lineage into two. How often do lineages undergo cladogenesis to give daughter lineages that will survive for long periods of evolutionary time? And what characteristics of species determine rates of successful cladogenesis? Such questions are tackled traditionally by using the fossil record (1-8), the quality of which limits the accuracy of the answers obtained (9). However, paleontological data could be usefully complemented with information from extant species if the dates when pairs of species last shared a common ancestor were known (10). Fig. 1 line A is a semilogarithmic plot of the number of lineages against time since the first bifurcation. As there is uncertainty about the calibration of the molecular clock pertaining to these data (15, 16), we measure time in arbitrary units since the time of the first bifurcation. The slope of this curve reflects the per-lineage rate of effective cladogenesis and, so, would appear to be a straight line, with stochastic wiggling, if the rate were constant through time. Instead, the rate appears to decrease quite smoothly over time. As the legend of Fig. 1 describes, the data are incompatible with a constant-rate model.Following the failure of the one-parameter constant-rate model, we fitted a two-parameter density-dependent model, in which the per-lineage rate of cladogenesis is a function of the form p/Na, where N is the number of lineages and a is a constant. The compatibility of this model with the data is good (Fig. 1), not only because there is an extra parameter to fit but also because of its qualitative form (the possession of a positive second derivative). This contrasts with the relatively poor performance of the two-parameter logistic model ofdensity dependence, p(l -N/K), which is commonly used in population biology.It has been suggested that the degree of molecular divergence between taxa is not related to time since divergence in a linear fashion, as we have assumed here, but that the genetic divergence between taxa was more rapid early in the history of an adaptive radiation (17). If this controversial (18,19) suggestion is true, the deceleration in cladogenesis was even more rapid than we have estimated (i.e., a larger a). The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.

A molecular assessment of phylogenetic relationships and lineage accumulation rates within the family Salamandridae (Amphibia, Caudata)

“…To obtain a visual perspective of the rate of lineage accumulation over time, we constructed lineage-through-time (LTT) plots (Nee et al, 1992) for 10 trees sampled from the posterior distribution (trees 1, 101, 201, 302, 401, 501, 601, 700, 801, and 900) and for the ML tree using the program LTT (written by L. Harmon). For each of these trees, we quantiWed the LTT patterns using the statistic (Pybus and Harvey, 2000;Pybus et al, 2002).…”

“…Plotting lineage accumulation as a function of estimated divergence time and integrating this information with null models of the birth and death of lineages (Nee et al, 1992) permit statistical testing of hypotheses of lineage diversiWcation over time (Paradis, 1997;Pybus and Harvey, 2000;Pybus et al, 2002). These phylogenetic approaches have yielded important insight in the tempo of evolutionary diversiWcation in diverse organismal groups including iguanian lizards (Harmon et al, 2003), marine Wshes (Ruber and Zardoya, 2005), mosses (Shaw et al, 2003), and plethodontid salamanders (Kozak et al, 2006).…”

The conditioned reconstructed process

“…Besides providing data for systematics and for taxonomy, phylogenies are the pattern of past diversification and so can be analysed to infer past macroevolutionary process. The first common step is to compare the reconstructed trees with expectations from neutral models of diversification (Gould et al, 1977;Mooers and Heard, 1997;Nee et al, 1992;Raup et al, 1973). The simplest class of neutral model are entirely homogeneous, and assume that throughout time, whenever a speciation (or extinction) event occurs, each species is equally likely to be the one undergoing that event.…”

Evolutionary models of phylogenetic trees

“…Simberloff et al 1981;Slowinski 1990;Guyer & Slowinski 1991, 1993Maddison & Slatkin 1991;Heard 1992;Nee et al 1992;Rogers 1993;Cunningham 1995;Aldous 1996Aldous , 2001Mooers & Heard 1997;HarcourtBrown et al 2001).…”