Evolution in our lives Flashcards
The relevance of evolutionary theory to our everyday lives:
Medicine
&
Agriculture
SARS-CoV2: Evolutionary biology’s key contributions:
1.Where did SARS-CoV2 come from?
Bats, pangolins snakes…?
Reason for pangolin concept was the similarity of the spike protein structure to pangolin viruses
Infact it is most likely to have evolved from Horseshoe bats
*SARS-CoV-2 most likely evolved in a bat
*However, it may have passed through other (as yet unsampled) hosts
Phylogenies are our best hypotheses from the information we have. - Future studies may reveal more details
SARS-CoV2: Evolutionary biology’s key contributions:
2.How and when did the pandemic unfold?
The first case in Europe: BavPat1
*Someone tested positive on 27 January, 2020 in Bavaria, Germany
*German officials contained an outbreak of 16 employees via rapid testing and isolation
*Initially, officials thought this outbreak was the source for the much larger outbreak in Lombardy, Italy (across the genome there was only 1 mutation difference between the two strains)
*BavPat1 is not likely to be the ancestor of Italy outbreak
*The Italian outbreak ancestor likely arrived from China in early February (Feb 7 on chart)
*The NYC outbreak ancestor likely arrived from Italy near the end of February
The first case in the U.S.: WA1
*A traveller from Wuhan arrived in Washington state on 15 Jan., experienced symptoms, and contacted health officials in Washington.
*Contact tracing and containment appeared to have prevented an outbreak.
Yet, toward the end of February, an outbreak was unfolding in Washington, leading officials to believe their containment measures did not work – however as seen below the WA1 variant was not infact the origin of the outbreak so they had infact contained this case.
“Assertions that these efforts had actually failed may have led to confusion about the utility of these approaches and contributed to a sense of the inevitability of the spread of the pandemic.”
Worobey et al 2020 (Science)
^This assumption allowed the pandemic to flare
SARS-CoV2: Evolutionary biology’s key contributions:
3.The nature of mutations: Are mutations bad?
Mutations are not always bad
SARS-CoV2 genome is continuously mutating, but:
*most mutations do not lead to differences in virulence (i.e., how damaging a virus is to human health)
*it mutates at the same rate as other coronaviruses (~10x slower than the influenza virus)
*these mutations allow us to understand how the pandemic unfolded by building phylogenetic trees
^as time progressed, variants of covid appeared to have functional differences – mutation resulting in spike protein change – this mutant had a faster growth rate and greater ability to enter human cells
Mutation favoured by pos selection? Or a surfing process happening due to a bottleneck?
SARS-CoV2 Mutations: Variants of concern (VOC)
Variants of concern (VOC)
*The tools of evolutionary biology have shed light on:
*Patterns of selection acting on different VOCs
*The evolutionary origins of the omicron VOC
*The early trajectory of the omicron wave
*Patterns of selection responsible for omicron
One way to look for evidence of selection at the level of individual genes is to consider the rate of non-synonymous vs synonymous change
dn/ds < 1 This suggests that deleterious non-synonymous changes are being removed by selection. We call this ‘purifying selection’.
dn/ds > 1 This indicates that positive selection has caused some amino-acid substitutions.
dn/ds = 1 This suggests that amino-acid substitutions have been neutral (or it could be a balance between positive and purifying selection).
Martin et al. 2021 tracked the ratio of non-synonymous vs synonymous substitutions early in the pandemic.
- Starting around November 2020, the number of sites that exhibit signatures of positive selection increased dramatically - What explains this? Exponential growth infecting a naïve population (humans had naïve immune systems initially) as resistance starts to develop this results in positive selection
Convergent evolution is compelling evidence for the action of natural selection across many VOC: VOC develop convergently, showing selection is a factor
The Omicron VOC
*First sequenced in mid-November 2021 in South Africa and Botswana
*Diversification models estimate a doubling time of 3.9 days
(far shorter than the delta VOC variant with a doubling time of ~11 days)
*Omicron was not closely related to other studied variants
*Researchers reconstructed point of origin (South Africa) and date of outbreak – although potentially this was introduced from a less observationally engaged country
* 15 amino acid substitutions in the receptor binding domain and higher level of human cell invasion
*Omicron overtook all other variants – positive selection resulting in Omicron being easier to spread
*Phylogenetic methods exist that can reveal signatures of positive selection acting on particular amino acids among different lineages in a phylogeny
*Analyses of non-synonymous mutations in omicron show that many mutation sites underwent positive selection and many of these were under purifying selection in other SARS-CoV-2 lineages
Some positively selected sites in omicron had an opposite pattern to other variants – other lineages of SARS CoV2 were neg selecting for the same sites
Why?
The Omicron VOC has a proximity of sites suggests positive epistasis (double mutation more effective than a single mutation)
Hypotheses:
*Incomplete surveillance – lack of detailed monitoring of the evolution of this strain
*Animal reservoir
*Chronic infections / immunocompromised patients – ability of genome to accumulate
SARS-CoV2: Evolutionary biology’s key contributions:
4.What other organisms may be susceptible?
SARS-CoV2 enters human cells via ACE2 receptor on cell membranes
primatologists checked amino acid complex of ACE2 in comparison to humans – to investigate how similar the proteins were in primates to the same receptor in humans.
Great apes and old world monkeys have the same ACE2 structure and so do some lemurs (with one mutation) therefore these animals were at risk of covid infection.
Evolution and agriculture
*Humans have been important selective agents, driving evolutionary changes in plants and animals that suit our needs.
*We can use tools from evolutionary biology to reconstruct the history of these changes.
*Ignoring evolutionary principles, e.g., by applying strong directional selection in the form of pesticides, can result in unintended, harmful consequences.
Example: the evolution of corn from teocinte
Popped Secret: The Mysterious Origin of Corn — HHMI BioInteractive Video:
https://www.youtube.com/watch?v=mBuYUb_mFXA
What reasons do scientists have for thinking that teosinte is the ancestor of maize?
Genetic similarity, able to hybridize, morphological similarity, transitional forms, ancient geographic distribution
How did scientists know where to look for evidence of the origins of maize?
Microfossils found on grinding stones which could be carbon dated using charcoal remains from nearby cooking areas.
Summary
1.Evolutionary thinking brings a new perspective to phenomena related to health, and may even point toward new medical treatments. Fever, for instance, is a highly conserved response to infection.
2.The tools of evolutionary biology have played an important role in understanding and responding to the ongoing SARS-CoV-2 pandemic
3.Agriculture is another prominent aspect of life thoroughly impacted by evolutionary biology
