The origin of Eukaryotes
All complex life in undeniably eukaryotic – multicellular organisms etc.
But did it arise from chance or necessity? – an inevitable consequence of natural
selection or due to opportunities from chance events (eg. Impact of asteroids, analogy –
the wipeout of dinosaurs gave mammals a chance to dominate)
A Origin of eukaryotic cells was a single event
In the 4 billion years of evolution – the common ancestor of eukaryotic cells arose
only once
Common traits of this LECA include: two step meiosis, syngamy, conserved positions
of introns, nuclear pore complex structure, phagocytosis, separation of
transcription and translation, cytoskeleton
- It is unlikely that all of these traits arose from lateral gene transfer or from
convergent evolution
- The most parsimonious explanation is that eukaryotic cells share common ancestry
- BUT – evidence for this is surprisingly elusive
Common ancestry assumes that all “protoeukaryotic lines” that gave rise to
eukaryotes would have been driven to extinction by eukaryotes dominating all the
niches of their ancestors
This cannot be addressed phylogenetically – all evidence of proto-eukaryotes lost,
or the existence of such lines cannot be proven
No evolutionary intermediates between prokaryotes and LECA
- Furthermore, the assumption of prokaryotes giving rise to more complex eukaryotes
is problematic in this sense – eukaryotes would have driven prokaryotes to
extinction (or major groups) but this hasn’t occurred
- Parallel niches have been established – archaea originally thought to only exist in
extreme environments also found in temperate oceans, picoeukaryotes compete
directly with prokaryotes in various environments
- If eukaryotic traits evolved step by step – each step has a selective advantage –
why did none evolve in prokaryotes?
- MUST BE CHALLENGED
B Eukaryotic Traits and Root of the Eukaryotic Tree of Life
Explosive radiation – short branch lengths between super groups near the root of
the tree – suggestive of a bottleneck
Phylogenetics does not tell much about how eukaryotic traits have arose
Root of the eukaryotic tree of life remains unknown – largely because numerous
characters conserved among eukaryotes lack homologs in bacteria and archaea –
difficult to find appropriate outgroup sequences for most molecular studies (Katz.
2012)
5-6 eukaryotic supergroups, unicellular groups contain most genetic diversity
(Koonin, 2010)
Best supported clade is the Opistokonta uniting animals, fungi and microbial
relatives – supported by numerous molecular characters
Excavata – Trichomonas and Giardia – elevated rates of evolution across their
, genomes, likely contributing to instability of Excavata
C Prokaryotes show no proclivity to evolve greater morphological complexity
3 billion year old microfossils show barely any morphological difference to modern
prokaryotes
Prokaryotes do possess some eukaryotic traits: introns and exons, linear
chromosomes, endosymbionts, cytoskeleton, DNA recombination
Bacteria compete mainly on replication speed
- Transcription and translation is linked
- Small cell volumes (usually 1-2µm diameter)
- Small genome sizes (up to 12Mb, eukaryotes up to 100 000Mb)
- Little non-coding DNA – almost no introns
- Operon structure of genes – multiple genes per transcription factor
Bacteria have DNA replication that is slower than cell division
- In bacteria a second round of DNA replication begins before DNA replication is
complete
- Both DNA replication and cell division are linked to the ATP/ADP ratio in bacteria
Orisomes create small bubble of unwound DNA in the replication origin, which
recruits the helicase – binding of DnaA unwinds the chromosomal replication origin
oriC
DnaA binds both nucleotides with equal avidity but only ATP-DnaA initates
replication
Several thousand molecules of DnaA which sense the ratio – ATP can produce ATP-
DnaA from ADP-DnaA (replication can only begin when cellular ATP/ADP ratio is
high)
What they lack is the simultaneous accumulation of these traits in one organism
complete with internal compartmentalisation and intracellular transport
Prokaryotes may be streamlined by selection to not evolve complexity – need small
genomes, remove unnecessary genes in favour of rapid replication, obtaining new
genes from metagenome via lateral gene transfer
- Environmental metagenomes
LECA was therefore a very complex cell, unknown why eukaryotes not streamlined
the same way as prokaryotes : numerous compartments, organelles, at least 3000
new gene families
D Cell fusions best explain the accumulation of metabolic traits
Evolutionary trees suggest that right after LECA appeared there was an immediate
radiation of forms and diversity – branching without a trunk
LECA was recognisably eukaryotic – there were no intermediates lacking one trait
over another, over evolutionary distance the tree of life
In order to achieve this ubiquitous acquisition of traits – evolution of eukaryotes
was rapid in a small population (if it was slow and in large – speciation would’ve
occurred)
, - Genomic evidence suggest that the
eukaryotic cell arose via a stochastic and
very rare endosymbiosis between 2
prokaryotes
- Based on 29 concatenated sequences of
highly conserved informational proteins and 63 concatenated protein sequences,
RNA trees with wider sampling arrive at the conclusion that the host cell was an
Archaeon (Williams, 2012)
- Suggests that there is really only 2 primary domains of life (Eocyte hypothesis)
Also likely that there was a tight bottleneck at the origin of eukaryotes
Environmental bottleneck – only best adapted group survives:
a) oxygen (GOE 2.4 bya – but some metazoans – Loriciferans strictly anaerobic)
b) temperature – oceans 20 – 30oC by 4 billion years anyway
Snowball Earth – non-global glaciations common through Earth history
c) Nutrient starvation – shortage of nitrate Fe, Mo, phosphate forces cooperation
between organisms – no evidence of endosymbiosis
Prediction: Forms arising later must have been outcompeted to extinction by eukaryotic
cells
There should not been any evolutionary and ecological intermediates
- 1980’s Cavalier-Smith identified Archezoa – diverse group of primitive
amitochondriate eukaryotes – this is false
- Morphological and genetic studies support that all archezoa did possess
mitochondria at some point but lost them through evolution to hydrogenosomes and
mitosomes – around 1000 species of protest lack mitochondria by reductive
evolution
- They are ecological intermediates which underwent reductive evolution from ore
complex eukaryotic ancestors
Giardia have mitosomes discovered by Tovar et al. (2003) which are vestigial
mitochondria – disovered when proteins that make iron-sulphur clusters in
mitochondria also present in Giardia
Furthermore – Giardia and Trichomonas known to be nested in clades of
mitochondria-containing lineages
Biological bottleneck – the acquisition of mitochondria (more likely?)
- Raises another question if the restrictive bottlneck is true – what about bacterial
structure that stopped them from evolving greater complexity?
- The answer – mitochondria (acquisition of mitochondria and origin of the eukaryotic
cell could have been the same event)
E Acquisition of mitochondria-transformed selection pressures acting on a
prokaryotic host cell
- Mitochondria were acquired prior to divergence of extant eukaryotes
- Acquisition of mitochondria was an early event – endosymbiosis supported by
genome wide phylogenetic studies
All complex life in undeniably eukaryotic – multicellular organisms etc.
But did it arise from chance or necessity? – an inevitable consequence of natural
selection or due to opportunities from chance events (eg. Impact of asteroids, analogy –
the wipeout of dinosaurs gave mammals a chance to dominate)
A Origin of eukaryotic cells was a single event
In the 4 billion years of evolution – the common ancestor of eukaryotic cells arose
only once
Common traits of this LECA include: two step meiosis, syngamy, conserved positions
of introns, nuclear pore complex structure, phagocytosis, separation of
transcription and translation, cytoskeleton
- It is unlikely that all of these traits arose from lateral gene transfer or from
convergent evolution
- The most parsimonious explanation is that eukaryotic cells share common ancestry
- BUT – evidence for this is surprisingly elusive
Common ancestry assumes that all “protoeukaryotic lines” that gave rise to
eukaryotes would have been driven to extinction by eukaryotes dominating all the
niches of their ancestors
This cannot be addressed phylogenetically – all evidence of proto-eukaryotes lost,
or the existence of such lines cannot be proven
No evolutionary intermediates between prokaryotes and LECA
- Furthermore, the assumption of prokaryotes giving rise to more complex eukaryotes
is problematic in this sense – eukaryotes would have driven prokaryotes to
extinction (or major groups) but this hasn’t occurred
- Parallel niches have been established – archaea originally thought to only exist in
extreme environments also found in temperate oceans, picoeukaryotes compete
directly with prokaryotes in various environments
- If eukaryotic traits evolved step by step – each step has a selective advantage –
why did none evolve in prokaryotes?
- MUST BE CHALLENGED
B Eukaryotic Traits and Root of the Eukaryotic Tree of Life
Explosive radiation – short branch lengths between super groups near the root of
the tree – suggestive of a bottleneck
Phylogenetics does not tell much about how eukaryotic traits have arose
Root of the eukaryotic tree of life remains unknown – largely because numerous
characters conserved among eukaryotes lack homologs in bacteria and archaea –
difficult to find appropriate outgroup sequences for most molecular studies (Katz.
2012)
5-6 eukaryotic supergroups, unicellular groups contain most genetic diversity
(Koonin, 2010)
Best supported clade is the Opistokonta uniting animals, fungi and microbial
relatives – supported by numerous molecular characters
Excavata – Trichomonas and Giardia – elevated rates of evolution across their
, genomes, likely contributing to instability of Excavata
C Prokaryotes show no proclivity to evolve greater morphological complexity
3 billion year old microfossils show barely any morphological difference to modern
prokaryotes
Prokaryotes do possess some eukaryotic traits: introns and exons, linear
chromosomes, endosymbionts, cytoskeleton, DNA recombination
Bacteria compete mainly on replication speed
- Transcription and translation is linked
- Small cell volumes (usually 1-2µm diameter)
- Small genome sizes (up to 12Mb, eukaryotes up to 100 000Mb)
- Little non-coding DNA – almost no introns
- Operon structure of genes – multiple genes per transcription factor
Bacteria have DNA replication that is slower than cell division
- In bacteria a second round of DNA replication begins before DNA replication is
complete
- Both DNA replication and cell division are linked to the ATP/ADP ratio in bacteria
Orisomes create small bubble of unwound DNA in the replication origin, which
recruits the helicase – binding of DnaA unwinds the chromosomal replication origin
oriC
DnaA binds both nucleotides with equal avidity but only ATP-DnaA initates
replication
Several thousand molecules of DnaA which sense the ratio – ATP can produce ATP-
DnaA from ADP-DnaA (replication can only begin when cellular ATP/ADP ratio is
high)
What they lack is the simultaneous accumulation of these traits in one organism
complete with internal compartmentalisation and intracellular transport
Prokaryotes may be streamlined by selection to not evolve complexity – need small
genomes, remove unnecessary genes in favour of rapid replication, obtaining new
genes from metagenome via lateral gene transfer
- Environmental metagenomes
LECA was therefore a very complex cell, unknown why eukaryotes not streamlined
the same way as prokaryotes : numerous compartments, organelles, at least 3000
new gene families
D Cell fusions best explain the accumulation of metabolic traits
Evolutionary trees suggest that right after LECA appeared there was an immediate
radiation of forms and diversity – branching without a trunk
LECA was recognisably eukaryotic – there were no intermediates lacking one trait
over another, over evolutionary distance the tree of life
In order to achieve this ubiquitous acquisition of traits – evolution of eukaryotes
was rapid in a small population (if it was slow and in large – speciation would’ve
occurred)
, - Genomic evidence suggest that the
eukaryotic cell arose via a stochastic and
very rare endosymbiosis between 2
prokaryotes
- Based on 29 concatenated sequences of
highly conserved informational proteins and 63 concatenated protein sequences,
RNA trees with wider sampling arrive at the conclusion that the host cell was an
Archaeon (Williams, 2012)
- Suggests that there is really only 2 primary domains of life (Eocyte hypothesis)
Also likely that there was a tight bottleneck at the origin of eukaryotes
Environmental bottleneck – only best adapted group survives:
a) oxygen (GOE 2.4 bya – but some metazoans – Loriciferans strictly anaerobic)
b) temperature – oceans 20 – 30oC by 4 billion years anyway
Snowball Earth – non-global glaciations common through Earth history
c) Nutrient starvation – shortage of nitrate Fe, Mo, phosphate forces cooperation
between organisms – no evidence of endosymbiosis
Prediction: Forms arising later must have been outcompeted to extinction by eukaryotic
cells
There should not been any evolutionary and ecological intermediates
- 1980’s Cavalier-Smith identified Archezoa – diverse group of primitive
amitochondriate eukaryotes – this is false
- Morphological and genetic studies support that all archezoa did possess
mitochondria at some point but lost them through evolution to hydrogenosomes and
mitosomes – around 1000 species of protest lack mitochondria by reductive
evolution
- They are ecological intermediates which underwent reductive evolution from ore
complex eukaryotic ancestors
Giardia have mitosomes discovered by Tovar et al. (2003) which are vestigial
mitochondria – disovered when proteins that make iron-sulphur clusters in
mitochondria also present in Giardia
Furthermore – Giardia and Trichomonas known to be nested in clades of
mitochondria-containing lineages
Biological bottleneck – the acquisition of mitochondria (more likely?)
- Raises another question if the restrictive bottlneck is true – what about bacterial
structure that stopped them from evolving greater complexity?
- The answer – mitochondria (acquisition of mitochondria and origin of the eukaryotic
cell could have been the same event)
E Acquisition of mitochondria-transformed selection pressures acting on a
prokaryotic host cell
- Mitochondria were acquired prior to divergence of extant eukaryotes
- Acquisition of mitochondria was an early event – endosymbiosis supported by
genome wide phylogenetic studies
