INTRODUCTION

     One of the goals of science is to recognize patterns and order in the natural world.  Are there patterns in the biota (sum total of all living organisms that have ever lived)?  Can we recognize any patterns that may be present and use the patterns to order the biota.  The answer to both of these questions is yes.  Can we use the patterns to help us understand Earth and biotic processes that account for the diversity of the biota.  Again, the answer is yes.

     The key to understanding the evolution and diversity of the Earth's 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 (evolutionary relationships).

TAXONOMY:  The classification of organisms (the science of classifying organisms).  A grouping of organisms is called a taxon (taxa, plural).  Taxonomy is not just naming groups of organisms - species and higher taxa reflect evolution.

ORGANIC EVOLUTION:  The change of organisms over time.  As Darwin (1859) put it: "Descent with modification".

DIVERSITY:  The different types of organisms.  Diversity of the biota (all organisms alive and extinct) is measured both in time and in space.  Diversity in time is reflected by evolutionary change.  Diversity in space is reflected by the geographic distribution of organisms (biogeography).

BIOGEOGRAPHY:  The geographic distribution of organisms.  For ancient organisms we use the term PALEOBIOGEOGRAPHY.

SYSTEMATICS:  Refers to the combination of the above.  Systematics goes beyond just traditional taxonomy (naming and classification of organisms).  Systematists (scientists who study systematics) look at past and present geographic distributions of organisms (biogeography and paleobiogeography), diversity of both modern organisms and past organisms, evolutionary history, and the total pattern of natural diversity to provide the basic framework for all of biology and paleontology.

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 connect 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 organism).  Thus, shared characters among organisms are important in classifying them as belonging to group of related organisms.

     General Characters (also called 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 and both birds and frogs inherited a backbone from a common ancestor that had a backbone).  Specific Characters (also called derived characters) 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).
 

PHYLOGENY, HEIRARCHY, AND CLADISTICS ( Journey into the World of Cladistics)

     Cladistics (also called Phylogenetic Systematics) is a form of systematics that attempts to determine the phylogenetic relationships of organisms based on unique shared characters.  Cladists construct cladograms.  Cladograms are branching diagrams to show a hierarchical distribution of shared characters.  To construct cladograms we used 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.  Biologists define species as a population of naturally interbreeding organisms (in other words, members of the same species share a common gene pool).  Of course, paleontologist cannot use this definition directly. Paleontologist define morphologic species. A morphologic species (morphospecies) is defined by similarity of anatomical or morphological characters within a fossil group.  

     So the manner in which organisms are related is defined as their phylogenetic relationships.
 

Organic Evolution

     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", however, this expression is often misunderstood.  Survival of the Fittest really means that the organisms that survive to reproduce or reproduce more offspring than other members of their species will selectively pass on more of their traits to their offspring (thus a change will occur in the gene frequencies of the gene pool, thus evolution will take place).  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.  Paraphyletic groups are groups that do not include all the descendants of a common ancestor.

From: http://www.ucmp.berkeley.edu/glossary/gloss1/phyly.html   

      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 and have descended from a common ancestor. Therefore, Organic Evolution is a Fact.  Overwhelming evidence supports the Darwin-Wallace Theory of Evolution by Natural Selection.  Thus, natural selection is the means by which evolutionary change takes place.  [Note:  Creationist jump on the debate about evolution by scientists, but scientists argue the mechanisms and rates of evolution, not whether evolution has occurred].

     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 (or homologies).  Thus, homology refers to two or more features that share a common ancestry.

     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.

    Analogues (Analogous Structures) perform a similar function in two different organisms, but may or may not trace back to a common ancestor.  For example, the wings of an insect and the wings of a bird are not homologues, but are analogues; they also cannot be traced back to a single structure in a common ancestor (thus, they have a different embryological origin).  Homoplastic structures look similar, but may or may not be analogous or homologous.  Sometimes organisms evolve structures that look similar to structures in other organisms, but these structures cannot be traced back to a similar structure in the ancestors of two different organisms; the structures may also not perform the same function in two different organisms, although they may look superficially similar.  One example of homoplasy is when organisms evolve structures that mimic the structures on other organisms (like large spots on the wings of a moth that resemble eyes, perhaps to fool a potential predator).

     Understanding evolution requires the recognition of homologous structures (including homologous molecular structures).

   Obvious (but often ignored) evidence of evolution is the hierarchical distribution of homologous characters in nature.  Some homologous characters are present in all organisms (such as DNA and/or RNA and cell membranes).  Some homologous characters are present in smaller groups.  And some homologous characters are very restricted to small groups.
 

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) (a good web 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. (Here is another good web site dealing with cladistics  Lecture 6 - Cladistics )

     Cladograms are hierarchical branching diagrams that allow us to show shared derived characters (synapomorphies) 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.

     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.  Polyphyletic groups do not share a common ancestor.

    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 (plesiomorphs).  Features that arise for the first time in a new taxon are advanced characters or derived characters (apomorphies). 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 in different distantly related organisms.  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 (pleisomorphic) for Homo sapiens, but derived (apomorphic) 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.
 

Let Us Try to Construct a Cladogram

     The first thing that we want to do to show the evolutionary relationships of a group of organisms is to choose characters and construct a character matrix.  For example, let us choose the following organisms for which we want to show the evolutionary relationships: a clam (bivalve), a shark, a bluegill (fish), a salamander, an iguana (lizard), an alligator, a crow (bird), a racoon, and a human.  Now let us choose the characters that we are going to use to show the evolutionary relationships.  We will choose the following characters: backbone (vertebral column or possession of vertebrae), bony skeleton, four limbs (2 pairs of appendages with digits at the end - the tetrapod condition), amniotic egg (egg with membrane and/or mineralized shell around an amniotic fluid that baths the embryo), hair, two openings in the skull behind the eye socket, and an opening in the skull in front of the eye socket (antorbital fenestra).  Now we will construct a table (matrix) of the taxa versus the characters.  If the organism has the character (derived condition) we will place a 1 in the appropriate box, but if it doesn't (primitive condition) we will place a 0 in the box.
 

     Now that we have a character matrix for the chosen taxa, we can construct a cladogram that clusters the taxa that have shared derived characters.
 

     Now we have a cladogram that is a hypothesis of the evolutionary relationships of the organisms that we have chosen.  Notice that the alligator and crow have a more recent common ancestor than the alligator and iguana, therefore, the alligator and the crow are more related in an evolutionary sense than is the alligator and iguana.  The clam does not share any of the derived characters (that we have chosen) with the other taxa and is considered the outgroup (for fixing {polarizing} the derived characters).  We could choose other characters to separate the human and racoon (like opposable thumb and large brain for humans and not for the racoon), however, this is not necessary just to group them together (as we see from the above cladogram).  We could also choose other characters to separate the alligator from the crow (like possession of feathers for the crow and not the alligator), but again, this is not necessary at this stage.
 

Parsimony

     If fewer steps in a cladogram provide an explanation of the derived characters, then we assume it is the correct cladogram until we have evidence to the contrary.   So, we start with the simplest hypothesis and consider it in the context of new or independent evidence (such as adding new characters or new taxa to our cladogram).

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

     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). 

     Now let us test the cladogram that we have presented above.  Let us predict that the Late Jurassic meat-eating (theropod) dinosaur Allosaurus is more closely related to the crow (thus birds) than to the alligator. We will look at the characters that we have already looked at, but we will need to add some more characters to test this hypothesis.  So, let us add Allosaurus to our table with the new characters added also.  We we will add the following characters: hole in the hip socket, 4th and 5th fingers on hand lost,  and three-toed foot (with digits 2, 3, and 4).
 

     Based on the additional characters that we have added, our original hypothesis is supported by the new data.  Thus, based on the data we have looked at, we would conclude that Allosaurus has a more recent common ancestor with the crow than with the alligator. Our cladogram now may be modified to include Allosaurus.

Other Methods of Determining Phylogenetic Relationships

Phenetic Phylogeny

     Until recently (the last couple of decades) most biologists and paleontologists used a method of phylogenetic analysis known as phenetic phylogeny.  In phenetic phylogeny comparisons are made between  taxa based on overall similarity.  Both primitive (plesiomorphic) and derived (apomorphic) characters are used in this method.  Whether characters are homologues or analogues is basically ignored.  Computers are used to compare a large number of randomly chosen characters (usually 50 or more).  The characters are clustered using coefficients of similarity among different taxa.  From this the phylogeny is constructed.  This method is objective and repeatable, but may not always show the best evolutionary relationships.
 

TAXONOMY

      Taxonomy is the process of classifying organisms into groups based on their similarities and of naming organisms.  Our present system of classification of organisms into major groups was devised by the Swedish naturalist Carolus Linnaeus (1707-1798).  The Linnaeus system of classification is a hierarchical scheme, as one proceeds up the classification ladder the categories become more inclusive.

Major Subdivisions                        Example

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

Binomial Nomenclature

     Linnaeus also said each organism should have two names (a binomen) to define it, the generic (genus) name and the specific (species) name.  For example, Tyrannosaurus rex or Homo sapiens (modern man).  Linnaeus, although not trying to show evolutionary relationships, lumped organisms that had similar traits into the same groups.  Of course, this implies phylogenetic relationships.

     Modern biologists and paleontologists use cladistics to relate modern and fossil organisms in an evolutionary sense (i.e., determine their phylogenies).  They still name organisms based on the Linnaean system and may place their phylogenetic groupings into the Linnaean hierarchy.  However, biologists and paleontologists recognize the arbitrary nature of the Linnaean categories (for example, some dinosaur paleontologists might refer to Saurischia as an order of the Dinosauria, whereas others may consider it to be a superorder), and thus may prefer that groupings on cladograms not be placed in formalized Linnaean categories.  On the other hand, some biologists and paleontologist do prefer to use the Linnaean system, once the evolutionary relationships have been worked out using cladistics.

    However, biologists and paleontologists always name organisms at the genus and species level according to the Linnaean system and must follow international codes of zoological and botanical nomenclature (for example, the International Code of Zoological Nomenclature. The International Code of Zoological Nomenclature provides the rules that must be used when naming animals (a similar code exists for naming plants).  Names at the genus and species level are latinized and italicized (or underlined).  Particular endings are required for different Linnaean categories (for example: order usually has the suffix “a”; family has the suffix “idae”, etc.).  However, there is much freedom in the naming of organisms. For example: a big carnivorous dinosaur found by John Osborn in 1905 in Montana [that was different than all other carnivorous dinosaurs known then] was named Tyrannosaurus rex, meaning Tyrant Lizard + King or King of the Tyrant Lizards (Note: This is the type specimen for T. rex, to which all others must be compared, and is now housed at the Carnegie Museum of Natural History in Pittsburgh).

     Priority of the name is another rule of naming organisms.  No two different organisms (extant or extinct) can have the same scientific name (binomen).  Also if two organism belong to the same taxon, they cannot be given different names; the one that was named first is the correct name.  For example, the Yale paleontologist O.C. Marsh in 1877 named a partial sauropod dinosaur skeleton (found in Colorado) to the genus Apatosaurus (deceptive + lizard).  A couple of years later (1879) he found an almost complete skeleton of a sauropod dinosaur in Wyoming and gave it the genus name Brontosaurus (thunder + lizard).  Many years later, it was determined by paleontologists that the two skeletons were of the same creature, thus Apatosaurus was ruled to be the correct genus name by priority.
 

 DIVERSITY OF LIFE ON EARTH

Introduction

     Life started as quite simple organisms, basically as a cell membrane enclosing some cytoplasm (cell fluid) and DNA (or RNA in some simple forms).  Over time, life on Earth has evolved into an extremely diverse array of organisms.  Starting as simple prokaryotic single-celled organisms sometime between about 4 billion years ago and about 3.5 billion years ago, that were no doubt heterotrophic and anaerobic, life has evolved diverse metabolic mechanisms and survival strategies, from simple one-celled organisms into complex multicelled organisms.  By 3.5 billion years ago, prokaryotes similar to todays Cyanobacteria had evolved into photoautotrophs that were capable of making their own food by photosynthesis and expelling molecular oxygen as a waste byproduct.   By about 2 billion years ago, prokaryotes evolved symbiotic relationships that ultimately led to the eukaryotic cell.  With the larger eukaryotic cells also came the ability to reproduce sexually and thus allow for more variation in the offspring, thus creating variants that natural selection could work on more effectively to evolve new species.  Sometime around 1.2 billion years ago, some colonial eukaryotes were experimenting with multicellularity to form various types of algae and by approximately 700 million years ago primitive multicelled animals were present on Earth.  With multicellularity, three basic and different lifestyles evolved to gain nutrients from the environment, plants photosynthesize to make their own food, fungi absorb nutrients from their environment, and animals ingest nutrients (usually other organisms). 

Prokaryotes

• Bacteria (Eubacteria)
  • Some are autotrophs: photoautotrophs (ex. Cyanobacteria) and chemoautotrophs (ex. nitrogen fixing bacteria)
  • Heterotrophs - many of the harmful bacteria
• Archaea (Archaebacteria)- grow only in anaerobic environments (like the atmosphere of the young earth.
  • Thermophiles - hot springs 70-75 degrees Celsius (160 deg. F), hydrothermal vents on sea floor - 100 deg. C (212 deg.F)
  • Halophilic - salt-loving.  briney stagnant lakes.
  • Methanogens - produce methane gas as a byproduct of anaerobic respiration - swamps, stomachs of ruminants, etc.

Eukaryotes (Protists, Plants, Fungi, and Animals)

    Protists

• Protists (not monophyletic) - some are photosynthetic and some are not.  Most are unicellular, but some are multicellular.
• Algae - red, brown, and green.  Photosynthetic.   Make up much of the phytoplankton - phytoplankton are the base of the food web in both marine water and freshwater ecosystems.
• Sarcodina - amoebas and foraminifera (forams).  Forams are like amoebas with a calcium carbonate exoskeleton surrounding their protoplasm.
• Flagellates - protists with a whiplike flagellum (aids in locomotion).

    Plants

• Plants arose from green algae during the Silurian period (or perhaps late Ordovician).
• Had to overcome desiccation and gravity to move onto land.
• Root and shoot system evolved.  Roots anchor plant and find water in nutrients in the soil.
• Shoot system (with leaves) collects carbon dioxide and sunlight for photosynthesis.
• Shoot system covered by waxy layer (cuticle) to help prevent desication.
• Walls of cells are often reinforced with lignin for additional support.
• Most plants have a vascular tissue (like a circulatory system) to bring water and nutrients to the shoot (above ground portion) and sugars from the shoot to the roots.
• Reproduction - alternation of generations. Sporophyte (2n) and Gametophyte (n) generations.

  Bryophytes (mosses)

  • most lack vascular tissues, true roots and lignin in their cell walls.  Spores. Live in damp, shady places. Common even in near polar environements.

Pteridophytes (ferns and related forms)

• Evolved by late Devonian time (about 360 million years ago).
• seedless vascular plants.  Rhizosome. Fronds.  Spores.
• Prominent alternation of generations.
• During the late Paleozoic (Mississippian and Pennsylvanian Periods in particular) formed great forests in the tropics.  Lignin and vascular tissue for support, allowed some to reach heights of 120 feet.  Lycopods (Lepododendron and Sigillaria - scale trees) - prolific in the great coal swamps of the Carbonifierous.

The Vascular Seed Plants (Gymnosperms and Angiosperms)

• The Seed - small capsule with a seed coat, plant embryo (fertilized zygote), and supply of nutrients.  Different approach for dispersal than the spore, however, spores may survive extremes of temperature and moisture also.
• Seed plants also produce pollen (a much reduced male gametophyte).  Some of the cells in the pollen develop into sperm.  Pollen grains are also very resistant to extremes of temp. and moisture.  

Gymnosperms (conifers and related forms, pine, fir, redwood, spruce, cedar, and juniper)

• First true seed plants to evolve.
• Evolved during early Carboniferous (Mississippian Period)
• Began to rise to prominence in late Pennsylvanian time as swamps dried up and the climate became cooler and drier on the continents.
• The tree is the sporophyte generation.
• The scales of the cones are modified leaves.
• In female cones the scales protect the ovule, where the tiny female gametophyte develops and forms eggs.
• The male gametophyte in located in the male cones and produces pollen grains that contain sperm.
• Pollination - the pollen falls onto the female cone and produces sperm that enters the ovule and fertilizes the egg.
• The ovule forms the seed - with protective coating, nutrients, and the plant embryo.

Angiosperms (flowering vascular seed plants)

• Evolved in the early Cretaceous Period of the Mesozoic Era.
• Became the dominant land plants by late Cretaceous.
• Flowers distinguish angiosperms from all other plants.
• Flower is modified leaves.
• Stamen (female organs), Carpel (male organs).
• Pollinators (most often insects) are attracted to  the flower and transfer pollen from one flower to another (however, self-pollination may occur in some species).
• Pollen is produced in the Anther, pollen grains are the male gametophyte.
• Pollen sticks to the Stigma of the Stamen and sperm travel down the Style into the Ovule to fertilize the egg.
• A second sperm fertilizes another female cell which develops into endosperm (that contains nutrient for the embryo) within the ovule.
• The swollen base of the carpel is the ovary with holds the eggs.
• After fertilization, the ovary ripens into fruit.

 

Fungi

• Not plants.  Fungi are heterotrophs.
• Contain chitin (nitrogen containing polysaccharides) in cell walls as supporting material.
• Absorb nutrients from the substrate to which they are attached.
• Secret digestive enzymes to dissolve the substrate, then they absorb the released nutrients.
• With bacteria, Fungi are the principle decomposers in the forest.
• Fungi are composed of cellular hyphae-thin filiments that allow free flow of cytoplasm through them.
• The Fruiting Body is the reproductive structure and the Myelium is the feeding network that permeates the substrate.

 

Animals