The Lone Ranger
07-30-2008, 09:43 AM
An Introduction to Zoology
Chapter One: Classification, Taxonomy, Phylogenies, and the Diversity of Life
Introduction:
I thought it might be fun to start a series of articles on the subject of Zoology. In it, we’ll look at the diversity of animal life on the planet. Hopefully, it’ll prove to be an interesting subject.
We’ll start out with some general concepts, such as what phylogenies (http://www.freethought-forum.com/forum/showthread.php?t=17135&garpg=3#content_start) are and how organisms are classified (http://www.freethought-forum.com/forum/showthread.php?t=17135&garpg=3#content_start). Once that’s done, we’ll discuss what, exactly, makes an organism an “animal.” We’ll also discuss the terminology used in the field of zoology. Finally, once all of the relevant introductory material has been dealt with, we’ll get into the meat and bones of the articles – the various animal groups, their characteristics, and what makes each of them interesting and unique.
What is Zoology?:
Biology is the study of life. The word comes from the Greek roots “bios,” meaning “life,” and “logos,” meaning “study.” The subset of biology that deals specifically with the study of animals is zoology (from the Greek “zoon,” meaning “animal.”)
So, to properly understand what zoology is, we must first understand what an “animal” is. That brings us to the disciplines of systematics and taxonomy.
Classification, Systematics, Taxonomy, and Phylogenies:
Biologists classify organisms into groups called taxa (singular = taxon), based upon characteristics shared by those organisms. Classification of organisms involves two closely-linked disciplines, systematics and taxonomy.
Systematics, broadly speaking, is the study of the diversity of life on Earth. As you can imagine, this is a very broad field indeed. Taxonomy is a subset of systematics that involves the practice of classifying organisms into groups (taxa) based upon shared characteristics, and also the principles by which these classification schemes are justified.
[b]Phylogeny:
Well before Darwin’s time, it was understood that organisms share characteristics, and that organisms can therefore be placed into groups according to those shared characteristics. For example, one might classify organisms that share the characteristics of being multicellular and of using the molecule chlorophyll to trap solar energy into a single group and call that group of organisms “plants.” One might classify multicellular organisms that lack chlorophyll but have specialized organs called “nerves” and “muscles” into a separate group and call them “animals.” And so forth.
What the principle of biological evolution does is provide an explanation for why organisms share characteristics and can be classified into taxa. After all, if two different species are both descended from a common ancestor, it’s only natural that they’ll share some characteristics in common, since they will have inherited those characteristics from the same ancestor.
The phylogeny of an species or of a group of related species is its evolutionary history. Ideally, then, when constructing a classification scheme, a taxonomist uses characteristics that species share because they inherited them from common ancestors. Any proper classification scheme should do more than simply group species together according to how similar they happen to look; it should help illuminate how the different species are related to each other.
[b]Binomial Nomenclature:
The common names for species vary widely from region to region, and are often quite imprecise. For example, consider four different kinds of “fishes” – a jellyfish, a crayfish, a starfish, and a silverfish. A jellyfish is a cnidarian. A crayfish is a crustacean. A starfish is an echinoderm. A silverfish is an insect. None of these organisms is actually a fish.
To avoid confusion and ambiguity, biologists therefore use a system called “binomial nomenclature” in order to formally identify each species. Under this system, every recognized species has a two-part (i.e. “binomial”) name, usually in Latin. The advantage of this system is that it is the same worldwide, which neatly eliminates confusion and ambiguity.
The first part of a species’ “scientific name” is the name of the genus to which it belongs. For example, we humans belong to the genus Homo (which is from the Latin for “man”). You’ll notice that the genus name is always capitalized and it is always italicized (or underlined). The second part of a species’ name is called the “specific epithet.” Often, though by no means always, the specific epithet provides some sort of description of the organism. The specific epithet for our species is sapiens (from the Latin for “wise”).
Put the two parts together and you have a species’ proper name. In our species’ case, for instance, it’s Homo sapiens. This translates, roughly, as “man the wise.” One can debate the appropriateness of this name, of course.
[b]What is a Species?:
You’d probably be surprised by how difficult a question that is. There are actually several different definitions of the word “species,” but for each of them, there are some organisms to which it applies poorly or not at all. That shouldn’t be surprising, given the reality of biological evolution. Evolution is not a nice, neat process that instantly splits organisms into separate, easily-identifiable groups. Rather, evolution is usually a gradual process. As such, there are inevitably going to be organisms that are intermediate between two different species and that cannot be unambiguously classified into one species or the other.
Still, in most cases, we can say whether or not two different organisms belong to the same species with a fair degree of confidence. According to the biological species concept, a “species” is a group of organisms that can and does interbreed freely, and that produces fertile offspring in the process – and that does so in nature.
For instance, despite our superficial outward differences, all extant humans comprise a single species, Homo sapiens. Because humans of all ethnic groups are perfectly capable of interbreeding to produce fertile offspring, and are prone to doing so, we’re all members of the same species by definition.
For contrast, consider the two closely-related species Canis lupus (Grey Wolf) and Canis latrans (Coyote). Wolves and coyotes can interbreed, and they produce fertile offspring when they do so. But even when they’re found in the same region, they rarely interbreed. Since they don’t normally interbreed, coyotes and wolves are considered separate species.
[b]Hierarchical Classification:
Different species can be grouped into more inclusive taxa, based upon characteristics they share as a result of common ancestry. This means that there is a hierarchy of classification, from the least-inclusive taxon (the species) up to the most-inclusive taxon (the domain).
A group of related species makes up a genus. A group of related genera makes up a family. A group of related families makes up an order. A group of related orders makes up a class. A group of related classes makes up a phylum (or division*). A group of related phyla makes up a kingdom. Sometimes it’s useful to include an even higher level of classification, the domain.
There are times when it’s useful to subdivide taxa even further. For example, a taxon that’s more inclusive than the class but less inclusive than the phylum is the “superclass.” A taxon that’s less inclusive than the class but more inclusive than the order is the “infraclass.” And so forth.
Still, for the most part, the traditional seven taxa are sufficient: Kingdom, Phylum (or Division), Class, Order, Family, Genus, and Species. There are all sorts of mnemonics out there that can help you to remember the proper order. One I frequently teach my students is: “King Phillip Chooses Oranges For Green Salads.” The students in one of my classes decided that “King Phillip Came Over For Good Sex” was more easily-remembered, though.
http://www.freethought-forum.com/forum/gallery/files/5/0/taxonomy_examples_original.jpg
Classification of three representative eukaryotic species.
http://www.freethought-forum.com/forum/gallery/files/5/0/rhododendron-catawbiense_original.jpg
Rhododendron catawbiense, a member of the Kingdom Plantae.
http://www.freethought-forum.com/forum/gallery/files/5/0/snape.jpg
Homo sapiens, a member of the Kingdom Animalia.
http://www.freethought-forum.com/forum/gallery/files/5/0/morchella.jpg
Morchella esculenta, a member of the Kingdom Fungi.
*The terms “Phylum” and “Division” mean exactly the same thing, for practical purposes. The difference is that Botanists (those who study plants) and Mycologists (those who study fungi) have traditionally used the term “Division,” whereas Zoologists have traditionally used the term “Phylum.” Old habits die hard, I suppose, and this is still the way things are done.
Up until fairly recently, it was thought that plants and fungi were closely-related, so the fields of botany and mycology have generally been fairly closely linked. This is one reason why botanists and mycologists tend to use the same terminologies. Recently, molecular analyses have shown quite conclusively that fungi are, in fact, much more closely related to animals than they are to plants. The old habits persist, nonetheless.
[b]Monophyletic, Paraphyletic, and Polyphyletic Taxa:
As I mentioned earlier, a classification scheme ideally shows how species are related to each other – that is, it reflects phylogenies. Sometimes, though, people insist on using classification schemes that don’t properly reflect species’ phylogenies (http://www.freethought-forum.com/forum/showthread.php?t=17135&garpg=3#content_start).
http://www.freethought-forum.com/forum/gallery/files/5/0/clade_original.jpg
Various taxa within the subphylum Vertebrata.
To help illustrate why this is sometimes done, consider the diagram I’ve posted just above. It shows the relationships between the various groups of animals in the subphylum Vertebrata. The vertebrates have in common a number of features, including an internal skeleton made of cartilage and/or bone that largely surrounds the central nervous system (the brain and the spinal cord).
As you can see from the diagram, the vertebrates can be subdivided into two major groups, the fishes and the tetrapods. The tetrapods have legs; fishes do not. The red dot on the phylogenetic tree that is marked with a “1” indicates the evolution of legs and, therefore, the evolutionary split between fishes and tetrapods.
The tetrapods can be subdivided into the amphibians and the amniotes. Amniotes produce amniotic eggs that are surrounded by three layers of tissues (the chorion, the allantois, and the amnion); amphibians do not. The red dot on the phylogenetic tree that is marked with a “2” indicates the evolution of the amniotic egg and, therefore, the evolutionary split between the amphibians and the amniotes.
The amniotes can be subdivided into the mammals and the “reptiles.” (Why I put “reptiles” in quotes should be clear soon.) In mammals, the lower jaw (mandible) is made of a single bone (the dentary); in “reptiles,” the mandible is made of more than one bone. The red dot marked with a “3” indicates the evolutionary split between the mammals and the “reptiles.”
The “reptiles” can be subdivided into the testudines and the diapsids. In testudines, the skull has no openings in the temporal region; in diapsids, there are two openings in the temporal region of the skull. The red dot marked with a “4” represents the evolutionary split between the testudines and the diapsids.
The diapsids can be subdivided into the lepidosauria and the archosauria. The archosauria have distinctive openings in the skull called antorbital fenestrae, just in front of the eyes. Lepidosaurs lack antorbital fenestrae. The red dot marked with a “5” represents the evolution of antorbital fenestrae and, therefore, the evolutionary split between the lepidosaurs and the archosaurs.
The surviving archosaurs can be subdivided into the crocodylia and the aves. The aves have a distinctive body covering called feathers, and most can fly; the crocodylia lack feathers. The red dot marked with a “6” represents the evolution of feathers and, therefore, the evolutionary split between birds and crocodilians.
Now, this is a correct phylogeny, so far as we’ve been able to determine. That is, by the data available, the chart correctly shows the evolutionary relationships between various members of the subphylum Vertebrata. But notice that it shows the birds and crocodiles to be closely-related animals. So what?
In a phylogeny, a [b]clade is a group that includes the common ancestor of that group and all of its descendents. All the members of a clade share a set of unique characteristics because they all inherited them from their common ancestor. A clade is referred to as a monophyletic group, meaning that all the members of the clade are descended from a single common ancestor, and that the taxon contains all the descendants of that common ancestor.
If you look at the chart above, you can easily see that the archosaurs are a monophyletic group and, therefore, comprise a clade. Similarly, the diapsids are a monophyletic group. But what about the reptiles?
http://www.freethought-forum.com/forum/gallery/files/5/0/monophyly_original.jpg
The “Reptiles” as a monophyletic taxon.
In this chart, I’ve shown the “reptiles” as a true clade – that is, I’ve shown them as a monophyletic group. But the only way that you can do this is by classifying birds as “reptiles.” Some people find this unsettling and don’t like to think of birds as “mere” reptiles.
The problem is, if you exclude the birds, then “reptiles” is not a clade. So any taxonomy that insists on classifying birds as “not-reptiles” does not accurately depict the evolutionary relationships between the birds and the other amniotes
[BREAK=Paraphyletic Taxa]
http://www.freethought-forum.com/forum/gallery/files/5/0/paraphyly_original.jpg
The “Reptiles” as a paraphyletic taxon.
A paraphyletic group is one that includes some, but not all of the descendants of its most recent common ancestor. A paraphyletic group, by definition, is not a clade and is instead referred to as a [b]grade. For example, if I don’t like thinking of birds as reptiles, I might define the “reptiles” as including all of the descendants of the original reptile ancestor except for the birds. That’s how I’ve defined “reptiles” in the chart above.
This is how most people define “reptiles” – not as a clade, but as a grade. But any classification scheme in which birds (or, for that matter, mammals) are not classified as “reptiles” is not correctly showing the evolutionary relationships between vertebrate animals. So, whether you think it sounds “proper” or not, birds are reptiles, strictly speaking.
http://www.freethought-forum.com/forum/gallery/files/5/0/polyphyletic_original.jpg
The “Endotherms,” a polyphyletic taxon. Awkward, isn’t it?
There’s yet another way to construct a taxon. Suppose I want to put both birds and mammals together into a group, because they both share the characteristic of being endotherms – that is, they generate significant amounts of body heat and can maintain a more or less constant body temperature. The problem is that endothermy evolved independently in birds and mammals; there was no common ancestor of both birds and mammals from which they inherited endothermy. So if I insist on inventing a taxon called “endotherms” and putting birds and mammals together into it, my classification scheme again fails to show the true evolutionary relationships between vertebrates.
A taxon that includes organisms which share similar characteristics not because they inherited them from a common ancestor, but because of convergent evolution is known as a polyphyletic group, since the members of this taxon are descended from more than one ancestor.
By now, it should be clear that, when classifying organisms, biologists strongly prefer to use groups that are monophyletic. If you use only monophyletic groups when constructing you classification scheme, then each taxon is a clade, and the classification scheme will accurately reflect species’ phylogenies. (To the best of our ability to determine them, of course.) Even so, there are times when people will insist on using paraphyletic or even polyphyletic taxa.
If you have come to suspect that, as a zoologist, I don’t like the term “reptiles,” you would be correct. To me, a bird is a reptile, but most people look at you strangely when you insist that “technically, a bird is a reptile.”
[b]The Diversity of Life:
http://www.freethought-forum.com/forum/gallery/files/5/0/tree_of_life_original.jpg
As the “Tree of Life” diagram illustrates, all known living things can be classified into three domains. These domains are the Archaea, the Bacteria, and the Eukaryota. The archaea and the bacteria, though only distantly related, share the common characteristic that they’re prokayrotes.
All living things are made of cells, and almost all prokaryotes are unicellular. That is, they are single-celled organisms. The cells of prokaryotes are relatively small and simple; they lack nuclei or other distinctive organelles.
By contrast, the cells of eukaryotes are much larger and more complex than are those of prokaryotes. Eukaryotic cells have specialized subunits called organelles, which perform various tasks within the cells. The largest organelle within a eukaryotic cell is typically the one where the cell’s main genetic material (DNA) is stored – the nucleus.
[b]Eukaryotes:
The eukaryotes are often subdivided into four kingdoms – the Protista, the Plantae, the Fungi, and the Animalia.
The members of the Kingdom Plantae have in common that their cells are surrounded by more or less rigid cell walls made of a substance called cellulose. All plants are multicellular, by definition, and the great majority use the molecule chlorophyll to capture solar energy. The plant uses the captured solar energy to manufacture food in the process known as photosynthesis.
The members of the Kingdom Fungi also have cell walls, but their cell walls are made largely of a substance known as chitin, rather than cellulose. Most fungi are multicellular, but unlike plants, they cannot manufacture their own food. Instead, fungi feed by secreting digestive enzymes and then absorbing their food.
The members of the Kingdom Animalia lack cell walls. Like plants, animals are multicellular by definition, and like fungi, they are incapable of manufacturing their own food. Animals typically feed by ingesting their food and digesting it inside their bodies. Most animals have two specialized types of body cells that are found in no other organisms – neurons (which can form nerves) and muscle cells that are specialized for movement.
Finally, there is the Kingdom Protista. It is not really a “proper” kingdom, because we generally classify any eukaryotic organism that is not clearly an animal, plant or fungus as a “protist.” In other words, if we know it’s a eukaryote but don’t know what else the hell to call it, we call it a “protist.” Protists are often divided into the “animal-like protists,” the protozoans, the “plant-like protists,” the algae, and the “fungus-like protists,” including the slime molds.
In the next chapter, we will consider in more detail the defining characteristics of the Kingdom Animalia. We’ll also discuss some of the terminology used in the field of zoology.
Chapter One: Classification, Taxonomy, Phylogenies, and the Diversity of Life
Introduction:
I thought it might be fun to start a series of articles on the subject of Zoology. In it, we’ll look at the diversity of animal life on the planet. Hopefully, it’ll prove to be an interesting subject.
We’ll start out with some general concepts, such as what phylogenies (http://www.freethought-forum.com/forum/showthread.php?t=17135&garpg=3#content_start) are and how organisms are classified (http://www.freethought-forum.com/forum/showthread.php?t=17135&garpg=3#content_start). Once that’s done, we’ll discuss what, exactly, makes an organism an “animal.” We’ll also discuss the terminology used in the field of zoology. Finally, once all of the relevant introductory material has been dealt with, we’ll get into the meat and bones of the articles – the various animal groups, their characteristics, and what makes each of them interesting and unique.
What is Zoology?:
Biology is the study of life. The word comes from the Greek roots “bios,” meaning “life,” and “logos,” meaning “study.” The subset of biology that deals specifically with the study of animals is zoology (from the Greek “zoon,” meaning “animal.”)
So, to properly understand what zoology is, we must first understand what an “animal” is. That brings us to the disciplines of systematics and taxonomy.
Classification, Systematics, Taxonomy, and Phylogenies:
Biologists classify organisms into groups called taxa (singular = taxon), based upon characteristics shared by those organisms. Classification of organisms involves two closely-linked disciplines, systematics and taxonomy.
Systematics, broadly speaking, is the study of the diversity of life on Earth. As you can imagine, this is a very broad field indeed. Taxonomy is a subset of systematics that involves the practice of classifying organisms into groups (taxa) based upon shared characteristics, and also the principles by which these classification schemes are justified.
[b]Phylogeny:
Well before Darwin’s time, it was understood that organisms share characteristics, and that organisms can therefore be placed into groups according to those shared characteristics. For example, one might classify organisms that share the characteristics of being multicellular and of using the molecule chlorophyll to trap solar energy into a single group and call that group of organisms “plants.” One might classify multicellular organisms that lack chlorophyll but have specialized organs called “nerves” and “muscles” into a separate group and call them “animals.” And so forth.
What the principle of biological evolution does is provide an explanation for why organisms share characteristics and can be classified into taxa. After all, if two different species are both descended from a common ancestor, it’s only natural that they’ll share some characteristics in common, since they will have inherited those characteristics from the same ancestor.
The phylogeny of an species or of a group of related species is its evolutionary history. Ideally, then, when constructing a classification scheme, a taxonomist uses characteristics that species share because they inherited them from common ancestors. Any proper classification scheme should do more than simply group species together according to how similar they happen to look; it should help illuminate how the different species are related to each other.
[b]Binomial Nomenclature:
The common names for species vary widely from region to region, and are often quite imprecise. For example, consider four different kinds of “fishes” – a jellyfish, a crayfish, a starfish, and a silverfish. A jellyfish is a cnidarian. A crayfish is a crustacean. A starfish is an echinoderm. A silverfish is an insect. None of these organisms is actually a fish.
To avoid confusion and ambiguity, biologists therefore use a system called “binomial nomenclature” in order to formally identify each species. Under this system, every recognized species has a two-part (i.e. “binomial”) name, usually in Latin. The advantage of this system is that it is the same worldwide, which neatly eliminates confusion and ambiguity.
The first part of a species’ “scientific name” is the name of the genus to which it belongs. For example, we humans belong to the genus Homo (which is from the Latin for “man”). You’ll notice that the genus name is always capitalized and it is always italicized (or underlined). The second part of a species’ name is called the “specific epithet.” Often, though by no means always, the specific epithet provides some sort of description of the organism. The specific epithet for our species is sapiens (from the Latin for “wise”).
Put the two parts together and you have a species’ proper name. In our species’ case, for instance, it’s Homo sapiens. This translates, roughly, as “man the wise.” One can debate the appropriateness of this name, of course.
[b]What is a Species?:
You’d probably be surprised by how difficult a question that is. There are actually several different definitions of the word “species,” but for each of them, there are some organisms to which it applies poorly or not at all. That shouldn’t be surprising, given the reality of biological evolution. Evolution is not a nice, neat process that instantly splits organisms into separate, easily-identifiable groups. Rather, evolution is usually a gradual process. As such, there are inevitably going to be organisms that are intermediate between two different species and that cannot be unambiguously classified into one species or the other.
Still, in most cases, we can say whether or not two different organisms belong to the same species with a fair degree of confidence. According to the biological species concept, a “species” is a group of organisms that can and does interbreed freely, and that produces fertile offspring in the process – and that does so in nature.
For instance, despite our superficial outward differences, all extant humans comprise a single species, Homo sapiens. Because humans of all ethnic groups are perfectly capable of interbreeding to produce fertile offspring, and are prone to doing so, we’re all members of the same species by definition.
For contrast, consider the two closely-related species Canis lupus (Grey Wolf) and Canis latrans (Coyote). Wolves and coyotes can interbreed, and they produce fertile offspring when they do so. But even when they’re found in the same region, they rarely interbreed. Since they don’t normally interbreed, coyotes and wolves are considered separate species.
[b]Hierarchical Classification:
Different species can be grouped into more inclusive taxa, based upon characteristics they share as a result of common ancestry. This means that there is a hierarchy of classification, from the least-inclusive taxon (the species) up to the most-inclusive taxon (the domain).
A group of related species makes up a genus. A group of related genera makes up a family. A group of related families makes up an order. A group of related orders makes up a class. A group of related classes makes up a phylum (or division*). A group of related phyla makes up a kingdom. Sometimes it’s useful to include an even higher level of classification, the domain.
There are times when it’s useful to subdivide taxa even further. For example, a taxon that’s more inclusive than the class but less inclusive than the phylum is the “superclass.” A taxon that’s less inclusive than the class but more inclusive than the order is the “infraclass.” And so forth.
Still, for the most part, the traditional seven taxa are sufficient: Kingdom, Phylum (or Division), Class, Order, Family, Genus, and Species. There are all sorts of mnemonics out there that can help you to remember the proper order. One I frequently teach my students is: “King Phillip Chooses Oranges For Green Salads.” The students in one of my classes decided that “King Phillip Came Over For Good Sex” was more easily-remembered, though.
http://www.freethought-forum.com/forum/gallery/files/5/0/taxonomy_examples_original.jpg
Classification of three representative eukaryotic species.
http://www.freethought-forum.com/forum/gallery/files/5/0/rhododendron-catawbiense_original.jpg
Rhododendron catawbiense, a member of the Kingdom Plantae.
http://www.freethought-forum.com/forum/gallery/files/5/0/snape.jpg
Homo sapiens, a member of the Kingdom Animalia.
http://www.freethought-forum.com/forum/gallery/files/5/0/morchella.jpg
Morchella esculenta, a member of the Kingdom Fungi.
*The terms “Phylum” and “Division” mean exactly the same thing, for practical purposes. The difference is that Botanists (those who study plants) and Mycologists (those who study fungi) have traditionally used the term “Division,” whereas Zoologists have traditionally used the term “Phylum.” Old habits die hard, I suppose, and this is still the way things are done.
Up until fairly recently, it was thought that plants and fungi were closely-related, so the fields of botany and mycology have generally been fairly closely linked. This is one reason why botanists and mycologists tend to use the same terminologies. Recently, molecular analyses have shown quite conclusively that fungi are, in fact, much more closely related to animals than they are to plants. The old habits persist, nonetheless.
[b]Monophyletic, Paraphyletic, and Polyphyletic Taxa:
As I mentioned earlier, a classification scheme ideally shows how species are related to each other – that is, it reflects phylogenies. Sometimes, though, people insist on using classification schemes that don’t properly reflect species’ phylogenies (http://www.freethought-forum.com/forum/showthread.php?t=17135&garpg=3#content_start).
http://www.freethought-forum.com/forum/gallery/files/5/0/clade_original.jpg
Various taxa within the subphylum Vertebrata.
To help illustrate why this is sometimes done, consider the diagram I’ve posted just above. It shows the relationships between the various groups of animals in the subphylum Vertebrata. The vertebrates have in common a number of features, including an internal skeleton made of cartilage and/or bone that largely surrounds the central nervous system (the brain and the spinal cord).
As you can see from the diagram, the vertebrates can be subdivided into two major groups, the fishes and the tetrapods. The tetrapods have legs; fishes do not. The red dot on the phylogenetic tree that is marked with a “1” indicates the evolution of legs and, therefore, the evolutionary split between fishes and tetrapods.
The tetrapods can be subdivided into the amphibians and the amniotes. Amniotes produce amniotic eggs that are surrounded by three layers of tissues (the chorion, the allantois, and the amnion); amphibians do not. The red dot on the phylogenetic tree that is marked with a “2” indicates the evolution of the amniotic egg and, therefore, the evolutionary split between the amphibians and the amniotes.
The amniotes can be subdivided into the mammals and the “reptiles.” (Why I put “reptiles” in quotes should be clear soon.) In mammals, the lower jaw (mandible) is made of a single bone (the dentary); in “reptiles,” the mandible is made of more than one bone. The red dot marked with a “3” indicates the evolutionary split between the mammals and the “reptiles.”
The “reptiles” can be subdivided into the testudines and the diapsids. In testudines, the skull has no openings in the temporal region; in diapsids, there are two openings in the temporal region of the skull. The red dot marked with a “4” represents the evolutionary split between the testudines and the diapsids.
The diapsids can be subdivided into the lepidosauria and the archosauria. The archosauria have distinctive openings in the skull called antorbital fenestrae, just in front of the eyes. Lepidosaurs lack antorbital fenestrae. The red dot marked with a “5” represents the evolution of antorbital fenestrae and, therefore, the evolutionary split between the lepidosaurs and the archosaurs.
The surviving archosaurs can be subdivided into the crocodylia and the aves. The aves have a distinctive body covering called feathers, and most can fly; the crocodylia lack feathers. The red dot marked with a “6” represents the evolution of feathers and, therefore, the evolutionary split between birds and crocodilians.
Now, this is a correct phylogeny, so far as we’ve been able to determine. That is, by the data available, the chart correctly shows the evolutionary relationships between various members of the subphylum Vertebrata. But notice that it shows the birds and crocodiles to be closely-related animals. So what?
In a phylogeny, a [b]clade is a group that includes the common ancestor of that group and all of its descendents. All the members of a clade share a set of unique characteristics because they all inherited them from their common ancestor. A clade is referred to as a monophyletic group, meaning that all the members of the clade are descended from a single common ancestor, and that the taxon contains all the descendants of that common ancestor.
If you look at the chart above, you can easily see that the archosaurs are a monophyletic group and, therefore, comprise a clade. Similarly, the diapsids are a monophyletic group. But what about the reptiles?
http://www.freethought-forum.com/forum/gallery/files/5/0/monophyly_original.jpg
The “Reptiles” as a monophyletic taxon.
In this chart, I’ve shown the “reptiles” as a true clade – that is, I’ve shown them as a monophyletic group. But the only way that you can do this is by classifying birds as “reptiles.” Some people find this unsettling and don’t like to think of birds as “mere” reptiles.
The problem is, if you exclude the birds, then “reptiles” is not a clade. So any taxonomy that insists on classifying birds as “not-reptiles” does not accurately depict the evolutionary relationships between the birds and the other amniotes
[BREAK=Paraphyletic Taxa]
http://www.freethought-forum.com/forum/gallery/files/5/0/paraphyly_original.jpg
The “Reptiles” as a paraphyletic taxon.
A paraphyletic group is one that includes some, but not all of the descendants of its most recent common ancestor. A paraphyletic group, by definition, is not a clade and is instead referred to as a [b]grade. For example, if I don’t like thinking of birds as reptiles, I might define the “reptiles” as including all of the descendants of the original reptile ancestor except for the birds. That’s how I’ve defined “reptiles” in the chart above.
This is how most people define “reptiles” – not as a clade, but as a grade. But any classification scheme in which birds (or, for that matter, mammals) are not classified as “reptiles” is not correctly showing the evolutionary relationships between vertebrate animals. So, whether you think it sounds “proper” or not, birds are reptiles, strictly speaking.
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The “Endotherms,” a polyphyletic taxon. Awkward, isn’t it?
There’s yet another way to construct a taxon. Suppose I want to put both birds and mammals together into a group, because they both share the characteristic of being endotherms – that is, they generate significant amounts of body heat and can maintain a more or less constant body temperature. The problem is that endothermy evolved independently in birds and mammals; there was no common ancestor of both birds and mammals from which they inherited endothermy. So if I insist on inventing a taxon called “endotherms” and putting birds and mammals together into it, my classification scheme again fails to show the true evolutionary relationships between vertebrates.
A taxon that includes organisms which share similar characteristics not because they inherited them from a common ancestor, but because of convergent evolution is known as a polyphyletic group, since the members of this taxon are descended from more than one ancestor.
By now, it should be clear that, when classifying organisms, biologists strongly prefer to use groups that are monophyletic. If you use only monophyletic groups when constructing you classification scheme, then each taxon is a clade, and the classification scheme will accurately reflect species’ phylogenies. (To the best of our ability to determine them, of course.) Even so, there are times when people will insist on using paraphyletic or even polyphyletic taxa.
If you have come to suspect that, as a zoologist, I don’t like the term “reptiles,” you would be correct. To me, a bird is a reptile, but most people look at you strangely when you insist that “technically, a bird is a reptile.”
[b]The Diversity of Life:
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As the “Tree of Life” diagram illustrates, all known living things can be classified into three domains. These domains are the Archaea, the Bacteria, and the Eukaryota. The archaea and the bacteria, though only distantly related, share the common characteristic that they’re prokayrotes.
All living things are made of cells, and almost all prokaryotes are unicellular. That is, they are single-celled organisms. The cells of prokaryotes are relatively small and simple; they lack nuclei or other distinctive organelles.
By contrast, the cells of eukaryotes are much larger and more complex than are those of prokaryotes. Eukaryotic cells have specialized subunits called organelles, which perform various tasks within the cells. The largest organelle within a eukaryotic cell is typically the one where the cell’s main genetic material (DNA) is stored – the nucleus.
[b]Eukaryotes:
The eukaryotes are often subdivided into four kingdoms – the Protista, the Plantae, the Fungi, and the Animalia.
The members of the Kingdom Plantae have in common that their cells are surrounded by more or less rigid cell walls made of a substance called cellulose. All plants are multicellular, by definition, and the great majority use the molecule chlorophyll to capture solar energy. The plant uses the captured solar energy to manufacture food in the process known as photosynthesis.
The members of the Kingdom Fungi also have cell walls, but their cell walls are made largely of a substance known as chitin, rather than cellulose. Most fungi are multicellular, but unlike plants, they cannot manufacture their own food. Instead, fungi feed by secreting digestive enzymes and then absorbing their food.
The members of the Kingdom Animalia lack cell walls. Like plants, animals are multicellular by definition, and like fungi, they are incapable of manufacturing their own food. Animals typically feed by ingesting their food and digesting it inside their bodies. Most animals have two specialized types of body cells that are found in no other organisms – neurons (which can form nerves) and muscle cells that are specialized for movement.
Finally, there is the Kingdom Protista. It is not really a “proper” kingdom, because we generally classify any eukaryotic organism that is not clearly an animal, plant or fungus as a “protist.” In other words, if we know it’s a eukaryote but don’t know what else the hell to call it, we call it a “protist.” Protists are often divided into the “animal-like protists,” the protozoans, the “plant-like protists,” the algae, and the “fungus-like protists,” including the slime molds.
In the next chapter, we will consider in more detail the defining characteristics of the Kingdom Animalia. We’ll also discuss some of the terminology used in the field of zoology.