Fundamentals Of Ecology Lecture notes PDF

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FUNDAMENTALS OF ECOLOGY - BS2460 WEEK 1 LECTURE 1 - Introduction “Nothing in biology makes sense, except in the light of evolution – but nothing in evolution makes sense except in the light of ecology” (Dobshansky) Definition of Ecology • From Greek “oikos” meaning “house” or “place to live” • The scientific study of the interactions between organisms and their environment (Ernest Haeckel 1869) • “Ecology is the scientific study of the interactions that determine the distribution and abundance of organisms” (Krebs 1972) “The scientific study of the distribution and abundance of organisms and the interactions that determine distribution and abundance” (Begon et al. 2006). • Key elements: o Where organisms occur, o How many occur there, o and Why Mathematically quantifying nature • Energy flows • Nutrient flows Evolution acts on phenotypic variability at the level of the organism, but indirect coevolutionary and group selection processes act at higher levels (populations, community, ecosystem). Organisms

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Variation within species o Genetic variation among individuals within a population o Genetic diversity o Presence/absence specific genes o Local adaptation o Gene flow Species & speciation Adaptive & neutral selection Life history & sexual selection Geographic variation across populations: ecotypes

Populations • The distribution and abundance of an organism o Where? – What are the patterns of abundance? o Why? – What factors influence local population abundance?

Communities/Assemblages

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A community is “any assemblage of populations of organisms living in a prescribed area or habitat” (Krebs) Metapopulations and communities

Ecosystems • Often concerned with the biotic interactions between individuals, populations and communities and the physical (abiotic) environment • Linkages are through nutrient cycles and energy flows Pure v Applied ecology Pure • • •

Natural systems Theory/concepts Natural Perturbations o (eg. drought, wildfire, predation, cyclical change)

Applied • Focussed on how ecological knowledge can be used or applied by people • Human influenced systems o (eg. agroecosystems, fisheries, forestry, reserves) • Human impacts o (eg. pollution, overharvesting, climate change) Anthropocene • New geological epoch o Human imprint is large enough to rival some of the great forces of nature and its impact on Earth’s systems • Biodiversity and functioning natural ecosystems are in crisis due to human impacts o Climate change, pollution, exploitation, invasive species We need to find a sustainable balance between human activities and needs and the healthy functioning of natural systems and to minimize the accelerating loss of global biodiversity. How do we do this? • By studying, advertising, minimizing and mitigating human impacts through the study of the ecology of change •

LECTURE 2 – Aquatic vs Terrestrial Ecosystems Most processes are the same - Competition and importance of density dependence - Predation as a dominant selective agent - Social organisation - Sexual selection Processes are similar BUT, the expressions are different (space and time scales) due to physical nature of each environment Fundamental differences in medium Terrestrial

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Environmental conditions (e.g. temperature, water availability) MUCH more variable over short time scales Requirement for support structures More energy devoted to movement Climate and climatic variability is critical Demographic interactions between species very important (e.g. predator-prey cycles)

Aquatic - Environmental conditions (e.g. temperature, pH, salinity) much more stable over short time scales - Medium is supportive  more tissue to eat! - Low energy devoted to movement - Dynamics strongly affected by processes external to the local - (e.g. oceanography like upwellings). - Dominance of ectotherms even at higher trophic levels

Generation times differ…

Food webs Terrestrial - production, scavenging, and decomposition tightly linked Marine Marine food webs are more complex -

Spatial disconnect between the processes of production, scavenging, and decomposition Marine carnivores sit 1.3 trophic levels higher than terrestrial carnivores Marine mammals are largely carnivorous and have larger predator–prey ratios compared with their terrestrial counterparts o (i.e., marine mammals are going for smaller prey).

Ontogenetic shifts in roles of vertebrates is common in aquatic systems. Aquatic - Change in trophic category with age Survival

Marine reproductive success - Reproductive success (population level) dependent on o physical dispersal o relatively predictable food cycles - Decoupling of adult and larval phase makes concepts of r - k selected life histories not applicable to aquatic systems o r – selected: high per capita population growth, but poor competitive ability, short lived (e.g., insects, rats). o K – selected: stable populations, slow development, good competitors, long lived (e.g., humans, elephants). Terrestrial – parental care in many vertebrates, less parental care in aquatic Fishes often flexible in sexuality

Hermaphrodites Protogynous (Humbug damselfish) – female first Protandrous (Clownfish, Baramundi) – male first Bidirectional (Gobies, Dottybacks) Simultaneous hermaphrodites (some grouper) Very easy to change sex as they just alter what’s in paired sacs by hormonal changes.

Aquatic egg/larval stages have an amazing ability to disperse - Eggs passively by currents - Larvae through active swimming - Many small dispersive larvae is typical of many aquatic organisms – invertebrates, fishes. - Dispersal a short period of overall life, but links disparate populations through unpredictable recruitment - For fish & invertebrates poor Stock-Recruitment relationship o Dispersive larvae rather than parental care in aquatic Kin selection and altruism – central to ecology theory for terrestrial invertebrates Open life cycles of most aquatic organisms means it’s hard to get positive feedback to promote kin selection Competition Terrestrial – strongly density dependent growth & survival, especially for juveniles Aquatic – poorly known in marine ecosystem (pelagic environment) for egg and larval stages; strong for juveniles Predation is central to dynamics and behaviour of both ecosystems

Predator-prey size relationships…

Key notes • Many of the processes that underlie community dynamics are the same between terrestrial and aquatic ecosystems Major differences are: • Short term stability of environmental conditions • Environmental conditions (i.e., oceanography) transport nutrients and food from outside the local community in aquatic systems • Aquatic systems rely on primary producers that are small, plentiful, with high turnover rather than a high standing biomass • Dominance of ectotherms even at higher trophic levels in marine systems • Marine organisms typically have life histories with high early mortality • Marine organisms usually have low parental care, a dispersive early life stage, and a flexible sexuality

WEEK 2 LECTURE 3 – Principals of sampling Rules of thumb Remember:  the more times you detect a pattern, then the more likely it is to be true;  The more places you detect a pattern, then the more likely it is to be true;  An effect cannot be demonstrated without a comparison with controls  The life histories of many organisms are complex, understanding the biology of your target taxa will help to frame questions and plan your sampling. Our goal is to infer characteristics of a population by analysing the characteristics of a sample (usually small) taken from that population PARAMETERS Two common measures are used to describe a population: Measure of central tendency eg. MEAN Measure of dispersion eg. VARIANCE These may be calculated for the POPULATION. POPULATION PARAMETERS: Population mean:  (Greek: mu); Population variance: 2 (Greek: sigma) (squared) SAMPLE STATISTICS These are estimates of population parameters Sample mean: xbar Sample variance: s2

NOTE: PARAMETERS ARE CONSTANT FOR A POPULATION AT A PARTICULAR TIME, BUT SAMPLE STATISTICS WILL VARY FROM SAMPLE TO SAMPLE FOR SAMPLES TAKEN FROM THE SAME POPULATION. The spread of these sample estimates is known as the SAMPLING VARIATION

CONFIDENCE IN OUR GENERALISATIONS  Sampling variation arises because we can never ensure that two samples (or experiments) will be exactly alike.  Our generalisations must therefore take into account the sampling variation - an element of uncertainty.  We must be careful how we sample to minimise the variation among samples so we have confidence in our conclusions (this should be under our control).  Animals are inherently patchily distributed due to: o different behaviours o genetics o response to habitat/environment o developmental stages, histories etc.  In ecology we are seeking to draw conclusions of known reliability despite the large sampling variation inherent in biological systems.

1. FORMING A QUESTION

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Logic of hypothetico-deductive argument Any sampling survey must begin with a clearly stated question. Your results will only be as coherent as your initial conception of the problem.

2. a) REPLICATION  A fundamental principal of survey design is the need to take replicate samples within each combination of time, location and any other variables of interest. b) REPLICATION AT DIF LEVELS OF DESIGN  beware pseudo replication  where treatments or factors of interest (eg. habitats below) are not replicated, though samples within may be.

3. RANDOMISATION  Replicates MUST be allocated at RANDOM so that all individuals have an equal chance of being sampled. 4. ACCURACY OF SAMPLING METHOD  Verify that your sampling device is sampling the population you think it is sampling o Eg. avoid trap happy o Eg. Life sampling characteristics – animals may occupy sub habitats at dif life stages  Make sure that accuracy is the same over the entire range of sampling conditions to be encountered - variation in efficiency among areas/ times will bias comparisons o eg. Searching for animals in complex habitats to compare with abundances in open habitats

5. SIZE OF SAMPLING UNIT – PRECISION  You must verify that your SAMPLE UNIT SIZE is appropriate to the size, density and dispersion of the organisms you are sampling.  Then estimate the NUMBER of replicate samples required  Both of these are done to maximise PRECISION. Precision is the degree of concordance among a number of estimates of the same population (repeatability). It is defined as the Standard Error: Mean Ratio. As a rule of thumb, it is advisable to have a precision of 0.1 or smaller (ie. The SE should be 10% of the mean) SE xbar

P=

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Large quadrats/transects are harder and more costly to survey than smaller ones Many quadrats/transects are more expensive to survey than only a few PATCHINESS VARIES WITH SPECIES - SO OPTIMISATION IS REQUIRED

6. PILOT STUDIES  Preliminary sampling must be carried out to provide a basis for evaluation and refinement of the sampling design and statistics to be used.

7. STRATIFICATION

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If the area to be sampled has a large-scale environmental pattern (eg. Discrete habitats or strata), break the area up into relatively homogeneous subareas Allocate samples randomly within each habitat or stratum

8. CONTROLS  To test whether a treatment has an effect you MUST collect samples both where the condition operates AND where it is absent  All of the sampling methods, effort etc... have to be the same.  An impact can only be demonstrated in comparison with CONTROLS 9. ANALYSIS  Decide on the appropriate statistical analysis during the design phase of the study.  Run the analysis on a ‘dummy’ dataset or real data from a pilot study to test the appropriateness of the analysis.  You may need to adjust your design to make the tests more sensitive 10. ASSUMPTIONS  All parametric statistics have assumptions (e.g. t-test, ANOVA, correlation).  These must be checked to make sure that data conforms to these assumptions. o When violated  Transformations can be used to alter the shape 11. ACCEPT YOUR RESULTS  Having gone through the previous procedures and used the best design and statistical procedure for testing your hypothesis YOU MUST STICK WITH THE RESULT. 12. STATISCAL/BIOLOGICAL SIGNIFICANCE  Do not confuse STATISTICAL SIGNIFICANCE with BIOLOGICAL IMPORTANCE - Statistical Significance: probability of obtaining this result under the null hypothesis is < 5% - Biological Importance: refers to the magnitude of the effect relative to a pattern in question or a theoretical hypothesis o Small, undetected effects may be important o Small, detected effects may be trivial LECTURE 4 – Natural selection and adaptation Charles Darwin and Alfred Russel Wallace presented the theory of natural selection in 1858 mechanism through which organisms adapt to their environments

NATURAL SELECTION Nat select - differential success (survival and reproduction) of individuals within a population - interactions with the environment are the selective agents Two conditions are required  variation in a trait, which must be heritable  Trait-driven differences in survival and reproduction among individuals through environmental interactions ADAPTATION  Adaptation - a heritable trait that maintains or increases the fitness of an organism under a given set of environmental conditions o Can be behavioural, morphological, or physiological  The study of adaptation is key to understanding the distribution and abundance of species - concepts central to this class and to ecology in general FITNESS  the contribution made by an individual to future generations  in a particular environment, individuals with characteristics that confer higher rates of survival and reproduction have more progeny (e.g., seeds or offspring)  those characteristics are then more frequent in the next generation Traits are passed through genes  DNA encodes genetic information transmitted from parent to offspring  Genome = all of the DNA in a cell  A gene encodes the information needed to produce an RNA molecule. This is usually messenger RNA, which results in the synthesis of a protein Alleles  Alleles are alternative forms of the same gene  most multicellular organisms are diploid  They have two copies of each chromosome, therefore two copies of each gene (homozygous and heterozygous)  Genotype = alleles present at each gene within an organism’s genome Requirements for evolution by nat selec. 1. Individuals in a population of a species are not identical 2. At least some of this variation is heritable 3. Populations have very high reproductive potential, but seldom achieve it due to mortality (selective pressure) 4. Different individuals leave different numbers of descendants (differential fitness) 5. The number of descendants an individual has depends on the interaction between the traits of the individual and its environment Genotype - Genes of an individual Phenotype - Physical characteristic expressed in an individual

- Genotype + environment Environmental effects - Can alter gene expression  changes in phenotype are not genetically inherited - Temperature, precipitation, sunlight, predation - These changes can cause phenotypes to vary continuously  phenotypic plasticity o Eg. temperature effects body colours of many insects Acclimation  phenotypic plasticity in response to environmental conditions that is reversible o Seasonal changes in temperature tolerance in fish o fish have upper and lower limits to temperatures they can tolerate - these change as water temperature changes Natural selection acts on the phenotype  Phenotypic evolution - a change in the mean or variance of the phenotype across generations  Results from changes in allele frequencies that arise from differences in fitness among genotypes  Natural selection acts directly on the phenotype

PROCESSES OF EVOLUTION GENETIC MUTATIONS  Random process  may be beneficial, neutral or harmful  Beneficial mutations are favoured by natural selection, and harmful mutations are removed by natural selection  Permanent alteration to the DNA sequence o Source of genetic diversity o Can affect a single DNA base or large chromosome section GENETIC DRIFT  Change in allele frequency as a result of random chance  the smaller the size of the population, the more it is affected by genetic drift  alleles can be lost through genetic drift – random walk

SEXUAL REPRODUCTION  Sexual reproduction – random recombination of alleles through o crossing over and independent assortment during meiosis & fertilization  Offspring have a subset of the alleles that their parents carry

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The larger the population, the greater the probability that most alleles will be represented in the next generation at about the same frequency

MIGRATION  The movement of individuals among local populations  Leads to gene flow – the movement of genetic information among populations  Reduces variation among populations by keeping allele frequencies more similar What not to expect of natural selection and adaptation  Necessity of adaptation – an environmental change need not necessarily lead to new adaptations  Perfection – natural selection can only act on available phenotypes, and may be subject to constraints and trade-offs  Progress – measurements of “improvement” or “efficiency” must be relevant to each species’ special niche or task  Harmony and the balance of nature – in general, cooperation among organisms requires special explanations  Morality and ethics – science describes only what is, not what ought to be Key points  Natural selection is the mechanism by which adaptations evolve  Natural selection acts on the phenotype  Different genotypes can have different capacities for acclimation  Mutations are a primary source of genetic diversity  Other processes in addition to natural selection can lead to genetic change in populations

WEEK 3 LECTURE 5 – Plant ecophysiology Photosynthesis  Energy in sunlight drives a series of reactions that result in the fixation of CO2 and the release of O2  This light energy is converted to the chemical bond energy in sugars  Other molecules (complex carbohydrates, proteins, fatty acids) are made in other parts of the plant using the chemical bond energy from these sugars Photosynthesis: CO2 + H2O + Light energy CH2O + O2    

Chlorophyll is a pigment in the chloroplasts that absorbs light energy in the form of photons Absorption of a photon raises the energy level of chlorophyll to an excited state Chlorophyll then donates an electron to an acceptor molecule, transferring energy to the acceptor This starts the photosynthetic electron transport chain:

o synthesizes ATP o reduces NADP+ to NADPH  These two molecules carry energy to the light independent reactions (dark reactions) Dark reactions:  Chemical bond energy in ATP and NAPDH is used to incorporate CO2 into simple sugars  Carboxylation: RuBP (a five-carbon molecule) combines with CO2 and fixes it to a solid form o this reaction is catalysed by an enzyme, Rubisco  The reaction produces two molecules of 3-PGA (phosphoglycerate, a three-carbon molecule): C3 cycle  3-PGA, ATP, and NADPH are used to synthesize the energy rich sugar G3P (glyceraldehyde 3-phosphate)  Some G3P is used to produce sugars and starch and some is used to synthesize new RuBP to continue the process  Light availability limits the light-independent reactions by controlling ATP and NADPH production Photorespiration  The C3 pathway has one major drawback  Rubisco is also an oxygenase o It catalyses a reaction between O2 and RuBP o This results in photorespiration, which costs energy and results in the loss of CO2  Photorespiration reduces the efficiency of C3 photosynthesis by as much as 25%  Some plants have ada...