Chapter 29: Evolutionary Genetics

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Welcome back to The Deep Dive.

Today we're diving into something pretty mind -bending, actually.

Developmental biologists recently found that the eyes of, well, all sorts of different species.

We're talking fruit flies, frogs, mice, even us.

They're all profoundly influenced by the exact same gene.

It's called Pax6.

Yeah, Pax6.

It's incredible when you stop and think about it.

Right.

So let's unpack this a bit.

How can something as complex,

as vital as an eye, be controlled by essentially the same genetic instruction across such different creatures?

That's a fantastic question.

And it leads us straight into today's topic,

evolutionary genetics.

Exactly.

So our mission in this deep dive is to give you a shortcut, basically, to understanding the core ideas in this field.

We're pulling mainly from chapter 29 of genetics, analysis and principles, the seventh edition by Robert J.

Brooker.

And at its heart, evolution is the accumulation of heritable changes in a population or species over generations.

Changes that stick.

Okay.

So heritable changes.

And you mentioned different scales.

Right.

So on one level, you have micro evolution.

These are the smaller, sort of measurable shifts in allele frequencies within a population.

You can actually see this happening.

Like bacteria getting resistant to antibiotics,

or maybe bird beak size is changing with the season.

Precisely.

Those kinds of things driven by mutation, genetic drift, migration, natural selection.

Even inbreeding can play a role.

It's evolution you can almost watch in real time, relatively speaking.

Gotcha.

And the other end of the spectrum.

That's macro evolution.

The big picture stuff.

The processes that over vast stretches of time lead to entirely new species emerging.

Wow.

Okay, so today we're going to dig into the genetic nuts and bolts behind all this.

Look at some examples, maybe clear up some terms, basically get you comfortable with these key ideas.

Sounds good.

So let's start at the beginning almost.

Where do new species actually come from?

And you know, what did someone like Charles Darwin figure out way back in the 19th century, long before anyone knew what a gene even was?

Ah, Darwin.

It's genuinely fascinating how he pieced it together without the genetic knowledge we have now.

His thinking was really shaped by a couple of key influences.

Like who?

Of course, the geologist Charles Lyell.

Lyell argued for uniformitarianism, this idea that the earth is incredibly old, and that slow, steady geological processes acting over time cause huge changes, like mountains rising, canyons forming.

Okay, so slow and gradual change.

Exactly.

And Darwin thought, well, maybe life changes gradually like that too.

Then there's Thomas Malthus, an economist.

Pub Malthus, the population guy.

That's the one.

His big idea was that populations, including humans, tend to grow faster than their resources can keep up.

This leads to a struggle for existence.

A struggle, meaning not everyone makes it.

Precisely.

For Darwin, the key takeaway was stark.

Not all offspring are able to survive and reproduce.

There's competition.

So geology gave him the timescale, and Malthus gave him the struggle.

You got it.

And by the mid -1840s, he'd pretty much formed his theory.

He almost got scooped, actually.

Alfred Russell Wallace came up with basically the same idea independently.

They even co -published briefly in 1858.

No kidding.

Wallace.

Yep.

But then Darwin published On the Origin of Species, his big book, and that really set the world talking.

He called his idea adaptive evolution,

or more famously, descent with modification through variation and natural selection.

Descent with modification, variation and selection.

Let's break that down.

Okay.

So genetic variation is the raw material.

Observable differences, phenotypes.

But at the gene level, it comes from random mutations, changes in alleles, changes in chromosomes,

stuff that affects how an organism turns out.

And that variation is just random.

Largely, yes.

The mutations themselves happen randomly.

Then comes natural selection.

This is the struggle for existence part.

Individuals with traits that happen to be more favorable for their specific environment, well, they're more likely to survive, reproduce,

and pass those traits on.

So the environment sort of selects the winners generation after generation.

That's a good way to put it.

Leading to better adaptation and reproductive success over time.

Okay.

That makes sense for how species change.

But this brings up something you touched on earlier.

How do biologists even define what a species is today, especially if they look super similar?

Oh, that's a huge challenge.

Seriously.

There's no single perfect definition that works for everything.

How different do two groups need to be?

Is it beak shape, song pattern, DNA sequence?

It depends on the organism, I guess.

It really does.

Defining an insect species might use different criteria than defining a bacterial species.

But generally, scientists look at a combination of things.

Morphology, the physical traits, ability to interbreed, or rather the inability to what we call reproductive isolation, molecular features like DNA, ecological factors, their niche, and their evolutionary history, their relationships.

Let's talk about that reproductive isolation.

That seems like a pretty clear line, right?

If two groups can't make fertile babies together, they're separate species.

It's often considered the gold standard, especially for animals and plants that reproduce sexually.

If they can't successfully interbreed, something's keeping them distinct.

And there are different ways that can happen.

Yeah, broadly two types.

Presigotic isolating mechanisms kick in before fertilization even happens.

Maybe their mating rituals are different.

Maybe their reproductive organs don't fit.

Maybe the sperm can't fertilize the egg.

Okay, prevents the zygote from forming.

Right.

And then there are post -zygotic isolating mechanisms.

These happen after fertilization.

The hybrid zygote might form, but it might not survive.

Or if it does survive, it might be sterile, like a mule.

Ah, okay.

But you said it's not always straightforward.

Well, yeah.

It can be tough to actually test in the wild.

Sometimes species that can interbreed in a lab setting just don't, in nature, they stay separate.

Think of some yucca plants and their specific moth pollinators.

And crucially, this definition doesn't work for organisms that reproduce asexually, like bacteria.

Right, no interbreeding there.

And obviously you can't test if extinct species could interbreed.

So it's a useful concept, but it has limitations.

So if breeding isn't the whole story, what about looking directly at the DNA, the molecular features?

That's become incredibly powerful.

We can compare DNA sequences directly.

Looking at specific genes, like the 16S ribosomal RNA gene in bacteria, that's a standard method for telling bacterial species apart.

16S rRNA, why that specific gene?

Ah, well, we'll get more into that later, but it's universal, essential, and changes relatively slowly.

We also look at gene order on chromosomes, chromosome structure, even the number of chromosomes.

But again, there's a judgment call, isn't there?

How much difference is enough?

Like, is a 2 % difference in the whole genome enough to say new species?

Exactly.

That's often the tricky part.

Where do you draw the line?

It's an ongoing area of research and debate.

Okay, so we have some ideas about what defines a species.

Now, how do new ones actually form?

What's the process?

That process is called speciation, the formation of new species through evolution.

And does that usually mean one species just slowly morphs into another one over time?

It can happen.

It's called antigenesis.

One lineage just changes.

But what seems much more common and what really drives biodiversity is cladogenesis.

Cladogenesis sounds like branching.

That's exactly it.

It's the division of a single species into two or more distinct species.

Think of it like a branch budding off the evolutionary tree.

This increases the total number of species.

Okay, branching is the main way.

Are there different ways that branching can happen?

Yes, based mainly on geography.

The classic mode is allopatric speciation.

Allo meaning different, Patrick meaning homeland.

This happens when a population gets geographically split.

Like a river changes course or some individuals colonize a new island.

Perfect examples.

A small group gets isolated.

Now gene flow between the new group and the original population is cut off.

In that new isolated environment, different mutations might arise.

Genetic drift can have a big effect.

And natural selection might favor different traits.

Over time, they diverge enough to become a new species.

So isolation is key there.

What if populations aren't fully separated but maybe just

mostly separate?

Ah, that leads to parapatric speciation.

Para meaning beside.

Here you have populations with ranges that touch or slightly overlap.

There might be a hybrid zone where they can interbreed a bit.

But they still become distinct species.

How?

Well, for speciation to complete, gene flow across that hybrid zone needs to be limited.

One way this can happen is if the two populations accumulate different major chromosomal changes like inversions or translocations.

How does a chromosome inversion stop gene flow?

Remember, during meiosis, homologous chromosomes pair up.

If one chromosome has a big inverted segment compared to its partner, they can't pair up properly in that region.

This can lead to messed up chromosomes in the gametes produced by hybrids, duplications, deletions,

making the hybrids less fertile or even sterile.

It creates a genetic barrier even without a mountain range.

Wow, okay.

Chromosomes themselves acting as barriers.

Now, you mentioned one more type, sympatric speciation.

Semim meaning same.

So same homeland.

Exactly.

This is the trickiest one to explain, but it happens within the same geographic area.

No physical separation.

How on earth does that work?

If they're all living together, shouldn't they keep interbreeding?

You'd think so.

It usually requires some sort of abrupt genetic change that causes reproductive isolation almost instantly.

Maybe a mutation affects mate recognition suddenly.

A subgroup only recognizes and mates with others carrying the same mutation.

Or a really common mechanism, especially in plants,

is polyploidy.

Polyploidy.

Many chromosomes.

Right.

An organism ends up with more than two complete sets of chromosomes.

For instance, an error in meiosis might create diploid gametes instead of haploid ones.

If two diploid gametes fuse, you get a tetraploid offspring, four sets of chromosomes.

And that makes it a new species just like that.

Often, yes.

Take a plant example, Galeopsis tetrahit, the common hemp nettle.

It's an allotroploid meaning its extra chromosomes came from two different ancestral species.

It has 32 chromosomes.

It's likely ancestors, G.

pubescens and G.

speciosa are diploid with 16 chromosomes each.

Okay.

Now, this tetraploid G tetrahit can reproduce just fine with other tetraploids.

But if it tries to cross back with one of its diploid ancestors, the offspring would be triploid, three sets of chromosomes.

Triploids are usually sterile because their chromosomes can't segregate evenly during meiosis.

They produce unbalanced aneuploid gametes.

Boom.

Instant reproductive isolation.

Created by a changing chromosome number right there in the same field, potentially.

Precisely.

Sympatric speciation through polyploidy.

It's been a major force in plant evolution.

Okay.

That's fascinating how new species can arise.

So once we have all these species branching off, how do scientists figure out their relationships?

How do they build those evolutionary family trees?

That's the realm of phylogenetics.

Building phylogenetic trees to visualize how species are related based on common ancestry.

Like a genealogy, but for species.

Kind of, yeah.

A key concept is the monophyletic group, or clade.

This is a group that includes a common ancestor and all of its descendants.

Not just some, but all of them.

If you snip a branch off the tree, everything on that branch is a clade.

So you can't just pick and choose descendants.

It has to be the whole lineage from that point.

Exactly.

And the main way we build these trees now, using the cladistic approach, is by looking for shared derived characters, or synepomorphies.

Synepomorphies.

Fancy word.

What does it mean?

It's a trait that a group of organisms shares, which they inherited from their common ancestor, but which is different from the trait found in more distant ancestors.

It's an evolutionary novelty for that group.

Can you give an example?

Sure.

Think about mammals having hair.

Hair is a shared derived character for mammals.

The common ancestor of mammals had hair and passed it on, but more distant ancestors, like reptiles or amphibians, didn't.

Or whale and dolphin flippers, those are derived from the front limbs of their terrestrial ancestors.

It's a modification specific to that lineage.

Okay.

So finding these shared new traits helps group organisms together.

And how do you actually build the tree, say, using DNA?

Well, you compare homologous gene sequences, genes that share a common ancestry across the different species you're interested in in your in -group.

You also include a more distinctly related species, the out -group, for comparison.

Why the out -group?

The out -group helps you figure out which character states are ancestral, present in the distant ancestor, and which are derived,

evolved later within the in -group.

You look for patterns of shared derived characters, often using computer programs to find the simplest tree structure, the one requiring the fewest evolutionary changes, that fits the data.

And this molecular data has really changed the game, hasn't it?

Absolutely revolutionized it.

We can compare organisms that look wildly different, or even study relationships deep in the past, using genes that everyone has.

Like those ribosomal RNA genes you mentioned, 16S and 18S.

Yeah, exactly.

Genes like 16S RNA in prokaryotes, or 18S RNA in eukaryotes, are fantastic for deep phylogeny.

Why?

Well, first, they're universal.

Almost all organisms have them.

Second, they code for ribosomal RNA, which is essential for making proteins so their function is ancient and highly conserved.

Meaning they change very slowly.

Right.

Most mutations would probably be harmful, so they get weeded out.

But they do change slowly over vast timescales.

And because they're pretty long molecules, they contain a lot of information to compare.

So you can trace relationships way back.

You can.

And you can even get quantitative.

Like, comparing humans and chimps, there are about 145 nucleotide differences per 10 ,000 nucleotides in many genes.

If you assume a relatively constant rate of change, that suggests maybe 72 or 73 changes happen in the human lineage, and 72 or 73 in the chimp lineage, since we split from our common ancestor millions of years ago.

That's cool.

But evolution isn't always just parent to offspring, right?

You mentioned something else.

Horizontal transfer.

Ah, yes.

So vertical evolution is the standard picture.

Genes pass down from parent to offspring, accumulating changes along lineage.

But horizontal gene transfer, HDP, is different.

It's when an organism gets genetic material from another organism that isn't its parent, like picking up DNA from the environment, or via viruses.

Sideways evolution.

Kind of.

It's super common in bacteria and anarchy.

It's a major way they acquire new traits quickly, like antibiotic resistance genes spreading through a population.

Less common in animals like us.

Much less common.

Especially getting genes into the germ line to be passed on.

Multicellularity.

Sexual reproduction.

These act as barriers.

But HGT definitely complicates the simple tree of life idea, especially early in life's history.

It might have been more like a web of life back then, with genes swapping all over the place.

So thinking about these shared genes,

what does this tell us about our own genetic past?

Or even about extinct species?

It all comes back to homology similarities due to common ancestry.

Homologous genes are genes in different organisms, or even within the same organism that ultimately trace back to a single ancestral gene.

And there are different types?

Yeah.

Two main types to know.

Orthologous or homologous genes found in different species.

They started diverging when the species themselves diverged.

The Pac -6 gene we started with.

The human Pac -6 and the fly Pac -6 are orthologs.

Hawks genes controlling body plans are another classic example.

And we can use orthologs to study extinct things.

Sometimes yes, if we can get ancient DNA.

There's an amazing study on the extinct moas of New Zealand, those giant flightless birds.

Scientists managed to get DNA, specifically the 12S rRNA gene, another mitochondrial gene often used, from museum specimens.

Yo, what did they find?

Everyone assumed moas were most closely related to the kiwis, the other flightless birds still in New Zealand.

But the DNA told a different story.

Kiwis are actually more closely related to Australian emus and cassowaries, and the moas.

Their closest relatives seem to be tinamis from South America.

Whoa, so flightless birds must have colonized New Zealand at least twice independently.

Looks like it.

DNA completely rewrote that evolutionary story.

That's the power of comparing orthologs.

Incredible.

Okay, so orthologs are homologous genes in different species.

What's the other type?

Paralogs.

These are homologous genes found within the same species.

They arise from gene duplication events.

An ancestral gene gets accidentally copied, and then the two copies can evolve slightly different functions over time.

Like backups that then specialize.

Sort of.

Think of the globin genes.

In humans we have genes for alpha -globin, beta -globin, myoglobin, fetal -globin.

These all make oxygen -carrying proteins, but they're slightly different and used at different times or in different tissues.

They form a gene family, all descended from a single ancestral globin gene through duplication and divergence.

They are paralogs of each other.

Orthologs across species.

Paralogs within a species.

Got it.

Now,

you mentioned estimating time earlier with the human -chimp split.

Can we really put dates on these evolutionary divergences?

Well, that's the idea behind the molecular clock.

It's a concept, maybe more of a hypothesis, that some genes or proteins evolve at a relatively constant rate over time, at least for certain types of changes.

Can mutations just tick away steadily?

Primarily neutral mutations, that's the key.

If a mutation doesn't really affect the organism's fitness, it's neither good nor bad, then its fate is mostly down to chance, to genetic drift, not natural selection.

The idea is that these neutral mutations accumulate at a roughly constant rate.

So if you compare the number of neutral differences between two species orthologs, You can estimate how long it's been since they shared a common ancestor.

If you can calibrate the clock somehow, maybe using fossil evidence for one divergence point.

And this ties into the neutral theory of evolution.

It does.

Proposed by Motu Kimura, this theory was pretty radical.

It suggests that most of the genetic variation you see within a population and most of the differences between species at the molecular level are actually due to the random fixation of neutral or nearly neutral mutations, not positive selection driving adaptations.

So evolution isn't always about adaptation.

A lot of it is just drift.

According to the neutral theory, yes.

Most mutations are either harmful and get quickly eliminated or neutral.

Beneficial mutations are rare.

So the background rate of molecular change is dominated by the neutral ones drifting through the population.

What's the evidence for that?

Several lines.

First, if you look at proteins, regions that are less critical for the proteins function tend to evolve faster.

They accumulate changes more quickly than essential regions where almost any change would be bad.

Makes sense.

More tolerance for change there.

Right.

Think of introns versus exons.

Introns get spliced out.

Exons code for the protein.

Introns evolve much faster.

Also, look at the genetic code itself.

Changes in the third position of a codon, the wobble base, often don't change the amino acid anyway.

These silent substitutions are much more common than substitutions that do change the amino acid.

So changes that don't matter happen more often or at least stick around more often.

Exactly.

And even among amino acid changes, substitutions between chemically similar amino acids conservative changes, are more frequent than changes between very different amino acids, non -conservative changes.

All points towards selection mainly acting to preserve function while neutral changes slip through.

Okay, so molecular clocks and neutral theory suggest a lot of evolution is about steady random change.

What about bigger changes like those chromosome rearrangements we talked about earlier?

Absolutely.

Changes in chromosome structure inversions, translocations, fusions, fissions,

and changes in chromosome number like polyploidy are definitely part of the evolutionary picture too.

Like the human chromosome 2, isn't that a fusion of two chromosomes that are still separate in chimps and gorillas?

That's the classic example.

Strong evidence for our shared ancestry and a specific event in the human lineage.

Orangutans also show a large inversion on their chromosome 3 compared to other great apes.

These large -scale changes might not always change the phenotype drastically, but as we discussed with parapatric speciation, they can contribute significantly to reproductive isolation driving the formation of new species.

Okay, let's maybe pivot slightly.

We've talked about the concepts, the theories, but how do scientists actually do this stuff in the lab?

What are the tools they use to get this genetic information?

Yeah, the methods.

Understanding the techniques is pretty crucial.

A lot of it relies on fundamental molecular biology tools, the kind you'd find detailed in, say, an appendix of a textbook like Brooker's.

Like basic stuff you need before you can even sequence a gene.

Exactly.

First, you often need to grow cells, maybe bacteria or yeast or even animal cells.

That's cell culturing.

Growing them in vitro, either in liquid media to get large quantities or on solid media like agar plates to get colonies, where each colony ideally starts from a single cell, a clone.

Okay, grow the cells, then what?

You need to get the molecules out, right?

The DNA, RNA, proteins.

Right, you need to break open the cell's disruption, maybe using detergents or physical force like sonication.

Then you need to separate the components you're interested in.

How do you separate molecules you can't even see?

Various ways.

Centrifugation is a big one.

Spinning samples at high speed separates things based on density, size, and shape.

You can use it to pellet cells, separate organelles, or even separate DNA from RNA using density gradients, like with caesium chloride.

Spinning things really fast, what else?

Chromatography is another workhorse.

It separates molecules based on their chemical or physical properties as they move through a column packed with some material.

Ion exchange chromatography separates by charge.

Gel filtration separates by size.

Affinity chromatography uses specific binding, like isolating a specific protein that binds to a known DNA sequence.

So different columns for different jobs.

Pretty much, and then there's gel electrophoresis.

You've probably seen pictures of these gels with glowing bands.

Yeah, the DNA fingerprinting thing.

Sort of, yeah.

You load your sample, usually DNA or RNA or protein, into wells in a gel matrix and apply an electric field.

The molecules migrate through the gel based mainly on size.

Smaller ones move faster.

You can then visualize them, often using stains like ethidium bromide for DNA, which glows under UV light.

It lets you see the sizes of your fragments.

Okay, so you can separate them.

How do you know how much you have or detect specific things?

Good question.

For concentration,

a spectrophotometer is common.

It measures how much light of a specific wavelength the sample absorbs.

Different molecules absorb maximally at different wavelengths, like DNA at 260 nanometers.

Measuring light absorption.

Clever.

And if you're working with radioactive labels, which used to be very common, you'd use scintillation counting to detect the radioactive emissions.

Or, for detecting specific proteins or other molecules, even in tiny amounts, techniques like radioimmunoassay, RIA, are used.

RIA uses specific antibodies linked to a radioactive tag to detect and quantify an antigen, like a hormone.

Wow, okay.

So it's a whole toolkit, culturing, breaking, separating, detecting that lets scientists actually get the molecular data needed to study evolution.

Exactly.

These foundational techniques underpin almost everything we've discussed, from sequencing the Pac -6 gene to comparing RNA in MOAs and Kiwis.

So bringing it all together.

From Darwin puzzling over barnacles and finches, to us today looking at DNA sequences and using molecular clocks.

This whole deep dive into evolutionary genetics shows this incredible story of continuous change, doesn't it?

Interconnected change.

It really does.

That initial mystery of the Pac -6 gene controlling eye development across such diverse animals, it suddenly clicks into place, doesn't it?

It's evidence of a deeply shared ancestry, a fundamental genetic toolkit that's been modified and tinkered with by evolution over hundreds of millions of years.

It's not that the fly eye and the human eye are the same, but the master switch, that initial instruction,

is conserved.

It's amazing.

And the discoveries just keep coming, refining our understanding of life's incredibly intricate tapestry.

It shows how these seemingly small genetic shifts accumulating over immense time generate the staggering diversity we see all around us.

And importantly, how that shared genetic heritage really does link all the life from bacteria to us.

It makes you think.

If these evolutionary mechanisms are always operating, constantly shaping life,

what about our own impact?

How might human actions, things we do intentionally, like genetic modification or unintentionally, like climate change or pollution,

how might those be influencing the future evolution of other species?

And maybe even our own species?

That's a profound question to ponder, isn't it?

The evolutionary story is far from over and we're now a major character in it.

Indeed.

Well, thank you for joining us on this exploration.

We hope this deep dive into evolutionary genetics has given you some food for thought, maybe sparked some curiosity about life's ongoing grand story.

Thanks for being part of the Deep Dive family.