In general, evolutionary biologist are interested in understanding how all the different creatures that are present today arose and how these creatures interact with each other and the environment to generate the ecosystems we see today. So evolutionary biology involves researchers in many fields, for example cladistics, paleontology, genomics, population genetics and ecology, and developmental biology.
Cladistics is the discipline of reconstructing the relationships between organisms. That is, when did two discrete organisms last share a common ancestor? As the relationships between individual species and among related clades become better resolved based upon morphological and molecular similarities, complex familial relationships can be inferred and represented as a tree like network where the closest relatives represent adjacent tips on large branches. The network of all living things is called the tree of life.
Paleontologists study the fossil record to trace back morphological features that can be used in cladistic studies. Genomics is the accumulation and annotation of the genetic codes for living organisms. Once an organism’s genome sequence is known, it can be compared with the sequences from other organisms to determine relatedness. Additionally, genomic researchers can look for patterns in the genes that are present in one group of animals but not others and in the way the genes are arranged with respect to each other and other non-coding sequences to gain further insights into how genomes and thus animals evolve.
Population genetics study the frequency of the different alleles for a gene in a population and the effects of population size, life strategies, and environmental effects on the frequency of these alleles over time.
Comparative developmental biology tries to understand the molecular and cellular differences that have resulted in the disparate morphologies among organisms, i. e. why is a butterfly’s wing different than a fly’s wing.
C. elegans, or the worm, is a model developmental organism. This means that along with a small group of additional animals and plants (such as fruit flies, mouse, zebra fish, and Arabidopsis), it has been chosen as a system for detailed molecular and cellular studies. The worm’s strengths are its easy laboratory handling and its tremendous amenability for genetic and cellular manipulation.
Over the past fifty years, studies in these systems have indicated that all animals share a large set of common molecules for their growth and development and that these molecules often associate with each other in common pathways to synthesize structural components, to allow communication between cells and tissues for coordinated growth of the organism, and to interact with the environment. This was perhaps the first major observation of evolutionary developmental biology and C. elegans was crucial in providing many of the inroads in understanding cell signaling, for example many of the founding members of the TGF-ß pathway, the EGF pathway, and the Notch pathway were first molecularly identified in the worm. Likewise, many cellular and regulatory processes that are proving to be of importance throughout the tree of life were also recognized and investigated in the worm at a very early stage, for example programmed cell death, nonsense mediated decay of mRNAs, post transcriptional regulation by micro RNAs (miRNAs), and the existence of RNA mediated interferences by short interfering RNAs (siRNAs).
While the last fifty years of comparisons have stressed how similar the metabolism and development of living things are, little has been learned about how animals evolve to have differences. This is perhaps the principal focus of much research today. What changes occurred to make all the different morphologies and life strategies we observe in organisms today? Is there a pattern to what kind of changes can occur at a molecular level and how do both molecular and environmental constraints affect the evolution of morphologies and life strategies?
It is easy to see that organisms use the same pathways for very different purposes. For example, flies use the EGF pathway for eye development and worms use the same pathway for vulva development. So, identifying difference has not been difficult. What has been problematic is explaining how the same pathway came to be used for two very different structures. Similarly, organisms often use the same pathways for putatively homologous structure that have vastly different morphologies. For example, flies have legs and humans have legs, but these two structures are very different from each other. Nevertheless, the development of both structures is dependent upon many of the same genetic pathways.
While we know the genes that regulate these two structures are the same, the structural components they target are so radically different between these animals that it is difficult to explain how the novelties between the resulting limbs evolved from a common ancestor. Thus, knowledge from organisms closely related to those well studied is required. This allows the opportunity to look for differences in morphologies and in genetic pathways in an organism where direct cellular and molecular homologies can be implied and allows the putative change resulting in a novelty to be directly investigated by experimentation and comparison. These species closely related to the model organisms are called satellite model systems.
Several nematodes are in use as comparative systems with C. elegans. Depending on the time of separation with Caenorhabditis elegans, these other nematodes can be used to ask a variety of questions. The two nematodes Caenorhabditis briggsae and Caenorhabditis remanei are very closely related to C. elegans and offer the potential to investigate the importance of highly conserved elements to cellular and genetic processes in this genus of worms, i.e. these elements (either nucleic acid or amino acid sequences) are maintained due to selective forces while elements without a necessary function are under no constraints and can change. Often however, as the animals are so closely related they appear morphologically identical and few differences can be observed. Thus, these species are best for the study of very quickly evolving traits like sex determination.
In these close satellite species, molecular players often have seemingly identical roles, thus if a difference is seen a hypothesis about the molecular players that have changed can be quickly formulated and tested. Nematodes a bit farther away from C. elegans in the tree of life, such as Oscheius tipulae and Pristionchus pacificus, allow an easier identification of morphological and cellular differences, for example differences in body patterning and organogenesis. They also open up investigation in cellular processes and pathways that evolve more slowly. However, a greater divergence time results in many more molecular changes having occurred. Thus, using data from C. elegans to make hypotheses about the molecular changes that underlie morphological novelties becomes less direct and a greater amount of experimental manipulation and data collection may be required to give insights.