Recent reconstructions of evolutionary history are often...

Recent reconstructions of evolutionary history are often dependent on assigning divergence in terms of changes in amino acid or nucleotide sequences. For example, a comparison of cytochrome c shows 10 amino acid differences between humans and dogs, 24 differences between humans and moths, and 38 differences between humans and yeast. Such data provide no information as to the absolute times of divergence for humans, dogs, moths, and yeast. How might one calibrate the molecular clock to an absolute time clock? What problems might one encounter in such a calibration?

Recent reconstructions of evolutionary history are often dependent on assigning divergence in terms of changes in amino acid or nucleotide sequences. For example, a comparison of cytochrome
c shows 10 amino acid differences between humans and dogs, 24 differences between humans and moths, and 38 differences between humans and yeast. Such data provide no information as to the absolute times of divergence for humans, dogs, moths, and yeast. How might one calibrate the molecular clock to an absolute time clock? What problems might one encounter in such a calibration?

Key Concepts

Fossil Record Limitations

The fossil record, while useful for calibration, has inherent limitations such as incomplete preservation, dating uncertainties, and biased representation of species. These issues can lead to inaccuracies in estimating the true divergence times when used as a calibration tool.

Rate Heterogeneity

Rate heterogeneity refers to the observation that mutation rates can vary among different organisms, genes, or lineages. Such variability poses a challenge to the molecular clock hypothesis since the assumption of a constant mutation rate may not hold true universally, complicating the calibration process.

Molecular Clock

This concept involves the idea that genetic mutations accumulate at a relatively constant rate over time, allowing researchers to use the number of observed differences in nucleotide or amino acid sequences to estimate the time since two species diverged. It forms the basis for relating genetic differences to evolutionary timelines.

Calibration Methods

Calibration of the molecular clock involves anchoring molecular divergence times to absolute times, typically using independent evidence such as fossil records, known geological events, or biogeographic data. This process is essential to convert relative genetic distances into actual chronological dates.

Transcript

00:01 In order to answer this question, we have to first understand what a molecular clock is.

00:05 So let's just review the definition real quick.

00:08 A molecular clock is defined as the average rate, a gene or an amino acid, or basically a section of a genetic code, mutates over generational time.

00:22 For instance, we might have these two genes or gene segments.

00:27 It could even be like individual bases along each path that mutates, say, five times each generation.

00:36 And these mutations could be silent substitutions or they could be non -sanonymous substitutions.

00:43 So, yeah, there is no real way of knowing exactly just yet.

00:47 This is just a general example.

00:50 In comparison, though, we might have these other genes or gene components that mutate 15 times each generation.

00:57 And so there's, that's why we're only looking at certain proteins or certain genetic code, not the genome as a whole, because different sections might mutate at different rates depending on different factors.

01:15 And i know you might now be thinking, okay, well, now that we have this down, what are those factors? well, as we can see, sometimes there are internal factors or inherent factors that just mean certain sections of a genome mutate more, certain proteins or more tended to certain mutations or changes, perhaps based on certain biochemical interactions or the type of dna polymerase, etc.

01:46 But there are also a lot of external factors.

01:48 And by external factors, i'm talking about things beyond the biochemical genome and proteins themselves.

01:56 And this question in particular mentions two important things.

02:01 It mentions population size and generation time.

02:08 So now that we have two examples of factors that might affect molecular clocks and why we might not be able to, you know, know, use this data in order to make certain assumptions about how often genetic changes happen over time and how we can use that to make phylogenic trees, we first have to address these things that can cause differences in the rates and why they might not be comparable in certain circumstances.

02:45 And so first, let's address the most apparent factor, which is generation time.

02:51 And note how on the first slide i mentioned that this is the average rate of gene or amino acid or protein mutates over generations.

03:01 This is because genetic mutations can be passed down through a population, not just as a function of time, like year to year, but as a function of how often those genes will get passed down, which is a measure of the generation time or how often a new generation arises.

03:24 And this changes depending on the organism.

03:27 So some species, like humans, we live an average of 70 to 80 years, and because of our longer development time, usually about every 20 to 30 years we might have a new generation.

03:46 And so every 20 to 30 years, that means that this is the timeline of when these mutations might take hold in a population, when we can actually see changes in the molecular clock, basically.

04:02 In comparison, some species of drosophila can have 10 to 20 generations per year.

04:14 And so drosophila species obviously live on a much shorter timeline than humans do, and so they have to reproduce a lot more often in order to maintain their population size...

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