Eukaryote evolution + Mitochondria Flashcards
What innovations are currently boosting discoveries of new major groups and evolutionary relationships of eukaryotes?
DNA sequencing innovations such as metagenomics and single-cell genomics
What are metagenomics?
when all the DNA in an environment is sequenced and genomes are pieced together
What are single-cell genomics?
when single cells are isolated and genomes are sequenced from them
T or F: most eukaryotes are multicellular
false, most are single-celled
What are the major groups of eukaryotes? How many are there?
it’s constantly being revised
but there’s a bunch?
Ex. Archaeplastida (plants, algae) Amorphea (animals, fungi)
most are single celled protists
unknown which groups are ancestral
What is the major message regarding the new tree of eukaryotes?
it’s incredibly dynamic and is always changing
Which eukaryote branch/super group is the ancestral root?
we have no idea
What new supergroup has recently been discovered? (“the lions of the microbial world”)
Nibbleromonas quarantinus and Nebulomonas marisrubri
two microbial predators
How does Nibbleromonas quarantinus predate other protists?
by eating chunks from them
How does Nebulomonas marisrubri predate other protists?
consuming the entire organism
Where do the newly discovered Nibbleromonas quarantinus and Nebulomonas marisrubri sit in the phylogeny of eukaryotes?
they’re in the super group Provora
but they are a separate and diverged lineage
even the two species are extremely distinct from one another (ex. as different as humans and yeast)
What was the first eukaryote?
unknown
Did prokaryotes or eukaryotes emerge first?
prokaryotes
What are some major eukaryotic genome features/innovations? (ie., differences between eukaryotes and prokaryotes)
nuclear membrane
organelles
cytoskeleton
introns and spliceosomes
mitosis and meiosis
larger gene number
larger cell size and cell number
etc.
What is the most accepted evolutionary model to explain the emergence of eukaryotes?
symbiogenic models
Describe the symbiogenic model and how it relates to the origin of eukaryotes
basically symbiosis between two prokaryotic cells to make the first eukaryotic cell
states that an “archaeal host cell” and an “alphaproteobacterial endosymbiont” merged
How are eukaryotes related to prokaryotes?
prokaryotes and Archaea are closely related and then there’s a very long branch (distance) between them and eukaryotes
T or F: eukaryotes evolved from Archaea
true
Why is it now accepted that eukaryotes emerged from archaeal lineages? what does this suggest?
newly discovered archaea (sisters of eukaryotes) genomes have features previously believed to be eukaryote-specific -
this suggests that maybe eukaryotic ancestor is more complex - challenging previous beliefs
Where were the archaea that are sisters of eukaryotes discovered? What kind of data was used to study these?
Loki’s castle, the hydrothermal vents between Norway and Greenland
metagenomic data used
What is an example of a protein that is characteristic of eukaryotes and was found in the newly discovered Loki archaea? what does this suggest?
actin: a major structural protein previously though to only be in eukaryotic cells
this provides evidence that eukaryotes and archaea are related
Up until 2020, how was Archaea studied in the labs? what changed?
just based on sequences
the first ‘Asgard’ archaea from deep sea vents was cultured over 13 years = it was GROWN in a lab, not just sequenced
What is the evidence for the symbiogenic hypothesis of eukaryotic cell origin?
There is likely a hybrid origin of genes from Archaea and Prokaryotes but this is hard to resolve because the two groups have very different ancestries
T or F: endosymbiosis is an incredibly important process in the evolution of eukaryotes
true
What gave rise to all eukaryotes via endosymbiosis?
mitochondria (alphaproteobacterial origin)
What gave rise to all photosynthetic organisms?
Chloroplast (cyanobacterial origin)
What was the result of endosymbiosis?
the acquisition of a ton of new genes and functions (acquired an entire new organism and its entire genome)
new metabolic potential
new niches become accessible (ex. photosynthesis, respiration)
What was the most important step in the evolution of eukaryotes?
acquiring the mitochondrion
T or F: some extant eukaryotes were descended from an ancestor without a mitochondrion
false! all extant eukaryotes, and all eukaryotes that have ever lived (as far as we know) have descended from an ancestor with a mitochondrion
What evidence suggests mitochondria originated from a bacterial symbiont (alphaproteobacterial origin)?
the mitochondrion has:
its own genetic material that is associated with bacteria
a separate genome (separate from the nuclear genome that exists in all cells) descended from bacteria
- it’s usually circular
- it’s non-recombining
features resemble ancient engulfment of a bacteria
has phylogenetic bacterial origin
T or F: the mitochondrion has a separate genome from the nuclear genome
true
Describe the features of the mitochondrial genome
it’s usually circular
it’s non-recombining
it’s separate from the nuclear genome
What is the phylogenetic origin of the mitochondria?
bacterial
T or F: in all eukaryotes the mitochondrion contains its own genome
false, in some eukaryotes, not all this is true
Where are the genes of the mitochondrion encoded?
either:
encoded in the mitochondrial genome and function in the mitochondrial genome
mitochondrial origin, but encoded in the nuclear genome and return to the mitochondrion to function
encoded in the nuclear genome and function in the mitochondrion
What does having genes from 3 different places suggest about the evolution of mitochondria?
it shows the symbiogenic origin - that mitochondria evolved from an alphaproteobacterial symbiont
How big are mitochondrial genomes?
very small (from 2-100 coding genes depending on the organism)
Why have mitochondria lost so many genes?
evolving from the free-living alphaproteobacteria, they are now contained within cells = they don’t require as many coding genes so they can afford to lose some
How many protein coding genes does the human mitochondrial genome have?
13
Where do all of the lost genes from the mitochondrial genome go?
they’re transferred to the nuclear genome
T or F: the mitochondrial genome is larger than the mitochondrial proteome?
false,
the proteome is larger than the genome because the proteome includes the genes that began in the nuclear genome and transferred to the mitochondrial genome
describe the state of the transfer of genes from the mitochondrial genome to the nuclear genome and vice versa
it’s dynamic and continual
functional and pseudogenes are continually transferred
T or F: some eukaryotes have lost their mitochondrial genome
true
What do the eukaryotes that have lost their mitochondrial genome have instead?
an organelle containing some genes of mitochondrial origin that have been transferred to the nuclear genome
What type of organisms are eukaryotes without a mitochondrial genome?
they’re anaerobic and usually parasites/pathogens of medical significance
What is an example of a eukaryote that has lost its mitochondrial genome? describe it
Giardia lamblia - a single-celled, anaerobic protist that causes beaver fever
it has a nuclear genome with genes of mitochondrial origin that are concentrated in small organelles called mitosomes
How do mitosomes differ from mitochondria?
mitosomes are tiny organelles that exist in organisms without a proper mitochondrion to permit anaerobic respiration
Are there any eukaryotes that have completely lost their mitochondrion (no genome, no organelle)?
only one so far
Monocercomonoides sp. - a microbe isolated from chinchilla guts
Are there examples of eukaryotes that never had a mitochondrion? why/why not?
Not yet. Why not?
maybe they haven’t been discovered yet
maybe they went extinct and haven’t been preserved well in the fossil record
maybe they never existed because the acquisition of a mitochondria is the defining feature of eukaryotes
What are the 4 major features of evolution in eukaryotes?
typically diploid
sexual reproduction and recombination
cellular and genomic complexity
wide range of population sizes - changes what type of evolutionary forces are at work
How do the features of eukaryotic evolution compare to that of bacteria and archaea?
typically, eukaryotes are diploid, whereas bacteria are haploid
eukaryotes reproduce sexually and have recombination, whereas bacteria reproduce asexually (but can still have recombination events)
eukaryotes have larger and more complex genomes and more complex cells (ex. mitochondrial genome and nuclear genome)
eukaryotic populations can range a lot in size, whereas generally, prokaryotic populations are all very large (natural selection is main force)
How might having a smaller population size, for example, as seen in multicellular eukaryotes, influence their evolution?
evolution will be more strongly influenced by genetic drift when the populations are smaller than by natural selection
How might population size explain the differences in evolutionary patterns seen between prokaryotes and eukaryotes?
eukaryotes can have much smaller population sizes than prokaryotes, so whether there’s genetic drift or natural selection occurring, evolution will look different
Does horizontal gene transfer occur in eukaryotes?
yes, but much less common than in prokaryotes
What is an example of a time when horizontal gene transfer in eukaryotes is beneficial?
it may be a good way to adapt to a new ecological niche by picking up genes that are already adapted to the ecology, the population will save evolutionary time adapting to the environment
What are the potential outcomes of horizontal gene transfer?
a new piece of DNA has entered the germline…
it can:
be expressed
not be expressed
be passed on to offspring and spread
not be spread
become fixed
become lost
What’s an example of horizontal gene transfer in eukaryotes? explain
red aphids - clearly contain carotenoids (red pigmentation)
animals have lost the genes to synthesize their own carotenoids, but carotenoids are essential so they must be acquired through diet
the aphid diet of phloem, however, does not contain carotenoids
studies have shown now that the red aphids have re-acquired the carotenoid biosynthesis genes via horizontal transfer from fungi
How have red aphids used horizontal gene transfer?
all animals have lost the carotenoid biosynthesis genes because they’ve been able to get carotenoids from their diet
red aphids do not get carotenoids from diet, but have re-acquired these carotenoid synthesizing genes by integrating them into their genome FROM FUNGI (horizontal gene transfer), expressing them, and passing them on to offspring = these genes are being maintained by vertical gene transfer
Why is fungi likely the source for the horizontal acquisition of the carotenoid biosynthesis gene in red aphids?
it’s parsimonious
when looking at the phylogenetic relationship of carotenoid synthases (enzymes) in aphids, the closest relatives were fungi
Describe eukaryotic genomes
big
filled with junk (a lot of redundancy and clutter, ie., noncoding DNA)
Why is the eukaryotic genome referred to as filled with junk?
it has accumulated a lot of non-coding genes and is very large and redundant
How does the eukaryotic genome compare to that of a prokaryotic genome?
eukaryotic genomes are large and contain a lot of redunancy and non-coding genes, whereas prokaryotic genomes tend to be streamlined, small, consisting of mostly coding genes and little non-coding
T or F: there’s a huge diversity in genome sizes within eukaryotes
true
how is eukaryotic genome size related to organismal complexity? how does this compare to prokaryotic genomes and organismal complexity?
it’s not related in eukaryotes
in prokaryotes, the bigger genome = more genes, complexity of organism
What is the C-value paradox or enigma?
C-value = content of nuclear DNA (ie., genome size)
the paradox = eukaryotic genome size is unrelated to the complexity of the organism
Explain and give an example that supports the C-value paradox
related organisms, even from the same species, may have differences in genomic sizes
ex. D. melanogaster flies from one location have genomes that range from 169.7-192.8 Mbases of DNA == huge variation in sizes within a population of the same species
Which eukaryotes have the biggest genomes?
Amoeba (single-celled) has the largest
Why are larger genomes often under-studied/why is there a bias in our understanding of eukaryotic genomes?
because the bigger the genome, the longer they take to sequence
T or F: most DNA in eukaryotic genomes is noncoding vs most DNA in prokaryotic genomes is coding
true
What kind of questions can we ask about the non-coding DNA in large eukaryotic genomes?
is it, or any of it, functional?
is it, or any of it, junk?
How can we apply the Spandrels/Panglossian metaphor to the presence of non-coding DNA in large eukaryotic genomes?
eukaryotic genomes have large amounts of non-coding DNA - is it there for a reason? Is it because of natural selection?
we’ve seen in prokaryotes that natural selection favours a smaller genome size, so no, these genes are not there for a reason - likely just no pressure to get rid of them/have a streamlined genome?
What percentage of the human genome is coding genes? What percentage is transposable elements?
protein-coding genes = ~1.5%
transposable elements = ~44%
What are transposable elements?
“jumping genes”
DNA sequences that break the Mendelian rules of inheritance and can move around the genome to be inherited more often
What does the onion test tell us about using Spandrel/Panglossian ideology to explain the size of a eukaryotic genome?
onions have a genome that’s 5x larger than the human genome…
basically, does every gene in a genome actually have to be assigned a function/reason to be there? No = not everything is there for a reason
What is an NUMT?
A nuclear-mitochondrial transfer of DNA
basically, mitochondrial DNA (pseudogenes and non-coding genes) being transferred into the nuclear genome
How common are human NUMTs? How big are they?
rare and the common ones are small
How do NUMTs relate to the size of the human genome and it’s large proportion of non-coding genes?
the mitochondria are continuously transferring pseudogenes and non-coding genes out to the nuclear genome to streamline the mitochondrial genome
this increases the size of the nuclear genome and its proportion of non-coding DNA
What was the result of the study on human NUMT and size?
high frequency of very rare NUMTs ranging in size but none were fixed
common NUMTs were small and some became fixed
What are 3 key features of mitochondrial evolution (genes encoded in the mitochondrial genome)?
mitochondrial genes have:
uniparental inheritance (usually from mother)
different mutation rates (ex. high in animals)
no recombination (a feature from bacterial origin) = mitochondrial genome is circular like bacteria and is inherited as one piece
What are the consequences in mitochondrial evolution of no recombination?
neighbours matter!
genetic hitchhiking
essentially reproducing asexually - can cause accumulation of deleterious mutations, especially in small population sizes
T or F: animal mitochondrial DNA has high mutation rates
true
Why does animal mitochondrial DNA (MtDNA) have very high mutation rates?
- mitochondria is the site of respiration = high levels of free oxygen radicals (mutagenic)
- replication of non-dividing cells (errors increased)
- some pathways for DNA repair are absent
Why is animal MtDNA used as a marker for molecular evolution, ecology, and species identification?
because animal MtDNA has very high mutation rates
T or F: Muller’s ratchet can apply to animal mtDNA - why/why not?
true because MtDNA does not undergo recombination
What are the consequences of Muller’s ratchet/no recombination in MtDNA?
an accumulation of slightly deleterious mutations over time because there’s no way to recombine them out of the genome
overall decline in fitness
What are two examples of human mitochondrial diseases?
Leber’s hereditary optic neuropathy (LHON) = blindness in male adolescents
Leigh syndrome = subacute necrotizing encephalomyelopathy
caused by mutations of mitochondrial genes
How has LHON (a mitochondrial disease) been linked to founder effects? discuss the example of French Canadians / Les Filles du Roy
the relatively high frequency of LHON amongst French Canadians has been traced back to a single woman who was sent as part of a founding population to Nouvelle-France (Quebec City) in the 1600s
she was a carrier of the mitochondrial mutation and passed it on to her descendants
the genes from the founding population are still influencing the current population = founder effect
what did the study of LHON in French Canadians show regarding the fitness of males vs. females in terms of survival past the 1st year? what does this mean for the heritability of the mutation?
females showed no differences in survival
males with the mitochondrial mutation haplotype for LHON had significantly lower fitness and reduced survival past 1 year than males that did not have the haplotype and than females
= the mutation is mitochondrial and only inherited from a carrier mother by offspring and expressed only in males
What is the “Mother’s Curse”?
mitochondrial mutations that are passed through females but don’t have deleterious outcomes will not be removed in females and will be then passed on to sons in which it may be deleterious
What does the Mother’s Curse, Les Filles du Roy, and LHON haplotype tell us about the patterns of evolution for mitochondria vs. nuclear genomes?
the patterns of evolution are different for the two genomes and heritability and gene expression are different
Is there conflict between mitochondrial and nuclear genomes? if so, when does it occur?
sometimes, when they are not totally aligned
What is an example of conflict between the mitochondrial and nuclear genomes?
cytoplasmic male sterility (CMS)
How are mitochondrial genes passed to offspring in gymnosperms?
uniparentally through males
What is CMS? what type of plants is it most common in?
a mitochondrial trait that sterilizes male flowers
it’s common in plants that produce male and female flowers (especially in agricultural crops)
used as a way to prevent self-fertilization
How do plants with CMS display conflict their between mitochondrial and nuclear genomes?
CMS is a mitochondrial trait that sterilizes male flowers
in flowers that produce both male and female plants, and that have sterilized male flowers because of CMS, the nuclear genome will act to restore fertility of male flower = co-evolution
When/why does conflict arise between the nuclear and mitochondrial genomes?
as a consequence of transmission because mitochondrial genes are inherited only through one sex, so the nuclear genome may not be aligned
What is an example of a selfish mitochondria?
mitochondrial genomes or haplotypes that sterilize male reproductive parts
What is a selfish mitochondria?
mitochondrial genomes or haplotypes that are transmitted more or unequally between sexes
like “jumping genes”
Are selfish mitochondria more common in plants or animals?
plants - ex. Cytoplasmic male sterility
Why would cytoplasmic male sterility be used as a tool by crop breeders?
to prevent self-fertilization, control crosses, and artificially select desired traits
