Inbreeding and Fitness

[haryonob (hary)]

Thank you all for pointing me to the right direction, will read up on these asap

[sfmatheson (Stephen Matheson)]

@haryonob

we just keep breeding the dogs that are the most hairy to get what we want right? But it seems that this is not what is happening on a large evolutionary scale?

Well, in the case of avian dinosaurs, the big changes aren’t actually conceptually very big. I know that’s a crude way to put it, but both wings and feathers arose from pre-existing structures that are clear in the fossil record and that can be understood at developmental and molecular levels. I think birds are amazing, and I think powered flight is an astonishing thing (birds are just one major lineage that can do it). But the evolution of powered flight in birds is not peculiarly mysterious. Feathers are modifications of skin appendages that were common (and diverse) in various dinosaurs. Wings are modifications of a tetrapod body plan, easily and clearly related to the forelimbs of other tetrapods (including us).

I don’t mean to suggest, even slightly, that the evolution of birds isn’t intensely interesting and even awe-inspiring. I do mean to say that there are no clear biological mysteries–not genetically, not developmentally, not even physiologically–that would have to be solved to fully understand how it happened.

[Rumraket (Mikkel R.)]

@John_Harshman

Check out the faces of swallows, swifts, and nightjars for a good example.

Thanks. Found some good pictures of the swallow and nightjars “whiskers” on google:

[sfmatheson (Stephen Matheson)]

@John_Harshman

Sexual selection could indeed be another part of it. So we have four possible functions of feathers […] All those are found in modern birds.

I am partway through Richard Prum’s The Evolution of Beauty and look forward to discussing it with others who have read it (including my kid who gave it to me). It’s both riveting and maddening. The former because the intensity of sexual selection in birds, and the outcomes, are both incredibly interesting, as in wow-you-can’t-make-this-sh*t-up interesting. The latter because his diatribes about Darwin and Wallace and others (Wallace is the Bad Guy in his narrative; there’s a new angle) are shrill and tediously repetitive.

I do think it’s a good book for laypeople to read, since it’s so entertaining, but it’s really not about the basic evolutionary processes that gave us birds in the first place.

[John_Harshman]

Prum is a fine scientist and has done a lot of great work on several subjects, including the evolution of feathers. But I think his view of sexual selection is just wrongheaded in multiple ways. It may be his one flaw.

[Mercer (John Mercer)]

@haryonob

Does anyone have a link to articles that explain the process of non-avian to avian evolution of dinosaurs? Preferably one suitable for general public understanding.

The first thing to understand, and that you’re obviously missing, is that evolution does not happen to individuals. It is a population-level phenomenon.

[haryonob (hary)]

Thank you everyone, now I can see how the ‘feather mutation’ could have spread out to a large population from one single dinosaur. As long as the population is large, there will not be any immediate issues or hurdles with inbreeding.

But what happens when this huge population start to undergo speciation? Do we always have to assume a large enough population for the resulting species to ‘‘overcome’’ inbreeding issues and evolve?

It is stated that one of the effects of inbreeding is: With continuous inbreeding, genetic variation is lost and homozygosity is increased, enabling the expression of recessive deleterious alleles in homozygotes.

From a layman’s view, doesn’t this mean that during the process of speciation, the dinosaurs who had the feather mutation (not yet expressed as any physical trait) had to keep on reproducing with closely-related relatives (inbreeding), in order for the feather mutation to be ‘‘maintained’’ in the species and finally be expressed as a physical trait in the thousands or millions of years ahead? And yet the speciation process could also result in genetic variation being lost?

Please feel free to correct me, but would all these 4 scenarios be acceptable in the evolution of non-avian to avian dinosaurs:

Using alphabets to represent gene variation, the non-avian dinosaur started with a gene variation of ABCDE, and the feather mutation is represented by O. F and G represent other mutations.

1. ABCDE + O (net gain of gene variation)
2. ABCDEFG + O (more net gain of gene variation)
3. ABCF + O (neutral gene variation)
4. ABF + O (net loss of gene variation)

In order for the evolution of diverse and complex lifeforms, does it mean that cases 1 and 2 have to occur more often than cases 3 and 4?

After more googling in regards to Inbreeding, I came across a paper that seems to be relevant: http://research.amnh.org/users/rfr/inbreeding.pdf

The title of the paper is ‘‘Inbreeding effects in Wild Populations’’, and conclude that ‘‘Inbreeding and inbreeding depression do occur commonly in nature and can be severe enough to affect
the viability of small and isolated populations.’’

Would it be fair to say that in the process of evolution, it is a constant tug of war between mutation of new genes vs loss of genetic variation due to inbreeding?

[Dan_Eastwood]

@haryonob

Thank you all for pointing me to the right direction, …

Thank you for sparking an interesting discussion!

@Timothy_Horton

There are two competing hypotheses for the evolution of flight in feathered dinosaurs (feathers evolved first for thermal regulation and/or display). The first is the Tree Down idea - small dinos began by gliding down from tree limbs to catch small prey, eventually added flapping to the gliding.

This seems plausible scenario to me. For a small insect eating dinosaur, climbing trees for food and living in trees for safety would be a survival advantage. This new habitat brings a risk of falling, so “falling slowly” becomes a new advantage. Flying insects would be a rich food source (with few if any existing predators) and the ability to leap in the air, catch a tasty meal, and land safely would be a big advantage.

I’m speculating, mostly, but each step has a food source to allow an advantage. In a world with no flying insect-eating dinosaurs, even flying poorly has potential to open up new fitness advantages that did not exist before.

[John_Harshman]

@haryonob

From a layman’s view, doesn’t this mean that during the process of speciation, the dinosaurs who had the feather mutation (not yet expressed as any physical trait) had to keep on reproducing with closely-related relatives (inbreeding), in order for the feather mutation to be ‘‘maintained’’ in the species and finally be expressed as a physical trait in the thousands or millions of years ahead?

There is no such thing as “the feather mutation”. I have no idea why you think inbreeding is necessary in order for feathers to appear. And I think you have an odd, though at the moment unclear, view of what speciation is. It’s the evolution of reproductive isolation between two populations. No reduction of population size or inbreeding is required, and it’s not synonymous with morphological change. Some change is necessary in at least one population, but only the change that produces isolation, perhaps, for example, a change in what sort of colors females prefer in mates. Recessive alleles are not particularly relevant, and alleles are generally not silent for millions of years waiting to be expressed.

Again, there is no such thing as “the feather mutation”. Your scenario makes no obvious sense.

@haryonob

Would it be fair to say that in the process of evolution, it is a constant tug of war between mutation of new genes vs loss of genetic variation due to inbreeding?

No. Genes and alleles are constantly being gained and lost through all sorts of processes: mutation of many varieties, selection, drift. Inbreeding certainly happens, but I see no evidence that it’s an important force in evolution and, as your source says, it can result in extinction in small populations. Note again that small populations have no particular connection to speciation.

[Mercer (John Mercer)]

@haryonob

But what happens when this huge population start to undergo speciation?

You have multiple, fundamental misunderstandings about evolution.

There’s no such thing as “starting to undergo speciation.” Species is a label applied retrospectively to a fuzzy process.

@haryonob

Do we always have to assume a large enough population for the resulting species to ‘‘overcome’’ inbreeding issues and evolve?

Large, outbred populations tend not to become extinct. Small, inbred ones do. Neither is an absolute.

@haryonob

It is stated that one of the effects of inbreeding is: With continuous inbreeding, genetic variation is lost and homozygosity is increased, enabling the expression of recessive deleterious alleles in homozygotes.

That’s impossible; only viable deleterious alleles can be tolerated with continuous inbreeding. Look at inbred lab mice. They are completely and continuously inbred, so they can have no recessive lethal alleles like most of us do.

Do you know what an allele is?

@haryonob

From a layman’s view, doesn’t this mean that during the process of speciation, the dinosaurs who had the feather mutation (not yet expressed as any physical trait) had to keep on reproducing with closely-related relatives (inbreeding), in order for the feather mutation to be ‘‘maintained’’ in the species and finally be expressed as a physical trait in the thousands or millions of years ahead?

Your layman’s view misses a fundamental understanding. As John Harshman pointed out, there’s no “feather mutation.” Feather evolution was gradual, as shown by fossils. We know that feathers aren’t a product of a single gene.

@haryonob

Would it be fair to say that in the process of evolution, it is a constant tug of war between mutation of new genes vs loss of genetic variation due to inbreeding?

Not really. There is zero chance that you will understand evolution of any vertebrate if you do not understand the distinction between genes and alleles.

Basically, if you see any writing about evolution that contains “the gene for X” or “the X gene,” or mentions genes without mentioning alleles, it’s a good idea to stop reading it.

[swamidass (S. Joshua Swamidass)]

I urge everyone to be careful to explain in a positive way what the science shows on this.

@haryonob is asking good faith questions that I hear all the time from the public.

[sfmatheson (Stephen Matheson)]

@haryonob

Thank you everyone, now I can see how the ‘feather mutation’ could have spread out to a large population from one single dinosaur. As long as the population is large, there will not be any immediate issues or hurdles with inbreeding.

Oh gosh, the notion of a “feather mutation” is a big red flag, suggesting that you are picturing single-event, large-effect mutations as the main or only drivers of evolution. That’s wrong.

The size of the population is not the simplistic limitation you suggest; in fact, genetic drift is thought to be a significant factor in evolution of populations of moderate size.

@haryonob

But what happens when this huge population start to undergo speciation? Do we always have to assume a large enough population for the resulting species to ‘‘overcome’’ inbreeding issues and evolve?

No. Inbreeding is not a relevant factor in speciation.

@haryonob

From a layman’s view, doesn’t this mean that during the process of speciation, the dinosaurs who had the feather mutation (not yet expressed as any physical trait) had to keep on reproducing with closely-related relatives (inbreeding), in order for the feather mutation to be ‘‘maintained’’ in the species and finally be expressed as a physical trait in the thousands or millions of years ahead?

Nope. The mutation (more accurately, the variant) can be maintained in the population through various well-known means. You are, btw, assuming the mutation is recessive.

As long as you are focused on “inbreeding,” you will be unable to understand evolution and population genetics. My suggestion is to get more basically up to speed on population genetics and basic evolutionary biology before jumping in with questions that begin with flawed (or completely false) premises. Good luck!

[swamidass (S. Joshua Swamidass)]

@sfmatheson

Oh gosh, the notion of a “feather mutation” is a big red flag, suggesting that you are picturing single-event, large-effect mutations as the main or only drivers of evolution. That’s wrong.

I think he is speaking colloquially, meaning “a mutation important to feather evolution”, not claiming that it is a Single Large effect mutation that makes a feather out of nothing.

@sfmatheson

No. Inbreeding is not a relevant factor in speciation

Separation of populations is important. Isn’t that a type of inbreeding from one perspective? After all we use the term interbreeding to discuss mating between populations. Inbreeding is just the opposite term.

[John_Harshman]

It may be that Stephen J. Gould, Niles Eldredge, and Ernst Mayr are partially responsible for @haryonob’s confusion, through their advancement of the peripatric speciation theory. In peripatric theory (and its descendent punctuated equilibria), most evolution happens during speciation, and speciation happens in small, geographically isolated populations in which loss of genetic diversity is a major factor.

It can’t be emphasized too strongly that there is little evidence for any of the components of that theory. Peripatric speciation is likely rare, with ordinary allopatric speciation the dominant mode. Large populations are not prevented from evolving. Molecular evolution, at least, proceeds at a steady clip. Evolution due to selection is likely episodic but not correlated with speciation. There are no “genetic revolutions”.

[John_Harshman]

@swamidass

Separation of populations is important. Isn’t that a type of inbreeding from one perspective?

No, any more than Luke’s father was dead “from a certain point of view”.

[T_aquaticus]

@haryonob

But what happens when this huge population start to undergo speciation? Do we always have to assume a large enough population for the resulting species to ‘‘overcome’’ inbreeding issues and evolve?

There are examples of species that were founded by just a few individuals, such as the cheetah:

Will evolution doom the cheetah? - Understanding Evolution

Cheetahs do experience issues due to inbreeding depression. From my reading on the subject, cheetahs are the exception. Most speciation events occur in larger populations of at least thousands of individuals, more than is needed to avoid most issues related to inbreeding depression.

@haryonob

From a layman’s view, doesn’t this mean that during the process of speciation, the dinosaurs who had the feather mutation (not yet expressed as any physical trait) had to keep on reproducing with closely-related relatives (inbreeding), in order for the feather mutation to be ‘‘maintained’’ in the species and finally be expressed as a physical trait in the thousands or millions of years ahead?

Not at all. If the allele is dominant then you only need one copy of the gene. If it is a recessive allele then it can still be spread to distantly related ancestors further down the family tree who can mate and produce homozygotes. If two individuals are 4th or 5th cousins, as it were, then there is a much, much lower risk associated with inbreeding.

@haryonob

Would it be fair to say that in the process of evolution, it is a constant tug of war between mutation of new genes vs loss of genetic variation due to inbreeding?

That wouldn’t be fair. In the vast majority of species and speciation events the population is large enough to avoid inbreeding depression.

[sfmatheson (Stephen Matheson)]

@swamidass

I think he is speaking colloquially, meaning “a mutation important to feather evolution”, not claiming that it is a Single Large effect mutation that makes a feather out of nothing.

That could be, and besides (hi @haryonob) it’s a reasonable honest mistake for a layperson. Thing is, once we agree that we’re not talking about single large-effect mutations, then we quickly realize that “inbreeding” or bottlenecks or whatever… are wholly irrelevant.

@swamidass

Separation of populations is important. Isn’t that a type of inbreeding from one perspective?

No, it’s not.

To help laypeople understand why this conversation is about misunderstandings of evolution and popgen, maybe we could try going through the concept of a selective sweep. It’s just a thought, but it seems clear to me that @haryonob has some important concepts so wrong that the opposite is true. Only under very strong selection do we start to think about loss of genetic diversity as a problem. It’s not “inbreeding” but it can be a factor. A conversation about that could help this layperson learn more about evolution.

[Rumraket (Mikkel R.)]

@Mercer

There’s no such thing as “starting to undergo speciation.” Species is a label applied retrospectively to a fuzzy process.

I think perhaps haryonob might have been thinking about a particular scenario of allopatric speciation, where a smaller subsection of the population gets isolated from the main one, and the subsequent reproductive isolation is what facilitates speciation. One could imagine the offshoot population to be quite small and thus be at greater risk of inbreeding problems.

It’s just that we don’t have to assume such a scenario in order to explain the evolution of feathers, nor that this is the normal or most likely scenario of speciation.

[swamidass (S. Joshua Swamidass)]

It certainly is a common mechanism in some contexts, such as island speciation.

[John_Harshman]

You’re talking about founder effect speciation, perhaps. Even that doesn’t seem to be common. In most speciation on islands, geographic isolation and environment are much more important factors than population size, even if the founding population is small.