Phylotypic Stage
The most comprehensive taxonomic category for classifying animals is that of phylum. Thirty-something phyla have been distinguished (the exact number depends on the taxonomy adopted) and each phylum involves a unique set of traits. For example, at some point during development, all chordates share a dorsal nerve cord, notochord, gill slits, and a postanal tail. These traits are present only in chordates, and thus they define the phylum’s body plan. Each existing phylum represents a unique body plan and the taxonomic divisions below the phylum level (e.g., class, order, family, genus, species) represent variations of this basic body plan.
In the phylotypic stage, the basic features of a phylum’s body plan are first distinguished. Karl von Baer (1792-1876) noticed that early in development it is difficult to determine whether a particular embryo is a frog, a bird, or a mammal (Figure 1.3). Structures specific to the class, order, family, genus, and species developed subsequently, making the organism progressively more recognizable. Developmental processes both before and after the phylotypic stage are variable across species within a phylum. For example, before the phylotypic stage, vertebrate embryos differ in terms of egg size and the structures that developed during early stages; after the phylotypic stage, differences in adult morphology across vertebrates speak for themselves. Development appears to be constrained to pass through a highly conserved stage, common to all species within a given phylum.
The stability of phylotypic stages suggests limits to natural selection. Variations in body plan organization were established early in metazoan evolution and have remained stable since then. The difficulties of tinkering with phylotypic stages may be in part responsible for the post-Cambrian stability of animal phyla. In turn, changes in genetic expression profiles during phylotypic stages may be responsible for the evolution of novel body plans leading to a new phylum, whereas changes in gene expression that occur after the phylotypic stage may lead to evolutionary changes leading to a new genus or species (Levin, Hashimshony, Wagner, & Yanai, 2012). The emergence of a new phylum could require reorganization of the early stages of development for the resulting body plan to be significantly different from that of the ancestral condition (e.g., the evolution of chordates from some ancestral echinoderm) . By contrast, the evolution of new species often involves relatively small changes that may be accomplished by readjustment of later developmental stages (e.g., Galapagos finches differing in body size and beak shape; see Chapter 1).
Several gene clusters are maximally active during the phylotypic stage. Importantly, these genes are remarkably stable across animal phyla, suggesting deep links of homology. One example is provided by I lox (or homeotic) genes. These are regulatory genes (i.e., genes whose protein products affect the expression of other genes) containing a sequence of 180 bases, called the homeobox. The homeobox is shared by all studied animal phyla. Hox genes are distributed in series in a strain of DNA and expressed in the anterior-posterior axis of the animal in the same order in which they are located in the DNA strain.
Hox genes were discovered in the fruit fly Drosophila melanogaster and called homeotic because their mutation usually leads to the development of similar structures in segments of the body normally exhibiting different anatomy. For example, a mutation of Hox gene number 7, known as ultrabithorax, leads to the development of four wings in Drosophila. Since fruit flies belong to the Order Diptera (literally, two-winged), this homeotic mutation alters the dipteran body plan.
Hox genes are expressed in the same sequence in species from different phyla. Figure 3.2 summarizes the distribution of these genes in several species, aligning those that were shown to be homologous on the basis of similarity in base sequence. Two features of Hox genes have implications for an understanding of evolution. First, the number of genes in the Hox
Figure 3.2 Hox genes identified in species from widely divergent phyla. Genes considered to be homologous. on the basis of the degree of similarity in the sequence of bases in the DNA molecule, are aligned vertically. Changes include gene additions, deletions, and, in vertebrates, quadruplication of the entire linkage group (Hox-A to Hox-D). These linkage groups are called paralogous genes and are located in different chromosomes.
cluster varies across species, even within the same phylum. Hox genes have evolved by a process of duplication and change. In some taxonomic groups, new genes have been added, whereas in others, specific genes have been deleted. Second, unlike in most other groups, in vertebrates the basic cluster has been extended by at least four additional genes (number 10 to 13), and the entire cluster has been quadruplicated, with each strain located in a different chromosome (clusters are known as Hox-A, B, C, and D). These variations may be related to the evolution of some vertebrate traits, such as the postanal tail, a structure unique to chordates and highly developed in vertebrates.
In addition to the Hox cluster, other genes are expressed along the anterior-posterior axis. For example, the genes known as orthodenticle and empty spiracles are expressed in the anterior end in both mice (chordate) and fruit flies (arthropod). These genes, as well as the Hox genes, do not determine the type of structure (i.e., compound eyes, wing, hind leg, etc.) that would develop in a particular region. Rather, they determine the relative position of structures in the anterior-posterior axis of the organism. For example, Hox genes determine that one end of the embryo would develop into a head, but additional genes are needed to determine the structures that would develop in the head (e.g., compound eyes in insects, but single-lens eyes in vertebrates).
