Lecture 6-9 Flashcards
What is biological evolution?
Gradual change in the inherited traits of a population.
Survival: maintain internal homeostasis, respond to external stimuli, consume and produce energy
Reproduction: reproduce and have a form of heredity
Survival + reproduction = natural selection
Change in allele frequencies in a pop. over time
Driven by variation in reproductive success (fitness)
What is the Darwinian Revolution?
Publiction of “On the Origin of Species”
1) The tree of life: all species on Earth have evolved from other species (perhaps, ultimately, from just one)
2) Natural Selection: organisms are well-adapted to their environments because they accumulate, over the generations, traits that enable them to survive and/or reproduce better than organisms lacking those traits
What is natural selection?
Individuals in a pop. differ in their traits
Some traits confer an advantage (in a given environment)
- by that advantage, those traits allow certain individuals to survive and reproduce more
Individuals that have these traits survive and reproduce better than others
- i.e. selection is on phenotype (expression of trait)
If differences are heritable, the frequency of advantageous traits will increase in the next generation
- i.e. evolution is due to changing “genotype” (genetic coding for traits)
Gene definition
A self replicating DNA unit that occupies a specific location on a chromosome and determines a particular characteristic in an organism
Allele definition
A variant (different) form of a given gene (section of DNA) that codes for smt (e.g. a trait)
What is fitness in terms of biological evolution?
Fitness translates to reproductive success
I.e. how many surviving offspring does one have compared to others in the pop.
What is a phenotype?
Interaction between genotype and environment
Even individuals with the same genotype have different expressions depending on the environment (plasticity)
Why do individuals’ genetics vary?
mutuation
mode of reproduction
How do prokaryotes transfer info from generation to generation?
An enzyme gently break apart fhe two DNA strands
Other enzymes attach complementary bases to each of the old strands
Another enzyme checks for mistakes (proof-reading) and a DNA repair enzyme fixes them
Result: two strands virtually identical to the original
Mutation: mistakes happen! inital source of all variation
What is the reproduction in prokaryotes?
Binary fission
Replication of the circular chromosome followed by fissioning of the cell
Transmission of DNA-coded info across generations
DNA replication: cell fission (splitting) placing replicated DNA into daughter cells
What is binary fission?
Asexual reproduction in prokaryotes, creates new prokaryotes and some genetic diversity via mutation (identical apart from mutations)
What are some other ways prokaryotes transmit genetic info (not equal to reproduction)?
All do not = reproduction, but introduces genetic variation
Conjugation: sharing plasmids (separate ring of DNA)
Transformation: a prokaryote picks up a plasmid (genetic material) from the environment
Transduction: a virus relocates DNA from one prokaryote to another via viral replication cycles
What is different about the genetic structures of eukaryote cells?
Genetic material organized into multiple linear chromosomes
Each chromosomes consists of one long molecule of DNA
After DNA replication, two identical “sister chromatids” form
What is mitosis?
Duplicate chromosomes lines up and are pulled to opposite sides of parent cell
The cell then divides (fission) to produce daughter cells
What are the steps of asexual reproduction in a single-celled eukaryote?
Start off with a haploid (N) cells - 3 chromosomes
Duplication: chromosomes and DNA duplicate
Mitosis/fission: results in two identical haploid (N) cells with 3 chromosomes
What are the steps of sexual reproduction?
Gametes: 2 haploid (N) cells, each with 3 chromosomes but from different mating strains (2 parents)
Gametes fuse to form diploid (2N) zygote
6 chromosomes become uncondensed inside the new nuclear membrane
Meiosis: we start off with a diploid (2N) zygote
Reassortment or reassortment + recombination: Chromosomes duplicate, and homologous chromosomes line up in center of cell (random process )
Reassortment: homologous chromosomes separate and move to opposite sides of cell
2 groups of 3 chromosomes (each with replicated sister chromatids)
Sister chromatids separate
Now 4 groups of 3 chromosomes each
What creates more possible combinations in gametes during reassortment?
More chromosomes
Example:
N=2 –> 4 possible gametes
N=3 –> 8 possible gametes
N=4 –> 16 possible gametes
What are the benefits of sexual reproduction compared to asexual reproduction?
Generates a lot of variation
What are the consequences of sexual reproduction?
Mate searching costs
- as pop. size grows smaller, probability to find a mate decreases –> can lead to extinctions
Competition
Display costs
Only half of pop. generates offspring
What conditions favour sexual reproduction?
High number of environmental factors (complex)
high genes per trait
Low background mortality
Strong soft selection
Low mutation rate
Periodic catastrophes
What is hard selection?
Extra mortality (reduced reproduction) for maladapted individuals
What is soft selection?
No extra mortality, but who dies depends on fitness of other individuals
What are direct advantages of sex?
DNA repair mechanism
Masking mutations – higher chance that one copy works
What is the biochemical evidence for Archean ancestor to eukaryotes?
DNA sequence data from genes in the nucleus of eukaryotes suggests that eukaryotes are more closely related to Archeae than to bacteria
What is the biochemical evidence for bacterial ancestor to eukaryotes?
Mitochondria and chloroplasts (eukaryote organelles) have their own circular DNA and prokaryoteic-type ribosomes. Most similar to bacteria
What is endocytosis?
A substance gains entry into a eukaryotic cell; the cell membrane wraps itself around the particle and pinches off a vescicle inside the cell
Steps:
- Food particle taken in by endocytosis
- Fusion forms secondary lysosome
- Food particles digested
- Products of digestion
- Exocytosis of waste
Is simple observation and measurement sufficient to assess descent using comparisons involving phenotypic traits?
No, it does not account for environmental influence on phenotpes, ontogenetic changes, identification of “derived” traits. There is also insufficient data from living and fossil organisms to unambiguously trace changes in time as well as a lack of universal traits.
What needs to happen to have the chance of finding a fossil?
Chance of dying in one piece, being fossilized, remaining undisturbed, being exposed, being found, and being recognized.
The probability of all of these events occurring is extremely small.
What are the advantages of assessing descent through comparisons involving molecular traits?
Nucleotide sequences provide a direct record of all info stored in the genome.
No environmental or ontogenetic effects on the observed traits
Potential for universal traits
What are the disadvantages of assessing descent through comparisons involving molecular traits?
Traits observed only with use of sophisticated technology.
Inferring patterns of change in time not intuitive.
Back mutation at a site in the sequence is possible and complicates analysis.
Assuming constant molecular clock.
What are the steps to reconstructing phylogeny (lines of descent)?
1) Acquire nucleotide sequence data
- sampled part of a genome depends on how far back in time the relationships of interest lie
2) Align sequences from different organisms
- allow for mismatches due to point mutations, insertions, and deletions
3) Reconstruct most likely lines of descent
- assess the minimal number of steps requires to change from one sequence to another and use this as a measure of relatedness across all the organisms in the analysis
What are Acritarchs?
Early marine plankton.
A group of eukaryote fossils probably including algae, ciliates, dinoflagellates, radiolarians, foraminiferans.
Many acritarchs had tests (shells)
- example of structural complexity
- better source of fossil material
Why did diversity increase and what were the processes involved?
Increase in size of genome (more proteins, enzymes coded for)
Sexual reproduction (meiosis increases possible variation/mixing)
Increase in structural complexity (locomotion, protection)
Ecological changes (O2, energy sources, physical/biological landscape, photosynthesis in shallow water)
What are the origins of multicellular life?
Colonial protists and algae illustrate intermediate stage of complexity
Colonial life allows evolution of separate functions for individual cells
- feeding, reproduction, locomotion, etc.
- different metabolic pathways turned on and off
Ediacaran diversity
Variety of forms (vendian animals)
- leaflike fronds, round pads, worms
Some resemble jellyfish, sponges
Most are unique and unlike known animals
What was the ediacaran seascape in the late precambrian era (around 570 MA)?
Small shelly fossils in ocean sediments
Soft parts not preserved –> no idea what organism construced the shells
Burgess Shale Diversity
Ancestors of many modern groups
Arthropods, worms, sponges, jellyfish
But also many mystery organisms (failed lines of evolution? victims of chance?)
What is the Pikaia?
Ancestor of chordates, vertebrates, mammals and humans
What happened during the Cambrian Explosion?
Diversification in the animal kingdom
From Ediacarans (+/-570 MA) to early Cambrian animals (+/-540 MA)
All modern animal body plans established in less than 25 million years
Changes since then are just variations on those established plans
What is fitness landscape?
used to visualize the relationship between genotypes and reproductive success
What defined the Cambrian ecology?
Burrowing priapulid worms
Predators of small molluscs with spines
Swallowing prey all face the same way
Well-developed feeding behaviour
Give an example of a predator-prey “arms race”
Predator behaviour –> burrowing
Dig for prey –> hard sclerites
Jaws –> spines/completes shell
Modified hunting behaviour
Is there purpose in evolution?
No
Variations arise through chance mutations
Some mutations are positive, some negative, many neutral
Selection, not the organisms, decides which variations will survive of succees
Always interpret evolution in terms of chance variations, selection, probabilities of survival, not purpose and progress towards an objective
What does the predator-prey arms race mean in terms of evolution?
Interpret the sequence of events in the predator-pre arms race in the context of random mutations, variations and selection
Co-evolution
What can mutations create variations in?
Structure of the exoskeleton or skin, mouthparts, organs of locomotion, sensor structures
Behavioural traits
Physiological and metabolic pathways
What is co-evolution?
Selection of favourable mutations in a biotic interaction between different organisms
Evaluate the predator-prey arms race through a random mutation lens
Predator behaviour
- scavengers randomly swallow live organisms - more nutrient
- some scavengers have mutations that allow digestion
Burrowing
- organisms with structural and behavioural that allow them to burrow in mud will not be encountered by scavengers
Dig for prey
- surface scavengers with longer legs penetrate deeper into the mud to find food - burrowing organisms are encountered
Hard sclerites
- burrowers with mutations that result in thicker skin may be harder to swallow - they will survive
–> many possible variations at each step in the process
What are some putative mechanisms for explosion of diversity during the Cambrian?
Tectonic activity
CO2 degassing rate
Heating and melting of Snowball Earth
Increased photosynthesis
Increase pO2 50-75% during Ediacaran period/beginning of Cambrian
Enough to support energy requirements for larger predators
What are some characteristics of the Proterozoic?
Photosynthesis evolved
Eukaryotes (cells with nucleus evolved)
Proliferation of bacterial mats
Great Oxygenation Event
- O began building up in the atmosphere
- Formed the ozone layer (filters out harmful UV radiation)
Near the end of the Proterozoic: multicellular photosynthesizers begin to appear (algae). Soft animals and hard bodied animals appear
What are some characteristics of the Cambrian?
Shells and hard bodies start to dominate in the fossil record
Animals become more motile (predation)
Explosion of evolution of new body types in animals
The first chordate (animal with a long central nerve). The lineage that would go on to give rise to all vertebrates
What are some characteristics of the Ordovician?
Mix of continents and shallow ocean shelves, rising and falling sea levels
First true vertebrates (fish with jaws) evolve from Pikaia
What are some barriers to adapting to land?
Harmful UV radiation
Desiccation
Gas exchange
Buoyancy
Temperature fluctuations
Mineral nutrition
Reproduction
Vision and hearing
How is harmful UV radiation a barrier ot adapting to land?
Water could filter UV light and protect light
Oxygen changed everything –> created an ozone shield which filters out enough UV radiation that life can survive on land
How is desiccation a barrier ot adapting to land?
Aquatic organisms are adapted to being surrounded by water, dry out easily
Cannot be waterproof: need to allow for the passage of water and gases in and out of the body
Smaller organisms dry out faster
- greater surface area to volume ratio
- internal space = water storage
- surface area = water loss
How is gas exchange a barrier ot adapting to land?
Gases (CO2 and O2) are absorbed differently depending on whether they are in air or dissolved in water
- need a new system of gas exchange
How is buoyancy a barrier ot adapting to land?
Water and water pressure supports body tissues, air does not (for example, most of the weight of blue whales is supported by the environment around them)
Land plants and animals need supporting structures
How are temperature fluctuations a barrier ot adapting to land?
Seawater: slow and little change (sea surface has changed as little as 4 degrees C over the past few centuries)
Land: quickl, large changes (as much as 30 degrees in 24 hours)
How is mineral nutrition a barrier ot adapting to land?
Water contains dissolved minerals for added nutrition
Many aquatic animals are sessile (immobile) –> need a way to supplement on land
On land, nutrients are sometimes less concentrated and less accessible
How is reproduction a barrier ot adapting to land?
Aquatic organisms need water to facilitate reproduction
Male and female gametes (egg and sperm) released into the water for fertilization and development (both animals and photosynthesizers)
How is vision and hearing a barrier ot adapting to land?
Light and sound waves move differently through water compared to air –> needed to adjust vision and hearing
Evolved sense need modification before they can work in the atmosphere
What are the traits of the first land colonizers?
From early cyanobacteria, green algae (eukaryotes, incl. mutli-cellular) appeared approx. 0.75 bya
Photosynthetic organisms tend to grow at the surface (get their energy from the sun). Wave action can throw organisms on shore, periodically exposing them to desiccation –> can still access nutrients in water, but still challenged to temporary life on land
Advantageous to grow near the surface (near light), in shallow waters, on coastal shelves
Selective force to tolerate desiccation
What is the evolution of green algae?
Pop. of green algae exposed to periods of drought in the intertidal.
- selection for individuals which could tolerate extended periods of desiccation
- i.e. existing species had traits which likely predisposed them to being able to adapt to the terrestrial environment.
Over time, evolved from green algae to more complex forms that could survive entirely on land
Algae –> moss and liverwort (no vascular system)
What is the evidence of the evolution of green algae into moss and liverwort?
Spores resembling modern liverwort spores found in Ordovician fossil record (no known species of aquatic liverworts)
Molecular clock of all modern plants –> work backwards to calculate the date when the began to diverge (use genetic info to build phylogenetic tree –> little difference in genetic code)
How did plants adapt to desiccation on land?
Developed multiple cell layers and a layer of surface wax (the cuticle)
Evolved roots or tooth-like structure that direct movement of water into the body
How did plants adapt to gas exchange?
Evolved specific pores (stomata) to allow for gas to enter
Could be closed to prevent the plant from drying out
How did plants adapt to reproduction?
Evolved spores which could survive desiccation
- still depended on water to move them
Eventuall evolved seeds –> more desiccation-tolerant than spores (disperse genetic material)
How did plants adapt to buoyancy?
Evolved strong fibers and compounds such as lignin and celluose for structural support
Big plants can have a skeleton
How did plants adapt to temperature fluctuations?
Traits evolved to prevent desiccation eventually helped plants survive extreme temp. fluctuations
- much later, plants evolved methods (e.g. dormancy) to survive in extreme environments (deserts, winter)
How did plants adapt to mineral nutrition?
Roots allowed plants to take minerals right out of the soil
Some plants formed symbiotic associations with microbes: exchange minerals for sugars
Why did plants move on land before animals?
Plants are at the base of the food chain
First animals on land
Multiple animal groups independently moved onto land
Cambrian era fossils show arthropod tracks on land even before plants. However, no permanent terrestrial species at this point. Footprints believed to have been made by animals fleeing predation in water
Which animal group was the first group to move on land?
Arthropods: scorpions, millipedes, springtails all present in Devonian (410-360 MA)
Rapid increase in diversity after that time
Which animal that moved onto land was our ancestor?
Tikaalik - Late Devonian (375 MA)
A lobe-finned fish
Shared ancestor of all tetrapods (amphibians, mammals, reptiles)
A transition fossil
Sturdy jointed arms for terrestrial support
Evolved to later form
- progressive evolution of limbs
- lived on land but still closely ties to water for reproduction
Are lobe-finned fish extinct?
Though to be extinct, yet there are remnant populations
Why could so many groups colonize land?
Structures that evolved for other uses are also effective for living on land
- e.g. exoskeleton of arthropods, verterbrate skeleton, types of movement
How did animals adapt to desiccation on land?
Terrestrial animals have different mechanisms to prevent desiccation on land
Physical (waxy caoting on exoskeleton) –> arthropods
Scales –> reptiles
Behvarioural (live in damp habitats, active at night) –> amphibians
Concentrate waste, remove water and excrete waste as uric acid (drier, less water) –> reptiles
How did animals adapt to gas exchange on land?
Must keep the membranes wet in dry air without losing water
Evolved lungs –> large surface area for gas exchange
Insects: small openings in exoskeleton (spriracles), network of tubes branching throughout bod (tracheae)
- limits the size of insects since there is not enough O to diffuse fast enough
Vertebrates: small opening (tracheae), sacs with large surface area and many blood vessels for gas exchange (lungs)
How did animals adapt to reproduction on land?
Internal fertilization
- keep ova inside body to prevent desiccation
- fertilize inside female (prevents gametes from drying out)
Internal fertilization also maximizes the probability of gametes encountering one another
Terrestrial organisms are much more conservative –> internal fertilization makes it so that there is a higher chance that egg is fertilized
Zygote inside female –> need to get embryo outside
- modify egg for terrestrial life (self contained world, major energy investment by female)
- protects from desiccation, provides nutrients, gas exchange and waste disposal
What is the amniotic egg?
Major evolutionary adaptation in reptiles
- allowed eggs to be laid on dry land
Temperature fluctuations still a problem
- bur in temperature-buffering material
- incubation behaviour
Fewer eggs produced
- need more resources per egg
Nesting parent is easy prey (vulnerable to predation)
What is viviparity and what are the pros and cons of viviparity (live birth)?
Viviparity evolved multiple times in diverse groups. An internal egg is retained by the female after fertilization. Even fewer young that species with amniotic eggs
Pros: Increase parental investment is believed to allow for the increased survival of offspring
Cons: more parental investment (more energy)
How did animals adapt to buoyancy on land?
Arthropods (e.g. insects): exoskeleton made of chitin
Molluscs: external shell (calcium), hydroskeleton (fluid pressure inside body)
Vertebrate (e.g. mammals): internal skeleton of cartilage and bone
How did animals adapt to temperature fluctuations on land?
Homeothermy: the ability to regulate internal body temp.
Both active and passive strategies:
1) metabolism: Regulate own body temp. (constant internal body temp.), costly in terms of energy (must eat a lot)behavioural)
2) Poikilotherms: tolerate temp. (body temp. changes with external temp. –> reptiles)
Homeotherms
Higher metabolism
Higher food requirement
How did animals adapt to vision on land?
Sealed chamber filled with fluid (as opposed to early eyes that were filled with water from the environment)
How did animals adapt to hearing on land?
Adaptations specialized in some species to airborne wavelengths
- cochlea in mammals still contains fluid for sound transmission
What is the kingdom, phylum, class, order, family genus and species of humans?
Kingdom: Animalia
Phylum: Chordata
Class: Mammalia
Order: Primates
Family: Hominidae
Genus: Homo
Species: H. sapiens
Who is our closest relative?
Chimpanzees, genus Pan
How far back do we have to go in western scientific literature to recognize that humans and apes are related?
1735
What were Lamarks suggestions?
First to suggest that apes and humans had a shared evolutionary history
Thought ancestral humans were likely tree dwelling, like apes today
- increasingly walked on the ground on two feet
- through acquired characteristics and over many generations, became bipedal and lost the ability to climb trees
Why was there a lot of debate surrounding human evolutionary record?
We had only found a fraction of the fossil record that we have today.
Until the 1800s, no fossils found of ancient human species, only a few stone tools
Why do the tropics not produce good fossils?
Things decay quickly (environmental conditions)
What does the fossil record tell us about human evolution?
Based n many fossils from Kenya and around the Qorld, we now know there were many species of homo, starting 2-2.5 MYA
Our lineage split from what would become chimps around 5-13 MYA, with many intermediates
Was hominid evolution a straight line (i.e. one species became another, all are our ancestors)?
Number of branch poitns that gave rise to more than one lineage
Lineages existed at the same time (different species of homo coexisted)
All of the lineages went extinct with the expections of homo-sapiens
Australopithecus chacteristics
Bi-pedal, ape-like (Lucy)
Small brains, but some made and used tools
Change in diet
Greater sexual dimorphism
Habitat in Africa about 4.2-2 MYA
Homo habilis characteristics
Brain is getting bigger, teeth smaller
Definitely made stone tools (the handyman)
Habitat in Africa about 2.4-1.5 MYA
Homo erectus characteristics
Most successful human species identified to date
Believed to be the first to leave Africa
Big brains, tools, hunters
Fire, art, proto-speech?
Habitat in Africa, East and West Africa about 1.9 MYA to 150 000 years ago
Homo antecessor characteristics
Sister species to H. sapiens
Suggests entire other lineage of human evolution
Habitat in Western and Southern Europe about 1.2 million-800 000 years ago
Homo heidelbergensis characteristics
overlapped with (evolved from) H. erectus
New study 2020: shared Africa with H. sapiens
Habitat in Asia, Europe and northern Africa about 700 000-200 000 years ago
Homo florensis characteristics
Species which live at the same time as our own
May have experienced insular dwarfism
Many primitive features
Habitat in Flores, Indonesia about 200 000?-50 000 years ago
Homo neanderthalensis characteristics
Sister species to us (both evolved from a single common ancestor)
Had many technologies we recognize
Bred with Homo sapiens
Habitat in Europe and central Asia aobut 400 000-40 000 years ago
Denisovans chracteristics
Another sister species to us
Believed descended from the same immediate common ancestor
No skull identified to date –> no official species name (not using the term homo)
The only human species identified solely by DNA
Habitat Western and Central Asia about 700 000-15-000 years ago
Homo sapiens characteristics
Only extant species in the homo genus
Skull morphology has changed distinctly over time
Evolved in Africa nad left 185 000 years ago
Interacted with other homo species
Habitat originally Africa and now current global distribution about 300 000 years ago -today
What drove human evolution?
Evolution associated with physical (e.g. bi-pedalism, larger brains) and technological (e.g. stone tools) changes that opened up new niches
Natural selection is driven by the fit between an organisms and its environment
The climate has changed around us over the last 2 MY
- climatic variability (temp. rainfall) and ecosystem changes
- favourable periods allowed expansion
- hominids adapted more climate extremes (seasonality, altitude)
What is a roadblock in using morphological traits to evaluate evolution?
Difficult to distinguish chronospecies
Difficult to tell apart natural variations within species from differences separating species
What is a roadblock in using DNA (molecular phylogeny) to evaluate evolution?
Half life of DNA is 521 years
Most recent extinction of other Homo likely H. neanderthalensis at 20 000+ years ago
We could not extract DNA to analyze –> widely believed we would never be able to analyze DNA past its half-life –> enter ancient aDNA
What is ancient aDNA?
Current theoretical upper limit for analysis: 1.5 MY
PCR lets us amplify even very tiny samples. Then can build ancient genomes from fragments by comparing them to modern ancestors
What are some drawbacks with ancient aDNA
Possibility of contamination
What is the Neanderthal Genome Project
International effort to sequence entire genome of H. neanderthalensis from two bones
Used computer programs designed to eliminate bacterial DNA from sequence reads
- Resulting sequences were compared to modern H. sapiens DNA, and mapped by comparison to the modern human genome
What were the discoveries from the Neanderthal Genome Project?
H. neanderthalensis likely started with a very small founder pop. of 3000 individuals
H. neanderthalensis had a gene mutation we believe to be required for complex speech
H. sapiens and H neanderthalensis hybridized and produced fertile offspring
What did ancient aDNA uncover about the denisovans?
Only a finger bone and a few teeth
Denisovans interbred with H. sapiens and H neanderthalensis
As much as 17% of the genome of the Denivosan girl is from a Neanderthal genome
What is eDNA?
DNA found in environments
DNA can be relatively stable especially when preserved in sediments (unlike RNA)
What are the DNA kits we see nowadays?
DO not use complete genome analyses, but rather seqeunce a small subet of regions of interest
Many large-scale correlational analyses
Some traits have very simple genetic basis, example hair and eye colour
Characteristics such as height and freckles –> multiple genetic regions that can contribute to these traits
Where is the greater proportion of deleterious mutations found?
In european populations (expected in a recent founder pop.)
Where is the greater proportion of rare alleles found?
In african populations
Rare alleles are likely to be lost in founder populations, unless they become dominant
