aDNA in climate change, systematics, speciation and gene flow Flashcards
(21 cards)
Why is it useful to study aDNA?
By studying the past, we can better understand our present and future. Modern populations may not be representative of past populations bc of bottlenecks, founder effects, population extinctions/replacements and introgression. So we need the temporal resolution available in aDNA, it allows for a lot of background history not available in modern data that we can inform the present and future by. Such as the threat of extinctions due to current climate change.
Past climate change affected entire ecosystems, how did Warm vs cold periods affect ecosystems respectively?
Warm periods (interglacials/interstadials): Increase in forest-dwelling taxa such as boreal trees, squirrel-like species, termites etc.
Cold periods (glacials/stadials): Decrease in boreal taxa-Increase in steppe/tundra taxa such as low-growing shrubs, herbs, large herbivores…
Why is increased greening of arctic environments problematic?
Warming → increased greening → less heat reflected off Earth → more warming. Increased greening enhances competition between species which normally don’t come into contact, e.g. the Arctic fox and the red fox.
What can we learn from past ecosystem dynamics?
We can learn a lot from studying past ecosystem dynamics:
- How to identify ecosystems under threat, as well as resilient ecosystems that might act as refugia in the future.
- How biodiversity is affected by increased warming - Diverse ecosystems are more resilient.
- How trophic interactions are affected by climate change - For example, the disappearance of large herbivores has been linked to an increase in forest vegetation, and a decrease in large carnivores.
Why is it generally easier to study the impact of climate change in small mammals rather than big? Provide an example.
Because small mammals were likely not hunted in the same way that the bigger mammals were, which allows you to study the impact of climate in isolation.
For example, collared lemmings which are small, cold-adapted rodents that are restricted to the dry treeless environment of the arctic tundra. During the last glacial period, there were connectivity in arctic climate, and five stratigraphically distinct lineages have been found using aDNA, while only one remains today. Looking at lineage turnover events for the last 50000 years, they found four, that coincided with warm periods –> during warm periods, populations have likely gone extinct. They also found that samples from Russia often occupied basal positions in phylogenies - possible source population (refugia?) which supports recolonization from the east during cooler periods.
Another study looking at complete mitogenomes from samples found that most of the diversity we see today occurred after the last interglacial (Eemian) which further supports that many populations went extinct during warm periods while a small surviving population then functioned as source for recolonization during colder period. Clade 5 (only surviving) arose ~27 ka BP and encompasses all modern diversity (geographically distinct subclades).
Ptarmigans is another example, but as opposed to the collared lemmings, they show continuity until todays populations - habitat tracking and evidence of suitable climate (cold) in Europe over time. So climate change seem to affect species differently.
How is range size for megafauna related to effective population size over the last 50 000 years?
In a study by Lorenzen et al (2011) they looked at range sizes and Ne, they found that for all megafauna they looked at, showed a decrease in range size over time with corresponding decreases in Ne. All showed an increase in population size at transition between MIS3 and MIS2 (around LGM) to then decrease gradually afterwards.
If we want to study cold adaptation, with questions like: What kind of genes might we expect to be related to cold adaptation? Do cold-adapted species have mutations in these genes? What are the functions of these mutations? Describe how one would approach this to answer these questions.
First: Examine non-synonymous mutations across the genome of species surviving in the cold for long compared to reference genome/ancestral state and look for mutations that cause amino-acid changes that could potentially affect function of the gene. Also, one can look if mutations in these genes are overrepresented in cold-adapted species.
Example: mutations in gene TRPA1 which is involved in sensing cold has been found both in woolly mammoth and woolly rhino, this is one of 89 genes that they shared non-synonymous mutations in, which indicates convergent evolution in cold-adapted megafauna.
What are some genes that are linked to cold adaptation in woolly mammoths?
Hair and skin development:
AHNAK2= hair follicle development
TCHH + PADI3= uncombable hair syndrome
DSP= woolly hair syndrome
Fat storage and metabolism:
ACADM-breaking down fatty acids
TET1= regulates cold tolerance through beige adipocyte tissue (fat tissue that forms in response to cold exposure)
Thermosensation:
SCN10A= pain sensation, essential for perception of extreme cold feeling painful
…Among others!
700 ka Chukochya mammoth already had 88,7% of the protein-coding changes found in late Woolly mammoths. This was found through deep-time paleogenomics which makes it possible to find out when mutations arose using aDNA.
What is important to remember about using aDNA to study past climate change?
Ancient DNA is biased and can mostly be applied to understand the effect of past climate change in the Arctic, but this will hopefully change in the future!
What is systematics?
Systematics = the study of relationships between groups of organisms (phylogenetics) and their classification (taxonomy).
Define the terms monophyletic vs paraphyletic group.
Monophyletic group: a group of organisms that are all descendants of a common ancestor.
Paraphyletic group: a group only including some descendants of a common ancestor.
Name the 8 different levels of taxonomic classification in order from lowest resolution/classification to highest.
The 8 different levels of taxonomic classification in order from lowest resolution/classification to highest is: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.
For a red fox this would be Domain=Eukarya, Kingdom=Animalia, Phylum=Chordata, Class=Mammalia, Order=Carnivora, Family=Canidae, Genus=vulpes, Species=vulpes vulpes.
Out of all species that have ever existed, how many percent have gone extinct?
Over 99% of all species that once lived have gone extinct. Extinction is part of life.
What are the two main mechanisms of speciation from a traditional viewpoint?
- Allopatric speciation (geographical isolation)
- Sympatric speciation (reproductive isolation)
But speciation is not so simple, genetics adds more complexity and nuance!
Define the term “Gene flow”.
Gene flow is the exchange of viable genetic information between populations.
Gene flow often makes phylogeny harder!
There are two types of gene flow, which and how do they differ?
If the gene flow is unidirectional = “introgression”, e.g. some individuals coming in an mixing with another population. In the end the introduced genes will get diluted over time.
If the gene flow is bidirectional = admixture, e.g. offspring from admixture are included in both populations, over time this leads to more persistence of the introduced genes and makes phylogenies mush more complex.
If the gene flow is between distinct species = hybridization, e. g. between horse and donkey = mule offspring. This term holds even if offspring of hybrid is not viable (but then there is no gene flow)
How is taxonomy done today?
Today, all taxonomy is handled by the international commission of zoological nomenclature (ICZN) who sets names and species based on description in the literature, a type specimen (holotype) and go off of principles of priority (first name sticks) and synonymity (is something have been called a name for a while, it’s impractical and unclear to change it, unless new info comes that warrants it).
Explain briefly how the gene flow method D-statistic works.
The D-statistic helps identify gene flow, where alleles from one population are introduced into another population. The D-statistic analyzes four groups (1, 2, 3, 4) to determine if two non-sister groups (e.g., 1 and 2) share more similarities with each other than expected based on the species tree. It looks at allele similarities - alleles shared pairwise between the pops, e.g. 1 and 2, 1 and 3 and so on. if D = 0 it means that there is no evidence of gene flow. If D = -1>0 there is evidence for gene flow between A and C, if D = 0<1 there is evidence of gene flow between 1 and 3.
What is “Pseudo-haploidization”?
Pseudo-haploidization is a method used to represent low-coverage ancient DNA (aDNA) data as if it were haploid, meaning it contains only one set of chromosomes instead of the usual two. If a polymorphic (SNP) site is represented by more than one read, then an allele is randomly selected in the final resulting genome. This is one way to handle PMD.
This is done because aDNA samples often have low sequencing depth, making it difficult to confidently call diploid genotypes. This is useful because many statistical methods, e.g. D-statistic and PCA can’t handle heterozygous SNPs.
What is the AMBER plot useful for?
The AMBER plot is useful to assess reference bias. As the higher the quality and the longer the reads of a sample, the better it will map to a reference genome. When there is no close reference and when working with highly fragmented aDNA one can use the AMBER plot to evaluate the percentage divergence from the reference.
Name three cases where we have been able to use aDNA to solve species mysteries.
- Moas: giant new Zealand birds that were thought to be three different species due to size differences, with aDNA studies, we found that they clustered based on island, not acc to the presumed species. Instead, it was a case of extreme reversed sexual dimorphism within one species, where the females were much bigger.
- Camelops, an extinct member of the llama and camel tree: It was long thought to be more closely related to llamas because of morphology, but aDNA showed that Camelops was instead more closely related to Afro-Eurasian camels (Dromedary and Bactrian camels) than South American camels (llamas, alpacas, guanacos).
- Wolves and dogs: aDNA showed that Wolves and dogs trace their ancestry a late pleistocene expansion from Beringia, and spread to both Eurasia and NA. Found that eastern and red wolves are products of admixture between coyotes and Grey wolves.
All in all, admixture is more a rule than an exception - very common in paleogenetic data!
