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Phylogeny: Reconstructing the Diversification of Life

Scientists who study phylogeny (from the Greek phylum meaning "group" and genesis, meaning "origin") use both systematics and taxonomy to organize the vast diversity of life into meaningful units that reflect evolutionary history and relatedness.

A taxon (plural: taxa) is one or more organisms judged by a systematist to form a unit. In modern systematics, a taxon is constructed based on evidence of evolutionary descent from a single, common ancestor.

A character is a trait (morphological, physiological, biochemical, molecular, etc.) used by a systematist to help determine evolutionary relationships between different taxa. The specific value of a particular character is known as its character state.
For example...


A character state may be compared to other character states of the same trait, and be determined to be

In comparing homologous characters across groups of organisms, the systematist also considers both

...in attempting to reconstruct evolutionary histories.

You already are familiar with the concept of analogous characters.

Evolutionary biologists usually use the term homoplasy to describe a character shared by a set of species,
but not present in their common ancestor.

A homoplasy is a character that has originated independently in different lineages, and is not the product of common ancestry. Homoplasies are analogous characters.


Phylogenetic Trees: Visualizing Evolutionary Histories

  • The evolutionary history of a species is its phylogeny.
  • A phylogeny can be represented as a diagram called a phylogenetic tree

    The metaphor of a branching tree is often used to represent origin and diversification from a common source. For example, one could draw such a tree to represent the origin and diversification of different branches of Christianity (redrawn from Kirk and Falk, 2010).

    So, too, can the relationships of living things be represented as a tree.
    Each branch point (node) represents the common ancestor of all taxa above that node on the tree.
    The endpoints of the tree's branches represent the taxonomic units included in that particular phylogeny.


    Characters that appear in a particular ancestral lineage are inherited by the descendants above that ancestor on the tree.
    These characters are synapomorphies, unique to those descendants.
    The blue hashmarks on the tree below represent synapomorphies that separate the taxa above them from all other taxa.


    The Three Domains of Life

    In November 2000, Dr. Carl Woese won the National Medal of Science for his work on classifying living organisms into three major Domains, based on the nucleotide sequence of different types of RNA (e.g., small subunit rRNA).

    The divergence of RNA sequences can be used as an index of how much time has passed since various taxa diverged from a common ancestor.

    Ribosomal RNA is an appropriate molecule to use because

    Woese proposed that all life be classified into three Domains:

    The diagram you see above is a phylogenetic tree, and such trees can be represented any number of ways, graphically, including sideways:

    As an emerging spiral:

    ....and several other ways. But they all say essentially the same thing: This is how the groups on the endpoints of the tree are related by descent from common ancestors, going back through time.

    In an attempt to make sense of the vast biodiversity around us, we use classification systems that reflect common evolutionary ancestry.


    Why Classify?

    Why bother to classify organisms?

    1. As an aid to memory
    It's more efficient to remember the characteristics of an entire group of organisms than to recall the characteristics of individual group members over and over.

    2. As an aid to prediction
    If one knows that all members of a particular taxon have a particular set of characteristics, then there's a good chance that a new member of that taxon may share some of those (useful?) characteristics. (e.g., antibiotic production, edibility, etc.)

    3. As an aid to explaining evolutionary relationships
    I think we've already made that pretty clear.

    4. To provide a stable, relatively unchanging system of internationally recognizable names.
    You can call it kaninchen, taulai, usagi, conejo, sungura, or any other language variant, but unless you use the formal scientific name, Oryctolagus cuniculus in your scientific paper, your scientific colleagues won't know you're writing about a rabbit.

    (Use your Dictionary of Word Roots and Combining Forms by Donald Borror when you encounter a scientific name or term you don't know. Fun and instructive!)


    Taxonomy: Describing, Naming, and Classifying Living Organisms

    In the earliest studies of biodiversity...

    Carl to the Rescue

    Carl Linnaeus was born on May 23, 1707 in Stenbrohult a town in the Swedish province of Småland.

    He became a medical doctor, but his first love was plants, and he ultimately spent most of his adult life pursuing the study of botany.

    His most enduring work is Systema naturae (the full title of which was Systema Naturae: Creationis telluris est gloria Dei ex opere Naturae per Hominem solum), in which he outlines a method for naming and classifying living things according to specific rules.

    The last part of the work's title translates as "The Earth's creation is the glory of God, as seen from the works of Nature by Man alone."

    Like many scientists of his day, Carl Linnaeus was deeply religious, and saw his scientific efforts as a form of worship to a divine creator.

    Systema naturae outlined a new way to classify and name living things that we still use today (sometimes referring to it fondly as the Linnaean System of classification), although--unlike Carl--we don't base our taxonomic groupings primarily on shared similarities. As we'll see shortly, each species has a unique name that is written in Greek or Latin, or at least Latinized (if the term is a name or term from another language).

    In the spirit of his work, Carl Linnaeus started to call himself Carollus Linnaeus, and today we simply recall the Father of Modern Taxonomy as Linnaeus.

    In the Linnaean system, each species is nested into successively more inclusive taxonomic groups above it:

    The most inclusive group (domain) includes the less inclusive groups below it, all the way down to species.

    (Insert clever mnemonic device here)

    Classification is organized as a nested hierarchy.

    And this hierarchy is reflected in the proper designation of taxa on the phylogenetic tree:

    Every species has its own, unique scientific name consisting of its genus and species written in Greek or Latin, or Latinized.

    Example: Strongylocentrotus purpuratus and Strongylocentrotus franciscanus


    Abbreviations of Scientific Names in Publications

  • In a publication, a species name is written out completely the first time it appears in the paper (Canis latrans), but after its first appearance, the genus is designated by only its capital letter, with the specific epithet spelled out (C. latrans).

  • If more members of the same genus appear in that paper, then the genus is not written again a second time. The abbreviation is understood ("The investigators applied census techniques to two native species, Canis latrans and C. lupus.")

  • If multiple species in a given genus are being considered, but it is not important to name each species individually, this concept can be conveyed by using "spp." to represent "multiple, unnamed species of Genus X" (Canis spp.).


    What's in a Name?
    Would a Frog by any other name be as sticky?
    Scientific names have a specific meaning, often physically describing the species. For example, Eleutherodactylus planirostris, the Greenhouse Frog:

    (So what do you suppose this frog looks like?)

    Many species are at least partially named after people, but these proper names, too, must be Latinized:

    And sometimes they're just weird, such as Upupa epops

    Here are some entertaining scientific names.


    Taxonomy: What is a Taxon?

    As we're already aware, taxon is a generic term used to describe a group of organisms that has been classified together at any given taxonomic level (phylum, order, family, etc.), but without specifying that level.

    The Three Aspects of a Taxon
    1. The taxon's name

    2. The taxon's rank

    3. The taxon's content

    Classification and Levels of Taxonomy

    The systematist must use all tools available to determine recency of common descent, and must often choose the best tool for the job at hand.


    Now that Linnaeus is Gone, Who Keeps Track of All This?
    As you might imagine, there must be rules for describing and naming organisms to prevent descent into chaos. Nomenclature is defined as a system of names used in a particular discipline (biology, chemistry, medicine, pharmacology, etc.). A standard system of nomenclature presupposes the existence of an organized classification of the entities within that field. And so we do have systems of nomenclature in Biology...

  • In 1901 the International Commission on Zoological Nomenclature (ICZN) was formed.
  • In 1930, the botanists branched (ha!) off on their own with the International Commission on Botanical Nomenclature (ICBN).
  • In 1947, the first International Code of Nomenclature of Bacteria was published.
  • There's even a Nomenclature Code for Viruses (they may not be alive, but they do need names).


    A Few Basic Rules of Biological Nomenclature


    Practical Application of Taxonomy
    Why should we care about correctly identifying species? Here's an excellent overview of the importance of phylogenetic systematics from the University of California at Berkeley Museum of Paleontology. Understanding classification at the alpha, beta and gamma levels can save you and the ecosystems around you.

    A Parasite's Tale

    The Evil Weevil

    Whale Meat: Illegal, or not?
    Tracking Bioterrorism

    Systematics: Reconstructing Evolutionary Relationships

    A taxon has dimensions in space (its geographical range) and time (its evolutionary history). The systematist is interested in both these aspects in reconstructing how different extant taxa are related to one another by common ancestry. Consider the apes (Family Pongidae):

    It has been well established with other data that the Great Apes (indicated in red on the tree) are more closely related to each other than they are to the Lesser Apes. The next closest relatives to the apes are the Old World Monkeys, and then the New World Monkeys.

    This particular phylogenetic tree (from Human Molecular Genetics - Evans, et al., 2004) is based upon amino acid sequences in a protein known as ASPM (Abnormal spindle-like microcephaly associated), believed to be involved in the formation of the central nervous system (brain and spinal cord) in vertebrates.

    But how do the investigators determine what the original, primitive condition of the ASPM protein (and its gene) was? Notice the taxa on the tree that are NOT apes. These are known as outgroups.

    Outgroup Analysis
    The method that provides the most parsimonious explanation for which characters are primitive and derived is known as outgroup analysis.

    The outgroup is a taxon related to the assemblage of interest (the ingroup), but not included within it. This means that all taxa of the ingroup should share about the same level of evolutionary relationship with the outgroup.

    Characters that are found in both the ingroup and the outgroup are most likely to be primitive, as it would require additional events for such characters to have arisen independently in each ingroup lineage. Characters unique to the ingroup (or a subset of the ingroup) are thus considered to be derived with respect to the outgroup.

    In the ASPM phylogeny, the outgroup shown is the Owl Monkey, classified within Order Primates, but in Family Cebidae--not Hylobatidae (Gibbons) or Pongidae (Great Apes). The authors also sequenced ASPM for other mammals, but did not include them in this phylogenetic tree. These, too, can establish the primitive character state, and can be considered outgroups.

    The phylogenetic tree of Family Canidae we saw earlier also shows an outgroup.

    The more synapomorphies common to subsets of the ingroup, the more recent their common ancestry. For example, if the phylogenetic tree of the Great Apes above is correct, you can surmise that humans and chimpanzees exhibit more synapomorphies (shared, derived characters) than do humans and gorillas. Similarly, gorillas, chimpanzees, and humans exhibit more synapomorphies (as a group) than do Gibbons and humans.


    Constructing Phylogenies That Reflect Common Ancestry In modern systematics, the goal is to reconstruct accurate phylogenies that indicate recency of descent from a common ancestor. This means that all members of any valid taxonomic group should share a common ancestor.

    In some cases, phylogenies do not accurately reflect evolutionary relationships.

    Viewed another way:

    The main difference between polyphyletic and paraphyletic taxa is whether the ancestors are included in the taxonomic groups being considered. By correcting a poly- or paraphyletic taxon's rank at the ancestral level, one can create a monophyletic group out of either type.

    In some cases, true evolutionary relationships cannot be determined with available data. Members of such a group may be placed (hopefully temporarily) into a form taxon or morphotaxon--formed on the basis of shared similarities in morphology--until more informative data become available. Many fossils will forever dwell in morphotaxa.


    A Brief History of Systematics

    Historically, there have been three major schools of thought used to classify living organisms

  • Classical Evolutionary
  • Phenetic
  • Cladistic

    Classical Evolutionary System


    The Phenetic System


    The Cladistic System
    Devised by German biologist Willi Hennig and published in 1950, this system is used almost exclusively by modern systematists. It is also known as phylogenetic systematics.

    A phylogenetic tree constructed with cladistic methods is called a cladogram.

    Four Tenets of Cladism:


    In the Cladistic System:


    A recent cladogram of terrestrial vertebrate relationships can be seen here, at the Tree of Life.
    A favorite tree shows the relationships of the vertebrates known as Amniota.
    (Hey, look! There's us!)

    This Introduction to Cladistics will tell you pretty much all you need to know about cladistics.