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BIOL1006 Full Notes Semester 1 Introduction Humans have always been biologists Welcome to the Anthropocene

• Anthropocene: last 40 years of human history

• Overall worldwide death rate has declined at a steady rate. Estimated that by 2035, child mortality rate in almost all countries will be as low as in USA in 1980

• Share of world living in absolute poverty has steadily declined since 1820 –projections for 2015 were at 9.6% Significant people

• Normal Borlaug –green revolution

• Carolyn Brooks Other facts and graphs

• Arable land per crop production index for world since 1961: steady decline. After 50 years, the world uses 6% less land to produce the same amount of food

• World population 1950-205: from less than 3 billion to over 9 billion –steady incline o Leads to 70% increase in demand for food

• Extent of global arable land projection 2010-2060: slow but steady decline Emerging diseases

• Continuing to mutate and evolve to develop resistances –already noted in plants and pesticide resistance

• Also in humans –antibiotic resistance

Biodiversity and the Tree of Life Problems with counting species

• Inaccessible habitats e.g. deep sea

• Definition of a species e.g. micro-organisms such as bacteria

• Complex life cycles e.g. jelly fish (in their early life cycles they look like plants)

• Cryptic species e.g. parasites

• Sampling bias e.g. holiday locations Number of species

• Estimates range from 3-100 million

• Current estimate 8.7 million o Estimated through analysis of current species well known and hence extrapolated –stats

Number of unnamed species

• 86% terrestrial life unnamed

• 91% marine life unnamed

• estimates of % discovered: o mammals: 98% o birds: 96% o reptiles: 80% o fish: 72% o crustaceans: 31% o molluscs: 43% o arachnids: 17% o insects: 20%

• generally, the smaller the organism, the more yet to be discovered -20% of insects discovered suggests that most life on earth is insects

In summary

• there are lots of living things

• most are animals and insects

• we haven’t named most of them Classifying life

2 • order:

o life o domain o kingdom o phylum o class o order o family o genus o species

• it is a hierarchical system

• LIFE DIRECTION: KEEP PONDS CLEAN OR FROGS GET SICK Mas Sibylla Merian

• Entomologist

• Developed own classification system –not used today Categorising life Carl Linneaus

• Swedish botanist –interested in plant classification

• Described 7300 species of plants

• Introduced binomial nomenclature

• Journeys experienced 405 mortality arte

• Separated life into 2 kingdoms –plants and animals o Plants: don’t move o Animals: do move

Anthonie van Leeuwenhoeck

• In 1683, he noted small ‘animals” moving within the plaque he has scraped from his teeth –he named these Protista

• Identified 3 kingdoms: plants, animals and Protista Present day

• There is currently a 6-kingdom system. This is the most recent however can never be considered fully correct due to the vast amounts yet to be discovered –many Protista’s seem to not fit the classification of existing systems

Eukaryotes

• Contain nucleus, membrane bound organelles

3 • Distinguished by where they get their energy

o Plants: sun (photosynthesis) o Fungi: absorb molecules from environment o Animals: ingesting other organisms

Protista

• Unicellular organisms that do not fit anywhere else

• No nucleus, are not bound by membrane Bacteria

• Proposed as separate kingdom in 1977

• Membranes composed of glycerol-ether lipids Why are classification systems important?

• Classification provides us with logical, universal names

• Deducing relationships What is biodiversity

• Biodiversity: the diversity of life, the genetic information organisms contain, and the ecosystems that they create and live in

• Number, relative abundance and genetic diversity of organisms on earth

• Components: o Genetic diversity o Species diversity o Community diversity (see below) o Landscape diversity (continental/large scale)

• Species richness: the number of species that occur in an area –does not consider number of individuals present –simplest measure of biodiversity

• Species abundance: the count of the number of individuals of the same species in a habitat

• Species diversity: species richness and their abundance Community diversity

• Alpha: the number of species within a chosen area or community (CHOSEN AREA) Local diversity

• Beta: the difference in species between areas and communities (BETWEEN AREAS) species turnover

• Gamma: the diversity of a landscape or all areas combined (LANDSCAPE/AREAS COMBINED) regional diversity Measuring diversity

• Diversity indices: controls that there may be different numbers in a group

E.g. 1 Alpha diversity higher

E.g. 2 Beta diversity higher

E.g. 1 Alpha diversity higher

E.g. 2 Beta diversity higher

4 Simpsons index

𝐷 = 1 − ∑ [𝑛

𝑁] 2

𝑠

𝑖=1

• 0 = one species

• 1 = many species an very diverse Inverse Simpsons index

• Pi = the proportion of individuals in the i th species (pi = ni / N)

• ni = the number of individuals of species i in the sample

• N = the total number of individuals sampled

• Index values are high if there are many species or evenness (equitability) is high

Shannon-Weiner Index Problems with using species diversity in conservation

• Introduced species by humans may eradicate natural species e.g. decrease in mammal diversity

• Endemic: those species found exclusively in an ecosystem e.g. koalas Centres of biodiversity

• Biodiversity is not evenly distributed over the planet

• Conservation international has identified 25 biodiversity hotspots based on 3 criteria: o Number of species present o Number of endemic species o Degree of threat they face

Darwinian Selection Scientific Theory

• Repeatedly tested

• Withstand rigorous scrutiny

• The highest category of something, the equivalent of law in science

• Evolution is a key fundamental concept in biology Static world view

• Dark ages –first emergence of ideas of a changing world o Ibd Kahldun, 1377: “transformations of some existent things too” o Nasir al-Din, 1200’s: some organisms can gain new and more variable features –gain advantages

• Mary Anning: 1800’s Europe –discovery of dinosaur bones Catastrophism

• Wiping out of all life though a major event e.g. natural disaster Uniformitarianism

• The world is constantly changing all the time Inheritance of acquired characteristics Lamarkism

• Traits are acquired or lost during an organism’s lifetime –either by use of disuse. These are transmissible to offspring (!!! This idea was later unsupported by empirical evidence !!!)

• Lamark’s Giraffes Charles Darwin

• The voyage of the Beagle –voyage raised questions over diversity of some species but different origins

• Explained the “struggle for existence” The theory of natural selection

• More individuals are produced at each generation than survive to reproduce

• Variation in fitness exists between individuals within a population

• Fitter individuals contribute more to offspring to subsequent generations

• Differences between individuals are inherited Natural selection

• Requires 4 conditions

pi = the proportion of individuals in the i th species (pi = ni /N)

Index values are high if there are many species, or if evenness (equitability) is high.

Gurevitch, Scheiner, Fox 2002

Where the summation is over all species

ni = number of individuals of species i in the sample

N = the total number of individuals sampled

D= 1 /Σ pi2

Emphasises common species

Inverse Simpson’s Index

H'= - Σ [pi ln(pi)]

Shannon-Weiner index

Emphasises rare species

pi = the proportion of individuals in the i th species (pi = ni /N)

Index values are high if there are many species, or if evenness (equitability) is high.

Gurevitch, Scheiner, Fox 2002

Where the summation is over all species

ni = number of individuals of species i in the sample

N = the total number of individuals sampled

D= 1 /Σ pi2

Emphasises common species

Inverse Simpson’s Index

H'= - Σ [pi ln(pi)]

Shannon-Weiner index

Emphasises rare species

5 o Excess reproduction: more individuals produced at each generation than survive o Genetic variation: individual exhibit variation traits that are inherited –generated via mutation o Different genetic variants have different fitness: fitness is measure of capacity of an organism to not

only survive but produce viable and fertilise offspring –a trait that increases this fitness is known as adaptation

• Anatomical, physiological and behavioural characteristics are all influenced by natural selection Fitness

• Fitness: the measure of the capacity of an organism to not only survive but to produce viable and fertile offspring. A trait that increases fitness is known as adaptation

• The probability that individuals with certain characteristics will be more likely to reproduce in a population (i.e. will have higher fitness)

• Excess fecundity: females producing more offspring than survive –universal in nature

• Competition: for food, space, mates etc. –universal in nature

• Excess fecundity and the resultant competition is what Darwin referred to as “the struggle for existence” –this provides the precondition or the process Darwin called natural selection

Alfred Russel Wallace

• Independently proposed idea of natural selection at the same time as Darwin

• Wallace line Gregor Mendel

• Darwin constrained by lack of valid theory on inheritance

• Mendel studied inheritance in peas –breeding lines to produce evidence

• Particular inheritance explains transmission of traits across generations (e.g. monohybrid cross, backcross etc.)

• First published in 1886, rediscovered in 1900 Evolution

• A process that results in heritable changes in population Misconceptions 1. Evolution is only a theory 2. Evolution has never been observed 3. There are no transitional fossils 4. The theory of evolution says that evolution proceeds by random chance Breaking these misconceptions (2) evolution HAS BEEN OBSERVED

• E.g. insects and pesticide resistance (3) THERE ARE TRANSITIONAL FOSSILS

• Transitions may occur in a small population, in a small area and/or in a relatively small amount of time

• When any of these conditions hold, the chances of finding the transitional fossils goes down (4) Evolution DOES NOT PROCEED BY CHANCE

• Chance plays a part, but this ignores the fundamental role of natural selection –the opposite of chance

• Mutations arise by chance, providing genetic variation. The variations that continue through time are determined by natural selection –ability to develop a higher fitness

Phylogeny for life

• The fossil record: o Mary Anning, 1800’s o Trace fossils: footprints and tracks o Chemical fossils: organic compounds produced by organisms o Formation and location:

▪ Burial limits the breakdown of bacteria (anoxic environment) ▪ These are compacted and converted with sedimentary rock ▪ Often remains are dissolved however fossil mould is left revealing the shape of an organism sometimes

filled with other materials and forms fossil cast ▪ Insects can also be trapped in amber (hardened resin of conifers) ▪ Deposition on sea floor where oxygen is low = preservation of parts of organism with a thin carbon film

o Dating: ▪ Relative dating methods (before measurement of rock age): observing layers of sedimentary rocks

(stratigraphic sequencing) –layers at base were older

6 ▪ Sometimes the same stratigraphic sequence of fossils can be found in different areas suggesting that

they are all the same age ▪ Radioactivity: discovered at end of 19th century –allowed for absolute dating although one 1% error

remains (equates to millions of years) ▪ time scale divided into eras and periods: originally era boundaries defined by changed in fossil record

• artificial selection: domestication of species (hybrid vigour) Summary

• evolution: process of change and divergence in populations i.e. changes in allele frequency across generations

• evolution is different to the initial origin of life

• Natural selection: consequences of the difference in reproduction or individuals with certain phenotype compared to individuals with other phenotypes in a population

• Fitness: the extent to which an individual contributes to future generations. A difference in survival or fecundity of individual with certain phenotypes compared to individuals with other phenotypes

Evolution of earth Formation of the earth

• Big bang: 13.75 billion years ago

• Earth formed: 4.52 billion years ago

• Oldest rocks: 4 billion years old

• First evidence of life: 3.5 billion years old Hadean earth

• ‘hellish earth’

• surface dominated by volcanic emissions

• lack of oxygen would have resulted in reducing environment –allowed for the formation of organic molecules without the input of as much energy as in an oxygen rich atmosphere

Most basic functions needed to make a life form

• Hereditary: life form can replicate itself, passing of cellular information for parent(s) that bears likeness to parent(s) cells. Capacity to alter cellular information, allowing populations to change over time and adapt to environment

• Compartmentalisation: all functions concentrated and contained ina space surrounded by barrier or membrane

• Metabolism: metabolic activity occurs, with chemical reactions making and breaking down complex molecules with both input and extraction of energy

Hypothesis of the origin of life

• Abiogenesis: the original evolution of life or living organisms form inorganic and intimate substances o Primordial soup o Hydrothermal vents o Created in reducing environment

• Panspermia/exogenesis: the hypothesis is that life originated elsewhere in the universe and came to earth via meteoroids, asteroids, comets etc.

• Major issues: o organic compounds o replicating molecules o membranes o cells/protocells

Miller-Urey experiment

• in this experiment, they showed that in a volcanic environment, the input of energy can generate spontaneously many of the basic molecules of life including: