Phylogeny

Phylogeny traces the history of life on Earth through the study of how animals and plants have developed over time and how they are related to one another. It is similar to taxonomy—the science of classifying organisms based on their structure and functions. Taxonomists create family trees of living and extinct species to discover the origins and lines of descent of various forms of life. Very few family trees are complete to their fossil origins, however, because of gaps in the fossil record. The first system of classification was devised by the eighteenth-century Swedish scientist Carolus Linnaeus. Linnaeus classified life-forms based on their appearance. The more they resembled each other in size, shape, and form, he believed, the more closely they were related.

The theory of evolution developed by nineteenth-century naturalist Charles Darwin was based on accumulated changes over time through natural selection and led to a new way of looking at the history of life and to the development of phylogeny as a method of classification. The new system classified the living world by similarities in ancestry rather than appearance. Life histories of species were derived from the study of comparative anatomy (the search for common features in different species), embryology (the study of the development of life from the egg to birth), and biochemistry (the study of invisible chemical characteristics of cells that link species that can look very dissimilar). Modern technology allows scientists to measure differences in deoxyribonucleic acid (DNA) molecules among species. DNA carries the genetic material of an organism and plays a central role in heredity. The degree of difference between two species helps scientists determine how much modern species have evolved and to estimate when important events in evolution occurred. If a sufficient fossil record exists, biochemists can determine the timing of a major change that led to the development of a new characteristic, such as a longer neck in giraffes or different-sized eyeballs in bats.

Classifying Earth’s Species

Studies of evolutionary change suggest that anywhere from three million to twenty million species exist, with millions more having become extinct. The Earth began about 5 billion years ago, and it has been occupied by living organisms for about 3.5 billion years. For about 2.5 billion years, the planet was populated only by single-celled bacteria. The earliest forms of life evolved by chance during a long period of chemical reactions. Random encounters between chemicals in the seas and the atmosphere produced amino acids and proteins. Small drops of proteins, made up of carbon, hydrogen, oxygen, nitrogen, and sulfur, somehow bound together and became organisms; that is, they began to reproduce themselves, which is the quality that makes them life-forms.

Every living thing is given a two-part Latin name under a system of binomial nomenclature. This name is usually based on an evolutionary, phylogenetic relationship. The first part of the name indicates the organism’s genus; the second part identifies the specific species. For example, Acer saccharum (sugar maple), Acer nigrum (black maple), and Acer rubrum (red maple) are all kinds of maple trees. They share the genus Acer, and their species names mean sugar, black, and red, respectively. No rules govern species names, though frequently, they refer to a prominent feature—color or characteristic—such as in the case of Homo sapiens, the Latin name for humans, which literally means “the thinking one.”

Of the classic five kingdoms model of life-forms, one (containing the bacteria) is made up of prokaryotes; the other four are eukaryotes. Prokaryotes do not have cell nuclei; eukaryotes do. In prokaryotes, cells are smaller and simpler in structure, and the DNA is not organized into chromosomes. Chromosomes, the threadlike structures found in the cell nucleus of all eukaryotes, determine the characteristics of individual organisms, with offspring receiving an equal number of chromosomes from each parent. In bacteria, however, reproduction takes place by a simple division of the parent into two masses that eventually separate. Bacteria do not share chromosomes with other members of the species; in other words, reproduction is asexual.

Other classification models have been proposed, including a six-kingdom model that divides the Prokaryotes into the kingdoms Archaebacteria and Eubacteria, which were later modified to become Bacteria and Archaea. This model has been highly controversial among scientists, but it is the most widely accepted classification model after the classic five-kingdom system.

The Nonanimal Kingdoms

All bacteria belong to the kingdom Prokaryotae. They are, in terms of total numbers, the most successful form of life in the universe. Some bacteria, which are germs, can cause disease, while some bacteria, such as antibiotics, can be used to cure disease. Bacterium-like fossils found in rocks from an Australian gold mine are about 3.5 billion years old. Cyanobacteria bacteria, also called blue-green algae, and Stromatolites are the most commonly found fossilized bacteria. Bacteria are found in every climate and habitat and are the first to invade and populate new habitats. Forty-two species of bacteria are known to exist, and none can be seen without a microscope.

The four other kingdoms of living things and the common names given to their most important phyla are Protoctista (algae, protozoa, slime molds), Fungi (mushrooms, molds, lichens), Animalia (sponges, jellyfish, flatworms, ribbon worms, rotifers, spiny-headed worms, parasitic nematodes, horsehair worms, mollusks, priapulid worms, spoon worms, earthworms, tongue worms, velvet worms, insects, beard worms, starfish, arrowworms, and chordates), and Plantae (mosses, ferns, and pine-bearing and flowering plants). Phyla are based on similarities in evolutionary development. Life-forms are divided into many phyla. There are forty-five phyla in the kingdom Prokaryotae; forty-five in Protoctista; seven in Fungi; thirty-five in Animalia, and fourteen in Plantae. Each phylum is divided into classes, then orders, families, genera (the singular form is genus), and finally, species. The last two divisions are based on the most recent evolutionary differences. Some phyla have only a few genera and species, while others, such as those in Animalia, have millions. A species consists of a group of similar individual organisms that can breed and reproduce offspring. A genus contains similar species, but members of a genus cannot reproduce; only members of a species can.

Protoctista (also called Protista) means the “very first to establish.” It is the kingdom made up of living forms that are neither animals, plants, nor fungi. It includes red, green, and brown algae, seaweeds, water and slime molds, and most protozoa (single-celled life-forms including amoebas). The phyla in this kingdom are found mostly in water habitats, such as rivers, freshwater lakes, and oceans.

The kingdom Fungi (from a Greek word meaning “sponge”) may have descended from the kingdom Protoctista. The oldest fossil Fungi is a fungus found in the Canadian Arctic that is about one billion years old. There are more than 150,000 identified species, including bread molds, yeasts, and mushrooms. Thousands more species are believed to exist but have yet to be identified.

The Animal Kingdom

All plants, from mosses to giant redwoods, belong to the kingdom Plantae (from a Latin word for “plant”), and most animals belong to the kingdom Animalia. This kingdom contains all multicellular, heterotrophic, diploid organisms that develop from an egg and sperm. A heterotrophic animal takes food into the body and digests it, or breaks it down, into energy for use. A diploid organism has two sets of chromosomes, one derived from the female parent and the other from the male. The characteristic that defines all Animalia, however, is that they develop from a blastula, a hollow ball of cells found in animal embryos (the earliest stage of development, when the egg just begins to divide) but not in plants. The blastula forms a layer around a central open space or cavity in the embryo.

Animalia (from a Latin word meaning “soul” or “breath”) is the kingdom with the largest number of life-forms, from Placozoa, a phylum with four tiny species usually found growing on aquarium walls, to the phylum Arthropoda (from a Greek word meaning “jointed foot”) that contains more than a half million identified species, including spiders, scorpions, beetles, shrimp, lobsters, crayfish, crabs, flies, centipedes, millipedes, butterflies, moths, and all other species of insects. About half of the phyla in Animalia are various kinds of worms found in the shallow and deep water of lakes, rivers, and oceans and in the ground. In the phyla Arthropoda is an enigmatic group of tongue worms, Pentastoma, that consists of more than 130 species that live exclusively in the tongues, lungs, nostrils, and nasal sinuses of dogs, foxes, goats, horses, snakes, lizards, and crocodiles. Another phyla, Platyhelminthes, consists of worms that live in bat dung and other equally unusual environments. Only two of the phyla, Arthropoda and Chordata (animals with nerve cords), spend significant time on land. Among the phyla, Arthropoda has the largest number of identified species, more than a million, and possibly millions more not yet identified. Most of the species of Animalia that have ever lived are now extinct. Thirty-two of the thirty-three phyla are invertebrates, which means they lack backbones.

The History of Life-Forms

The phylogenetic method of classifying life, using animals as an example, begins with the earliest known fossil records. Exactly when and which members were the first animals is subject to debate and ever-evolving as scientists make new discoveries. However, evidence supports that the earliest ancestor of the Animalia kingdom is a single-celled organism that was likely similar to modern-day choanoflagellates that lived about 565 million years ago. Ediacaran biota, or early animal life, evolved in the late Proterozoic Era. Sponge fossils have been discovered that date back 890 million years.

Between 545 to 525 million years ago, the Cambrian explosion occurred. This period was a time of extensive diversification and development among animal life-forms, including clams, snails, arthropods, crabs, and trilobites. Tens of millions of years later, echinoderms (starfish and sea urchins) appear in the fossil record and eventually chordates, out of which emerged fish and mammals.

The periods of explosive growth and massive extinction of life-forms are believed to have been caused by some major environmental changes, the exact nature and cause of which have not been determined. Scientists believe an explosion of new life could have been caused by an increase in atmospheric oxygen, which would allow life-forms to live out of water, and a mass extinction could have been the result of gigantic dust clouds, large enough to darken the sun’s light for millions of years, stirred up by huge meteors crashing into the Earth. Such a critical darkening of Earth is believed to have taken place about sixty-five million years ago, plunging temperatures to near freezing and killing off thousands of species, including all the dinosaurs.

The Phylum Chordata

Despite the tremendous losses resulting from the extinction of as much as 95 percent of the existing species, life-forms continued to survive and evolve. The most successful of the new forms emerged from the ancestors of the phylum Chordata (from a Latin word for “cord”). This phylum includes all mammals, birds, amphibians, reptiles, and species with backbones (vertebrates). More than 80,000 species of chordates exist. Three key features are used to classify members of the phylum. A member must have a single nerve cord along its back. In mammals, this cord has developed into the spinal cord and brain. It must also have a notochord, a bony rod located between the nerve cord and the digestive tract, which supports the body and the muscles and is found in the embryo and the adult. The last requirement is that members have gill slits in the throat at some stage of development, whether in the embryo stage, as is true with land animals, or throughout their entire life, as in fish. Gill slits show that land animals developed from sea creatures.

The phylum Chordata includes two superclasses, Agnatha (jawless vertebrates) and Tetrapoda (four-limbed forms). There are two classes of living Agnatha, Chondrichthyes (boneless creatures), which includes sharks, skates, and rays, and Osteichthyes (bony fish), a class that contains about twenty-five thousand species. The earliest fish fossils are about 500 million years old. Among the Tetrapoda classes are Amphibia, Reptilia, Aves, and Mammalia.

The class Amphibia contains about 81,000 species of frogs, toads, and salamanders. Members of this class evolved about 370 million years ago and were the first vertebrates to live on land. Amphibia must lay their eggs in water and must live close to water, or their soft skin will dry out and cause death.

The class Reptilia has more than twelve thousand species. It includes turtles, lizards, snakes, and crocodiles. Reptiles develop from an egg, live on land, and have dry, scaly skin. The largest reptiles, the dinosaurs, died out more than sixty million years ago. Reptiles are cold-blooded,—which means they cannot control the temperature of their blood—they breathe air through lungs, and they are not required to lay their eggs in water. They probably evolved out of an amphibian species between 300 million and 320 million years ago.

The class Aves contains over eleven thousand species of living birds, with thousands more extinct. Aves evolved from dinosaur species perhaps 200 million years ago. Unlike reptiles, Aves class members can regulate their internal temperature and have feathers rather than scales, but they lack teeth.

The fourth class is Mammalia, which has more than fifty-five hundred living species, including human beings. Mammals are classed into Metatheria (marsupials) and Eutheria (placentals). Metatheria, such as kangaroos, have external pouches to carry their young. Eutheria have vaginas through which the fully developed young pass during birth. Most mammals are members of Eutheria. This includes the orders of Insectivora (hedgehogs, shrews, and moles), Primates (lemurs, monkeys, apes, and human beings), Carnivora (dogs, cats, and bears), and Pinnipedea (seals and sea lions.)

The Benefits of Classification

Life on Earth includes millions of different types of organisms. Phylogeny is one method of making sense out of so many different life-forms. It provides a system that links organisms together based on their evolutionary history of development. By grouping vast numbers of forms into related groups, phylogenetics helps bring some order to what seems like chaos. Attempts to classify life-forms have always been controversial, and there still is much disagreement in the scientific community over various types of classification. However, phylogeny is the most widely agreed upon system.

Developments in techniques used to analyze molecules and DNA in the 1980s shed light on the evolutionary development of species and demonstrated new links among living plants and animals. The information gleaned using these techniques can also be used to trace the ancestry of modern species back to the earliest fossil evidence available from 575 million years ago. Molecular comparisons have shown that the development of species from spores and eggs into embryos and adult stages is very similar across a wide range of phyla.

These techniques produce data that consist of long sequences of the four nucleic acids that make up the information contained in DNA. The patterns formed by the acids are very similar among related organisms. The more closely related the sequence of nucleic acids, the more closely the species are related. Closely related species differ only very slightly in the way their DNA is structured. The more species differ in their DNA structure, the more distant they are in evolutionary terms. By measuring and comparing the differences in a gene that controls basically the same function in various species, scientists can construct an evolutionary tree. Species can be placed on the tree at the points where they begin to diverge from other genus members. In this way, examinations of the phylogenetic development of organisms can be used to create a tree of life showing the close relationships among all organisms. The tree also shows that all forms of life are related because they originally came from the same source in some ancient pool where the right chemicals just happened to bump into one another, mix, and begin to produce offspring.

Principal Terms

Deoxyribonucleic Acid (DNA): The genetic material of most living organisms

Evolution: The process by which the variety of plant and animal life has developed over time from the most primitive to the most complex life-forms

Kingdom: The highest category into which organisms are classified; there are believed to be five kingdoms

Molecule: The smallest part of a chemical compound

Phylum: A group that consists of several closely related classes

Species: A group of organisms that can produce offspring with each other

Bibliography

Copeland, Herbert F. The Classification of Lower Organisms. Pacific Books, 1956.

Gould, Stephen Jay. Wonderful Life: The Burgess Shale and the Nature of History. Norton, 2007.

Margulis, Lynn, and Michael J. Chapman. Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth. 4th ed., Elsevier Science, 2009.

Romer, A. S. The Vertebrate Story. U of Chicago P, 1971.

Schram, Frederick R., and Stefan Koenemann. Evolution and Phylogeny of Pancrustacea: A Story of Scientific Method. Oxford UP, 2021.

"Understanding Phylogenies." Berkeley, evolution.berkeley.edu/evolution-101/the-history-of-life-looking-at-the-patterns/understanding-phylogenies. Accessed 10 Sept. 2024.

Wilson, Edward O. The Diversity of Life. Folio Society, 2019.