BIOS 1620 Central Michigan University Biology Worksheet

BIOS 1620 Ecology and Evolution
LAB 4. PLANTS!
Please bring your lecture notes and textbook to this week’s lab.
This week’s lab workbook will be built by you, as you examine specimens and answer questions
throughout the booklet. Use your lecture notes and textbook to help you answer the questions,
complete the figures and fill out the tables.
Lab Objectives
At the end of the lab, students should be able to:
1. provide scientific and common names of the plant groups observed in lab;
2. recall the number of species found in each group;
3. describe the general form (plant body) of plants in each group;
4. explain the major evolutionary innovations displayed in each of these groups of plants,
including
a. the generalized plant life cycle known as the alternation of generations;
b. the specific life cycles exhibited by bryophytes, ferns and club mosses, and seed
plants, and how they differ in the dominant phase of the life cycle.
5. explain why some of the evolutionary innovations were important in the transition to life on
land in early plants, why some of these innovations allowed certain plant groups to inhabit
diverse habitats, and why still other innovations contributed to the success of seed plants
and angiosperms specifically.
Related lectures: Systematics and Phylogenetics; Plant lectures.
Related textbook chapters: Chapters 31, 32.
Complete before lab: Read lab handout. Complete questions 1-7.
I. The major plant groups
Our survey of plants covers major groups that are primarily distinguished on the basis of
characters involved with adaptation to terrestrial life (i.e. evolutionary innovations). Some
traits are exhibited by all plants groups, some are not. During this week’s lab, you’ll work to
identify the different plant groups, understand which traits are found in which groups, and map
these traits on a phylogenetic tree.
Plants are remarkably diverse. They range from mosses that are small, unassuming, and easily
overlooked to some of the largest organisms on earth, the redwood trees of California and
Oregon, the tallest of which reaches a staggering 380 feet tall. Yet, these distinct organisms are
grouped within the Kingdom Plantae because they share common characteristics: with few
exceptions, plants:
1. are autotrophic,
2. contain chlorophyll a,
3. have cell walls containing cellulose.
4. have a life cycle described as an alternation of generations.
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BIOS 1620 Ecology and Evolution
1. What term describes traits that are common to all members within a clade? If all members of
a clade exhibit these traits, when did the traits evolve?
2. Name the algal group that are the closely living relatives to land plants. What is the name of
the life cycle they exhibit.
3. Plants and this algal group share the trait of cellulose-rich cell walls. Does this change your
answer to when this trait evolved? Explain your reasoning.
4a. Draw a simple phylogenetic tree showing: the most recent common ancestor of plants and
the algal group identified in Question 2; two branches showing these two groups; and a line
mapping the origin of the alternation of generations.
4b. Map the origin of cellulose-rich cell walls.
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BIOS 1620 Ecology and Evolution
5. List here the 9 plants groups, including both common names and scientific names, that were
discussed in lecture. These are the plant groups you’ll study in lab this week.
6. Add to this list the number of known species alive today for each of the plant groups.
7. List here the evolutionary innovations (EIs) discussed in lecture in relation to reproduction
without water (4) and life on land (3). Later in the lab, we’ll add additional innovations shown in
the most recently evolved plant groups.
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BIOS 1620 Ecology and Evolution
II. Plant bodies
On each bench in the lab, you’ll find live specimens of the plant groups you listed above (any
exceptions will be announced by your TA).
Examine these specimens and complete Table 1 (at the end of the lab booklet).
Answer the following questions, referring to particular evolutionary innovations as appropriate.
Use your notes and textbook to help you.
Which three evolutionary innovations are present in land plants (but not all land plants) that
allowed them to live on land? Explain why each trait was important in the transition to life on
land.
Do all the plant groups express each of these innovations? Refer to your table to see the
pattern that exists in which group have which traits.
Why are there such differences in the size of the plant bodies? Refer to a specific evolutionary
innovation in your answer.
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BIOS 1620 Ecology and Evolution
Do you think all plant groups will be found in both wet and dry environments? Explain.
Based solely on the innovations of the bodies of plants, which plant groups would you predict
will be found only in wet or moist environments? Why?
Summary: Plant bodies
EI-1 ____________________ and EI-2 ____________________ prevent water loss from plant
bodies.
EI-3____________________ moves water through the plant body.
Given that EI-3 is absent in bryophytes, water moves through plant bodies through the process
of osmosis. You might then expect bryophytes to live only in moist environments (Is this what
you predicted above?). Actually, some mosses do live in extreme environments such as
deserts, but also the Arctic, Antarctic and mountaintops. Mosses can withstand these extremes
because they are able to dry out and become dormant when conditions are difficult. When
conditions become favorable mosses rehydrate, begin photosynthesis again and reproduce.
Seedless vascular plants and seed plants display all three evolutionary innovations. Vascular
tissue originated in the common ancestor of these two plant groups. Vascular tissue is
specialized for conducting water, nutrients and photosynthetic products through the plant.
Vascular tissue is a key evolutionary innovation that allowed land plants to decrease their ties
to water habitats: vascular tissue allows the transportation of water from tissue that had direct
access to water to tissue that did not.
The cells of vascular tissue are reinforced with a strong polymer called lignin that strengthens
the plant body and allows it to grow upright. This explains why the largest plants on earth are
species with vascular tissues. In the case of the redwoods, the strength of lignin is reinforced by
the strength of the woody tissue, as well.
If we only consider evolutionary innovations in plant bodies, we’d be hard pressed to explain the
distribution of ferns and club mosses. These two plant groups also live primarily in moist
environments. The reason why lies not with plant bodies, but with plant reproduction. This is the
next topic for discussion.
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BIOS 1620 Ecology and Evolution
III. Plant reproduction
All plants show four evolutionary innovations for reproducing on land. All seed plants have one
additional innovation, and the flowering plants another two. Your next task is to examine
specimens that demonstrate the evolutionary innovations found in land plants that allowed them
to reproduce on land. While doing so, complete Table 2, which will compare and contrast
different aspects of the life cycle of the different plant groups.
i. The plant life cycle: alternation of generations
The concept of alternation of generations is critical for understanding plant reproduction and life
cycles, which vary among different plant groups. In this section, work through the questions and
complete the life cycle to demonstrate your understanding.
Land plants display a life cycle known as an “alternation of generations”. In the alternation of
generations, life cycles through or alternates between two multicellular phases that differ in
having one or two sets of chromosomes. That is, one stage is haploid and the other diploid.
How does this compare to the life cycle of humans? Do humans exhibit two multicellular
phases? Explain.
What are the names of the two phases of the plant life cycle? Which stage is haploid and which
is diploid?
Note that there are several major differences between the plant and animal life cycles, which
makes generalizing between them difficult and also makes the idea of an alternation of
generations difficult to understand. Here are some fundamental differences between animal and
plant life cycles:
1. Animals produce gametes by meiosis; plants do it by mitosis.
2. The haploid stage in the life cycle of animals consists only of gametes. Plants have a
multicellular haploid stage.
3. Animals do not have the equivalent of spores. Plants produce spores by meiosis.
Take the time to understand these differences; they are profound! With your notes nearby, work
through the land plant cycle shown in Figure 1. Several plants groups show this form of the life
cycle.
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BIOS 1620 Ecology and Evolution
Figure 1. The generalized life cycle of plants showing the alternation between the
diploid and the haploid phases of the life cycle.
On this figure, indicate where meiosis and mitosis occurs during this generalized life cycle. Hint:
meiosis occurs once, mitosis three times. To get you started, a. and b. show two times when
cell division occurs. Fill in the correct type.
Make sure you can fill in all the blanks in this figure. What is structure is produced as a result of
fertilization – see point c? What is the name of the structures at point d?
Although all the stages of the generalized plant life cycle are recognizable in all plants, there
have been several significant evolutionary trends. As you proceed through your study of
plants, keep in mind the following questions.
What are the major differences between the two phases of the life cycle across the
major plant groups?
What modifications in the life cycle occurred in the major groups of plants, and
how have they contributed to success on land?
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BIOS 1620 Ecology and Evolution
The plant life cycle is also known as the sporic life cycle. It’s an evolutionary innovation. Why?
Different plant groups vary in the life phase that is dominant. What does it mean to say that one
of the multicellular phases is dominant?
ii. Specialized reproductive structures for gametes
Terminology associated with plants will be unfamiliar to most of you and is another aspect of the
challenge of learning the plant life cycle. To start you off, consider the gametangia, which is a
specialized structure where male or female gametes are produced and protected. In land plants,
gametangia are found on gametophytes. Examine specimens showing gametangia and be sure
you understand the specialized role of these structures and why they are considered
evolutionary innovations.
What is the name of the female gametangia? What specifically does this structure produce?
What is the name of the male gametangia? What specifically does this structure produce?
What is the chromosome number of gametes?
How do male gametes get to the female gametes in bryophytes and ferns? How does this limit
where these organisms can live?
iii. Protection of the embryo and sporophyte
The sperm have made it to the eggs and fertilization occurs. A zygote has formed.
What is the chromosome number of a zygote?
The zygote will grow out of the female gametangia, which provides protection to the developing
embryo. This embryo becomes the new sporophyte.
What is the chromosome number of a sporophyte?
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BIOS 1620 Ecology and Evolution
As you learned in lecture, not only does the female gametangia protect the developing
sporophyte, it actually transfers energy to it as well until it becomes fully photosynthetic. Plants
care for their young.
iv. Protection of the spores
Once the sporophyte is mature, it produces spores. Spore production occurs in specialized
structures on plant bodies.
What’s the name of the structures in bryophytes and ferns that houses the spores?
How are these structures different in seed plants? Why?
What’s the chromosome number for spores?
What type of cell division led to the formation of spores?
The final part of the life cycle involves the movement (known as dispersal) of spores, at least in
most plants. In moss and ferns, the structure that houses the spores (known as a
_______________) bursts open and the spores scatter in the environment. Some of these
spores will land in suitable habitat, germinate, and then grow to become a gametophyte. The
dispersal phase is risky and it’s possible that conditions aren’t favorable for the spore. But, at
least for short periods of time, the spores are protected by a special polymer called
__________________. This polymer is an evolutionary innovation.
Plant reproduction challenge! To fully understand the plant life cycle across plant groups, you
need to visualize each stage and each evolutionary innovation. And you need to do this for each
plant group, so that you see the similarities and differences among the groups.
Below are two figures showing the alternation of generations in a moss and a fern. Complete
the diagrams by labelling the different structures, naming each phase in the life cycle and
indicating where meiosis and mitosis occur. You’ll do the same for the seed plants later in lab.
Key terms – did you use these terms in your answers and in the labelling of the plant life
cycles? If not, make sure you do.
•
•
•
•
•
gametophyte
sporophyte
sporangium (sporangia)
spores
sporopollenin
•
•
•
•
•
gametangia
antheridia
archegonia
sperm
egg
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BIOS 1620 Ecology and Evolution
Figure 2. The life cycle of a moss. Label each structure. Which structures are haploid;
which are diploid? Which phase is dominant?
Figure 3. Life cycle of a fern. Label each structure. Which structures are haploid; which
are diploid? Which phase is dominant?
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BIOS 1620 Ecology and Evolution
IV. Evolutionary innovations in seed plants
And now, the seed plants! Seed plants include evergreens and deciduous trees that are all over
our campus. The major evolutionary innovations in these plants are seeds, pollen and the
related concept of heterospory. The evolution of each of these traits triggered a massive
adaptive radiation of seed plants beginning about 290 million years ago, as these traits
permitted seed plants to occupy new and drier environments. Angiosperms display additional
innovations, flowers and fruit, that allowed them to become the most diverse land plants living
today.
What four plant groups are considered seed plants? Provide common and scientific names and
examine specimens of each.
What is heterospory?
What is homospory? What groups show this trait?
Why was heterospory important? What two other structures evolved as a result of the origin of
heterospory?
Unlike plants that are homosporous, in species with heterospory, sporangia developed into two
types. Name them here:
What’s produced in each?
What does a microspore develop into?
What does a megaspore develop into?
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BIOS 1620 Ecology and Evolution
What does the microsporangia look like on a pine or spruce tree? And the megasporangia?
Draw examples of both.
Figure 4. Diagram of the life of a heterosporous vascular plant.
Identify each stage of the life cycle here on the live specimens. Don’t just memorize the
life cycle, but visualize what each part actually represents on a living plant.
A major difference between seed plants and the plants discussed earlier is that seed
plants don’t require water to transfer sperm to eggs. This is accomplished by pollination,
which is the transfer of pollen to the receptive surface of the female cone. In gymnosperms,
pollen is transferred by the wind to the ovulate cones and after this event, another year (or
more) passes before the ovule produces a mature female gametophyte. Pollen will then
germinate and each pollen grain grows a pollen tube into the archegonium and delivers a
haploid nucleus to the egg for fertilization. Fertilization produces a zygote. The zygote divides
by mitosis to produce an embryonic sporophyte. After a short developmental period, the
embryo becomes dormant. At this time, a seed has formed, and it is composed of (1) the
embryo sporophyte surrounded by (2) nutritive tissues from the parent gametophyte, which in
turn is encased in (3) protective tissues from the parent sporophyte that forms the seed coat.
Explain how the male and female (micro and mega) gametophytes fit into the life cycle of pines.
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BIOS 1620 Ecology and Evolution
Another major difference between seeds plants and the other plants involves the dispersal of
genetic material away from parent plants.
Which stage in a pine involves the dispersal of genetic material? How is this different from
bryophytes and ferns?
Mature
sporophyte
(2n)
Megaspore
Ovule
cone
Meiosis
Pollen
cone
Egg (n)
Megasporangium
Mitosis
Microspores
Pollen grain (n)
Female gametophyte (n)
Megasporangium (2n)
Archegonium (n)
KEY
Microsporangium
Haploid
Diploid
Sperm
Embryo (2n)
Mitosis
Fertilization
Male gametophyte (n)
Figure 5. Life cycle of pine. Which is the dominant phase of the life cycle in conifers?
Summary: Gymnosperms
Gymnosperms are seed plants that bear their seeds on the surface of highly modified leaves,
called cones. Gymnosperms were the first to evolve pollen and seeds.
Several evolutionary trends apparent in the seedless vascular plants have been continued in the
gymnosperms. For instance, while the basic “alternation of generations” life cycle can still be
seen in gymnosperms, it is highly modified. Instead of producing spores that disperse to
germinate into free-living gametophytes, the dominant sporophyte stage retains its spores on
specialized reproductive leaves where they develop directly into tiny gametophytes, which are
supported by the sporophyte.
Unlike the ferns, club mosses and bryophytes, the spores of gymnosperms are not
dispersed into the environment; rather the gametophyte is highly reduced, stays on the
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BIOS 1620 Ecology and Evolution
parent plant, and it is the fertilized seed that disperses into the environment. In
gymnosperms, the female gametophyte is retained on the parent sporophyte in the
megasporangium, which means that the gametophyte no longer requires a moist habitat for
development. Moreover, pollen allows sperm to find and fertilize eggs even in very dry habitats.
In gymnosperms (and angiosperms), there are two kinds of spores and two kinds of
gametophytes: a microspore develops into a microgametophyte (or male gametophyte) that
in turn develops into a pollen grain that is released form the parent sporophyte; and a
megaspore develops into a megagametophyte (female gametophyte) that produces an egg,
which will be fertilized with a nucleus from the pollen grain.
To understand the differences between plant groups, take the time to compare and contrast
the life cycles drawn in Figures 2, 3 and 5 (as well as Figure 6 below).
V. Evolutionary innovations in flowering plants
Let’s focus now on only the flowering plants and the innovations that contribute to their
overwhelming dominance among living plants. Over 250,000 species of flowering plants have
been described. They thrive in diverse habitats, from deserts to tropical forests to freshwater.
With the exception of northern and high-elevation forests in which conifers dominate, flowering
plants are the most abundant plant group in terrestrial environments.
The importance of angiosperms to human life as well as other organisms can simply not be
overstated. In most environments, it is angiosperms that supply food for almost all other
species. We eat the vegetative structures of angiosperms (roots, stems and leaves), and the
seeds and fruit from angiosperms are staples of human culture throughout the world.
Provide two other names for flowering plants?
In addition to the evolution of heterospory, pollen and the seed, the spectacular success of
angiosperms is due to two additional evolutionary innovations.
1. The flower, which greatly increases the efficiency of pollen transfer (and probably
increases speciation rates). Whereas gymnosperms rely solely on wind for transfer of
enormous amounts of pollen, pollination of many flowers is accomplished by insects,
birds and bats (as well as other animals). Pollination by animals in advantageous
because it increases the probability of cross-fertilization between distant plants, allowing
for the possibility of increased genetic variation. Flowers have two reproductive
structures, the stamens and the carpels that are responsible for heterospory. The
carpel encloses the ovary where eggs are found (angiosperm means “encased-seed”).
The stamens enclose the microsporangia, and microsporocytes from which pollen are
produced
2. The evolution of the ovary enabled the evolution of fruit, which is a structure that is
derived from the ovary of the flower and encloses the seeds. Fruit helps disperse the
young sporophyte. Seeds develop with the ovary of the flower, which then matures into
fruit. Fruit provides protection for the new sporophyte and many animals that eat large
and brightly colored fruit inadvertently act as to disperse seed over potentially large
areas. In other species, tissue from the ovary forms structures that aid in wind dispersal.
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BIOS 1620 Ecology and Evolution
Angiosperms still show the basic “alternation of generations” life cycle, but it is highly
modified. Like that of gymnosperms, the dominant sporophyte stage retains its spores on
specialized reproductive leaves (the flowers) where they develop directly into tiny
gametophytes. Also, like gymnosperms, angiosperms display heterospory. There is a
microspore that develops into a microgametophyte (or male gametophyte) that in turn
develops into a pollen grain that is released form the parent sporophyte. A megaspore
develops into a megagametophyte (female gametophyte) that produces an egg that will be
fertilized with a nucleus from the pollen grain.
The developing female gametophyte is completely enclosed in a structure called a pistil, which
constitutes the female part of a flower. A pistil may have single or multiple carpels, which in
turn consist of ovary, stigma and style. Within the ovary is the ovule (female gametophyte plus
protective layers), which develops into a seed, as with the gymnosperms. However, the ovary
of the pistil develops into a fruit, which functions to protect and disperse the seeds. Also, in the
development of an angiosperm seed, there is double fertilization; two pollen nuclei enter the
ovule, one unites with the egg nucleus to form the zygote, and the other unites with two haploid
polar nuclei of the megagametophyte to produce a triploid tissue called the endosperm.
Endosperm functions as a nutritive tissue for the seed (when we eat a corn kernel, we are
eating mostly endosperm).
Figure 6. The structure of a flower showing a cross section through the ovary.
Examine available flowers. Do you see sepals, petals, stamens, pistil and ovaries?
Animals are attracted to flowers because they receive a reward (usually food, but sometimes
even sex pheromones!) when they enter or probe into a flower. Many flowers produce nectar,
a sugar solution, near the bases of the stamens and petals. Thus, insects in pursuit of food
must move past the sexual parts of the flower.
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BIOS 1620 Ecology and Evolution
Many flowers are highly specialized so that only a few kinds of animals can manipulate the
flower. Among insect-pollinated flowers, some are specialized for flies, bees, or butterflies.
Other plants have flowers that are specialized for birds (hummingbirds), bats. Some, including
most grasses, have extremely small flowers that are wind pollinated.
Figure 7. Life cycle of a flowering plant. Note the both the male and female
gametophyte are extremely reduced in angiosperms. The male gametophyte in the
pollen grain consists of only two cells and the female gametophyte in the
megasporangium consists of only eight nuclei!
Pollination and fertilization
Pollination is the transfer of pollen to a receptive surface of the stigma in angiosperms (In
gymosperms, pollen sticks to a drop of resin at one end of the ovule.). This process is critical in
angiosperm reproduction and is critical for us for food production. Once at the stigma, the pollen
grain germinates and a pollen tube grows through the stigma and style to the ovary. Once the
pollen tube reaches the megagametophyte, it discharges two nuclei – one sperm fuses with the
egg to form the diploid zygote and the other fuses with the two polar nuclei to form a triploid
(3n) nucleus. This becomes the endosperm. The process is called double fertilization, which
is characteristic of angiosperms.
o What is the difference between pollination and fertilization?
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BIOS 1620 Ecology and Evolution
o Examine the electron micrographs on the pollen website
http://pollen.usda.gov/index.htm on the lab computers.
Seeds, fruits and dispersal
Seeds of angiosperms develop from the ovule, inside of which is the embryo and endosperm.
As the seed develops, the wall of the ovary gets larger and becomes the fleshy part of a fruit.
The fruit provides protection for the seeds, as well as aiding in dispersal. Fruits have co-evolved
with the animals that disperse them, so many fruit display characteristics that make them
attractive to animals. For example, they may be brightly colored, they may be fragrant and they
are often sweet. When animals eat the fruit, the seeds within them are protected by the
integument from digestion. When the animal defecates, these seeds get deposited with fertilizer,
which helps the seeds germinate. Fruits and seeds are both adaptations that promote the
dispersal of plants. Fruits can be fleshy, like apples, or they can be dry, like peas and nuts. Dry
fruits crack at maturity and release their seeds.
Major fruit types include:
A. Fleshy fruits.
1. Simple fruits develop from a single ovary. The flesh of the fruit develops from the ovary.
If the layer enclosing the seed is hard and there is only one seed per fruit, the fruit is
called a drupe (e.g. olive, cherry, coconut). The layer enclosing the seed is fleshy and
there are many seeds per fruit, the fruit is called a berry (e.g. tomato, grape, green
pepper).
2. Complex fruits develop from more than one ovary. The fruit may form from many carpels
on a single flower, and these fruits are called aggregate fruits (e.g. strawberry,
raspberry). Alternatively, complex fruits can be derived from many carpels of many
flowers, which fuse together. These are called multiple fruits (e.g. pineapple).
B. Dry fruits
3. Dry fruits include those that split open when they are mature. Legumes, such as peas
and beans, are dry fruits that split across a seam in the ovary. All the seeds are borne on
one half of the split ovary. Capsules are fruit in which the seeds are released through
pores or multiple seams (e.g. poppies, irises).
4. The other type of dry fruits does not split at maturity. Nuts are fruit with a hard and thick
wall, which has a cup at its base (e.g. acorns, chesnut). Samaras are fruit with thin and
winged walls (e.g. maple, ash, elm). Achenes are dry fruits that have a hard wall, which
is thin, but not winged (e.g. sunflower).
Examine the seeds and fruit on display. Try to figure out the methods by which the fruit is
dispersed (wind, water, gravity, animal, or adhesion to fur).
As you complete this lab, you have created a study guide about plants for Exam 2.
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BIOS 1620 Ecology and Evolution
Table 1. Innovations in plant bodies.
Evolutionary innovations – present or absent?
Size range of
Group name
plants
Habitats
1.
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2.
3.
BIOS 1620 Ecology and Evolution
Table 2. Innovations in plant reproduction.
Moss
Fern
Club moss
Scientific name for group
Produces spores (y/n)
Distinct gametophyte
Gametophyte develops by
mitosis (y/n)
Gametopyte haploid (y/n)
Where egg is produced
Where zygote is formed
Sporophyte develops by
mitosis (y/n)
Structure where spores
produced
Spores haploid (y/n)
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Conifer
Angiosperm
BIOS 1620 Ecology and Evolution
Summary questions
1. Compare ferns and bryophytes. What structures and features do ferns possess that
bryophytes do not that may have contributed to the success of ferns in more environments?
2. What are the advantages of vascular tissues in land plants? hat groups have vascular
tissues? What groups do not?
3. What problems did plants face as they moved into terrestrial environments? What features
of mosses, liverworts, ferns and other seedless vascular plants are relevant to the
transition?
4. Describe the general alternation of generation life cycle in plants. How does this basic life
cycle differ between mosses and ferns?
5. Two friends are planning to sell ferns at the local farmers’ market. And they think it’s going to
be easy. They collect thousands of spores from a fern they find in the forest and plant these
spores in individual pots. They carefully tend to the pots and wait for the plants to grow. Why
will they fail?
6. A species of Equisetum has a diploid number of 22. How many chromosomes do you expect
in a spore? In a zygote? In a cell from the sporophyte? What would the pattern be if you
were examining a liverwort?
7. How is the sporic life cycle different in ferns and pines?
8. How are the environmental agents for uniting sperm and egg different in pines and
bryophytes?
9. Fill in the phylogeny on the next page with the names of the major plant groups and the
major evolutionary innovations shown by each as they made the transition to land.
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BIOS 1620 Ecology and Evolution
Figure 2. Map the evolutionary innovations (EI). When did the EIs discussed in lab and
lecture first originate in the evolutionary history of plants?
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Introduction to Phylogenetics
“Nothing in Evolution Makes Sense Except in the Light of
Phylogeny”
– Jay Savage, Presidential Address to Systematic Biologists
Are dinosaurs extinct?
A Peregrine falcon ——> is a dinosaur!
Dinosaurs
Introduction to Phylogenetics
All of life is organized by phylogenetic relationships
You are here
Outline:
1.Understand how to read phylogenies
The cotton in your
shirt came from here
2.How do we find the best tree?
3.How how we use phylogenies?
The E.coli
in your gut
is here
Download wall poster from: http://www.zo.utexas.edu/faculty/antisense/DownloadfilesToL.html
(see Science 300:1692-1697)
Phylogenetics: a historical science
Systematics – biological
discipline that studies
organismal diversity
1) Phylogenetics
2) Taxonomy
Phylogenetics: a historical science
Systematics – biological
discipline that studies
organismal diversity
1) Phylogenetics – forming
and testing hypotheses of
evolutionary relationships
among species
2) Taxonomy
Phylogenetics: a historical science
Systematics – biological
discipline that studies
organismal diversity
1) Phylogenetics – forming
and testing hypotheses of
evolutionary relationships
among species
2) Taxonomy – naming &
classifying organisms
Didelphis virginiana
Didelphidae
Didelphimorpha
Mammalia
Chordata
Animalia
Felis catus
Felidae
Carnivora
Mammalia
Chordata
Animalia
Leopard
Carl Linnaeus
Linnaean
classification rank based
grouping
originally based
on similarity
1707-1778; Swedish botanist
Taxonomy should be based on nested sets of relationships
Phylogenetics
•Phylogenies are
branching diagrams
that depict hypotheses
of evolutionary
relationships or
recency of common
ancestry.
human
chimp
gorilla
Anatomy of a phylogeny
human
chimp
gorilla
tips
Anatomy of a phylogeny
human
chimp
gorilla
tips
branches
Anatomy of a phylogeny
human
chimp
gorilla
tips
branch length – distance
from edge to edge
Anatomy of a phylogeny
human
chimp
gorilla
tips
lineages – branches
represent lineages, which
are a series of ancestor
descendent populations
Anatomy of a phylogeny
human
chimp
gorilla
tips
branches
nodes
nodes
nodes represent the Most
Recent Common Ancestor
(MRCA)
The MRCA is often unknown,
we just know they had one!
Anatomy of a phylogeny
sister taxa
human
chimp
gorilla
sister species – are any
two species that are each
others closest relatives
sister clades – any two
clades that are each others
closest relatives
Anatomy of a phylogeny
human
chimp
gorilla
Clade – group of taxa
sharing a more closer recent
common ancestry with one
another than with members
of another clade.
-nodes indicate clades
-clades are by definition
monophyletic
Monophyly- group of taxa derived from a common ancestor
and all descendants of that ancestor (monophyletic).
human
chimp
gorilla
orangutan
Hominini
Homininae
Hominidea
Hominoidea
gibbon
Monophyly- group of taxa derived from a common ancestor
and all descendants of that ancestor (monophyletic).
A monophyletic group is a clade.
human
chimp
gorilla
orangutan
Hominini
Homininae
Hominidea
Hominoidea
gibbon
Monophyly- group of taxa derived from a common ancestor
and all descendants of that ancestor (monophyletic).
human
chimp
gorilla
orangutan
Hominini
Homininae
Hominidea
Hominoidea
gibbon
Monophyly- group of taxa derived from a common ancestor
and all descendants of that ancestor (monophyletic).
human
chimp
gorilla
orangutan
Hominini
Homininae
Hominidea
Hominoidea
gibbon
paraphyly- group includes common ancestor and some but
not all descendants (paraphyletic)
human
chimp
gorilla
orangutan
Hominini
Homininae
Hominidea
Hominoidea
gibbon
paraphyly- group includes common ancestor and some but
not all descendants (paraphyletic)
human
chimp
gorilla
orangutan
Hominini
Homininae
Hominidea
Hominoidea
gibbon
polyphyly- group derived from two or more different common
ancestors (polyphyletic)
human
chimp
gorilla
orangutan
Hominini
Homininae
Hominidea
Hominoidea
gibbon
Are “fishes” monophyletic?
“Fishes”
“Paraphyletic”
Phylogenetics
A
B C
C A
B
•Topology (branching
arrangement) matters,
orientation does not.
-Nodes “swivel”
Are these trees the same?
Yes
Phylogenetics
Topology (branching
arrangement) matters,
orientation does not.
-Nodes swivel
Are these trees the
same?
Yes!
Phylogenetics
Are these trees the same?
YES!
How do we determine phylogenetic relationships?
“It’s one of those
hummingbird things”
How do we determine phylogenetic relationships?
“It’s one of those
hummingbird things”
How do we determine phylogenetic relationships?
“It’s one of those
hummingbird things”
How do we determine phylogenetic relationships?
“It’s one of those
hummingbird things”
Wings of dragonflies, birds bats
due to common ancestry?
How do we determine phylogenetic relationships?
“It’s one of those
hummingbird things”
How do we know this is wrong?
Wings of dragonflies, birds bats
due to common ancestry?
Descent (from a common ancestor) with
modification
Descendants B
C
Speciation
Ancestor (A)
Descent with Modification
Descendants B
C
Speciation
Ancestor (A)
Descent with Modification – organisms will share many
features with close relatives, because they both
inherited them from a common ancestor.
These “features” are homologous traits. For example,
hair and mammary glands in mammals are homologous.
Descendants B
C
Speciation
Ancestor (A)
About those wings….
Dragonflies
birds
bats
Homology – structures or traits due
to common ancestry, but not
necessarily retaining common form
& function
Homoplasy – Structures or traits
NOT due to common ancestry. Due
to convergence, likely for a common
function
Wings in these three species are not
due to common descent.
Descendants B
C
Ancestor (A)
We want to use homologous
traits called synapomorphies to
build phylogenies
Ungulates – hooved mammals
mammals
Hooves
Placenta
Discrete reproductive tract
mammary glands, hair
Phylogenetics
Synapomorphies
Shared derived
characters due to
common ancestry.
•These are used to
identify
evolutionary
relationships.
•Diagnose clades
Phylogenetics
Synapomorphies
Shared derived
characters due to
common ancestry.
•Diagnose clades
Amniotic egg is a synapomorphy for amniotes
Phylogenetics
Synapomorphies
shared derived
characters” are
shared due to
recent common
ancestry.
Four limbs is a synapomorphy for tetrapods
Phylogenetics
•Homoplasy refers to
characters that are
similar due to
convergence, not due
to common ancestry.
Homoplasy
wings in birds and bats
Phylogenetics
•But remember, the
phylogeny is a
hypothesis.
•These relationships
can change with new
data
•So how do we know
which tree is best?
Descent with Modification – organisms will share many
features with close relatives, because they both inherited
them from a common ancestor.
We can use this knowledge to in our favor!
•Parsimony: The
hypothesis that invokes
the fewest ad-hoc
hypotheses is most likely
to be correct.
Descendants B
C
•In other words, the best
tree should be that with
the least homoplasy.
Ancestor (A)
Phylogenetics
Hair
Milk
Placenta
Hair
Milk
Placenta
Wings
7 Steps
(each tick
mark is a
“step”)
Phylogenetics
Wings
5 Steps
Hair
Milk
Placenta
Wings
Phylogenetics
To find the best
tree you search for
the topology
(arrangement) that
requires the fewest
steps – most
parsimonious.
Wings
Hair
Milk
Placenta
5 Steps
Wings
Why was this a shortsighted (but still awesome) decision?
Why was this a shortsighted (but still awesome) decision?
Phylogenies are testable hypotheses that change with new evidence
What can we do with phylogenetic tree?
“Nothing in Evolution Makes Sense Except in the Light
of Phylogeny”
– Jay Savage, Presidential Address to Systematic Biologists
Answer: We can’t do anything without phylogenetic trees!
Applications of Phylogenetics
• The tree itself
• Discover surprising relationships
• Character evolution
• Biogeography
• Disease evolution
• Forensics
Applications of Phylogenetics
• The tree itself
• Discover surprising relationships
• Character evolution
• Biogeography
• Disease evolution
• Forensics
Several years ago, a
physician was
accused of injecting
his ex-girlfriend with
HIV positive blood
from one of his
patients.
Richard P. Schmidt vs.
The State of Louisiana
Richard P. Schmidt vs.
The State of Louisiana
How does HIV infection work?
Descendants B
C
Ancestor (A)
Richard P. Schmidt vs.
The State of Louisiana
HIV from general
population
Convicted of attempted murder
-serving 50 years
First use of phylogenetics in criminal case
Using the same principles and approach, we can
determine the origins of HIV in humans
Phylogenetic prediction
of the future of influenza:
Which current strains
will lead to the epidemics
of tomorrow?
years samples
were taken
Bush et al., 1999
(Science 286:1921-1925)
Applications of Phylogenetics
• The tree itself
• Discover surprising relationships
• Character evolution
• Biogeography
• Disease evolution
• Forensics
Which came first?
It turns out, you can answer this question!
Announcements
Quiz 3 due
Sunday
Lecture: History of Life on Earth
The History of Life: what features define life?
Biology is the study of life!
Life:
(C) Tiffany Schriever
The History of Life: what features define life?
Life:
o Cells – Keep the outside
out, and the inside in.
All organisms have cells
Smallest & simplest unit of
life
New cells come from preexisting cells
Cell Theory
(C) Tiffany Schriever
The History of Life: what features define life?
Life:
o Metabolism & Homeostasis
o Regulate cells
o Use energy – photosynthesis
and metabolism
o Maintain stable conditions
(C) Tiffany Schriever
The History of Life: what features define life?
Life:
o Interaction with the environment
(C) Tiffany Schriever
The History of Life: what features define life?
Life:
o Growth & development
o Get bigger
o Characteristics, function
(C) Tiffany Schriever
The History of Life: what features define life?
Life:
o Reproduction
o Hereditary materials -ability to store
and transmit information
o DNA
o RNA
(C) Tiffany Schriever
The History of Life: what features define life?
Life:
o Cells
o Metabolism & Homeostasis
o Interaction with the environment
o Growth & development
o Reproduction
o Hereditary materials
o Ability to evolve
o All species are related by
evolutionary history
(C) Tiffany Schriever
Tree of Life
Age of the Earth and timeline for various
major events in Earth’s history
http://www.npr.org/2016/11/22/502920622/watch-earthshistory-play-out-on-a-football-field
(C) Tiffany Schriever
The History of Life:
3.8 BYA Life!
How did life begin?
4.6 Billion Years
(C) Tiffany Schriever
The History of Life: abiotic synthesis
• Spontaneous formation of organic molecules from nonliving matter
> Prebiotic soup
Hypotheses for the mechanism of how and where organic molecules
originated
Experimentally tested!
Reducing atmosphere
Extraterrestrial origin
Deep-sea Vents
(C) Tiffany Schriever
The History of Life: abiotic synthesis
Miller and Urey Experiment
Test reducing atmosphere
hypothesis- organic
compounds form from simpler
molecules
Simple molecules in a reducing
(adding electrons) atmosphere.
Watch this

(C) Tiffany Schriever
The History of Life
1. Spontaneous formation of organic molecules from nonliving mattersmall molecules
2. More complex molecules formed
• RNA, DNA or proteins
• Potential to have formed on clay surface
3. Boundary layer around molecules
• Protobiont- aggregate of molecules and macromolecules with a boundary
layer (allowed for separation of internal and external environment)
(C) Tiffany Schriever
Origin of Life

Which
molecule
made life
possible?
(C) Tiffany Schriever
Origin of Life
Which molecule made life possible?
Protein – Can perform tasks, but no replication, no storage
DNA – Ideal for replication & information storage. But can’t
perform tasks alone, requires enzymes. Rely on protein to
function
RNA – store information and perform functions.
–Catalytic activity – metabolic activity of breaking down
molecules
(C) Tiffany Schriever
RNA world Hypothesis
The Man Who Rewrote the Tree of Life
The RNA Origin of Life
• http://www.pbs.org/wgbh/nova/next/evolution/carl-woese/
• Self replicating RNA formed, multiplied, and evolved
• Mutation into double helix of DNA
(C) Tiffany Schriever
first living thing?
(C) Tiffany Schriever
Geological time
• The earth is how old?
– 4.6 BYA
• First fossils appeared
– 3.5 BYA
A Billon years went by!
(C) Tiffany Schriever
Geological time
• The Earth is 4.6 BYA
Eons
• Concept of time
• Compartmentalize into time bits
we can grasp (sort of!)
• Boundaries between time
periods – mass extinctions
(C) Tiffany Schriever
Eras
Periods
Epochs
Extinction
loss of species
(C) Tiffany Schriever
Extinction
Baseline extinction rate
• Normal or standard rate
• rate of about one to five species
per year
• Natural phenomenon
Mass extinction
• Widespread and sudden loss of a
large number of species (50%)
• Caused by asteroid strikes,
volcanic eruptions, and natural
climate shifts
• Any new events causing mass
extinctions?
(C) Tiffany Schriever
Environment’s role in life on Earth
• Influences what types of
organisms live and where they
live
• Extinctions
• New types of organisms
• Temperature
• Atmosphere
(C) Tiffany Schriever
Environment’s role in life on
Earth
• Temperature
• Atmosphere
• Landmasses
• Continental drift – process by
which major landmasses have
moved and changed shape over
billions of years
• Floods and glaciations
• Volcanic eruptions
• Meteorite impacts
(C) Tiffany Schriever
The History of Life: Fossils
3.5 BYA: first fossils
Fossils are preserved
remains of past life
(C) Tiffany Schriever
The History of Life: Fossils
3.5 BYA: first fossils
Stromatolites: Layered
rocks that are formed
through the cementing of
sediments by bacteria.
Single-celled organisms use
O2
Suggests life originated
before 3.5 Billion years ago
(C) Tiffany Schriever
The organism that changed the world
• Video
• https://www.youtube.com/watch?v=dO2xx-aeZ4w&feature=youtu.be
(C) Tiffany Schriever
3.8 – 2.5 BYA
Little oxygen
Prokaryotic
cells
Archaean Eon
> organisms were anaerobic
> Bacteria and archaea
> First cells were heterotrophs
First life: prokaryotes
• Bacteria and archaea
• a microscopic single-celled
organism that has neither
a distinct nucleus with a
membrane nor other
specialized organelles.
Cyanobacteria!
(C) Tiffany Schriever

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