Genomic changes in the extinction process, museomics and aDNA in selection Flashcards
(30 cards)
Late Pleistocene was a time of many extinctions, invasions and dramatic population declines within still existing species. What was the cause?
One factor alone cannot explain the numerous extinctions. Climate and human interference are indicated in many extinctions, where a combination of the two is likely, for some species it seems like one or the other had a greater impact, for example mammoths on the mainland looks like they were hit hard by hunting, while climate was a cause to unstable populations but not likely to be the last straw. Data suggest the opposite for rhinos. It is important to factor in that responses to environmental fluctuations are species-specific. All in all, it’s hard explain the cause to the final straw, as its hard to capture the last moments before extinction.
What data can we use to better track & understand extinctions?
- The fossil record is great for detecting extinctions, but the causes is much harder.
- Morphological & modern genomics data = incomplete picture
- mtDNA for short markers were used in the beginning of the field, but today we have better methods that are still improving.
Overall, More data = higher resolution. More detail on genomic processes at play and more data that can be used to study long-term population histories.
The number of known species increasing, why?
Taxonomical oversplitting/inflation has been a subject of debate for a while now. Most of it is not due to new discoveries, but rather subspecies that are now considered new species and changes to the species concept. Much of it is due to conservation interests (higher priority to save a species than a subspecies).
There are three modes of decline in the context of extinctions, which and what is the typical cause?
- Sudden decline: previously stable population, until a point of very rapid population decline (few generations). This typically occurs due to extreme changes in the environment and Human interference.
- Gradual decline: Slowly approaching extinction, easier to detect with genetic data as there is no distinct point to find.
- Terminal refugium decline: Severe population bottleneck with only a portion of population left, but in spite of this the population survives for thousands of years more.
Give two examples of species that underwent sudden decline before extinction.
- The Dodo: a flightless bird that was endemic to the island Mauritius. Extinct in 1662 due to human hunting.
- Tasmanian tiger (Thylacine): a marsupial carnivorous wolf native to Australia. Extinct in 1936 on Tasmania but on mainland ~3,500 kya, probably due to human hunting, out competition by Dingo’s and climate change.
- Passenger pigeons: Last individual died 1914, but in 1800’s there were billions of individuals that carried letters and communications. After not being needed anymore, they were considered a pest, were overhunted as cheap meat and suffered from habitat loss.
Why are endemic island populations so vulnerable to sudden decline?
Endemic island populations are generally small population sizes, low genetic diversity due to founder effects and are adapted to an environment highly distinct from mainland. Because of this they are vulnerable to sudden decline through extensive overhunting, introduction of predators
or diseases all of which they are not adapted to.
The brown bears versus cave bears comparison is classic in terms of gradual decline. Why?
Cave bears and brown bears have very similar life history traits and shared habitats, but ~50 000 kya the cave bear population started to decline to then go extinct ~24 000 kya, whereas the brown bear population remained steady. So what affected cave bears negatively but left brown bears undisturbed? There are many theories, but the population decline started long before the cooling of the climate in the LGM, so that is not it. Theories:
- Cave bears were predominantly herbivorous so they were potentially more sensitive to climate changes causing vegetation shifts.
- Hibernation strategies: It’s possible that the cave bears were outcompeted by humans in terms of caves to hibernate in. Cave bears more reliant on caves for hibernation than brown bears?
- Even though population decline started before the cooling that led up to LGM, it could have led to problems though other routes that led to them struggling even more when the cooling started.
Provide an example of a species extinction that followed a terminal refugium decline pattern.
The best example of a terminal refugium decline is the woolly mammoth. They had been around since ~700 kya, and was super abundant during the LGM. Then ~12 000 ya, around the time of the start of Holocene (interglacial) very few remained and at 10 000 ya, they were extinct on the mainland likely bc of warming climate and overhunting, but survived isolated on what today is St Paul and Wrangel island in the arctic ocean (but were highlands during glacial period) for thousands of years. On St Paul island they went extinct 5,500 ya - probably due to lack of freshwater. On Wrangel island they went extinct ~ 4 000 ya (after 6000 years of isolation) on an island with a carrying capacity of 149-819 individuals. The last samples showed high levels of inbreeding (up to 28-fold increase in FROH) and accumulation of harmful mutations. In the end, they had high genetic debt = not large enough population to remove harmful mutations and as they were last extant pop, there was no possibilities for rescue.
What are the genetic consequences of population declines?
When the population gets small, there is an increase ion inbreeding and random genetic drift (loss of alleles stochastically) which both lead to loss of genetic variation, which in turn leads to reduction in individual fitness (due to increased homozygosity in recessive deleterious alleles) and adaptability (Strong genetic drift can lead to fixation of deleterious alleles despite natural selection - reduced fitness). Which can cause lower reproduction and higher mortality (purging of deleterious alleles), which leads to an even smaller population and this goes on an on in a spiral/vortex and can lead to extinction.
Give one example of a tool that can be used to study genomics of extinction.
GenErode - A bioinformatics pipeline to study genomic erosion.
How is studying extinctions relevant today?
By studying extinctions, endangered species, and small populations that have persisted in stable populations for thousands of years we can inform the present and the future in conservation efforts. Can species adapt during the extinction process? Are they in terminal refugia? Have they escaped extinction due to species-specific behavioral strategies? Genetically adapted to a small population size during the decline?
There is still much we don’t know, but we are getting there!
What is the Anthropocene?
The Anthropocene is a Proposed geological epoch dating from the commencement of significant human impact on Earth ~1950. in 2024 it was rejected as a formal unit of geological time, but is still a valuable descriptor of human impact on the Earth system for the public at large. This period of human impact has come with many consequences:
- Wildlife has been declining drastically since the 1970s
- in the last 200 years, the population sizes of mammals have decreased by 38%, amphibians 81% and marine life populations have declined with 36% - alarming as small populations are more vulnerable to extinction, both through genetic processes but also stochastic events.
Explain the term “Inbreeding depression”.
Small populations leads to increased inbreeding, which in turn leads to reduced heterozygosity and is unmasking deleterious recessive alleles, which leads to the the reduced fitness (survival and reproduction) of offspring = inbreeding depression - resulting in even smaller populations and so on.
Explain the term “Mutational meltdown”
Mutational meltdown is the accumulation of deleterious alleles that comes from small populations being subject to genetic drift and “relaxed” purifying selection.
What is conservation genomics?
Conservation genomics applies genomic tools and data analysis to aid in the preservation of biodiversity and the viability of populations.
The main question in conservation genomics is: Can we tell if a species is endangered by looking at its genome? Can we?
Not really, we can sequence the genomes of possibly endangered species, check heterozygosity and sort then as endangered if high, and not endangered if low, but this really doesn’t say much. A way to find the most severe cases is to sequence a bunch of species, compare the heterozygosity and generate a priority list of highest to lowest which can be useful in where to place conservation efforts. However, high heterozygosity and populations size is only weakly correlated, and heterozygosity and red list status in not correlated at all - so this is clearly not enough.
So, if interspecific comparisons of contemporary genomic erosion indices are poor proxies for conservation status of wild organisms, what can we use instead?
An alternative strategy for finding out if a species in endangered is using conservation paleogenomics, which also takes diverse population histories (i.e. ancient bottlenecks), species-specific life history traits and reproductive strategies into account.
How is conservation paleogenomics done in practice? what is the resulting data useful for?
In conservation paleogenomics, historical samples function as a baseline (H0) and is used to quantify “delta indices” or genomic erosion in modern samples (h1): Δh = h1-h0. This Δh value can be used to quantify genome-wide heterozygosity, inbreeding coefficient, mutational load, or structural variants (i.e. deletions).
This temporally sampled data is then useful for:
- Validating theoretical predictions about small populations (i.e. woolly mammoth)
- Provide comparable trends for modern-day endangered populations (gorillas, Sumatran rhinoceros, kakapo).
- Monitoring and informing decisions regarding red list status and conservation methods.
What is museomics?
Museomics is the study of genomic data obtained from ancient DNA (aDNA) and historic DNA (hDNA) specimens in museum collections. Natural history museums are vaults for DNA, that include billions of specimens including bones, pelts, tissues in wet collections, herbaria, dry pinned insects, etc. This was a previously untapped source of aDNA and recent advances in next-generation sequencing technology, and subsequent development of techniques for preparing and sequencing historical DNA, have recently made working with collection specimens an attractive option - but still in it’s infancy!
What are the challenges with museomics?
The challenges with museomics are similar to aDNA studies:
- Destructive sampling: Museums collect samples to display and some are rare, so finding the least destructive method of sampling is key. Museum policies still apply, so they can say no.
- Contamination: Varies a lot in museum specimens, handling and storing not ideal: most is not kept cold or sterile, and some samples are kept in batches so DNA from one can leech into others. Sources of contamination includes: human DNA, pests, fungi, other unknown sources.
- DNA fragmentation: aside from DNA fragmentation due to age, some chemicals used to minimize contamination and preservation can cause DNA damage and fragmentation. Not super big issue today with NGS, but can introduce biases. (i.e. formalin interstrand cross-linking)
Give three examples of case studies where conservation paleogenomics have provided insights into endangered species/conservation efforts. What were the key takeaways?
- Gorillas the last 100 years (2018): 123 gorilla mitogenomes sequenced dating from 1914-2014, both Grauer’s gorillas and mountain gorillas. Grauer’s-Lower genomic diversity, increased inbreeding and increased geneticload. Mountain- No changes in diversity, inbreeding or genetic load even though they had less to begin with and much smaller range.
- Sumatran rhinos: Less than 100 individuals left in the wild. Population declined 70% since the 40s. Malay population extinct, Reduced heterozygosity, increased inbreeding, but reduced mutational load - purging? Borneo overall declining, showing same patterns as Malay but also increased mutational load, should be prioritized for conservation efforts.
Kakapo: Extinct on mainland, that pop had high mutational load and number of LoF variants, but extant pop on Stewart island seem to be fine in that sense, even though they have lower diversity and higher inbreeding - seems like there has been some purging of deleterious LoF variants.
more case studies from slide 50-72.
A classical example of selection is that of the Peppered moth, explain it briefly.
Peppered moths in England were initially adapted to be camouflaged on tree bark, and was therefore white with black speckles or “peppered”. During the Industrial Revolution of
mid-19th century, their
environment changed and many of the trees were covered in soot, resulting in having an all black color phenotype became more advantageous as it provided camouflage, and the alleles for this phenotype increased in frequency. This is a classic example both because it’s so clear and happened so quickly, but also says something about how human interference can change natural processes.
Mutations arise randomly and evolve according to their affect on fitness, what four types of selection are there? How does each affect the frequency?
The four forms of selection on mutations are:
- Neutral: a mutation that doesn’t affect fitness. This will generally not be subject to selection and the frequency of it will depend on stochasticity.
- Positive: Mutations that increase fitness usually increase in frequency and eventually gets fixed in the population. Fixed = everyone has it.
- Negative: If a mutation that arise affects the fitness of the individual negatively, the mutation will decrease in frequency until it is purged.
- Balancing: When a mutation arises that leads to increased fitness of those that are heterozygous for it, selection will maintain multiple alleles at that gene locus within a population, instead of leading to the fixation of one allele.
Provide two examples of balancing selection.
- Sickle cell anemia: When homozygous = anemia or no protection towards Malaria, when heterozygous = only slightly anemic and protected against malaria which is much better.
- Negative frequency dependence in dragonflies: If all have the same color, their predators learn that. they are safe to eat. If they are different colors, they are safer = better fitness.
Remember: One SNP can be selected for but surrounding SNPs can “follow along” due to proximity.
