Vertebrate Cladistics

Though numerous traditional taxonomic groups have been confirmed by phylogenetic analysis, many others have been overturned. For example, think back to Module 2 and our explorations of the former “Kingdom Protista:” why did that group get revised? Sometimes, traditional groupings leave out members, essentially referring to a common ancestor and some but not all of its descendants. This typically happens when a group member evolves novel characteristics that make it look different than other group members. Take Reptilia, for example. The name “Reptilia” traditionally refers to a group that includes lizards, snakes, crocodiles, and dinosaurs - and leaves out some important descendants of reptilian ancestors (birds & mammals). Unless birds and mammals get included within Reptilia in classificatory schemes, it doesn’t reflect a true evolutionary group. This type of group is called a paraphyletic group (Figure 2).

At other times, traditional classifications have pulled together organisms that only share a distant common ancestor. Instead of sharing their similarities due to that common ancestry, they share features because they evolved them convergently. An example of this type of group is one that Linneaus  actually created himself. Since both birds and mammals are the only warm-blooded organisms on earth, he decided they should belong to the same group. He united them within a group called “Homeothermia.” But now that we know more about the evolution of these two groups, we know that birds are specialized dinosaurs, and that mammals descend from a completely different group of reptiles! For this reason, we can say that the evolution of warm-bloodedness evolved independently (it converged). These types of groups are termed polyphyletic groups (Figure 2), just like the organisms in the former  “Kingdom Protista” we explored in Module 2.

A monophyletic group is a group of species descended from a single common ancestor. Sometimes a particular environment causes traits to appear similar even when they are not descended from a common ancestor. Instead of homology, this is known as homoplasy, or in some cases as convergent evolution. For instance, fish and whales have fins that have historically caused scientists to group the whales and dolphins as fish, but this is in fact convergent evolution due to their aquatic habitat. In addition, traits can reverse to an older condition (reversal). To find the best answer, we will need to construct the most parsimonious tree - the hypothesized tree that requires the fewest evolutionary changes to explain.

Willi Hennig, a German entomologist, established the first numerical approach to building evolutionary trees and testing out hypotheses about the pattern of evolution in 1950. Hennig’s method is called cladistics. During the 1970s-1980s there was a raging debate about the best way to classify organisms: should groups be based on overall similarity (phenetics) or based upon only characteristics that were derived from a common ancestor (aka “shared derived characters” or “synapomorphies”) (cladistics). The earliest systematists constructed phylogenies with morphological data only. Today, systematists can employ both morphological, behavioral and molecular (ie. DNA or RNA) data to answer questions about relationships among organisms.

In the cladistic approach, a matrix is constructed in which each row refers to the species or taxa (singular: taxon) included in the study. Each column refers to the characters the scientist has chosen to work with (Characters and Taxa are reversed in Figure 3a below, but you get the idea). Different character “states” are assigned a simple numerical code so that they can be easily recorded in the matrix. For example, in the matrix below, each character has two states that are coded: absent (0) or present (1) (Figure 3a).

You can imagine that there might be lots of possible ways to arrange the character-taxa data on a tree. You’d be right! In fact, there are so many possible options that it is pretty much impossible for us to do it in our heads or by hand for most natural taxonomic groups with more than a handful of organisms (though it IS possible!). To make the job more manageable, most scientists use computer programs employing particular algorithms to help us determine which arrangement of the data is best - therefore finalizing a hypothesis of evolutionary relationships. Several laboratories here at GWU are devoted to this pursuit for a number of groups including the Clark-Forister Labs (dinosaurs), the Hormiga Lab (ironically, spiders not ants as the primary investigator’s name would suggest), the Orti Lab (fish), and the Pyron Lab (snakes).

In cladistics, we can choose among alternative arrangements of the data by employing the principle

of parsimony, which states that: “the simplest answer is probably right.” In an evolutionary sense, this means that we try to minimize the number of times characteristics evolve in the group that we are interested in. If organisms share a common ancestor and inherit their common traits from that ancestor, then the most parsimonious phylogenetic tree, or cladogram (Figure 3b) will illustrate each character evolving only a single time. “Treelength” is thus minimized in order to discover the most parsimonious tree.

It sounds simple enough, but a perfectly parsimonious tree hardly ever happens in nature! Instead, we may discover that characteristics must have evolved more than once – when they do, it indicates that the two species, or clades, have evolved those characters convergently. How do we determine which character states have evolved only once, and which have evolved multiple times? It requires a mathematical algorithm that applies the principle of parsimony across the entire dataset. This process will find the tree shape (topology) that maximizes parsimony. What? Huh? Put another way, it chooses the topology that minimizes the total number of evolutionary changes across the entire tree

(thus minimizing convergence among similar features).

/

If we’d accidentally used convergently evolved characters when we created our taxonomy, our hypothesis would be proven wrong! We would’ve created a non-monophyletic group based on a superficial similarity, and we’d have to go back to the drawing board and revise our taxonomy to bring it in line with our new understanding of evolution. Cool, right? Yes. However, you can easily imagine that it may result in some scientific controversy, where experts may not always agree upon the best possible phylogenetic tree. In the short term, that is. In the long term, new data and new techniques will become available to resolve such a dispute. That’s all good and confirms that the scientific process

is working.

Introduction Part 2: Animals in Brief

When you think of animals, what comes to mind? Maybe it is a cat, or dog, or fish. These are among the most visible and largest animals, but if diversity and absolute numbers are any measure of evolutionary success, we must discuss the invertebrates. Invertebrate animals are a group that accounts for all animals without a notochord in their development; that includes 96% of all animal species. The small minority not included is Chordata, the vertebrates, the phylum including animals like us that have notochords (e.g. fish, mammals, reptiles, birds, and amphibians). Invertebrate animals are incredibly diverse in structure, behavior, and ecology, but we still know relatively little about them. In fact, it is realistic to hypothesize that we know anything about less than half of the invertebrate life on Earth!

Most animal phyla originate from the Cambrian Explosion, a fast (on a geologic scale, 20 million years) diversification and radiation of life forms about 540 million years ago. Invertebrate organisms you will learn about today have an unbroken lineage from that time until now, which explains some of the enormous diversity we observe. Their fossils also provide morphological characters for study in how animals have changed over time. Consider going to the Smithsonian National Museum of Natural History exhibit on the Burgess Shale; there you will find many fossil examples of these early animals.

A Small Subset of Invertebrate Phyla:

We will be observing a few invertebrate phyla in this lab and building a cladogram. There are currently 35 recognized invertebrate phyla, each of which form their own monophyletic group according to the best modern evidence and methodologies. Each of them are interesting in their own right, but unfortunately we could not hope to cover all 35 in detail in this one lab. We will focus on the following multicellular Phyla, as a simplified offering of the diversity of invertebrates life on earth. Our samples include living organisms, recent remains, and fossils dating back many millions of years.

Phylum Porifera

Poriferans (pore-bearing), or sponges, are unique among animals because they lack so many animal-like features. They are sessile as adults, asymmetrical, have no true tissues, and can reproduce sexually or asexually by budding, fragmentation and regeneration from broken off parts. Sponges do not have nervous, digestive or circulatory systems. Instead, sponges' bodies consist of a non-living jelly-like mass (mesohyl) sandwiched between two main layers of cells. Sponges are filter feeders that draw water into a central cavity through pores in their body. Their internal skeleton is made of spicules, which are small structures used for skeletal support and protection. Spicule morphology figures prominently in sponge classification. There are about 5,000 species of sponges which have a variety of forms, ranging from relatively simple tubes to ones with complex channel systems or a brain-like appearance.

Phylum Cnidaria

Cnidarians are named for their cnidocytes, which are stinging cells that swimmers may know all too well. This phylum includes jellyfish, sea anemones, and hydra. Bearing some similarity to the sponges, their bodies consist of mesoglea, a non-living jelly-like substance, sandwiched between two layers of epithelium (meaning they are diploblastic) that are mostly one cell thick. Unlike sponges, the cnidarians have true tissues, composing a simple muscular and nervous system. Some members even developed rudimentary sensory organs like photosensitive eyespots. They have radial symmetry, two germ layers, and radically different forms in their life cycle. These are the sessile polyp phase, and the mobile medusa phase. The medusa is what we usually term jellyfish. Cnidocytes are cells with a hair-like trigger, the cnidocil, which, upon contact, explosively activates the cnida, an organelle which, depending on its morphology, can either penetrate prey cells, injecting poison; sticks in a glue-like fashion to its prey; or, in a lasso-like fashion wraps around its prey. Cnidaria have only one body opening, usually surrounded by tentacles. While somewhat fragile, they can grow to be up to 200 kg and dozens of meters in length, particularly the Nomura’s jellyfish as well as the Portuguese man-of-war.

Phylum Nematoda

Nematodes are roundworms, which have a complete digestive tract (alimentary canal) with a separate mouth and anus. Their mouth often includes a sharp stylet, which the animal can thrust into its prey to begin food processing. Despite these adaptations for feeding, they lack a true stomach chamber, with their mouth connected directly to a muscleless length of intestine that reaches their anus. They have a resilient cuticle that allows internal muscle attachment. Though these seem like basic characteristics, nematodes are very diverse and abundant with both free-living (frequently in soil and associated with decomposition) and parasitic forms. They can range from being somewhat large (e.g. Ascaris) to quite small.

An example of one such small species is the well-known Caenorhabditis elegans. The Nobel Prize for Chemistry in 2002 was awarded to biologists who had developed it into a model organism for the study of embryological development. A curious attribute of adult members of this phylum is the near constancy of their cell numbers. For example, the adults of the free-living C. elegans have precisely 959 cells, which can be tracked from their generation during embryogenesis to their inevitable cell death, which is valuable for numerous descriptive and experimental studies. Furthermore, its entire DNA sequence was one of the first to be published, making it popular for genetic studies as well.

Phylum Annelida

Annelids are ringed-worms (annulus = ring). The Annelids are bilaterally symmetrical, triploblastic (have three primary germ layers), invertebrate organisms. There are over 22,000 identified species and counting, with common representatives include segmented roundworms, earthworms, and leeches. In addition to their segmentation, annelids have a closed circulatory system (more similar to chordates than other invertebrates!), developed musculature, developed central nervous system, and cephalization. Mesoderm lines their entire body cavity. Their bodies are covered by a cuticle (outer covering) that does not contain cells but is secreted by cells in the skin underneath, is made of tough but flexible collagen and does not molt (in contrast to arthropods).

Annelids may be parasitic or free-living. Some annelids are helpful to humans: earthworms are excellent decomposers and soil aerators, and leeches have medical uses including restoring circulation, reducing swelling, inhibiting clotting, and as a local anesthetic.

Phylum Mollusca

Mollusks are a diverse clade of soft-bodied organisms, often with hard protective covering. They are the second most diverse clade of invertebrates, after arthropods, with over 85,000 recognized species to date. Mollusks are characterized by a radula, or rasping, tongue-like organ. The two other universal features defining modern molluscs are a mantle with a significant cavity used for breathing and excretion and the complex & incredibly unique structure of the nervous system. Like most invertebrates, they have an open circulatory system.

This phylum contains many body forms and life histories; chitons, clams, oysters, snails, slugs, squids, and octopi are all mollusks. While the cephalization in mollusks like snails and octopi is quite apparent, protection and filter-feeding have modified mollusks like clams into organisms that one can scarcely tell are bilateral. Cephalopods (squid, octopi, nautiloids, and cuttlefish) are deserving of special mention due to their intelligence, speed, internal shell, ability to change color, and ink defense, making them unique organisms for morphological, behavioral, and cognitive study.The largest living invertebrates are the giant and colossal squids, deep sea giants which can weigh in excess of 1,000 lbs and be over 30 ft in length.

Phylum Arthropoda

Arthropods (arthro = jointed, poda = feet or legs), are the most successful group of animals on the planet, based on their diversity and ubiquity across the globe. They number in the millions of species, dwarfing other groups. About 75% of all animal species belong to this group. Beetles alone may represent over 25% of all animal species alive today. Major groups of arthropods are the insects (six-legged arthropods, usually with wings), chelicerates (eight-legged arthropods with modified fang-type mouthparts; includes spiders, scorpions, and mites), crustaceans (usually aquatic arthropods, including crabs, shrimp, and crayfish, though some are terrestrial like sowbugs/pillbugs), myriapods (centipedes and millipedes), and the extinct trilobites. In general, in addition to jointed limbs, arthropods have bilateral symmetry, segmentation, open circulatory system, a hardened exoskeleton (frequently composed of the protein chitin), tagmosis (segment fusion), well- developed cephalization, and specialized appendages.

Phylum Echinodermata

Echinoderms (echino = spiny, derm = skin) are deuterostome invertebrates with radial symmetry. In deuterostomy, the developing embryo's first opening (the blastopore) becomes the anus, while the mouth is formed at a different site later on. Echinoderms share this trait with Phylum Chordata, but with NO OTHER Phyla in this lab module. Echinoderms include sea stars, brittle stars, sea cucumbers, sea urchins, and crinoids. They are slow-moving but still effective predators. They also frequently rely on external protection ranging from a leathery texture on sea cucumbers to skin covered in tiny pincers in sea starts to poisonous spikes in sea urchins (hence the phylum name). While they lack many of the features we consider ‘advanced’ in animals, this phylum is closely related to the chordates. They are actually bilaterally symmetrical as larvae and become radially symmetrical as adults. Echinoderms possess a unique water vascular system, a network of fluid-filled canals derived from the coelom (body cavity) that function in gas exchange, feeding, sensory reception and locomotion.