5.3 CLASSIFICATION OF BIODIVERSITY
Nature of science: Looking for patterns, trends and discrepancies—there are common features in the bone structure of vertebrate limbs despite their varied use. (3.1
Understandings:
• The binomial system of names for species is universal among biologists and has been agreed and developed at a series of congresses.
• When species are discovered they are given scientific names using the binomial system.
• Taxonomists classify species using a hierarchy of taxa.
• All organisms are classified into three domains.
• The principal taxa for classifying eukaryotes are kingdom, phylum, class, order, family, genus and species.
• In a natural classification, the genus and accompanying higher taxa consist of all the species that have evolved from one common ancestral species.
• Taxonomists sometimes reclassify groups of species when new evidence shows that a previous taxon contains species that have evolved from different ancestral species.
• Natural classifications help in identification of species and allow the prediction of characteristics shared by species within a group.
Applications and skills:
• Application: Classification of one plant and one animal species from domain to species level.
• Application: Recognition features of bryophyta, filicinophyta, coniferophyta and angiospermophyta.
• The binomial system of names for species is universal among biologists and has been agreed and developed at a series of congresses.
• When species are discovered they are given scientific names using the binomial system.
• Taxonomists classify species using a hierarchy of taxa.
• All organisms are classified into three domains.
• The principal taxa for classifying eukaryotes are kingdom, phylum, class, order, family, genus and species.
• In a natural classification, the genus and accompanying higher taxa consist of all the species that have evolved from one common ancestral species.
• Taxonomists sometimes reclassify groups of species when new evidence shows that a previous taxon contains species that have evolved from different ancestral species.
• Natural classifications help in identification of species and allow the prediction of characteristics shared by species within a group.
Applications and skills:
• Application: Classification of one plant and one animal species from domain to species level.
• Application: Recognition features of bryophyta, filicinophyta, coniferophyta and angiospermophyta.
the binomial system of names for species
You have a name that you were given when you were born, but you also have a scientific name based on your species: Homo sapiens. This system of naming organisms using two names is called binomial nomenclature. ‘Bi’ means two, ‘nomial’ means name and ‘nomenclature’ refers to a system used to name things.
The first name in the binomial nomenclature system is always capitalized and it refers to the genus; the second name always begins with a small letter and refers to the species. Both are always written in italics when typed, or underlined when written by hand. Most words used in binomial nomenclature are Latin or Greek in origin. For example, Lepus arcticus is the scientific name for the Arctic hare; both terms come from Latin. This is why the term Latin name is often used, although this is an oversimplification because other languages are also involved.
This system of naming organisms was consolidated and popularized by the dynamic Swedish naturalist Carolus (Carl) Linnaeus. In his book Systema Naturae (The Natural World, 1735), he listed and explained the binomial system of nomenclature for species that had been brought to him from all over the world. Although he was not the first to use the idea of genus (plural genera), he popularized its use along with the species name in a consistent way.
There are three main objectives to using binomial nomenclature and its associated rules: (1) to be sure that each organism has a unique name that cannot be confused with another organism; (2) so that that the names can be universally understood, no matter what nationality or culture is using the name; and (3) so that there is some stability in the system by not allowing people to change the names of organisms without valid reasons.
naming new species
In the early days of classification, all known organisms were classified into only two kingdoms: plants and animals.
As the centuries went by, and as the study of biology became more systematic, tens of thousands of new species were discovered in forests, deserts, and oceans, some of which showed characteristics of both plants and animals, and some of which were not like either plants or animals.
With the invention of the microscope in the mid 1600s, many new creatures were discovered that were nothing like plants or animals. In effect, the microscope revealed that there is an entire world of invisible organisms living throughout the biosphere.
If a botanist finds a new species of orchid, for example, he or she would have to describe the plant, describe the location it was found in, name it using the proper rules of binomial nomenclature as set out by the International Code of Botanical Nomenclature (ICBN), and publish the findings in a publically accessible publication. In addition, it is important to put a sample specimen in a public location where other botanists can examine it. Such an example specimen is called a holotype. One of the rules of nomenclature is that a scientific name is not considered valid if a specimen is not available for verification.
As the centuries went by, and as the study of biology became more systematic, tens of thousands of new species were discovered in forests, deserts, and oceans, some of which showed characteristics of both plants and animals, and some of which were not like either plants or animals.
With the invention of the microscope in the mid 1600s, many new creatures were discovered that were nothing like plants or animals. In effect, the microscope revealed that there is an entire world of invisible organisms living throughout the biosphere.
If a botanist finds a new species of orchid, for example, he or she would have to describe the plant, describe the location it was found in, name it using the proper rules of binomial nomenclature as set out by the International Code of Botanical Nomenclature (ICBN), and publish the findings in a publically accessible publication. In addition, it is important to put a sample specimen in a public location where other botanists can examine it. Such an example specimen is called a holotype. One of the rules of nomenclature is that a scientific name is not considered valid if a specimen is not available for verification.
examples of binomial nomenclature
Sometimes scientific names for organisms are relatively easy to decipher because they contain their common names:
• Amoeba amazonas
• Equus zebra
• Gekko gecko (this lizard gets its name from the sounds it makes).
• Gorilla gorilla
• Paramecium caudatum (caudate means having a tail). Sometimes, it is more difficult to guess their common name:
• Apis mellifera (honeybee, although you might have guessed this if you know that beekeeping is also called apiculture)
• Aptenodytes patagonicus (king penguin, although you can probably guess where it lives from its species name)
• Loxodonta cyclotis (African forest elephant)
• Malus domestica (apple tree).
• Amoeba amazonas
• Equus zebra
• Gekko gecko (this lizard gets its name from the sounds it makes).
• Gorilla gorilla
• Paramecium caudatum (caudate means having a tail). Sometimes, it is more difficult to guess their common name:
• Apis mellifera (honeybee, although you might have guessed this if you know that beekeeping is also called apiculture)
• Aptenodytes patagonicus (king penguin, although you can probably guess where it lives from its species name)
• Loxodonta cyclotis (African forest elephant)
• Malus domestica (apple tree).
three domains of life
At the top of the hierarchy are the three largest groupings for organisms, called domains. The names of these three domains are the Archaea domain, the Eubacteria domain and Eukaryote domain. All living organisms are classified into one of these three. Note that viruses are not in this list because they are not alive and do not necessarily share a common ancestry with each other, two major conditions necessary to fit into this classification system.
-Archaeans are single-celled organisms that are distinct from bacteria and are very ancient. Archaean species thrive today in diverse habitats, from extreme conditions such as hydrothermal vents and hot springs, to the guts of mammals
-Eubacteria is the domain in which we find the bacteria you are most familiar with: the kind that makes your yogurt taste good, the kind that helps your intestines work properly, and also the kind that might give you an infection.
-Eukaryote is the domain in which we find all other life besides Archaea and bacteria, from the microscopic single-celled yeast that helps bread to rise, to enormous organisms such as sequoia trees and blue whales. A eukaryote is recognizable by its membrane-bound nucleus and membrane-bound organelles.
-Archaeans are single-celled organisms that are distinct from bacteria and are very ancient. Archaean species thrive today in diverse habitats, from extreme conditions such as hydrothermal vents and hot springs, to the guts of mammals
-Eubacteria is the domain in which we find the bacteria you are most familiar with: the kind that makes your yogurt taste good, the kind that helps your intestines work properly, and also the kind that might give you an infection.
-Eukaryote is the domain in which we find all other life besides Archaea and bacteria, from the microscopic single-celled yeast that helps bread to rise, to enormous organisms such as sequoia trees and blue whales. A eukaryote is recognizable by its membrane-bound nucleus and membrane-bound organelles.
seven principal taxa
In order to classify the hundreds of thousands of different types of organisms on Earth, scientists have agreed to use a seven-level hierarchy of taxa. Each of the three domains is subdivided into these seven taxa:
• kingdom
• phylum
• class
• order
• family
• genus
• species.
The taxa that are higher up this list contain the most numbers of organisms, and the taxa at the bottom of the list contain the least number. For example, although there are hundreds of thousands of named animals in the Eukaryote kingdom (most of which are insects), there is only a single known species of humans on Earth today: Homo sapiens.
• kingdom
• phylum
• class
• order
• family
• genus
• species.
The taxa that are higher up this list contain the most numbers of organisms, and the taxa at the bottom of the list contain the least number. For example, although there are hundreds of thousands of named animals in the Eukaryote kingdom (most of which are insects), there is only a single known species of humans on Earth today: Homo sapiens.
The system of kingdoms and taxa is used for identifying and naming organisms, but there are countless other ways to classify organisms. Here are some examples:
• by feeding habits: carnivore/herbivore
• by habitat: land dwelling/aquatic
• by daily activity: nocturnal/diurnal
• by risk: harmless/venomous
• by anatomy: vertebrates/invertebrates
• by feeding habits: carnivore/herbivore
• by habitat: land dwelling/aquatic
• by daily activity: nocturnal/diurnal
• by risk: harmless/venomous
• by anatomy: vertebrates/invertebrates
a common ancestral species
In biology, one of the objectives of classification is to represent how living (and extinct) organisms are connected. This means we are interested in natural classification, classifying organisms by their descent from a common ancestor. The best way to establish a natural classification is to base it on DNA sequences. When the sequences are not available, the next best way is to look at derived characteristics, such as whether or not an organism can produce milk. When genetic similarities are found, a genus can be established in which all similar species are placed. The members of this genus will have all evolved from a common ancestor, and this will be evident in the similarities between their gene sequences.
reclassification
Linnaean classification was limited to observable characteristics, and in Linnaeus’s time little effort was made to classify organisms by their ancestry because nothing was known about the genetic connections between species. The consequence of this is that sometimes organisms were put in the same genus even though they are not in fact closely related to each other. With a better understanding of cell structure and metabolism, as well as the new techniques of gene sequencing developed over the past few decades, we now know that some organisms that were put into the same categories in the 1700s should not be together in the same genus or even the same order.
natural classification
Natural classification uses ancestry to group organisms together, whereas artificial classifications use arbitrary characteristics, such as whether or not a plant or animal tastes good, or is useful to the textile industry, or whose name begins with the letter ‘c’. You may laugh, but early classification systems were often based on listing the species by alphabetical order, the way a dictionary lists words. The reasons for putting living organisms into groups according to a natural classification rather than an artificial one are numerous, and include:
• trying to make sense of the biosphere
• showing evolutionary links
• predicting characteristics shared by members of a group.
If you find a type of sea creature that you have never seen before, you should be able to find an identification key that was made by the experts who classified it. If you do a comprehensive search in the published literature of organisms that have already been identified and do not find a name for the organism, it is possible that you have discovered a new species. To put it into its appropriate category, you would find currently existing taxa that contain similar organisms.
You would determine whether it had a backbone or not, if it had stinging cells or not, and so on, until you reached a family or genus that it fit into. Once you find that genus, you can look at the list of characteristics of the species in that genus and make predictions about your new species. You might be able to predict what it eats, how long it lives, whether or not it produces certain enzymes, or even certain characteristics about its cell structure or biochemistry.
• trying to make sense of the biosphere
• showing evolutionary links
• predicting characteristics shared by members of a group.
If you find a type of sea creature that you have never seen before, you should be able to find an identification key that was made by the experts who classified it. If you do a comprehensive search in the published literature of organisms that have already been identified and do not find a name for the organism, it is possible that you have discovered a new species. To put it into its appropriate category, you would find currently existing taxa that contain similar organisms.
You would determine whether it had a backbone or not, if it had stinging cells or not, and so on, until you reached a family or genus that it fit into. Once you find that genus, you can look at the list of characteristics of the species in that genus and make predictions about your new species. You might be able to predict what it eats, how long it lives, whether or not it produces certain enzymes, or even certain characteristics about its cell structure or biochemistry.
examples of plant phyla
Of the several phyla of plants, four represent many of the types of plants you are probably most familiar with.
• Bryophyta: the bryophyte phylum includes plants of very short stature, such as mosses.
• Filicinophyta: this phylum includes ferns and horsetails, among others.
• Coniferophyta: the conifer phylum includes cedar, juniper, fir, and pine trees, among others.
• Angiospermophyta: the angiosperm phylum includes all plants that make flowers and have seeds surrounded by a fruit.
Bryophyta
Bryophytes, such as the liverwort shown below, are referred to as non-vascular plants because they do not have true vascular transport tissue inside them, such as xylem tissue (which transports water and minerals up from the roots) or phloem tissue (which transports water and nutrients from the leaves towards the stem and roots).
Filicinophyta
Members of the Filicinophyta, on the other hand, are vascular plants, as are the other two phyla described in this section. Ferns are recognizable by the absence of flowers and by their triangular fronds made up of many smaller long thin leaves.
Coniferophyta
Conifers can be recognized by the fact that all of them produce woody stems and their leaves are in the form of needles or scales.
Angiospermophyta
The most obvious vegetative characteristic that allows angiosperms (i.e. members of the Angiospermophyta) to be identified quickly are their flowers and fruit. If the fruit has any seeds inside, the plant is an angiosperm.
• Bryophyta: the bryophyte phylum includes plants of very short stature, such as mosses.
• Filicinophyta: this phylum includes ferns and horsetails, among others.
• Coniferophyta: the conifer phylum includes cedar, juniper, fir, and pine trees, among others.
• Angiospermophyta: the angiosperm phylum includes all plants that make flowers and have seeds surrounded by a fruit.
Bryophyta
Bryophytes, such as the liverwort shown below, are referred to as non-vascular plants because they do not have true vascular transport tissue inside them, such as xylem tissue (which transports water and minerals up from the roots) or phloem tissue (which transports water and nutrients from the leaves towards the stem and roots).
Filicinophyta
Members of the Filicinophyta, on the other hand, are vascular plants, as are the other two phyla described in this section. Ferns are recognizable by the absence of flowers and by their triangular fronds made up of many smaller long thin leaves.
Coniferophyta
Conifers can be recognized by the fact that all of them produce woody stems and their leaves are in the form of needles or scales.
Angiospermophyta
The most obvious vegetative characteristic that allows angiosperms (i.e. members of the Angiospermophyta) to be identified quickly are their flowers and fruit. If the fruit has any seeds inside, the plant is an angiosperm.
examples of animal phyla
Of all the phyla of animals, we will consider seven here. Some of these you may be familiar with, but others you probably do not know much about. Only one of the categories of animals in these seven phyla has a backbone or vertebral column; they are called vertebrates. The other six categories are all invertebrates: they do not have a backbone.
• Porifera: this phylum consists of the sponges.
• Cnidaria: this phylum includes sea jellies (jellyfish) and coral polyps, among others.
• Platyhelminthes: this phylum is made up of flatworms.
• Annelida: this phylum is made up of segmented worms.
• Mollusca: this phylum contains snails, clams, and octopuses, among others.
• Arthropoda: this phylum includes insects, spiders, and crustaceans, among others.
• Chordata: these are the vertebrates, the animals that have a backbone.
• Porifera: this phylum consists of the sponges.
• Cnidaria: this phylum includes sea jellies (jellyfish) and coral polyps, among others.
• Platyhelminthes: this phylum is made up of flatworms.
• Annelida: this phylum is made up of segmented worms.
• Mollusca: this phylum contains snails, clams, and octopuses, among others.
• Arthropoda: this phylum includes insects, spiders, and crustaceans, among others.
• Chordata: these are the vertebrates, the animals that have a backbone.
vertebrates
We will now explore the characteristics used to classify vertebrate organisms into the following five classes:
• fish
• birds
• amphibians
• mammals.
• reptiles
Fish
From goldfish to sharks, fish are a class of very diverse aquatic organisms that possess gills to absorb oxygen, and have skulls made of bone or cartilage. Great white sharks are well known for their jaws and teeth, and the vast majority of fish have these features, although they are not always visible. A small number of fish, such as lampreys, are jawless and use their mouths as suckers to stick onto a surface.
Amphibians
Amphibians include organisms such as frogs and salamanders; they start their lives in water. Their larval forms usually have gills to breathe underwater, but their adult forms develop lungs for breathing air. Most amphibians can also absorb oxygen through their skin. Most have four legs when they are adults, but there is a legless group called caecilians that resemble large worms or small snakes. They eat a wide variety of food, which they can chew with teeth. They might seem similar to reptiles, but their eggs do not have a membrane around the embryo.
Reptiles
Organisms such as snakes, lizards, turtles, and alligators are classified as reptiles in part because they produce amniote eggs. Amniote eggs are characterized by having a membrane around the developing embryo to protect it, which is seen not only in reptiles with soft or hard-shelled eggs but also in birds and mammals.
Birds
All living species of birds are bipedal (have two legs) and possess wings, most of which are adapted for flight. All birds have feathers and lay eggs with hardened shells. Bird skeletons are often very lightweight, making them well-adapted for flight. Their low density is achieved by having hollow bones.
Mammals
Mammals include animals such as foxes, hippopotamuses, squirrels, and camels, and can be recognized by the fact that they have hair on their bodies and the females produce milk in specialized glands to feed their young. There are nearly 5500 species of known mammals in the world, most of which have four limbs adapted for life on land. Some mammals, such as whales and dolphins, are adapted for life in the water, and others, such as bats, are adapted for flight. Mammals are capable of thermoregulation: they maintain their body temperature at a fixed level.
• fish
• birds
• amphibians
• mammals.
• reptiles
Fish
From goldfish to sharks, fish are a class of very diverse aquatic organisms that possess gills to absorb oxygen, and have skulls made of bone or cartilage. Great white sharks are well known for their jaws and teeth, and the vast majority of fish have these features, although they are not always visible. A small number of fish, such as lampreys, are jawless and use their mouths as suckers to stick onto a surface.
Amphibians
Amphibians include organisms such as frogs and salamanders; they start their lives in water. Their larval forms usually have gills to breathe underwater, but their adult forms develop lungs for breathing air. Most amphibians can also absorb oxygen through their skin. Most have four legs when they are adults, but there is a legless group called caecilians that resemble large worms or small snakes. They eat a wide variety of food, which they can chew with teeth. They might seem similar to reptiles, but their eggs do not have a membrane around the embryo.
Reptiles
Organisms such as snakes, lizards, turtles, and alligators are classified as reptiles in part because they produce amniote eggs. Amniote eggs are characterized by having a membrane around the developing embryo to protect it, which is seen not only in reptiles with soft or hard-shelled eggs but also in birds and mammals.
Birds
All living species of birds are bipedal (have two legs) and possess wings, most of which are adapted for flight. All birds have feathers and lay eggs with hardened shells. Bird skeletons are often very lightweight, making them well-adapted for flight. Their low density is achieved by having hollow bones.
Mammals
Mammals include animals such as foxes, hippopotamuses, squirrels, and camels, and can be recognized by the fact that they have hair on their bodies and the females produce milk in specialized glands to feed their young. There are nearly 5500 species of known mammals in the world, most of which have four limbs adapted for life on land. Some mammals, such as whales and dolphins, are adapted for life in the water, and others, such as bats, are adapted for flight. Mammals are capable of thermoregulation: they maintain their body temperature at a fixed level.
using a dichotomous key
When biologists encounter a species they do not recognize, they use a dichotomous key to establish which taxa it belongs to. If you have ever played a guessing game in which the rule is that you can only ask ‘yes’ or ‘no’ questions, then you already know how a dichotomous key works. Here are the basic principles.
1 Look at the first section of the key, which has a pair of sentences, (a) and (b), describing characteristics.
2 Next, look at the organism to see if the particular characteristic described in the first line (a) is present in the organism.
3 If the answer is yes, then go to the end of its line and find the number of the next pair of statements to look at, follow the number given and continue until the end. If the end of the line contains a name, it is the taxon for the organism.
4 If the answer is no, then go to the second statement just below it (b) and that one should be true, so go to the end of its line and find the number of the next pair of statements to look at. Follow the number given and continue until the end.
1 Look at the first section of the key, which has a pair of sentences, (a) and (b), describing characteristics.
2 Next, look at the organism to see if the particular characteristic described in the first line (a) is present in the organism.
3 If the answer is yes, then go to the end of its line and find the number of the next pair of statements to look at, follow the number given and continue until the end. If the end of the line contains a name, it is the taxon for the organism.
4 If the answer is no, then go to the second statement just below it (b) and that one should be true, so go to the end of its line and find the number of the next pair of statements to look at. Follow the number given and continue until the end.
Theory of knowledge:
• Evolutionary history is an especially challenging area of science because experiments cannot be performed to establish past events or their causes. There are nonetheless scientific methods of establishing beyond reasonable doubt what happened in some cases. How do these methods compare to those used by historians to reconstruct the past?
• Evolutionary history is an especially challenging area of science because experiments cannot be performed to establish past events or their causes. There are nonetheless scientific methods of establishing beyond reasonable doubt what happened in some cases. How do these methods compare to those used by historians to reconstruct the past?