Organismal Biology — Notes

STUDY GUIDE and VOCABULARY
BIOLOGY / SCIENTIFIC METHODS / EVOLUTION

Biology: Biology is the science of living systems.   These systems exhibit metabolism, irritability, homeostasis, growth, population structure, reproduction, hereditary information, and mutability.   (See the vocabulary below for the meanings of these terms.) Science and its methods: Science is a method of inquiry based on formulating falsifiable hypotheses and then testing them vigously. Steps in the scientific method include: A problem is formulated (or a question asked). An idea is proposed Any idea (called a hypothesis) is proposed;  it must be falsifiable. The hypothesis is tested, vigorously and repeatedly. Some hypotheses are tested by experimentation in which an artificial test is contrived by a scientist and set up in order to test one or more hypotheses. This method is extensively used in chemistry, physics, physiology, and cell biology. Hypotheses can also be tested by naturalistic observation and comparison, taking advantage of variations in natural conditions to test hypotheses beyond the ability (or desire) of scientists to manipulate. This method is extensively used in astronomy, geology, ecology, and evolutionary biology. Any cluster of related hypotheses that has been repeatedly tested without falsification becomes a theory. Biological ideas before Darwin: In many folk tales, one species could quickly change into another, but Francesco Redi showed that flies developed from eggs and did not arise spontaneously. Local naturalists studied the species in their local area and came to recognize their discreteness (they didn't intergrade), their constancy (they did not arise suddenly, and their offspring resembled their parents), and their diversity. Divine order was commonly invoked to explain these findings. Before 1859, most scientists and philosophers insisted that species were fixed and unchanging. Most scientists also believed in the divine creation of each species. To explain diversity, most scientists before 1830 believed that Species were arranged in an unchanging, unbroken order of perfection, the Great Chain of Being (Scala Naturae).   This idea was used to justify the social order (hierarchy), class structure and social oppression, the "divine right of kings", "Man's place in nature", and, later on, racism, sexism, and the search for "missing links". Adaptation was usually attributed to divine benevolence. Lamarck tried to explain environmental adaptations by his theory of use and disuse. Geoffroy Saint-Hilaire explained adaptation by direct effects of the environment. Both Lamarck's and Geoffroy's theories rely upon inheritance of acquired characteristics, a concept later disproved by Weismann and others. Around the time of the French Revolution, social hierarchies (and monarchies) came into question. New ideas of the Enlightenment included "progress" and environmental determinism: Maupertius and Lamarck re-interpreted the Chain of Being as a time sequence; Lamarck described a unilineal sequence of change which he called "La Marche de la Nature." Lamarck and Geoffroy attributed adaptations to environmental influences; they both thought that species could adapt to their environments by changes occurring within individual lifetimes. Cuvier's used comparative anatomy to argue against the Chain of Being. Hutton and Lyell reformed geology, emphasizing slow change and immense time spans. William Paley ("Natural Theology") used adaptations as proof of God's existence. Darwin and Evolution: A voyage around the world aboard H.M.S. Beagle convinced Darwin of several facts that earlier theories could not explain: Different continents had very different species, even in very similar climates. Species sharing a land mass or island group were often related. Island species were usually related to those of the nearest continent. Similar environments did not always produce the same species or related species  (contrary to Lamarckism and Geoffroyism). Darwin's ideas developed among many lines: Reading Malthus' Essay on Population convinced him that overpopulation and competition could occur in any species. Observations of animal breeders showed him how artificial selection produced heritable changes within a few generations. His experiences with earthquakes and coral reefs on board the Beagle convinced him of slow change throughout geologic time. His work on barnacles helped him develop his ideas of branching descent. Wallace's letter led to the publication of the Linnaean Society papers (1858) In 1859, Darwin published On the Origin of Species, in which he developed two new theories: He explained diversity by branching "descent with modification". He explained adaptation by natural selection. Evidences for branching evolution ("descent with modification"): Patterns of common descent are reflected in classifications, forming "groups within groups". Related species share many internal similarities (anatomical, biochemical, or embryological homologies) despite different adaptations. These homologies may include vestigial remnants of once-useful parts. Similar adaptations often occur under similar circumstances, even in unrelated species (convergent adaptations). Related species often inhabit certain land masses or island groups. Fossils can often be arranged in evolutionary sequences. Some species vary from place to place, and the differences are inherited. Natural selection: All living species tend to over-reproduce. Most seeds, eggs, or hatchlings die without reproducing. All living species are extremely variable. Many of these variations are inherited. Inherited differences in survival and reproductive ability (natural selection) bring about change in each generation. Evidence for natural selection: All living species are highly adapted to their way of life. Many adaptations cannot be explain by environmental influence alone. Examples: Unrelated but ecologically equivalent species live on different continents. Some embryonic structures (e.g., a flap in the human heart that seals closed at birth) develop before they become useful. Some behavior (like bird migration or nest building) occurs in advance of its usefulness. Mimicry (see below) Some adaptations are less than perfect, contrary to an earlier theory that used perfect adaptation to prove divine creation. Natural selection has repeatedly been documented (e.g., among peppered moths in England), and has resulted in changes over time in natural populations. Artificial selection by animal and plant breeders has produced many new adaptations, some of them similar to adaptations occurring naturally. Mimicry and camouflage:   Many species gain protection against predators by resembling their background (camouflage) or by falsely resembling other species (mimicry). In Batesian mimicry, a palatable species resembles a distasteful or harmful one. Mullerian mimicry is resemblance among distasteful or harmful species. Mimicry works only when certain models are present, a fact explained easily by natural selection, but not by Lamarckism or similar theories, nor by theories of special creation. Mimicry may vary geographically, with the same mimic species resembling different models in different places. Natural selection can explain this; Lamarckism cannot. MICROEVOLUTION is evolution below the species level. It results from: Variation, brought about by mutation, chromosomal changes, and genetic recombination through mating. Variation is a prerequisite for selection. Selection, which occurs whenever the chances of leaving offspring differ among genotypes. Genetic drift and other random forces. Mating patterns, and the resultant gene exchange within and between populations. Restricted gene flow, combined with differences in selection, which can lead to geographic variation. Restricted gene exchange between populations, including reproductive isolation, which can lead to species formation (speciation). Variation Origins of variation: sources of variability Mutations, chromosomal variations Variations in phenotypic expression Chromosome numbers and chromosomal family trees Recombination and recombination systems Sexual & asexual reproduction Factors tending to reduce variation: selection genetic drift Persistence of variability: mechanisms that allow variation to persist despite selection and drift (see below) Genetic variation in populations. Hardy-Weinberg equilibrium Departures from Hardy-Weinberg: mutations (unbalanced) migrations nonrandom mating (assortment, inbreeding) genetic drift natural selection Genetic drift ("Sewall Wright effect"): In smaller populations, gene frequencies can fluctuate randomly in either direction simply by chance.     This also occurs for rare alleles in larger populations.     Important subtypes include:         - "Bottleneck effect" in populations temporarily small         - "Founder effect" among founders of a new population (e.g., Dunkers) Natural selection: All living species tend to over-reproduce. Most seeds, eggs, or hatchlings die without reproducing. All living species are extremely variable. Many of these variations are inherited. Inherited differences in survival and reproductive ability (natural selection) bring about change in each generation. Evidence for natural selection as a cause of evolution: All living species are highly adapted to their way of life. Many adaptations cannot be explain by environmental influence alone. Examples: Unrelated but ecologically equivalent species live on different continents. Some embryonic structures (e.g., a flap in the human heart that seals closed at birth) develop before they become useful Some behavior (like bird migration or nest building) occurs in advance of its usefulness. Natural selection can explain mimicry (see below). Some adaptations are less than perfect, contrary to an earlier theory that used perfect adaptation to prove divine creation. Natural selection has repeatedly been documented (e.g., among peppered moths in England), and has resulted in changes over time in natural populations. Artificial selection by animal and plant breeders has produced many new adaptations, some of them similar to adaptations occurring naturally. Types of selection: In all types of selection, genotypes contribute genes unequally to the next generation, either by differences in mortality and survival, by differences in mating success, or by differences in fertility and fecundity (leaving offspring). Natural selection is differential contribution by natural processes. The peppered moths of England, selected by predators (birds), are an example. Artificial selection is selection of captive species by humans. Sexual selection is selection based on success in mating. Selection against a dominant trait can eliminate the trait rapidly. Selection against a recessive trait works very slowly and becomes much less effective once the recessive allele becomes rare. Selection against heterozygotes can result in either allele becoming lost and the other taking over 100% of the gene pool. Selection favoring heterozygotes over both types of homozygotes results in balanced polymorphism in which both alleles persist indefinitely. Sickle-cell anemia is an example of this situation. Directional selection shifts the population mean. Examples shown in class include lizards (Aristelliger), corn, fruit flies. Disruptive selection increases population variance. Centripetal or stabilizing selection (very common) reduces variance (e.g., Bumpus' sparrows) Agents of selection: Artificial selection (by human agency) Natural selection (by natural agency) by predators by pathogens, parasites, & other diseases by starvation by environmental (climatic) extremes (of temperature, etc.) other physical agents: fire, landslides, etc. sexual selection Adaptation includes: Structural adaptations Biochemical adaptations Color & pattern adaptations:   camouflage, industrial melanism, mimicry Mimicry and camouflage: see above for details. MENDEL'S DISCOVERIES: Particulate inheritance (Mendel's "first law"): The determinants of heredity behave as particles (now called genes) that do not blend; they maintain their identity even when hidden or masked by other genes. Most genetic traits exist in dominant and recessive variants (alleles). Heterozygous individuals display the dominant phenotype. Independent assortment (Mendel's "second law"): The inheritance of one gene is statistically independent of other genes; we now know that this is true only for genes located on different chromosomes. GENES IN POPULATIONS: Hardy-Weinberg law:   Large, random-mating populations will, under certain assumptions, reach a genetic equilibrium in which genotypic proportions tend to remain constant. These assumptions include: no unbalanced mutation, no unbalanced migration, and no selection of any kind.   Equilibrium frequencies under these conditions are given by the equation p2 AA + 2pq Aa + q2 aa = 1 or, more simply, p2 + 2pq + q2 = 1 p stands for the frequency of A; q for the frequency of a;   p + q = 1 p2 is the frequency of AA homozygotes; gametes are all A 2pq represents the frequency of Aa heterozygotes.     Half of their gametes (pq) are A, the other half are a. q2 is the frequency of aa homozygotes; gametes are all a To find the new frequency of allele A, add p2 + pq = p (p + q) = p (1) = p, so the frequency of allele A remains p. To find the new frequency of allele a, add pq + q2 = q (p + q) = q (1) = q, so the frequency of allele a remains q. A Hardy-Weinberg equilibrium can be established in a single generation of random mating. Exceptions to the Hardy-Weinberg law: If the population is not large, genetic drift occurs: gene frequencies can fluctuate randomly in either direction simply by chance. Populations may not mate at random. Inbreeding (increased mating among related individuals) results in more homozygotes. Assortative mating is mating according to phenotype, with mating between phenotypically similar individuals being either more frequent (positive assortment) or less frequent (negative assortment). Mutation in only one direction can cause one allele slowly to replace another. Mutation in both directions results in an equilibrium with frequencies determined by the mutation rates. Migration between populations always causes the gene frequencies of the receiving population to shift towards those of the immigrants. Selection occurs whenever different genotypes contribute genes unequally to the next generation. Persistence of variability: Importance of maintaining variability Forces that erode variability: natural selection; genetic drift Maintaining variability cytologically Negative assortment Selection by pathogens/parasites and "rare male" effects Difficulties of selecting against rare alleles Maintaining variability ecologically: polymorphism; maintaining balanced polymorphism (balanced disadvantages, seasonal differences, habitat differences, etc.) Measuring genetic variability in populations; electrophoresis Neutral gene theory, etc. Geographic variation: Natural selection in different environments causes populations to differ. Gene flow reduces the opportunities for populations to differ; restricted gene flow allows enhanced differences. Populations of some geographically widespread species may differ so much that they may become unable to interbreed. If barriers to breeding accompany differences in visible traits, the species may become divided into subspecies. Continuous geographic variation is usually described in terms of clines (character gradients across a map). Geographic variation is usually the first step in species formation. SPECIES AND SPECIATION (THE MODERN SYNTHESIS OF EVOLUTIONARY THEORY): Species are evolutionary units within which gene flow occurs. Natural populations belong to the same species only if they can interbreed and leave fertile offspring. Different species are reproductively isolated from each other. Most new species originate geographically. Hugo DeVries and the Mutation Theory (1903) Controversy, 1900-1940 Resolution: Population genetics: Fisher (1930), Wright, Haldane Studies of geographic variation: Dobzhansky, etc. "Modern Synthesis":  Huxley (1940, 1942), Mayr (1942) Importance of species: Species characteristics are passed from parents to offspring. Species were long considered real and important because these characteristics seemed to be constant and unchanging. Morphological (typological) species definition: Each species is defined by characteristics thought to be "essential" or "typical". (Problems arise under this definition with sexually dimorphic species and with sibling (cryptic) species.) Biological species definition: Species are groups of interbreeding populations that are reproductively isolated from other species. reproductive isolation reproductive isolating mechanisms (premating, postmating) example: mallards and pintails sibling species, e.g., Drosophila pseudoobscura and D. persimilis Reproductive isolating mechanisms that act prior to mating: Ecological isolation: Potential mates do not meet because they live in different habitats or breed at different times or seasons. Behavioral isolation: Mating calls or mating rituals differ. Mechanical isolation: "Lock and key" mismatch of genitalia. Reproductive isolating mechanisms that act after mating: Gametic mortality: Gametes die before fertilization. Zygotic mortality: Fertilized eggs fail to divide properly. Embryonic or larval mortality: They die prematurely. Hybrid inviability: Hybrids never reach reproductive age. Hybrid sterility: Hybrids cannot reproduce, as in mules. F2 breakdown: Offspring of hybrids are inviable. Geographic variation: Natural selection in different environments causes populations to differ. Gene flow reduces the opportunities for populations to differ; restricted gene flow allows enhanced differences. Populations of some geographically widespread species may differ so much that they may become unable to interbreed. If barriers to breeding accompany differences in visible traits, the species may become divided into subspecies. Continuous geographic variation is usually described in terms of clines (character gradients across a map). Geographic variation is usually the first step in species formation. Importance of geographic variation Occurence of (or absence of) geographic variation Gene flow at habitat boundaries (ecotones) example: mine entrances (Antonovics) Altitudinal "races" Clines Insular & continental patterns Subspecies and polytypic species; pocket gophers and other examples What is speciation? Phyletic transformation (anagenetic; no new RIM) True speciation or splitting (cladogenetic; new RIM must evolve) Geographic speciation: Most speciation occurs geographically. Stages of geographic speciation: A species develops geographic variation over its range. Geographic barriers prevent contact between populations. Reproductive isolation may now evolve. Geographic isolation ends, with two possible outcomes: No reproductive isolation-- still a single species. Reproductive isolation is effective-- two species now exist; selection will enhance differences between them. Incomplete speciation: clines of reproductive isolation (e.g., Rana pipiens) clines with circular overlap (e.g., Parus major,   Ensatina) species in statu nascendi (e.g., Drosophila paulistorum) "Semigeographic" or "parapatric" speciation if adjacent ranges touch. Character displacement Many other models of speciation have been proposed; some are now rejected; some are still controversial:     Phyletic transformation (anagenetic; no new RIM)   and the problem of allochronic species     True speciation or splitting (cladogenetic; new RIM must evolve): SUDDEN speciation: Genic, by "mass mutation" or "hopeful monster" (DeVries, Goldschmidt)-- rejected because does not produce new species Chromosomal, by aneuploidy, etc. (M.J.D. White)-- no longer supported-- rejected because does not produce new species Polyploidy:   doubling or tripling of chromosome number in plants. GRADUAL speciation: Sympatric speciation (sometimes claimed, but controversial; few believers) Nonsympatric speciation (spectrum of possibilities): Parapatric or "semigeographic" speciation if adjacent ranges touch Alloparapatric (begins allopatric, becomes parapatric) Allopatric or Geographic— the prevaling model by crossing pre-existing barriers with new barriers developing by extinction of intervening populations in a cline ?Symparapatric or "stasipatric"-- (sometimes claimed, but controversial; few believers) Hybridism and polyploidy hybridism and its effects speciation by polyploidy MACROEVOLUTION and the FOSSIL RECORD: Evolution above the species level (macroevolution) consists of two distinct processes: changes within a lineage (anagenesis) and the branching of lineages (cladogenesis). Evolutionary trends are adaptive and are usually opportunistic, following no plan or goal but rather taking the path of least resistance. Cladogenesis fills the biosphere with an ever-increasing number of species, arranged into classifications which reflect descent. Species that fail to adapt to changing conditions become extinct. The geological time scale divides the last ~530 million years into 12 periods. Fossils differ in the degree to which smaller structural details are preserved and in the degree of chemical alteration of the original material. The fossil record allows us to test various evolutionary theories against the actual long-range history of life on Earth. Lineage: An ancestor-to-descendent sequence of species. Trend: Continued morphological change within a lineage. Parallelism: Independent occurrence of the same or similar trends in different lineages. Convergence: Similar adaptations in unrelated lineages. Cladogenesis: The branching of lineages by speciation. Anagenesis: Evolution within a lineage, between branching points. Evidence for the adaptiveness of trends: Trends often persist for a long time. Parallel trends often occur independently. Evolutionary rates vary: trends speed up or slow down; they may even stop altogether or reverse direction. Trends in different characters do not always go together but occur independently (mosaic evolution) and at different rates and times. For this reason, transitional species like Archaeopteryx are a mosaic of primitive and advanced features mixed together. Opportunism: Evolution follows no plan or goal, but instead takes the path of least resistance. Cladogenesis fills the biosphere with more and more species (and niches). Diversity among the descendents of a single species (adaptive radiation) often results. Functional problems are often solved differently in different lineages (multiple solutions, such as diversity among eyes). The same trend often occurs repeatedly (iterative evolution). Convergence (and its imperfections) show that similar adaptive opportunities may arise independently more than once. Organs that change function usually serve both old and new functions simultaneously during the transition. Rates and modes of evolution: Evolutionary rates may measure either anagenesis or cladogenesis or both. Rates calculated in different ways are usually not comparable. Since Darwin, most evolutionists have viewed evolution as a continuous, gradual process. Many scientists now view evolution as a series of steady equilibria punctuated by infrequent episodes of very rapid change (the punctuated equilibrium theory). Results of evolution: The results of macroevolution can be seen in the diversity among species that is reflected in their anatomical structure and in our classifications. These results include: Adaptations: Features which help organisms cope with and exploit their environments. Analogy: Similarity among species resulting from adaptations to similar functional requirements. Homologies: Deep-seated resemblances reflecting common ancestry, often despite adaptive differences. Evolutionary classifications: Descent with modification results in classifications that contain groups within groups; these groups have always been considered "natural," even by pre-evolutionary taxonomists. Whenever new technology allows new types of variation to be studied (e.g., DNA sequences), most variation follows the groups established by earlier methods. Extinction: Species that cannot adapt to change become extinct. Extinction may come either early or late in the history of a group. Extinction may occur at times of either low or high diversity. Some paleontologists believe that rates of speciation and extinction tend to be approximately equal for many large groups. Geologic time scale: The Earth is about 4.6 billion years old, but only the last (approximately) 530 million years is well documented by fossils. Precambrian Era (up to about 530 million years ago, sometimes divided into Azoic and Archaeozoic): Includes the earliest fossils, about 4.2 million years old. Precambrian fossils are very rare; most are microscopic fossils of procaryotic organisms. Palaeozoic Era (up to about 250 million years ago): The time when invertebrates dominated the oceans and when fishes, insects, amphibians, and land plants first flourished. Divided into 7 periods: Cambrian (oldest) Ordovician Silurian Devonian Mississippian (=lower Carboniferous) Pennsylvanian (=upper Carboniferous) Permian (most recent) Mesozoic Era (up to about 65 million years ago): Sometimes called the "Age of Reptiles" because dinosaurs and other large reptiles dominated the land while marine reptiles (and ammonoid mollusks) flourished in the seas. Mesozoic time is divided into 3 periods: Triassic (oldest) Jurassic Cretaceous (most recent) Cenozoic Era ("Age of Mammals"): The last 65 million years, divided into 2 periods: Tertiary (from about 65 to 2 million years ago) Quaternary (the last 2 million years, including Pleistocene and Recent epochs) Fossils and Paleontology Paleontology: The study of fossils. Fossils: Remains or other evidence of life of past geologic ages. Fossils containing original material: Unaltered remains. Example: frozen mammoths Compressions: Flattened and dehydrated, but unaltered otherwise, with cellular details often preserved. Replacement fossils (with original material largely replaced): Permineralization, impregnation, and embedding: Gradual addition of minerals by ground water, preserving many internal details. Carbonization: Volatile compounds lost, leaving carbonized skeleton only. Mineralization: Complete replacement of original material by minerals. Casts and molds: Impressions in fine-grained sediments, preserving only surface shapes. Casts are solid objects; molds are hollow. Trace fossils: Tracks, trails, footprints, burrows, and other traces of activity. Examples: Amber (fossil tree sap or resin); coprolites (fossil dung). Lessons learned from studying the fossil record: The fossil record can be used to test various theories against the actual record of life on Earth. No proposed theory or evolutionary mechanism is acceptable if it conflicts with this historical record. The fossil record shows a historical process of branching and diversification, not just a single linear sequence. "Evolution is a bush, not a ladder." Cope's rule: Size increases frequently and decreases far less often. Williston's rule: Repeated parts (like multiple legs or segments) often become less numerous and more different from one another. Dollo's law: Like other historical processes, evolution never repeats itself exactly. Because of probability considerations, small, simple changes may reverse, but larger and more complex changes never do. Evolution is thus constrained (limited) by its own history. ORGANIC DIVERSITY AND TAXONOMY: Biological diversity is expressed by arranging organisms into kingdoms, phyla, classes, orders, families, genera, and species. These groups reflect evolutionary history and common ancestry as much as possible. Evolutionary relationships responsible for these arrangements are often depicted in family trees. The aim of phylogenetics is to reconstruct family trees and base classifications on them. Binomial nomenclature: Each species has a two-word name. The first word (capitalized) is the name of the genus; the second (lower case) is the name of the species. Example: Homo sapiens. The Linnaean system: Uses binomial nomenclature throughout. Species are grouped into genera and genera into higher groups. Any one of these groups, at any level, is called a taxon (plural, taxa). The complete Linnaean hierarchy (ranking) of groups is as follows: Kingdom (the most inclusive group)     Phylum (plural, phyla, sometimes called a "division" in plants)         Class             Order                 Family                     Genus (plural, genera)                         Species (same spelling in both singular and plural) (Mnemonic: "King Philip Came Over For Good Soup") Extra ranks are added to this hierarchy as needed, such as subphylum (just below phylum) or superfamily (just above family). Example: Humans belong to the Kingdom Animalia, Phylum Chordata, subphylum Vertebrata, class Mammalia, order Primates, family Hominidae, genus Homo, species Homo sapiens. Phylogeny: A family tree of species. Phylogenetics: The study of family trees. Phylogenetic methods use both the fossil record and resemblances among living species as evidence to reconstruct phylogenies. Species sharing many similarities are considered to be descendents of a common ancestor that also shared these similarities. When conflicting evidence arises from different characters, further study is undertaken to see whether some of the similarities could have evolved by convergence. An important task in phylogenetics is therefore recognizing homology (resemblance due to common ancestry) and distinguishing it from analogy or convergence. The aim of classification based on phylogenetics is to group together those species that derive their similarities from a common ancestor. That means that, insofar as possible, each taxon should be made monophyletic by including the common ancestor within the taxon. Taxonomy is the theory behind the making of classifications. Phenetic taxonomy: Classifications based on resemblance alone have long been in disfavor because they do not distinguish convergence from other causes of resemblance. Phylogenetic taxonomy: Modern classifications are based on phylogenetics, meaning that species that share a common ancestry are grouped together as much as possible. Strict adherence to this principle is the basis of cladistics. Cladistic taxonomists construct family trees first, then base their classifications strictly on the geometry of branching, ignoring such matters as the diversity or degree of change within each branch. Monophyletic group (clade):  A group which includes a single ancestor and all of its descendants (a natural group). Paraphyletic group: A group which includes a common ancestor and some but not all of its descendants (an incomplete group). Polyphyletic group: An unnatural group whose common ancestor is not part of the group. Plesiomorphy: A primitive trait, possessed by an ancestor. Symplesiomorphy: A shared plesiomorphy, often defining a paraphyletic group. Apomorphy: A derived trait, possessed by a descendant but not by an ancestor. Synapomorphy or homology: A shared trait, derived from a common ancestor, thus defining a monophyletic group. Homoplasy: A misleading resemblance (such as a convergence), defining a polyphyletic group. Evolutionary (phylogenetic) classification is based on branching descent: Biological classification reflects the results of a branching evolutionary process. Insofar as possible, classifications should be genealogical. Each taxon should ideally represent one branch of the evolutionary tree, with the smaller included taxa representing its sub-branches. Three domains and six kingdoms: Most biologists now arrange organisms into three domains containing six kingdoms: Domain Archaea contains only the Kingdom Archaebacteria, a group of oxygen-intolerant procaryotes with RNA sequences different from those of all other organisms. Domain Bacteria (or Eubacteria) contains only a single kingdom of the same name, including the majority of procaryotes. Domain Eucarya contains four kingdoms of eucaryotes: Kingdom Protista: Simple eucaryotes, generally one-celled, containing neither tissues nor embryos Kingdom Mycota: Fungi, with cell walls but no plastids. Kingdom Plantae: Plants, containing plastids and chlorophyll. Kingdom Animalia: Multicellular animals, developing from blastulas. Things to know and explain: Explain the general characteristics of living systems. Explain the role of hypotheses, experimentation, and naturalistic observation in the scientific method. Explain how early naturalists thought about species, their constancy, and the reasons for their diversity. Explain how Darwin confronted these earlier ideas in order to establish his new theories. Describe Darwin's theory of evolution, and how it differed from earlier ideas such as Lamarck's. Describe some of the evidence used by Darwin to support his theory. Explain the concept of natural selection and the evidence showing how it works. Describe artificial selection and compare its results with those of natural selection Describe the importance of variation as preceding selection Describe the Hardy-Weinberg equilibrium Perform simple calculations using the Hardy-Weinberg equation Describe changes that happen when equilibrium conditions are not met Describe the changes brought about by selection in populations over time Describe the principal phenomena contributing to evolution below the species level Describe genetic drift and its effects over time Explain some of the factors that lead to geographic variation within species Define species according to the biological species concept Explain the relationship between species and reproductive isolation Distinguish among several types of reproductive isolation Explain the theory of geographical speciation Explain the major processes that result in ongoing change (anagenesis) and branching (cladogenesis) Explain some of the reasons for evolutionary trends and for opportunism Describe several types of fossils Describe some of the highlights of the history of life on Earth Describe Dollo's law and a few other lessons learned from the fossil record Describe how evolution results in organic diversity Describe some of the modern methods used to construct family trees and classifications Describe how biologists classify species into taxonomic groups based on family trees VOCABULARY TO KNOW:         Biology:   The science of living systems.         Metabolism:   The ability to take in energy-rich matter from the surroundings, convert this matter into lower-energy material             which is discarded, and use the energy provided.         Selective response (irritability):   The ability to respond to certain stimuli but not to others.         Homeostasis:   The ability to maintain tolerable conditions or to restore extreme conditions to within tolerable limits.         Growth and biosynthesis:   The ability to incorporate externally acquired matter into one's own body system.         Reproduction:   The ability of biological systems (especially organisms) to make others like themselves.         Hereditary information:   Information or arrangement that persists in the reproduction of biological systems.         Mutability:   The ability of hereditary information to change slowly over time.         Mechanism:   The belief that living systems are made of nothing more than nonliving ones, obeying only the laws             of physics and chemistry.         Vitalism:   The belief that living systems contain more than just physical-chemical materials and thus contain a "vital             principle" not subject to the laws of physics and chemistry.         Reductionism:   The belief that each level of complexity can be explained as the workings of the more detailed levels, or             that a science like biology can be "reduced" to a special branch of chemistry.         Compositionism (holism):   The belief that new principles and new phenomena (such as "life") emerge at each level of             organization that are meaningless or not explainable at the simpler levels.         Science:   A method of inquiry based on formulating falsifiable hypotheses and then testing them.         Hypothesis:   An idea to be tested.         Verifiable:   Capable of being shown to be true (or verified).   IMPORTANT: This doesn't mean that the idea is true, just             that you can specify what data or observations would make you to believe it to be true.         Falsifiable:   Capable of being shown to be false (or falsified).   IMPORTANT: This doesn't mean that the idea is false, just             that you can specify what data or observations would make you to believe it to be false.         Theory:   A cluster of related hypotheses that has been repeatedly tested without being falsified.         Paradigm:   A theory plus its special ("theoretical") vocabulary, customary methodology, values, and way of thinking,             along with the scientific community that supports it.         Evolution:   The process of long-term change in biological systems.         Acquired characteristics:   Changes in traits during the life of an individual, such as muscle enlargement with continued use.         "La Marche de la Nature" (Nature's Parade):   A unilineal (single-file) evolutionary sequence envisioned by Lamarck.         "Descent with modification":   A branching pattern of evolution proposed by Darwin.         Natural selection:   Unequal contributions of different variations (or genotypes) to future generations in nature.         Artificial selection:   Selective breeding of domestic species by animal and blant breeders.         Homology:   Similarity (resemblance) due to common ancestry or common origin.         Analogy:   Similarity (resemblance) due to similar adaptation, often despite different ancestries.         Vestigial:   Structures currently small and useless, but resembling once-useful structures in an ancestor or other species.         Convergence:   Independent evolution of similar adaptations (analogies) in unrelated lineages.         Mimicry:   False or deceptive resemblance of another species, often with selective advantage.         Model:   The species that a mimic resembles.         Batesian mimicry:   Mimicry in which a palatable species resembles a distasteful or harmful one.         Mullerian mimicry:   Mimicry in which distasteful or harmful species resemble one another.         Microevolution:   Evolution below the species level.         Hardy-Weinberg equilibrium:   Equilibrium of stable allele frequencies in large, random mating populations without             unbalanced mutations, unbalanced migrations, or natural selection.         Genetic drift:   Random, erratic changes in gene frequencies due to chance, especially in small populations.         Sexual selection:   Selection due to mate choice and mating success.         Directional selection:   Selection that changes the mean value of a quantitative character.         Disruptive selection:   Selection against values near the mean (a rare occurrence).         Centripetal or Stabilizing selection:   Selection against extreme values, favoring values near the mean.         Particulate inheritance:   Genes behave as discrete particles, maintaining their identity without blending.         Independent assortment:   Different genes (if located on different chromosomes) are inherited independently of one another.         Inbreeding:   Increased mating with related individuals.         Positive assortative mating:   Preferential mating among phenotypically similar individuals.         Negative assortative mating:   Preferential mating among phenotypically different individuals.         Morphological species definition:   Definition of individual species by their morphological characteristics.         Biological species definition:   Definition of species as groups of interbreeding populations that are reproductively             isolated from other species.         Sibling species (cryptic species):   Reproductively isolated species that are difficult to tell apart.         Reproductive isolating mechanism:   Biological characteristics of individuals that prevent matings between species.         Cline:   A geographic character gradient.         Speciation:   The evolution of reproductive isolation, and thus of a new species.         Anagenesis:   The process by which one species evolves into another without branching.         Cladogenesis:   The branching of evolutionary lineages by speciation.         Polyploidy:   Increases in chromosome number by doubling or other whole-genome increases.         Allopatric:   Living in separate geographic ranges.         Sympatric:   Living in the same or broadly overlapping geographic ranges.         Parapatric:   Living in adjacent geographic ranges that marginally touch one another.         Lineage:   An ancestor-to-descendent sequence of species.         Trend:   Continued morphological change within a lineage.         Parallelism:   Independent occurrence of the same or similar trends in different lineages.         Opportunism:   The theory that evolution follows no plan or goal, but instead takes the path of least resistance.         Adaptive radiation:   Diversity among the descendents of a single species, often arising when many new             opportunities become available.         Paleontology:   The study of fossils.         Fossil:   The remains or other evidence of life from past geologic ages. (See above for various types of fossilization.)         Taxonomy:   The theory behind the making of classifications.         Phylogeny:   A family tree of species.         Phylogenetics:   The study of family trees.         Phylogenetic taxonomy:   The making of classifications based on phylogenies.         Monophyletic group (clade):   A natural group, including a single ancestor and all of its descendants.         Paraphyletic group:   An incomplete group, including a common ancestor and some but not all of its descendants.         Polyphyletic group:   An unnatural group that includes no ancestor common to all group members.         Plesiomorphy:   A primitive trait, possessed by an ancestor.         Symplesiomorphy:   A shared plesiomorphy, often defining a paraphyletic group.         Apomorphy:   A derived trait, posessed by a descendant but not by an ancestor.         Synapomorphy or homology:   A shared trait, derived from a common ancestor, thus defining a monophyletic group.         Homoplasy:   A misleading resemblance (such as a convergence), defining a polyphyletic group. MORE DETAILS are contained in the following outlines: 01.Biology     02.Science     03.BeforeDarwin     04.Descent     05.Selection     Mendel 06.Popul.Genetics     07.Taxonomy     08.Microevol     09.Synthesis     10.Speciation     11.Macroevolution THIS GUIDE will continue to be revised. It is still tentative.

Index             Syllabus

rev. Nov. 2015