Download Set 2 (download file)

Evidences of Evolution
1. African Elephants
2. Pod Mrcaru Lizards
3. E.coli: >45k Generation Lab Expts
Elephants
•One of the slowest reproducing mammal
•Tusk: source of Ivory
•Larger the tusk, more is the value
•Large tuskers: competitive advantage over other male elephants
•Disadvantage vis‐a‐vis poaching
•Human hunting and evolutionary pressure
•Smaller tusk as a function of evolutionary pressure
•Millennia to be detected OR within one human life time Tusk Weight in Ugandan Elephants
Tusk Weight in Ugandan Elephants (Linear Regression Analyses of licensed kills over 1925‐1960)
• Strong Selection against large tusk? OR
• Strong natural selection leading to gene frequency increase?
• Case of a RAPID EVOLUTION started >1925
POD MRCARU LIZARDS
Croatian coast: Two small islets – Pod Kopiste, Pod Mrcaru
Mediterranean lizard Podcaris sicula: Pod Kapiste
5 pairs introduced in 1971 in PodMrcaru
1985 the lizards from 2 islets compared
Pod Mrcaru lizard(evolved?): large heads
Larger heads‐ >bite force
Plant cell walls stiffened with cellulose
Herbivores: millstone like teeth, massive jaw muscles‐ grind cellulose
• Carnivores and animals: no cellulose digestion
• Harbor symbionts (bacteria): caecum – fermentation chamber
• Analyze their diet: retained insect as feeds?
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Summer Diet of Lizard on
the two Adriatic islands
Evolution evident in <40 years!
(~18‐19 generations)
Herrel et al JEvolBiol (2004), PNAS, USA (2008)
Evolution during 45000 Generations
E.coli expt of R Lenski et al @ MSU
•E.coli multiplies ~20 mins
•Preserve them indefinitely by freezing and bring back to life again: Living
Fossil record!!
•Hundred bn bn, ~ a bn in our large intestine
•Mutn frequency ~10-9, ~every gene in the genome would have mutated
somewhere in the world!
•Asexual reproduction:simple cell division – make genetic clones very easily
•Glucose as a carbon source, protein extract etc
•Arabinose (sugar) + tetrazolium dye
•Plate cultures vs Shake flask
•Ara+ = white colonies; Ara- = red colonies
•Founding population, 12 flasks (tribes?): ara+ ara_ 50:50
•Growth curve reach plateau: Glucose a limiting source
•100th aliquoted at plateau to fresh broth, cycle renewed every day, 20 yrs
•~7k flask generations, 45k bacterial generations
•45k human generations = ~Mn yrs back : Homo erectus
•Sampled 12 flasks at regular intervals thru out 20 yrs: Progress of evolution
•Evolutionary pressure: Glucose
•“Fossil” bacteria vs “modern” bacteria
Lenski experiment: Bacterial
body size in twelve tribes
Lenski experiment: Bacterial
body size in one tribe
Lenski experiment: Increase
in fitness
Lenski experiment: Some
take home lessons
• When “modern” and “fossil” bacteria grown together in same flask : No evidence of fitness of fossil (Ara screen)
• All 12 tribes survived better in Glu limiting conditions
• Grew still faster in successive generations
• Average bacterial body size increased
• 1st ‐2000 gen most fitness achieved
• All 12 tribes showed differential evolution of fitness: some bit
slow, some bit fast
• In all 12 tribes 59 genes changed • May have had different evolutionary lineages responsible?
• Gradual change, perhaps too gradual?
• Increase in fitness is a stepped‐up event: waits for the next “good” mutation
Lenski experiment:
Population density
•One tribe went bersek, as though more glucose was added at the 33k gen?
•Analyze the molecular event: ability to utilize citrate
•Additional mutation at gen 33k in one tribe
•At ~30k gen ALL genes would have mutated •Sequence of mutation matters A‐B‐C not A‐C‐B
PNAS, USA (1994); PNAS, USA (2008)
Evolution of whales from land creatures, showing the numerous
transitional fossils now documented from Eocene beds of Africa and
Pakistan (Drawing by Carl Buell)
OTHER EVOLUTION THEORIES Creationist
Intelligent Design
Lamarckism
© 2008 Paul Billiet ODWS
Creationist Theory of Evolution
(Biblical View)
Lord Almighty created all living forms in six days
Humans were the last of the species created in the present form within the last 10k yrs
Human race is derived from a single couple (Adam and Eve)
© 2008 Paul Billiet ODWS
Intelligent Design
Theory promoted by Discovery Inst and Access Res Inst, USA
Biological systems at molecular level: ‘irreducibly complex’
Complicated parts and systems: put in place before system can perform any useful function
E.g. eye: it is beneficial ONLY if it functions as an eye –
must be functioning from beginning‐ all or none
Complex forms are NOT created by divine intervention (read GOD) but by an ‘Intelligent Designer’
LAMARCKIAN EVOLUTION
Jean Baptiste LAMARCK
1744 – 1829
© 2008 Paul Billiet ODWS
Adaptation and Specialisation
• Lamarck noticed that organisms adapted to a particular niche had well developed specialised organs
• For example a carnivore will have long canine teeth to grip its prey
• The only methodical evolution theory preceding Darwin
• A linear continuous evolvement from simple to complex creatures
• These changes passed on to future generations
© 2008 Paul Billiet ODWS
Vestigial organs
• Small non‐functional organs (vestigial organs) • e.g. the appendix in humans, the internal hind limbs of whales and the internal legs of some species of snakes
• Comparative anatomy showed that these organs resembled those which were much more developed, with particular functions, in other species
© 2008 Paul Billiet ODWS
Two Main Features of Lamarck’s Theory: The Law of Use and Disuse; The Inheritance of Acquired Characteristics
• Individuals lose characteristics they do not use and develop and strengthen those useful
• If it is not used it will atrophy
• The law of use and disuse
© 2008 Paul Billiet ODWS
The Inheritance of Acquired Characteristics
• if an organism developed a characteristic feature through adapting to a new way of life during its lifetime, it would pass
this on to its offspring
• Classic example: giraffe’s neck
• As the giraffe’s ancestors searched for a richer food supply they stretched to reach higher branches in trees
• Thus their stretched bodies were passed onto their offspring
© 2008 Paul Billiet ODWS
Lamarck vs Darwin
• Lamarck’s theory required adaptation to create new variations
• This was followed by the inheritance of these characteristics
• Darwin’s theory requires random hereditary variation first, followed by selection of the variations
• The argument was over when Mendel’s laws of genetics were rediscovered at the end of the 19th century
• Variations are due to hereditary traits passing from one generation to the next in predictable frequencies
Disproving Lamarck
• Characteristics acquired during the lifetime of a parent are not passed onto the offspring
• An athlete who develops a large muscle mass through training does not have children who already possess this large muscle mass
• Ernst Haeckel
In an attempt to disprove Lamarckism he is said to have cut off the tails of mice for several generations
• The babies born from this line of tailless mice still grew tails as long as their ancestors
• This was not exactly a fair test as the mice had not stopped using their tails in an attempt to adapt to their environment
• They still found their tails useful
Relevance of Lamarckism today
• Behaviour can be different
• Some behaviour patterns are innate and will also evolve in by natural selection
• Learned behaviour patterns can be changed within a generation
• Members of a social group who have acquired the behaviour in their lifetimes will pass these learned skills onto others including their children
• This pattern of evolution resembles the Lamarckian pattern
• The evolution of learnt behaviour is much faster than genetic evolution and it plays an important role in human cultural evolution
How general is bacterial bleaching of corals?
Bleaching of P. damicornis by Vibrio coralliilyticus at 24-25oC
Infected coral
Control coral
Ben‐Haim & Rosenberg 2002
(Koch’s postulates satisfied)
Ben‐Haim, Thompson et al. 2003
Partially bleached Oculina patagonica
Fine & Loya, 1994
Vibrio shiloi is the causative agent of bleaching
of Oculina patagonica
All of Koch’s postulates were demonstrated.
Kushmaro et al Nature 1996
Infection of coral Oculina Patagonica by Vibrio shiloi
RESISTANCE OF O. patagonica TO V. shiloi
1. From 1995-2002, V. shiloi was readily isolated from
30/30 bleached corals.
From 2004 to the present we are unable to isolate V. shiloi from
bleached corals (0/20)
2. From 1995-2002, all strains of V. shiloi caused
bleaching in aquaria
From 2004 to present, none of the same V. shiloi strains bleach
corals
3. From 1995-2002, V. shiloi adhered to the coral,
penetrated into the exoderm and multiplied
Now, V. shiloi adheres, penetrates and dies
Coral resistance to Vibrio shiloi infection
2000
2006
How did the coral become resistant?
• Corals have a primitive immune system (no antibodies)
Coral Probiotic Hypothesis
1. Exposed to pathogens, but no less healthy than
organisms with adaptive immune system.
2. The Coral Probiotic Hypothesis was proposed to
explain the development of resistance to
infection. Beneficial bacteria (probiotics) were
acquired (epidemic?) which kill V. shiloi.
Reshef et al. Environ Microbiol (2006)
Role of Microorganisms in the Evolution of Animals and Plants: The Hologenome Theory of Evolution
Rosenberg et al. Nature Rev. Microbiol. 2007
Zilber‐Rosenberg & Rosenberg. FEMS Microbiol. Rev.2008
• Holobiont: The animal or plant with all of its
associated microorganisms
• Hologenome: The sum of the genetic information
of the host and its microbiota
The hologenome theory of evolution
considers the holobiont with its hologenome
as the unit of natural selection.
The Theory is based on four generalizations:
1. All animals and plants establish symbiotic relationships
with microorganisms; often the genetic information of
the diverse microbes exceeds that of the host.
2. Symbiotic microbes are transmitted between
generations with fidelity.
3. The association between the host and symbionts
affects the fitness of the holobiont within its
environment.
4. Variation in the hologenome can result from changes in
either the host or microbial genomes. Under
environmental stress the microbial component of the
hologenome can change more rapidly than the host
genome.
Host
Estimated number of microbial species
References
Tunicate
30
Martínez‐García et al. (2007)
Drosophila melanogaster
70
Mateos et al. (2006)
Marine sponge
1700
Webster et al. (2001)
Coral Oculina patagonica
400
Koren & Rosenberg (2006)
Termite gut
350
Hongoh et al. (2005)
Human gut
>1000
Rajilić‐Stojanovićet al. (2007)
Human subgingival plaque
400
Paster et al. (2001)
Bovine rumen
350
Edwards et al. (2004)
Pig gut
400
Leser et al. (2002)
Reindeer rumen
700
Sundset et al. (2007)
Leaf of Trichilia catigua
600
Lambais et al. (2006)
Seed of Norway spruce
50
Cankar et al. (2005)
Roots of Zea mays
70
Chelius & Triplett (2001)
Invertebrates
Vertebrates
Plants
Table :‐ Examples of microbial species associated with specific animals and plants Holobiont: Microbiota
Mode of transmission of microorganisms
Microbial contribution References
Physical contact with parents and via food contaminated with feces and sputum
Provision of all Dehority (2003), nutritional needs from Russell & Rychlik cellulose
(2001)
Physical contact with mother
Provision of nutritional Herwig et al. (1984), needs from chitin and Olsen et al. (1994), other complex Olsen et al. (2000)
organics
Via physical contact and from environment
Protection against pathogens; stimulation of immune system; angiogenesis; vitamin synthesis; fiber breakdown; fat storage
Vertebrates
• Cow rumen: Microbiota
• Whale forestomach: Microbiota
• Human gut and mouse model: Microbiota
Hooper et al. (2002), O'Hara & Shanahan (2006), Ley et al.
(2006a), Xu et al.
(2007)
Table :‐ Modes of transmission of symbionts and their contribution to the fitness of the holobiont Helicobacter pylori and Ancestry
Epidimiological studies have shown that
transmission occurs predominantly within
families, mostly mother to child (Blomstergren et al. Gene. 2004)
and has been used as a window into
human migration
(Devi et al. BMC Genomics 2004)
POINT 3
Contribution of symbionts to the fitness of the holobiont
Holobiont microbiota
Microbial contribution
Aphid - Buchnera
Provides essential amino acids
Termite - Microbiota in hind gut
Nitrogen fixation, etc.
Anthropods – Wolbachia
Effects fertility
Squid light organ - Vibrio fischeri
Camouflage against predators
Cow rumen microbiota
Nutritional needs from cellulose
Human gut - microbiota
Stimulation of immune system
Protects against pathogens
Angiogenesis and muscle
thickness
Vitamin synthesis
Fiber breakdown
Fat storage
Land plants - Fungi
Supply minerals from soil
Legumes - Rhizobium
Nitrogen fixation
POINT 2
Examples of Modes of Transmission of Symbionts
Holbiont:Microbiota
Mode of transmission of
microorganism
Aphid - Buchnera (primary
endosymbiont)
Present in eggs
Termite - microbiota in hind
gut
Feces of adult fed to juveniles
Squid light organ - Vibrio
fischeri
From surrounding water
Bovine rumen - microbiota
Physical contact with parents;
Feeding on grass contaminated
with feces and sputum
Human gut – microbiota
Via physical contact, starting at
birth
Land plants - mycorrhiza fungi
Seeds on ground and vegetative
reproduction*
POINT 4
Contribution of Symbionts to Genetic Variation of the Holobiont
(raw material for evolution)
• Host variation
Sexual reproduction
Chromosome rearrangement
Mutation
• Microbiota – Same three plus:
Horizontal gene transfer
Acquisition of novel strains from environment
Microbial amplification
The hologenome can change rapidly under environmental stress,
such as a new food source, temperature increase or decrease, etc.
DISTINGUISHING FEATURES OF THE THEORY
1. Considers all of the diverse symbionts in the evolution of
the holobiont, not only the primary symbiont.
2. Fusion of neo-Darwinism and Lamarckism
Individual genomes evolve by mutation followed by natural
selection and genetic drift (neo-Darwinism)
Holobionts can also evolve by Lamarckian principles:
(a) Use and disuse (of microbes)
(b) Inheritance of acquired characteristics (microbes)
CONCLUSION
The hologenome theory of evolution posits that symbiont microorganisms play an important role in the evolution of animals and plants,
by helping them survive and multiply during times of environmental stress. This can allow the time necessary for the host genome to evolve.
Hologenome Theory of Evolution
Holobiont (host + all of its symbiotic biota) is the UNIT of selection in evolution, a dynamic entity
Genetic variation in Hologenome (host genome + genome of symbiont) can be transmitted to progeny
Variation in holobiont can also occur by:
amplification of existing microorganisms
acquisition of novel strains from environment
Regulated by
use and disuse of microbes
transmission of variations in hologenome to offspring (
Lizard example)