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Evolution > Eukaryote evolution + Mitochondria > Flashcards

Eukaryote evolution + Mitochondria Flashcards

1
Q

What innovations are currently boosting discoveries of new major groups and evolutionary relationships of eukaryotes?

A

DNA sequencing innovations such as metagenomics and single-cell genomics

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2
Q

What are metagenomics?

A

when all the DNA in an environment is sequenced and genomes are pieced together

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3
Q

What are single-cell genomics?

A

when single cells are isolated and genomes are sequenced from them

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4
Q

T or F: most eukaryotes are multicellular

A

false, most are single-celled

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5
Q

What are the major groups of eukaryotes? How many are there?

A

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

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6
Q

What is the major message regarding the new tree of eukaryotes?

A

it’s incredibly dynamic and is always changing

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7
Q

Which eukaryote branch/super group is the ancestral root?

A

we have no idea

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8
Q

What new supergroup has recently been discovered? (“the lions of the microbial world”)

A

Nibbleromonas quarantinus and Nebulomonas marisrubri

two microbial predators

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9
Q

How does Nibbleromonas quarantinus predate other protists?

A

by eating chunks from them

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10
Q

How does Nebulomonas marisrubri predate other protists?

A

consuming the entire organism

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11
Q

Where do the newly discovered Nibbleromonas quarantinus and Nebulomonas marisrubri sit in the phylogeny of eukaryotes?

A

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)

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12
Q

What was the first eukaryote?

A

unknown

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13
Q

Did prokaryotes or eukaryotes emerge first?

A

prokaryotes

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14
Q

What are some major eukaryotic genome features/innovations? (ie., differences between eukaryotes and prokaryotes)

A

nuclear membrane
organelles
cytoskeleton
introns and spliceosomes
mitosis and meiosis
larger gene number
larger cell size and cell number
etc.

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15
Q

What is the most accepted evolutionary model to explain the emergence of eukaryotes?

A

symbiogenic models

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16
Q

Describe the symbiogenic model and how it relates to the origin of eukaryotes

A

basically symbiosis between two prokaryotic cells to make the first eukaryotic cell

states that an “archaeal host cell” and an “alphaproteobacterial endosymbiont” merged

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17
Q

How are eukaryotes related to prokaryotes?

A

prokaryotes and Archaea are closely related and then there’s a very long branch (distance) between them and eukaryotes

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18
Q

T or F: eukaryotes evolved from Archaea

A

true

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19
Q

Why is it now accepted that eukaryotes emerged from archaeal lineages? what does this suggest?

A

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

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20
Q

Where were the archaea that are sisters of eukaryotes discovered? What kind of data was used to study these?

A

Loki’s castle, the hydrothermal vents between Norway and Greenland

metagenomic data used

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21
Q

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?

A

actin: a major structural protein previously though to only be in eukaryotic cells

this provides evidence that eukaryotes and archaea are related

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22
Q

Up until 2020, how was Archaea studied in the labs? what changed?

A

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

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23
Q

What is the evidence for the symbiogenic hypothesis of eukaryotic cell origin?

A

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

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24
Q

T or F: endosymbiosis is an incredibly important process in the evolution of eukaryotes

A

true

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25
Q

What gave rise to all eukaryotes via endosymbiosis?

A

mitochondria (alphaproteobacterial origin)

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26
Q

What gave rise to all photosynthetic organisms?

A

Chloroplast (cyanobacterial origin)

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27
Q

What was the result of endosymbiosis?

A

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)

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28
Q

What was the most important step in the evolution of eukaryotes?

A

acquiring the mitochondrion

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29
Q

T or F: some extant eukaryotes were descended from an ancestor without a mitochondrion

A

false! all extant eukaryotes, and all eukaryotes that have ever lived (as far as we know) have descended from an ancestor with a mitochondrion

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30
Q

What evidence suggests mitochondria originated from a bacterial symbiont (alphaproteobacterial origin)?

A

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

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31
Q

T or F: the mitochondrion has a separate genome from the nuclear genome

A

true

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32
Q

Describe the features of the mitochondrial genome

A

it’s usually circular
it’s non-recombining
it’s separate from the nuclear genome

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33
Q

What is the phylogenetic origin of the mitochondria?

A

bacterial

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34
Q

T or F: in all eukaryotes the mitochondrion contains its own genome

A

false, in some eukaryotes, not all this is true

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35
Q

Where are the genes of the mitochondrion encoded?

A

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

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36
Q

What does having genes from 3 different places suggest about the evolution of mitochondria?

A

it shows the symbiogenic origin - that mitochondria evolved from an alphaproteobacterial symbiont

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37
Q

How big are mitochondrial genomes?

A

very small (from 2-100 coding genes depending on the organism)

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38
Q

Why have mitochondria lost so many genes?

A

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

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39
Q

How many protein coding genes does the human mitochondrial genome have?

A

13

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40
Q

Where do all of the lost genes from the mitochondrial genome go?

A

they’re transferred to the nuclear genome

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41
Q

T or F: the mitochondrial genome is larger than the mitochondrial proteome?

A

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

42
Q

describe the state of the transfer of genes from the mitochondrial genome to the nuclear genome and vice versa

A

it’s dynamic and continual

functional and pseudogenes are continually transferred

43
Q

T or F: some eukaryotes have lost their mitochondrial genome

A

true

44
Q

What do the eukaryotes that have lost their mitochondrial genome have instead?

A

an organelle containing some genes of mitochondrial origin that have been transferred to the nuclear genome

45
Q

What type of organisms are eukaryotes without a mitochondrial genome?

A

they’re anaerobic and usually parasites/pathogens of medical significance

46
Q

What is an example of a eukaryote that has lost its mitochondrial genome? describe it

A

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

47
Q

How do mitosomes differ from mitochondria?

A

mitosomes are tiny organelles that exist in organisms without a proper mitochondrion to permit anaerobic respiration

48
Q

Are there any eukaryotes that have completely lost their mitochondrion (no genome, no organelle)?

A

only one so far

Monocercomonoides sp. - a microbe isolated from chinchilla guts

49
Q

Are there examples of eukaryotes that never had a mitochondrion? why/why not?

A

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

50
Q

What are the 4 major features of evolution in eukaryotes?

A

typically diploid

sexual reproduction and recombination

cellular and genomic complexity

wide range of population sizes - changes what type of evolutionary forces are at work

51
Q

How do the features of eukaryotic evolution compare to that of bacteria and archaea?

A

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)

52
Q

How might having a smaller population size, for example, as seen in multicellular eukaryotes, influence their evolution?

A

evolution will be more strongly influenced by genetic drift when the populations are smaller than by natural selection

53
Q

How might population size explain the differences in evolutionary patterns seen between prokaryotes and eukaryotes?

A

eukaryotes can have much smaller population sizes than prokaryotes, so whether there’s genetic drift or natural selection occurring, evolution will look different

54
Q

Does horizontal gene transfer occur in eukaryotes?

A

yes, but much less common than in prokaryotes

55
Q

What is an example of a time when horizontal gene transfer in eukaryotes is beneficial?

A

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

56
Q

What are the potential outcomes of horizontal gene transfer?

A

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

57
Q

What’s an example of horizontal gene transfer in eukaryotes? explain

A

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

58
Q

How have red aphids used horizontal gene transfer?

A

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

59
Q

Why is fungi likely the source for the horizontal acquisition of the carotenoid biosynthesis gene in red aphids?

A

it’s parsimonious

when looking at the phylogenetic relationship of carotenoid synthases (enzymes) in aphids, the closest relatives were fungi

60
Q

Describe eukaryotic genomes

A

big
filled with junk (a lot of redundancy and clutter, ie., noncoding DNA)

61
Q

Why is the eukaryotic genome referred to as filled with junk?

A

it has accumulated a lot of non-coding genes and is very large and redundant

62
Q

How does the eukaryotic genome compare to that of a prokaryotic genome?

A

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

63
Q

T or F: there’s a huge diversity in genome sizes within eukaryotes

A

true

64
Q

how is eukaryotic genome size related to organismal complexity? how does this compare to prokaryotic genomes and organismal complexity?

A

it’s not related in eukaryotes

in prokaryotes, the bigger genome = more genes, complexity of organism

65
Q

What is the C-value paradox or enigma?

A

C-value = content of nuclear DNA (ie., genome size)

the paradox = eukaryotic genome size is unrelated to the complexity of the organism

66
Q

Explain and give an example that supports the C-value paradox

A

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

67
Q

Which eukaryotes have the biggest genomes?

A

Amoeba (single-celled) has the largest

68
Q

Why are larger genomes often under-studied/why is there a bias in our understanding of eukaryotic genomes?

A

because the bigger the genome, the longer they take to sequence

69
Q

T or F: most DNA in eukaryotic genomes is noncoding vs most DNA in prokaryotic genomes is coding

A

true

70
Q

What kind of questions can we ask about the non-coding DNA in large eukaryotic genomes?

A

is it, or any of it, functional?
is it, or any of it, junk?

71
Q

How can we apply the Spandrels/Panglossian metaphor to the presence of non-coding DNA in large eukaryotic genomes?

A

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?

72
Q

What percentage of the human genome is coding genes? What percentage is transposable elements?

A

protein-coding genes = ~1.5%
transposable elements = ~44%

73
Q

What are transposable elements?

A

“jumping genes”

DNA sequences that break the Mendelian rules of inheritance and can move around the genome to be inherited more often

74
Q

What does the onion test tell us about using Spandrel/Panglossian ideology to explain the size of a eukaryotic genome?

A

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

75
Q

What is an NUMT?

A

A nuclear-mitochondrial transfer of DNA

basically, mitochondrial DNA (pseudogenes and non-coding genes) being transferred into the nuclear genome

76
Q

How common are human NUMTs? How big are they?

A

rare and the common ones are small

77
Q

How do NUMTs relate to the size of the human genome and it’s large proportion of non-coding genes?

A

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

78
Q

What was the result of the study on human NUMT and size?

A

high frequency of very rare NUMTs ranging in size but none were fixed

common NUMTs were small and some became fixed

79
Q

What are 3 key features of mitochondrial evolution (genes encoded in the mitochondrial genome)?

A

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

80
Q

What are the consequences in mitochondrial evolution of no recombination?

A

neighbours matter!

genetic hitchhiking

essentially reproducing asexually - can cause accumulation of deleterious mutations, especially in small population sizes

81
Q

T or F: animal mitochondrial DNA has high mutation rates

A

true

82
Q

Why does animal mitochondrial DNA (MtDNA) have very high mutation rates?

A
  • 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
83
Q

Why is animal MtDNA used as a marker for molecular evolution, ecology, and species identification?

A

because animal MtDNA has very high mutation rates

84
Q

T or F: Muller’s ratchet can apply to animal mtDNA - why/why not?

A

true because MtDNA does not undergo recombination

85
Q

What are the consequences of Muller’s ratchet/no recombination in MtDNA?

A

an accumulation of slightly deleterious mutations over time because there’s no way to recombine them out of the genome

overall decline in fitness

86
Q

What are two examples of human mitochondrial diseases?

A

Leber’s hereditary optic neuropathy (LHON) = blindness in male adolescents

Leigh syndrome = subacute necrotizing encephalomyelopathy

caused by mutations of mitochondrial genes

87
Q

How has LHON (a mitochondrial disease) been linked to founder effects? discuss the example of French Canadians / Les Filles du Roy

A

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

88
Q

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?

A

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

89
Q

What is the “Mother’s Curse”?

A

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

90
Q

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?

A

the patterns of evolution are different for the two genomes and heritability and gene expression are different

91
Q

Is there conflict between mitochondrial and nuclear genomes? if so, when does it occur?

A

sometimes, when they are not totally aligned

92
Q

What is an example of conflict between the mitochondrial and nuclear genomes?

A

cytoplasmic male sterility (CMS)

93
Q

How are mitochondrial genes passed to offspring in gymnosperms?

A

uniparentally through males

94
Q

What is CMS? what type of plants is it most common in?

A

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

95
Q

How do plants with CMS display conflict their between mitochondrial and nuclear genomes?

A

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

96
Q

When/why does conflict arise between the nuclear and mitochondrial genomes?

A

as a consequence of transmission because mitochondrial genes are inherited only through one sex, so the nuclear genome may not be aligned

97
Q

What is an example of a selfish mitochondria?

A

mitochondrial genomes or haplotypes that sterilize male reproductive parts

98
Q

What is a selfish mitochondria?

A

mitochondrial genomes or haplotypes that are transmitted more or unequally between sexes

like “jumping genes”

99
Q

Are selfish mitochondria more common in plants or animals?

A

plants - ex. Cytoplasmic male sterility

100
Q

Why would cytoplasmic male sterility be used as a tool by crop breeders?

A

to prevent self-fertilization, control crosses, and artificially select desired traits

Evolution (11 decks)

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