Chapter 9. Ontogeny and Phylogeny

Ontogeny is development. It’s most often thought of as the series of stages multicellular organisms go through, beginning with the fusion of an egg and sperm to form a zygote, continuing into adulthood, and perhaps even to death of an individual. As an organism completes development, it takes on the characteristics of whatever species it may be.

Phylogeny is the evolutionary history of a group of organisms, most often expressed as a pattern of relationships among species. A phylogeny can be traced by examining the characteristics that one species shares with another species, or the features that groups of species share with each other, including the fossils of species long gone, but it is the individual organism that expresses species membership. Species are expressed through the development of individuals – this subject was of great interest to Jack and Cy, and others, and I became interested as well.

Individuals of the same species can interbreed, or put up vegetative shoots from underground rhizomes, or somehow make more of themselves; they are usually anatomically and behaviorally similar. Individuals can be catalogued into species, and species can be grouped at higher levels, following a pattern of evolutionary relationships based on the evidence of shared characteristics.

“Ontogeny recapitulates phylogeny.” Many biology students have heard this old phrase, suggesting that each individual goes through a series of “ancestral states” as it develops. As an embryologist, Cy Finnegan offered comments and some historical perspective on this notion: “Early in the 19th century Karl von Baer observed a comparatively large group of various developing Vertebrate embryos and reached certain conclusions (principles). The general characteristics of the groups were the first to appear in development and were followed in time by the less general. Subsequently, the more specific (features) appeared in development until finally the individual characteristics were present in the developed forms. At no time did the forms resemble extant adults, but rather approximated the embryos of associated forms. Later, Ernst Haeckel, an expert in the Protista (a collection of eukaryotic organisms, some single-celled, some more complex, that are not green plants, animals or fungi) asserted that he observed a recapitulation in the Protists and extrapolated it to all development. Von Baer fought this aphorism mightily, noting it was embryos resembling embryos, if they resembled anything at all, and not adults.”

The idea that ontogeny recapitulates phylogeny – that as an individual, multicellular organism develops, it passes through many of the earlier evolutionary stages of its ancestry, lacks descriptive accuracy. Though ancient patterns sometimes appear to manifest themselves during development, they may vanish as organisms reach maturity. As Cy summarized: “Embryos resemble only embryos,” and not adult forms. It seems that a developing organism reads and translates genetic and other information, changing its physical form and manifesting distinct features as it moves along a developmental trajectory, “which to a considerable extent is predetermined, given no external interferences,” Cy adds. Species membership is “predetermined” as the information the organism possesses constrains the forms its development can take.

After he finished a Master’s degree with Jack, Mishtu spent some years traveling in an analytical and programming universe looking, in part, for empirical ways to approach ontogeny and other interesting phenomena. In paraphrasing Cy’s point, Mishtu described the difficulty in collecting developmental data: “Development is characterized by increasing specification. Vague patterns early in development become distinct categories later in development. To make a measure on a developing system assumes we can first identify the category of what we are about to measure – and that the category even exists at the point of observation. That is, in the course of development, measurable variables emerge, and the ability to measure emerges.”

Perhaps the original saying, “ontogeny recapitulates phylogeny” should be amended to read: “Phylogeny, or evolutionary history, is expressed by organisms closer to the endpoint of development.” For multicellular organisms, species membership can only occur through the phenomenon of ontogeny. Individual organisms exhibit emergence; an organism has properties not possessed by its collective parts, or even by its embryonic self – the eventual adult has become something quite different. As they develop, young individuals expand along a trajectory that will eventually take them to their adult forms, but the trajectories aren’t absolutely identical. Each organism expresses some uniqueness as it develops; in many ways the adult endpoint is predictable, but there’s always a little bit of a surprise. Much of this surprise may be the result of an organism reacting to a continually changing environment in its particular way. As an organism passes through development and reaches adulthood, it finally takes on the characteristics of its species. As it changes form, it manifests a developmental program, a program partly based on the information captured in its DNA. Humans and chimpanzees share a lot of genetic information, but their developmental outcomes are pretty different. Perhaps DNA doesn’t tell an organism how to develop or what to become, but instead each organism interprets the information on its chromosomes according to its species membership. In later years, Jack & Cy studied this idea with Edwina Taborsky, as something of a feedback effect (Taborsky et al., 2004)

Jack Maze was very interested in the relationship between ontogeny and phylogeny, not in recapitulation, but in finding methods to explore the connections. For plants that live more than a single year, development is something of an ongoing event, or something that starts up again every spring, and botanists have the option of studying more than embryos. In his comparative studies of grasses and conifers, Jack could look at younger or older structures and be able to use the same variables for both ages. Most grasses become dormant and die back to the ground in the winter, putting up a new set of shoots the following spring. Although the plants are already mature and no embryos are involved, this repeated spring growth is still development of new, unquestionably homologous, organs. All of the little flowers on a grass inflorescence don’t mature at once, but once they have all of their parts, these flowers of different ages can be measured and compared at a single moment in time. Conifers, of course, don’t die back to the ground, but each year new shoots and needles grow from the older branches and these can also be compared. There are thousands of grass species in the world. Most of these have homologous parts, organs that arose from the same evolutionary source, reflected by their membership in the grass family, but the homologous parts are organized somewhat differently, depending on the species; taxonomists and systematists try to group these species into genera, tribes and sub-families based on morphological and molecular sources of evidence. The same is true of many conifers, and this allows for the study of development within an individual, as well as among individuals, populations and species. Jack compared the flower parts of grasses – lemmas, paleas, stamens, stigmas, ovaries – at different ages and among species. He looked for changes in biological organization through changes in variable correlations, and explored ways to summarize these variations. Similarly, Jack and student Rob S. tracked changes in variable correlations in the maturing ovules of the southern beech, as well as various grasses (add Refs.). These sorts of studies can be difficult to do, and the patterns are often unclear, but they are a necessary empirical approach to understanding the biological events produced through development and evolution. Genetics and other molecular studies are needed as well, but by themselves aren’t sufficient – it is the organisms we want to understand.

Development is tricky enough, but ideas about speciation and species themselves are at least as messy. These questions have been argued about over many years: What, if anything, is a species? Why and how does one species split into two (or more?) species? These are, or should be, ongoing debates in biology in spite of the tidy, but unsatisfactory, Biological Species Concept of E. Mayr that is still the common definition taught to students.

We usually think of a species as: “A distinct, identifiable group of individuals that regularly breeds together and is thought to be an evolutionarily independent group, generally distinct from other species in appearance, behavior, habitat, ecology, genetic characteristics, etc.” This is a fairly good operational definition for a first year biology class – it expects species to be “distinct” and “identifiable,” which they very often are, in addition to having sex. Sex is assumed to provide basic cohesion – it’s the glue that sticks the individuals of a species together so that there is constancy from generation to generation. But this becomes a problem in species that tend to bypass sex. Many people can recognize an aspen tree, and realize they tend to grow in groves under natural conditions. Aspens don’t have sex very often at all, but tend to reproduce themselves vegetatively. A single individual produces woody rhizomes that travel under the surface of the ground, producing new shoots that grow into trees here and there, sometimes forming extensive groves. Being aspens, the trees are all of one sex, male or female, so sexual reproduction is often not an option. On the one hand, there are the balsamroots engaging in hybridization when the opportunity presents itself, having sex both inside and outside of species boundaries. On the other hand, there are the quaking aspens, Populus tremuloides, skipping sex altogether and producing a big population of either female or male, genetically identical clones. Individuals replicate themselves and express species membership as they develop, but not always through sex. Humans think sex is ever so important, but other life forms may be less impressed. So, the glue of species cohesion may be something beyond sex alone, perhaps a shared history at other levels of cohesion. Present-day epigenetics is interested in molecules beyond DNA that alter the reading and expression of the information it holds, and this is perhaps a similar approach.

Other proposed definitions of species (according to a first year biology text) have been offered over the years to try and clarify the topic. “Morphological” species (or “morphospecies”) are defined as groups with measurably different anatomical features. Some biologists liked the “phylogenetic species concept,” where a species is defined as the smallest monophyletic group in a tree diagram representing populations. A monophyletic group is: “An evolutionary unit that includes an ancestral population, all of its descendents, and only its descendents.” This phylogenetic species concept seems a bit off – tree diagrams or cladograms usually represent species and not populations. If the populations are all of the same species, how will we distinguish the ancestral from the descendant, except maybe by geographical separation or other characters below the level of species? There might be some detectable mutations in alleles, in genes that vary somewhat in chemical details, but have the same function and generate the same product. It might be difficult to trace the sequence of these mutations and decide which could be ancestral without some other source of evidence. A change in allele frequencies within and among populations of the same species is often known as microevolution. This kind of change was going on in the pepper moth where there were two versions of wing color – one allele for dark wings and one for pale wings with dark spots. But “microevolution” is reversible, so it doesn’t qualify as evolution in the sense of irreversible speciation. For a moth to have two color forms may simply be the variability typical of that species, as it often is for other species. A major change in form resulting in the splitting off of a new species is sometimes called macroevolution. As an evolutionary process it is irreversible, but it’s not very clearly connected to the minor mutations of “microevolution.” Twenty microevolutionary allele changes don’t add up to a macroevolutionary speciation event. Or, if they do, the bridge principles linking them are not clear.

Rather than the biological, morphological or (so-called) phylogenetic species concepts, a clearer way to define a species is to point out one or more autapomorphies all of the individuals share. “Show me a unique character shared by a group of organisms, and I’ll show you a species, even if I can’t fully define it.” This paraphrases the argument of a systematist named Kluge (find ref.) who offered this operational definition of species and, until we learn more about them, I think it works pretty well. In addition, a monophyletic group might be better defined as a group of species sharing a unique evolutionary history as evidenced by the possession of one or more synapomorphies – all species with the defining characteristics are included in the group; all others are omitted. To require that a monophyletic group include an “ancestral” population (or species) might be asking a bit too much – how would we spot the “ancestor?” Do we really need one? It’s not so hard to demonstrate that a group of organisms or species shares a common ancestry – autapomorphies and synapomorphies provide evidence for this. But I’m not so sure about the search for the actual ancestor – evolution might not be exactly the same as a genealogy, where we can show the great-great grandparents and all of their descendants on the tree.

What happens during speciation, when a lineage splits, when a species bifurcates and becomes two species? Are we left with the older species plus a new one that has branched off from its ancestor, or does the “ancestral” form disappear altogether, leaving us with two new forms? Is speciation always a bifurcation, a splitting-in-two, or could there be more than two resulting species? Often, at least in plant systematics, one ends up with a phylogeny, a cladogram that is described as unresolved. This is where more than two species diverge from a single branching point. Most often we assume such a pattern is the result of poor data, but it might also be the result of speciation following hybridization, an event that’s fairly common in plants; the several species of wheat, for example, have arisen this way (ref?). Or, maybe the pattern reflects the possibility that more than two species can evolve from a single speciation event. We really don’t have an answer for this, but some additional patterns that accompany speciation have been discover over time.

Western North America is the center of diversity for plants such as balsamroots, lupines and fleabane daisies – most of them are native to this part of the world and there are many species within a relatively small geographic area. Textbooks call this pattern adaptive radiation, defined as: “Rapid evolutionary diversification within a single lineage, producing numerous descendant species with a wide range of adaptive forms.” I’m not sure about the meaning of “adaptive forms,” since all are adapted if they exist, but some life forms seem to have undergone rapid speciation, at least in geologic time. Speciation is often correlated with some sort of physical barrier that separates the populations of a species. This is known as allopatry or vicariance: “Speciation that occurs by the splitting of a population into smaller, isolated populations by a geographic barrier.” Even when split, speciation doesn’t always occur. Some moss species that were split apart by glaciers during the last ice age haven’t done much evolving at all. Jack Maze likes to point out that the Douglas fir trees on Vancouver Island haven’t exchanged genetic material with trees on the mainland, or in the Black Hills of South Dakota, for a very long time, yet they all remain Doug firs, though with a few differences. So, physical barriers are correlated with speciation, but they aren’t fully causal – something else must be going on in addition to separation to trigger bifurcation of a species. Evolutionary lineages sometimes seem to diverge and converge at the same time. My biology textbook addresses convergent evolution: “Evolution of similar traits in distantly related organisms due to adaptation to similar environments and a similar way of life…often produces analogous traits.” So, do the causal forces of evolution spring from the environment, or does the environment simply provide constraints, limiting evolution’s possibilities?

The idea of homology – that structures or other features arise from a single source, though they may have different functions – remains an important one. Conversely, analogs share a common function, but they come from different sources. Again, the classic example is the wings of insects and birds. They are analogous as both function in flight, but they are not homologous as they have a different evolutionary source. The arms of humans are homologous to the wings of bats or birds but they perform different functions. With the elucidation of DNA we thought we would be able to fully pinpoint and understand homologs. We hoped that each character would be coded for by one gene or maybe a simple set of genes. It turns out to be just a bit more complicated than that, and the DNA “Rosetta Stone” is still more like alphabet soup. We see the letters, but can’t read the language. Perhaps this is because, as with all languages, there’s more to the language than the letters.

This is one of the most basic, most studiously ignored problems in biology – we don’t know how we get from DNA to organisms. We need a good theory of morphogenesis, one that gives us reason to expect to see the translation of information from DNA into structure and behavior, and a theory that is amenable to evaluation using Hempel’s Covering Law Model. Certainly, genetics and molecular biology have discovered many things, but the methods frequently consist of shooting in the dark. In the genetic modification of organisms, we don’t really know what’s going on.

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