BIO1320 Class

Dr. Hale's Second Semester Biology

Reductionism

reduction of complex systems to simpler components

Emergent Properties

emerge from the arrangement and interaction of parts within a system

blind men and the elephant prinicple

Systems Biology

constructs models for dynamic behaviour of biological systems

Predator - Prey Model

Unity and Diversity of Life

the concept that living organisms are modified descendants of common ancestors

• accumulation of heritable changes contribute to differences in species

• lots of supporting evidence

~evolution~

Taxonomy

the branch of biology that names and classifies into groups of increasing breadth

Carolus Linnaeus

Natural Selection

is a process in which individuals with favourable inherited traits are more likely to survive and reproduce

Descent with Modification

refers to the view that all organisms are related through descent from an ancestor that lived in the past

proposition that natural selection could cause ancestral species to give rise to two or more descendent species

Lyell’s Principle of Uniformitarianism

states that the mechanisms of change are constant over time

The Geologists

• James Hulton

• Charles Lyell

proposed changes in Earth’s surface can result from slow continuous actions still operating today

Catastrophism

speculation that each boundary between strata represents a catastrophic event

George Cuvier

Evolutionary Trees

are hypotheses about relationships among different groups

• homologies form nested patterns in evolutionary trees

can be made using different types of data (anatomical or DNA sequence)

Biogeography

the study of the geographic distribution of species providing evidence of evolution

tracking/understanding Pangaea and continental movement to predict when and where different groups evolved

Endemic Species

species not found anywhere else in the world

Microevolution

is a change in allele frequencies of genes in a population over time

Mechanisms of Microevolution

1. Natural Selection

2. Genetic Drift

3. Gene Flow

Genetic Drift

describes the fluctuation of allele frequencies due to RANDOM CHANCE

• small populations are most susceptible

• tends to REDUCE genetic variation

two main types

• Founder Effect

• Bottleneck Effect

Founder Effect

occurs when a few individuals become isolated from a larger population

smaller founder population often very different from parent population

• the smaller founders LOSE genetic diversity

• harmful genotypes may occur more frequently

Bottleneck Effect

a sudden reduction in population size due to a change in environment

• volcano/flood/carrying capacity reached

the resulting gene pool may not contain the variation it once had

population with reduced diversity is vulnerable to further genetic drift

Gene Flow

consists of movement of alleles among populations

• exchange of alleles between populations

keeps different populations very similar - won’t become individual species

Measures of Gene Variation

two primary measures:

• gene variability (average heterozygosity)

• nucleotide variability

Average Heterozygosity

measure of the average percent of loci that are heterozygous in population

Heterozygosity

the state of having different alleles at a particular gene locus - measure of genetic variation within a POPULATION

Nucleotide Variability

is measured by comparing DNA sequences of pairs of individuals

rarely results in phenotypic variation

Gene Pool

consists of all the alleles for all loci in a population

Fixation

when all individuals in a population are homozygous for the SAME

Mendelian Population

a theoretical model of infinite size (no sampling error) consisting of:

• completely random mating

• No migration (in or out)

• No mutation

• No natural selection

Modes of Selection

• Directional Selection

  • favourable individuals at one end of the phenotypic range

• Disruptive Selection

  • favours individuals at both extremes of the phenotypic range

• Stabilizing Selection

  • favours intermediate variants and acts against extreme phenotypes

Sexual Selection

natural selections for mating success

• can result in SEXUAL DIMORPHISM (marked differences between the sexes in secondary sexual characteristics

Intrasexual Selection

a direct competition among individuals (males) for mates

Intersexual Selection

aka mate choice

when individuals (female) are choosy in mate selection

more of a performance than competition

Speciation

the origin of new species is at the focal point of evolutionary theory

evolution explains how new species originate and how they evolve

Biological Species Concept

states a species is a group whose members have the potential to interbreed in NATURE and produce Viable and Fertile offspring

based on potential to interbreed rather than physical similarity

Allopatric Speciation

gene flow is interrupted when a population is divided into Geographically Isolated Subpopulations

• definition of barrier depends on the ability of a population to disperse

• separate populations may evolve independently through mutations, natural selection and genetic drift

• reproductive isolation may arise as a result of genetic divergence

Sympatric Speciation

when speciation take place in a geographically overlapping populations

can occur if gene flow is reduced by factors including:

• polyploidy

• sexual selection

• habitat differentiation

Polyploidy

the presence of extra chromosome sets due to ACCIDENTS during cell division

two main subtypes:

• Autopolyploid

• Allopolyploid

Autopolyploidy

when an individual has more than 2 chromosome sets derived from A SINGLE SPECIES

tetraploids

Allopolyploidy

a species with multiple sets of chromosomes derived from DIFFERENT SPECIES

Habitat Differentiation

the appearance of new ecological niches within the same geographical range

Hybrid Zones

a region in which members of a different species mate and produce hybrids

• between species with incomplete reproductive barriers

3 potential outcomes

• reinforcement

• fusion

• stability

Reinforcement Hybrid Zone

when hybrids are less fit than parent species

• reinforces reproductive barriers

Fusion Hybrid Zone

if hybrids are a fit as parents

substantial enough gene flow between species to fuse into a single species

Stability Hybrid Zone

continued/steady production of hybrids

extensive gene flow outside the hybrid zone can overwhelm selection for increased reproductive isolation inside hybrid zone

Phylogeny

the evolutionary history of a species or group of related species

Systematics

the discipline that classifies organisms and determines their evolutionary relationships

uses:

• phenotypic data

• fossils

• molecular data

• genetic data

Homoplasies

analogous structures or molecular sequences that evolve independently

Molecular Systematics

uses DNA and other molecular data to determine evolutionary relationships

Cladistics

the process that groups organisms by common descent

Monophyletic Clade

signifies that is consists of the ancestor and ALL its descendants

Paraphyletic Clade

consists of ancestor but NOT ALL of its descendants

Polyphyletic Clade

grouping includes distantly related species but not their most recent common ancestor

avoided at all costs

Maximum Parsimony

assumes the shortest number of events is the best way to build the evolutionary tree/pathway

Maximum Likelihood

states that the rules of how DNA changes reflects the most likely evolutionary pathway

DNA Barcodes

species can be identified using their CYTOCHOME OXIDASE (COI) gene sequence as barcode

used to compare molecules to infer relatedness

Key Factors of Genetic Evolution

• rRNA code changes very SLOWLY making it useful for branch-point investigation

• mtDNA evolve rapidly making it useful to explore recent evolution

Orthologous Genes

same gene in different species as a result of divergent speciation

99% of human genes are orthologous with mice

Paralogous Genes

two copies of a gene in one species

creates a larger genome

Molecular Clock

uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change

Taxis

in a heterogenous environment bacteria may exhibit the ability to move toward or away from a stimuli

Phototaxis, Chemotaxis, Geotaxis

Genetic Recombination in Prokaryotes

combining DNA from two sources

3 methods:

• transformation

• transduction

• conjugation

Genetic Recombination: Transformation

the passive/random take up and incorporation of DNA from surroundings

Genetic Recombination: Transduction

movement of genes between bacteria via BACTERIOPHAGE

Genetic Recombination: Conjugation

the process where genetic material is transferred between prokaryotes directly via the SEX PILUS

requires F-Factor

Conjugation in 3 Steps

1. a donor cell (cell containing F-Factor) attaches to a recipient

2. donor pulls recipient closer

3. donor donates DNA

the F-Factor is transferable via conjugation

Metabolic Cooperation

intraspecies cooperation to allow individuals to use resources more easily

occurs in biofilms

Proteobacteria

the largest group of Gram Negative bacteria

examples:

• E. Coli

• Salmonella

• Campylobacter

Firmicutes

largest group of Gram Positive bacteria

examples:

• bacillus + clostridium

• staphylococcus

• streptococcus

• lactobacillus

Extremophiles

archaea that live in extreme environments

Extreme Halophiles

live in high saline environment

Extreme Thermophiles

thrive in very hot environments

Methanogens

archaea that live in swamps. and marshes and PRODUCE METHANE as waste

strict anaerobes

Exotoxins

are secreted and cause disease even if prokaryote is not present

Endotoxins

are released only when bacteria die and their cell walls break down

common in gram negative bacteria

Protists

• unicellular eukaryotes

• exhibit more structural and functional diversity then any other group of eukaryotes

• nutritionally diverse

  • photoautotrophs

  • heterotrophs

  • mixotrophs

• some reproduce asexually others sexually or via meiosis/fertilization

Supergroups

eukaryotes can be divided into 4 supergroups including protists

1. Excavata

2. SAR

3. Archaelplastidia

4. Unikonta

Supergroup: Excavata

some have a groove on one side of the cell body

includes parasites, many predatory and photosynthetic species

examples:

• Diplomonads

• Euglenozoans

Excavata - Diplomonads

have modified mitochondria (MITOSOMES)

anaerobic biochemical pathways

2 equal sized nuclei and multiple flagella

often parasites → Giardia

Excavata - Euglenozoans

spiral or crystalline rod inside their flagella

some are mixotrophic

Supergroup: SAR

diverse monophyletic group

named for 3 major clades

• STRAMENOPILES

• ALVEOLATES

• RHIZARIANS

a controversial group due to lack of evidence

examples:

• Diatoms

• Dinoflagellates

• Ciliates

• Apicomplexans

• Brown Algae

SAR - Diatoms

unicellular algae

unique 2-part, glass-like wall of silicon dioxide

major component of phytoplankton

highly diverse

SAR - Dinoflagellates

2 flagella and reinforced by cellulose plate

abundant component of phytoplankton

cause toxic red-tides

SAR - Ciliates

large and varied group of protists

use cilia to move and feed

have large MACRONUCLEI and small MICRONUCLEI

exchange haploid micronuclei via conjugation

SAR - Apicomplexans

parasites

spread via SPOROZOITES

one end = the APEX

• contains a complex of organelles specialized for penetrating host cells/tissues

have sexual and asexual stages that require two or more host species for completion

SAR - Brown Algae

largest and most complex algae

multicellular

mostly marine

have plant-like structures:

• rootlike → HOLDFAST

• stemlike → STIPE

• leaflike → BLADES

includes some species of ‘seaweed’

Supergroup: Archaeplastidia

a monophyletic group

descended from protists that engulfed cyanobacterium

examples:

• Red Algae

• Green Algae

• Land Plants

Archaeplastidia - Red Algae

reddish due to PHYCOERYTHRIN accessory pigment that masks chlorophyll

usually multicellular → largest seaweeds

most abundant large algae. in tropical coastal waters

Archaeplastidia - Green Algae

aka - CHLOROPHYTES and CHAROPHYTES

named for grass-green chloroplasts

ancestor of plants

paraphyletic group

most are freshwater some marine

Chlorophytes can live as symbionts in lichens, in high visible light and UV light environments

Supergroup: Unikonta

extremely diverse - including aminals, fungi and some protists

2 main clades

• AMEOBOZOANS

• OPISTHOKONTS

root of eukaryotic tree (unclear timline)

example = Slime Molds

Slime Molds

resembles fungi due to convergent evolution

2 lineages

1. Plasmodial Slime Molds

2. Cellular Slime Molds

Plasmodial Slime Molds

brightly pigmented (usually yellow or orange)

PLASMODIUM = a mass formed during lifecycle

not multicellular

undivided by membranes

contains many diploid nuclei

extends pseudopodia

Cellular Slime Molds

form multicellular aggregates

cells separated by their membranes

cells feed individually but can aggregate to form a fruiting body

Traits of Charophytes and Land Plants

1. rings of cellulose

2. structure of flagellated sperm

3. formation of cell plate during cell division

4. shared genes for nucleus, chloroplasts, and mitochondria

Derived Traits of Land Plants

1. Alteration of Generations

2. Multicellular Dependent Embryos

3. Walled Spores

4. Multicellular Gametangia

5. Apical Meristems

also:

• the Cuticle

• Mycorrhizae Relationships

Gametangia

organs responsible for producing gametes

• Female Gametangia = ARCHEGONIA

• Male Gametangia = ANTHERIDIA

Leaf Categories

1 - Microphylls = single vein

2. -Megaphylls = highly branched vascular system