Bios 101

Biology of Populations and

Communities
Dr. Alan Molumby
molumby@uic.edu
3084 SEL
What is Out There?
Reading: Freeman Chps. 1 and 57
Biology is the study of life, but
what is life?
processes that define a living
thing
Organization and Information
Need for an Energy Source
Reproduction and Evolution
Organization and
Information
Living things are born and living things die.
Although true by definition, this underlies an
essential property-they are organized.
So long as an organism maintains a given level
of organization, it is alive. When this
organization breaks down, it dies.
Living things impose organization on nonliving
matter by growth, development, and
reproduction.
In death and decomposition, this organization
breaks down.

Homeostasis
A critical aspect of life's organization is a
constant internal environment, called
homeostasis, which makes the complex
biochemical machinery of life possible.
Information
Living things use a template to impose order
on nonliving things and to maintain order
within their own bodies.
In all present-day living things, this template
is DNA (many viruses use RNA, but are they
living?.)
This template makes proteins, which are
responsible for our structure, function, and
metabolism-it is copied every time living
things reproduce.
DNA
DNA is the prime substance of life itself
(on this planet, at least), it is as close to
the basis of life as we can get.
DNA is the information template for life
on earth. Without DNA, living
organisms could not reproduce or
function.
Need for and Energy Source
All living things require constant input of
energy to survive.
This is because life exists in a state of
dynamic equilibrium.
A dynamic equilibrium is an organized
system that requires a constant input of
energy to maintain itself.
Without input of energy, the organization
breaks down and death is imminent.
Humans are Heterotrophs
Humans, like other animals, are
heterotrophs. We process energy that was
originally captured by other living things.
Unlike plants, we cannot fix energy from
sunlight, nor can we fix energy by reducing
hydrogen sulfide these organisms are
autotrophs and chemoautotrophs
respectively.)
All of the energy we use to survive, and most
of the nutrients, were taken from another
organism.
Reproduction and Evolution
All living things are able to make copies
of themselves.
It is in this area that the ambiguous nature
of viruses becomes apparent. A virus
alone is inert. It does not use energy and
cannot reproduce. In the presence of the
right living cells, however, viruses can
direct the production of million copies of
themselves.
On Earth, living things fall into (more
or less) discrete categories called
species
The term species is fundamental to our
understanding of biology, and yet, there are
multiple, competing definitions.
Basically, species are groups of organisms that
1-can interbreed and produce fertile offspring
(biological species concept) and/or
2-share a set of traits in common that distinguishes
them from other such groups (morphological
species concept) and
3-is an evolutionary lineage that persists, ancestor
to descendant, over time (systematic concept)
How Many Species are Out
There?
There are approximately 2 million described species on
Earth, true number has been estimated to be 8.7 million,
though it may be much higher.
This total was published online 23 August 2011 | Nature
doi:10.1038/news.2011.498. There are other estimates
Currently there are at least 1 million named insect species
There are approximately 53 000 vertebrate species
of which approximately 25 000 are fish, 5 000 are
mammals, 10 000 are birds, 8 000 are reptiles and 5
000 are amphibians)
There are about 250 000 flowering plant species.
If prokaryote species are recognized, the true total can
be as many as 100 million.
Most of what is out there remains
undescribed.
The process of describing a species is time-consuming,
and demands special skills which are in short supply.
There is no central database of species, though several
projects are underway to change this.
There is also an attempt to create a central database of
phylogenetic information.
There are difficulties with the species concept;
cryptic species, species named more than once,
and polymorphic species.
As a result, only a small fraction of species are named
and described, some existing species have been
named several times.
When we extend this concept back in time,
we must acknowledge that most extinct,
ancient species never fossilized, and will
never be known.
Scientific names are given to fossil species,
though it is acknowledged that these names, at
best, represent morphological species based on
limited data.
For instance, there is only one recognized
species of Allosaurus, a very well-known
predatory dinosaur-Allosaurus fragilis.
There is a great deal of variation among specimens
attributed to that species-and in reality, the fossils we
have may have represented several species.
The largest specimens are often placed in the
genus Epanterias, or Saurophagnax-but we do not
really know whether they were simply big
individuals of A. fragilis.
Some taxa are known much better than
others.
For example, birds, mammals, flowering
plants, and butterflies are well known,.
Most species in these groups have been
described and named.
Most insect groups, such as the
chalcidoids and beetles, are less well-
known, but becoming much better-
understood.
Only a fraction of the insects have a name
and a description.
For some groups, including most
microorganisms, we are only beginning
to comprehend their true diversity.

Above is a chalcidoid, named and described,
Below are microbes from a Greenland glacier,
no formal description yet
From E.O Wilsons Biodiversity
This figure is fairly old, the numbers of described species
In each group have increased, but the proportions have remained
fairly similar.
The Tree of Life
All organisms on Earth descend from a single,
common ancestor.
This ancestor may have been a single species, or a
cluster of organisms freely exchanging genetic
material.
If other, unrelated forms of life existed, they have
gone extinct by nowwe know this because:
Except for a few viruses, which may have undergone
retrograde evolution, all forms of life on Earth use DNA as
the genetic material.
All forms of life share a common, virtually-identical genetic
code.
All forms of life rely on the same biomolecules-amino
acids, sugars, etc.
In scientific terms, the tree of life is a diagram
representing the actual diversification of
organisms from a common ancestor.
The Old Classification
This five kingdom scheme of classification replaced the old
animal kingdom vs. plant kingdom scheme in the 1970s. It is an
excellent grouping of organisms based on their characteristics, but
it does not reflect evolution very well.
The Tree Within a Tree Phenomenon
Very often, groups of organisms appear to be
similar when they are really not very similar at all.
This similarity is superficial, however, because very
different organisms often possess the ancestral state
for many characteristics, and we overlook differences.
When organisms are classified objectively and
scientifically, it becomes apparent that much of the
diversity we see in nature is variations on a theme
created by a single, very successful, common
ancestor.
An important adaptation has enabled diversification
This pattern is repeated many times in evolution.
New ideas on the tree of life
Modern methods of sequencing
DNA, and a modern approach
to systematics allows a greater
understanding of the true
tree of life

The tree on the left, based upon
ribosomal RNA, which is very
evolutionarily conservative
endicates that there are three major
domains of living things.

The prokaryote archaea are closer
To eukaryotes than the bacteria.
From paleos.com
This image is on Wikipedia
http://en.wikipedia.org/wiki/File:Tree_of_life_with_genome_size.
svg
To surf the tree of life in depth, go to http://www.tolweb.org
From wikipedia.com
Prokaryotes
Prokaryotes are the most ancient,
most abundant, and most metabolically
diverse organisms.
This term describes a state of organization
(no nucleus) rather than a taxonomic
group.
Prokaryotes include the:
Bacteria
Archaea
Bacteria
Some major groups of bacterica
include:
Proteobacteria
Cyanobacteria
Gram-Positive Bacteria
Chlamydias
Spirochetes
Proteobacteria
The proteobacteria are a large and
diverse group that includes
photoautotrophs, chemoautotrophs, and
heterotrophs.
There is no taxonomic divide between good
bacteria, those that are essential to the
functioning of the biosphere, and bad
bacteria, those that can kill us.
Pathogenic bacteria occur within many different
groups.
Among the
proteobacteria are
the myxobacteria,
interesting gliding
bacteria that
produce fruiting
bodies under
conditions of
starvation.

Myxobacteria live
in the soil, and
glide along
solid surfaces via
a polysaccharide
slime.
www.biology.ed.ac.uk/.../microbes/myxococc.htm
Among the
proteobacteria are
the ancestors of
mitochondria.
Also included are
Rhizobium species
that live in the roots
of plants,
and the
rickettsias, tiny
pathogens that
live within the
cells of animals
bioinfo.bact.wisc.edu/.../Effects.html
Spirochetes
These are among
the most
distinctive bacteria
they move by a
spiraling
corkscrew motion.
They can be free
living or parasitic.
Syphilis and
Lymes disease
are caused by
spirochetes
Archaea
Although we know very little about them, the archaea are
some of the most abundant, and important, organisms on
the planet.
The group is very ancient-some bear a striking
resemblance to fossils dated at more than two billion
years old and many exploit ecological niches that were
probably more important billions of years ago.
Though the majority live in ordinary habitats, the
group includes many extremophiles.
These include, but are not limited to;
methanogens-live in anerobic conditions and break down
methane
extreme thermophiles-live in incredibly hot environments
extreme halophiles-live in extremely salty environments
Eukaryotes
Eukaryotes, organisms with nuclei and usually
possessing membrane-bound organelles, are a
single branch on the tree of life.
It is likely that the original eukaryote was an
amalgam of prokaryote species, and possibly
a viral component as well.
Modern studies of eukaryote taxonomy indicate
there are probably between 11 and 20 eukaryote
kingdoms. These kingdoms include many groups
formerly classed simply as protists, such as
diplomonads and parabasalids.
From Baldauf, SL Science, 2003, Jun 13 1703-6
Protists
Protists are simply eukaryotes that are
unicellular for most of their life cycle.
There are many groups of distantly related
protists, which are now thought of as kingdoms
in their own right.
Several groups have independently acquired
photosynthesis, and become algae, others
have evolved multicellularity.
One group of multicellular protists evolved into
animals.
Another lineage evolved into fungi.
There are several multicellular lineages, such as
slime molds, that neither plant nor animal nor fungi.
Fungi
Fungi are a kingdom of organisms that
includes decomposers, parasites, and
mutualisms.
There are four major groups;
Chrytridomycots
Zygomycots
Ascomycots
Basidiomycots
EO Wilsons Biodiversity again
Viridiplantae
This group includes the green plants
and the basal bush from which they
originated. They have chlorophyls a
and b, as well as certain other
distinguishing characteristics.
Green Algae-Chlorophytes
Charophytes
Plants
True Plants
These include several
groups of multicellular,
terrestrial
photosynthesizers,
including
Bryophytes-mosses,
etc.
Pteridophytes-ferns.
Gymnosperms
Angiosperms-flowering
plants
Animals
Animals are a true lineage
of multicellular organisms
evolved from one line of
protists (probably
resembling a group called
the choanocytes).
They have evolved many
different body plans, each of
which represents a phylum.
There are about 30 present-
day animal phyla, there
were probably more in the
distant past.
Organisms Create
Habitats for Other
Organisms.

Many individuals of
a single species
are called a
biological
population

Populations of
organisms tend
to assemble into
biological
communities
Biodiversity
The concept of biodiversity includes many
different ideas regarding the diversity of living
things. It encompasses:
The Genetic Diversity within Populations
Diversity of Populations Within Species
Diversity of Species or Lineages (Taxonomic Diversity)
in a given habitat (alpha diversity)
accounting for the diversity of habitats, and the change
in species from one habitat to the next (beta)
total number of species (gamma)
Communities and Ecosystems
Genetic Diversity
An example of biodiversity
that includes genetic
diversity within a species is
varieties of cultivated
plants.
The tomato, Solanum
lycopersicum, is a single
species of plant, originally from
the Andes.
There are over 7500 varieties of
tomatoes, each with its own
characteristic allele pool.
These include hundreds of
heirloom varieties.
Taxonomic Diversity
Every ecosystem, habitat, or location can, at
least hypothetically, be assessed for the
number of different species it contains.
In practice-this assessment depends a great deal on 1)
who is looking, 2) how much effort and how long the
look, and 3) what lineages the observer expects to see
or is interested in counting.
A herpetologist can get a very good measurement of
how many lizards are living on an island in just a few
days, but a botanist might need weeks or months to
produce an estimate of ALPHA DIVERSITY for the
island, because identification of plants often depends
upon flowers or structures that are seasonal in
occurrence.

For instance, this is a complete list of snakes
that occur in California:
http://www.californiaherps.com/snakes/snakes.html
It includes 73 species, in various families.
Some Major Areas of
Unexplored Biodiversity
Tropical Rainforests; Harbor much of
the planets biodiversity-are becoming
increasingly well-understood even as
we destroy them.
Ocean Floor; Almost entirely
unexplored.
Microbial World; We are just scratching
the surface of what is out there.

Tropical rain forests cover 6% of the
Earths land area, and harbor a significant
proportion of its biodiversity, and account
for a great deal of its primary productivity.
More than 4/5 of all plant species and
animals and nearly half of all animal
species reside here.
The reasons for this are a bit of a mystery,
but are likely some combination of;
a) History,
b) Productivity
c) A heterogeneous environment, with
biodiversity begetting more biodiversity.
Below; neotropical orchid bees, flowers of the
Theobroma tree, a poison-dart frog. Each
organism exists in complicated mutualisms with
other creatures, fostering biodiversity.
The ocean covers 70% of the earths
surface and provides about half the air we
breathe, courtesy of the microscopic,
oxygen-producing phytoplankton floating in
it.
As of the year 2000, the National Oceanic
and Atmospheric Administration (NOAA)
estimated that as much as 95 percent of the
world's oceans are unexplored.
In the 19
th
century, it was thought that the
deep oceans were uninhabitable to living
things. This is not true.

The Census of Marine Life, a decade-long
international study of the planet's oceans,
uncovered more than 1,200 new species, excluding
microbes, since the project began in 2000, and this
is a very small fraction of what is out there.
Below-Abyssal sea cucumber, and carnivorous
harps sponge.

The Microbial World
We are just scratching the surface of microbial
biodiversity.
Even the definition of a species needs to be reconsidered
when dealing with microbial fauna, because prokaryotes
(which make up the lions share of these organisms) do not
reproduce sexually, and have systems of gene exchange
that do not lend themselves to distinct boundaries among
species.
Additionally, most microbes cannot be cultured in the
laboratory setting.
Challenging environments, such as glaciers, deep drilling
cores, and hydrothermal vents, have yielded unexpected
biodiversity.
Ecology and Evolution
The sciences of ecology and evolutionary biology are
often taught together, and at many universities, the
two sciences are part of a single academic
department.
This is because the mechanisms that drive
evolution are fundamentally ecological, and the
participants in ecological interactions are products
of evolution.
The two subject areas interrelate so extensively that
some areas of research, such as life history
evolution, biogeography, coevolution, and
macroevolution, are inextricably entwined in both
sciences.
They provide an answer to the question of why there are so
many species are out there, as well as an answer to the
question of why they take the forms they do.
Example: Pollination Syndromes in
Flowers
Naturalists have long observed that flowering
plants, in a wide variety of taxa convergently
evolve characteristics which match one of
several pollination syndromes.
The same pollination syndromes evolve in
widely disparate types of plants. Likewise,
widely disparate types of pollinators will
evolve to exploit these syndromes.
These syndromes are discrete sets of floral,
nectar, and pollen characteristics that match the
sensory abilities, metabolism, and biology of their
pollinators, and act to ensure efficient pollination by
manipulating the behavior of the pollinator.
Pollinators evolve in response to these floral
characteristics, the result being a coevolutionary
interaction that intensifies the relationship.
.

To the left is an image of the
earliest known pollinatora
thryp, with pollen grains attached
to its abdomen.

The first pollinators were
probably
herbivores attracted to pollen as
a source of food.
Example;
A flower evolves a long corolla to ensure that
hawkmoth visitors must reach deeply into a
flower in order to reach the nectar reward
provided by the flower, thus placing their
faces in the appropriate location to receive
pollen.
The hawkmoths respond by evolving longer
tongues, to enable them to more easily reach
the nectaries of the flowers.
This, in turn, places selective pressure on
the flowers, and intensifies the relationship.
The longer nectary, in turn, makes it
nearly impossible for long-tongued bees
to visit the flowers, and drives the system
toward an obligate mutualism, rather than
a looser, facultative mutualism
Charles Darwin was fascinated by
pollinators.
Upon examination of a Madagascar
Star orchid, (Angraecum
sesquipedale), which has a nectar
tube over ten inches long, he
famously predicted that there must
be a hawkmoth with a tongue ten
inches long to pollinate it.
At the time, only the orchid had
been discovered.
40 years later, the moth was
discovered, Xanthophan morgani
praedicta, now called Darwins
hawkmoth.
In this particular scenario, part of
the selective pressure driving the
system is that the moths are safer
from predatory spiders, but less
effective as pollinators, if they never
get too close to the flowers as they
feed.
In addition to the evolutionary consequences of these
syndromes, they have ecological aspects as well.
Under some circumstances, flowers effectively compete
for pollinators. Flowers that are more conspicuous, and
offer greater rewards, get more pollinators, but since these
syndromes restrict the types of pollinators that can visit
flowers, they restrict the scope of competition.
Pollinators very often compete for nectar, and for pollen.
Specialist pollinators that visit only one type of flower are
sometimes protected from interspecific competition
(sometimes not, pollinator specialization does not imply that
the flower can only receive one type of visitor), but at the
cost of extreme ecological specialization.
This specialization causes the pollinator to evolve behavior
and life history to match the appearance of the flowers they
pollinate.
Other pollinators are generalists, able to visit a wide
variety of flowers within their own pollination syndrome.
For instance, the squash
bee, Peponapis pruinosa
feeds on the nectar and
pollen of squash,
exclusively. Though other
bees visit squash, it is the
most effective pollinator.
Males hide in squash
flowers day and night,
waiting for females to mate
with in the early mornings
as they forage for pollen.
The abundance of this
pollinator makes squash
and pumpkins easy to
cultivate, even though
most gardeners do not
know the squash bee
exists. Squash bees time
their emergence to late
summer.
The most common pollination
syndromes:
Most flies and generalists (most beetles)-open flowers, easy
to reach pollen, accessible nectaries. Large amounts of
pollen because most of the visitors are after pollen. Usually
early spring.
Long-tongued bees-moderately long corollas, flowers are
white, blue, yellow, infrared, sucrose-concentrated nectar,
sometimes a landing pad for bees, and sometimes petals
that must be pushed apart for the bee to reach the nectar.
Scented flowers, open in daytime. Sticky pollen that bees can
easily collect and transport, nectar guides.
Short-tongued bees-white, yellow, infrared flowers, short
corollas with easily available pollen, no special tricks with
petals, but usually asymmetric. Scented flowers open in
daytime. Sticky pollen. Sucrose-dominated nectar.
Bumblebees, Amigillia bees-as with long-tongued bee
flowers, but bee must hang upside and buzz to release
pollen.

More pollination syndromes
Hawkmoths-very long corollas that effectively force the
moth to push its face into the stamens in order to reach
reward (moths are not after pollen, so they must be
tricked into transporting it), white flowers that are heavily
scented and open at night, small amounts of
concentrated nectar.
Butterflies-as above, but flowers run more to the pink or
lavender and have a landing platform.
Bee flies -as above, no landing platform
Hummingbirds-red flowers (only vertebrates see that
color well) with very long corollas and large amounts of
dilute nectar, flowers open in daytime, and bird is forced
to push face into stamens in order to feed. No scent.
Bats-large amounts of dusty pollen that will stick to
mammal hairs, very big flowers that bats can reach into
with their faces, open at night,
Carrion beetles and flies-flowers smell like carrion and
offer large amounts of pollen

African baobab-bat
pollinated.
Day-flying sphinx
moth nectaring on
African vervain.
Syrphid fly on a
crocus flower.