A flock of sheep somewhere in Punjab, India.

Biological Diversity, Nested Hierarchies, and Parsimony

Aaron Mboma
808 Computing

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Twelve years ago, I picked up a biology textbook and memorized the taxonomic ranks used in biological classification. I actually still remember the mnemonic the book used: Da Kine Philip Came Over For Good Spaghetti (Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species). Of course, I didn’t know then how significant this information was. Neither did I imagine that years later it’d be my primary area of research. Well, here we are.

Our planet is home to so many organisms, coming in different shapes and sizes: mosquitoes, blue whales, crows, sponges, jellyfish, earthworms, sheep, etcetera. These all belong to the animal kingdom (Kingdom Animalia). But what makes them animals? What even is an animal? Taxonomy is a field concerned with the identification, classification and naming of organisms. The Kingdom is customarily considered the broadest rank and the Species the narrowest, i.e., all mosquitoes are animals but not all animals are mosquitoes.

I will not discuss the intricacies of taxonomy, but classification is generally based on meaningful similarities and/or differences among organisms. Meaningful in the sense that, even though bats can fly, they are not birds. When giving scientific names to species, two ranks are used: the Genus name and the Species name. For example, the scientific name of a chimpanzee is Pan troglodytes. Different species can belong to the same Genus, Family, etcetera. The bonobo (pygmy chimpanzee) is another species in the Genus Pan. It bears the scientific name Pan paniscus. These two Pan species share a lot in common with each other than each share with other organisms. Now that we are up to speed, let us dive in.

Domestic sheep (Ovis aries) are my favorite livestock. The genus they belong to — Oviscontains 6 other species (not breeds), including the mountain sheep (Ovis ammon) and the bighorn sheep (Ovis canadensis). Collectively, all sheep species share some characteristics with animals in the Genus Bos (cattle) and the Genus Capra (goats), such as having a four-chambered stomach. Cattle, goats, and sheep characteristically have unbranched horns, and together they make up the Family Bovidae. Other members of this family include antelopes and buffalo. Bovidae belongs in the Order Artiodactyla, which roughly means even toes. A defining feature of the many families that belong in this order is that they all walk on an even number of toes, e.g., sheep walk on two toes while hippos walk on four toes. In contrast organisms in the Order Perissodactyla walk on an odd number of toes, e.g., rhinos walk on three toes while modern horses walk on one toe. These two orders belong in the Class Mammalia, alongside orders such as Carnivora (carnivores), Primates (monkeys, humans, lemurs), Rodentia (rodents), etcetera. The most obvious feature of all mammals is the possession of mammary glands. Class Mammalia, together with classes such as Amphibia and Reptilia, make up the Phylum Chordata, which then is found in the Animal Kingdom together with Phylum Porifera (sponges), Arthropoda (insects, spiders, scorpions), Mollusca (snails, octopuses), and many others. This idea of groups within groups is what is known as a nested hierarchy.

Biological evolution posits that all organisms have descended from some common ancestor. Darwin called this descent with modification. Be it as it may, it seems nonsensical to think that sheep and humans have descended from a common ancestor. How can it be? Alternatively, it would not be as ridiculous to consider that our 7 sheep species descended from a common ancestor. The latter would obviously be more acceptable than the former because it appears to be a difference of degree, not kind.

The utility of a nested hierarchy lies in demonstrating to us what characteristics supposedly are ancestral and what are new (unique). Therefore, while all sheep species have unique identifying characteristics, the characteristics they have in common must have been present in their common ancestor. This train of thought extends to higher ranks. If cattle, goats, and sheep (bovids) have some characteristics in common, then it is quite likely that their common ancestor (whatever it looked like) must have possessed these characters. Ideally, the ancestor of all sheep (Ovis) is more recent than the ancestor of all bovids. By extension, the ancestor of all bovids is more recent than the ancestor of all Artiodactyla.

A phylogenetic tree of the SRY gene, constructed in MEGA 11 using the Maximum Parsimony method, showing a nested hierarchy. From the tree, the African buffalo and cattle share a more recent common ancestor, just like the goat and sheep. Collectively, they share a more recent common ancestor than they do with the horse.

Why assume common ancestry? Why not consider that they somehow independently developed these characteristics? This rests on the principle of parsimony (a.k.a. Occam’s Razor). This principle asserts that a hypothesis requiring the fewest assumptions should be preferred. In this case, a ‘single sheep ancestor’ has fewer assumptions than alternatives. By extension, it is more parsimonious to hypothesize that all mammals have mammary glands because they all share a common ancestor that had mammary glands; and while they diversified into different kinds, they have maintained their ancestral characteristics.

Adopting a nested-hierarchy way of thinking helps avoid common pitfalls such as ‘if we evolved from monkeys, why aren’t monkeys evolving into humans?’ Taxonomically, the term ‘monkey’ is very broad, referring to all anthropoid organisms in the Order Primates. Meanwhile ‘humans’ — in the strictest sense — would refer to organisms in the Genus Homo (sapiens, erectus, neanderthalensis, denisova). Humans belong to the Family Hominidae, which includes chimpanzees and other great apes, while what are commonly considered monkeys belong to the Family Cercopithecidae (Old World monkeys) or Parvorder Platyrrhini (New World monkeys). Therefore, humans and chimpanzees share a more recent common ancestor than they do with old world monkeys.

A phylogenetic tree of the SRY gene in some primates. The Olive baboon and the Diana monkey are Old World monkeys, while the Tufted capuchin is a New World monkey. The Bonobo, Chimpanzee, and Gorilla are great apes, and their common ancestor is more recent than one between them and the Old World monkeys.

Here is a cool fact to take with you: all animals, from houseflies to blue whales, sheep to humans, share the same genes that regulate their body plans, known as Hox genes. Parsimony would therefore have us consider that these genes are ancestral to all animals, and despite their immense diversity, all animals fundamentally run on the same, albeit modified, code.

‘There is grandeur in this view of life… from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.’ — Charles Robert Darwin.

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808 Computing
808 Computing

Published in 808 Computing

scientific computing and business intelligence

Aaron Mboma
Aaron Mboma

Written by Aaron Mboma

Zoologist: Butterfly Systematics, Molecular Phylogenetics, Speciation, Evolutionary Genetics. Malawian. https://www.researchgate.net/profile/Aaron-Mboma-2