bio term 1
Classification
Classification or ‘taxonomy’ is the science of naming, describing, and grouping organisms.
Why classify?
Classification is done for three main reasons
1. Organisation – Massive information can be easily accessed and interpreted.
2. Communication – a global system that allows scientists to share ideas despite language barriers
3. Further study – patterns and trends are easier to recognise when organisms are accurately grouped.
How does it work?
Initially, scientists just grouped organisms that looked similar. There were only two groups: plants and animals. Over time new theories and evidence came together and changed the system. It is important to remember that the classification system is a human construct, it is not perfect and is constantly being changed and improved.
The system we use today is based on “Linnaean classification.” Linnaean classification has 8 grouping levels called ‘taxa’ or taxonomic levels. This system is ‘hierarchal’ meaning that the higher the taxonomic level, the more organisms there are in that group.
The order of taxonomic levels
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
The order of taxonomic levels All primates are mammals and all mammals are animals. Each level becomes more specific. Reptiles are animals but not mammals.
Major groupings
The order of taxonomic levels
Remember the system is hierarchal so each level becomes more specific. The levels at the top must be distinguished by major differences between organisms.
Domains and kingdoms are separated by major differences on a cellular level.
3 Domains (Eukaryotes) (Prokaryotes) Eukarya – All contain nucleus and membrane-bound organelles.
Bacteria – simple single-celled organisms
Archaea – Single-celled organisms that typically live in extreme conditions. No nucleus or membrane-bound organelles.
6 kingdoms
Animalia
Plantae
Protista
Fungi
Bacteria
Archaea
Animalia
Eukaryotic (Cells have a nucleus)
Multicellular
Heterotrophic (eat to gain energy)
No cell wall
Plantae
Eukaryotic
Multicellular
Autotrophic (make their energy)
Cell wall of cellulose
Fungi
Eukaryotic
Mostly multicellular but can be single-celled
Heterotrophic - Extracellular digestion
Cell wall made of chitin Eg. mushrooms, toadstools, moulds, and yeasts
Protista
All eukaryotes that don’t fit into fungi, plant, or animal
Unicellular
Heterotrophic but can be autotrophic (varies)
No cell walls All live in moist conditions
Bacteria vs. Archaea
For a long time,e both were in the same grouping (Monera). Archaean DNA studies determined they are more like eukaryotes than bacteria.
Prokaryotic (no nucleus or membrane-bound organelles)
Unicellular
Can be autotrophic or heterotrophic (varies)
Both have cell walls but differ in structure.
Archaea are often found in extreme locations.
Major Animal Phyla
Chordata (vertebrates)
Arthropoda (crustaceans, millipedes, centipedes, insects, arachnids) Annelids (segmented worms)
Echinodermata (starfish, sea urchin)
Mollusca (shellfish) Nematoda (roundworms)
Platyhelminthes (flatworms)
Cnidaria (jellyfish, sea anemones)
Porifera (sponges)
There are 35 in total
Characteristics for classification
Characteristics Organisms are classified into taxonomic groups based on a series of distinct characteristics.
The main categories of characteristics used are:
Physical (Morphological)
Reproductive
Genetic
Physical characteristics
Physical classification was the first means of organising organisms.
Can occur at the macro level with features such as “has wings” or “thin tail”
But also, at the cellular level with features such as “cells have a nucleus.”
Physical characteristics
Skeletal structure is a common characteristic for physical classification:
Exoskeleton: External skeleton
Endoskeleton Internal skeleton
Hydrostatic skeleton: No skeleton – held together by internal fluid pressure.
Symmetry
Symmetry or asymmetry (no symmetry).
Bilateral symmetry: Division into two equal (approx.) sides (left and right or up and down). Radial symmetry: Any number of divisions if it’s cut through a central axis. Segmentation: Division into repeating sections. Reproductive methods
Reproduction
Sexual reproduction: gametes (sex cells) from two individuals
Asexual reproduction: Single organism reproduction Reproductive methods
Asexual reproduction-
Fragmentation: The splitting of an organism's body. Both fragments then regenerate into whole organisms
- Binary fission cell division
- Spores: release of genetic material which can be activated later
- Parthenogenesis: female-only reproduction
Sexual reproduction: Common characteristic used to distinguish organisms that use sexual reproduction is the method of birthing. Many organisms lay eggs whilst others live young. Some organisms have very long gestation times, others very brief.
Genetic characteristics
Since the discovery of molecular sequencing, there has been a massive leap forward in the ability to classify organisms and observe evolutionary relatedness.
DNA, RNA, and protein sequences are all indicative of relatedness.
The greater the similarity, the more closely related the organisms.
Deoxyribonucleic acid. (DNA)
4 bases: adenine, thymine, cytosine, and guanine.
The sequence of these bases determines the sequence of RNA.
Ribonucleic acid (RNA)
4 bases: Cytosine, Guanine, Adenine and Uracil.
The sequence of these bases determines which amino acids will be connected to make a protein.
Cladograms
Classification:
The modern classification reflects evolutionary relationships.
The theory of evolution is founded on two key concepts.
1. All life forms share a common ancestor
2. Populations change over time due to selective pressures
Speciation
Speciation refers to the formation of new and distinct species because of progressive evolution. It refers to the splitting of a single evolutionary lineage.
At this point – the two groups cannot successfully reproduce 2 species.
Cladograms
Information about speciation events can be represented in evolutionary tree diagrams.
cladograms or phylogenetic trees
There are different ways of representing these diagrams but the most common are shown below. Each division (circled) shows a special event.
Several assumptions are made when putting cladograms together: The more characteristics two organisms share, the more related they will be.
Characteristics in a group might not be shared with more distantly related groups. Sometimes, there is more than one potential way of organising the cladogram.
Usually, the simplest explanation is the most likely to be correct.
Clades Organisms can be grouped into clades: A clade is all descendants of one ancestor. If we consider Darwin’s finches, they could all be classified as one clade, as they all share a common ancestor.
Monophyletic: a group (clade) containing all descendants of the oldest ancestor. Paraphyletic: a group that does not contain all the descendants of the oldest ancestor. Polyphyletic: a group of organisms from different branches.
Biodiversity
Definition: The full range of different living things in a particular area.
3 types of biodiversity
1. Genetic
2. Ecosystem
3. Species
Genetic biodiversity: Differences in the gene pools amongst a single species.
Homo sapiens have different coloured eyes, different coloured skin, different immunities, different deficiencies, all of which are a product of genetic diversity.
Genetic diversity importance: Allows a population to effectively evolve and adapt through natural selection.
With no genetic diversity, a species could easily be wiped out. It provides resistance to extinction.
Ie. S. Aureus is the cause of a common skin condition.
Originally it had little genetic diversity: easily cured with antibiotics. An increase in genetic diversity leads to antibiotic resistance. A recessive genetic condition that affects the red blood cells of humans. Usually detrimental to health, however, it provides significant resistance against malaria.
Ecosystem diversity
Organisms can live in complex communities in vastly different physical environments. Ecosystem diversity looks at the variation between biotic(living) and abiotic (non-living) factors of different ecosystems.
Often the productivity of one ecosystem can affect others surrounding it.
Rainforests can contribute significantly to the recycling of oxygen in the atmosphere.
Bodies of water are excellent ways of maintaining temperature.
Note that many organisms inhabit different ecosystems during various stages of their lives.
If all ecosystems were the same, then there would be minimal biodiversity across the planet.
Species biodiversity
It looks at the number of varied species present within an ecosystem.
Species diversity, the more diverse a population, community or ecosystem is, the more resistant to extinction it becomes
Measuring biodiversity
Biodiversity
We know the greater the diversity of an ecosystem, the more resistant to destruction i.t
Biodiversity Measurements/metrics
Species richness
Species evenness
Biodiversity index
Species richness:
Total number of different species in an ecosystem.
This is expressed as a number – the greater the number, the more diverse the ecosystem.
Species evenness:
Measure of the proportions of populations in an ecosystem.
An ecosystem with one very dominant species could be considered less diverse than one with evenly spread populations of several species.
Biodiversity index:
Best measure of the biodiversity of a region is as it takes into account both the richness and evenness of an ecosystem.
There are many different types of biodiversity indices, some more specific than others.
Simpson’s Biodiversity index
This is a number that states how diverse an ecosystem is.
It does not have any units and can only be used to compare ecosystems.
Note that this equation we are using is a modified version.
In this version the bigger the index, the greater the diversity.
Biodiversity hotspot
When a region's biodiversity is determined, it may be considered a biodiversity hotspot.
There are two major conditions for an area to be considered a biodiversity hotspot.
1. There must be a substantial number (1500+) of endemic species (found nowhere else in the world)
2. Over 70% of the habitat needs to have already been destroyed.
Extra info
In WA: Over 7000 endemic plant species and 1500 endemic vertebrates.
Environments
Biosphere: All the living things on the planet
Biome: Major category of ecosystems over a large geographical area
Ecosystem: An interacting system of living and non-living things in an area
Community: All living members of an area
Population: All the members of a species in a particular area
Individual: A single organism
Habitats and environments
Habitat: Specific geographic location
Environment: Set of biotic and abiotic factors in an area There can be many habitats in one environment. Environment
Environments - abiotic
Physical factors include:
Temperature
Amount or intensity of light
Availability of water
Probability of rain
Texture/particle size of soil
Movement of water Humidity
Wind speed Environments
Abiotic-chemical factors include:
pH of the soil
Concentration of significant gases
Concentration of significant nutrients
Salinity
The largest division in environments is the classification of aquatic or terrestrial environments.
Abiotic factors
• Rainfall (terrestrial)
• Movement of water
• Salinity
• pH
• Depth/pressure
• Soil size (terrestrial)
• Availability of light
• Distance from shore
• Dissolved oxygen
• Nitrate content (fertilizer) (terrestrial)
Temperature Australia’s Temperature Patterns:
Air temperatures in Australia vary widely due to the continent-spanning 30° of latitude (north and south). Temperatures not only affect organisms directly, but they also influence humidity and moisture conditions on land, as well as dissolved oxygen in water.
The Australian Environment:
Apart from Antarctica, Australia is the driest continent on earth. Two-thirds of Australia’s land surface receives less than 500 mm of unreliable rainfall. This results in desert conditions. Regions receiving more than an average of 500 mm of rain are restricted to a belt of just 500 km wide.
Australian Vegetation:
Australia is an arid land, and the distribution of its vegetation depends primarily on rainfall patterns. The vegetation types include rainforest, sclerophyll forest, woodlands, shrubland, grassland, and heath. These vegetation types correspond to different ecosystems.
Ecological sampling
Distribution:
When trying to understand ecosystems, it is important to understand how organisms distribute themselves.
Very rarely will organisms be spread evenly across an entire area.
We generally refer to a populations distribution as being either: Clumped, Random or Uniform. Distribution
By knowing how organisms live, certain strategies can be used to make them easier to study. Once we know how organisms distribute themselves, we try to find out how many organisms are present.
Abundance:
Determining the population size of a species can be a very difficult task.
There are a number of different methods that scientists can use to determine the size and distribution of the population in an area. Some of these include:
Direct observation
Quadrats Transects
Capture-recapture
Note that these methods generally give an estimate rather than an exact number.
Direct observation: Sitting down and counting all of the ants.
Advantages:
Accurate
Don’t need much equipment
Disadvantages:
Can be intrusive/damaging to environment or stressful to wildlife
Inefficent
Quadrat sampling: Variation of direct observation, in which only small areas are looked at. A quadrat is a square. The size of the square depends on the size of the area being studied. Rather than measuring the whole area, we can measure a small part and extrapolate.
Quadrat sampling
Advantages:
Faster than other methods
- Cheap (not much equipment is needed)
- Less intrusive than other methods
Disadvantages
Can be less accurate if not done effectively
Can be subject to bias
Not good for rare or mobile species
Quadrats
Average density of a species = total number of individuals counted/(area of quadrat x number of quadrats)
Population size = Avg Density x total sample area
Percentage cover:
For some species, such as plants or coral, it is more useful to mark out the area covered than to count individuals.
To do this we can create percentage cover maps.
An estimate of the proportion of the ecosystem that is taken up by each species
An average percentage cover can be determined for the whole area by finding the average percentage cover across each of the quadrats.
Line transects:
Imagine you drew a line across a map and recorded everything that touched that line.
You would have a line transect.
Transects are particularly useful when studying environments that have significant changes in environmental factors.
Often abiotic factors are measured along the transect to show how changes in
salinity,
pH
soil type
changed through the environment. These factors can affect the distribution and abundance of species and give insight into which organisms live where.
Transect sampling
Advantages
Fast
Cheap
Shows how changes in the environment may affect populations.
Not very intrusive
Disadvantages
Not good for moving populations
Doesn’t always reflect entire area
Capture-recapture:
A number of individuals from a certain population are trapped, collected and marked.
They are then released back into the environment.
Later, another lot of individuals are captured.
Some of these may have been marked previously.
The number of marked individuals can be used as an indicator of the total population.
We can use this concept to mathematically estimate the population size
Remember that this is an estimate, and accuracy is dependent on sample size
Larger sample (More catching) = more accuracy
Capture-recapture relies on at least one individual being captured twice.
If there are no marked individuals in the second capture, the sample is invalid and needs to be repeated with a larger capture size.
Bias in capture samples: estimates can be skewed for a number of reasons:
If done too close together, there is a higher chance that the same individuals get caught
f done too far apart, the caught population might have died or left the ecosystem
Some individuals may be more likely to be caught twice (old, slow, injured, friendly )
Advantages and Disadvantages
Advantages -
Good for moving populations
Accurate when sample sizes are large
Disadvantages
Can be harmful or disruptive to the species
Timing can be difficult
Can be subject to bias
Community Ecology
Competition
One of the biotic factors that can be limiting is competition.
Competition can be both intraspecific (amongst the same species) or interspecific (amongst other species).
Competition occurs when two organisms need the same resource.
Example: Sunflowers need water and nutrients from the soil in order to grow. They grow quite slowly. Weeds also need water and nutrients but grow very quickly.
Competitive exclusion
The competitive exclusion principle : Two similar species that occupy the same ecological niche cannot co-exist.
Competitive exclusion: When the two species were grown together they competed for the food.
The P. aurelia was slightly better at obtaining the food and so dominated the competition until the P. caudatum died out.
Competitive exclusion
Firstly, not all resources that organisms compete for are limiting.
Two organisms might compete for both food and shelter but only the amount of food is limiting.
The second reason is that most organisms are adaptable enough to have found their own ecological niche.
An ecological niche is the way an organism functions in an ecosystem.
Can include
food they eat,
the time they eat,
where they live
how they reproduce
when they reproduce
Ecological niche: A niche is the role of an organism in its community.
Organisms that are very good at what they do, generally hold their ideal niche. They are not in any threat of competitive exclusion
Some organisms are under threat of competitive exclusion and so they do whatever job they can to get by(relised niche)
We call these terms the fundamental and realised niches.
Fundamental niche: ideal niche that an organism would occupy if there were no biotic restrictions (competitors or predators etc.)
Realised niche: Actual niche that an organism occupies as a result of those restrictions.
Resource partitioning:
One component of niches is the partitioning of resources.
Resource partitioning is the observable separation of resources in to categories where each specific species can occupy and exploit that resource.
Example:
The warblers are a genus of birds that all live in spruce trees.
Due to competition, they cannot live in the same part of the tree.
Instead the tree is partitioned into segments where each species lives and feeds.
Symbiosis: the relationship between individuals of different species where at least one of the species benefits
Collaboration: intraspecific interaction
Individuals of the same species work together to benefit each other
Along with competition, collaboration and disease, symbiotic relationships are important factors in maintaining and controlling population sizes.
There are three categories of symbiotic relationships:
Mutualism: both species benefit from the relationship
Parasitism: one species benefits but the other is harmed
Commensalism: one species benefits but the other is unaffected
Population dynamics
Population growth formula: N=(b+i)-(d+e)
N= The population size
b=births
i=immigrants
d=deaths
e=emigrants
Population growth rate:Often expressed as a decimal or percentage of the original population
Lag phase(low population growth) could be due to:
The limited number of mates in a particular area taking a while for individuals to find each other to then reproduce.
Initial time it takes to reproduce/gestate.
Log/exponential phase
Population is large enough that it is easy to find mates, the population increases exponentially.
Stationary phase
As the population increases more resources begin to become :limiting. Which slows the population growth. Eventually the population will not be able to grow any more and will remain at a relatively constant size.
If some event occurs to change the amount of available resources or a new limiting factor is added to the environment, The species may enter the death phase, during which the population will decrease. Growth is shaped by environmental resistance.
Environmental resistance: Collective group of potentially limiting biotic and abiotic factors that act on a population.
Examples:
The availability of food, shelter, disease.
As the population increases in size, the environmental resistance increases as well. This is what stops the population at carrying capacity.
Lag phase: the r value is small
Log phase: the r value is large
Stationary phase: the r value is zero (or very close to!)
Death phase: the r value is negative
Carrying capacity: Size of a population that an ecosystem can comfortably support. This is the point at which the resources are being used at an optimum level.
If populations exceed the carrying capacity something will happen to reduce the population size. Relationships and interactions between living things
Predator and prey
Density-dependent factors
Some limiting factors can be considered density dependent.
Density-dependent factors: influence changes depending on the size of the population in the area.
Other factors can be considered density-independent: Not affected by the size of the population.
It is important to understand that both types of factors will change the size of a population.
The difference is whether the degree of impact changes when applied to a dense population or a sparse population
r and K selection
Survivorship indicates the chances of survival at different stages of life.
It shows the relationship between populations at birth and populations at death. There are three categories of survivorship
Survivorship
Type 1(I) – High chance of survival until old age.
Type 2(II)- Constant chance of survival through entire lifespan.
Type 3(III)- Low chance of survival at early stages of life, increasing with age.
r and K selected species
When describing population growth, we use the following letters:
N = population size
r = population growth rate
(∆N/N) K = carrying capacity
Charecteristics of R-selected species
Focus on the growth phase
They are often referred to as ‘boom and bust’ species.
Quick colonization then rapidly die
Opportunists that will often be able to survive in unstable environments
They are poor competitors
Generally small in size so need few resources.
Reach reproductive maturity quickly.
Short gestation periods.
High fecundity (can produce many offspring in a lifetime) And generally have minimal parental care for offspring.
Often associated with type III survivorship.
Include many insects, weeds, fish and amphibians.
K-selected species
Focused on the stationary phase and reaching carrying capacity.
More stable and longer living species.
Generally take time to establish themselves in an ecosystem.
Depend on stable ecosystems.
Good competitors (out compete the r-selected)
Larger in size on average
Longer gestation periods
More parental care required
Longer time to reach sexual maturity
Low fecundity
Generally associated with Type I and Type II survivorship