Biology Unit 3 Summary PDF

Biodiversity The interactions between species (all species in the world) in their ecosystems (all of the ecosystems in the world) Measurement (levels): ▪ Genetic diversity: the number of different alleles possessed by a species ▪ Species diversity: the number...

Biodiversity The interactions between species (all species in the world) in their ecosystems (all of the ecosystems in the world) Measurement (levels): ▪ Genetic diversity: the number of different alleles possessed by a species ▪ Species diversity: the number of different species present in an ecosystem ▪ Ecosystem diversity: the various biomes and different ecosystems Species Richness Tally of the number of different species within a particular area Calculating species richness: ▪ The more samples that are taken (e.g. quadrats), the more accurate the sample ▪ Construct a species accumulation curve ▪ As the graph plateaus, that is the point where sufficient samples have been taken and the rarest species have been identified ▪ The greater the species richness, the more samples will need to be taken 𝑠 ▪ 𝑆= √𝑁 o S is species richness o s is the total number of different species in the sample o N is the total number of individual organisms in the sample Species Evenness Species evenness (or relative species abundance) is the measure of the number of individuals of that particular species in relation to the total number of individuals of all species in the area Calculating species evenness: ▪ Using percentage cover ▪ Percentage cover is a calculation of the percentage of a given area covered by a particular organism, usually a plant ▪ 𝑃𝑒𝑟𝑐𝑒𝑛𝑡𝑎𝑔𝑒 𝑐𝑜𝑣𝑒𝑟 = 𝑝𝑒𝑟𝑐𝑒𝑛𝑡 𝑎𝑟𝑒𝑎 𝑜𝑓𝑜𝑛𝑒 𝑠𝑞𝑢𝑎𝑟𝑒 × 𝑡𝑜𝑡𝑎𝑙 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑠𝑚𝑎𝑙𝑙 𝑠𝑞𝑢𝑎𝑟𝑒𝑠 𝑐𝑜𝑣𝑒𝑟𝑒𝑑 𝑏𝑦 𝑠𝑝𝑒𝑐𝑖𝑒𝑠 ▪ There are four ways to measure percentage cover: o Basal cover (stem/soil level) o Ground cover (area of soil/leaf litter) o Leaf cover (determined by shadows) o Canopy cover (total area covered by a plant)  Percentage frequency: ▪ The percentage of quadrats in which a species appears 𝑡𝑜𝑡𝑎𝑙 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑞𝑢𝑎𝑑𝑟𝑎𝑡𝑠 𝑖𝑛 𝑤ℎ𝑖𝑐ℎ 𝑠𝑝𝑒𝑐𝑖𝑒𝑠 𝑜𝑐𝑐𝑢𝑟𝑒𝑑 ▪ 𝑃𝑒𝑟𝑐𝑒𝑛𝑡𝑎𝑔𝑒 𝑓𝑟𝑒𝑞𝑢𝑒𝑛𝑐𝑦 = × 100 𝑡𝑜𝑡𝑎𝑙 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑞𝑢𝑎𝑑𝑟𝑎𝑡𝑠 𝑠𝑡𝑢𝑑𝑖𝑒𝑑 Simpson’s Diversity Index (SDI) Represents the probability that two individuals randomly selected from a sample will belong to a different species Gives a number between zero (no diversity) and one (infinite diversity) Low species diversity (numbers close to 0) suggest: ▪ Relatively few successful species in the habitat ▪ The environment is quite stressful with relatively few ecological niches and only a few organisms are well adapted to that environment ▪ Food webs are relatively simple ▪ Change in the environment would probably have serious effects High species diversity (numbers close to 1) suggest: ▪ A greater number of successful species and a more stable ecosystem ▪ More ecological niches are available and the environment is less likely to be hostile ▪ Complex food webs ▪ Environmental change is less likely to be damaging to the ecosystem as a whole SDI accounts for both species richness and species evenness More species richness and species evenness increases the index Calculating SDI: ∑𝑛(𝑛−1) ▪ 𝑆𝐷𝐼 = 1 − ( 𝑁(𝑁−1) ) o n is the total number of individuals of each species o N is the total number of individuals of all species Abiotic factors Nonliving, chemical and physical components of the environment Each species has a set of environmental conditions within which it can best survive and reproduce These conditions are the ones for which it is best adapted Many different abiotic factors influence where species live  Abiotic factors: ▪ Climate: o Precipitation (rain) o Temperature o Wind: affects salinity (coast lines), precipitation (more near the coastline), contributes to the water cycle as it influences transpiration and wind acting on plants supports biodiversity o Cloud cover o Sunshine ▪ Substrate: o Soil o In tropical climates, soil can be influenced by the amount of rain and sunlight: large amounts of rain, sunshine and quick organic decay improves plant growth and then increases biodiversity but lots of rain forces nutrients to leach out of the soil o In colder climates, the amount of biodiversity tends to reduce due to the limited plant growth because of the harsh conditions and fewer consumers o Soil quality is determined by thickness, pH, structure and porosity, nutrient content and salinity o Soil can be broken down into layers called horizons o Soil texture and soil structure influence water holding capacity, nutrient retention and supply, drainage, and nutrient leaching o Soil classification depends on the mixture of sand, clay and silt o The textural triangle describes the relative proportions of sand, clay and silt in various types of soils: Biotic Factors Living members in the environment which affect the survival of species in a particular habitat Biotic factors: ▪ Bacteria ▪ Fungi ▪ Plants ▪ Animals ▪ Food availability ▪ Disease Species Interactions (Symbiosis) Spatial Scales and Temporal Scales Both biotic and abiotic factors determine species distribution and abundance. Their combined effects result in measurable changes in communities over time and distance Species distribution is affected by interactions amongst other living organisms (biotic factors) and the physical (abiotic factors) in their environment.  Scientists determine the effect of these factors by observing how communities change over time (temporal scales) or over space and distance (spatial scales) Ecosystems can be compared across spatial and temporal scales based on a number of factors: ▪ SDI ▪ Species interactions ▪ Abiotic factors ▪ Disease Spatial scale: ▪ How much area a studied ecosystem covers ▪ Spatial factors are factors that affect the biodiversity of a habitat: o Distance from equator o Size of habitat o Depth of habitat ▪ Spatial differentiation is measured at microlevels (individual biomes), meso levels (named area or locations) or macrolevels (countries or continents) Temporal scale: ▪ The time period over which an ecosystem is studied ▪ Can be short term (over 24 hours), midterm (seasonal changes) or long term (years) ▪ Temporal factors refer to the change in seasons or time across a habitat: o Some organism have a high tolerance to change while others have low tolerance o Organisms function best at optimum range o If an organism has low tolerance to change the might migrate, hibernate, die, etc and can lead to changes in the biodiversity within the habitat ▪ Temporal differentiation can be measured in days, years or decades Distribution Patterns Limiting Factors A limiting factor is a resource or environmental condition which limits the growth, distribution or abundance of an organism or population within an ecosystem Physical (abiotic) factors: ▪ Temperature ▪ Water availability ▪ Oxygen ▪ Salinity ▪ Light ▪ Food ▪ Nutrients Biological (biotic) factors: ▪ Interactions between organisms: o Predation o Competition o Parasitism o Herbivory Environmental factors: ▪ Any abiotic of biotic factor that influences living organisms ▪ Variations in geography, climate and time all impact the biodiversity of an ecosystem ▪ Vegetation is also different throughout the year depending on the season ▪ Geography also impacts an ecosystem if it is very large ▪ Ecosystems vary over time and as the area changes, the ecosystem also change (succession) making a new ecosystem replace another until it is stable Resources such as food, water, light, space, shelter and access to mates are all limiting factors If an organism, group or population does not have enough resources to sustain it, individuals will die through starvation, desiccation and stress or they will fail to produce offspring Shelford’s Law of Tolerance For each abiotic factor, an organism has a range of tolerances within which it can survive Towards the upper and lower extremes of this tolerance range, that abiotic factor tends to limit the organism’s ability to survive  As well as a tolerance range, organisms have a narrower optimum range within which they function best and will usually be most abundant where the abiotic factors are closest to the optimum range Outside this range the organism suffers physiological stress decreasing its functioning until its tolerance limits are reached Beyond its tolerance limits it cannot survive (intolerance range) The distribution of a species in response to a limiting factor can be represented as a bell-shaped curve with 3 distinct regions: ▪ Optimal zone: central portion of curve which has conditions that favour maximal reproductive success and survivability ▪ Zones of stress: regions flanking the optimal zone, where organisms can survive but with reduced reproductive success ▪ Zones of intolerance (or death): outermost regions in which organisms cannot survive (represents extremes of the limiting factor) The wider an organism’s tolerance range for a given abiotic factor, the more likely it is the organism will be able to survive variations in that factor Classification An ecosystem is all the living and non-living factors of an area and how they interact with each other Every organism occupies an ecological niche and the community of all living organisms interacting with one another and the physical abiotic factors around them forms a specific type of ecosystem Ecosystems are composed of various habitats which may be as small as a sweat gland pore inhabited by bacteria (microhabitat), or a massive ecoregion covering a large biogeographical area  Common separations in ecosystems include natural and artificial ecosystems which may be subdivided into terrestrial and aquatic ecosystems Four Major Types of Ecosystem Classification Systems Holdridge life zone system: ▪ Global system predominately based on climate ▪ Classifies based on: o Average annual precipitation (rainfall mm or snow) o Mean annual biotemeperature o Potential evapotranspiration rate (rate of water loss via evaporation and transpiration combined) o Humidity levels o Latitudinal regions o Altitudinal belts  Specht’s classification system: ▪ Classifies ecosystems by their dominant type of vegetation (plants) and canopy cover Australian National Aquatic Ecosystem classification system (ANAE): ▪ A semi-hierarchical system designed to classify different aquatic (water- based) ecosystems ▪ Considers region, landscapes, climate, hydrology and topography European Nature Information System habitat classification (EUNIS): ▪ Used to classify all types of natural and artificial habitats including aquatic, terrestrial and benthic marine habitats (sea floor) ▪ An interactive, criteria-based key that involves progressing through a sequence of questions to arrive at a classification Effective Ecosystem Management Why we classify: ▪ By describing, classifying and tracking ecosystems, we can study complex processes and functions beyond individual species interactions, such as those in old-growth forests, productive soils and coral reefs ▪ Conservationists rely on this information to protect a wide range of ecosystems, thus maintaining habitats for common species and allowing species biologists to focus on protecting endangered species ▪ Many ecosystems also provide essential services like flood control, water quality, storm surge protection, and erosion prevention Old-growth forests: ▪ An old forest that has not been significantly disturbed so it exhibits unique ecological features and can be classified as a climax community (an established community that remains relatively unchanged unless disturbed by a natural disaster or human intervention) with features such as many trees that provide a diverse wildlife habitat which increases biodiversity ▪ Are valuable for economic reasons and for the ecosystem services they provide. This is a point of contention when the logging industry may want to cut down forests for timber, but environmentalists seek to preserve them for maintenance of biodiversity, water regulation and nutrient cycling. Productive soils: ▪ The health of the soil is directly linked to its ability to support the growth of plants which affects the consumers that eat the plants ▪ Factors that can affect soil: o Continuous growth of a monoculture (e.g. sugar cane) can affect soil chemistry (pH, nitrogen, etc) o Constant grazing of an ecosystem can cause compacted soil & prevent further growth o Tillage (breaking the soil with a plough) can result in water loss or erosion Soil management: ▪ Using plants to cover the soil to keep it anchored and prevent erosion ▪ Rotating monoculture crops with other legume-based crops (can increase nitrogen in soil) ▪ Mulching the soil to reduce erosion and water loss Coral reefs: ▪ Protect coastlines from damaging effects of waves and storms, while providing essential nutrients, shelter and habitats for marine organisms  ▪ Coral bleaching is caused by an increase in water temperature, lowering of pH, presence of various chemicals (e.g. pollutants, sunscreens) or increased sediments from runoff Sampling Methods (Planning) Stratified sampling: ▪ Can be used to highlight the characteristics of a particular subgroup or to compare the features of a different subgroups ▪ As all subgroups are sampled, it gives a better representation of a population than random sampling, which can miss sampling smaller populations ▪ Can be used for: o Estimating population o Calculating population density o Looking at distribution of organisms o Studying the effect of gradients and profiles o Studying zonation o Looking at stratification (layering) Systematic sampling: ▪ Samples are collected from locations at regular intervals ▪ Surveyed sites are predetermined Random sampling: ▪ Samples are not regularly collected ▪ They are randomly chosen so that each measurement in the study has an equal chance of being selected as part of the sample Surveying Techniques (Counting) A line transect is made by running out a tape measure or marked line across the area to be sampled. Observer works along line recording the name and position of each species the line passes over, under or through. A belt transect is similar to a line transect, but all species between two different, parallel lines are recorded and this is usually achieved by sampling a quadrat at set intervals along the transect line.  A quadrat is a square, rectangle of circular frame used to mark out an area which is to be sampled (size will vary depending on environment/location) ▪ Measurements taken from a quadrat: o List of all species compiled o Abundance can be estimated for both density (number of a particular species per unit area) and cover (percentage of ground covered by the species) Minimising Bias in Samples Need to carefully consider the size and number of samples being collected (usually 10−20% of an area if possible) with the sample size in each subsection being representative of that subsection size To determine where samples should be taken, quadrats can be used at random, using random number generators to help select the sampling points within each stratum The greater the number of samples taken, the greater the possibility the sample taken is an accurate representation of the community When counting the organisms, consistent rules need to be applied (e.g. counting a plant that is half in the quadrat or excluding and remaining consistent) Be careful to calibrate all equipment before use and note the level of precision measured Data Analysis Data can be used to classify the ecosystem, identify habitats within the ecosystem and identify relationships between organisms Data can be used to look at population ratios for predator-prey relationships and the preferred habitats of endangered species Data collected over time can show a rate of succession of species in a recolonisation of an area or after a catastrophic event Data is important for conservation and preservation management plans Different Types of Classification Linnaean system: ▪ Based on observable features ▪ Taxonomy is the science or technique of classification ▪ Binomial nomenclature: o Two-part naming system which uses Latin words to name a species o The first word is the genus and the second word is the species name o This classification system has seven levels: o Kingdom o Phylum o Class o Order o Family o Genus o Species o Drawbacks of the Linnaean system are that physical characteristics can be misleading (e.g. when observing organisms from the fossil record, similar structures can be thought to come from a common ancestor, but this is not always the case) Reproductive methods: ▪ Asexual reproduction: o One parent produces offspring which are genetically identical to it ▪ Sexual reproduction: o Gametes are produced by two parents and join through fertilisation to produce offspring o It is through meiosis that each gamete is a unique combination of genetic information and so the offspring show variation ▪ r selection is where organisms live in an unstable environment, so they show traits such as: o Small size o Fast reproduction o Many offspring o Short life expectancy o e.g. oysters, corals, dandelions ▪ K selection is where organisms live in a stable environment so they exist I numbers close to the carrying capacity for the environment and show traits such as: o Large size  o Slow reproduction o Few offspring o Longer life expectancy o e.g. elephants, whales, humans ▪ Some organisms can show a mix of r and K selected traits (e.g. turtles have a long life expectancy but produce many eggs requiring little care) Molecular sequencing: ▪ Involves the sequencing of molecules such as DNA and proteins ▪ The degree of similarity between these molecules in different species is an indication of how closely related they are and can be used to determine how organisms have evolved ▪ This system suggests all Eukaryotes are related (animals, plants, protists and fungi) ▪ The bacteria kingdom is split into 2 domains of bacteria and archaea Cladistics (molecular phylogeny): ▪ Molecular analysis allows us to classify organisms based on phylogeny (assumed evolutionary relationships between organisms) ▪ Phylogenetic classification ties names to clades, so it is often called cladistics ▪ A clade is a taxonomic group that consists of a common ancestor and all its descendants (monophyletic group) ▪ The characteristics used for assigning organisms to a clade can be molecular or morphological (structure) ▪ Cladogram: o Root – initial ancestor common to all organisms within the cladogram o Nodes – each node corresponds to a hypothetical common ancestor that branched to give rise to two new species o Outgroup – the most distantly related species in the cladogram which is used for comparison o Clades – a common ancestor and all its descendants ▪ Assumptions of cladistics: o Common ancestry - Diversity of life on earth is due to the reproduction of existing organisms. It originated only once and hence all the organisms are related to one another in some way.  Groups of related organisms have descended from a common ancestor whose relationship can be studied on any given group of organisms and significant deductions can be drawn. o Bifurcation - According to this assumption, new kinds of organisms evolve when existing species divide into exactly two groups. This assumption is controversial, as biologists believe that multiple new lineages can evolve from a single population at the same time with a possibility of interbreeding between distinct groups. o Physical Change - Cladistics assumes that the features of living organisms change over time, allowing one to observe and recognize different lineages or groups. In cladistics, the original feature is called a plesiomorphic/primitive feature whereas the changed feature is called an apomorphic/derived feature. ▪ Phylogram: o Built by placing taxa in a branching sequence according to their shared biological characteristics o Use branch length to indicate the length of time a group has remained cohesive (without divergence or splitting) in evolutionary history o The more ancestral the character, the more likely it is to be present in a greater number and variety of organisms  o Taxa groupings: Interpreting Molecular Data If two populations are isolated from each other, they will accumulate differences in their DNA over time due to mutation The greater the number of genetic differences between populations, the longer it is assumed to be since they shared a common ancestor Mutations are assumed to occur at a standard rate so the differences in the DNA of two populations can act as a ‘molecular clock’ to estimate when organisms diverged from one another (assumption is flawed) Different protein chains have different mutation rates. Proteins with a slow mutation rate are generally involved in functions that are essential for survival. DNA for analysis can be found in the nucleus but also in the mitochondria. Mitochondrial DNA comes from the mother only, often having a faster mutation rate than nuclear DNA and is sometimes easier to harvest in useful quantities as most cells contain many mitochondria Biological Species Definition Two organisms are from the same species if they can breed with each other to produce healthy, fertile offspring Sometimes, two similar/closely related organisms can breed together to produce offspring, but they are sterile (unable to reproduce themselves) ▪ According to the biological species definition, this would mean the two organisms are still different species as their offspring are unable to reproduce ▪ E.g. a mule is the offspring of a female horse and male donkey  Limitations of the biological species model include times that whether two organisms can produce healthy, fertile offspring cannot be tested: ▪ Asexual reproducers: o Many species reproduce asexually (bacteria, some lizards and sharks, many plants) so this definition is irrelevant for these cases ▪ Extinct species: o When all there is only fossils or preserved specimens, we cannot know if these different animals were able to breed together ▪ Practicality: o If an organism is rare or there are no individuals in captivity, it is often impractical to attempt to interbreed it with similar organisms to determine if they are the same species ▪ Physical isolation: o Two organisms that are far and never come into contact with each other cannot breed naturally that does not mean they cannot produce viable offspring if together ▪ Habitat differences: o There are no physical or genetic reason that two organisms cannot interbreed but they do not in nature because of their different habitat preferences ▪ Incomplete speciation: o Speciation is a gradual accumulation of differences over evolutionary timescales which means there are points at which groups of organisms are partly reproductively separated but not entirely ▪ Races and sub-species: o Sometimes there is a range of different populations of a type of organism, some of which can produce viable offspring but some of which cannot Population Ecology Carrying Capacity Represents the largest population size that can be supported indefinitely on the available resources of the ecosystem A population can overshoot (exceed) the carrying capacity which would lead to an increase in competition, predation and disease but also resource destruction The population will tend to fluctuate around a set point which corresponds to ecological homeostasis Carrying capacity is not static  Limiting factors: ▪ Limitations to population growth are either density-dependent (often biotic factors) or density-independent (often abiotic factors) o Density-dependent factors affect a population through increasing or decreasing birth and death rates in a way that is directly related to population density (e.g. disease, crowding, parasitism and predation) o Density-independent factors refer to any influences on a population’s birth or death rates regardless of population density (e.g. temperature, pollutants, climate extremes and catastrophic factors) ▪ A resource or environmental condition which limits the growth, distribution or abundance of an organism or population within an ecosystem ▪ Living within the limits of an ecosystem depends on factors such as: o The amount of resources available in the ecosystem o The size of the population and/or individuals o The amount of resources each individual is consuming Population Size Populations are groups of organisms of their same species living in the same area at the same time defined by: ▪ Population size is the number of individuals in the population ▪ Population density is how many individuals are in a particular area ▪ Population growth is how the size of the population is changing over time The change in size of a population over time is determined by four key factors: ▪ Natality/birth increases to population size through reproduction ▪ Immigration increases to population size from external populations (immigrants) ▪ Mortality/death decreases to population size as a result of death ▪ Emigration decreases to population size due to loss to external populations (emigrants) Calculating population change/growth: ▪ 𝑟 = (𝑏 − 𝑑) + (𝑖 − 𝑒) o r is population change/growth o b is number of births o d is number of deaths o i is number of immigrants o e is number of emigrants (𝑏−𝑑)+(𝑖−𝑒) ▪ 𝑃𝑒𝑟𝑐𝑒𝑛𝑡 𝑝𝑜𝑝𝑢𝑙𝑎𝑡𝑖𝑜𝑛 𝑐ℎ𝑎𝑛𝑔𝑒 = 𝑡𝑜𝑡𝑎𝑙 𝑜𝑟𝑖𝑔𝑖𝑛𝑎𝑙 𝑝𝑜𝑝𝑢𝑙𝑎𝑡𝑖𝑜𝑛 × 100 Lincoln Index Used to estimate population size based on the capture-mark-release-recapture method This method is a means of estimating the population size of a motile species so marking must not be easily removable or adversely affect the animal’s survival prospects Calculating using Lincoln index: 𝑀×𝑛 ▪ 𝑁= 𝑚 o N is estimated population o M is the number of individuals caught, marked and released initially o n is the number of individuals caught on second sampling o m is the number of individuals recaptured that were marked It requires that the following assumptions to be true: ▪ All individuals in a given area have an equal chance of being captured (sampling must be random) ▪ Marked individuals will be randomly distributed after release (one individual cannot be allowed to influence another) ▪ Marking individuals will not affect the mortality or natality of the population The accuracy of of this index can be improved by a number of means: ▪ Increasing the size of the capture samples (larger samples will be more representative but also more difficult to collect) ▪ Taking repeated samples in order to determine a statistical average Population Growth Models Mathematical models are used to model population dynamics (how populations change in size and composition over time) An exponential growth (J curve) occurs in an ideal environment with unlimited resources and no competition to place limits on rate of growth ▪ Initially, population growth will be slow as there is a shortage of reproducing individuals that may be widely dispersed ▪ As population numbers increase, the rate of growth will also increase resulting in an exponential curve and the growth rate will keep increasing over time in proportion to the size of the population ▪ The maximal growth rate for a given population is known as its biotic potential and is represented as the ‘uptick’ section of the curve ▪ Exponential growth can be seen in populations that are initially very small and need to recover, where a previously exploited species is protected  and also in species that have short generation time and large numbers of offspring (r-strategists) A logistic growth (S curve) occurs when environmental pressures decrease the rate of growth and it slows as the population reaches the carrying CapCut of the environment ▪ When the number of individuals gets large enough, resources start to get used up which slows the growth rate ▪ Eventually, the growth rate will evenly off so that birth and death rates are equal ▪ As the population approaches its carrying capacity, environmental resistance occurs which slows rate of growth ▪ This results in a sigmoidal growth curve that plateaus at the carrying capacity ▪ Logistic growth will eventually be seen in any stable population occupying a fixed geographic space  Population crash (or more informally, a ‘boom and bust’ pattern) is when a previously readily available resource becomes scarce due to environmental change, human intervention or the rapid exponential growth of the population going beyond the ecosystem’s carrying capacity, the population can rapidly die out If carrying capacity is exceeded, the growth curve will typically follow four key stages: ▪ Lag phase: the new population takes time to settle and mature before breeding begins and as doubling of small numbers does not have a big impact on the total population size, the line of the graph rises only slowly with time ▪ Log (exponential) phase: there are no limiting factors so there is rapid breeding and the increase in population and steady multiplying of numbers per unit of time produces a straight line ▪ Stationary phase: limiting factors (e.g. shortage of food) causes the rate of reproduction to slow down and there are more deaths so as the birth rate and death rate become equal, the line of the graph becomes horizontal ▪ Death phase: as food runs out, more organisms die than are born so the number in the population drops  Other population growth patterns can be present as populations can fluctuate/vary in density in many different patterns and have regular cycles of boom and bust: ▪ Cyclical oscillations are repeating rises and drops in the size of the population over time and are controlled by a combination of limiting factors