Phylogeny and Classification

Phylogeny and Classification Student Learning Guide

1. Phylogeny shows evolution’s branching pattern

Imagine the scenario that’s depicted in the series of diagrams to the left.

The scenario starts with one ancestral songbird species. This is species “A,” which lives on continent “w.” In a storm (indicated by “1”), a small population of individuals from species “A” is blown to island “x.”

Island “x” is beyond “A’s” normal flying range. As a result, this new island population is cut off from its parent population. In the subsequent years, a series of events involving migration, genetic drift, and adaptation by natural selection to the differing environments on each island result in repeated instances of speciation. At the end, four new species — B, C, D, and E —  evolve on these islands, while “A” continues to exist on the mainland.

Such a scenario is thought to explain the evolution of the finches on the Galapagos Islands, an island chain located about 1000 kilometers off the Pacific coast of Ecuador, in South America. Six of the Galapagos finch species are shown below, along with its proposed common ancestor.

The diagram above tells a story of adaptive radiation, a process by which an ancestral species diversifies into an array of descendant species. In the case of the Galapagos finches, each descendant species has evolved a different beak phenotype (as well as other differences). Each species is adapted to a specific ecological niche.

Phylogeny is the study of evolutionary history and relationships among individuals or populations. To represent these relationships, biologists construct phylogenetic trees. The one that follows shows the phylogeny of six of the Galapagos species (though not the same ones as those shown directly above).

In this diagram, “A” represents the common ancestor of all of the species shown in on the right side of the diagram. A group that consists of a common ancestor and all of its descendants is called a clade. A clade can be a group of species, a single species, or a population within a species.

To make the subsequent history clearer, I’ve added shading to the diagram (see below). The clade that’s descended from species “A” is numbered as clade “1.”

For any clade that consists of more than one species, the common ancestors are located at nodes. The nodes are labeled “A” through “E.” Because nodes are where speciation events occur, they’re also called branch points.

A speciation event at node “A” created two new clades, “2” and “3.” A second speciation event at node “B” produced two more clades (“4” and “5.”). Another speciation event at “C” produced clades “6” and “7.” Speciations at nodes “D” and “E” produced additional clades, each consisting of a single species.

A phylogenetic tree shows the branching pattern typical of evolution. It also indicates change within a single line of descent, or a lineage. Imagine that you could examine allele and phenotype frequencies in the lineage leading up to the Green Warbler Finch. The population at “p” would be different from that at “q,” which in turn would be different from  “r.”

Whatever is at the tip of the branches of a phylogenetic tree is called a terminal taxon. In the example immediately above, the Green Warbler is a terminal taxon. A taxon is any named group of organisms (or other evolving entities).

One goal of classification is to create taxa (the plural of taxon) that are clades. And with that in mind, let’s continue by looking at how organisms are classified and named. But before that, take the following quiz.

2. Phylogeny Introduction: Checking Understanding

3. Naming and Classifying Species

3a. Binomial nomenclature, or scientific naming

The practice of naming species or varieties and organizing them into categories has probably been going on, at some level, for our entire history as a species. During the mid-1700s, a Swedish botanist, zoologist, and physician named Carl Linnaeus developed the modern system of taxonomy: the “science dealing with the description, identification, naming, and classification of organisms” (Dictionary.com).

Let’s begin with naming. A species is a group of organisms that can successfully interbreed to produce fertile offspring, and which is isolated from other such groups. In the Linnaean system, every species has a two part name. The first part of the name identifies a genus. For example, the genus to which humans belong is Homo. We’re the only species within this genus, which we share with a few other extinct species. The second part of the name is the specific epithet. Ours is “sapiens.” That makes our species name Homo sapiens, which in Latin means “wise man.”

In the Linnaean system,

1. species names are in Latin, and italicized.
2. The genus begins with a capital letter,
3. the specific epithet begins with a lower-case letter.

Here are a few examples of familiar species and genera (plural of genus). Dogs are in the species Canis lupus. That species contains both dogs and wolves. In the same genus is the coyote (Canis latrans), which is considered to be a distinct species from dogs and wolves (though Canis latrans and Canis lupus are so closely related that they can interbreed successfully). Apples are Malus domesticus.  If you have ants in your house, it’s very likely the Argentine ant, Linepithema humile, an invasive species from South America.

Because the names in the Linnaean system have two parts, the system is called binomial nomenclature. You’ll also see these names referred to as binomials, as scientific names, or as Latin names.

The Linnaean system avoids the confusion associated with the common names we have for species. For example, if you live in North America, the robin in front of your house or apartment is Turdus migratorius. But if you’re in Europe, what’s called a robin is Erithacus rubecula.

Common name	Robin	Robin
Region	North America	Europe, North Africa
Scientific name	Turdus migratorius	Erithacus rubecula

 

Similarly, what’s been called an anteater on 3 different continents is not the same species.

Common name	Spiny Anteater	Cape Anteater	Giant Anteater
Region	Australia	Africa	South America
Scientific name	Tachyglossus aculeatus	Orycteropus afer	Myrmecophaga tridactyla

3b. Classification

No one knows how many species there are on our planet. In 2011, a joint study led by researchers at the University of Hawaii estimated that the number could be 8.7 million, with a margin of error of plus or minus 1.3 million. Over 1.25 million species  have been formally named and described.

To organize all of these species, scientists classify them into increasingly general groups above the species level. Related species are grouped into a common genus. Related genera (plural of genus) are grouped into families. Related families are grouped into orders, which are grouped into classes, which are grouped into phyla, which are grouped into kingdoms, which are grouped into domains.

The image on the left shows the classification of the red fox, Vulpes vulpes. Each group is a taxon. Canidae is a taxon at the family level. In addition to foxes, it includes wolves and dogs. The taxon Carnivora is at the order level. In addition to dog-like mammals, carnivora includes bears, cats, weasels, raccoons, and walruses. As you move higher up, the taxa become more general and inclusive. As you move down, they become more specific and exclusive.

If you need to memorize the classification categories, you can use these mnemonics:

1. Daring kings play chess on fine gray satin.
2. Dear King Phillip came over for good soup.

4. Checking Understanding: Phylogenetic Trees, Binomial Nomenclature, and Classification

In addition to classification, this quiz reviews some of  the material on phylogeny above,

5. Phylogenetic trees: A deeper look

5a. Ingroups, Outgroups, and Shared Derived Features

Let’s look at a phylogenetic tree that shows the phylogenetic relationships among seven different vertebrate taxa. Note that you can scroll the text below the phylogenetic tree below so that you can look at the tree and read the text.

MISCONCEPTION ALERT: In a horizontally organized phylogenetic tree, like this one, the vertical arrangement of the terminal taxa says nothing about how closely related these taxa are. For example, a frog is no more closely related to a lizard than it is to a gorilla. That’s because the lineages in a phylogenetic tree can rotate around the nodes. A useful mental trick is to think of them as a mobile sculpture, with the root attached to the ceiling.

In other words, these two phylogenetic trees are equivalent.

But if you can’t identify the closest relationship by who’s next to whom, then how can you tell? You tell by moving back in time and finding the most recent common ancestor. Alligators and robins, for example, have a common ancestor at node “F.” Alligators and lizards have a common ancestor at “E.” Because the ancestor between robins and alligators is more recent than the common ancestor between alligators and lizards, you can conclude that alligators and robins are more closely related than alligators and lizards (something you might not have expected, because alligators and lizards are both classified as reptiles: more on this below).

5b. Connecting Phylogeny and Classification

Any clade (a group derived from a common ancestor) could be a taxon. For example,  there’s a name for the clade shown below.

This group is called the amniotes. In addition to possessing the shared derived trait of claws or nails, these tetrapods (four limbed vertebrates) produce a complex egg with an internal, fluid-filled sac that surrounds and nourishes an embryo (shown at 11 at left). This watery internal environment is called an amnion (12). It’s surrounded by an amniotic sac (10) — the same sac that ruptures when a woman’s “water” breaks shortly before birth. The “water” is actually the amniotic fluid. The amniotic egg is what allowed reptiles, birds, and mammals to live a truly terrestrial life, as opposed to amphibians, whose simpler, fish-like eggs must be laid in water.

While all clades can be taxa, the reverse is not necessarily true. The group we call reptiles, for example, is not a clade.

That’s because it consists of lizards and alligators (along with other reptiles that aren’t shown here, like snakes), but it excludes birds. Is there a taxon that includes all of these animals? Yes, but it’s not commonly known. It’s called sauropsida, and if you’re interested, you can read more about it at this article in Wikipedia.

Take a look at the groups shown in the  phylogenetic trees below. Note that all four trees have the same branching pattern. What’s different are the shaded branches, which indicate different taxa.

The shaded areas in trees 1 and 2 are both clades: they consist of the common ancestor of the clade, and all of its descendants. Such groups are said to be monophyletic.

The shaded group in tree 3 consists of lineages that derive from two separate ancestors. Such a group is said to be polyphyletic. The now-outmoded taxonomic group called protists (single celled eukaryotes) is a polyphyletic group. So are groups like “marine mammals,” or “trees.”

A paraphyletic group is descended from a common ancestor, but doesn’t include all of the descendants. Unless you consider chickens (and all other birds) to be dinosaurs, then the group we consider to be dinosaurs is a paraphyletic grouping (because it excludes the birds, which should be part of this group). Reptiles are another paraphyletic clade.

5c. Phylogenetic trees can be represented in a variety of ways

All of the phylogenetic trees shown in this tutorial so far have been drawn with lines going either horizontally or vertically. Another style of phylogenetic trees is drawn with diagonal lines.

The trees shown below and the taxa within them are exactly equivalent to the ones above. In the quiz that follows, and in textbooks, websites, etc, you’ll see both.

Finally, note that a distinction can be made between a cladogram and a phylogenetic tree.

Strictly speaking, a cladogram shows the branching pattern of evolution only, with no reference to time. A phylogenetic tree, by contrast, is usually scaled, with branch lengths being proportional to the amount of time between the events indicated on the tree. Many sources, however, use the terms interchangeably.

 

 

 

 

5d. Phylogenetic Trees, Checking Understanding

 

6. Using Character Tables to Create Phylogenetic Trees

To create a phylogenetic tree, biologists start from character tables. A character is any quantifiable, heritable trait. Here are some examples of characters:

• The presence or absence of any inherited trait: wings, legs, eyes, etc.
• A nucleotide sequence for a gene that’s shared among several species
• An amino acid sequence for a shared protein, such as cytochrome c or hemoglobin
• The number of segments in an animal’s backbone.

6a. Inferring a phylogeny based on morphology

The best way to understand how phylogenetic trees are built is to build one!

6b. Watch out for confusion related to convergent features

In terms of interpreting and creating phylogenies, not all inherited characters are of equal value. Characters are only useful if they’re homologous (derived from a common ancestor). They’re even more useful if they’re highly conserved. But if they’re analogous traits — ones that come about from convergent evolution — they can put you off track in determining phylogeny.  This is shown in the following example.

Let’s say that you were assigned the task of figuring out a phylogenetic tree for the following four organisms: a rat, a bat, a bird, a frog, and a fish.

6c. Molecular data can also be used to infer phylogenetic relationships

In the examples below, we’ll see how similarities and differences in amino acid and nucleotide sequences can be used to determine phylogenetic relationships.

7. Molecular Clocks

In all phylogenetic trees, there’s an underlying assumption of the passage of time.

For example, in the phylogenetic tree above, you can assume that clade E emerged more recently than clade C, which emerged more recently than clade B. But there’s no explicit scale.

In other phylogenetic trees, the branch lengths are proportional to the passage of time.

These branch points can be dated from fossil evidence. But increasingly they’re dated based on what are called molecular clocks. 

The basic idea behind molecular clocks is that for any specific protein or nucleic acid, the rate of change caused by accumulated mutations is constant over time. If you can calibrate the amount of change in a gene or protein to when two species split apart (a node in the tree), then you can

1. Determine a rate of change in that gene or protein,
2. Use that rate to determine when other species split in the tree split apart.

Here’s an imaginary example. Imagine a specific sequence of DNA that’s 100 nucleotides long, and it’s shared by all of the primates shown above. In Gibbons and Siamangs, that stretch of DNA is identical except for 10 substitutions. Based on fossil evidence, we learn that the split between Gibbons and Siamangs occured 10 million years ago.

That means that the rate of change in that nucleotide sequence is

• 10 mutations/10 million years, or
• one mutation/million years.

If we find that there are six nucleotide differences between in the same stretch of DNA that’s shared by humans and chimps, then a little algebra tells us that humans and chimps would have had a common ancestor about 6 million years ago.

8. Horizontal gene transfer makes the phylogeny of early life a tangled web

The only image in Darwin’s Origin of Species is this phylogenetic tree—one of the first phylogenetic trees  ever published.

If you start from “A” or “I” above you see two events: branching evolution, and extinction.

What Darwin didn’t know about is that throughout the history of life, and particularly during life’s earliest phases, lineages don’t only split apart. They sometimes fuse together, particularly at the genetic level.

The process by which this happens is called horizontal gene transfer. In horizontal gene transfer, genes are transferred from one species to another. This is very different from vertical gene transfer, in which genes are transmitted from parents to offspring.

The most significant instance of horizontal gene transfer in life’s history involved the uptake of a bacterial cell by an archaeal host. The cell that was taken up evolved into  the mitochondrion, and the endosymbiotic merger that resulted gave rise to the eukaryotes. Later, an early eukaryote engulfed a cyanobacteria, and the endosymbiotic merger that resulted led to the algae and plants. In both cases, there’s was widespread transfer of genes from mitochondria or chloroplasts into the genomes of their hosts.

In addition, horizontal gene transfer can involve any of the following mechanisms.

• Plasmids can transfer genes between bacteria— even bacteria of different species. This process is called conjugation.
• Through transformation, bacteria can take up foreign DNA from the environment and incorporate it into their genomes.
• Through transduction, viruses can move DNA from one species to another.

Through these mechanisms, and possibly others, animals, ranging from humans to rotifers, have taken up genes from bacteria. Plants have similarly taken up bacterial genes, as well as genes from other plant species.

The takeaway is that this highest level phylogeny of the three domains in life is almost certainly incomplete.

So when you think about tree of life, it might be more accurate to think of this:

“1” shows the last universal ancestor of all living things. “2” is the lineage leading to bacteria, while 3 leads to Archaea and eukaryotes (“Eukarya”). Eukaryotes only emerge, however, after horizontal mergers that lead to all eukaryotes (“4” indicates the acquisition of mitochondria, creating the entire eukaryotic clade) and to plants (“5 indicates the acquisition of chloroplasts, leading to the plants).

But even that’s probably inadequate. Taking into account other instances of horizontal transfer, a more accurate tree of life might look like this.

The base is a seething mass of ancient cells, freely transferring genes with one another. The transfers that led to all eukaryotes are shown in the lateral line labeled “mitochondria.” A later lateral line labeled “plastids” leads to the plants and algae. Later, horizontal transfers through plasmids, viruses, and other mechanisms continue right up to the present day.

9. Phylogeny and Classification: Cumulative Quiz

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