ORGANIC EVOLUTION

ORGANIC EVOLUTION

• Organic Evolution is the changes that have occurred (and are occurring) to organisms on Earth through time.  The changes that have occurred (and are occurring) are inheritable.
• As Charles Darwin put it: "Descent with modification."
• Fossil evidence provides strong support of organic evolution, but is not the only line of evidence in support of organic evolution.  Other lines of evidence include embroyology, genetics, comparative anatomy (similarities of morphologic structures) (our basis for classification of organisms), and biochemistry (similarities of DNA, blood proteins, etc. among organisms).

THE EVOLUTION OF ORGANIC EVOLUTION

• The ancients Greeks had some thoughts on evolution (but not much was passed on to later generations).
• During the Middle Ages, and even from the time of Aristotle, not much thought on organic evolution.
• In fact, Aristotle believed that species were fixed (immutable) and cound not change.
• Also, traditional interpretations of the bible (particularly during the Dark Ages and Middle Ages and prior to the 1700's) stressed the immutablitity of species.
• During the 1700s attitudes toward organic evolution started to change (at least by some naturalist).
• Erasmus Darwin (1731-1802) (Charles Darwin's grandfather) was the first to actually propose an idea of gradual evolution of organisms.
• Jean Baptist de Lamarck (1744-1829) - Botanist and geologist.  Lamarck proposed the "Inheritance of Acquired Characteristics" and was the first person who was taken seriously relative to concepts of organic evolution.  Giraffe example:  the giraffe's neck became longer with time because the parents stretched their neck to get the higher leaves, and the longer necks were passed on to the next generation, etc.  Actually, not too crazy an idea for his time, remember there was no concept of genetics then.  Lysenko affair: Soviet Union, belief in Lamarckian evolution destroyed agriculture in U.S.S.R. (read perspective 5.1 in your text).
• Charles Darwin (1809-1882) and Natural Selection -  From: The C. Warren Irvin, Jr., Collection of Charles Darwin and Darwiniana at http://www.sc.edu/library/spcoll/nathist/darwin/darwin.html (this is a nice website, it would be worth your time to visit this website).
•      Charles Darwin, an English naturalist (GO TO THIS SITE TO READ ABOUT DARWIN), conceived many of his ideas on organic evolution while serving as a naturalist (1831-1836) on the British ship, the HMS Beagle.  Darwin first published his book Voyage of the Beagle in 1839, with the popular version in 1845.  In this publication, Darwin demonstrated that evolution had occurred in the past and was still occurring in his time.  His study of the different adaptations of finches on the Galapagos Islands is a classic.  However, after returning from his voyage on the HMS Beagle, and for many studious years following, Darwin still did not have an acceptable mechanism for evolution.  However, by about 1838, based on his studies of domestic breeding (artificial selection) and the reading of an essay by Thomas Malthus on population growth, Darwin was starting to formulate his ideas on natural selection (even though he still did not know how traits were actually transmitted and retained in a population of interbreeding organisms)
• .
• Alfred Russel Wallace (1823-1913)
• (From:  Alfred Russel Wallace (1823 - 1913) is one of the forgotten fathers of modern science http://www.iol.ie/~spice/alfred.htm)
•      During the summer of 1858, Alfred Russel Wallace (also an English naturalist), then on a collecting expedition in Indonesia, wrote a note to Darwin outlining his ideas on a mechanism for evolutionary change, the mechanism being "NATURAL SELECTION BY MEANS OF SURVIVAL OF THE FITTEST".  Darwin was shocked, he had been thinking along the same lines himself and now it appeared that Wallace was going to publish his ideas before Darwin could publish.  At the urging of Charles Lyell and Joseph Hooker, friends of Darwin and fellow members of the prestigious Linnaean Society of London, it was arranged for Darwin and Wallace to independently present papers at the same session of the Linnaean Society in 1858, outlining their ideas on evolution by means of natural selection.  Darwin published his famous On the Origin of Species by Means of Natural Selection (usually shortened to The Origin of Species) the following year, 1859.  (An online version of Origin of Species is located at this website: Online Literature Library - Charles Darwin - The Origin of Species ).  (Another website that you may find interesting, and which discusses evolution, is my Paleobiology of Dinosaurs site at:  GEOLOGY 307. Check out parts of lectures 2, 3, and 4).
•      Darwin believed that natural selection was a very gradual process involving natural selection and minute mutations which were advantageous to the organism.  Many followers of Darwin today (Neodarwins) also believe in gradualistic evolution.  However, fairly recently several noted paleontologists and evolutionary biologists have questioned gradualism and have proposed that evolution may have occurred by "jumps and leaps" followed by very slow evolutionary change for long periods of geologic time.  This concept, known as the Punctuated Equilibrium Model of Evolution, has spread rapidly in scientific circles since Stephen Gould of Harvard University and Niles Eldridge of the American Museum of Natural History published several articles on the subject in 1971 and 1972 (Gould and Eldridge have enhanced ideas orginally suggested by Ernest Mayr of Harvard in the 1950s and 60s).  Steven Stanely, of John Hopkins University, is also an adament disciple of the Punctrated Equilibrium Model and preaches the theory eloquently in his book The New Evolutionary Timetable...Fossils, Genes, and the Origin of Species (1981).

THE DARWIN-WALLACE MODEL OF ORGANIC EVOLUTION BY NATURAL SELECTION

• Direct quote from Darwin's 1859 The Origin of Species, first paragraph of the chapter on Natural Selection:

"How will the struggle for existence, discussed too briefly in the last chapter, act in regard to variation? Can the principle of selection, which we have seen is so potent in the hands of man, apply in nature? I think we shall see that it can act most effectually. Let it be borne in mind in what an endless number of strange peculiarities our domestic productions, and, in a lesser degree, those under nature, vary; and how strong the hereditary tendency is. Under domestication, it may be truly said that the, whole organisation becomes in some degree plastic. Let it be borne in mind how infinitely complex and close-fitting are the mutual relations of all organic beings to each other and to their physical conditions of life. Can it, then, be thought improbable, seeing that variations useful to man have undoubtedly occurred, that other variations useful in some way to each being in the great and complex battle of life, should sometimes occur in the course of thousands of generations? If such do occur, can we doubt (remembering that many more individuals are born than can possibly survive) that individuals having any advantage, however slight, over others, would have the best chance of surviving and of procreating their kind? On the other hand, we may feel sure that any variation in the least degree injurious would be rigidly destroyed. This preservation of favourable variations and the rejection of injurious variations, I call Natural Selection. Variations neither useful nor injurious would not be affected by natural selection, and would be left a fluctuating element, as perhaps we see in the species called polymorphic."

• 1.  There is natural variation among the individuals of a population of a given species.  This variation controls characteristics such as color (like flower color), size, shape, and many other morphologic and physiologic characteristics.  Darwin and Wallace were not aware of genetics, but they assumed that characters must be controlled by traits within the organisms that could be transmitted to the offspring (i.e., the traits were inheritable).
• 2.  Certain variations are more beneficial to the organism than others and those variations will give the organisms that have them a selective advantage in the stuggle for existence.
• 3.  Most organisms produce many more offspring than can survive to maturity.  Of course this is to help ensure that some of the offspring have the beneficial variations that will allow them to reach maturity.
• 4.  Those individuals of a population that have the more beneficial variations are the ones most likely to survive to sexual maturity and pass on their favorable combinations of variable characteristics (i.e., the survival of the fittest).
• How would Darwin and Wallace explain the evolution of a long neck in the giraffe?
• Note:  After publishing The Origin of Species, Darwin did not argue for his theory.  He left that
• to others, most notable Thomas Henry Huxley (1825-1895) ("Darwin's Bulldog"). (Check out his site relative to Huxley: Thomas Huxley ,  (From: http://www.ucmp.berkeley.edu/history/thuxley.html)
• and this one: Huxley From Devil's Disciple to Evolution's High Priest - Adrian Desmond )  Of course Darwin's book made a real stir in Victorian England.

GREGOR MENDEL AND GENETICS

• Critics of natural selection said that Darwin and Wallace could not account for the origin of variation and how variation is maintained in populations.
• Gregor Mendel (1823-1884), an Austrian Monk (and called the Father of Genetics), solved this problem and founded the science of genetics. {Go to these websites and read about Mendel: 1)  Gregor Mendel (1823-1884) , 2) Gregor Mendel's Legacy }
• Mendel did experiments with true breeding, self-fertilizing pea plants to establish that variable characters could be passed on to offspring and would not be blended out by combination with other characters.  Mendel did his work in the 1860s and his results could have helped Darwin and Wallace in their arguments for natural selection.  However, Mendel published his results in an obscure journal that did not draw much attention.  He did send Darwin a copy of his paper, but evidently Darwin did not read it.  In fact, Mendel's results went almost unnoticed by the scientific community and was independently rediscovered about 1900 by several researchers.
• Mendel's Pea Experiments: Mendel looked at characters like height, flower color, seed coat color, seed shape, etc. in his pea experiments.  Pea plants normally self-fertilize (self-pollinate). Mendel mechanically (surgically) removed the anther (male flower part that contains the male sex gamate - pollen) so he could cross-fertilize peas with different characteristics.  Typically, in self-fertilization pollen from the anther falls on the stigma (female flower part that produces the eggs).  The pollen contains sperm nuclei which fertilizes the egg, forming a zygote.  The zygote (having recieved genetic material from the male part and female part) develops into an embryo.  The embryo is coated with an envelope of nutrients and a coat to form a seed.  The seed can then develp into a new individual.
•      When Mendel crossed red flowered pea plants with white flowered pea plants all the offspring were red in the first generation cross (F-1 cross).  Mendel then let the F-1 generation self-fertilize to give an F-2 generation.  In the second generation (F-2), white flowers would again reappear, with a ratio of about 3 reds to 1 white (Mendel did a large number of trials).
•      Mendel treated the results mathematically and based on the outcomes of his experiments he concluded that traits must appear in pairs.  These pairs must combine and recombine according to laws of probability. GO TO THIS WEBSITE AND READ ABOUT MENDEL'S EXPERIMENTS, MONOHYBRID CROSSES, PUNNETT SQUARES, PHENOTYPES, AND GENOTYPES:  Gregor Mendel's Legacy .
•      Mendel's traits (he called them factors) we now call genes.  Different expressions of genes (such as red flowers verus white flowers) we now refer to as alleles.  Mendel stated four laws of inheritance, restated as follows:
• MENDEL'S LAWS OF INHERITANCE:
• 1) Mendel concluded that genes occur in pairs, each member of a pair is called an allele (however, there may be several alleles for a particular character trait; example for eye color: brown, blue, green, etc.).
• 2) Mendel concluded tha a pea seed got one allele from the pollen and one allele from the ovule (egg in the stigma).  In general, when sex cells are formed, the two alleles of each pair separate from one another, and each sex cell recieves only one allele of each pair.  This is called the Law of Segregation.
• 3) When two alternative forms of the same gene (i.e., two different alleles) are present in an individual, often only one of the alleles is expressed.  This is called the Law of Dominance.
• (Things are not always this simple, there are many cases of incomplete dominance and the crosses will have intermediate charateristics)
• 4) Mendel concluded that, if two or more separate characteristics are considered in a cross, flower color, tallness, etc., each trait is inherited without relation to other traits.  Thus all possible combinations of independently inherited characteristics will occur in the sex cells (gamates).  This is called the Law of Independent Assortment (however, as we now know, this is only true for genes located on different chromosomes).

	R	r
R	RR	Rr
r	rR	rr

• Example of a Punnett sqaure of a F-2 cross (letting F-1 peas self-fertilize).  This results in phenotypes of 3 red pea flowers and 1 white pea flower (ratio of 3:1 for phenotypes; so 75% red phenotypes and 25% white phenotypes).  However, the genotypes will be 1 RR, 2 Rr, 1 rr (ratio of 1:2:1 for genotypes, so 25% or 1/4 are RR; 50% or 1/2 are Rr; 25% or 1/4 are rr).  This is the result of a simple monohybrid cross in the F-2 generation of one gene with two possible alleles.  RR is said to be homozygous dominant; Rr is heterozygous; and rr is homozygous recessive.
•      The importance of Mendel's work is that factors (genes) controlling characteristics (traits) are transmitted as discrete entities, and even though not always expressed, are not lost.
•      Thus some variation is accounted for by alternate expression of genes and variation can be maintained.

GENES AND CHROMOSOMES

• Only sex cells pass on genetic information, thus variations and mutations of genes can only be transmitted by the sex cells.
• Genes are located on chromosomes (composed of DNA) - thread-like structures in the cell nucleus.
• The number of chromosomes is specific for a particular species, thus varies among different species.
• Humans have 46 chromosomes.  Horses have 64.
• Chromosomes always occur in pairs, so humans have 23 pairs whereas horses have 32 pairs.
• Sex cells have only one-half of the number of chromosomes as do body cells.  Sex cells undergo a type of division called meiosis (see page 110 in text and diagram below).  This reduces the number of chromosomes to one-half (called the haploid number).  Sex cells end up with one each of the paired chromosomes.  Body cells undergo a different type of cell division called Mitosis (see page 110 in text and diagram below).  In mitosis each daughter cell has the same number of chromosomes as the parent cell (called the diploid number).
• COMPARISON OF MEIOSIS AND MITOSIS:
• 
• From:  Meiosis at http://www.accessexcellence.org/AB/GG/comparison.html
• Each chromosome is made up of thousands of genes.
• Paired chromosomes are said to be Homologous Chromosomes. Study the diagram below to see homologous chromosome pairs, allelic genes vs. non-allelic genes, etc.
• 
• Thus for every characteristic in a simple monohybrid cross, one allelic gene is supplied from each parent (or from each sex gamate)  (in many cases it is much more complex than this and several genes may control a specific trait).  However, in a simple monohybrid cross and based on the laws of probablity, we can predict the possible combinations.
• 

• So genetics shows how variation was maintained in a population.  The concept of mutation illustrates how variations may arise in a population. A mutation is just a mistake in the genetic code and may occur during the duplication process.
• However, geneticists during the early 20th century believed that mutation alone, rather than natural selection, was the main mechanism by which evolution occurred.
• During the 1930sand 1940s ideas of geneticists, paleontologists, population biologists, evolutionary biologists, anatomists, and others were brought together to form the Modern Synthesis (Neodarwin) view of evolution.
• 1.  Chromosome theoryy of inheritance incorporated.
• 2.  Mutations were accepted as one form of variation in populations.
• 3.  Lamarckism (Inheritance of Acquired Characteristics) was completely rejected as a mechanism for evolution.
• 4.  Natural Selection reaffirmed as the primary process of organic evolution.
• 5.  Emphasized that evolution is a gradual process (Gradualistic Evolution).

• Sources of Variation:
• Most phenotypic variation in populations can be explained by sexual reproduction and the recombinations of gene alleles from generation to generation, thus a large gene pool develops in a population.
• However, all new variations that are introduced into a population must be the result of a mutation in the sex cells.  Only mutations in sex cells are inheritable.  Mutations are random with respect to fitness.
•  Chromosomes (via genes) direct the synthesis of proteins (based on the genetic code in DNA molecules) by selecting the right amino acids and arranging the amino acids in a particular sequence.  These proteins determine the characteristics of the organism.
• Any change in the information (DNA) directing protein synthesis is a mutation.
• Most mutations are not beneficial to the organism, but if the environment changes a mutation may become beneficial.

SPECIATION AND THE RATE OF EVOLUTION

• IMPORTANCE OF SPECIES

The species is the fundamental taxonomic unit of biological entities, it is real.  All other taxonomic categories are arbitrary and constructed by man, but the species has a reality in nature, not just in the minds of scientists.  However, how we define species is another matter.

• Typolocial Species Concept: Pre-Darwinian view that God created the ideal type for each species.  Any deviation from the ideal type was viewed as an imperfection from God's blueprint.  Species were fixed and unchanging.
• With Darwin's publication of "On the Origin of Species by Means of Natural Selection", it became apparent that species were not static and did not fit a "blueprint" type.  Because of the natural variation in populations, changes in species would occur with time because of the continued struggle for existence and the continued selection for the most fit.
• Biological Species Concept: "a species is an array of populations which are acturally or potentially interbreeding, and which are reproductively isolated from other such arays under natural conditions." (Ernst Mayr, 1963, also check out this link: What is a Species, and What is Not?  ).  Or, in other words, a species is a group of naturally interbreeding or potentially interbreeding populations with a common gene pool and reproductively isolated from other species. (See this link,  Species Concepts ).
• Morphological Species Concept: "a species is a diagnosable cluster of individuals within which there is a pattern of ancestry and descent, and beyond which there is not." (Eldredge and Cracraft, 1980).  Of course this definition implies morphologic similarity, but also evolutionary relationships.  Perhaps the above definition, because of the evolutionary implications, is really that for a biolgical species.  Morphological species are defined soley by morphological criteria and are also referred to as morphospecies.  The morphospecies concept is most often used by paleontologist to define species, however, paleontologists are really using the morphospecies concept as a way to recognize ancient species, they are not (or perhaps should not be) really defining a species with this concept.  Even biologists, in practice, use the concept of the morphospecies (we can't always actual observe living populations interbreeding).  However, most biologists (and paleontologists should) recognize that the morphospecies concept is not a definition of species, but rather a  useful concept in the recognition of different species.
•  Paleontological Species Concept: Alan Shaw (1964) describes a paleontological species in the following manner: ".....objects of organic origin that are of sufficiently distinctive and consistent morphology so that a competent paleontologist could define them so that another competent paleontologist could recognize them."  In practice, of course, this is typically how paleontologists recognize species.  However, perhaps paleontologists should use the biological definition of what a species is and is not.  Certainly, biologists have information about modern species that is not available to the paleontologists, however, paleontologists have information that may help in the recognition of species in the biological sense; such as paleoecologic relationships, biostratigraphic data, paleobiogeographical distributions, and sedimentological information which may help in recognizing fossils as valid biological species.
• The following definition of the paleontological species is offered by Maddocks, 1999 (see this link,  GEOL 3330: THE SPECIES ): "A paleontological species is a group of fossil populations showing similarity and range of variability within, and differing from other such populations, such that the best explanation of these relationships is that in life they were members of a species."  Of course, here she means members of a biological species as biological species has been defined above.
• Some other species concept terms:
• Ecological Species Concept:  no two biological species occupy the same niche, so this concept basically has the same meaning as the biological species concept.
• Asexual Species: difficult situation.  Certainly, the biological species definition doesn't apply well here.  Organisms that reproduce asexually surely are very similar genetically (which would isolate them from other species).  For fossils, often the best thing we can do here is use morphologic traits to recognize different asexual species.
• Sibling Species: Some modern organisms that are very closely related and have very similar morphologic characteristics may not be part of a naturally interbreeding (or potentially interbreeding) population (i.e. they are reproductively isolated), yet it is morpholoigcally difficult to tell them apart.  However, in modern sibling species we can often observe their behavior and reproductive habits and determine that they are separate species.  This is much more difficult for extinct organsims.  Perhaps, in most cases, sibling species cannot be differentiated from fossils.

• Reproductive Isolation: most speciation occurrs as a result of reproductive isolation. How does this reproductive isolation come about?
• Peripherally isolated populations: If a portion of the population becomes isolated to the fringe of the main population, then the gene pool is smaller and any unusual gene frequencies (say from original variability in the population or from new alleles introduced by mutation) have a higher probability of becoming dominant in the peripheral population (i.e. there is no longer gene flow with the main population).  Eventually, the gene pool of the peripheral population may become so different that they are reproductively isolated from the main population, even if other isolating barriers are removed.
• Allopatric Speciation Model: Geographically isolated portions of a population.  Over time, these isolated variants become reproductively isolated from the parent population and become new species.  Most speciation is thought to result from allopatric speciation.
• Sympatric Speciation: Any factor which causes reproductive isolation results in speciation.  Speciation is not always a result of sharp geographic isolation.  Note: sympatric means living together in the same area, allopatric means living in different areas.

• Anagenesis: phyletic gradualism in the geologic record and the problem of pseudoextinction.  If there is a gradual change of one species into another, where do you draw the boundary?  And when you do arbitrarily cut one species off and start a new one, are you causing the pseudoextinction of one species and pseudoevolution of another species.
• Punctuated Equilibria: Eldredge and Gould (1972) first formally proposed this idea.  This concept basically says that species do not change much (stasis, i.e. in stable equilibrium) over long periods of time, but that speciation occurs rapidly (i.e. stasis is punctuated by the sudden introduction of new species, either due to migration of peripherally isolated variants back into a particular area or perhaps by environmental stress that results in rapid change in the gene pool, and thus speciation).  The Punctuated Equilibria Model appears to be the best explanation of what we observe in the fossil record, however, there are examples of phyletic gradualism.  (See these links:  Punctuated Equilibria ,  Evolutionary Genetics )
• Diagram illustrating the difference in phyletic gradualism versus punctuated equilibrium.  In the phyletic gradualism model there is slow continuous morphologic (or other) change as one species evolves into another.  In the punctuated equilibrium model, there are long periods of no or very little change (stasis) punctuated by rapid evolution of new species.  The figure (caption mine) from: http://www.zoology.ubc.ca/~bio336/Bio336/Lectures/Lecture23/Overheads.html.  This is the same concept as Figure 5.11 in your text.

Divergent, Convergent, and Parallel Evolution

• Divergence occurs when one species evolves into two (or more) species, which continue to change over time and become less and less alike.  As time goes on and more divergence occurs of these related forms (with a common ancestory), we say that adaptive radiation has occurred.  Adaptive radiation involves numerous divergences of an ancestral stock (common ancestor) into a number of descendants that have exploited different niches in the environment.  For example, when the dinosaurs became extinct at the end of the Mesozoic Era, the ancestral mammal stock (which was present when the dinosaurs were alive) diverged  and adaptively radiated into many niches that had been occupied by dinosaurs.
• Adaptive radiation of the ancestral mammal stock into many different forms of mammals occupying different niches (Figure from:  Evolution - The Evidence at http://bioserve.latrobe.edu.au/vcebiol/cat3/u4aos2p4.html#Divergent ) (By the way, this is an excellent site, you should go there and take a look at it.)
• Parallel Evolution also involves divergence from a common ancestor, but the descendants evolve similar morphologic characteristics as time goes on (most likely in response to similar environmental parameters, i.e., occupying a similar niche).  So, parallel evolution is the development of similar characteristics in closely related organisms.
• Parallel Evolution in the elephant and wooly mammoth (From:   Evolution - The Evidence at http://bioserve.latrobe.edu.au/vcebiol/cat3/u4aos2p4.html#Divergent)
• Convergent Evolution is the development of similar morphology in distantly related groups.  As with parallel evolution, this is in response to adapting to similar habitats and niches.  An excellent example of this is the modern dolphin and the ichthyosaurs of the Mesozoic Era (see Figure 5.22, p. 118 in Wicander and Monroe).
• Some examples of convergent evolution from three very distantly related organisms (From: Evolution - The Evidence at http://bioserve.latrobe.edu.au/vcebiol/cat3/u4aos2p4.html#Divergent).

EVOLUTIONARY TRENDS

     Based on the fossil record and working out the evolutionary history of a group of organisms (i.e. phylogeny), we can recognize certain trends in evolution.

• An increase or decrease in size.  This may be for the whole body or certain parts (such as teeth, brain, horns, etc.).
• A reduction or increase in the number of certain body parts, such as ribs, toes, fingers, teeth, etc.
• An increase in the complexity of certain body parts, such as sutures (ammonites), brain, armor (dinosaurs), etc.
• Not much change at all.  Some organisms did not change much over very long periods of time.  Ones that are still living (extant) are called living fossils (examples: the brachipod Lingula, the opossum, the coelocanth (Latemeria).

DETERMINING PHYLOGENETIC RELATIONSHIPS (CLADISTICS AND CLADOGRAMS)

    The key to understanding the evolution and diversity of the organisms is to determine their phylogeny (how they are related to each other and to the rest of the biota).  In order to do this we need to understand some of the principles of evolution, classification (taxonomy), and phylogeny.

• PHYLOGENY:  The history of descent of organisms.

• TAXONOMY:  The classification and naming of organisms.(Note: some would say that taxonomy should only deal with the naming of organisms and that classification is intimately related to the phylogenetic relationships of organisms)

• EVOLUTION:  The origin and change of organisms over time.

Hierarchy

• We can organize the biota into a heirarchy (rank or order of the features of the biota).  For example:  Living Organisms -- things that are alive; Vertebrates  -- living organisms that have a backbone; Mammals – living organisms that have a backbone and have fur and mammary glands.
• Thus mammals are a subset of all animals that have backbones.  All of the biota is connected by the sharing of features in a hierarchy.  Thus most organisms could be described as having a primitive body plan with variations  (but the original, unmodified body plan is always present in the biota).  Life is not really infinitely diverse, but is connected by the sharing of certain features in a hierarchy.

Characters

• To recognize the heirarchy we must identify features of organisms.  These features are referred to as characters.  The distribution of characters among a selected group of organisms has meaning, but a single feature of a specific organism does not have much meaning (except to separate it from other organisms).  Thus, shared characters among organisms are important in classifying them as belonging to a group of related organisms.

• General Characters (primitive characters) are characters of larger groups that are not specific to smaller groups within the larger group (for example, birds have a backbone – this is not specific to birds because frogs also have a backbone).  Specific Characters (derived charaters, also called evolutionary novelties) are usually restricted to a smaller group within a larger group (thus feathers are specific to birds, which belongs to the larger group of vertebrates; frogs, which are also vertebrates, do not have feathers and thus can not be grouped with birds using the specific character of possession of feathers).

Cladograms ( Journey into the World of Cladistics)

• Cladograms are branching diagrams to show a hierarchical distribution of shared characters.  To construct cladograms we use shared observable characters (not functions – we can't observe functions).  We can group anything using shared characters, thus it is not restricted to living organisms.  However, when we group living organisms into a heirarchy based on shared characters, we are implying that the organisms have an evolutionary relationship (i.e. they share a common ancestor).  The history of descent of organisms is referred to as phylogeny.  The phylogeny of a group of organisms shows their evolutionary relationships. Phylogenies are determined by constructing cladograms.
• Each branch (or bundle of branches) of a phylogeny is called a clade (from "clados" meaning branch).  A divergence is a split on a cladogram.  Convergence is the evolution of similar features in two unrelated (or distantly related) clades.
• Groups of organisms shown on a phylogeny are called taxa (singular taxon).  For very detailed work, the species level taxon is used.  (Note:  Biologists define species as a population of naturally interbreeding organisms.  Of course, paleontologist cannot use this definition directly.  Paleontologist define morphologic species.  A morphologic species is defined by similarity of anatomical characters within a fossil group).
• So the manner in which organisms are related is defined as their phylogenetic relationships (or evolutionary relationships).

     In order to understand the history of life, we have to understand the patterns of evolution.  Darwinian Evolution is the most accepted theory of evolution today.  First proposed by Charles Darwin (1859) in“On the Origin of Species by Means of Natural Selection”.  This concept is sometimes expressed as Survival of the Fittest.  For Darwinian evolution we use phylogeny to show relationships of ancestors to descendants.

     Evolution means descent with modification. In order to understand the history of life, we have to understand the patterns of evolution.  We use phylogeny (Greek: phylum = tribe, genos = birth or origin) to show relationships of ancestors to descendants, therefore, phylogeny explains the history of descent of organisms.

     In modern phylogenetic methods, we use cladograms to show monophyletic groups (natural groups that descended from a common ancestor).  Polyphyletic groups are groups that do not share a closest common ancestor, and thus are not of value in determining phylogeny.

     If we, as scientists and students of science, are capable of understanding the world around us and the ways of science, then organisms have changed over time.Therefore, Organic Evolution is a Fact (Fastovsky and Weishampel, 1996).  [Note:  Creationist jump on the debate about evolution by scientists, but scientists argue the mechanism and rates of evolution, not whether evolution has occurred].(GO TO THIS SITE AND READ ABOUT SOME OF THE MISCONCEPTIONS ABOUT EVOLUTION AND EVOLUTIONARY THEORY)

     The biota has evolved!!!  As Darwin said, descent with modification.  The mechanism of evolution, as first proposed by Charles Darwin and Alfred Russell Wallace in a joint presentation to the Linnaean Society of London in 1858, is natural selection.

     Evolution (in morphology, genetic make-up, behavior, etc.) by natural selection involves modification such that ancestral (primitive) features (characters) are retained and new (derived) features are evolved.

     Relationships in anatomical features is one line of evidence for the evolutionary relationship of organisms.  When two anatomical structures can be traced back to a single structure in a common ancestor, we say that the two structures are homologous.  Thus homologous structures are called homologues.  For example, our hands (as with all mammals) are homologous to the digits on dinosaur forelimbs and the common ancestor to both mammals and dinosaurs had digits on the forelimb.

From: Evolutionary Genetics at http://www.zoology.ubc.ca/~bio336/Bio336/Lectures/Lecture5/Overheads.html

    Analogues (Analogous Structures) cannot be traced back to a single structure in a common ancestor.  For example, the wings of an insect and the wings of a bird are not homologues, but are analogues; they cannot be traced back to a single structure on a common ancestor (thus, they have a different embryological origin).

• Understanding evolution requires the recognition of homologous anatomical structures.

Cladograms and the Reconstruction of Phylogeny

     If evolution has occurred (and it has), there must be a single phylogeny.  In this course we will normally not use “Trees of Life” or “Evolutionary Trees”, but we will primarily use cladistics (also called Phylogenetic Systematics) CHECK OUT THIS SITE (Journey into the World of Cladistics) to show relationships among organisms and thus reconstruct phylogeny based on these relationships.  We want to reconstruct evolutionary patterns.

     Cladograms are hierarchical branching diagrams that allow us to show shared derived characters that presumably relate organisms.  A cladogram is a testable hypothesis.  We can't test an “evolutionary tree”.  How can we ever know for sure that a particular organism is ancestral to another.A cladogram specifies particular derived characters that are either present, or not present, in the organisms being compared.

Cladogram showing the phylogenetic relationships of vertebrates (From: American Museum of Natural History: Understanding Cladistics at http://www.amnh.org/Exhibition/Fossil_Halls/cladistics.html).

     If derived characters are shared between two taxa, then cladistics argues that the two taxa are closely related.  Shared primitive characters do not reveal phylogenetic similarities.  Shared derived characters results in a cladogram that is monophyletic.  A monophyletic group includes the common ancestor and all the descendants of the common ancestor. From: Monophyletic Group at http://rainbow.ldeo.columbia.edu/courses/v1001/monophl.html

Polyphyletic groups do not share a common ancestor.

From:
Monophyletic Group at http://rainbow.ldeo.columbia.edu/courses/v1001/monophl.html

Paraphyletic groups exclude some of the descendants of a common ancestor.

From: Monophyletic Group at http://rainbow.ldeo.columbia.edu/courses/v1001/monophl.html

    How do we identify derived characters?  It is not always easy.  But………..when a new taxon originates, it inherits features from its ancestor.  These inherited characters are primitive characters. Features that arise for the first time in a new taxon are advanced characters or derived characters.  These derived characters unite organisms (or fossils) into closely related groups, but only if the derived characters arose only once in related groups.  If the derived characters arose more than once (in unrelated groups) then the features are not representative of closely related groups.

     In fact, evolutionary convergence is where derived characters have arisen more than once.  For example, wings in birds, insects, and bats.  These groups are not closely related, but share derived characters (wings).  Of course, if we recognize that these are analogous structures, rather than homologous structures, we know the derived character of possessing wings does not necessarily relate these organisms.  So, we only want to compare homologous shared derived characters to show phylogenetic relationships.  Convergent evolution of characters presents the greatest threat to cladistic analysis.  We must recognize that convergence has occurred.

     Only homologous shared derived characters provide evidence of natural (monophyletic) groups.

    A cladogram depicts monophyletic groups within monophyletic groups.  For example, warm bloodedness (endothermy) is ancestral (primitive) for Homo sapiens, but derived for mammals.  We can add other organisms into the hierarchical scheme without altering the basic structure.

    Therefore, a cladogram is a hypothesis of evolutionary relationships.
 

Parsimony

     If fewer steps in a cladogram provide an explanation of the derived characters, then we assume it is the correct cladogram.

    So, we start with the simplest hypothesis and consider it in the context of new or independent evidence.

HYPOTHESIS: CLADOGRAM
TEST: NEW OR INDEPENDENT EVIDENCE (i.e. we consider more derived characters and whether they fit the cladogram).

Bird, Dog, Bat example (see p. 118, figure 5.21 in Wicander and Monroe, 2000).

     Thus, cladograms are hypotheses.  They are more robust if they survive falsification attempts.  The addition of characters may result in the rejection of a certain cladogram (if the addition results in a character distribution which is not the most parsimonious).

     Can we really test a “tree of life” (“evolutionary tree”).  Isn't it more of a story, rather than a testable scientific hypothesis.

EXTINCTIONS

• Extinction is the disappearance of a species (or other taxon).  The species ceases to exist.
• Pseudoextinction: a species evolves into a new species, so not really due to the dieing off of a species (but that particular species ceases to exist).
• Terminal Exstinction: a species dies off but does not evolve into a new species, so this lineage is gone forever.
• Mass Extinction: the extinction of a very large number of species such that larger taxonomic levels (such as families and orders) become extinct.
• The most severe mass extinction to affect the organsims on Earth was the extinction event at the end of Permian time (at the end of the Paleozoic Era).  About 90% of all marine species were wiped out and about 70% of terrestrial species.
• The extinction at the boundary between the Cretaceous Period and Tertiary Period (at the end of the Mesozoic Era) (called the K/T Extinction Event) that wiped out the dinosaurs and many other groups was significant, but less severe than the end of Permian extinction event.
• Other severe mass extinction events occurred at or near the ends of the Cambrian Period (decimated the trilobites and they never completely recovered), Ordovician Period, Devonian Period, and Triassic Period.

EVIDENCE FOR EVOLUTION

     We have already discussed much of the evidence for evolution in the forgoing discussion, however, let's summarize the evidence here and discuss some aspects in a little more detail.

• Classification of Organisms: classifying organisms into groups based on their similarities.  A formal classification of organisms into major groups was devised by the Swedish naturalist Carolus Linnaeus (1707-1798) during the late 1700s.  The Linnaeus system of classification is

a hierarchical scheme, as one proceeds up the classification ladder the categories become more inclusive. Obviosuly Linnaeus used similarities of shared characters to relate organisms into groups, however, he believed in the immutability of species and thought his classification reflected God's plan, from simple primitive organisms to complex organisms with man at the apex.  However, the fact that organisms share many characters in common is a very good line of evidence for evolution.  Why would organisms share so many homologous characters if they were not related to a common ancestor?  The probablity is very low that such similar characters would evolve by chance and if by special creation, why would such similar body plans be present in so many organisms (particularly since some characters and body plans could have been made better for the niche that they occuppy if they were not the result of modification of an ancestral body plan)?

The Linnaean Classification Scheme:

Major Subdivisions                        Example

Kingdom                                        Animalia
  Phylum                                           Chordata
     Subphylum                                      Vertebrata
        Class                                                Reptilia
            Order                                               Theropoda
                 Family                                             Tyrannosauridae
                     Genus                                             Tyrannosaurus
                         Species                                            Tyrannosaurus rex

• Embryology: similarities in the development of embryos in the early stages for closely related organisms (for example: gill slits and tails in humans, that our ancestors possessed), with later divergence in the development.
• Comparative Anatomy:
• the comparsion of homologous structures among various organisms.  We have already discussed the idea that organisms that share homologous structures (like tetrapod limbs that have been modified as wings in birds, flippers in whales, and arms and hands in humans) should be related to a common ancestor that had that structure and that these structures have a similar embryological development.  Homologous structures have a similar structure, but the function may have been modified.
•  Analogous structures, on the other hand, cannot be traced back to a common ancestor that shared these structures and they do not have a similar embryological development.  Analogous structures are due to convergent evolution and are structures without a common origin, but funcion in a similar manner among organisms being compared (in most cases due to adaptation to a particular mode of life, i.e., niche).
• Vestigial structures or organs: structures or organs that are nonfunctional or only partially functionally (like the human appendix and wisdom teeth, whale and snake pelvises, horse toes and dewclaws in dogs).  These structures or organs may be fully functional in other organsims or were in the ancestors of organisms that have them.
• Biochemistry: The similarity of DNA, blood proteins, and other organic molecules among organisms must be related to organisms that share a common ancestor.
• DNA Molecule:
• From:  DNA Molecule - Two Views at http://www.accessexcellence.org/AB/GG/dna_molecule.html
• The four nucleotide bases in DNA.
• From: BIOL 1400 -- Lecture Outline 21 at http://www.accessexcellence.org/AB/GG/dna_molecule.html
• The similarity of DNA among organisms is considered by many as the strongest line of evidence in favor of evolution.
• Small scale evolution: examples: insecticide/antibiotic resistance (insects and bacteria), industrial melanization (moths).
• Fossils: The rock record shows that organisms have changed over time.  Fossils groups from the past show differences as compared to modern organisms.
• The farther back in time the more simple, less diverse, and different are the fossils as compared to modern organisms.
• The youngest rocks contain the fossils that are most similar to modern organisms and contain more complex and diverse forms.
• Mosaic Evolution and "Missing Links:
• Example: Archaeopteryx from the Jurassic Solnhofen Limestone - Link between dinosaurs and birds.  Has both reptilian and bird characteristics.  Archaeopteryx had the characteristics of a small theropod dinosaur, but had feathers, so is considered the first bird.

Archaeopteryx skeleton with feather impressions and reconstruction of a Jurassic scene with the crow sized Archaeopteryx capturing a meal (from:  Evolutionary Genetics at http://www.zoology.ubc.ca/~bio336/Bio336/Lectures/Lecture5/Overheads.html)