Unit 7: Biodiversity (copy)

Evolution

Change in heritable characteristics in a population / Change in allele frequencies of a population gradually over time

• Acquired changes that are not genetic in origin are not regarded as evolution

• Darwinian evolution ≠ Lamarckism

Evidence for Evolution (Sequence data)

Sequence data gives powerful evidence of common ancestry

• Universality of DNA genes & code for proteins

• Same genes are present in organisms that evolved from a common ancestor

  • Mutations accumulate gradually at a constant rate → Differences in the base sequence

The more similar the sequences of DNA are, the more closely related the organisms are. Closely related species have similar gene and protein sequences, as there will be a small number of mutations because they diverged from a common ancestor.

Evidence for Evolution (Selective Breeding)

Variation between different domesticated animal breeds and varieties of crop plant + Variation between “ VS original wild species shows how rapidly evolutionary changes occur

• Selective Breeding = Process of humans choosing plants / animals with desirable traits to breed together and produce offspring with more desirable traits

  • Dogs ~ Domesticated from wolves by humans (Docility, size, color of fur)

  • Brassica oleracea → (Selection for…)

    • Terminal buds → Cabbage

    • Lateral buds → Brussel sprouts

    • Stem → Kohlrabi

    • Leaves → Kale

    • Stems & flowers → Broccoli

    • Flower clusters → Cauliflower

Evidence for Evolution (Homologous Structures)

Homologous structures = Similar in structure, different in funtion

• Present in organisms that have common ancestor

• Pentadactyl limbs = Any limb with five digits

  • Found in mammals, reptiles, and amphibians

  • In humans → Carrying tools

  • In dogs → Running

  • In birds → Flying

  • In whales → Swimming

Convergent Evolution

Origin of analogous structures

• Analogous structures = Same function, different evolutionary origins

  • Wings for flight ~ In birds, bats, and insects

  • Wing flaps for gliding ~ Sugar glider & Flying squirrel

Speciation

Speciation = Formation of new species (Only way) through evolution / splitting of pre-existing species; Speciation ≠ Gradual evolutionary change in species

• Speciation increases the total number of species on Earth

• Extinction decreases it

Speciation ~ Reproductive Isolation & Differential Selection

Reproductive isolation = Occurs when barrier prevents individuals from reproducing → Speciation; Due to geographical isolation e.g. rivers, mountains, or different islands

• Bonobos VS Common chimpanzees by Congo river

  • Chimps → North // Bonobos → South

  • Divide is maintained by apes’ inability to swim across the Congo river (Geographical isolation) → Unable to reproduce with each other (Reproductive isolation)

  • Different traits were selected: Aggressiveness in chimps VS Peacefulness in bonobos

Differences and Similarities Between Sympatric and Allopatric Speciation

Reproductive isolation can be geographic, behavioural, or temporal

• Sympatric = Behavioural OR temporal isolation → Reproductive isolation; Population divides into new species while inhabiting same habitat; Faster

  • E.g. Mating behaviour in Western & Eastern meadowlarks

    • Have overlapping habitats / capable of reproducing

    • Use different songs to attract mates

  • E.g. Reproducing times in Cicadas

    • Different cicada species → 13 or 17 year-long life cycle

    • Remain as larvae underground until end of life cycle → Adult cicadas of different lifespans will not be present simultaneously

• Allopatric = Geographical isolation; Physical separation of two populations; Slower

  • Once separated, different selective pressures in its environment causes them to evolve into different species → Unable to interbreed

Adaptive Radiation

Adaptive radiation = Source of biodiversity; Evolution of single ancestral species into many species which become adapted to new environmental niches due to different selection pressures (Divergent evolution)

• Allows closely related species to coexist without competing, thereby increasing biodiversity in ecosystems where there are vacant niches

E.g. Darwin’s finches (18 species) on Galápagos Islands

• Fruit / Insect / Cactus / Seed eater ~ Parrot / Grasping / Probing / Crushing beak

• Variation in beak shape = Genetically controlled characteristic

Barriers to Hybridisation + Mechanisms for Preventing Mixing of Alleles Between Species

Hybrids = Rarely formed due to pre-zygotic or post-zygotic barriers

• Pre-zygotic barrier:

1. Behavioural isolation
   Courtship behaviour prevents hybridisation

2. Temporal “

3. Geographical “

4. Mechanical “
   Physical differences between organism prevents intercourse

• Post-zygotic barrier:

1. Hybrid inviability
   Offspring do not survive to become sexually mature adults

2. " infertility
   Offspring are incapable of producing functioning gametes; Sterile due to genetic incompatibility between species
   E.g. Mule ~ Offspring of male donkey + female horse

3. “ breakdown
   2nd generation of offsprings are unable to reproduce

Abrupt Speciation in Plants by Hybridisation and Polyploidy

Polyploidy = Sympatric speciation; Having 2+ sets of homologous chromosomes

• Occurs commonly in plants due to errors during meiosis

• Self-fertilisation / Asexual reproduction allows polyploid individuals to produce a breeding population → Immediate speciation (Organism contains different # of chromosomes)

E.g. Knotweed

• Polyploid plants often produce bigger fruits

• Japanese knotweed (octoploid) + Giant “ (tetraploid) = Bohemian “

  • Most are hexaploid (66 chr)

Natural Selection

Mechanism driving evolutionary change; Operates continuously and over billions of years, resulting in the biodiversity of life on Earth

• Variation

• Competition

• Selection

• Reproduction

• Heritability

Roles of Mutation and Sexual Reproduction in Generating Variation

Mutations generates new alleles

• Typically has no effect on phenotype of organism

• Can be disadvantageous OR advantageous

• Low rate in population

Sexual reproduction generates new combinations of alleles

• Meiosis ~ Random orientation of homologous chromosomes during Metaphase I + Crossing over

• Fertilisation of different possible gametes (Variation between sperms and ova from same individual)

Factors that Promote Natural Selection

Overproduction of offspring & competition for resources that limit carrying capacity

• E.g. Competition for food, mates, space

  • Predation, parasitism, disease

Selection Pressures (Abiotic Factors)

Abiotic selective pressures = Density-independent factors; Population density does not influence ability to affect individuals / species

• E.g. High or low temperatures that may affect survival of individuals in a population

  • 15º decrease in temperature → 50% less bacterial activity

  • Increase in temperature → Naegleria fowleri amoeba parasite moves North

  • Wind, air pollution, cold stress, nutrient deficiency, soil salinity, water deficit, high temperature, extreme radiation → Plants

Intraspecific Competition

Differences between individuals in adaptation, survival, and reproduction as the basis for natural selection

• Fitness = How well adapted an individual is to its environments

  • If advantageous in terms of it being well-adapted & help organism survive, trait has survival value

  • Reproductive potential = Maximum number of offspring an organism can produce if it survives to reproductive age

Requirements of Traits for Evolutionary Change

Characteristics acquired during an individual’s life due to environmental factors are not encoded in the base sequence of genes and so are not heritable

Selection Pressures (Sexual Selection)

Differences in physical and behavioural traits, which can be used as signs of overall fitness, can affect success in attracting a mate and so drive the evolution of an animal population

• Sexual dimorphism = Males and females of a species looks very different

• E.g. Evolution of plumage of (male) birds of paradise

  • Peacocks: Display of vibrant and large plumage

  • Bowerbirds: Construction of elaborate bowers decorated with colorful objects (flowers, leaves, & plastic); Based on attractiveness & complexity

  • Mandrills: Fight for dominance + Bright coloration on face and rumps (which becomes more pronounced when excited or displaying)

Endler’s Experiment (Guppies)

• Mean number of spots on male guppies increased → Sexual selection (Females preferred highly spotted male guppies, leading them to have more offspring)

• Under different conditions…

  • No predation = Sexual selection continues, mean number of spots increase

  • Mild predation = Similar to no predation as threat is not strong enough to overcome female preference

  • Voracious predation = Imposed sexual selection; Since highly spotted males were more likely to be preyed on, mean number of spots decreased → Dull-colored male population

Gene Pool

Consists of all genes and their different alleles present in a population

Changes in Allele Frequency (Random Event)

• Genetic Drift = Change in composition of gene pool due to random events; occurs more prominently in small populations

• Can change significantly when large population is reduced to small population

  • Population bottleneck = Occurs when event reduces population size by order of magnitude (50%)

    • Due to natural disasters or human-induced

    • E.g. Northern elephant seals have reduced genetic diversity (compared to Southern) due to overhunting

  • Founder Effect = Occurs when small group separates from larger population to colonise new territory

    • Subset of population has less diversity → Divergent gene pool over time; Original population remains largely intact

    • E.g. Some Amish communities have higher incidence of polydactyly  due to inter-marriage

Changes in Allele Frequency (Natural Selection)

Changes in allele frequency due to natural selection between individuals according to differences in heritable traits

• Darwin developed theory of evolution by natural selection → Biologists subsequently integrated genetics with selection to form Neo-Darwinism

  • Favourable traits may increase and unfavourable traits may decrease

Differences Between Directional, Disruptive, and Stabilising Selection

All three types result in change in allele frequency

• Directional selection = One phenotypic extreme is favoured; Usually due to gradual / sustained environment changes

  • Normal / Gaussian → Distribution is shifted to left / right

  • Typically followed by stabilising selection

  • E.g. Flowers producing more nectar

• Stabilising selection = When moderate phenotype is favoured over two extremes; Usually due to cost-benefit trade-off or when environment is stable and competition is low

  • Normal / Gaussian → Narrow width of distribution; Removal of extremes

  • E.g. Similar human baby weights

• Disruptive selection = Two extreme phenotypes are favoured over one intermediate (Opposite of stabilising); Occurs when environment fluctuates (e.g. seasons)

  • Normal / Gaussian → Bimodal spread

  • Over time may lead to speciation

  • E.g. Proliferation of black or white moths in regions

Hardy-Weinburg Equation

Calculates for allele frequencies & genotypes

• p = dominant allele frequency

• q = recessive allele frequency

• p² = homozygous dominant genotype

• q² = homozygous recessive genotype

• 2pq = heterozygous genotype

If genotype frequencies in population do not fit equation, 1+ conditions are false

• No selection

• No mutation

• No migration

• Large population

• Random mating

Artificial Selection

Artificial selection = Deliberate choice of traits

• Carried out in crop plants and domesticated animals by choosing individuals for breeding that have desirable traits

• Unintended consequences of human actions

  • E.g. AMR

Variation Between Organisms as Defining Feature of Life

No two individuals are identical in all their traits

Patterns of variation = Complex; Basis for naming & classifying organisms

Linnaeus’ “Species”

Morphological concept – Species as groups of organisms with shared traits

Biological Species (Official)

Species = Group of organisms that can breed and produce fertile offspring

• Possible challenges associated with definition

• E.g. Fertile pizzly bears & coy wolves

Karyotyping & Karyograms

Evidence for hypothesis that chromosome 2 in humans arose from the fusion of chromosomes 12 and 13 with a shared primate ancestor

• Vestigial (small, defunct remnant) centromeres in chr 2

• Telomere (end cap) sequences in the middle

• Size of chr 2 in humans = ~Double the size of 2a and 2b in chimps

• DNA in C2 is almost identical to 2a and 2b

Diversity of Genomes Within Species & Among Eukaryotes

Genome = All genetic information of organism

• Mostly shared in same species

• Variations such as SNPs give diversity

  • E.g. BTC gene

• Genome size greatly varies in eukaryotes

  • As measured by # of base pairs or C-value (total mass of DNA in single haploid nucleus)

Current + Potential Future Uses of Whole Genome Sequencing

Currently…

• Increasing speed 

• Decreasing costs

• Used for research into evolutionary relationships

In the future…Personalised medicine?

Chromosome # as a Shared Trait Within a Species

Cross-breeding between closely related species is unlikely to produce fertile offspring if parent chromosome numbers are different

• Uneven # of chromosomes affects viability

Biodiversity

Variety of life

• Ecosystem diversity = Variety of different ecosystems or habitats present within specific geographic area

• Species diversity = Number of different species and the relative abundance of each species in a given area

• Genetic diversity = Variety of genes within same species

Past VS Now Levels of Biodiversity

• Millions of species have been discovered, named and described but there are many more species to be discovered

• Evidence from fossils suggests that there are currently more species alive on Earth today than at any time in the past

Causes of Anthropogenic Species Extinction + Examples

North Island giant moas

• Loss of terrestrial megafauna; Hunted to extinction

Caribbean monk seals

• Loss of marine species; Hunted for its oil to use in lamps + for food

American mastodon

• Over-hunted + Stressed by changing climate

Causes of Ecosystem Loss + Examples

Deforestation for wood, agriculture, mining, climate change, and hunting

Loss of mixed dipterocarp forest in Southeast Asia

• Tropical rainforests with many hardwood trees

• Disappearing by rate of 1% per annum

• Land clearing for palm oil plantations (Monoculture; Reduces biodiversity)

Amazonian rainforest

• Land clearing for cattle ranching & gold mining

Evidence for Biodiversity Crisis

• Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) reports

  • Results from reliable surveys of biodiversity in a wide range of habitats around the world indicate “Human actions threaten more species with global extinction now than ever before.”

• Surveys need to be repeated to provide evidence of change in species richness and evenness

Causes of Current Biodiversity Crisis

• Human population growth = Overarching cause

+ Hunting & other forms of over-exploitation

+ Deforestation & clearance of land for agriculture with consequent loss of habitat loss

+ Pollution & spread of pests, diseases, and invasive species due to global transport

Need for Several Approaches to Biodiversity Conversation

No single approach by itself is sufficient, and different species require different measures.

• in situ conservation of species in natural habitats

  • Management of nature reserves

  • Rewinding & reclamation of degraded ecosystems

• ex situ conservation of species outside natural habitats

  • Zoos and botanic gardens

  • Storage of germplasm in seed / tissue banks

Rationale of EDGE

Prioritising evolutionarily distinct and globally endangered (EDGE) species allows for efficient resource distribution to execute effective conservation and maximum recovery of threatened species

Need for Classification of Organisms + Difficulties + Alternatives

• Immense diversity of species

• After classification, broader range of further study is facilitated

  • BUT may not accurately reflect evolutionary relationships due to divergence created by evolution → Cladistics (Classified organisms based on shared derived characteristics)

Advantages of Classification Based on Evolutionary Relationships

(Can be predicted)

Clade, Cladograms, & Methods

Clade = Groups of organisms with common ancestry and shared characteristics

• Most objective evidence for placing organisms in same clade = DNA sequences or amino acids sequence of proteins

• Morphological traits can be used to assign organisms to clades as well

Base sequences of genes or amino acids of proteins as basis for constructing cladograms

• Parsimony analysis = Determines the simplest explanation for observed data; Selects cladogram requiring fewest changes to character states

• Node = Represents hypothetical common ancestor

• Other features of cladogram include root, terminal branch, and …

Basis for Estimation of Clades Divergence from Common Ancestor

Gradual accumulation of sequence differences

• Molecular clock = Based on accumulation of genetic mutations over time

  • Only give estimates because mutation rates are affected by length of generation time, size of population, and intensity of selective pressures

  • Useful for tracing evolutionary history, understanding spread of pathogens, etc. 

Use of Cladistics + Case Study

For investigating whether classification of groups corresponds to evolutionary relationships

• E.g. Reclassification of figwort family via chloroplast DNA and amino acid sequences instead of phenotypes

Classification of Organisms into Domains

Revolutionary reclassification with extra taxonomic level above kingdoms proposed in 1977 → Archaea, bacteria, & eukarya

Using evidence from rRNA base sequences

• rRNA = Ribosomal RNA; Crucial for protein synthesis 

  • Due to its slow evolution, reliable for evolutionary analysis