Human Haplogroups rule out humans descending from....

[laymanB]

I am not a professional in this field so please bear with my ignorance. I try to be science literate where ever I can.My question is: Do genetics broadly and haplogroups more specifically rule out humans descending from more than one gene pool of common ancestors?To put it another way: Could it be possible that there was more than one beginning of Homo Sapiens than a single population in Africa 200-300K years ago?Thanks.

 

[mfb]

How exactly would you distinguish between "a single population" and "multiple populations"? Can't you just consider everyone contributing to the current gene pool part of the single population, or arbitrarily split it into subgroups?

 

[jim mcnamara]

A population can be defined in part by how little gene flow exists between other groups. For speciation (make a new species) there has to be a way to prevent gene flow.

Let me answer your question in that context. And in mostly non-science terms

First, in order to get a new species, there must be genetic changes (mutations, genetic drift) in a group. Next, if the group is isolated somehow then those changes can become very common in that 'cut off' group. Why? Because if they were interbreeding a lot with outside groups then their relatively uncommon "new" genes would be swamped by "old" genes.

How to isolate populations of animals - examples
1. change mating times - earlier or later in the year
2. change mating signals - example bird calls, pheromones
3. geographic isolation - examples: island populations, glaciers form between two populations that were once interbreeding
4. hybrid infertility - any hybrid (a cross with outside population) cannot produce offspring.
5. Founder effect - massive die out leaves a small population with unusual genes very isolated long enough to allow adaptive changes to take over.
Genetic drift drives differences in small isolated populations (see speciation link below for genetic drift)

So what you ask is: Can two isolated populations later come together and then undergo speciation? Sure. BUT. The new population still has to be genetically isolated from other populations. Otherwise you are back to square one. Some way to block gene flow (interbreeding outside the group) has to exist. What you are proposing is simply 'putting off isolation'

Read about peripatric speciation, allopatric speciation, and so on here (Some scientific terms defined):

https://en.wikipedia.org/wiki/Speciation

 

[Noisy Rhysling]

OP, are you looking for a Eastern Mediterranean origin?

As for there being separate gene pools, Lee Berger, Wits U., Johannesburg, has dated his Homo naledi finds at 330 million to 225 million years ago. They lived in the same area as H. sapiens, possibly right along side.

 

[jim mcnamara]

@Noisy Rhysling I think you have too many zeroes in your dates. The dinosaurs would have been snacking on H naledi.

https://en.wikipedia.org/wiki/Homo_naledi

Does ~3 hundred thousand years ago look better?

 

[Noisy Rhysling]

@Noisy Rhysling I think you have too many zeroes in your dates. The dinosaurs would have been snacking on H naledi.

https://en.wikipedia.org/wiki/Homo_naledi

Does ~3 hundred thousand years ago look better?

Let me double check. Yeah. https://news.nationalgeographic.com/2017/05/homo-naledi-human-evolution-science/

 

[jim mcnamara]

One of the problems in archeology by example

US Football (not soccer) has more rules than any other physical sport. They have changed over time, let's look from say, 1900 to the present.

Our goal: work out what the rules for the game were and how they have changed. We know them now.

Now the fun part! data:
We have a small number of video examples, each less than 5 seconds long, which we have use other means to date. We also have many samples of helmets, cleats, and some other things like shoulder pads which we can date to ±10 years. Which helps date the video clips.

Now work out all of the rules changes and when they happened. Good luck.

We have found relatively few complete individual human fossils that date before 50000ya (like the video clips), many stone tools and random teeth and bone bits (like the helmets in the example).

So archeologists and other researchers have done an amazing job, considering what they have had to work with. But as this thread shows there are lots of "maybes" that well meaning folks who are not expert can logically inject into consideration.

 

[laymanB]

How exactly would you distinguish between "a single population" and "multiple populations"? Can't you just consider everyone contributing to the current gene pool part of the single population, or arbitrarily split it into subgroups?

That's part of my question; How would you discriminate, based on genetics, two isolated populations that later came together to mate?

 

[laymanB]

OP, are you looking for a Eastern Mediterranean origin?

I am looking for whether genetics constrains the interpretation of human history based on the data. Or if the data can be interpreted with a multiregional hypothesis with isolated groups of hominids evolving into Homo Sapiens and later coming together to breed?

 

[laymanB]

So what you ask is: Can two isolated populations later come together and then undergo speciation? Sure. BUT. The new population still has to be genetically isolated from other populations. Otherwise you are back to square one. Some way to block gene flow (interbreeding outside the group) has to exist. What you are proposing is simply 'putting off isolation'

Thanks Jim. Let me make my questions more specific.

Is it possible that more than one group of hominids (say Homo Erectus for example) evolved into Homo Sapiens independently and then later came together to interbreed?

If so, would we expect the genetic data and specifically hapolgroups to look differently than they do now? Or could that hypothesis be sustained with the current genetic data?

 

[fresh_42]

What about homo neanderthalensis as an example of two independent populations of homo sapiens and whose genes are still alive today?

 

[jim mcnamara]

No, it is extremely unlikely to have completely parallel evolution like that. Changes occur in a random manner:
local geologic changes and disasters
new parasites/diseases evolve in one place not the other
Plain old random chance mutation

Re mutation by chance:
If you had two shuffled decks of cards with 100,000 (approximate size of human genome) cards one in New York, one in Mumbai, what do you think the chances of them dealing the exact order of cards is? My answer: so close to zero it would make sense to consider it zero. This is by no means a perfect analogy, but I'm trying to convey the idea of improbable.

 

[laymanB]

No, it is extremely unlikely to have completely parallel evolution like that.

I understand what you are saying. So let's not talk "complete parallel evolution" with the same genotypic and phenotypic changes exactly. But if you had two isolated populations with unique Y-DNA and mtDNA (say one in Africa and another in a different part of the world) and they came together to produce offspring, would there be any genetic evidence of the extinct population? And by extinct I mean where one of the population’s Y-DNA and mtDNA is no longer represented after X number of generations.

 

[laymanB]

What about homo neanderthalensis as an example of two independent populations of homo sapiens and whose genes are still alive today?

Are these genes only present in the nuclear DNA or are they also traceable through Y-DNA and mtDNA?

 

[laymanB]

Changes occur in a random manner:

I understand the paradigm here about the randomness of genetic change being the source for novel variation and new alleles. But aren't there a number of reputable biologists who think that genetic change and the resulting expression of genes is not a one-way street?

https://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080

http://www.thethirdwayofevolution.com/

 

[laymanB]

What about homo neanderthalensis as an example of two independent populations of homo sapiens and whose genes are still alive today?

Let me try another question in case some of my other questions got convoluted.

If we had not sequenced the DNA of neanderthals, could we have come to the conclusion that their DNA was present in non-African haplogroups? If so, how?

 

[Ygggdrasil]

Some background on the topic for those posters who may not be so familiar with human evolution (though I am also not an expert on human evolution):

All hominid species evolved in Africa and there have been multiple waves of hominid species that migrated from Africa to other regions (e.g. the Neanderthals in Eurasia). Of course, all of these hominid species have since gone extinct except for the modern Homo sapiens (i.e. us). Scientists, however, do debate the evolution on Homo sapiens. The most widely accepted theory is the "Out of Africa" hypothesis, which states that modern humans arose from a single population of hominids that arose in Africa then subsequently spread throughout the world replacing other hominid species that were present. An alternative theory, the multiregional hypothesis, posits that some of the other hominids that migrated out of Africa prior to Homo sapiens contributed to the genetics of modern humans.

The strongest evidence for the Out of Africa hypothesis comes from studies of human mitochondrial DNA extracted from people all across the world. These studies indicate that all Homo sapiens share a recent human ancestor between 140,000 and 290,000 years ago. Because the first hominids began migrating out of Africa up to ~ 1.8 million years ago, this evidence suggests that it is unlikely that some of these early hominid populations contributed to modern Homo sapiens.

Recent studies of Neanderthal DNA, however, has shown that a small percentage of DNA in modern humans does derive from Neanderthals, providing some support for multiregionalism. There is likely a false dichotomy between the Out of Africa hypothesis and multiregionalism as there is room for both to be true (modern humans emanate from one major population that replaced other hominids, but interbreeding between Homo sapiens and other hominids did occur to allow for some horizontal gene transfer between hominid populations).

As I am not an expert in the area, I don't know more detail about the methods to analyze modern DNA sequences for evidence of admixture with other populations of hominids. Given the recent discovery of Neanderthal sequences in modern human DNA it does seem possible that we may just have not been able to detect evidence of multiregionalism, but this is still likely an active area of research.

Here's a helpful page from Nature which discusses some of these issues: https://www.nature.com/scitable/topicpage/human-evolutionary-tree-417

 

[laymanB]

Because the first hominids began migrating out of Africa up to ~ 1.8 million years ago, this evidence suggests that it is unlikely that some of these early hominid populations did not contribute to modern Homo sapiens.

Thanks for the reply and the information.

So if there was a group of humans or hominids capable of reproducing with the population that contained Y-chromosomal Adam (Y-CA), circa 240 kya, and this other population had Y-chromosomes that had a most recent common ancestor (MRCA) in the distant past with Y-CA, how could we tell how much admixture this other population contributed to the nuclear DNA? It seems Y-CA's Y-chromosome won out over all other descendants, based on the empirical genetic data of people around the globe today. I guess this question is similar to my #16 post.

 

[laymanB]

So what you ask is: Can two isolated populations later come together and then undergo speciation? Sure. BUT. The new population still has to be genetically isolated from other populations. Otherwise you are back to square one. Some way to block gene flow (interbreeding outside the group) has to exist. What you are proposing is simply 'putting off isolation'

I do get your point about speciation not happening when gene flow is allowed between populations.

 

[jim mcnamara]

Species defined or not define?

Okay. Let me try this. Suppose that our existing definition of species has problems. It most likely does, in fact. See, for example, the "Panda's Thumb" by S J Gould.

Nature does not dictate anything about the boundaries or definitions of species. Or even that species must exist. The concept of species, to a small extent at least, was humans imposing mental templates on something for understanding. Templates that do not always work well. So, for long time any anatomically distinct human skull from long years back was deemed a separate species. Which we would interpret as:

Homo neanderthalensis should not interbreed with humans with modern man and create viable offspring. And that has proven false. Neanderthal skulls are different from ours. And modern humans met and interbred with them sometime in the past. And note - that although there was some genetic divergence - they still interbred. "Interbred" implies a separate species or at least a varying variety. See? Our terms corner us to limit what logic we must apply. That they are probably not separate species is another point of view. Therefore, how you define species makes the answer to your question a possibly a yes or probably a no.

So does that mean that your model is viable? If you want to interpret it that way, it is probably not a standard view. The out of Africa model is standard at the moment. The problem is with our definition of species, IMO. I am leaving it at that.

I would commend the last link in @Ygggdrasil's nice post, it will help. My research in evolution was limited to plants and birds.

 

[Ygggdrasil]

IIRC from a talk by one of the groups studying admixture with Neanderthal DNA, one of the main methods they used to search for introgressed squences is by looking for linkage disequilibrium (large segments of DNA from a very different genetic background will not have had time to show recombination). Because modern humans migrated from Africa circa 240 kya, we would likely need to search for admixture occurring within the past ~ 200,000 years. These methods should not require knowing the sequence of the other hominid with which humans interbred. However, it will be easier to detect more recent examples of admixture than admixture occurring more distantly in the past.

Here are a few papers discussing these methods that I found which you may be interested in. They are somewhat old, so I have probably missed more recent developments in the field:
http://www.genetics.org/content/154/3/1271
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0020105

 

[Ygggdrasil]

Homo neanderthalensis should not interbreed with humans with modern man and create viable offspring. And that has proven false. Neanderthal skulls are different from ours.

There is quite strong genetic evidence for interbreeding between Homo sapiens and Neanderthals as DNA originating from Neanderthals can be detected in modern day humans and DNA originating from Homo sapiens can be detected in Neanderthals:
http://humanorigins.si.edu/evidence/genetics/ancient-dna-and-neanderthals/interbreeding
http://www.nature.com/news/evidence...ding-bonanza-in-ancient-human-species-1.19394
https://www.nature.com/nature/journal/v524/n7564/full/nature14558.html
https://www.nature.com/nature/journal/v530/n7591/full/nature16544.html
http://science.sciencemag.org/content/343/6174/1017

 

[laymanB]

Here are a few papers discussing these methods that I found which you may be interested in.

I knew that population genetics was complicated, so I was hoping there was at least one population geneticist on here to explain it to me. Maybe one will swing by and read this thread. If not, I'll slog through the literature in time.

 

[r8chard]

It's all about reproduction. Specifically the ability to cross-breed. Carnivores have descended from an ancient bear-dog. As far as I know, modern bears can usually reproduce with one another. I am unsure whether or not that includes Pandas? Canines can certainly all cross-breed, The trouble is trying to stop them! Cats, some can cross-breed. However, among Equines, horses and asses crossbreeding produces mules. So the issues can get pretty complex.

Homo Sapiens can all cross-breed and since there have been found traces of Neanderthals, Denisovans, and others, defining Human is still in play.

Personally I think the term Homo Sapiens should be retired as a bad concept from the racist pseudo-science of eugenics. It would be a lot more accurate to designate ourselves as Homo Anthropophagus.

 

[BillTre]

The first human populations evolved in Africa and had (and still have) high genetic diversity there.
Humans started migrating out of Africa and spreading over the rest of the world.
These population that migrated out were sub-populations and should have only a sub-set of the sequence diversity found in the original population. This is the founder effect that @jim mcnamara referred to above. It happened repeatidly, each step reducing genetic diversity to some extent.
Before modern humans, the precursors of Neanderthals and Denisovans (and perhaps others) migrated out an established population outside of Africa (for >100,000 years).
These populations may have been isolated and undergone selection to their environments and/or random genetic drift which would make their genomes more distinct from that which they were derived from.
Eventually modern humans would migrate out of Africa as another sub-set of the Africa population (having less genetic diversity than the African populations).
Various groups of these modern humans interbred with some of the extra-Africa populations which added parts of their genetic diversity to that which the African sub-population of modern humans which migrated out of Africa.

This has a variety of modern day results.
Population diversity is greatest in Africa (as a whole).
As modern human sub-groups migrated away from Africa and into newer areas (presumably in a series of steps). They have reduced genetic diversities at greater distances from Africa.
Some of these populations have acquired genes from interbreeding with Neanderthals and/or Denisovans as they migrated out and moved around. These acquired genes can be 5% of a genome. They have added to genetic diversity in that way. Some of their sequences are probably adaptive since they seem to have replaced some of those from the out of Africa migrating populations genes.
How much genetic inheritance modern humans have from these more archaic sources (Neanderthals and Denisovans) varies among different modern human populations. It is very low or non-existent in modern humans from Africa.

Therefore, to me, it is unlikely that genetics from more than one separate breeding population were important in generating the genome of modern humans (consider the modern humans of Africa).

 

[laymanB]

Thanks @BillTre

 

[ZapperZ]

According to 23andMe, I have 270 Neanderthal variants, and they make up about 4% of my DNA.

I'm using that as the excuse for my poor table manners.

Zz.

 

[Drakkith]

Personally I think the term Homo Sapiens should be retired as a bad concept from the racist pseudo-science of eugenics. It would be a lot more accurate to designate ourselves as Homo Anthropophagus.

I can't see how the term Homo Sapiens is a bad concept/term. It didn't even come from eugenics.

 

[BillTre]

Here is recent Science news article on this subject.