Exam 2

An Introduction to Population Genetics:

a. In earlier lectures, we learned that natural selection acts upon the individual, but its

results (evolution) are measured at the population level. Until now, we have been

concentrating on the state of inheritance and variation at the level of the individual.

b. In this, and the next few lectures, we will focus on how things occur at the population

level. That is, how genes/alleles change in a population over time, how species are

created, and how populations grow, will be our topics of class time over the next 2-3

weeks.

c. The key question to be answered within this lecture is: How do we know when the genes

of a population have changed? In other words, how do we know evolution has taken

place?

II. Let’s start back with the Monohybrid Cross:

a. The mating of two purebred individuals having a trait that is caused by 2 alleles within a

population yields an F1 generation of heterozygous individuals (See below).

b. The crossing of these hybrids yields an F2 generation of individuals that have one of two

phenotypes, but three distinct genotypes.

Example: P1: RR x rr

F1: Rr Rr x Rr

c. If the alleles in question (R and r) did not come from a single organism (as in our

previous work), but were randomly selected in pairs from a pool of independently

occurring alleles within the population, the resulting genotypes, and their probabilities,

would be represented by:

(R x R) + (r x R) + (R x r) + (r x r) = 1.0

Combined to: R2 + 2Rr + r2 = 1.0

R r

R

r

F2: RR Rr

rR rr

d. We can say that the alleles R and r represent the frequencies at which the alleles R and r

occur in our population.

e. The allele frequencies are multiplied together (e.g., (R x R) and (R x r)) because the

alleles are independently passed from one generation to the next, and represent the

probability that those particular alleles will be paired up in our random draw and

subsequent mating.

f. The total accumulation of these genotypes equals 1.0, because they represent the entire

(100%) population.

g. The equation R2 + 2Rr + r2 = 1.0 is a representation of the frequency of the different

genotypes within the generation created by the hybrid parents.

h. By convention, we refer to p as the frequency of one allele in the gene pool and q as the

frequency of the second allele at the same locus in the gene pool.

i. Since there are only two alleles at this locus in the pool, the sum of their frequencies must

equal 100% of the alleles.

Therefore, p + q = 1.0

And their combined genotypic frequencies can be

expressed as:

p2 + 2pq + q2 = 1.0

This equation is referred to as the Hardy-Weinberg Equilibrium equation.

j. If more than 2 alleles are present in a population at the same locus, their combination is

still a product of the sums of the alleles.

i. Ex. If there are 4 alleles (p, q, w, z), then p + q + w +z = 1.0 and

(p + q + w +z) x (p + q + w +z) = 1.0.

The resulting genotypic frequency is:

p2 + 2pq + 2pw + 2pz + q2 + 2qw + 2qz + w2 + 2wz + z2 = 1.0

k. Obviously, the genotype represented by p, q, w, and z cannot exist in a single organism

where only two alleles are allowed (they are diploid after all!), the combination of the 4 alleles

and their frequencies can be assembled in an imaginary individual that represents an average

individual (of sorts) in the population that has each of the alleles at the given frequencies.

III. What does the Hardy-Weinberg Principle do for us?

a. Before H-W we thought:

i. Dominant traits would eventually go to fixation in a population and recessive

traits (unless they were selected for) would go away.

ii. Or alleles would get distributed equally (50/50 in a 2 allele set),

iii. And/or the only way alleles change frequency was through sexual reproduction.

b. H-W says:

i. p is always the same generation after generation.

ii. q is always the same generation after generation.

Example, if 2 alleles at one locus are A and a

A = p = 0.7 and a = q = 0.3 and p + q = 1.0

The genotypic frequency of AA in the next generation is 0.49 (=p2), aa=0.09

(=q2), and Aa = 0.42 (=2pq). That is to say, the genotype AA is 49% of the

available allelic combinations (or genotypes) in this population.

The allele frequencies in this generation are:

p = 0.49 + ½(0.42) = 0.7

and q = 0.09 + ½(0.42) = 0.3

0.49 (or 0.09) because 100% of those gametes coming from homozygous

individuals will contain just A (or a) plus half the gametes from Aa will be A (or

a).

c. Assumptions of the H-W model

i. Random mating

ii. No mutation

iii. No migration

iv. Infinite population size

v. No natural selection

d. Notes about the assumptions:

i. Assumptions are with respect to particular alleles at locus in question.

ii. If any one of these assumptions is violated, then H-W does not apply.

iii. If the allelic frequency does not match from one generation to the next, then

something is happening to the population.

iv. Points to one or more of the assumptions as the culprit.

e. How do we tell when there is change in a population over time?

H-W as a Null Hypothesis

i. The H-W equilibrium hypothesis acts as a null hypothesis for the sake of

determining whether genetic changes are taking place at a particular locus within

a population.

1. For now, know that a null hypothesis is a standard, caused by

randomness, that we compare our actual data against to determine

if change has occurred. If the change in our data from one

generation to the next is greater than what randomness would

allow for (the H-W model), then we say that the null is rejected (H-

W is rejected) and the population has evolved (change in allele

freq. over generations). If the change in data is within what

randomness would predict, then the population has not changed,

and evolution has not taken place.

ii. Therefore, if you detect change in a population (and H-W says you shouldn’t) you

must assume that H-W does not fit your population (you reject it) and that

something is causing the changes (likely a violation of one of the assumptions).

iii. Your job then becomes one of finding out what it is that is causing the change

(which is the more fun aspect of population ecology).

iv. Typically, researchers do not go through the process of testing first whether H-W

is violated. They usually see what they think is a change, hypothesize what is

causing the change, develop an experiment to test it, and form conclusions.

Researchers use the genetic change in a population as evidence that one of the

violated assumptions is causing a change in the population (i.e., the population

has evolved).

Summary:

An Introduction to Population Genetics outlines the principles of how evolution is measured at the population level. Natural selection acts on individuals, but evolutionary changes are observed through gene and allele frequency shifts over time in populations. This lecture series introduces key concepts like the Monohybrid Cross, where the mating of purebred individuals leads to an F1 generation of heterozygous offspring. The resulting genotypes can be predicted using allele frequency equations. The Hardy-Weinberg Equilibrium (H-W) principle states that allele frequencies (p and q) remain constant under specific assumptions, including random mating and no selection. If these assumptions are violated, it indicates that evolution has occurred within the population. The H-W model serves as a null hypothesis to identify genetic changes, and researchers often investigate the reasons behind these changes if they are detected, suggesting a complex interplay of factors influencing population genetics.

—

Week 6 (2/25) - Ways in which populations change, thus violating H-W assumptions: - Bottlenecks: - Significant reduction of the gene pool leads to lower allele diversity. - Example: Cheetahs have experienced bottlenecks causing non-random mating and small population sizes. - Genetic Drift: - Constant changing of allele frequencies in a population over time due to random mating. - Changes are not adaptive and are most influential in small populations. - Can lead to fixation or loss of alleles without increasing overall diversity. - Gene Flow: - Movement of individuals and alleles between populations. - Often equilibrates allele frequencies, increasing diversity in the recipient population. - Non-random Mating: - Violates randomness assumptions of the H-W model. - Includes Assortative Mating, Inbreeding, and Sexual Selection. - Assortative Mating: Mates are selected based on similar or dissimilar phenotypes. - Inbreeding: Mating of closely related individuals causing inbreeding depression. - Sexual Selection: Non-random selection often favors traits that help obtain mates, leading to sexual dimorphism.

Changes in Population Genetics and other Mechanisms in Evolution

Ways in which populations change, thus violating H-W assumptions:

a. Bottlenecks:

i. One of the more frequent causes of H-W assumption violation is in the form of

Bottlenecks

ii. A bottleneck is where a gene pool is significantly reduced for some reason and a

relatively small allele diversity remains.

1. For example, Imagine a population has the alleles A, a, B, b, C, c, D, d, E,

and e in it at one locus. If something happens that eliminates some of the

alleles at that locus (fire destroys that part of the population with those

alleles, the few members with one or two specific alleles migrate away,

etc.), the population is left with a smaller diversity of alleles in the gene

pool. As a result of the lower allele diversity, the population may be more

subject to environmental stressors.

iii. It is thought that cheetahs have gone through 2 bottlenecks in their history.

These bottlenecks have caused them to directly violate 2 of the assumptions of the H-W

hypothesis: They have non-random mating, and small population sizes. As a

result, their populations are experiencing severe genetic problems (See inbreeding

depression below) and are declining significantly.

b. Genetic Drift

i. Genetic Drift is the constant changing of allele frequencies (that percentage of all

alleles any one, or more, allele occupies in a population) in a population over

time, due to random mating.

ii. Random mating has the effect of changing how frequently an allele is found in a

population. For example, imagine a population consisting of allele A at 60%

frequency (0.6) and allele a at 40% (0.4). If by random chance many of the aa

individuals do not mate, the next generation may have a different allele frequency

distribution, say 70% of the alleles are A and 30% are a. In the next generation,

by chance, some of the individuals with A die off (and thus have no offspring).

The resulting offspring may have a new allele frequency, say 55% A and 45% a.

iii. Keys to understanding genetic drift are that

1. Genetic drift is Random

2. Any change in allele frequency is due to chance.

3. Allele frequencies are constantly drifting up and down over time.

4. Allele changes are not adaptive

5. Drift is most influential in small populations (know Bottlenecks and

Founder events/effects)

6. Drift can lead to the fixation or loss of alleles

7. Genetic drift does not increase allele frequency distribution in a

population. In other words, drift cannot increase the diversity of alleles in

a population, it only changes the relative abundance of existing alleles

within a population.

8. Drift from generation to generation is not a violation of H-W, because the

allele changes are within what randomness would predict is ok, and one of

the assumptions of the H-W equilibrium is that randomness is occurring.

c. Gene Flow

i. The movement of individuals and their alleles from one population to another is

referred to as Gene Flow.

ii. Gene flow typically results in equilibrating allele frequencies between

populations. That is, flow makes the populations look more alike genetically.

iii. Gene flow into a population is one of two ways in which allele frequency

distribution (i.e., allele diversity) increases. Although it may cause a decline in

allele diversity in the population that the individuals are emigrating from. The

other way to increase allele diversity is mutation.

d. Non-random Mating

The H-W model is based on mates being selected at random. However, random

mate selection is not the norm in insects, vertebrates and many other animals. Even in

organisms that broadcast gametes, population mixing is not entirely homogeneous.

For example, grasses are pollinated by wind carrying pollen from plant to plant. A

particular plant is more likely to be pollinated by a plant nearby, than one farther away.

This is not random with respect to the entire interbreeding population.

There are three different ways in which non-random mating occurs: Assortative

Mating, Inbreeding, and Sexual Selection.

i. Assortative Mating

1. An individual is more likely to mate with another that is similar in

phenotype to itself (Assortative Mating), or mate with another that has a

different phenotype from itself (Disassortative Mating).

2. Examples:

A. People

B. Plants

C. Blister beetles

D. Wolves.

ii. Inbreeding

1. Inbreeding is the mating of individuals that share a recent common ancestor.

“Recent” is relative to the organism in question and the intent to introduce

novel alleles into the offspring, or maintain allele frequency distributions the

way they are. As an example, consider the cheetahs from earlier in the

lecture. The species as a whole is so similar genetically, that almost any

mating between two cheetahs might be considered inbreeding, even if the

two mates and their ancestral lines have been separated for many

generations. The resulting offspring may exhibit inbreeding depression (see

below). Those that are involved in trying to increase the numbers, and

species health, of cheetahs keep strict records of genetic lines and who

mates with whom, so as to maximize genetic diversity in resulting offspring.

Alternatively, an ancestral line of pea plants may be able to inbreed parent

to offspring for multiple generations without seeing much of an effect.

(Note: this is not necessarily specific to animals vs. plants. See example of

Cardinal flower below.)

2. Inbreeding individuals are likely to share alleles they inherited from their

common ancestor, causing Inbreeding Depression.

Inbreeding depression is the loss of fitness as homozygosity in resulting

offspring, future generations, and the population increases and

heterozygosity decreases. Evolution does not occur here since allele

frequency does not change. Only the genotypes do.

Why is homozygosity a problem?

3. Inbreeding examples from humans

4. Inbreeding example of Cardinal flowers

iii. Sexual Selection

1. Special case of natural selection that favors individuals with traits that

increase their ability to obtain mates.

2. Acts on males more so than females because females are typically the higher

investment sex. Since females invest so much in their offspring, they should

be choosy about what males they mate with. They should choose males that

appear the most healthy, wealthy, and/or wise. Males invest little.

Therefore, they should be willing to mate with any female. Therefore,

females of many species look less showy/large.

3. Examples of sexual selection: pea-fowl, guppies.

Female Choice

4. Females will often choose males with good alleles. But, how do they tell if

males have good alleles?

5. Those that have a healthy body can “afford” to have bright feathers/beaks,

long tails, colorful bodies. Those that are not healthy, spend their energy in

body maintenance, and cannot develop such “extras”. Therefore, females

choose mates that are brighter, showier, larger, or have more resources.

(Careful, though; sometimes males lie!)

6. Sometimes though they choose mates on other criteria, like a willingness to

provide resources, care for young, defend territories, etc.

Male- Male Competition

7. Sometimes males compete with one another for mates. Typically, the

biggest and strongest are the ones that get the mates. Often, this is

interpreted as females choosing the biggest and strongest mates (i.e. female

choice). However, the traits that are being selected for here are sorted out

by the males not the females. See the white-tailed deer example.

8. Both forms of sexual selection can lead to Sexual Dimorphism, the

tendency of the two sexes of a species to look different. Careful, not all

species that exhibit sexual dimorphism are that way due to sexual selection.

### Changes in Populations and Violations of Hardy-Weinberg Assumptions - **Bottlenecks**: - Significant reduction in gene pool leads to lower allele diversity (e.g., cheetahs). - Results in issues like non-random mating and small population sizes, causing genetic problems. - **Genetic Drift**: - Random changes in allele frequencies over time, especially in small populations. - Can lead to fixation or loss of alleles without increasing overall diversity. - Drift is random and does not induce adaptation; does not violate H-W if changes are due to chance. - **Gene Flow**: - Movement of alleles between populations, equilibrating allele frequencies. - Increases diversity in recipient populations but may decrease diversity in donor populations. - **Non-random Mating**: - Violates assumptions of random selection in H-W model. - Includes assesses causes like assortative mating (similar phenotypes), inbreeding (mating of closely related individuals), and sexual selection (traits that aid in mate acquisition). - Inbreeding can lead to decreased fitness in offspring (inbreeding depression).

WEEK 6, Pt. 2

Week 6 (2/27)

Species and Speciation

I. History of Taxonomy and Nomenclature

Throughout time, people have been interested in understanding the diversity of life around

us: how the different forms were created, why they were created, how they should be

organized, etc.

Up until the 18th century, scientists were frequently confused by the several names that

existed for individual plant specimens. Local scientists would have their own names for

common plants and would use those names when talking with others from different areas.

Entire conversations would be held between botanists from different areas about the virtues

of plants they thought were specific to their areas, and then, maybe, they would find out in

the end that they were talking about the same species.

Additionally, the scientific names given to plants consisted of very long strings of Latin

words that could be changed at the will of the person studying them. Frequently, when a

scientist would discover a name used in a different locale for a plant they already knew,

they would just add the new name to the existing one. Some plants had names consisting

of 15-20 words!

In the 1700’s Carolus Linnaeus (the Latinized name Karl von Linné gave himself) began

the task of creating a set of rules for the naming of plants and attempted to classify all the

plants he could get his hands on. He eventually classified and named over 12,000 plants

and animals! Not only was he doing this to help standardize the naming of plants for

scientific purposes, but he felt that by organizing and naming all the plants (and then

animals) in the world, he (and scientists) would have a better understanding of God, and,

thus, be closer to God.

Although binomial nomenclature (two descriptive words given to identify a species) is

credited to Linnaeus, he did not invent it. He just used it to such a degree that most give

him credit for establishing its use.

II. The Taxonomic Hierarchy

Linnaeus also provided us with one of our first real taxonomic hierarchies

A. What is a taxonomic hierarchy?

1. A Taxonomic Hierarchy is a system of classifying and naming species for the

purpose of understanding and establishing relatedness between species or larger

groupings.

2. The taxonomic hierarchy has 7 basic levels: Kingdom, Phylum, Class, Order,

Family, Genus, and Species. The last two (Genus and Species) are the words

used to name an individual type of organism. They are used in text by either

underlining the words or writing them in italics (because they are Latin).

Additionally, the genus name (plural: genera) uses a capital letter at its start

where the species name (singular and plural: species) starts with a lower case

letter (See example below.).

3. In some systems of classification, you may find the prefixes super- and sub-

(e.g., Superorder, or Subfamily) to describe further refinement of groupings

above and below a certain level, respectively.

B. How many kingdoms are there?

1. Linnaeus divided all life into two kingdoms: Plantae and Animalia.

2. Some have used a 3-kingdom hierarchy: Plantae, Animalia, and Fungi.

3. Until recently, the most commonly used hierarchy included 5 kingdoms:

Monera, Protista, Plantae, Fungi, and Animalia. Many now use the Domains

(level above Kingdom) Bacteria and Archaea instead of Monera and then use

the other four groups to describe all the rest (included in the domain

Eukarya).

C. Example: White-tailed deer (Odocoileus virginianus). Note, the descriptions for each

level are not complete for that given level (i.e., hair and mammary glands are not all

that go into identifying mammals), but are provided for some descriptive guidance.

Domain Eukarya

1. Kingdom: Animalia - animal

2. Phylum: Chordata – has a spinal cord

3. Class: Mammalia – has hair, mammary glands

4. Order: Artriodactyla – quadruped with even number of digits

5. Family: Cervidae – bony antlers

6. Genus: Odocoileus – small groups, white hair under tail

7. Species: virginianus – Odocoileus virginianus - antler points extend from

single main beam

III. What is a species?

A species is an evolutionarily independent group, meaning that mutation, selection, and

drift act on the group independently of what’s happening in other groups.

Remember, gene flow between groups causes allele frequencies to be the same. If gene flow

stops, then mutation, selection, and drift begin to work independently between groups.

Although these things are working all the time at some level. If new alleles arise in one

group, there is no way for it to get to the other group. If allele frequencies change

sufficiently over time, populations become distinct species.

There are 3 different criteria for designating species. They involve the Biological,

Morphological, and Phylogenetic species concepts.

A. Biological Species Concept:

1. If two populations do not interbreed in nature, or do so but fail to produce viable

offspring – they are separate species.

2. There are two ways in which groups can be prevented from forming viable

offspring:

a. Prezygotic isolation - prevention of individuals from mating and creating

a zygote – fertilized egg (Example: lightning bugs).

i. temporal- breeding at different times

ii. habitat- breed in different habitats

iii. behavioral – courtship displays differ

iv. gametic barrier – eggs and sperm are incompatible

v. mechanical – genitalia incompatible

b. Postzygotic isolation – (zygote) offspring of individuals do not survive or

reproduce (Example: horse, donkey, and mule)

i. hybrid viability – offspring die as embryo

ii. hybrid sterility – offspring mature, but are sterile

3. The biological species concept is problematic for distinguishing species in the

fossil record and for organisms whose populations do not overlap (they cannot

interbreed).

B. Morphospecies Concept:

1. Differences between groups in size, shape, or other morphological features

(and sometimes in behaviors), indicate the two groups are different species.

2. Logic is that in order to be this different, the populations must have been apart

and separated long enough to become distinct species.

3. The morphospecies concept works with sexual, asexual, and fossilized/extinct

species.

4. Problems arise because traits are often subjective. Differences seen between

groups of organisms may represent variation within the species, the effects of

genetic drift, mutations, and/or natural selection.

5. Example: Cooper’s and Sharp-shinned hawks.

C. Phylogenetic Species Concept:

1. Phylogenetics is the reconstruction of the evolutionary history of populations.

2. This concept takes into account a variety of traits specific to the population in

order to establish relatedness between groups, and, therefore, distinction

between them. Species are determined by populations having distinctions

from other populations, whether these distinctions are morphological,

behavioral, or genetic.

3. Phylogenetic analysis results in a Phylogenetic Tree – a branching diagram

that depicts relatedness/distinction among groups.

4. Branches within the tree represent a population through time.

5. Nodes (where branches come together) are points in time when an ancestral

group split into 2 or more descendant groups, each group represented by each

branch.

6. Terminal nodes at the ends of branches represent a group (species, or larger)

- living or extinct.

7. Phylogenetic analyses are performed using one of two methods:

a. Phenetics – Grouping of species by similarity of traits, whether those

traits are ancestral or more recently derived.

b. Cladistics – Grouping of species by shared, recently derived

characters only.

i. Monophyletic group – Most recent common ancestor and all its

descendants

ii. Paraphyletic group – Most recent common ancestor and not all of

its descendants. This is not a really useful tool to studying

phylogenies, but is often used when trying to clarify the loss of

evolved traits and convergence.

iii. Cladistics is largely based on the idea that species with recently

evolved traits are likely closely related. In other words, the

independent evolution of a trait in multiple genetic lines is much less

likely than it evolving once in an ancestor and that ancestor passing

that trait to its various descendent lines, especially for those traits

relatively recently evolved.

8. In theory because we can track genetic differences between almost all

populations within a species, (and even between individuals within a pop), we

could end up with a huge number of species (each individual is one). That’s

one of the problems with this system.

9. Another is that if you do not choose the correct suite of traits to compare, you

could end up with garbage.

10. Other terms in phylogenetics:

a. Homology – traits are similar due to a shared ancestry

b. Homoplasy – traits are similar due to other reasons than common

ancestry.

c. Convergent Evolution – the independent evolution (by natural

selection) of similar traits in distantly related organisms, where the

common ancestor does not have the trait. (most common cause of

homoplasy)

d. Parsimony – the most likely explanation or pattern is the one that

implies the least amount of change (i.e., the simplest).

D. The designation of a species is typically done with a variety of methods. Consider the

Golden-winged vs. Blue-winged Warbler example.

E. The use of phylogenetics to solve problems of maintaining genetic diversity is highly effective, if done right (See the example of the Dusky Seaside Sparrow).

IV. How do we get new species?

A. The creation of new species from old species is a process that is based on isolation of one or more groups from an ancestral group, and the genetic divergence between th new and ancestral groups. Remember, populations are continuously changing.

Speciation is not one group separating into two new species then those separating into two new species, etc. Speciation occurs when subgroups are isolated (reproductively) and divergence occurs during this separation. The ancestral population may continue to look roughly the same for a very long time (i.e., they maintain their species identity), while the new group diverges dramatically, or the two groups may diverge more or less equally.

B. Speciation can occur in Allopatric and Sympatric populations.

C. Allopatric speciation. Allopatric speciation occurs when subpopulations are

separated by some physical barrier. The two subpopulations remain reproductively

isolated (no gene flow) and, over time, diverge from each other (due to genetic drift,

accumulation of mutations, and/or by natural selection differences between

populations). After enough genetic divergence has taken place, the two populations

may be classified as distinct species. Allopatric speciation may occur due to:

1. Dispersal – When a group emigrates from an area, and they are isolated long

enough to have allele changes that eventually lead to a new species.

2. Vicariance – When a population is divided by a change in the geologic

landscape. If the sub populations remain separated long enough, allele

frequencies will change enough to call them separate species.

D. Sympatric Speciation. Sympatric speciation occurs when new species are created in

areas where there is no physical barrier between subpopulations, meaning they could

interbreed. Traditionally, scientists thought you couldn’t get sympatric speciation.

Gene flow between groups would overwhelm differences that occur.

However, if parts of a population prefer certain foods or habitats, they may eventually

become separate species. This is what happened with the Golden-winged and Blue-

winged Warblers. Where they overlap, they prefer slightly different habitats,

(competition will be covered later). They did this long enough to separate

morphologically and genetically, but not biologically. Also consider Apple Maggot

Flies.

E. What happens if the newly formed species come back into contact? You may get:

1. Reinforcement of species – if pops. can interbreed, and produce young, and

hybrids have suppressed fitness (sterile or lowered fitness), then selection

would favor those that do not interbreed, then further separation will occur.

2. Hybrid zones – Areas where 2 populations overlap and hybrids exist. May be

small or large, short-lived or long-lived

3. New species through hybridization – hybrids contain a unique blend of

alleles from parents and therefore different characteristics. If these traits can

be selected for, then the genes are passed on to the next generation. A new species may be created as a result.

• History of Taxonomy and Nomenclature:

  • Linnaeus began standardizing plant names in the 1700s, creating binomial nomenclature.

  • Established a structured system for plant and animal classification.

• Taxonomic Hierarchy:

  • System of classification with 7 levels: Kingdom, Phylum, Class, Order, Family, Genus, and Species.

  • Linnaeus divided life into two kingdoms (Plantae and Animalia); later classifications include up to 5 kingdoms or more, considering Domains.

  • Example: White-tailed deer (Odocoileus virginianus) is classified under Domain Eukarya.

• What is a Species?:

  • A species is an evolutionarily independent group, undergoing mutation, selection, and drift separately.

  • Three criteria for defining species: Biological, Morphological, and Phylogenetic.

  • Biological Species Concept:

  • Distinguishes species based on reproductive isolation (prezygotic and postzygotic barriers).

  • Morphospecies Concept:

  • Identifies species by differences in size, shape, or other features.

  • Phylogenetic Species Concept:

  • Uses evolutionary history and traits to define species, illustrated by a phylogenetic tree.

• How Do New Species Form?:

  • Speciation occurs through reproductive isolation and genetic divergence of groups.

  • Types of speciation:

  • Allopatric Speciation: Groups are separated by physical barriers leading to divergence.

  • Sympatric Speciation: New species arise without physical barriers, often due to behavioral or habitat preferences.

  • When newly formed species come into contact, outcomes include reinforcement, hybrid zones, or new species through hybridization.

Week 7:

Lecture for week 7 (3/4)

Intro to Plants and Plant Diversity

I. Introduction

The Kingdom Plantae includes all the land and aquatic plants and the green algae, but recently the red algae

and an additional small, primitive algal group have been included in the Plantae. For our purposes though,

we will just include the green algae and land/aquatic plants as constituting the Kingdom Plantae, and

exclude other algae.

A. Some major characteristics of Kingdom Plantae.

1. Chloroplasts with chlorophyll a, b and β-carotene for wider spectral sensitivity – in green

algae and all land plants – evolved for early competition for sunlight.

2. Multiple membrane layers in chloroplasts [thylacoid condition = stacked and flattened vesicles

without connection to the inner of two membranes enclosing the chloroplast), for more

efficient extraction of radiant energy

3. Cellulose cell wall outside of flexible cell membrane (for greater protection – and structural

support)

4. Starch as an energy storage product

B. Conditions leading to the evolution of Plantae

1. Wavelength resource limitation

Photosynthesis evolved in early unicellular bacteria (Prokaryote: Cyanobacteria) with the

appearance of a pigment molecule able to absorb radiant energy and transform it into high-energy

chemical bonds that could be used as an energy source by the cell for many metabolic purposes.

Different pigments eventually evolved as the competition for different wavelengths of light

penetrating the sea surface intensified with the increased diversity of aquatic autotrophs.

Unfortunately, water also absorbs radiant energy, especially in the red end of the visual spectrum

(which makes ocean water appear blue). Thus, the radiant energy available to marine organisms

is much less just below the sea surface than a few centimeters above it (with the blue end of the

spectrum reaching farther down), and natural selection would favor early autotrophs able to reach

above the sea surface even if just for short periods.

2. CO2 was also becoming less available, and oxygen more available, in the shallow marine waters

congested with marine autotrophs. Here again, the air above the water had much more readily

available CO2 than was dissolved in sea water. Clearly, the early aquatic environment had

become saturated with early autotrophs competing for a shrinking resource base of energy and

CO2. Some early life forms at this time evolved the ability to attack other life forms for

food/energy instead of competing for solar radiation. And so, an evolutionary progression was

evident in the early oceans from autotrophy with different pigments, to heterotrophy (organisms

eating organisms as an energy source), and eventually to parasitism (nibbling the surface of larger

forms that couldn’t be engulfed). There were few available niches left in the early sea, at least for

single cell or simple multicellular organisms.

3. Evidence of early competition for energy sources in the aquatic environment:

a. Elongated cells in multicellular algae (to reach above neighbors to access sunlight and CO2)

in the very surface water. Elongated cells appear in multicellular algae to reach areas with

more light (e.g. kelp), sometimes 30 m above the sea floor. It is easier to diffuse substances

within parts of the same cell than transferring substances across cell membranes/cell walls,

even if intercellular pores are present.

b. Increased contractile fibers and cytoplasmic streaming to distribute energy products and

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gases within different parts of larger and elongated cells, and between cells, in multicellular

organisms. Larger cells evolved to reduce predation risk and to help expose at least some

plant parts to increased radiant energy, such as at or above water surfaces.

c. Cellulose, silicon and calcium carbonate were used by the photosynthetic protists (e.g.

diatoms) to strengthen their cell membranes against predation, with cellulose becoming the

common constituent of the cell wall of all land plants. This physical protection could also

protect those protists pushed to the edge of the sea in the splash zone along ancient shores.

4. New niches: Untapped possibilities (resources) were just centimeters away in the air above

very shallow water or on land: Land invasion and the evolution of land plants.

a. Resources out of the water

1) Sunlight unfiltered and unabsorbed by water, and hence energy is more available

2) CO2 is more available in air than in water, and photosynthetic organisms

were being driven to the most surface waters and even momentarily out of the

water and onto land to get enough CO2 [diffusion of CO2 occurs about 10,000

times faster in air than water]

3) Freedom from heterotrophs, at least early in the evolution of land plants

b. The important challenges of life on land

1) Dehydration and getting enough water for photosynthesis

2) Support of plant structure above ground (overcoming gravity)

3) Transport of water within the plant from buried or submerged cells to air-exposed cells

4) Transport of photosynthate sugars to non-photosynthesizing cells, such as “root” cells

5) Sexual reproduction in dry environments where flagellated sperm can’t swim.

6) Exposure to harmful ultraviolet radiation (blue end of the wavelength spectrum);

fortunately some pigments evolved to absorb blue wavelengths and offer protection.

II. Major Plantae Groups, showing an ever increasing ability to live out of water as aquatic and then

terrestrial niches gradually became more congested with different plant types: the competition observed in

the early seas among the bacteria and protists just continued out onto land, showing the structural

adaptations and concurrently the reproductive adaptations acquired to achieve gamete

union in a dehydrating environment. The plant groups below reflect this trend of increasing

structural complexity to deal with more harsh/competitive environments from the simplest to the most

highly evolved plants.

A. Non-vascular plants without cuticle: purely aquatic, simple plants with no major adaptations for

existence on land (e.g. green algae).

1. Mainly immersed in nearshore and freshwater habitats

2. Division (Phylum) Chlorophyta (Green algae)

Ex. Charales. An order of green alga believed to be the closest relatives of green land plants.

They are branched, multicellular, chlorophyll-using plants that grow in fresh water. They are

often called stoneworts, because the plants can become encrusted in lime (calcium carbonate) in

hard water. There is no specialized transport tissue.

The remainder of plant phyla are only briefly covered here.

B. Non-vascular plants with cuticle: Parts of plants out of water have a cuticle that gives dehydration

resistance, but lack of support structure (and vascular tissue) results in low, sprawling growth (e.g. true

mosses). Extending out of the water just a little greatly increases wavelength and CO2 availability.

1. Mosses have specialized conducting tubular cells,

2. First to have stoma,

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3. Water/nutrient intake and intercellular transport mainly by diffusion.

4. The gametophyte (haploid) is the dominant life cycle stage

5. Diversity: 3 Divisions (Phyla): mosses, liverworts and hornworts

a. Largest Phylum: Bryophyta (Mosses)

b. First land plants (mosses); but not the ancestors of higher plants.

c. Sphagnum moss during drought becomes dormant until water returns

C. Vascular, seedless plants: The first plants with true vascular tissue enabling them to grow to

greater heights, reaching above the non-vascular plants to compete for sunlight, but still limited

sexually to moist environments because of depending on flagellated sperm for reproduction (e.g.

ferns). Again, notice the evolutionary consequences of congested living.

1. Vascular system

2. The sporophyte (diploid) is the dominant life cycle stage, as in all higher (land) plants.

3. Diversity: 4 major Divisions: Club mosses, Horsetails, Whisk ferns, Ferns.

Largest Phylum: Pteridophyta (Ferns): largest leaves, many epiphytes, oldest vascular

plants, ancient 20 m high tree ferns.

D. Vascular, naked-seed plants (=gymnosperms): the innovation of pollen (~ air-borne sperm) and

dehydration-resistant seeds enable greater freedom (and dispersal) of sexual reproduction on land (e.g.,

cycads and conifer trees), but absence (= naked) of fruit (= developed ovary) compromises even

greater seed dispersal.

1. Seed is 1st major innovation:

(1) protects embryo against water loss, (2) protects the embryo against herbivores, (3)

permits dormancy, and (4) promotes dispersal.

2. Pollen is 2nd major innovation.

3. Cones of males (small) and females (large) usually in separate trees; scales partially protect

female megaspore (eggs).

4. Needles of conifers reduce the photosynthetic surface, but this feature in combination

with pollen allow conifers to thrive in more arid habitats.

5. Diversity: 4 major Divisions: Cycads, Ginkgos, Gnetophytes, Conifers (pines, spruces, firs)

a. Largest Division: Coniferophyta (Pines/spruces/firs)

b. Includes the largest (redwoods, sequoias) and oldest (Bristle cone pine ~ 4,900 yr) plants

E. Vascular plants with fruit-covered seeds (=angiosperms, the flowering plants). The fruit increases

the protection and dispersal of seeds; the largest number of species of all plants.

1. Flower: a major innovation over gymnosperms: they facilitate pollination by attracting animal

Pollinators (but many are wind- or water-pollinated).

2. Fruit = a mature, ripened ovary enclosing seed(s);

3. Diversity: One large Division: Anthophyta: the most widely distributed group of all land plants.

a. Traditionally separated into monocotyledonous and dicotyledonous plants. Monocots have

one leaf at germination, scattered vascular bundles, parallel leaf veins,

and flower petals in multiples of 3; dicots have 2 leaves at germination, a circular

arrangement of vascular bundles, branching leaf veins, and petals in multiples of 4 or 5.

b. Most angiosperm plants are annuals (die off at the end of the year leaving only seeds for the

next growing season) and herbaceous (are short-lived and non-woody [little or no lignin]).

SUMMARY:

The Kingdom Plantae encompasses land and aquatic plants, including green algae, while excluding red algae and some primitive groups. Key characteristics include chloroplasts with chlorophylls and β-carotene for light absorption, multiple membrane layers for energy extraction, cellulose cell walls for protection, and starch as an energy storage product.

Conditions Leading to the Evolution of Plantae:

1. Wavelength Resource Limitation: Early photosynthesis occurred in unicellular bacteria (Cyanobacteria) which evolved pigments to absorb sunlight, leading to competition for light in aquatic environments.

2. CO2 & O2 Availability: As marine environments became congested with autotrophs, CO2 became less available, prompting some organisms to shift towards heterotrophy or parasitism for energy.

3. Adaptations in Multicellular Algae: Elongation in cell structures helped access more light, while increased cell size and specialized walls using cellulose provided protection against predation.

4. New Niches on Land: The move to land offered untapped resources like unfiltered sunlight and more CO2, albeit with challenges like dehydration, structural support, and efficient nutrient transport.

Major Groups Within Plantae:

1. Non-Vascular Plants (e.g., Green Algae): Lack adaptations for land, primarily aquatic.

2. Non-Vascular Plants with Cuticle (e.g., Mosses): Developed cuticles for dehydration resistance, but limited vascular support leads to low growth.

3. Vascular, Seedless Plants (e.g., Ferns): First plants with vascular tissue, allowing for greater height and competition for light, yet still reliant on moist environments for reproduction.

4. Vascular, Naked-Seed Plants (Gymnosperms): Innovations like pollen and seeds enabled wider dispersal and adaptability to land, though lacking fruit for seed dispersal.

5. Vascular Plants with Fruit (Angiosperms): Present the highest diversity among plants, featuring flowers for pollination and fruits for seed dispersal, divided into monocots and dicots based on seed and structural characteristics.

WEEK 7 PT.2

Lecture week 7 (3/6)

Plant Form and Function

I. Introduction

We’ll mainly focus on the typical flowering plant, although since the gymnosperms are vascular

plants as well, much of the following description will be true for the gymnosperms. Emphasis will be

on basic morphology associated with the maintenance, growth and reproduction of the mature plant. The

purpose of this lecture is to provide you with a working map of a typical plant. Some variation is added

to provide detail and breadth.

II. Gross functional morphological

A. Root: usually the “below” ground plant part (as opposed to the above ground called the shoot), but

more accurately, that plant part not having leaves or nodes

1. General design

a. Tap root system: long central shaft to store nutrients and reach deeper water tables

b. Fibrous or diffuse root system – primary function is to support plant, secondarily to access a more shallow water supply

c. Tuber – sweet potato (swollen, energy-storing roots)

d. Adventitious (prop) root systems (root emerges from stem just above ground to help

support plants in shallow soils (e.g., tropics)

e. Snorkel roots (pneumatophores): emerge below ground but rise above ground to obtain

oxygen for

respiration within the root. Usually present in species that have roots in water

saturated soil or standing water.

2. General functions:

a. Provides moisture and inorganic nutrients (K, N, P) to plant

b. Attaches plant to the ground to enable them to reach for radiant energy above ground or

to climb (attach to) vertical surfaces for the same purpose, as with Ivy and strangler figs

c. Long term starch storage: carrots, sweet potatoes

d. Access oxygen – pneumatophores on mangroves

B. Stems/trunks/shoot (usually the above ground plant part, with nodes and leaves)

1. General design

a. Axial: central column with spire shape for strength and shedding snows (spruces);

palm trunks are bare to reduce lateral wind pressure in tropical storms

b. Dendritic: Sub-branching (for greater photoreception)

c. Buttressed trunk for greater support in thin tropical soils

2. Functions

a. Transport nutrients/water between leaves and roots

b. Access to available light above surrounding structures

c. Asexual reproduction: lateral stem runners above ground (stolons) and below (rhizomes)

d. Photosynthesis; in arid-dwelling plants, e.g. cactus

e. Water storage: cactus, certain vines

f. Protection: thorns are modified stems

g. Food storage: underground stems: white potato, yams

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C. Leaves

1. General designs

a. Simple

b. Compound

c. Doubly compound (increases lateral leaf reach with minimal increase in leaf mass)

d. Needles, giving maximum water conservation; reduced, but year-round photosynthesis

2. Functions

a. Photosynthesis– large, doubly compounded leaves like ferns with many spaces to

avoid rain damage

b. Water collectors with leaves angled down toward central stem and axil collection basin

c. Attachment to other vegetation for climbing – pea leaf tendrils

d. Defense: most cactus spines are modified leaves

e. Water storage - aloe vera, succulent plants

f. Obtaining supplementary nitrogen – carnivorous plants

III. Plant cell types. All plant cells have a thin cell membrane similar to animal cells, but then in

addition have an outer cell wall with cellulose called a “primary” cell wall. Some plant cells

produce an additional “secondary” cell wall inside the primary cell wall, and these cells then have 3

coverings: a cell membrane, a secondary cell wall, and an outer primary cell wall. The secondary

wall is defined by specialized chemical components corresponding with the cell’s specialized

function, e.g., waxy substances for the cuticle, lignin for maximum strength in xylem tissue. The cell

types below are given in order of their degree of specialization, beginning with the least specialized

cells (and having the greatest ability to become any cell type):

A. Meristematic cells: those undifferentiated, rapidly-dividing cells with just a simple primary cell

wall that comprise those layers of active plant growth: i.e. apical (stem & root tips) and lateral

meristems (cambium). One daughter cell remains undifferentiated and rapidly dividing, but the

other usually becomes slightly “differentiated”, mainly in being less mitotically active and more

ready to produce functionally differentiated cells. These cells do not have secondary cell walls,

and their primary cell walls are thin and flexible to enable the daughter cells to elongate.

B. Parenchyma cells: most common mature cells in the plant, close descendants of meristematic

cells, that are less-actively dividing but still totipotent because they can either revert back to

meristematic tissue or form repair tissue, dermal tissue (outer, single cell layer giving rise to root

hairs, trichomes, leaf guard cells, waxy cuticle), and ground tissue (e.g., leaf mesophyll cells,

root cortex cells. They remain alive and, importantly, make up the phloem cells (sieve-tube cells,

companion cells) of the vascular system. Only primary cell walls, thin and flexible.

C. Collenchyma cells: much less abundant in the plant; they have longer, thicker, primary cell walls

(but no secondary wall) with somewhat more cellulose; they function primarily in support (e.g,

of vascular bundles), but can still stretch and elongate (e.g., in elongation zones near apical

meristems). Celery stalks have strands made of collenchyme cells, as do most vascular bundles.

D. Sclerenchyma cells: cells have an extra, “secondary” cell wall impregnated with lignin; these

cells do not permit stretching and elongation, and are found in non-growth areas of the tree.

They also lose their cytoplasm and die when mature, leaving just the cell wall material. They

are the cell types making up the xylem (pitted Tracheid cells that retain a thin primary cell wall

at the pits, and pitted vessel elements that are larger and have large terminal openings devoid of

all tissue), and the purely supportive tissue of elongated fibers (for making rope, hemp, linen) or

short, tough sclereid cells (reinforce nut shells and seed coats).

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IV. Regional functional morphology

A. Leaf cross section (from top surface inward, although the majority of stomata are on the under

side of the leaf closer to the spongy mesophyll). Consult this diagram of a leaf cross section for

reference.

1. Epidermis

a. Waxy cuticle The cuticle reduces water loss, protects against pathogens, and protects

against herbivores.

b. Trichomes The trichomes thwart small herbivorous insects, reflect excess

incoming solar radiation, and conserve water.

c. Stomata (guard cells + pores); The kidney bean shape guard cells take in water and become

turgid (rigid) when moisture is present, opening a pore between them, but become

flaccid and close the pore during dry conditions. The stomata regulate water vapor

(transpiration) and gas passage into and out of the leaf.

2. Palisade mesophyll (elongated parenchyma cells; site of most photosynthesis)

3. Spongy mesophyll (space for gas and H2O exchange)

4. Vascular bundle in mesophyll (xylem, phloem and supportive collenchyme cells)

B. Stem/trunk cross section of dicotyledon (from bark inward).

Consider this diagram of a cross section of a tree. Be aware the diagram includes phloem as part

of the bark. We are not doing so for this class. The heartwood and sapwood in the diagram make

up the xylem, and the heartwood label would be better positioned in the darker center of the

diagram.

1. Bark (cork cells)

2. Cork cambium: produces cork cells, often with lignin, to outside the cork cambium layer

3. Secondary phloem cells (transport photosynthate, nutrients)

4. Secondary vascular cambium: produces secondary phloem cells to the outside, secondary

xylem cells to the inside, and parenchyma cells horizontally (rays) that transport

fluids/nutrients between inner and outer cells of the trunk

5. Secondary xylem cells (mentioned above) are active in water transport

6. Sapwood (light-colored xylem layer active in water transport).

7. Heartwood (dark-colored xylem in core of a tree that no longer transports water, but serves

as a depot for resin (anti-microbial and anti-fungal properties).

C. Root cross section (from surface inward). Check out this diagram of a root cross section.

1. Epidermis with lateral roots and root hairs (waxy cuticle layer reduced) increase root

surface area for water/nutrient absorption

2. Cortex – parenchyma food-storage cells in the “ground” tissue of the root

3. Vascular cylinder in center, or if multiple, dispersed vascular bundles in cortex

a. Endodermis – important barrier in plant root functioning, site of Casparian strip (See notes

on plant processes.)

b. Pericycle – layer from which lateral roots begin and grow

c. Phloem (primary)

d. Xylem (primary)

D. Growth Zones See this diagram of a root's growth areas. (first pic on the page)

1. Primary growth caused by apical meristems – increases length of root and shoots

a. Root system

1) Cellular Division Zone

a) Root cap (loose epidermal cells); mucigel lubricant secreted to facilitate

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growth through soil

b) Apical meristem – a tiny area of undifferentiated, but actively dividing tissue

c) Primary meristem (just above the apical meristem in root): cells begin to

differentiate.

2) Elongation Zone

3) Absorption Zone

b. Shoot system

Similar to root tip but with leaves and lateral buds instead of

root hairs.

2. Secondary growth caused by lateral meristems (= cambium), resulting in increased

girth (diameter) of the plant.

a. Lateral meristem = cylinder of actively dividing tissue running the length of the plant

and occurring just inside the perimeter of the stem or trunk.

b. Two types of lateral meristems:

1) Cork cambium located outside the secondary phloem cells and produces cork

Cells (bark) only to the outside of the cork cambium layer; no tissue layer is

generated to the inside, as with the vascular cambium)

2) Vascular cambium located inside the cork cambium layer

a) Produces phloem cells to the outside of the cambium layer; this layer

doesn’t increase in width much because, as new phloem cells are added,

older phloem cells disintegrate and are resorbed near the cork cambium

b) Produces xylem cells inside the vascular cambium next to previous xylem

tissue, and since old xylem tissue doesn’t disintegrate, the girth of the tree

increases. Several cell layers occur each growing season, the spring cells

are larger than late summer cells, with the entire seasonal record being one

growth ring.

E. Reproductive Zone (flowers, seeds and fruits)

The Flower

The primary design and function of flowers is to attract pollinating insects, bats, birds and small

mammals by visual and/or chemical information, sometimes just one pollinating species, tailored

by the pollinator (flowers facing down near ground for small mammals, high and facing

upwards for insects and birds). Also, to protect gametes, provide for sexual reproduction,

and promote seed dispersal through fruit formation (a reward for the seed dispersing animal).

1. Conventional Flower - Attracts pollinators, launches pollen, protects ova. Four

basic parts, variable in occurrence and elaboration. See this diagram of a typical flower.

a. Sepals - thicker, leaf-like, photosynthesizing structures that enclose the developing

flower bud and other reproductive structures, protecting them from insects and disease.

b. Petals - generally thinner, leafy, colorful, and scented structures located in a whorl inside

the sepals, serving to attract pollinators. A nectary at the petals’ base may occur, which

contains a nectar reward for pollinators. The entire petal assemblage is termed the corolla.

c. Stamen - the structure producing the male gametophyte (pollen) and composed of a

support shaft (filament) and a terminal pad of pollen (anther)

d. Carpel - the reproductive structure that produces female gametophytes (and eventually

eggs), each composed of a swollen basal ovary with ova, a tubular style, and a

terminal stigma upon which pollen lands and initiates growth of the pollen tube

conveying the male gametes to the ova for fertilization.

2. Seed – consists of a plant embryo, an endosperm as a nutrient source, and a seed coat (this is

roughly like the embryo, yolk and shell of a bird egg. The seed has a longer lifetime and is less

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vulnerable to environmental extremes than a eukaryote spore.

3. Fruit – develops from the ovary as the seed(s) develop in the ovary; they function to

protect the seed(s) from damage and predators during development, and may aid dispersal as

well by attracting predators to eat “ripened” fruit and in the process carry the seeds

elsewhere (the seed coat protects the seeds from digestion by the predator, a frugivore)

I. Introduction
Focuses on typical flowering and gymnosperm plants, emphasizing basic morphology for plant maintenance, growth, and reproduction.

II. Gross Functional Morphology
A. Roots:

1. General Design:
   a. Tap Root: Central shaft for nutrient storage and deep water access.
   b. Fibrous Roots: Support plant and access shallow water.
   c. Tubers: Energy-storing roots (e.g., sweet potatoes).
   d. Adventitious Roots: Support in shallow soils (e.g., tropical plants).
   e. Pneumatophores: Roots that rise above soil to gain oxygen.

2. General Functions:
   a. Supply moisture and nutrients (K, N, P).
   b. Anchor plants and climb vertical surfaces.
   c. Store starch (e.g., carrots, sweet potatoes).
   d. Access oxygen through specialized roots.

B. Stems/Shoots:

1. General Design:
   a. Axial: Central column for strength.
   b. Dendritic: Sub-branching for light access.
   c. Buttressed: Trunks for support in weak soils.

2. Functions:
   a. Transport nutrients/water.
   b. Access light.
   c. Asexual reproduction through stolons and rhizomes.
   d. Photosynthesis and storage.
   e. Protection (thorns).

C. Leaves:

1. General Designs:
   a. Simple, compound, doubly compound, needles for water conservation.

2. Functions:
   a. Main site for photosynthesis.
   b. Water collection and storage.
   c. Attachment (e.g., tendrils).
   d. Defense (cactus spines).

III. Plant Cell Types:
A. Meristematic Cells: Undifferentiated, rapidly dividing cells for growth.
B. Parenchyma Cells: Most common, involved in storage and tissue repair.
C. Collenchyma Cells: Supportive, flexible cell walls.
D. Sclerenchyma Cells: Thickened, non-stretchable, supportive cell walls.

IV. Regional Functional Morphology:
A. Leaf Cross Section:

1. Epidermis: Waxy cuticle, trichomes, stomata for regulation.

2. Palisade Mesophyll: Main photosynthesis site.

3. Spongy Mesophyll: Gas exchange storage.

B. Stem Cross Section: Includes bark, cork cambium, phloem, xylem.
C. Root Cross Section: Epidermis, cortex and vascular cylinder providing nutrient absorption and transport.

D. Growth Zones: Primary growth by apical meristems, secondary growth by lateral meristems increasing plant girth.

E. Reproductive Zone (Flowers, Seeds, and Fruits):

1. Flowers attract pollinators; composed of sepals, petals, stamens, and carpels for reproduction.

2. Seeds: Include embryo, endosperm, and protective seed coat.

3. Fruits: Protect seeds

WEEK 9, Pt. 1

Lecture week 9 (3/18)

Plant Processes

I. Introduction

All organisms require certain resources, first just to maintain themselves, then to grow, and then to

reproduce. For plants, the resources are sunlight, water, CO2, and nutrients. This lecture emphasizes

those internal processes focused on obtaining and distributing water and nutrients; sunlight and CO2 are

usually available to plants.

Understanding the movement of water and sugars is largely a process of understanding that fluids move

from areas where pressure is being applied (relatively positive pressure) to areas where pressure is being

alleviated (relatively negative pressure). Generally speaking, water flow goes from the roots (positive

pressure) to the leaves (where negative pressure is being applied). Sugars move from the leaves (positive

pressure) to roots where negative pressure exists. (Be aware, sugars are moved up the tree as well during

some parts of the year.) Do remember though, that sugars are traveling in an aqueous (water-based)

solution, and that the water spoken of below is water from the roots to the leaves. That which goes from

the leaves to the roots is referred to as some form of sugar, or photosynthate.

II. Water and sugar transport

A. Water flow up the xylem;

1. The root (positive) pressure pump: a minor factor

a. Endoderm cells (a single cell layer around xylem/phloem tissue in the root) secrete wax

on their surfaces, forming a Casparian strip, a barrier to all ion/water flow around the

endoderm cells. Thus, all ion/fluid movement in or out of the root has to pass through the

endoderm cells’ cytoplasm, which selectively controls which solutes pass into the vascular

tissues or out of the phloem into the cortex cells. These endoderm cells drive

high concentrations of potassium salts and sugars from the phloem cells to the cortex cells.

b. Plasmodesmata are small openings (with intercellular cytoplasmic connections)

between the endoderm and cortex cells that allow entry of water into and through the

cytoplasm of adjacent endoderm cells. The concentrated solutes in the root cortex

osmotically draw water into the root from the soil, and because the lignin-reinforced

cellulose in the root cells resists swelling, this positive water pressure in the root

drives water through the plasmodesmata and endoderm cytoplasm and then into and up

the xylem tissue. Water is restricted from flowing around the endoderm cells or back into

the cortex by the Casparian strip. This root pressure can drive water 2 m up the xylem, but

no further. The attraction (adhesion) of water molecules to the sides of tubes (capillarity;

especially in the vessel elements of the xylem) also contributes to the forces driving water

up the xylem. At night when photosynthesis stops (stomata close, reducing water loss via

evapotranspiration), the “draw” of water from the leaves stops, and the root pressure can

drive some water out the stomata of the leaves of small plants within 2 m of the ground,

collecting as H2O droplets on leaf tips (a process called guttation).

2. The leaf transpiration negative pressure (= tension) pump; a major factor

a. Spongy mesophyll parenchyma cells-stomata: the air surrounding the parenchyma

cells of the spongy mesophyll is at 100% relative humidity because of “puddles” of

water (menisci) coating the cell surfaces. The air outside the leaf almost always has a

lower relative humidity. A wet surface (puddles of menisci) on the spongy

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mesophyll cells is required for CO2 to be taken into solution for photosynthesis, and

the stomata almost always have to remain open during the day to take in CO2. The

result is a net escape of moisture out of the stomata, called transpiration.

b. Leaf vascular bundle (xylem tracheids and vessel elements): the evaporation of water

from the menisci draws water out of the adjacent parenchyma cells of the spongy

mesophyll, and in turn, out of the adjacent xylem cells, creating a “suction” (negative

pressure) that draws water up the xylem by bulk flow (especially through the hollow vessel

elements). The latter don’t collapse in response to the negative pressure because of the

lignin/cellulose reinforced cell walls of the sclerenchyma tissue that make up the xylem

elements. In addition, since hydrogen bonds in the water molecules hold the water

molecules tightly together, this negative pressure is “felt” all the way down the plant, and

can actually be measured by a small reduction in trunk circumference during active

daytime photosynthesis. It’s this major negative “draw” that works in concert with the

small root pressure to draw water up the tallest trees. Drinking a beverage with a straw is a

rough analogy: the mouth creates a negative pressure that is transferred all the way down

the straw to draw fluids up to the mouth, assuming the straw holds its shape and the

hydrogen bonds in the fluid keep the fluid molecules intact.

B. Translocation (movement of sugars up and down the phloem) – the (positive) Pressure-Flow

Hypothesis (from the source to the sink area; usually from leaf to root storage)

1. Phloem loading at leaf - From Palisade parenchyma cells to the companion &

sieve-tube cells of the leaf phloem. Active (energy-consuming) transport of relatively

moderate concentrations of sucrose in the palisade parenchyma cells to the higher concentrated

sugar locations in the companion cell of the phloem, and then by diffusion to the sieve-

tube cells of the phloem. The high sugar content in the phloem draws water from the leaf

xylem via osmosis (the sugar is blocked by semi-permeable membranes from entering the

xylem vessels). The elevated pressure in the phloem pushes the sugary water mix down

the phloem to the root, which experiences the increased water pressure.

2. Phloem unloading (= movement of sugar in the root phloem to the root companion cells and

then to the cortex cells of the root where the sugar is stored). – The root is experiencing

increased water pressure in the phloem, and water moves into the xylem, in essence replacing

the water that left the xylem tissue all the way up in the leaves. Because the membranes

between the phloem and xylem are not permeable to sugar, sugar diffuses into the companion

cells where it is then actively transported into storage areas in the root cortex. The combination

of water going from the xylem to the phloem in the leaf and from the phloem to the xylem in

the root creates a cycle of water movement that occurs through the growing season, except

during the early spring thaw when the direction of movement in the phloem is reversed. In

early spring, sugars are actively transported from the root cortex to the companion cells, and

then by diffusion pass into the root phloem. Water is then drawn into the phloem by osmosis

from neighboring xylem, and an upward, pressure-driven flow of the sugary mix is generated in

the phloem, which supplies energy for new growth higher in the plant. The flow of maple sap

in spring is the result of this temporary reverse flow in the phloem. Only in the phloem do we

see flow reversal depending on time of year; the xylem always has unidirectional flow upward.

Once leaves are formed and photosynthesis begins, the reversed phloem flow is over-ruled by a

greater sugary concentration in the leaf phloem tissue, greater osmosis of water from the leaf

xylem to the phloem, and a greater leaf phloem pressure driving the more concentrated sugary

mix downward to replenish the sugar supplies in the root cortex.

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III. Nutrient Relations

A. Introduction

1. Essential nutrients: those required for metabolism or new tissue

2. Hydroponic techniques are used to determine the exact concentrations of nutrients

required for maximum health.

B. Types of nutrients

1. Macronutrients – those required in relatively large quantities and are the building blocks

of nucleic acids, proteins, phospholipids, etc

a. Oxygen, carbon and hydrogen are available from the atmosphere or water; oxygen

and carbon combined make up 90% or more of the dry weight of a plant

b. Nitrogen, phosphorus and potassium are those acquired from the soil and generally

are considered to be limiting nutrients, meaning that a shortage of them often occurs and

results in reduced growth/reproduction

2. Micronutrients – those required in relatively small amounts, and usually function in

association with enzymes, e.g., chlorine, iron, manganese. These are required in such

small amounts that in nature they are seldom “limiting” (= limit growth).

C. Factors promoting nutrient uptake

1. Active Transport. Ion concentrations are usually higher in plants than the surrounding

soil, requiring epidermal cells to actively transport the desired ions against a concentration

gradient of those ions into the root cortex. Without the metabolic cellular engine pumping

these ions into the root, these ions would diffuse out into the soil. If certain ions like sodium or

calcium become too concentrated in soils, they can draw water out of the roots by osmosis,

even in saturated soils, causing plant death. This happens when “hard” water is used to water

house plants and the salt ions rejected by the plant roots (e.g., Ca) accumulate in the soils and

cause osmotic flow of water out of the roots, termed “salting out”.

2. Mycorrhizal fungi symbionts, because of their greater surface-to-volume ratio, supply N,

P, K & H20 in high concentrations to plants by wrapping their hyphae closely around the root

epidermal cells (Ectomycorrhizal fungi in northern forests) or actually invading the cell

walls of the roots (Arbuscular mycorrhizal fungi in grassland and tropical forests).

Greater than 90% of vascular plant species have such symbionts.

3. Root hairs in the maturation zone of roots increase the surface area for nutrient uptake,

although this surface area is still less than that of the fungal hyphae.

D. Environmental factors reducing nutrient availability

1. Acid soils shut down respiratory decomposition and therefore the release of nutrients from

dead organisms. Certain plants, especially Sphagnum mosses, elevate H+ concentrations

and therefore lower pH to around 3 or 4. Without adequate nutrients, some bog plants

(sundew, pitcher plants) evolve structures to kill insects in order to obtain the required

nitrogen; the plants generate plenty of sugars from their own photosynthesis.

2. Rapid decomposition by microbes in tropical soils generates high CO2 levels, which is

converted into carboxylic acid that lowers soil pH. Low pH combined with high precipitation

causes leaching away of soil nutrients, leaving only those elements that are most resistant to

acid leaching: iron oxide, hence reddish (laterite) soils.

3. Very sandy soils, even without low pH, favor leaching because water flows through easily.

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4. Very fine, clay soils favor positive ion retention and adhesion to the clay particles, which

attract positive charged ions like N, K and P, making them less available to the plant.

5. Saturated soils do not permit O2 to enter the soil from the air. O2 is required by the roots for

respiration and active transport (e.g., sugar into storage, sodium ions out of the plant). Soils

with moderate amounts of sand, or tunneled by earthworms, allow better aeration. Plants such

as mangrove trees with roots constantly under brackish or sea water have hollow secondary

roots (called pneumatophores) that rise above the ground (and water) to collect air for the roots.

All organisms need resources to maintain themselves, grow, and reproduce. For plants, these resources include sunlight, water, CO2, and nutrients. Internal processes focus on obtaining and distributing water and nutrients, with water flowing from roots (positive pressure) to leaves (negative pressure) and sugars moving from leaves to roots. ### Water and Sugar Transport 1. **Water Flow Up the Xylem**: - **Root Pressure Pump**: Minor factor where endoderm cells secrete wax, forming a Casparian strip to control ion/water flow. This drives water into the xylem from the soil through osmosis. - **Transpiration and Negative Pressure Pump**: Major factor where evaporation from leaf stomata creates suction, drawing water up from roots. 2. **Translocation of Sugars**: - **Phloem Loading**: Sugars are actively transported from palisade cells to phloem, creating high sugar concentrations that draw water in through osmosis, generating pressure that moves sugars down to roots. - **Phloem Unloading**: Sugars move into root cells via diffusion for storage. ### Nutrient Relations 1. **Essential Nutrients**: Necessary for metabolism and new tissue. Hydroponics help determine nutrient concentrations needed for health. 2. **Macronutrients**: Needed in larger quantities (O, C, H, N, P, K). 3. **Micronutrients**: Required in small amounts (e.g., Fe, Mn) and typically not limiting. 4. **Nutrient Uptake**: - Active transport helps concentrate ions in roots against gradients. - Mycorrhizal fungi assist in nutrient absorption. 5. **Environmental Constraints**: - Acidic soils limit nutrient availability. Sandy soils promote leaching. Saturated soils restrict O2 entry. Overall, understanding these processes highlights how plants obtain and utilize essential resources for life processes.

WEEK 9, PART 2

Lecture week 9 (3/20)

Animal Diversity

I. Introduction.

The early evolution of animals consisted of a gradual change in (evolution of) mechanisms for extracting

energy from other organisms, which became increasingly sophisticated as other organisms evolved defenses

from becoming prey. What follows are a few notes about some of the key characteristics of animals and

some of the traits used to define the major groupings within the kingdom. Additionally, there is a BRIEF

overview of the diversity of the animal kingdom and some of the key innovations for the phyla within this

kingdom.

II. What is an animal?

A. Basic animal characteristics.

1. Heterotrophic lifestyle, deriving nutrition by consuming other life forms.

2. Flexible cell membranes, (like plant cells ,but unlike them in that plant cells are surrounded by a

cell wall made rigid by cellulose) and associated Extracellular Matrix (ECM).

3. Glycogen, a carbohydrate energy storage product (compare to starch in plants).

4. Neuromuscular tissue, Associated with movement. The vast majority of animals show

locomotion, at least in their larval stages (in Chordates, only the adult sea squirts are attached to

their substrate).

B. Protist ancestors of Animalia

1. Choanoflagellate protists are the closest living relative of the animals.

2. The Phylum Porifera is the most ancient animal phylum with living representatives. There is a

similarity between the feeding cell members of the choanoflagellate and choanocyte cells of the

sponges. Choanocyte cells are cells with an attached cylinder of microfibrils within which a

flagellum resides.

3. “Micro-feeders” These “flagellated collar cells” not only show a phylogenetic connection

between protists and animals, but support the belief that these specialized cells evolved when only

the smallest suspended organisms were available as food (e.g., bacteria and early protists). No

animals, other than sponges, are able to capture such small food items.

III. Fundamental traits used to define major animal groups

A. Number of germ layers (layers of similar dividing cells (analogous to plant meristematic cells). Each

germ layer produces a characteristic subset of structures/organs in the adult animal.

1. No primary germ layer. Although different looking cells come together and function as a

multicellular organism, the cells remain totipotent (e.g., sponges).

2. Diploblastic. Two major germ layers form, from which different structures develop. 1) The

ectoderm – the outer layer and 2) the endoderm – the inner layer. The ectoderm gives rise to the

skin and nervous system structures, and the endoderm gives rise to the lining of the digestive tract

(e.g., Cnidarians).

3. Triploblastic. Three major germ layers. 1) The ectoderm and 2) endoderm form the same types

of structures as in 2 above. 3) The mesoderm (meso-meaning “middle”) gives rise to the

muscles, bones, and most organ systems (e.g., all other animals).

B. Body symmetry.

With higher levels of organization, the body becomes more symmetrical and cephalized (development of a

“head”), where sense organs and nerve tissues are concentrated at the leading edge of movement. There are

three main types of symmetry.

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1. Asymmetry. The animal cannot be subdivided into equal, but opposite, halves (e.g., sponge).

2. Radial Symmetry. Condition in which many planes will divide an organism into equal, but

opposite halves so long as the plane goes through the center of the animal. These animals have a

circular body with equally effective action/response in all directions (e.g., jellyfish).

3. Bilateral Symmetry. Condition in which only one plane will subdivide the animal into equal

halves (e.g., mammals).

C. Body Cavity

Among those animals with a mesoderm, the body cavity separates internal organs from the body wall,

allowing greater maneuverability.

1. Acoelomate. No body cavity exists (e.g., flatworms).

2. Pseudocoelomate. Animal has a body cavity without a mesodermal lining of organs, allowing

better diffusion of substances inside the organism and better maneuverability. However, a certain

amount of rubbing between the organs and body wall occurs in these animals (e.g., nematodes).

3. Eucoelomate. Animal has a body cavity and internal organs covered with a membrane derived

from mesoderm. This form provides the best protection from rubbing and foreign antigens

entering the coelom from a wound. This condition is found in most higher organisms.

D. Embryology

Within the triploblastic organisms, the fate of the embryonic blastopore helps to distinguish phyla. Those

that have the blastopore resulting in a mouth are considered Protostomes, and those where it becomes the

anus are called Deuterostomes.

IV. Classification of phyla

What follows is a classification of the 5 major groupings of animals. Contemporary organization is based on

DNA sequence data and the above (and other) morphological/embryological traits. The traits emphasized

include those for accessing energy sources/feeding, for without an energy source, maintenance, growth and

reproduction would be impossible.

A. Asymmetric animals without germ layers.

1. Phylum PORIFERA (sponges) –

The sponges represent a dead-end phylum (that is they did not give rise to any other existing phyla)

are benthic, sessile filter feeders with variable body sizes and complex water canals throughout their

bodies. Sponges had very few competitors in early seas (see micro-feeding above), but had the need

for defenses against predators, using both chemical and physical (sharp spicules) defenses. The

commercial sponge trade has been replaced by the invention of synthetic sponges.

B. The radiates – diploblastic animals with radial symmetry.

1. Phylum: CNIDARIA (animals containing cnidocyte cells – e.g. coral, anemones, and jellyfish) –

These animals evolved when macroscopic protists were abundant, well after sponges evolved. These

animals were sessile or slow-moving hunters that used attached paralyzing harpoons (nematocysts in

cnidocyte cells) to capture prey or for defense. Sessile forms (e.g., coral) supplement energy with a

mutualistic algae. Most cnidarians have a multipurpose, blind, gastrovascular cavity, extending to

most of the body tissues for nutrient delivery.

C. Lophotrochozoan protostomes – Triploblastic animals with bilateral symmetry, a blastopore becoming

a mouth, and showing growth by incremental additions to the body (without having to shed to grow).

1. Phylum: PLATYHELMINTHES (flatworms)

This phylum includes free-living flatworms and parasitic flukes and tapeworms. The most primitive

groups include bilateral symmetry, cephalization, and typical tube-within-a-tube design. The flat

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body maximizes surface area for diffusion of gasses (they have no respiratory system). This group

represents the first bottom-dwelling, flat, slow-moving scavengers, also including well-developed

chemoreceptors for localizing food.

2. Phylum: ANNELIDA (segmented worms)

This group likely evolved from a free-living flatworm and includes earthworms, predatory marine

worms, and leeches. Marine worms were the first annelids (and majority of existing annelids today).

Later annelids radiated into freshwater and onto land. Annelids have a hydrostatic (liquid-inflated)

skeleton and gripping setae, both of which assist in burrowing through substrate. Annelids have

repetition of body parts along the body axis (segmentation) allowing independence of body parts.

Earthworms are important in cycling nutrients in ecosystems.

3. Phylum: MOLLUSCA (chitons, snails, clams, squid, octopus and others)

The mollusks are the second largest phylum (first is Arthropoda) and extremely diverse, and are

likely to have evolved from an annelid ancestor. Adaptive radiation is due to several innovations,

including a mantle, protective shell, muscular foot, and a scraping radula, all allowing the early

mollusks to feed on suspended and attached algae near shore. Only snails moved onto land. Many of

the species are used for food. Some, like the Zebra Mussel, are problematic.

D. Ecdysozoan protostomes – Triploblastic animals with bilateral symmetry, a blastopore becoming a

mouth, and showing growth via repeated shedding of the outer body exoskeleton (ecdysis).

1. Phylum: NEMATODA (nematodes or roundworms)

Members of this phylum occur in most habitats, including other organisms, and likely evolved from a

flatworm ancestor. The number of individual nematodes is much greater than the number of all other

animals combined. Nematodes are tolerant of a variety of extreme conditions, including drought

(>39 years), freezing and boiling, O2 depletion, and low pH. Primary among their adaptations is the

evolution of a cuticle (protective, dehydration-resistant body covering that is shed to permit growth.

Nematodes play an active role in nutrient cycling. They are the most abundant multicellular

organism that feeds on bacteria and fungi in decaying plants and animals. Nematodes are also a

concern to animals, causing diseases like Trichinosis and Elephantiasis.

2. Phylum: ARTHROPODA (insects, crustaceans (crabs, lobster, shrimp, etc.), and spiders (mites,

ticks, scorpions, etc.))

The arthropods dominate our landscape in abundance and numbers of species (80% of all known

animal species – 70%of all animal species are beetles). Arthropods evolved from an annelid ancestor

(arthropids have segmentally arranged appendages/bodies). The chitinous external skeleton

(exoskeleton) was the innovation that met all the criteria for moving out of the water and onto land.

The mollusks had heavy shells. The marine worms were segmented for flexibility, but movement

with parapodia didn’t allow for speed on land. The arthropod’s exoskeleton has strength, is

economical, and allows for speed of movement. Later arthropods evolved a tracheae system (small

breathing tubes to the inner body parts) and a compound eye (for spotting food from a distance,

rather than just bumping into it.

E. Deuterostome Phyla – Deuterostomata = “second mouth”; the mouth is the second opening to develop

during embryonic growth, the anus being the first. In the Protostomes (= “first mouth”), the mouth is

the first opening to develop, the anus being the second. Early embryological differences like these

reveal the early divergence of two fundamentally different evolutionary lines of animal phyla, the

protostomes and deuterostomes. Animals in the deuterostome phyla have bilateral symmetry,

triploblastic germ layers, and eucoelomate body cavities.

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1. Phylum: ECHINODERMATA (starfish (sea stars), sea urchins, and sea cucumbers)

Echinoderms represent the closest non-chordate relative to the chordates, based on genetic

information and larval type. However, a common ancestor between echinoderms and the chordates is

unknown. Overall, echinoderms are slow-moving, omni-directional, heterotrophs, with spines for

protection. They have arms with gripping suction cups for locomotion and predation.

2. Phylum: CHORDATA (all with a notochord or more)

a. This phylum is comprised of progressively more mobile, more rigid-bodied heterotrophs. In

addition to an increase in cephalization, there are 4 key chordate characteristics.

i. Notochord – fibrous support rod along the back appearing at least during early development

(replaced by a vertebral column in the adult in later evolved chordates.

ii. Pharyngeal gill slits – initially used in filtering food suspended in water, but later just for

respiration.

iii. Dorsal hollow nerve cord – a single dorsal nerve for rapid sensory processing.

iv. Post-anal tail – a portion of a tail extends posteriorly past the anus (effective for

locomotion in early evolution).

b. There are 3 chordate subphyla: Urochordata, Cephalochordata, and Vertebrata. Within the

Vertebrata there are 6 major classes:

i. Chondrichthyes – cartilaginous fishes (sharks and rays) – first chordates with jaws.

ii. Osteichthyes – bony fishes – includes all feeding modes (mostly carnivorous, but also

algivores, suspension feeders, and scavengers.

iii. Amphibia – frogs, toads, and salamanders – first chordates to invade land, but have to stay

close to water.

iv. Reptilia – Lizards, snakes, turtles, and crocodiles – dry, keratinized skin allowed reptiles to

be fully terrestrial. Became the ruling terrestrial vertebrates in the Mesozoic Era (Age of

Reptiles).

v. Aves – birds – first chordates adapted for flight

vi. Mammalia – mammals – 3 major groups: Monotremes (egg-laying mammals), Marsupials

(pouched mammals), and Placentals (those with a placenta).

Introduction

The evolution of animals involved the development of sophisticated mechanisms for extracting energy from other organisms, leading to various adaptations against predation.

What is an Animal?

• Characteristics:

  1. Heterotrophic lifestyle (derive nutrition from other organisms).

  2. Flexible cell membranes without a rigid cell wall (unlike plants).

  3. Store energy as glycogen (compared to starch in plants).

  4. Possess neuromuscular tissue for movement, especially in larvae.

• Origins:

  • Closely related to choanoflagellate protists.

  • Phylum Porifera (sponges) is the earliest animal phylum, using specialized feeding cells (choanocytes).

Fundamental Traits for Major Animal Groups

• Germ Layers:

  • No germ layer (e.g., sponges).

  • Diploblastic: two layers (ectoderm and endoderm) (e.g., Cnidarians).

  • Triploblastic: three layers (ectoderm, endoderm, mesoderm) (e.g., most other animals).

• Body Symmetry:

  1. Asymmetry (cannot be divided into equal halves, e.g., sponges).

  2. Radial Symmetry (multiple planes can divide equally, e.g., jellyfish).

  3. Bilateral Symmetry (one plane divides equally, e.g., mammals).

• Body Cavity:

  1. Acoelomate (no body cavity, e.g., flatworms).

  2. Pseudocoelomate (body cavity without mesodermal lining, e.g., nematodes).

  3. Eucoelomate (body cavity with mesodermal lining, e.g., higher organisms).

• Embryology:

  • Protostomes develop a mouth first; Deuterostomes develop an anus first.

Classification of Animal Phyla

• Phylum Porifera:

  • Sponges; filter feeders with no competitors in early seas.

• Phylum Cnidaria:

  • Includes corals, anemones, jellyfish; use nematocysts to capture prey.

• Lophotrochozoan Protostomes:

  1. Phylum Platyhelminthes: Flatworms, lacking respiratory systems.

  2. Phylum Annelida: Segmented worms with hydrostatic skeletons, crucial for ecosystems.

  3. Phylum Mollusca: Diverse group including octopuses; adaptive radiation due to innovations like shells and radula.

• Ecdysozoan Protostomes:

  1. Phylum Nematoda: Roundworms; highly adaptable.

  2. Phylum Arthropoda: Most numerous group; exoskeleton allows land adaptation.

• Deuterostome Phyla:

  1. Phylum Echinodermata: Includes starfish; close relatives to chordates.

  2. Phylum Chordata: Characterized by notochords, Pharyngeal gill slits, dorsal nerve cord; includes:

  • Chondrichthyes (cartilaginous fishes);

  • Osteichthyes (bony fishes);

  • Amphibia;

  • Reptilia;

  • Aves (birds);

  • Mammalia (with subgroups: Monotrem

1) If a population is in Hardy-Weinberg equilibrium and has 64% of its members exhibiting the dominant phenotype,

what is the frequency of the dominant allele in this population?

A) 0.8

B) 0.64

C) 0.6

D) 0.4

E) 0.36

The 64% of the population showing the dominant phenotype includes both those with the homozygous dominant

genotype and those that are heterozygous. Mathematically, it includes those that are q2 and 2pq. Simply taking the

square root of 64% is not enough (choice A). Also, describing a group as having a particular phenotype is a reference

to their genotype, which includes two alleles. The question refers to the frequency of an allele, which is represented

by just a single allele (negating B and E). Since 64% of the population is dominant, then we know that 36% of the

population is recessive (64% +36% = 100% of the phenotypes). Since the population is in H-W equilibrium, we can

just backtrack to find the allele frequency by finding the square root of 0.36, which is 0.6. (q2 = 0.36 so q = 0.6). This

is the allele frequency of the recessive allele (negating C). Since p + q = 1.0, then p (the frequency of the dominant

allele) = 0.4.

2) Which of the following statements best explains the purpose of the Hardy-Weinberg model in population

genetics?

A) It describes the process of natural selection in a population.

B) It predicts the rate of mutation in a gene pool over time.

C) It measures the impact of environmental changes on gene flow.

D) It explains how genetic drift influences allele frequencies.

E) It provides the conditions under which allele frequencies remain constant in a population.

Yes, the H-W model predicts that allele frequencies do not change, but the model really describes the conditions that

must exist to get that result: random mating, no natural selection, etc.

3) A research team observes that over several generations, the allele frequencies in a fish population are changing,

even though no new mutations have occurred and there is no migration. Based on this information, which of the

following would be the most reasonable explanation for why the population is not in Hardy-Weinberg equilibrium?

A) Genetic drift is occurring due to the small population size.

B) The population is experiencing natural selection favoring one allele.

C) Random mating is occurring, but the population size is large.

D) A non-random pattern of mutation is increasing genetic diversity.

E) Environmental changes are causing mutations that favor survival.

This question was about identifying which of the H-W assumptions is being violated. No mutations are occurring, and

no migration is occurring. This leaves non-random mating, natural selection, or significant births/deaths as options.

Choice B is the only answer that provides one of these assumption as being violated.

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4) Which of the following statements about inbreeding is most accurate?

A) Inbreeding increases the number of homozygous dominant individuals in the population, but not the number of

homozygous recessive individuals.

B) Inbreeding depression is when the number of homozygous genotypes decreases in a population.

C) Inbreeding causes a decrease in heterozygosity because heterozygotes lose half of their offspring to

homozygosity.

D) Inbreeding occurs when homozygous dominant individuals mate with homozygous recessive individuals.

E) Inbreeding increases fitness, since the genotype of the offspring is similar to both parents.

When similar genotypes mate (inbreeding) offspring resemble their parents for those matings that include

homozygous genotypes. However, when heterozygotes mate, only half of their offspring resemble the parents. The

other half resemble those that are homozygous (1/4 dominant and ¼ recessive).

5) You are tasked with designing a conservation plan for a critically endangered animal species. Based on the Hardy-

Weinberg model, which of the following strategies would best help you ensure that the genetic diversity of the

population is maintained over time?

A) Selectively breed individuals with the most desirable traits to increase their frequencies in the population.

B) Introduce a small number of individuals from a genetically similar population to increase allele variation.

C) Allow natural selection to eliminate weaker individuals, ensuring that only the strongest genes persist.

D) Isolate the population from all other populations to prevent gene flow. (Maybe)

E) Allow random mating and protect the population from selective pressures, even if the population size is small.

Although random mating and no natural selection are requirements of the H-W model (choice E), a small population

is subject to the influences of genetic drift more than a larger population is (supporting B and negating D). Although

D could be considered to be correct if other nearby populations would dilute and diminish the genetic diversity

desired in the endangered population. Allowing selection to occur reduces allele frequencies in a population

(negating A and C).

6) A population of plants living in one field flowers from May to July. Each individual plant, however, only flowers

once during this time. Those that are in flower are pollinated by only those that are also flowering at the same time.

Therefore, although we consider all of the individuals to be part of the same population, they are not all

interbreeding. Which of the following statements about this scenario is most accurate?

A) The reproduction of flowers in this example is considered a form of assortative mating.

B) If the population is small enough we can consider this to be an example of a population in Hardy-Weinberg

equilibrium.

C) The flowers are exhibiting sexual selection.

D) This is an example of inbreeding depression.

E) Sexual dimorphism must exist in this population in order for it to persist over generations.

Assortative mating is the tendency for individuals to mate with another that is similar to themselves. I described the

situation in choice A as an example of this. H-W typically requires large populations (negating B). Sexual selection

(choice C) is natural selection where those traits that are selected for are those that increase the ability to gain

mates. It is not clear how sexual selection would work here as described in this question (even if it did exist among

plants – which I’m not sure of).

7) Two groups of birds are active at different times of day: one in daylight and one in darkness. When one group is

performing courtship displays and mating, the other is resting. Assuming there is no overlap in active times for the

two groups, which of the following is true?

A) This is an example of a temporal prezygotic isolation mechanism.

B) This is an example of an abiotic postzygotic isolation mechanism.

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C) This is an example of a hybrid viability isolation mechanism.

D) This is an example of a mechanical postzygotic isolation mechanism.

E) This is an example of a behavioral postzygotic isolation mechanism.

87% of students got this one. This is not a postzygotic mechanism (choices B, D and E), because a zygote is not

formed in this comparison. Hybrid viability (C) is a reference to postzygotic mechanisms as well.

10) Imagine a fossil record showing a species of marine mollusks with little morphological change over millions of

years, followed by the sudden appearance of several distinct but related species. How would this fossil evidence best

be explained by proponents of punctuated equilibrium, and how does this explanation contrast with that of phyletic

gradualism?

A) Punctuated equilibrium would explain the gaps as evidence of mass extinction events, while phyletic gradualism

would argue that these species diverged slowly but left no fossils during transitional periods.

B) Punctuated equilibrium argues that species evolved gradually, but fossilization occurred more frequently during

periods of stasis, whereas phyletic gradualism claims that gaps in the record result from species evolving during

catastrophic events.

C) Punctuated equilibrium suggests that the fossil gaps represent a period of rapid evolution, while phyletic

gradualism would interpret the gaps as incomplete fossil records that obscure slow, continuous change.

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e

c

d

b

a

#1 #2 #3 #4

D) Punctuated equilibrium would attribute the sudden appearance of new species to a long-term accumulation of

mutations, while phyletic gradualism would claim that species evolved in response to slow changes in environmental

pressures over time.

E) Punctuated equilibrium would suggest that evolution occurred continuously but was only recorded during rapid

speciation events, while phyletic gradualism would explain the fossil gaps as the result of rapid environmental

changes.

This was covered in lecture on Oct 10. Punctuated equilibrium suggests that evolutionary change should not be

viewed like a sloped hill (phyletic gradualism), but, instead, occurs as periods of slow, consistent change (gradualism),

or lack of change, interrupted by dramatic leaps forward in genetic radiation and the creation of new complex traits,

or even species (called cladogenesis). According to punctuated equilibrium gaps in the fossil record are the result of

rapid evolution where diversification gives the appearance of gaps: not time-based gaps, but diversity-based gaps.

Gradualism, since evolutionary change is slow, would see gaps in the fossil records as missing species in fossilized

form.

11) Which of the following is evidence that competition was a driving force in the evolution of plants moving onto

land?

A) Some plants evolved to have smaller and smaller cells to take advantage the limited spaces available.

B) Some plants evolved a loss of their cellulose, which is not needed on land.

C) Some plants evolved to grow extensions above the water to gather CO2 from the air above.

D) Some plants evolved lignin to better move fluids around inside their body.

E) Two of the above are correct.

12) According to the endosymbiosis theory, chloroplasts in modern plant cells originated from ancient free-living

photosynthetic bacteria. Which of the following experimental observations would best support this theory?

A) Chloroplasts are surrounded by a double membrane, similar to the membranes found in other eukaryotic

organelles.

B) Chloroplasts are able to produce energy through photosynthesis, just like modern-day plants.

C) Chloroplasts contain their own DNA, which is similar in structure to bacterial DNA.

D) Chloroplasts divide and replicate through binary fission, a process commonly found in all eukaryotic cells.

E) Chloroplasts have enzymes that function under similar environmental conditions as those in plant cells.

This one was also covered in lecture on 10/10, as a way to demonstrate how punctuated equilibrium works. I

presented 3 lines of evidence that the endosymbiotic theory of organelle evolution happened. First, there are 2 or

more membranes around chloroplasts and mitochondria. One of those membranes is typical of bacterial species and

the other is typical of Eukaryotes. Second, chloroplasts and mitochondria have their own genomes, which is similar

to bacteria and not eukaryotes. If they originated in a eukaryotic cell, they wouldn’t need their own genes, and if

they did, they should be more similar to that of the eukaryotic cell in which they live. Third, chloroplasts reproduce

on their own schedule, independent of the cell in which they exist, and their process of dividing is more similar to

what bacterial species do (fission) than what eukaryotes do (mitosis).

13) Which phylum includes non-vascular plants?

A) Bryophyta.

B) Pteridophyta.

C) Coniferophyta.

D) Ginkgophyta.

E) Anthophyta.

Bryophyta have internal vessels to move fluids throughout their plant bodies. However, this is not true vascular

tissue (xylem and phloem).

22) Which of the following is correct regarding the phylum Porifera?

A) They are the direct ancestors of the Radiates.

B) They are asymmetrical.

C) They are protostomes.

7

KJ

G

I

D F

E

H

CBA

D) Two of the above are correct.

E) A, B, and C are correct.

23) Which of the following is a benefit of being a pseudocoelomate over a eucoelomate?

A) Less friction between your organs and body wall as you move.

B) Protection from pathogens from entering the coelom from a wound.

C) Direct diffusion of nutrients from fluids to organs.

D) A more advanced development in cephalization.

E) Organs are covered with a thin, protective membrane.

24) Which of the following statements about the evolution of animals is accurate?

A) Animals showing asymmetry have a significant amount of cephalization.

B) Echinodermata develop such that their blastopore becomes the anus of the individual.

C) Diplobasts are pseudocoelomates and triploblasts are eucoelomates.

D) Lophotrochozoans show growth via repeated shedding of the exoskeleton.

E) The coelom referred to in a pseudocoelomate is the digestive tract.

25) The Cnidaria include which of the following?

A) Anemones.

B) Nematodes.

C) Squids.

D) Butterflies.

E) Sea stars.

26) Who are the closest living relatives of the Animalia?

A) Porifera.

B) Archaea.

C) Bacteria.

D) Cyanobacteria.

E) Choanoflagellates.