Bio 2 midterm

1/13/25: History of Life (p1)

How did life begin?

• 13-17 billion years ago = Big Bang formed the universe

• 4.6 billion years ago = solar system formed

• 4.55 billion years ago = Earth formed

• 4 billion years ago = Earth has cooled enough for outer layers to solidify and oceans to form

• 4 - 3.5 billion years ago = life emerged

• ! Life requires interplay between DNA, RNA, and proteins

  • Living cells come from pre-existing cells

• 4 overlapping stages:

  • Nucleotides and amino acids produced prior to existence of cells

  • Nucleotides and amino acids became polymerized to form DNA, RNA, and proteins

  • Polymers became enclosed in membranes

  • Polymers enclosed in membranes evolved cellular properties

Primitive Earth

• Reducing Atmosphere Hypothesis (1920s)

  • Primitive atmosphere

    • H2O vapor, N2, CO2

    • Small amounts of H2 and CO

    • Little free oxygen (reducing atmosphere)

    • Originally too hot for liquid water

    • As Earth cooled, water vapor condensed to liquid water

    • Primordial soup

• Spontaneous formation of organic molecules

• Monomers evolved and joined to form polymers

• Abiotic (prebiotic) synthesis

Primitive Earth - video

TAKE NOTES!!

First Biomolecules

• Miller’s and Urey’s Apparatus and Experiment (1953)

  • Showed that biochemicals could be produced from simple nonbiological sources

  • Primitive atmospheric gases

  • Strong energy sources

  • Yielded HCN, CH2O, glycine, sugars, amino acids, N-bases

• More recent:

  • Neutral environment – CO, CO2, N2, H2O

  • Organics can be made under a variety of conditions

Alternative Mechanisms

• Extraterrestrial Hypothesis

  • Organic carbon from asteroids and comets stocked prebiotic soup

  • Meteorite studies → Carbonaceous chondrites, lots of organic carbon, amino acid, nucleic acid bases

  • Controversy → destroyed by intense heat of impact?

• Deep-sea vent Hypothesis (1988)

  • Key organics arose at deep-sea vents

  • Superheated water (150 C) rich in H2S and Metal ions mixes with cold seawater

  • Organics formed in temperature gradient around vents

Origin of the 1st Cell

• Clay hypothesis

  • Simple organics polymerize on solid surface (clay, mud, inorganic crystals) into more complex organics

• Cell-like structures - Protobiont

  • Boundary (ex. membrane)

  • Polymers inside contain info

  • Polymers inside with enzymatic function

  • Self-replication

• Chemical Selection – RNA World

  • RNA in Protobionts

    • Can store info

    • Capacity for replication

    • Enzymatic functions (ribozymes)

• Stromatolites = mats of mineralized cyanobacteria

                                                                                             Replaced by DNA/RNA/Protein World

Advantages of DNA/RNA/Protein World

• Information storage

  • DNA would have relieved RNA of informational role and allowed RNA to do other functions

  • DNA = less likely to suffer mutations

• Metabolism and other cellular functions

  • Proteins have a greater catalytic potential and efficiency

  • Proteins can perform other tasks → cytoskeleton, transport, etc.

Fossil Dating

• Fossils = remains and traces of past life

• Paleontology = the study of the fossil record

• Most fossils are traces of organisms embedded in sediments

• Sediment converted to rock

• Becomes recognizable stratum in stratigraphic sequence of rocks

• Strata of the same age tend to contain the similar fossil assemblages

• Helps geologists determine relative dates of embedded fossils despite upheavals

Strata:

Index species

• Wide distribution

• Large number of individuals

• Fossilize easily

Factors that Affect the Fossil Record

• Anatomy

• Size

• Number

• Environment

• Time

• Geological processes

• Paleontology

Fossil Dating (Absolute)

• Half-lives !!

1/15/25: History of Life (p2)

Geologic Time Scale

• Changes in organisms result from:

  • Genetic changes

  • Environmental changes

• Patterns correlated with:

  • Climate/Temperature

  • Atmosphere

  • Land masses (continental drift 1-10cm/yr)

  • Floods/Glaciation

  • Volcanic eruptions

  • Meteorite impacts

Precambrian Time

• Includes ~87% of geologic time → Hadean, Archaeon, and Proterozoic Eons

• Little or no atmospheric oxygen

• Lack of ozone shield allowed UV radiation to bombard Earth

• First cells came into existence in aquatic environments

  • Prokaryotes ~3.5 billion years

  • Cyanobacteria left many ancient stromatolite fossils

  • Added first oxygen to the atmosphere

  • Evolution of aerobic species

• Eukaryotic cells ~2 billion years

• Multicellular organisms ~1.5 billion years

Ediacaran Period

• 635-541 million years

• Multicellular animals appear, including sponges

• Mudflat animals, unusual forms, no internal organs, no shells or bones

• Mass Extinction occurred

Mass extinctions

• Changes to the environment that dramatically increase the rate of extinction

Permian mass extinction

• Lost 95% of marine species

• Occurred over 500 thousand years

• Period of extreme volcanic activity

• Climate change – Earth warming 6 C, ocean acidification, etc.

Cretaceous mass extinction

• Lost 76% of marine species, but also 75% of all animals and plants

• Likely due to an asteroid impact – Chicxulub crater in Mexico

Paleozoic Era → Cambrian Explosion

• Warm, wet climate, O2, no ice at poles

  • All existent phyla developed (?)

  • No major reorganizations of body plans since

  • Many marine invertebrates – 520 million years

• High diversity of the Cambrian may be due to:

  • Favorable environment – oxygen

  • Evolution of Hox genes

  • Predator/prey “arms race” – shells, reef-building

Paleozoic Era – Ordovician Period

• Warm temperatures and atmosphere very moist

• Diverse marine invertebrates including trilobites and brachiopods

• Primitive plants and arthropods first invade land

• At end, abrupt climate change (large glaciers) resulted in mass extinction

Paleozoic Era – Invasion of Land

• Silurian Period

  • Stable climate, glaciers melted

  • Significant vertebrates (many fishes) and plants, coral reefs appeared

  • Large colonization by terrestrial plants (seedless vascular) and animals (arthropods)

• Devonian Period

  • North dry, South wet (oceans)

  • Many more terrestrial species

  • Gymnosperms emerge

  • Insects emerge

  • Tetrapods – amphibians emerge

  • Invertebrates flourish in the oceans

  • The Age of Fishes

Paleozoic Era – Carboniferous Period

• Rich coal deposits formed

• Cooler with land covered by forested swamps

• Plants and animals further diversified

• Very large plants and trees prevalent

• First flying insects

• Amphibians prevalent

• Amniotic egg emerges → reptiles

Paleozoic Era – Permian Period

• Continental drift formed supercontinent Pangea

• Interior regions dry with seasonal fluctuations

• Forest shift to gymnosperms

• Amphibians prevalent but reptiles became dominant

• First mammal-like reptiles appeared

• At the end → largest known mass extinction event

Mesozoic Era – Age of Reptiles

• Hot climate, dry terrestrial environments, little if any ice at poles

• Triassic Period

  • Gymnosperms dominant

  • Reptiles abundant (1st dinosaurs appeared)

  • 1st true mammals

• Jurassic Period

  • Dinosaurs achieved enormous size

  • Mammals remained small and insignificant

  • 1st bird

• Cretaceous Period

  • Dinosaurs began precipitous decline

  • Mammals began an adaptive radiation and moved into habitats left vacated by dinosaurs

Cenozoic Era – Age of Mammals

• Tropical conditions replaced by a colder, drier climate

• Mammals continued adaptive radiation (birds, fishes, insects diversified)

• Flowering plants already diverse and plentiful 

• Primate evolution began

  • Quatemary Period (1.8 mya to today)

  • Age of Man (hominids)

  • Homo sapiens appear 130,000 years ago

Primate Evolution

• Lemurs, tarsiers, monkeys, apes, humans

• Descended from tree-dwellers

• All adapted for climbing trees

  • Rotating shoulder joint

  • Big toe and thumb widely separated from others

  • Stereoscopic vision

• Also: larger brain, 1 offspring/pregnancy, upright body

• Humans (homo) → bipedalism, increased brain size, fully opposable thumb

6th Mass Extinction (Holocene, Anthropocene Extinction)

• Currently experiencing the worst spate of species die-off

• Humans = global superpredators

Living Planet Report 2020

• Average 68% decline in monitored populations of mammals, birds, amphibians, reptiles, and fish between 1970 and 2016

• Most significant declines in tropical subregions of the Americans and Africa

• Freshwater biodiversity declining faster than terrestrial or oceanic

• Megafauna particularly vulnerable

• Plant extinction risk is comparable to that of mammals and higher than for birds

• >⅕ of wild species are at risk of extinction this century due to climate change alone

1/20/25: Evolving Concepts of Evolution 

Evolution → heritable change in one or more characteristics of a population or species from one generation to the next

Species → group of related organisms that share a distinctive form

• Among species that reproduce sexually, members of the same species are capable of interbreeding to produce viable and fertile offspring

Population → members of the same species that are likely to encounter each other and thus have the opportunity to interbreed

Microevolution → changes in a single gene in a population over time

Macroevolution → formation of new species or groups of species

History of Evolutionary Thought

• Pre-Darwinian = influenced by myth, religion, and superstition

• Anaximander (611-547 BC) = Organisms evolve from other organisms

• Plato (427-347 BC) = Objects are temporary reflections of ideal forms

• Aristotle (384-322 BC) = All living things can be arranged in a linear hierarchy (Scala

• naturae)

• Creationism = a god is absolute creator of heaven and earth, out of nothing, by an act of

• free will; includes Christians, Jews, and Muslims

• Spontaneous Generation (5th - 14th century AD)

  • Sweaty rags in open jar with grain after 21 days produces mice

  • Rotting meat produces maggots

  • Dust gives rise to flies

Scala Naturae

• Establishes humans as dominant and a perfect form of life

• Sets humans above and apart from nature

• Incorporated into the religious belief that the Earth and its creatures are the result of special creation, that they have not changed since they were created 

History of Evolutionary Thought

• Taxonomy matured during late 17th to mid 18th century

  • John Ray

  • Carolus Linnaeus → fixity of species, binomial system of nomenclature

• Count George Buffon = catalog of all plants and animals, suggested life forms change over time

• Erasmus Darwin = suggested common descent, evidence in developmental patterns

• Georges Cuvier = first to use comparative anatomy to develop a system of classification, founded paleontology, proposed catastrophism

• Jean-Baptiste Lamarck = first biologist to propose evolution and link diversity with environmental adaptation

  • Concluded more complex organisms are descended from less complex organisms

  • Proposed inheritance of acquired characteristics = Lamarckism

• James Hutton and Charles Lyell = Earth is subject to slow but continuous cycles of erosion and uplift

  • Proposed Uniformitarianism, rates and processes of change are constant 

  • Principles of geology

Darwin’s theory of evolution

• Geological observations consistent with those of Hutton and Lyell

• Biogeographical observations:

  • The study of the geographic distribution of life forms on earth

  • Darwin saw similar species in similar habitats

  • Reasoned related species could be modified according to the environment

Galapagos Islands

• Tortoises → observed tortoise neck length varied from island to island, proposed that speciation on islands correlated with a difference in vegetation

• Finches → observed 13 species of finches on various islands, speculated they could have descended from a single pair of mainland finch

Darwin and Origin of Species

• Returned to England and wrote the Origin of Species about his voyages on the HMS Beagle and what he discovered

 Darwin’s Explanatory Model of Evolution by Natural Selection

1/22/25: Evidence of Evolution

Survival of the Fittest

• Fitness = the relative reproductive success of an individual

  • Most-fit individuals in a population capture a disproportionate share of resources

  • Interactions with the environment determine which individuals reproduce the most

• Adaptation

  • Changes that help a species become more suited to its environment

  • Product of natural selection

Evolution in Action – Industrial Melanism

• Before industrial revolution → peppered moths = 10% dark colored, 90% light

• After IR → soot in atmosphere, tree trunks darkened, lichens killed, peppered moths = 80% dark colored, 20% light (currently we have moved back to more light colored)

Adaptive Melanism

• Melanin = makes skin darker or lighter depending on amount, keeps us safe from UV sun rays

• Videos on slides

• Melanin genes targeted by evolution → ex. Pocket mice

• Evolution of bacteria on a mega agar plate petri dish

Evidence of Evolution – Comparative Anatomy

• Homologous Structures:

  • Anatomically similar because they are inherited from a common ancestor

  • May be functionally similar or not

• Analogous Structures:

  • Serve the same function

  • Not constructed similarly

  • Do not share a common ancestor

  • Convergent evolution

Convergent Evolution = similarity due to convergence

Evidence of Evolution – Comparative Anatomy

• Vestigial structures:

  • Fully-developed anatomical structure

  • Reduced or obsolete function

• Human appendix

• Male breast tissue/nipple

• Wisdom teeth in humans

• Human tailbone (coccyx)

• Erector pili and body hair

• Blind fish - Astyanax mexicanus

• Sex organs in dandelions

• Wings on flightless birds

• Hind leg bones in whales/snakes

• Fake sex in virgin whiptail lizards

Comparative Development

• All vertebrate embryos have:

  • A postanal tail

  • Paired pharyngeal (gill) pouches

  • Dorsal, hollow nerve cord

  • Notochord

Evidence of Evolution – Fossil Record

• Fossils record the history of life from the past

• Document a succession of life forms from the simple to the more complex

• Sometimes the fossil record is complete enough to show descent from an ancestor

Whales

• Fossil record spans 50 million years

• Terrestrial tetrapod to aquatic animal lacking hind limbs

• Order Cetacea: whales, dolphins, porpoises

Evidence of Evolution – Biogeography

• Alfred Russell Wallace - Father of Biogeography

  • Study of geographical distributions of plants and animals across Earth

  • Different mixes of plants and animals in areas separated by water, continents, and islands

  • Consistent with origin in one locale and then spread to accessible regions

Evidence of Evolution – Plate Tectonics

Evidence of Evolution – Molecular Homologies

• Almost all living organisms:

  • Use the same basic biochemical molecules

  • Utilize the same DNA triplet code

  • Utilize the same 20 amino acids in their proteins

  • Utilize ATP as an energy source

• Genetic homologies (DNA base-sequence differences)

  • When very similar, suggest recent common descent

  • When more different, suggest more ancient common descent

Evidence of Evolution – Genetic Homologies

Process of Evolution

1. Variations are produced by chance mutations and sexual reproduction

2. Natural selection selects the ‘fittest’ organisms

3. Natural selection leads to adaptation to a particular environment

4. Process occurs constantly in all species of life on Earth

• Natural selection acts on individuals in a species

• Evolution = a property of populations

• Occurs generation to generation

• Descendants are different from ancestors

• Change in allele (gene) frequencies; change in genetic makeup of population over time (generations)

Genes in Populations

• Populations genetics = study of genes and genotypes in a population

• Want to know extent of genetic variation, why it exists, how it is maintained, + how it changes over the course of many generations

• Helps us understand how genetic variation is related to phenotypic variation

Genes in Natural Populations

• Genes can be monomorphic (99% = 1 allele) 

  • Or polymorphic (2 or more alleles in population)

• Polymorphism comes about through various changes:

  • Duplication of gene region

  • Deletion of significant region of gene

  • Change in a single nucleotide (SNP) (smallest and most common change in a gene)

• Allele frequency = # of copies of a specific allele in a population/total# of all alleles for that gene in population

• Genotype frequency = # of individuals with a particular genotype/total # of individuals in a population

Hardy-Weinberg Principle

• 1908 → G.H. Hardy and W. Weinberg independently recognized that:

  • Genes remain in equilibrium (constant frequency) over time (in each succeeding generation of a sexually reproducing population) as long as 5 conditions are met

  • Relates allele and genotype frequencies in a population

  • Can be described by the binomial equation 

Using the Hardy-Weinberg Equation

p + q = 1

p^2 + 2pq + q^2 = 1 (expansion)

Hardy-Weinberg Equilibrium

• Conditions to be met:

  • No mutations → allelic changes do not occur, or changes in one direction are balanced y changes in the opposite direction (also no gene duplication, exon shuffling, or horizontal gene transfer)

  • No gene flow → migration of alleles into or out of the population does not occur

  • Random mating → individuals pair by chance and not according to their genotypes

  • No genetic drift → the population is very large, and changes in allele frequencies due to chance alone are insignificant 

  • No selection → no selective agent favors one genotype over another, all genotypes are equally adapted

• If p or q is changed in next generation → evolution has occurred!!

• Hardy-Weinberg identifies factors that cause evolution

• Evolution detected by noting any deviation from a Hardy-Weinberg equilibrium of allele frequencies in the gene pool of a population

• Equilibrium population = hypothetical population in which evolution does not occur

• Conditions for Hardy-Weinberg are rarely met

• Hardy-Weinberg population provides starting point for studying mechanisms of evolution

• Microevolution = accumulation of small changes in the gene pool of a population over a relatively short period of time

1/27/25: Micro and Macroevolution

Causes of Microevolution – Genetic Mutations

• The raw material for evolutionary change → source of genetic variability

• Source of new alleles → leads to new combinations of alleles

• Not goal-directed → not a result of environmental necessity

• Random events → can be good, bad, or neutral (depending on environmental conidtions)

• Other forces act to either maintain the variation or remove it from the population

Causes of Microevolution – Gene Flow/Gene Migration

• Movement of alleles between populations when:

  • Gametes or seeds (in plants) are carried into another population

  • Breeding individuals migrate into or out of population

• Continual gene flow reduces genetic divergence between populations

  • Typically increases genetic diversity within the population

• Populations of relatively sedentary organisms are more isolated from one another than populations of very mobile organisms (subspecies)

Causes of Microevolution – Non-random Mating

• Non-random Mating = when individuals do not choose mates randomly

• Assortative Mating

  • Individuals select mates with their phenotype and reject opposites

  • Increases the number of homozygotes

• Disassortative Mating

  • Dissimilar phenotypes mate preferentially

  • Increases the number of heterozygotes

• Inbreeding

  • Mating of 2 genetically related individuals

  • Chose a mate from same genetic lineage

Causes of Microevolution – Genetic Drift

• Changes to allele frequency due to random chance

  • Can cause the gene pools of two isolated populations to become dissimilar

  • Some alleles are lost (0%) and others become fixed (100%)

• Likely to occur:

  • After a bottleneck

  • With severe inbreeding

  • When founders start a new population

• A random event prevents a majority of individuals from entering the next generation → next generation composed of alleles that just happened to make it

• Stronger effect in small populations 

Bottleneck Effect

• African Cheetah

  • Fastest living land animals (70+mph)

  • Lost nearly all genetic variability (monomorphic for almost all genes)

  • Prolonged inbreeding following a Bottleneck (10-20,000 years ago)

  • Very low sperm count, motility, deformed flagella

• Northern Elephant Seals 

  • Low genetic variability

  • Human inflicted (1890’s)

  • Hunted to 20 individuals → now 100,000

  • May be susceptible to pollution/disease

Founder Effect

• When a new population is started from just a few individuals

• The alleles carried by population founders are dictated by chance

• Formerly rare alleles will either:

  • Occur at a higher frequency in the new population

  • Be absent in the new population

• Ex. Amish Ellis-van Creveld syndrome

Causes of Microevolution – Natural Selection

• Adaption of a population to the biotic and abiotic environment

  • Biotic = competition, predation, sexual selection

  • Abiotic = climate, water availability, minerals

• Requires:

  • Variation = the members of a population differ from one another

  • Inheritance = many differences are heritable genetic differences

  • Differential Adaptiveness = some differences affect survivability

  • Differential Reproduction = some differences affect likelihood of successful reproduction

• Results in:

  • A change in allele frequencies in the gene pool

  • Improved fitness of the population

• Major cause of microevolution

Types of Selection

• Directional Selection

  • Individuals at one extreme of a phenotypic range have greater reproductive success in a particular environment

  • Curve shifts in that direction

  • Ex. size of modern horse, industrial/adaptive melanism, DDT-resistant mosquitos

• Stabilizing Selection

  • Intermediate phenotype is favored

  • The peak of the curve increases and tails decrease

  • Ex. human babies with low or high birth weight = less likely to survive

• Disruptive (Diversifying) Selection

  • Two or more extreme phenotypes are favored over intermediates → bimodal distribution

  • Ex. Capeta snails vary because a wide geographic range causes selection to vary

Types of Selection (cont.)

• Balancing Selection

  • Maintains genetic diversity

  • Balanced polymorphism

    • Two or more alleles are kept in balance and therefore are maintained in a population over the course of many generations

  • Two common ways:

    • For a single gene, heterozygote favored

    • Negative frequency-dependent selection – rare individuals have a higher fitness (predator-prey)

Sexual Selection → a special case of Natural Selection

• Directed at certain traits of sexually reproducing species that make it more likely for individuals to find or choose a mate and/or engage in successful mating

• In many species, male characteristics affected more intensely than female (secondary sex characteristics, sexual dimorphism)

• Intrasexual – same sex

  • Males directly compete for mating opportunities or territories

• Intersexual – opposite sex 

  • Females choose with males possessing a particular phenotype

• Ex. birds of paradise

Maintenance of Variations

• Genetic variability 

  • Populations with limited variation may not be able to adapt to new conditions

  • Maintenance of variability is advantageous to population

  • Only exposed alleles are subject to natural selection

  • Natural selection does not cause genetic changes

  • Natural selection acts on individuals

  • Population evolves as gene frequencies change

Macroevolution = evolutionary changes that create new species and groups of species, accumulation of microevolutionary changes over long periods of time

• Speciation:

  • The splitting of one species into two = Cladogenesis

  • The transformation of one species into a new species over time = Anagenesis

What is a species?

• Typographical (Morphological) Species Concept

  • Species is defined by fixed, essential features

  • Each species has a unique structure that makes it distinct

• Biological Species Concept

  • A species is a reproductive community of populations (reproductively isolated from others) that occupies a specific niche in nature → interbreeding with common gene pool to produce viable, fertile offspring

  • Drawbacks = species have dimensions in space and time, sexual and asexual reproduction, unit of evolution and taxonomic category

• Ecological Species Concept

  • Using the ability of organisms to successfully occupy their own ecological niche or habitat, including their use of resources and impact on the environment → to distinguish species

• Phylogenetic (Evolutionary) Species Concept

  • A species is an irreducible group of organisms diagnosably distinct from other such groupings and within which there is parental pattern of ancestry and descent

  • Morphological, chromosomal, molecular characters used

Reproductive Isolating Mechanisms

• Reproductive isolating mechanisms inhibit gene flow between species and maintain distinctiveness of species

• Prezygotic Mechanisms

  • Discourage attempts to mate

    • Habitat isolation

    • Temporal isolation

    • Behavioral isolation

    • Mechanical isolation

    • Gamete isolation

• Postzygotic Mechanisms

  • Prevent hybrid offspring from developing or breeding

    • Hybrid inviability (zygote mortality)

    • Hybrid sterility

    • Hybrid breakdown

Modes of Speciation

• Allopatric Speciation

  • Two geographically isolated populations of one species

  • Become different species over time – gene flow interrupted

  • Can be due to differing selection pressures in differing environments

  • Ex. Kaibab and Abert squirrels on North vs. South rim of Grand Canyon = two different species now, Grunts of the sea = Panamic vs. Atlantic Porkfish

1/29/25: Systematics and Taxonomy

Classification of Living Things

• 1.75 million species described

• 10-100 million actually exist

Systematics and Taxonomy

• Systematics = the study of the biological diversity and evolutionary history of life on Earth

• Taxonomy = branch of biology concerned with identifying, naming, and classifying organisms

• Name → only 1 scientist gets to “name” a species

• Identify → anyone can with a key

• Classify → group a species with its closest relatives

• Began with the ancient Greeks and Romans

• Aristotle classified organisms into groups such as horses, birds, and oaks (Scala naturae)

• Every organism should have a set name (creds to John Ray)

Taxonomy

• Carolus Linnaeus (mid 1700s)

• Binomial System of Nomenclature

  • First word is GENUS name

  • Second word is SPECIFIC EPITHET

    • = refers to one species within its genus

  • Species is referred to by the full binomial name (Genus species) or Genus species (specific epithet)

  • Genus name can be used alone to refer to a group of related species

• Whole thing should be in italics

Scientific Names

• Some names are super long, some super short, some unusual, some after celebs

Classification Categories

• Modern taxonomists use the following classification:

  • Domain = one or more supergroups

    • Supergroup = one or more kingdoms

      • Kingdom = one or more phyla

        • Phylum = one or more classes

          • Class = one or more orders

            • Order = one or more families

              • Family = one or more genera

                • Genus = one or more species

                • Species 

• Whole thing is called the taxon

• Did King Phillip Come Over For Good Sushi? ACRONYM FOR MEMORIZATION!!

Classification Categories

• The higher the category → the more inclusive

• Organisms in the same domain have general characteristics in common

• In most cases, classification categories can be subdivided into additional categories → superorder, suborder, infraorder

• Distinguishing species on the basis of structure can be difficult

• Members of the same species can vary in structure

• Attempts to demonstrate reproductive isolation is problematic because:

  • Some species hybridize

  • Reproductive isolation is difficult to observe

Phylogenetic Trees

• Goals of systematics:

  • To discover all species

  • To reconstruct the phylogeny (evolutionary history) of a group

  • To classify accordingly

• Phylogeny often represented as a phylogenetic tree

  • A diagram indicating lines of descent

  • Each branching point:

    • = a divergence from a common ancestor

    • Represents an organism that gives rise to two new groups

Phylogenetic Trees

• Classification lists the unique characters of each taxon and is intended to reflect phylogeny

  • Primitive characters = present in all members of a group, present in the common ancestor

  • Derived characters = present in some members of a group, but absent in the common ancestor

Tracing Phylogeny

• Fossil Record

  • Fossil record = incomplete

  • Often difficult to determine the phylogeny of a fossil

• Homology

  • Refers to features that stem from a common ancestor

  • Homologous structures are related to each other through common descent

Tracing Phylogeny

• X Convergent Evolution – Analogy

  • The acquisition of a feature in distantly related of descent

  • The feature is not present in a common ancestor

• X Parallel Evolution

  • = the independent evolution of similar traits → starting from a similar ancestral condition

  • Several species respond to similar challenges in a similar way

Molecular Data

• Protein Comparisons

  • Immunological techniques

    • Degree of cross-reaction used to judge relationship

  • Amino acid sequencing

    • Similar sequence in same protein indicates close relationship

• RNA and DNA Comparisons

  • Systematics assumes:

    • 2 species with similar base-pair sequences are assumed to be closely related

    • 2 species with differing base-pair sequences are assumed to be only distantly related

Molecular Clocks

• Use non adaptive nucleotide sequences

• Assumed constant rate of (neutral) mutations over time

• Favorable mutations are rare

• Detrimental mutations are quickly eliminated

• → means most mutations are neutral

• mtDNA = 2% nucleotide changes/1 million years

• SSU(18S) rRNA = 1% sequence change/50 million years

DNA – DNA Hybridization

Traditional Systematics

• Mainly uses anatomical data

  • Classify organisms using assumed phylogeny with emphasis on phenotype

  • Stress both common ancestry and degree of structural difference among divergent groups

  • Construct phylogenetic trees by applying evolutionary principles to categories 

  • Not strict in making sure all taxa are monophyletic

• Monophyly

• Paraphyly = includes common ancestor but not all descendants

• Polyphyly = members traced to separate ancestors, does not contain the most recent common ancestor of the group

Cladistic Systematics

• Traces evolutionary history of the group under study

• Uses shared derived characters = Synapomorphies to:

  • Classify organisms

  • Arrange taxa into a cladogram

• Cladogram = special type of phylogenetic tree

• Clade = evolutionary branch that includes:

  • A common ancestor, together with:

  • All its descendant species

• Monophyletic group = taxon whose units all evolved from a single parent stock, most recent common ancestor and all of its descendants

Parsimony

• Cladists are always guided by the principle of parsimony

  • The arrangement requiring the fewest assumptions is preferred

  • This would:

    • Leave the fewest number of shared derived characters unexplained

    • Minimize the number of assumed evolutionary changes

• The reliability of a cladogram is dependent on the knowledge and skill of the investigation

Cladistic vs Traditional Phylogeny

Classification System – Previous

• Until the mid-1800s → biologists recognized only 2 kingdoms:

  • Plantae (plants)

  • Animalia (animals)

• Protista (protists) were added as a third kingdom in the 1880s

• Whittaker expanded to five kingdoms in 1969 by adding Fungi and Monera

The Three-Domain System of Classification

• The bacteria and archaea are so different that they have been assigned to separate domains 

• Distinguishable by:

  • Difference in rRNA base sequences

  • Plasma membrane chemistry

  • Cell wall chemistry

• Domain Eukarya

  • Uni- and multicellular organisms

  • Cells with a membrane-bound nucleus

  • Sexual reproduction common

  • Contains kingdoms – Fungi, Plantae, and Animalia

  • Protists, now New Kingdom = Hemimastigotes

2/3/25: Viruses

General characteristics

• Noncellular → cannot be classified with cellular organisms, generally <200nm in diameter

• Each type has at least 2 parts:

  • Capsid

    • Outer layer composed of protein subunits

    • Some enveloped by membrane, others non-enveloped or “naked”

    • Generally symmetrical

  • Nucleic acid core

    • DNA or RNA (3-100 genes)

    • Single or double-stranded, linear or circular

• 4 morphological categories → very diverse (over 4000 types)

  • Icosahedral

  • Complex

  • Helical

  • Spherical

Categorization

• Unique

  • Obligate intracellular parasites

  • Cannot reproduce outside a living cell

  • Can be cultured only inside living cells

  • Cannot move, metabolize, or respond to stimuli

  • All are infectious!

• Similar

  • Can make copies of themselves (although they need a host)

  • Can evolve/mutate

  • Are parasites/infect organisms

  • Contain genetic material as their instructions

  • Viruses can stay dormant until ideal conditions

  • Can respond to their environment

• Classification is based on:

  • Type of nucleic acid (DNA/RNA, single or double-stranded)

  • Size and shape

  • Presence/absence of outer envelope

Viral Replication

• Bacteriophages

• Portions of capsid adhere to specific receptor on the host cell

• Not easily recognized by host immune system

• Viral nucleic acid enters the cell

• Once inside, the virus takes over metabolic machinery of the host cell

Viral Assembly

• During assembly → the components of the virus that were produced during replication are organized into viral particles before being released by the cell

Viral Infections

• Viruses are best known for causing infectious diseases in plants and animals

• Most common entry point → respiratory tract, open wounds

• Herpes, HIV, cancer

  • Viruses lack metabolism → antibiotics have no effect

  • Controlled by preventing transmission (vaccines, antiviral drugs)

• Viroids

  • Naked strands of RNA

  • Many crop diseases

• Prions

  • Protein molecules with contagious tertiary structure

  • Some human and other animal diseases: TSE’s (Scrapie, Kuru, Mad cow)

Emerging Diseases

• An emerging disease is one that has appeared in a population for the first time, or that may have existed previously but is rapidly increasing in incidence or geographic range

  • AIDS

  • West Nile Encephalitis

  • SARS

  • Ebola Hemorrhagic Fever

  • Bird Flu

  • HPS

  • Chikungunya Virus

  • COVID-19

  • Re-emerging → cholera, plague, dengue hemorrhagic fever, yellow fever, malaria, tuberculosis

HIV and AIDS

• Human Immunodeficiency Virus (HIV) = causative agent of Acquired Immune Deficiency Syndrome (AIDS)

  • Primarily spread by sexual contact between infected and uninfected individuals

  • Can also be spread:

    • By transfusion of HIV-infected blood

    • By sharing of needles among drug users

    • From infected mother to unborn child

• Globally there are ~38 million people living with HIV as of 2019

• 65% of all new HIV infections are in Sub-Saharan Africa

Influenza Virus – the ‘Flu’

• The Flu = viral, respiratory disease with fevers, headache, cough, runny nose, muscle pain

  • 4 Influenza Viruses → A, B, C, D

  • Seasonal Flu → A, B

  • Characterized by surface antigens

• More health complications and hospitalizations, harder to prevent

• Mutates faster than others

• Hard to prevent with vaccination

SARS-CoV-2

• Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) = a strain of coronavirus that causes COVID-19, the respiratory illness responsible for the COVID-19 pandemic

• It is a positive-sense single-stranded RNA (+ssRNA) virus, with a single linear RNA segment

• SARS-CoV-2 is a strain of the species Betacoronavirus pandemic (SARSrCoV), as is SARS-CoV-1 (the virus that caused the 2002-4 SARS outbreak)

• The virus is airborne and primarily spreads between people through close contact and via aerosols and respiratory droplets

• It enters human cells by binding to angiotensin-converting enzyme 2 (ACE2), a membrane protein that regulates the renin-angiotensin system

SARS-CoV-2 strain tree

• There are many thousands of variants of SARS-CoV-2 → which can be grouped into the much larger clades

• Gives understanding of the evolutionary relationships between a set of species

• Designing vaccines, for ex. SARS-CoV2

2/5/25: Prokaryotes

The Tree of Life

Domains, Bacteria, and Archaea

• Fully functioning Prokaryotic cells

• More numerous than all other organisms

• Fossils to 3.5 billion years ago, alone on Earth for over 1 billion years

• Very diverse (50+ bacterial phyla)

• Horizontal gene transfer important in their diversification

• Differ from each other in metabolism, genetics, and membrane structure

Horizontal Gene Transfer

• Movement of one or more genes from one species to another

• Contrasts with vertical gene transfer from parent to progeny

• Increases genetic diversity

• Common among archaea and bacteria

• Can result in large genetic changes

• At least 17% of the genes present in E. Coli came from other bacteria

• About 80% of prokaryotic genes have been involved in horizontal transfer at one point or another

Prokaryotic Cell Structure  

Reproduction in Prokaryotes

• Prokaryotes reproduce asexually by means of binary fission

• Methods of genetic recombination:

  • Conjugation = sex pilus forms between 2 cells, donor cell passes DNA to recipient cell through pilus

  • Transformation = occurs when bacterium picks up free pieces of DNA from other prokaryotes, becomes incorporated into genome

  • Transduction = occurs when bacteriophages carry portions of bacterial DNA from one cell to another (vectors)

Endospores

• Response to unfavorable conditions

• Dormant stage

• Resistant to heat, radiation, disinfectants, and desiccation

• Difficult to eliminate from medical and pharmaceutical materials

• Frequent cause of contamination

• Exs. anthrax, tetanus, botulism, botox

• Some bacteria form resistant endospores

Prokaryotic Nutrition

• Oxygen requirements:

  • Obligate aerobes = unable to grow in the absence of free oxygen

  • Facultative aerobes = able to grow in either the presence or absence of free oxygen

  • Obligate anaerobes = unable to grow in the presence of free oxygen (botulism, gangrene, tetanus)

  • Aerotolerant anaerobes = do not use oxygen but are not poisoned by it

Autotrophic Prokaryotes

• Photoautotrophs

  • Some do not produce O2 (green/purple bacteria)

  • Some use solar energy to reduce carbon dioxide to organic compounds

  • Photosynthetic

• Chemoautotrophs

  • Oxidize inorganic compounds to obtain the necessary energy

  • Use it to reduce CO2 to an organic compound

  • Chemosynthetic

Heterotrophic Prokaryotes

• Most prokaryotes are chemoheterotrophs that take in organic nutrients

  • Aerobic saprotrophs decompose most large organic molecules to smaller molecules (detritivores)

  • Essential components of healthy ecosystem

  • May be free-living or symbiotic

    • Nitrogen fixation (diazotrophs)

    • Commensalism

    • Parasites

  • Commercial uses:

    • Produce chemicals (ethanol), butter, cheese, rubber, cotton, silk, coffee, cocoa, antibiotics, yogurt

Bacterial Cell Wall !!

• Gram-positive vs. gram-negative (GN much more virulent)

Bacteria

• Classified in terms of their five basic shapes:

  • Round (coccus)

  • Rod (bacillus)

  • Comma (vibrio)

  • Flexible Spiral (spirochete)

  • Rigid Spiral (spirillus)

Pathogenic Bacteria

• Sexually transmitted → Syphilis, Gonorrhea

• Systemic → Plague, Typhoid fever

• Respiratory → Strep throat, Scarlet fever

• Skin → Boils, carbuncles

• Digestive tract → Gastroenteritis, food poisoning

• Nervous system → Botulism, Tetanus

• Others → Tularemia, Lyme disease

Outbreaks

• Salmonella

  • Group of rod-shaped enterobacteria

  • Passed from infected feces of people/animals

  • Common sources → pet feces, reptiles, amphibians, poultry, beef, eggs, vegetables, milk, peanut butter

  • Symptoms → last 4-7 days, diarrhea, fever, abdominal cramps

  • 1.35 million American cases per year

  • Also causes typhoid fever

• E. coli

  • Hundreds of strains, most harmless

  • Reside in intestines of healthy humans and animals

  • Escherichia coli

  • 95,000 American cases a year

  • Infection often leads to severe stomach cramps, bloody diarrhea, and occasionally kidney failure.

  • Sources → undercooked ground beef, unpasteurized milk and juice, raw fruits and vegetables, contaminated water

2/10/25: Protists pt. 1

Evolution of the Eukarya Domain

Eukarya

• Paraphyletic group – very diverse

• Morphology:

  • All life activities carried on within limits of one membrane (mostly)

  • Most unicellular and microscopic, specialized organelles

  • Many with amazingly high level of structural and functional complexity

• Life cycles:

  • Asexual reproduction common

  • Sexual reproduction may occur when conditions deteriorate

  • Some life cycles simple, many extremely complex

Features of Eukarya

• Cells with nuclei surrounded by nuclear envelope with pores

• Chromosomes organized by histones

• Cytoskeleton of microtubules and microfilaments

• Mitochondria

• Cilia and flagella

• Mitosis

• Sexual reproduction – meiosis

• Cell walls (cellulose, chitin)

Ecology/evolution

• Protists are of enormous ecological importance

• Photoautotrophic forms:

  • Produce oxygen - primary producers in both freshwater and saltwater ecosystems

  • Major component of plankton → suspended in the water

  • Serve as food for heterotrophic protists and animals

• Many protists are symbionts (parasitism to mutualism)

  • Coral reefs greatly aided by symbiotic photoautotrophic protists in tissues of corals → Zooxanthellae

• Some with great medical importance → pathogenic/parasitic

• Difficult to classify

  • Plant-like = multicellular algae are not plants, do not protect gametes/zygote from desiccation

  • Fungi-like = lack flagella, no chitin in cell wall

  • Animal-like = heterotrophs but no embryonic development

Protists:

• Large group of eukaryotic organisms

• Live in water-based environments

• Majority of them are unicellular, microscopic, and motile

Archaeplastida – Red Algae

• Generally multicellular, light red to dark green, about 6500 species

• Marine (mostly in warmer seawater), can be as deep as 200m

• Some filamentous, most branched, feathery, flat

• Economic importance:

  • Agar, agarose → capsules, dental impressions, cosmetics, culture medium, electrophoresis, food prep.

  • Carrageen → emulsifying agent used in chocolate, low-fat foods, cosmetics

  • Reddish-black wrappings around sushi rolls consist of processed Porphyra blades

Archaeplastida – Green Algae

• Over 7000 species

• Variety of environments → oceans, freshwater, snowbanks, tree bark, turtles’ backs

• Many symbiotic with fungi, plants, or animals

• Morphology varied:

  • Majority unicellular, but many are filamentous or colonial

  • Some are multicellular and resemble leaves of lettuce

• Plants thought to be derived from Charophytes

  • Have a cell wall that contains cellulose

  • Possess chlorophylls a and b

  • Store excess food as starch

Amoebozoa – Amoebas

• Amoeboids are protists that move and ingest their food with pseudopods – phagocytize food

• Pseudopods form when cytoplasm streams forward in a particular direction

• Entamoeba histolytica – parasite of the human colon (50 million cases/year)

  • Causes amoebic dysentery

  • Can be fatal

• Naegleria fowleri

  • Primary amoebic meningoencephalitis (PAM)

Amoebozoa – Slime molds

• They are not actually molds

• Can be:

  • Plasmodial = single multinucleated cells

  • Cellular = single cells that can aggregate to form multicellular organisms

Opisthokonta

• Contrary to other protists, have a single flagellum at the back

• Choanoflagellates:

  • Animal-like

  • ~250 species

  • Marine and freshwater

  • Solitary or colonial

  • Attached or free-swimming

  • Single flagellum surrounded by collar of microvilli

2/12/25: Protists pt. 2

Rhizaria

• Many can make shells (tests) → varied shapes + materials, silica, calcium carbonate, etc.

• Important for the carbon and nitrogen cycles

• Cercozoans

  • Can have or lack a shell

  • Vampyrella = the vampire amoeba

Chromalveolata – Dinoflagellates

• About 4000 species of unicellular aquatic and marine organisms

• Morphology:

  • Cell = usually bounded by protective cellulose plates impregnated with silicates

  • Two flagella

    • One in a longitudinal groove with its distal end free

    • Other lies in a transverse groove that encircles the organism

• Some photosynthetic, some heterotrophic, some parasitic

• Symbiotic dinoflagellates in corals called Zooxanthellae

  • Dinoflagellates provide their host with organic nutrients

  • Corals provide wastes to fertilize the algae

Chromalveolata – Apicomplexans

• Non-motile obligate parasites

• Apical complex of organelles on merozoites/sporozoites → penetrate host

• Most serious parasitic human disease = malaria → caused by Plasmodium spp

  • Millions of cases, hundreds of thousands of deaths

  • Transmitted by the pregnant female mosquito

  • Pregnant women + children = most vulnerable

  • Few treatments + preventions

Malaria life cycle

Chromalveolata – Ciliates

• Ciliates are among the most complex of the protozoans

• Hundreds of cilia beat in coordinated rhythm

• Most are holozoic, swallowing food whole

• Divide by transverse binary fission during asexual reproduction

• Two nuclei of differing types:

  • Micronucleus – heredity

  • Macronucleus – metabolism

Chromalveolata – Diatoms + Golden Algae

• Diatoms = the most numerous unicellular algae in the oceans (also important in freshwater)

• Significant portion of phytoplankton

• Primary producers

• Cell wall

  • Two valves → larger valve acts as a lid

  • Contains silica

• Diatomaceous earth used as:

  • Filtering agents

  • Sound-proofing materials

  • Polishing abrasives

Chromalveolata – Brown Algae

• About 1500 species

• Most live in colder ocean waters along rocky coasts

• No unicellular or colonial brown forms

• Morphology:

  • Some small forms with simple filaments

  • Others large multicellular forms that may exceed 200m in length

• Pigments:

  • Chlorophylls A and C

  • Fucoxanthin (type of carotinoid pigment) gives them their color

• Excess food stored as a carbohydrate called laminarin

Excavata – Euglenozoans

• Euglenoids

  • Small freshwater unicellular organisms

  • Have 1 flagellum and an eyespot

  • 1 flagellum much longer than the other

    • Projects out of an anterior, vase-shaped invagination

    • Called a tinsel flagellum because of hair-like projections

  • Cell bounded by flexible pellicle

  • Chloroplasts:

    • Surrounded by three rather than two membranes

    • With a pyrenoid → which produces an unusual type of carbohydrate called paramylon

• Kinetoplastids

  • Colorless heterotrophs – unusual mitochondria

  • Most symbiotic and many parasitic

  • Well known for causing various diseases in humans

  • Trypanosomes

    • African sleeping sickness → tsetse fly

    • Chagas disease → kissing bug

  • Leishmania spp.

    • 12 million

    • Sand fly → vector

Life Cycles

2/17/25: Fungi pt. 1

Characteristics

• Over 150K species growing

• Mostly multicellular eukaryotes that share a common mode of nutrition

• Heterotrophic (Sapotrophic decomposers)

• Cells release digestive enzymes and then absorb resultant nutrient molecules

• Some are parasitic:

  • Millions of dollars of crop losses per year

  • Human diseases: ringworm, athlete’s foot, yeast infections, fungal infections = mycosis

• Several have mutualistic relationships

Structure

• The body of most fungi is multicellular mycelium

• Mycelium = a vast network of thread-like hyphae

  • Aseptate fungi – multinucleated

  • Septate fungi – hyphae with cross walls

  • Hyphae grow from tip (osmosis, cytoplasmic streaming)

  • Give the mycelium a large surface/volume ratio

• Cell walls of chitin

• Excess food stored as glycogen as in animals

• Produce pigments, including melanin

Reproduction

• Both sexual in most and asexual reproduction = results in nonmotile spores

• Spores = used for reproduction means of dispersal of organism

• Resistance to harsh conditions

Phylogeny

Zygomycota

• Bread molds (Zygospore Fungi)

• Mainly saprotrophs decomposing animal and plant remains, bakery goods in a pantry

• Some parasites of soil protists, worms and insects

• Black bread mold - Rhizopus stolonifer

Sac Fungi – Ascomycota

• Most as saprotrophs that digest resistant materials containing cellulose, lignin, or collagen

• Most are composed of septate hyphae

  • Neurospora = model organism

  • Morels and truffles, famous gourmet delicacies revered throughout the world

  • Many plant diseases → powdery mildews, leaf curl fungi, ergot of rye, chestnut blight, Dutch elm disease

  • Yeasts in baking/brewing, Aspergillus and Candida cause serious human infections

  • Penicillium spp. = source of penicillin

Sac Fungi – Asexual Reproduction

• Asexual reproduction is the norm

• Yeasts usually reproduce by budding

  • A small bulge forms on the side of cell

  • Receives a nucleus and gets pinched off and becomes full-size

• The other ascomycetes produce spores called conidia or conidiospores → spores are 1n

  • Vary in size and shape and may be multicellular

  • Spores are haplotype

  • Conidia usually develop at the tips of conidiophores

• Conidiophores differ in appearance and can be used for diagnostic

• Conidia are windblown

• Conidia of Cladosporium cause allergies

Sac Fungi – Sexual Reproduction

• Ascus = fingerlike sac that develops during sexual reproduction

• Asci usually surrounded and protected by sterile hyphae → fruiting body or ascocarp

  • In cup fungi → ascocarps are cup-shaped

  • In morels, they are stalked and pitted

• Haploid hyphae fuse to make diploid nucleus

• Mitosis and then meiosis produces 8 ascospores

• Spores are windblown

Sac Fungi – Yeasts

• Term ‘yeasts’ = loosely applied to unicellular fungi, many of which are ascomycetes

• Budding = common form of asexual reproduction

• Sexual reproduction → results in the formation of asci and ascospores

• When some yeasts ferment → they produce ethanol and carbon dioxide

• Yeast essential ingredient in making bread, beer, wine

Club Fungi

• Toadstools, mushrooms, bracket fungi, puffballs, stinkhorns

• Some deadly poisonous → Amanita spp. spreading across North America

• Plant diseases - smuts and rusts (parasitize cereal crops, often 2 hosts)

• Mycelium composed of septate hyphae

Club Fungi – Reproduction

• Usually reproduce sexually

• Haploid hyphae fuse, forming a dikaryotic (n+n) mycelium

• Dikaryotic mycelium forms fruiting bodies called basidiocarps

• Contain club-shaped structures called basidia

• Nuclear fusion followed by meiosis produces basidiospores (40 million/hr)

Humongous Fungus – World’s Largest Organism

• Weight = 605 tons

• Age = 2400 - 7200 years old

• Size = spread over 2384 acres

• Location = high elevation on a mountain in Oregon

• Known as = honey mushroom, shoestring rot

• Rhizomorphs take water and nutrients from tree roots, killing trees

• Mycelium = network of hyphae that increases the surface area for nutrient absorption, allowing fungi to efficiently decompose and absorb nutrients from their environment

Mushroom Life Cycle

• Mushroom = tightly packed hyphae whose walled-off ends become basidia

Poisonous Mushrooms

• Death cap

• Fly amanita

• Webcaps

• Etc.

Humans and Fungi

• Black mold

• Ringworm

• Athletes foot

• Dermatophytes

• Nail fungus

• Etc.

2/17/25: Fungi pt. 2

Some Drugs from Fungi

• Penicillin and Amoxicillin → antibiotic

• Streptomycin → antibiotic

• Cyclosporin A → immunosuppresant

• Cephalosporin → antibiotic

• Griseofulvin → antifungal

• Ergot alkaloids → circulation and neurotransmission

Chloesterol Lowering Agents (Mevinolin)

• Lovastatin (mevacor)

• Simvastatin (zocor)

• Pravastatin (pravachol)

• Atorvastatin (lipitor)

Symbiosis – Lichens

• Symbiotic association between a fungus (up to 3-2019) and a cyanobacterium or green algae (25,000 spp.)

• Specialized fungal hyphae penetrate photosynthetic symbiont

• Transfer nutrients directly to the fungus

• Possibly mutualistic, but fungal symbiont may be a parasite of photosynthetic symbiont

• Photosynthetic symbiont independent

• Fungal symbiont usually can’t grow alone

Lichens

• 3 morphological types:

  • Compact crustose lichens = seen on bare rocks or on tree bark

  • Fruticose lichens = shrub-like

  • Foliose lichens = leaf-like

• Can live in areas of extreme conditions and contribute to soil formation 

• Sensitive indicators of air pollution – no roots, absorb

Glomeromycota – Mycorrhizae

• Mutualistic relationships between soil fungi and the roots of most familiar plants (80-90%)

  • Give plant greater absorptive surface

  • Help plants acquire mineral nutrients in poor soil (P, Cu, Zn)

  • Hyphae may enter cortex of root, but not cytoplasm

• Ectomycorrhizae form a mantle that is exterior to the root, and they grow between cell walls, coat root surface

  • Ex. oak, beech, pine, spruce trees 

• Endomycorrhizae penetrate only the cell walls, grow along plasma membrane

  • Ex. apple trees, coffee, legumes

• Earliest fossil plants have mycorrhizae associated with them

• Some sac and cup fungi also form mycorrhizae