What happens to the number of characteristics shared by organisms as you move from kingdom to species?

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Principles of Classification

Think about an elephant.  Develop a mental image of it.  How would you describe it to someone who has never seen one?  Take a moment to consider carefully . . .

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your mental image was accurate.

Very likely your mental image was a visual one like the picture.  Humans primarily emphasize traits that can be seen with their eyes since they mostly rely on their sense of vision.  However, there is no reason that an elephant or any other organism could not be described in terms of touch, smell, and/or sound as well.  Think about an elephant again but this time in terms of non-visual traits . . .

Not surprisingly, biologists also classify organisms into different categories mostly by judging degrees of apparent similarity and difference that they can see.  The assumption is that the greater the degree of physical similarity, the closer the biological relationship.

On discovering an unknown organism, researchers begin their classification by looking for anatomical features that appear to have the same function as those found on other species.  The next step is determining whether or not the similarities are due to an independent evolutionary development or to descent from a common ancestor.  If the latter is the case, then the two species are probably closely related and should be classified into the same or near biological categories.

Human arm bones   (common bird, mammal, and reptile forelimb configuration)

Homologies

are anatomical features, of different organisms, that have a similar appearance or function because they were inherited from a common ancestor that also had them.  For instance, the forelimb of a bear, the wing of a bird, and your arm have the same functional types of bones as did our shared reptilian ancestor.  Therefore, these bones are homologous structures.  The more homologies two organisms possess, the more likely it is that they have a close genetic relationship.

There can also be nonhomologous structural similarities between species.  In these cases, the common ancestor did not have the same anatomical structures as its descendants.  Instead, the similarities are due to independent development in the now separate evolutionary lines.  Such misleading similarities are called homoplasies

.  Homoplastic structures can be the result of parallelism, convergence, or mere chance.

Parallelism

, or parallel evolution, is a similar evolutionary development in different species lines after divergence from a common ancestor that did not have the characteristic but did have an initial anatomical feature that led to it.  For instance, some South American and African monkeys evolved relatively large body sizes independently of each other.  Their common ancestor was a much smaller monkey but was otherwise reminiscent of the later descendant species.  Apparently, nature selected for larger monkey bodies on both continents during the last 30 million years.

Convergence

, or convergent evolution, is the development of a similar anatomical feature in distinct species lines after divergence from a common ancestor that did not have the initial trait that led to it.  The common ancestor is usually more distant in time than is the case with parallelism.  The similar appearance and predatory behavior of North American wolves and Tasmanian wolves (thylacines) is an example.  The former is a placental mammal like humans and the latter is an Australian marsupial like kangaroos.  Their common ancestor lived during the age of the dinosaurs 125 million years ago and was very different from these descendants today.  There are, in fact, a number of other Australian marsupials that are striking examples of convergent evolution with placental mammals elsewhere.

Australian Tasmanian wolf or tiger (now extinct)		North American wolf

Both parallelism and convergence are thought to be due primarily to separate species lines experiencing the same kinds of natural selection pressures over long periods of time.

Analogies

are anatomical features that have the same form or function in different species that have no known common ancestor.  For instance, the wings of a bird and a butterfly are analogous structures because they are superficially similar in shape and function.  Both of these very distinct species lines solved the problem of getting off of the ground in essentially the same way.  However, their wings are quite different on the inside.  Bird wings have an internal framework consisting of bones, while butterfly wings do not have any bones at all and are kept rigid mostly through fluid pressure.  Analogies may be due to homologies or homoplasies, but the common ancestor, if any, is unknown.

Problems in Classifying Organisms

Listing characteristics that distinguish one species from another has the effect of making it appear that the species and their distinctive attributes are fixed and eternal.  We must always keep in mind that they were brought about by evolutionary processes that operated not merely at some time in the distant past, but which continue to operate in the present and can be expected to give rise to new forms in the future.  Species are always changing.  As a consequence, they are essentially only a somewhat arbitrarily defined point along an evolutionary line.

Jaguar

It is also important to realize that most species are physically and genetically diverse. Many are far more varied than humans.  When you think of an animal, such as the jaguar shown on the right, and describe it in terms of its specific traits (fur color patterns, body shape, etc.), it is natural to generalize and to think of all jaguars that way.  To do so, however, is to ignore the reality of diversity in nature.

Another problem in classifying a newly discovered organism is in determining the specific characteristics that actually distinguish it from all other types of organisms.  There is always a lively debate among researchers over defining new species because it is not obvious what are the most important traits.  There are two schools of thought in resolving this dilemma.  The first defines new species based on minor differences between organisms.  This is the splitter approach.  The second tends to ignore minor differences and to emphasize major similarities.  This lumper approach results in fewer species being defined.  Ideally, this dispute could be settled by breeding experiments--if two organisms can mate and produce fertile offspring, they are probably members of the same species.  However, we must be careful because members of very closely related species can sometimes produce offspring together, and a small fraction of those may be fertile.  This is the case with mules, which are the product of mating between female horses and male donkeys.  About one out of 10,000 mules is fertile.  Does this mean that horses and donkeys are in the same species?  Whatever the answer may be, it is clear that species are not absolutely distinct entities, though by naming them, we implicitly convey the idea that they are.

Tigons and Ligers--what happens when tigers and lions mate        This link takes you to an external website.  To return here, you must        click the "back" button on your browser program.

Breeding experiments are rarely undertaken to determine species boundaries because of the practical difficulties.  It is time consuming and wild animals do not always cooperate.  Using this kind of reproductive data for defining species from the fossil record is impossible since we cannot go back in time to observe interspecies breeding patterns and results.  Likewise, we cannot carry out a breeding experiment between ourselves and our ancestors from a million years ago.  Comparisons of DNA sequences are now becoming more commonly used as an aid in distinguishing species.  If two animals share a great many DNA sequences, it is likely that they are at least closely related.  Unfortunately, this usually does not conclusively tell us that they are members of the same species.  Therefore, we are still left with morphological characteristics as the most commonly used criteria for identifying species differences.

The Linnaean scheme for classification of living things lumps organisms together based on presumed homologies.  The assumption is that the more homologies two organisms share, the closer they must be in terms of evolutionary distance.  Higher, more inclusive divisions of the Linnaean system (e.g., phylum and class) are created by including together closely related clusters of the immediately lower divisions.  The result is a hierarchical

system of classification with the highest category consisting of all living things.  The lowest category consists of a single species.  Each of the categories above species can have numerous subcategories.  In the example below, only two genera (plural of genus) are listed per family but there could be many more or only one.

order family family genus genus genus genus

species	species	species	species	species	species	species	species

Most researchers today take a cladistics 

approach to classification.  This involves making a distinction between derived and primitive traits when evaluating the importance of homologies in determining placement of organisms within the Linnaean classification system.  Derived traits are those that have changed from the ancestral form and/or function.  An example is the foot of a modern horse.  Its distant early mammal ancestor had five digits.  Most of the bones of these digits have been fused together in horses giving them essentially only one toe with a hoof.  In contrast, primates have retained the primitive characteristic of having five digits on the ends of their hands and feet.  Animals sharing a great many homologies that were recently derived, rather than only ancestral, are more likely to have a recent common ancestor.  This assumption is the basis of cladistics.

Copyright � 1998-2012 by Dennis O'Neil. All rights reserved.
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Page 2

The highest category in the traditional Linnaean system of classification is the kingdom.  At this level, organisms are distinguished on the basis of cellular organization and methods of nutrition.  Whether they are single- or multiple-celled and whether they absorb, ingest, or produce food are critical factors.  Based on these types of distinctions, the biological sciences define at least five kingdoms of living things:

Kingdom		Types of Organisms
Monera	bacteria, blue-green algae (cyanobacteria), and spirochetes
Protista	protozoans and algae of various types
Fungi	funguses, molds, mushrooms, yeasts, mildews, and smuts
Plantae (plants)	mosses, ferns, woody and non-woody flowering plants
Animalia (animals)	sponges, worms, insects, fish, amphibians, reptiles, birds, and mammals

Most macroscopic creatures are either plants or animals.  Of course, humans are animals.  The distinction between the plant and animal kingdoms is based primarily on the sources of nutrition and the capability of locomotion or movement.  Plants produce new cell matter out of inorganic material by photosynthesis.   They do not have the ability to move around their environment except by growing or being transported by wind, water, or other external forces.

Kingdom Animalia
Kingdom Plantae

In contrast, animals do not produce their own food but must eat other organisms to obtain it.  Animals are generally more complex structurally.  Unlike plants, they have nerves and muscles that aid in rapid, controlled movement around their environment.  Animal cells usually do not have rigid walls like those of plants.  This accounts for the fact that your skin and flesh are flexible and the trunk of a tree is not.

This simple dichotomy between plants and animals is not adequate to encompass all life forms.  Some organisms have characteristics which do not qualify them to fit neatly into either kingdom.  For instance, funguses and most bacteria do not photosynthesize and most of them lack a means of controlled locomotion.  Some organisms have attributes of both plants and animals.  For instance, there is a group of common single-cell species living in fresh water ponds called Euglena that photosynthesize and have their own means of locomotion (whip-like tail structures called flagella).  Because of these and other exceptions, new kingdoms of living things had to be created.

More information about the kingdoms of living things

Research done over the last half century has shown us that there are even stranger single-celled organisms known as archaeobacteria that live in extremely harsh anaerobic environments such as hot springs, deep ocean volcanic vents, sewage treatment plants, and swamp sediments.  Unlike other life forms, they usually get their energy from geological sources rather than from the sun. There are also microscopic things that are not quite alive by definition but have some characteristics that are similar to living things.  These are the viruses and prions.  It is easy to overlook the importance of these extremely small things because they cannot be seen with the naked eye.  However, there are very likely around ten times as many viruses as all living things put together.  There are about 50 million viruses in 1 cm� of ocean water.  It has been estimated that these viruses are responsible for the death of 20% of all oceanic bacteria every day, thereby keeping the phenomenal reproductive capability of bacteria under control.  There are also complex interactions between bacteria, viruses, and other microbial life forms within our own bodies.  Most of the time, there are about 10 times as many microbial cells within us as there are body cells.

Phylum

Immediately below kingdom is the phylum

level of classification.  At this level, animals are grouped together based on similarities in basic body plan or organization.  For instance, species in the phylum Arthropoda

have external skeletons as well as jointed bodies and limbs.  Insects, spiders, centipedes, lobsters, and crabs are all arthropods.

Phylum Arthropoda	Phylum Mollusca

In contrast, members of the phylum Mollusca

have soft, unsegmented bodies that are usually, but not always, enclosed in hard shells.  They also usually have at least one strong foot that helps them move.  Octopi, squids, cuttlefish, snails, slugs, clams, and other shellfish are mollusks.

Bilateral symmetry (phylum Chordata)

There are at least 33 phyla (plural of phylum) of animals.  Humans are members of the phylum Chordata

.   All of the chordates have elongated bilaterally symmetrical

bodies.  That is to say, the left and right sides are essentially mirror images of each other.  If there are two functionally similar body parts, they are usually found roughly equidistant from the center line, parallel to each other.  Note the location of the woman's eyes, nostrils, and cheeks relative to the center line of her body.

Gill slits (phylum Chordata)

At some time in their life cycle, chordates have a pair of lateral gill slits or pouches used to obtain oxygen in a liquid environment.  In the case of humans, other mammals, birds, and reptiles, lungs replace rudimentary gill slits after the embryonic stage of development.  Frogs replace them with lungs in the transition from tadpoles to adults.  Fish retain their gill slits all of their lives.

Chordates also have a notochord

at some phase in their life cycle.  This is a rudimentary internal skeleton made of stiff cartilage that runs lengthwise under the dorsal surface of the body.  Generally, there is a single hollow nerve chord on top of the notochord.  Among humans and the other vertebrates, the notochord is replaced by a more complex skeleton following the embryonic stage of development.

Members of the phylum Chordata also often have a head, a tail, and a digestive system with an opening at both ends of the body.  In other words, the body organization is essentially that of a tube in which food enters one end and waste matter passes out of the other.   The chordates include mammals, birds, reptiles, amphibians, fish, as well as the primitive lancelets (or amphioxus) and tunicates (or sea squirts).

Notochord in a lancelet (phylum Chordata)
	Tunicate (phylum Chordata)

Human skeleton

  
              Subphylum

The chordates are divided into three subphyla.  Humans are members of the subphylum Vertebrata

.  Among the vertebrates, the simple hollow dorsal nerve tube is replaced by a more complex tubular bundle of nerves called a spinal cord.  A segmented vertebral (or spinal) column of cartilage and/or bone develops around the spinal cord of vertebrates to protect it from injury.  At one end of the spinal cord is a head with a brain and paired sense organs that function together to coordinate movement and sensation.

Vertebrata is the most advanced and numerous subphylum of chordates.  It includes all of the fish, amphibians, reptiles, birds, and mammals.  Collectively, there are about 43,000 living vertebrate species in comparison to just over 1500 species in the other two invertebrate subphyla of chordates.

NOTE:  Because science is constantly expanding our knowledge of living things, the precise details of how organisms are classified in the Linnaean system are frequently in flux.  This is not due to confusion but rather to the evolution of our understanding brought about by new discoveries.  For instance, as a result of the discovery of a dramatically new form of life known as archaeobacteria, a growing number of researchers now use a classification level above kingdoms referred to as a domain.  They define 3 domains of living things: Archaeo (simple bacteria-like organisms that live in extremely harsh anaerobic environments--these are the archaeobacteria), Bacteria (all other bacteria, blue-green algae, and spirochetes), and Eukarya (organisms with distinct nuclei in their cells--protozoans, fungi, plants, and animals).

Copyright � 1998-2013 by Dennis O'Neil. All rights reserved.
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Page 3

The subphylum Vertebrata

includes all of the familiar large animals and some rare and unusual ones as well.  The 7 living classes of vertebrates are distinguished mostly on the basis of their skeletal system, general environmental adaptation, and reproductive system.

subphylum:	Vertebrata
class:	Agnatha	Chondrichthyes	Osteichthyes	Amphibia	Reptilia	Aves	Mammalia

Three of the vertebrate classes are fish.   The most primitive of these is Agnatha

.  It consists of jawless fish that do not have scales.  These are the lampreys and hagfish.  Fish that have skeletons consisting of hard rubber-like cartilage rather than bone are members of the class Chondrichthyes

.  These are the sharks and rays.  All of the bony fish are members of the class Osteichthyes

.  Tuna, bass, salmon, and trout are examples of Osteichthyes.

Ray (class Chondrichthyes) and bony fish (class Osteichthyes)

Animals in the class Amphibia

spend part of their lives under water and part on land.  Frogs, toads, and salamanders are amphibians.  Many of these species must keep their skin moist by periodically returning to wet areas.  All of them must return to water in order to reproduce because their eggs would dry out otherwise.  They start life with gills, like fish, and later develop lungs to breathe air.

Salamander and frog (class Amphibia)

The class Reptilia

includes turtles, snakes, lizards, alligators, and other large reptiles.  All of them have lungs to breathe on land and skin that does not need to be kept wet.  They produce an amniote

egg which usually has a calcium carbonate rich, leather hard shell that protects the embryo from drying out.  This is an advantage over fish and amphibians because the amniote egg can be laid on land where it is usually safer from predators than it would be in lakes, rivers, and oceans.

Tortoise, snake, and lizard (class Reptilia)
		Amniote egg

The class Aves

includes all the birds.  They also produce amniote eggs but usually give them greater protection from predators by laying them high off of the ground or in other relatively inaccessible locations.  In the case of both reptiles and birds, the eggs are fertilized within the reproductive tract of females.  There are other striking similarities between reptiles and birds in their anatomies and reproductive systems.  This is not surprising because birds are descendents of theropod dinosaurs (two-legged mostly carnivorous dinosaurs).

Birds (class Aves)

Dogs, cats, bears, humans and most other large animals today are members of the vertebrate class Mammalia

.  All mammals conceive their young within the reproductive tract of the mother and, after birth, nourish them with milk produced by their mammary glands

.  Mammals are heterodonts

with strong jaws.  That is to say, they have a variety of specialized teeth (incisors, canines, premolars, and molars).  This allows them to chew their food into small pieces before swallowing it.  Subsequently, they can eat any size plant or animal.  Many reptiles must swallow their prey whole, which limits them to hunting smaller game.

Mammalian heterodontism

Like birds, mammals are endothermic

, or warm blooded.  They are able to maintain a relatively constant body temperature regardless of external environmental conditions mainly by using internal physiological mechanisms.  In other words, they are homeothermic, or stable in core body temperature, as a result of endothermy.  All of the living species of insects, fish, reptiles, and amphibians are ectothermic

, or cold blooded.  They keep their body temperature in a normal range mainly by avoiding exposure to environmental temperature extremes.  For instance, reptiles usually remain in shaded areas on hot days to prevent fatal overheating.  On cold nights, their lowered body temperature can cause them to become sluggish and inactive.  In contrast, endothermic animals are able to remain active at night and often in the winter when the air temperatures are especially cold.  They can also move about in the heat of very warm days.  This ability most likely provided an advantage for the early small mammals in surviving alongside dinosaurs and other large reptiles, which apparently were mostly ectothermic.  The downside of endothermy is the need to consume far more calories relative to body size in order to maintain a constant core body temperature.  Small mammals, such as moles with their rapid metabolism rates, must eat insects or other high calorie foods every half hour or so in order to stay alive.  By comparison, cold blooded rattlesnakes usually eat only once every 3-6 weeks and have been known to go without food for as long as two years.

Aiding in mammal body temperature control is their insulating hair and sweat glands.  Sweating helps to dissipate heat by evaporative cooling.  Compared to most other land mammals, humans are relatively hairless, but they have far more sweat glands.  Mammals have four chambered hearts (like birds), complex nervous systems, and large brains relative to the size of their bodies.  This broad range of useful features has made mammals highly adaptive and successful.  They first appeared about 200,000,000 years ago, early in the age of dinosaurs, and replaced reptiles as the dominant class of land animals after 65,000,000 years ago.  As the rapidly changing environment at that time led to the mass extinction of most large reptiles, it left vast evolutionary possibilities which mammals took advantage of by rapidly diversifying through adaptive radiation.  

Important to mammalian success is their reproductive system.  Their bodies took the amniote egg revolution of reptiles and birds one step further.  In effect, the uterus

functions as the protective eggshell.  Young mammals spend a long period of their early development within their mother's uterus.  After birth, they are provided with protein and fat rich milk to eat and are usually protected until maturity.  Pregnancy and milk production require mothers to significantly increase their own calorie consumption in order to provide nutrients for their infants.  A nursing human female normally uses about 30% of her body's energy just to produce milk.

Mammalian mother and her baby

Despite their success, mammals still only make up about .4% of known animal species.  It is humbling to realize that all chordates together are only just over 3.7% of known animal species.  By comparison, well over 1/2 of all animal species are insects.

Copyright � 1998-2012 by Dennis O'Neil. All rights reserved.
illustration credits

Page 4

Mammal Subclasses and Infraclasses

Among the mammals, there are three major variations in reproductive systems.  This is the basis for dividing them into subclasses and infraclasses.

class: subclass: Theriainfraclass:

Mammalia
Prototheria
	Metatheria	Eutheria

Members of the subclass Prototheria

lay eggs like most non-mammalian vertebrates.  However, they feed their newborn with mammary gland secretions like all other mammals.  They lack nipples, but the skin over their mammary glands exude milk for their babies.  The Prototheria are also referred to as monotremes

, which literally means that they have one opening for excretion and reproduction.  This is similar to birds and reptiles.  The Prototheria are also similar to reptiles in some aspects of their skeletons.  Notably, their legs are on the sides of their bodies rather than underneath them.  This results in a reptile-like gait.  There are only three surviving rare species groups of Prototheria.  These are the Australian platypus and 2 echidna (spiny anteater) species of Australia and New Guinea.

Platypus (subclass Prototheria)		Echidna (subclass Prototheria)

To find out a little more about the strange lives of monotremes, select the "Echidna Reproduction" button below:

All other living mammalian species, including humans, are in the subclass Theria

. They have in common the fact that they give birth to live young.  Therian mammals apparently did not evolve from the Prototheria. The relatively primitive prototherian reproductive system evidently evolved after their evolutionary line separated from the other early mammals.

The oldest infraclass of therian mammals is the Metatheria

, or the marsupials

.  Their young are born very immature and cannot live without further development in the mother's pouch.  The word marsupial comes from marsupium, the Latin word for purse.  Marsupials include kangaroos, koalas, opossums, and many other similar animals.  Most of them are native only to Australia and New Guinea.

Kangaroo, koala, and opossum (infraclass Metatheria)

Human fetus in utero

Most mammal species, including humans, are in the infraclass Eutheria

.  They are also referred to as placental 

mammals.  Eutherian mothers carry their unborn children within the uterus where they are nourished and protected until an advanced stage is reached.  This is made possible by the umbilical cord and placenta which connects the fetus to the uterus wall and enables nutrients and oxygen to get to the offspring as well as provides a means of eliminating its waste.  At the same time, the placenta functions as a barrier to keep the blood cells and other components of the immune systems of the mother and her fetuses separate to prevent their destruction. 

Giant pandas are an exception among the placental mammals.  Their babies are born at only 1/4 the size predicted for the general placental mammal pattern.  Marsupial babies are born at an even more immature stage because their rudimentary placentas are comparatively inefficient in nurturing fetuses.

Placental mammals have been extremely successful in out-competing monotremes and marsupials for ecological niches.  This is mostly due to the fact that their babies are born more mature, which increases their chances of survival.  This is particularly true of herbivores that are predated on by carnivores.  Marsupials give birth to early stage fetuses.  Placental mammals give birth after fetuses are much more developed.  The downside is that pregnant placental mammals must consume significantly more calories to nurture their fetuses and themselves, especially during the second half of their pregnancies.  Like monotremes and marsupials, placental mammals feed their babies with milk from their mammary glands.  Species that have multiple births at the same time generally have more mammary glands.  The number ranges from 2 in primates, goats, sheep, and horses to 18 in pigs.

Placental mammals are found on all continents, in the air, and in the seas.  Primates, cats, dogs, bears, hoofed animals, rodents, bats, seals, dolphins, and whales are among the dominant placental mammal groups today.  Nearly 94% of all mammal species now are placental mammals (5,080 species out of 5,416).

Whale, dolphin, monkey, and zebra (infraclass Eutheria)

The next tutorial in this series, The Primates, investigates all of the Linnaean classification categories below the infraclass level for humans, apes, monkeys, and some other closely related animals.  This will take us from the "order" level down to "species."

NEWS:  A team of researchers led by Wesley Warren at Washington University School of Medicine reported their completion of a draft of the platypus genome sequence in the May 8, 2008 issue of the journal Nature.  This showed that the platypus has about 18,500 genes (about 2/3 as many as humans) and that 82% are shared with humans, mice, dogs, opossums, and chickens.  Other platypus genes show links to reptiles, including those related to egg-laying, vision, and venom production.  Adult male platypuses can inject their poison with a spur just above the heel of each hind foot.  Apparently, they use this as a weapon against other males during the mating season.  Platypuses are also unusual in having sensors in their bills that are used to detect faint electrical fields from their prey when they hunt them under water.

NEWS:  The results of a 5 year global project sponsored by the Union for Conservation of Nature to survey all living mammals has been completed.  The researchers concluded in October 2008 that one half of the 5487 mammal species are declining in numbers and at least 1/4 are now threatened with extinction due primarily to habitat destruction, hunting by humans, and climate change (Jan Schipper et al., Science 1165115, 2008).

Copyright � 1998-2012 by Dennis O'Neil. All rights reserved.
illustration credits