Biology 182

Evolution by Natural selection

1/13/20

Natural selection

● Explains how populations become well suited to their environments over

time

Evolution

● Evidence for change through time

○ Geologic time

○ Extinction

○ Transitional features

○ Vestigial traits

○ Change over time

Theory of evolution by natural selection

● Can explain what we see now

● Can help us predict what might happen in the future

Scientific theories - two components

● Pattern - statement about facts (how things are)

 ○ The organisms themselves and their properties - genes/genomes,

anatomy, morphology, diversity, time of occurence, biogeography,

ecology…(everything about organisms)

● Process - mechanism that produces patterns we see

○ How change has occurred over the course of years, generations of

million of years

○ Time frame - microevolution

Evolution by natural selection

● One of the most important and well supported theories in modern biology

○ Populations of organisms evolve or change through time

○ Charles darwin published about natural selection

○ Since that time considerable, consistent evidence for theory

Understanding natural selection importance

● How diseases evolve, differences among human influence responses to

treatment, how cancer cells have changed from the original cells, explains

why we need triple drug treatment for HIV

Before Darwin special creation

● Species are independent(unrelated)

● Life on earth is young(approx 6000 years old)

 ● Species are immutable(won't change)

Aristotle and the great chain of being

● Aristotle ordered known organisms into the linear great chain of being.

Ordered from least to most complicated. Similar to a hierarchy EX: Humans

on top, mammals, fish, bugs and lastly plants on bottom.

● Species were fixed types, species were organized based on increasing size

and complexity, sequence started with minerals and lower plants

Darwin and Wallace - change in species through time

● Does not follow a linear, progressive pattern

● Based on variation among individuals in populations

○ A population consists of individuals of the same species living in the

same area at the same time

Population thinking vs typological thinking

● Typological thinking - species are unchanging types and variations is not

important

Theory of evolution by natural selection was revolutionary

● Species are not static and unchanging

● Population thinking replaces typological thinking

● Scientific theory

○ Proposed a mechanism that could account for change through time

 ○ Predictions could be tested through observation and experimentation

Darwin and the voyage of the Beagle

● Traveled along the coast of S america stopping to examine nearby habitats

Charles Darwin

● Uniformitarianism - forces of nature (wind, rain, volcanism, etc) are constant

and have existed for all time, thus, can result in dramatic landscape

Origin of Species

● Descent with modification - all spece=ies have descended, without

interruption, from one or a few original forms of life

● Natural selection - the causal agent of evolutionary change

● Two predictions

○ Species change through time

○ Species related through ancestry

Fossils - traces of organisms that lived in the past

Found in sedimentary rock layers

Transitional features

● Traits in a fossil species that are intermediate between ancestral and derived

species

● For example, fossils show a gradual change from the aquatic fin to the

terrestrial limb
Vestigial trait

● Reduced or incompletely developed structure in an organism and has no (or

reduced) function

● But clearly similar to functioning organs or structures

● EX: nonfunctional hip and leg bones in some snakes or whales, reduced

wings in flightless birds, Coccyx bone (vestigial tail) and goosebumps in

humans

Homology in modern biology

● Carcinogens in humans can be studied in related animals such as mice,

zebrafish etc

● Test drugs for humans on related animals

● Compare biochemical pathways in closely and distantly related organisms

such as photosynthesis in land plants and green algae

1/15/20

Darwin's contribution

● Observed and carried out artificial selection

● Concluded - diverse pigeon breeds all descended from wild pigeons

Darwin's four postulates

1. Individuals in a population vary in trait

2. Some of these differences are heritable; they are passed onto offspring
 3. In each generation many more offspring are produced than can survive

a. Only some will survive long enough to reproduce

b. Some will produce more offspring than others

4. Individuals with certain heritable traits are more likely to survive and

reproduce

a. Natural selection occurs when individuals with certain traits produce

more offspring than do individuals without those traits

b. The individuals are selected naturally, by the environment

These four can be condensed into

1. Heritable variation leads to

2. Differential success

Testing darwin's postulates

● Variations occur in populations

● Variation is heritable

Natural selection acts on individuals, because individuals experience differential

success

Only populations evolve

Natural selection and Adaptation: misconceptions

● EX: individual organisms don't change over time (giraffe becks and

acclimation to higher elevations)

 ● Natural selection sorts existing variants--it doesn't change them

1/17/20

Evolution

● A change in allele frequencies and thus heritable traits, in population over

time

● Driven by four processes

○ Natural selection- the frequency of alleles that contribute to

reproductive success in a particular environment increase

○ Genetic drift- allele frequencies to change randomly

○ Gene flow- occurs when individuals leave one population, join

another, and breed

○ Mutation- modifies allele frequencies by continually introducing new

alleles. Can be defined as a change in the DNA sequence within a

gene or chromosome of a living organism

Genetic variation

● Number and frequency of alleles present in population

○ Lack of variation can make populations less able to respond

successfully to changes in the environment

○ EX: african cheetah has a lack of variation

Four main types of natural selection- influence type of change of phenotype of

population and amount of genetic diversity in population

● Directional selection

○ Changes average phenotype in population in one direction

○ Favored alleles: allele frequency moves toward 1 and may become

fixed in the population; the other alleles may become lost from the

population

○ Loss of disadvantageous alleles - purifying selection

○ Reduces the genetic diversity

○ EX: cold decreased amount of insects, birds with bigger bodies were

the majority of survivors. Hypothesis- larger birds had bigger fat

stores and did not get as cold as smaller birds. Directional selection

caused average body size to increase for the rest of the population

● Stabilizing selection

○ Mortality high for very small and very large babies, babies with

average size were more likely to survive. This leaves a very narrow

distribution

● Disruptive selection

○ Has the opposite effect of stabilizing selection

○ Extreme or divergent phenotypes are favored

 ○ Overall amount of genetic variation in the population is maintained

○ EX: occurred in a population of black bellied seacrackers. Birds with

very long or very short beaks survived and the birds with intermediate

phenotypes did not survive

● Balancing selection

○ No single allele has an advantage

○ Heterozygote advantage

○ The environment varies over time

○ Genetic variation is maintained

1/22/20

Phylogenies and the histories of life CH 25

Phylogeny - evolutionary history of a group of organisms

Phylogenetic tree

● Graphical summary of evolutionary history

● Hypothesis of ancestor - descendant relationships among texa (species),

individuals or genes

Hypothesis supported with data (characters)

● Morphology, anatomy, physiology

● DNA sequences - from one gene to whole genomes

Uses of phylogenetic trees (chart drawn in notes)

● Study host switching - transmission of viruses between species

○ Origin of HIV from SUV

● Helps identify species that are a conservation priority

Root - take organisms of interest and find its closest relative (hypothesize). Look at

similar characteristics.

Node - anytime the root branches

Branch - comes off a node

Tip - usually a species or population

Outgroup- a taxon that diverged prior to the taxa that are the focus of the study

Polytomy- a node that depicts an ancestral branch dividing into three or more

descendent branches

Creating a phylogenetic tree

● First determine which taxa to study

● Choose outgroup

○ Diverged earlier in time than taxa being studied

○ Outgroup used to establish whether a trait is ancestral(evolved before)

or derived(evolved after)

● Choose characters to study (morphology, physiology)

● Create a data matrix - rows are taxa and columns are characters
 ○ Taxa- four species and one outgroup

○ Characters - six characters- but only two show variation and thus

provide information about relationships

Cladistic methods - to estimate phylogenetic trees using data matrix that you just

constructed

● Based on synapomorphies - shared, derived character traits

○ Change in DNA sequence

● Feathers are a synapomorphy for birds

● Flowers are a synapomorphy for flowering plants

Ancestral trait - existed in an ancestor

Derived trait - modified from of ancestral trait, found in descendant

Monophyletic group - everything beyond the group (clades or lineages)

● Includes an ancestral population and all of its descendants

● Reptiles are monophyletic, but only if they include birds

Paraphyletic groups

● Includes an ancestral population and some, but not all of its descendants

● Reptiles are paraphyletic, if they do not include birds

Ancestral trait is scales

● Derived trait is feathers in birds

● Derived trait is hair in mammals

Ancestral trait is forelimb

● Derived trait is wings in birds

● Derived trait is wings in bats

Homology - similarity in organisms due to common ancestry

Polyphyletic group - an unnatural group that does not include the most recent

common ancestor

Homologous traits - similar due to ancestry

Homoplastic traits - similar for other reasons

● Convergent evolution

○ Natural selection favors similar solutions to similar environmental

pressures

■ Wings in bats and birds

■ Succulence and similar structure in cacti and euphorbias

■ Dolphins and ichthyosaurs

1/24/20 Bacteria and Archaea

Tree of life - tree based on analyses of small subunit rDNA sequences;

Bacteria and Archaea - prokaryotes - two of the three largest branches (domain) on

the tree of life

Eukarya - the eukaryotes - membrane bound nucleus, often multicellular

Microbes - microscopic organisms - bacteria, yeast, fungi

Bacteria and archaea interact or have relationships with all other organisms

● Crucial for understanding all other organisms

● Affect the physical environment, affect biochemical processes such as the

nitrogen and carbon cycles that all other organisms depend upon

Abundance - very large numbers of individuals

Biomass

● Mass of living organisms

● Wet weight or dry weight

Bacteria and archaea - may be up to 10% of the world's Biomass

Largest total volume - of living material on earth of all organisms

Bacteria and archaea

● Live almost everywhere

● As deep as 1600 meters beneath the world's oceans

● Depths of 10,000 m and in temperatures ranging from 0 to 121 degrees c

Extremophiles - are interesting research topics

● Industrial processes- extremophiles contain enzymes that function at

extreme temperatures and pressures; e. G. PCR (method of producing large

amounts of particular DNA molecules from a very small amount)

● How life on earth began - extremophiles may help explain this

 ● Search for extraterrestrial life - astrobiologists use extremophiles as model

organisms

Pathogenic Bacteria - cause disease

● Only a tiny fraction of bacterial species living on and in the human body are

pathogenic

● Pathogenic bacteria found in many lineages, thus pathogenetically

independently evolved

Virulence -

● ability to cause disease

● genetically determined

○ Heritable from one generation to the next

○ Varies among individuals in a population

● Some species have both pathogenic virulent strains and harmless strains

Endospores - tough, thick-walled, dormant structures formed during environmental

stress

● Resistant to high temperatures, UV radiation, freezing, desiccation, and

disinfectants

● Can resume growth under favorable conditions

● Ex; anthrax bacteria in soil and animal hides

Koch's postulates
 ● The microbe must be present in individuals suffering from disease and

absent from healthy individuals

● The organisms must be isolated and grown in pure culture away from host

organism

● If organisms from the pure culture are injected into a healthy experimental

animal disease symptoms should appear

● The organisms should be isolated from the disease experimental animal,

again grown in pure culture, and demonstrated to be the same as the original

organisms

Koch's experimental results were the first test of germ theory of disease

● Foundation in modern medicine

● In industrialized countries, improvements in sanitation and nutrition have
dramatically reduced mortality rates due to infectious diseases
1/27/20

2 types of cell walls exist - distinguished by Gram stain treatment

● Gram-positive - cells look purple after this treatment under a microscope

○ Gram-positive cells - extensive amount of peptidoglycan

● Gram-negative - cells look pink

○ Gram-negative cells - cell wall with two components

■ A thin layer containing peptidoglycan

■ An outer phospholipid bilayer

Cell-Wall composition

● Gram-Positive cells - retain crystal violet stain and stain dark purple

● Gram-Negative cells - do not retain crystal violet stain, but take up counter

stain (safranin) and are pink or red

Cyanobacteria - photoautotrophs

● Past global significance of Cyanobacteria

○ Responsible for the origin of the oxygen in the atmosphere on Earth

■ Thus origin of aerobic respiration that uses oxygen as an

electron acceptor

■ Thus evolution of lively multicellular organisms

● Current global significance

○ Produce much oxygen

○ Fix nitrogen - can produce nitrogen-containing compound usable by

other organisms from nitrogen gas

○ Produce organic compounds that feed other freshwater and marine

organisms

Bacteria - Spirochaetes(Spirochetes)

● Small bacteria lineage

○ Unique corkscrew shape and flagella

● Most spirochetes produce ATP via fermentation

 ● Very common in aquatic habitats; many species only in anaerobic conditions

● Some spirochetes

○ Live in the hindgut of termites and can fix nitrogen

○ Cause syphilis and Lyme disease

Archaea - Euryarchaeota

● Include some chemolithotrophs

● Live in diverse habitats;; for example, high-salt, high pH, and low pH

environments

● Some species of Euryarchaeota

○ Live in piles of waste rock and produce acids that pollute nearby

streams

○ Are methanogens, which contribute about 2 billion tons of methane

into the atmosphere each year

Global significance - Nitrogen Fixation and the Nitrogen Cycle

● All organisms require Nitrogen(N) to synthesize proteins and nucleic acids

● Molecular nitrogen(N2) is abundant in the atmosphere; most organisms

cannot use it directly

○ All eukaryotes and many prokaryotes must obtain nitrogen in a usable

form such as ammonia(NH2) or nitrate (NO3-)

1/29/20
Protists part 1

Domain eukarya - third domain on third tree of life

Eukaryotes - most share fundamental features

● A nuclear envelope

● Cells have more organelles and a cytoskeleton

● Multicellularity is common and many are large

Protists - include all eukaryotes except the land plants, fungi and animals

● Protists are a paraphyletic group

○ They represent some, but not all of the descendants of a single

common ancestor

Many protists are found in aquatic environments

● Open ocean - surface waters teem with microscopic protists such as diatoms

● Shallow coastal waters

● Intertidal habitats - sea palms

Biologists study protists because they are

● Medically important

● Cause plant and animal diseases including crops and domestic animals

● Ecologically important - photosynthesis and decomposition

● Understand evolution of plants, fungi, and animals

 ● Intrinsically interesting; note, can be related to events of human history as

well

Plasmodium - well studied, but difficult to find effective and sustainable measures

to control it

● Drug treatments- parasite has evolved resistance to drugs used to control it

● Vaccine development - difficult because it evolves so quickly

● Vector control - natural selection has favored mosquitoes resistant to

insecticides used to try to control the spread of malaria

Primary producers - species that produce chemical energy by photosynthesis

● Production of organic molecules by marine protists represent almost half of

total carbon dioxide

Plankton - diatoms and other small organisms that drift in the open oceans or lakes

Phytoplankton - photosynthetic plankton

Zooplankton - what is their mode of nutrition - organic in the form of other

plankton. Secondary consumers

Basis of food chains - organic compounds produced by phytoplankton in aquatic

environments

Global carbon cycle - movement of carbon atoms from carbon dioxide molecules

in the atmosphere to organisms in soil or ocean and then back to the atmosphere

1/31/20
Protists part 2

Direct sequencing and metagenomics

● Sample soil for water

● Analyze the dna sequence of specific genes/genomes in sample

● Use sequence data to place the organisms in the sample on a phylogenetic

tree

○ Discovery of several new lineages of eukaryotes, including many, tiny

protists the size of bacteria

Earliest eukaryotes

● Mitochondria

● A nucleus

● An endomembrane system

● A cytoskeleton

● No cell wall

○ Probably swam using a novel type of flagellum

Mitochondria - organelles that generate ATP

Endosymbiosis theory - the origin of mitochondria (and chloroplasts as well)

Endosymbiosis - occurs when an organism of one species lives inside cells of an

organism of another species, both benefit in this situation

Both benefit from relationship (Endosymbiosis and the origin of the

mitochondrion)

● Host cell supplied bacterium with protection and carbon compounds

● Bacterium produced much more ATP than host cell could synthesize on its

own

Data that support this theory - similarities of mitochondria and bacteria

Mitochondria

● Are about the size of an average bacterium

● Replicate by fission, as do bacteria

● Have their own ribosomes, manufacture their own proteins

● Have double membranes, consistent with the engulfing mechanism

● Have their own genomes that are circular molecules like bacterial

chromosomes

Structures provide support and protection for protists (evolution of protists:

structures for support and protection)

● Cell wall

● Hard external shells

● Rigid structures inside plasma membranes

● These structures sink to the bottom of aquatic environments thus have global

significance
Multicellularity

● Evolution of multicellularity, organisms with more than one cell

● First, cells stick together after cell division, then live as a colony

● Eventually, individual cells become specialized for different functions; not

all cells express the same genes

● Multicellularity arose independently in a wide array of eukaryotic lineages

● Thus some protist lineages like the stramenopiles have unicellular diatoms

and multicellular brown algae (kelp)

Phagocytosis - many protists ingest their food --- they eat bacteria, archaea or other

protists whole

Absorptive feeding - nutrients are taken up across the plasma membrane directly

from the environment, common among protists

● Decomposers - feed on dead organic matter for example, the plasmodial

slime molds

● Others live inside other organisms and absorb nutrients from host (if it

damages host, it is a parasite

Endosymbiosis theory - origin of chloroplasts

● Protist engulfed a cyanobacterium

Evidence similar in concept to evidence for endosymbiotic origin of mitochondria.

Primary endosymbiosis - occurred in the common ancestor of the plantae (thus in

common ancestor of land plants, green algae and red algae)

Four other major protists lineages include some group of species with chloroplasts

● But these chloroplasts surrounded by three or four membranes instead of two

Apicomplexans have a residual chloroplast

Early evolutionary split occurred between unikonts(one flagellum) and bikonts

(two flagellum)

Excavata - live inside animals, many mutualistically

● Includes free living, symbiotic, and parasite species

● Are all single celled

● Most swim using their flagella

○ Parabasalids

○ Diplomonads

Plantae

● Monophyletic group

● All subgroups descended from a common ancestor that engulfed a

cyanobacterium

Subgroups

● Glaucophyte algae

● Red algae
 ● Green algae

● Land plants

Rhizaria

● Single celled organisms that lack cell walls

● Some species have elaborate shell like coverings

● Move by amoeboid motion and produce long slender pseudopodia

11 major subgroups

Alveolata

● flattened , membrane bound vesicles, called alveoli, located just under their

plasma membranes

● Unicellular, but diverse in morphology and lifestyle

Some species are capable of bioluminesce

Stramenopila

● At some stage of life cycle, have flagella covered with distinctive hollow

hairs

○ Synapomorphy

2/7/20

Chapter 28: Green algae and land plants

An ecosystem consists of

● All the organisms in a particular location

 ● Non Living physical components of the environments such as

○ The atmosphere

○ The soil

○ The temperature

Ecosystem services - provided by green algae and land plants include

● Producing oxygen

● Building soil by providing food for decomposers

● Holding water in soil

● Holding soil and preventing nutrients from being lost to wind or water

erosion

● Moderating the local climate by providing shade and reducing the impact of

wind on landscapes

Land plants are the dominant primary producers in terrestrial ecosystems

Land plants are the key to the carbon cycle

● Take CO2 from the atmosphere and reduce it to make sugars

● Fix much more CO2 than they release

Artificial selection for plants with certain properties has led to dramatic changes in

plant characteristics

Plants provide us with important sources of raw material for clothing, rope, and

household articles such as towels and linens

 ● Woody plants provide

○ Lumber for houses and furniture

○ Fiber for papers

Medicines - at least one molecule derived from plants

Most of these compounds are synthesized by plants to repel herbivores

Biologists have long hypothesized that green algae are closely related to plants on

the basis of several key reasons

● Their chloroplast is the same

● Their thylakoid arrangements are similar

● Their cell walls, sperm, and peroxisomes are similar in structure and

composition

● Their chloroplasts synthesize starch as a storage product

Nonvascular plants

● Lack Vascular tissue (veins in plants)

○ Specialized groups of cells that conduct water or dissolved nutrients

throughout the plant body

● Include mosses

● Use spores, not seeds, for reproduction and dispersal

Seedless vascular plants

● Have well-developed vascular tissue

 ● Do not make seeds; use spores for reproduction

● Includes ferns

Seed plants

● Have vascular tissue

● Make seeds

○ Seeds consist of an embryo and a store of nutritive tissue, surrounded

by a tough protective layer

● Include angiosperms(encased seeds) or flowering plants and

gymnosperms(naked seeds)