Bios 101Biology 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 Wilson’s BiodiversityThis figure is fairly old, the numbers of described speciesIn 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 now…we 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 ClassificationThis “five kingdom” scheme of classification replaced the old animal kingdom vs. plant kingdom scheme in the 1970’s. 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 lifeModern methods of sequencing

DNA, and a modern approachto systematics allows a greaterunderstanding of the true“tree of life”

The tree on the left, based uponribosomal RNA, which is veryevolutionarily conservativeendicates that there are three major“domains” of living things.

The prokaryote archaea are closerTo 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 Lyme’s 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

EukaryotesEukaryotes, 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 Wilson’s 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 CreateHabitats for Other Organisms.

Many individuals ofa single speciesare called a biological population

Populations of organisms tendto assemble intobiological 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 planet’s 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 Earth’s 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) Productivityc) 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 earth’s 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 19th 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 lion’s 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 pollinator…a thryp, with pollen grains attached to its abdomen.

The first pollinators were probablyherbivores attracted to pollen asa 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 Darwin’s 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.