Analyzing Developmental Sequences Within a Phylogenetic Framework

Abstract

Heterochrony is important as a potential mechanism of evolutionary change. However, the analysis of developmental timing data within a phylogenetic framework to identify important shifts has proven difficult. In particular, analytical problems with sequence (event) heterochrony revolve around the lack of an absolute time frame in development to allow standardization of timing data across species. An important breakthrough in this regard is the method of "event-pairing," which compares the relative timing of developmental events in a pairwise fashion. The resulting event-pair-encoded data can be mapped onto a phylogeny, which can provide important biological information. However, event-paired data are cumbersome to work with and lack a rigorous quantitative framework under which to analyze them. Critically, the otherwise advantageous relativity of event-pairing prevents an assessment of whether one or both events in a single event-pair have changed position during evolutionary history. Building on the method of event-pairing, we describe a protocol whereby event-pair transformations along a given branch are analyzed en bloc. Our method of "event-pair cracking" thereby allows developmental timing data to be analyzed quantitatively within a phylogenetic framework to infer key heterochronic shifts. We demonstrate the utility of event-pair cracking through a worked example and show how it provides a set of desired features identified by previous authors.

The Architecture and Evolution of Life Cycles

“…Here Minelli outlines some of the problems that comparative embryologists encounter when trying to compare stages between different species. This is often not straightforward, because the development of some characters may be heterochronically shifted relative to others during evolution, so that a given stage in one species can be a mosaic of conserved, retarded, and advanced developmental events when compared with development of another species (see also Smith 1997;Schlosser 2001;Jeffery et al 2002). Some stages are more clearly delimited than others.…”

A New Technique for Identifying Sequence Heterochrony

“…Unfortunately, the very simplicity of the event-pair method makes interpretation of the apomorphic changes difficult (Jeffery et al, 2002b). For example, it is clear from the list of changes in Table 1 that there have been several changes in the developmental sequence from species X to species Y.…”

“…This method encodes the relative position of each item in the sequence, thereby allowing comparisons between species to be made. The use of relative timing is necessary because variation in the overall rate of development (both between species and to some extent between individuals of the same species) prevents the use of absolute timing data (e.g., in hours, minutes, and seconds) in phylogenetic comparisons (for a full discussion, see Nunn and Smith, 1998;Bininda-Emonds et al, 2002;Jeffery et al, 2002aJeffery et al, , 2002b.…”

Constructing (Almost) Phylogenetic Trees from Developmental Sequences Data

“…Using knowledge on, e.g., the rate of change, time-stamps are computed for the different splits. In this paper we show how to reconstruct such trees with a different kind of data, viz., the order of events in the development of an animal [1,2]. Examples of the events are the start of the development of the Heart or of the Eyes.…”