Archive for the ‘alleles’ Category
Did bonobos do it with chimps? Well, duh
bonobos or chimps? Or both? Or neither? What’s in a name…?
Canto: So we’ve been learning than we did it with Neanderthals, and that Neanderthals did it with Denisovans, and I remember hearing an anthropologist or palaeontologist saying that it’s likely that our split with our last common ancestor with chimps and bonobos – they call it the CHLCA (chimp-human last common ancestor, eliminating bonobos altogether, sigh) – wasn’t necessarily a clean break, which surely makes sense.
Jacinta: Well, yes, as we’ve read, the split was caused by the relatively sudden creation of the Congo River, but the word ‘relatively’, is, well, relative. So this raises the question of speciation in general. Think of those Galapagos finches that so intrigued Darwin. All about differently-shaped beaks, but it didn’t happen overnight.
Canto: Right, so here’s what a website with the rather all-encompassing title “Science” says about our topic:
Tens of thousands of years ago, modern humans slept around with Neandertals and swapped some genes. Now, it turns out one of our closest living relatives, chimpanzees, also dallied with another species. New research reveals that chimps mixed it up with bonobos at least twice during the 2 million years since these great apes started evolving their own identities. Although it’s not yet clear whether the acquired genes were ultimately beneficial or harmful, the finding strengthens the idea that such cross-species mating played an important role in the evolution of the great apes.
Jacinta: Interestingly this Congo River separation which led to a completely different species was repeated by other separations which led to four sub-species of chimps. Which leads me to wonder – what’s the difference between a new species and a sub-species? Why are bonobos ‘deserving’ of being called a different species?
Canto: Well the Science article has some fascinating further information. This was the work of Christina Hvilsom and colleagues, described as ‘conservation geneticists’. They were using any genetic differences they could find to work out where particular chimps were being caught or hunted. But, since the interbreeding of humans and Neanderthals, proven by DNA, had hit the headlines, Hvilsom wondered about the DNA of chimps. So, using the same methods that uncovered Neanderthal in humans –
she and her colleagues determined that 1% of the central chimpanzee’s genome is bonobo DNA. The genetic analysis indicates that this inbreeding happened during two time periods: 1.5 million years ago bonobo ancestors mixed with the ancestor of the eastern and central chimps. Then, just 200,000 years ago, central chimps got another boost of bonobo genes, the team reports today in Science. In contrast, the western chimp subspecies has no bonobo DNA, the researchers note, suggesting that only those chimps living close to the Congo River entertained bonobo consorts.
Jacinta: What this highlights, more than anything to me, is the importance and excitement of genetic and genomic analyses. Not that we’re experts on the topic, but it has clearly revolutionised the science of evolution, complicating it in quite exciting ways. Think again of those Galapogos finches. Separation, some interbreeding, more separation, less interbreeding, but with a few kinks along the way.
Canto: And we’re just beginning our play with genetics and genomics. There’s surely a lot more to come. Ah, to live forever…
Jacinta: So how did they know some inbreeding occurred? Can we understand the science of this without torturing ourselves?
Canto: David Reich’s book Who we are and how we got here tells the story of interbreeding between human populations, and how population genetics has revolutionised our understanding of the subject. With dread, I’ll try to explain the science behind it. First, the Science article quoted above mentions a split between bonobos and chimps 2 million years ago. Others I’ve noted go back only about a million years – for example a Cambridge University video referenced below. The inference, to me, is that there was a gradual separation over a fair amount of time, as aforementioned. I mean, how long does it take to create a major river? Now, I can’t get hold of the data on chimp-bonobo interbreeding in particular, so I’ll try to describe how geneticists detect interbreeding in general.
I’ll look at the human genome, and I’ll start at the beginning – a very good place to start. This largely comes from Who we are and how we got here, and the following quotes come from that book. The human genome consists of a double chain of 3 billion nucleobases, adenine, cytosine, guanine and thymine. That’s 6 billion bases (often called letters – A, C, G and T) in all. Genes are small sections of this base chain (called DNA), typically a thousand or so letters long. They’re templates or codes for building proteins of many and varied types for doing many different kinds of work, although there are segments in between made up of non-coding DNA.
Researchers have been able to ‘read’ these letters via machinery that creates chemical reactions to specific DNA sequences:
The reactions emit a different colour for each of the letters A, C, G and T, so that the sequence of letters can be scanned into a computer by a camera.
What anthropologists want to focus on are mutations – random errors in the copying process, which tend to occur at a rate of about one in every thousand letters. So, about 3 million differences, or mutations, per genome (3 billion genes, coding or non-coding). But genomes change over time due to these mutations and each individual’s genome is unique. The number of differences between two individuals’ genomes tells us something about their relatedness. The more differences, the less related. And there’s also a more or less constant rate of mutations:
So the density of differences provides a biological stopwatch, a record of how long it has been since key events occurred in the past.
As Reich recounts, it was the analysis of mitochondrial DNA, the tiny proportion of the genome that descends entirely down the maternal line, that became a corner-stone of the out-of-Africa understanding of human origins, which had been competing with the multi-regional hypothesis for decades. ‘Mitochondrial Eve’ – a rather ‘western’ moniker considering that the Adam and Eve myth is only one of a multitude of origin stories – lived in Botswana in Southern Africa about 160,000 to 200,000 years ago, given the variability of the genomic ‘clock’ – the mutation rate.
So, what does this have to do with chimps and bonobos? Well, The exact detail of how Hvilsom et al proved that their (slightly) more recent interbreeding events occurred is hidden behind a paywall, and you could say I’m a cheapskate but the reality is I’m quite poor, trying to bring up seven kids and a few dozen grandkids in a home not much bigger than a toilet, so… but truthfully I’m just getting by, and I just want to know in general the techniques used.
First, they have to find ancient specimens, I think. But, in a video referenced below, they raised the question – Can we ‘excavate’ ancient DNA from modern specimens? We’ve learned that many modern humans have a certain percentage of Neanderthal DNA, say around 2%, but each person’s 2% may be different. Aggregating those different segments can, if we analyse the genomes of enough humans, create a whole Neanderthal genome, though not one of any Neanderthal who ever lived! At least that’s how I’m reading it, in my dilettantish way. So what exactly does this tell us? I’m not at all sure – it’s a relatively new research area, and completely new to me.
The presenter of this video uses the heading, at least at the beginning of his talk, ‘A little Archaic introgression goes a long way’. So now I need to know what introgression means. A quick look-up tells me it’s:
‘the transfer of genetic information from one species to another as a result of hybridization between them and repeated backcrossing‘.
I’ve bolded two key words here. Hybridisation, in mammals, is ‘breeding between two distinct taxonomic units’. Note that the term species isn’t used, presumably because it has long been a questionable or loaded concept – life just seems too complex for such hard and fast divisions. Backcrossing seems self-explanatory. Without looking it up, I’d guess it’s just what we’ve been learning about. Canoodling after speciation should’ve ruled canoodling out.
But, looking it up – not so! It’s apparently not something happening in the real world, something like backsliding. But then… Here’s how Wikipedia puts it:
Backcrossing may be deliberately employed in animals to transfer a desirable trait in an animal of inferior genetic background to an animal of preferable genetic background.
This is unclear, to say the least. How could an animal, even a human, deliberately do this? We could do it to other animals, or try it, based on phenotypes. We’ve been doing that for centuries. What follows makes it more or less clear that this is about human experimentation with other animals, though.
Anyway, I’m going well off-topic here. What I wanted to do is try to understand the proof of, or evidence for, bonobo-chimp interbreeding. I accept that it happened, well after the split between these two very similar-looking species. What could be less surprising? Along the way I’ve been reminded inter alia, of homozygous and heterozygous alleles, but I’ve been frustrated that straightforward information isn’t being made available to the general public, aka myself. I’ll pursue this further in later posts.
Jacinta: What a mess. Phenotype isn’t everything my friend. To a bonobo, a chimp probably looks like a neanderthal – a real bonehead… They probably only had sex with them out of pity. ‘Boys, we’ll show you a good time – like you’ve never had before.’
References
https://www.science.org/content/article/chimps-and-bonobos-had-flings-and-swapped-genes-past
David Reich, Who we are and how we got here, 2018
https://www.newscientist.com/article/2110682-chimps-and-bonobos-interbred-and-exchanged-genes/
exploring genetics – Mendel, alleles and stuff
Canto: So I’d like to know as much as I can about genetics before I die, which might be quite soon, so let’s get started. What’s the difference between genetics and genomics?
Jacinta: Okay, slow down – but I suppose that’s as good a place to start as anywhere. I recently listened to a talk about the human genome project, which was completed around 2003, and the number I heard the guy mention was 3 billion genes, or something. But according to videos and other sources, each human has between 20,000 and 25,000 genes – though I’ve found another FAQ which estimates 30,000. So I gather from this that our genome is the number of genes we might possibly have – in the whole human population? Which raises the question, how do we know that the human genome project has captured or mapped all of them.
Canto: So there’s an individual genome, peculiar to each of us, and a collective genome?
Jacinta: Errr, maybe. We’re 99.9% genetically identical to each other, supposedly. And if this sounds very paradoxical, we need to zoom in on the detail. And with that, I’ve discovered that the 3 billion refers to base pairs, sometimes called ‘units of DNA’. So what’s a base pair? Well, we need to start with the structure of DNA, the genetic molecule. That’s deoxyribonucleic acid, which is made up of basic components called nucleotides. A nucleotide of DNA consists of a sugar molecule, a phosphate group and a nitrogenous base. The bases come in four types – adenine, guanine, thymine, and cytosine (A, T, G and C). The sugar and phosphate groups provide structure, allowing the bases to form a long string of DNA. Bonds form between the bases to create a double strand of DNA – hence base pairs.
Canto: Here’s how the World Health Organisation defines genomics, obviously from a health perspective:
Genomics is the study of the total or part of the genetic or epigenetic sequence information of organisms, and attempts to understand the structure and function of these sequences and of downstream biological products. Genomics in health examines the molecular mechanisms and the interplay of this molecular information and health interventions and environmental factors in disease.
Now you might think that this definition could cover genetics too, and maybe we shouldn’t be too worried about the distinction. Maybe, in general, genomics is about sequences of genes, especially in detailing whole organisms, while genetics is more about individual genes.
Jacinta: Genomics is the much more recent term, first coined in the 1980s, whereas genetics and genes date back to before we knew about DNA as the genetic molecule. Going back to Mendel and all, though I don’t think he used the term, he talked about ‘factors’ or some such.
Canto: So we know that there’s DNA, and there’s also RNA, another building block of life. How old are they, and which came first? And can species replicate without these molecules?
Jacinta: Oh dear – we’ll get there eventually, maybe. Genomics deals with the whole complement of genes in an organism, which we’ve gradually realised is necessary to evaluate, say, how prone that organism is to contracting a disease, or developing some immuno-deficiency, because individual genes often don’t tell us much. And there’s also the matter of dominant and recessive genes. Which takes us to inheritance. All those genes are combined together on chromosomes, of which there are 23 pairs in humans, which we inherit from our parents, 23 chromosomes each.
Canto: Combined together? Can you be more specific?
Jacinta: Okay, a chromosome is a thread-like structure, in which DNA is coiled around structural proteins called histones. Each chromosome has two ‘arms’, flowing from a constriction point called a centromere. These arms are labelled p and q. The p arm is shorter than the q. And these chromosomes contain genes, which may or may not code for proteins. The genes, as mentioned, consist of base pairs, which vary in number from hundreds to millions.
Canto: Okay, so what’s the difference between a gene and an allele?
Jacinta: Well, genes are codes for making proteins – and those proteins affect all sorts of things, to do with taste, smell, hair colour and type, height, and predisposition to various diseases, among many other things. You can call these things ‘traits’, which show up in our phenotype, our physical characteristics. And it should be pointed out that many of these traits are the results of not just one gene but different genes in combination. Now, as mentioned, these genes are in pairs of chromosomes – 23 pairs in humans. Now, say we isolate an area in a chromosome that codes for a particular trait. What about the other chromosome in that pair? Remember, each chromosome comes from a male or female parent, and they are different, genetically – or likely to be. That’s where alleles come in, and it takes us back to Mendel, who found that with pea plants, traits such as colour, or the alleles that carried those traits, could be dominant or recessive. So, for that trait, they could carry two dominant alleles, or two recessive alleles, or one of each. If one or both of those alleles is dominant, the trait will be expressed, but if both are recessive, it won’t be. But as I say, it’s more complicated than that, as traits expressed in phenotypes are generally carried by many genes.
Canto: So alleles are? – how to define them?
Jacinta: Google it mate. Here’s a quickly found definition: “each of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome”. So let’s continue with the work of Mendel. When we find a dominant trait, we use a capital, T. It might be paired with another dominant trait, TT, or with a recessive trait, Tt. On the other hand, both traits might be recessive, tt, and that’s all the combos you have, for single traits. Now, in noting this, and the way that alleles combine, Mendel came up with a ‘law of segregation’. Or rather, he noticed a process, which later became recognised as a law. In fact, he observed three fundamental processes, ‘segregation’, ‘independent assortment’, and ‘dominance’, which we now describe as laws. Now, I’ve used the term ‘trait’ but perhaps I should’ve used the term ‘allele’. So TT combines two dominant alleles. The law of segregation has been stated thus:
During gamete formation, the alleles for each gene segregate from each other such that each gamete formed carries only one allele for each gene.
Canto: Right. Uhhh, what’s a gamete again?
Jacinta: Sex cells, which carry only one copy of each chromosome. They’re created during meiosis, after which we end up with four cells each with only one allele for each gene. So indeed, alleles are segregated during gamete formation.
Canto: Oh dear. I’ll have to brush up on meiosis.
Jacinta: So now we have these segregated alleles, which will be recombined. The law of independent assortment comes next. This also occurs during meiosis. In the fourth or metaphase period of cell division, the chromosomes align themselves on the equatorial plane, also called the metaphase plate. This alignment is random, and that’s the key to the law of independent assortment – ‘genes for different traits assort independently of each other during gamete formation’. But obviously Mendel knew nothing about meiosis, though it was first observed in his lifetime, in sea urchins . Anyway, this law allows for many different combinations of alleles depending on how chromosomes become aligned on the metaphase plate. A dihybrid cross will provide more such combinations.
Canto: A dihybrid cross? Please explain.
Jacinta: Well, a monohybrid cross will be like this – TT x tt. Not much to be assorted there. A dihybrid cross might be like this – TtCc x TtCc, creating four different assortments for each cross. So now to the third law, of dominance. This law simply states that ‘some alleles are dominant while others are recessive. An organism with at least one dominant allele displays the effect irrespective of the presence of the recessive one’. So the phenotype will present the dominant allele regardless of whether it’s double-dominant or single-dominant. Though the terms used are homozygous (TT), or heterozygous (Tt).
Canto: So are we going to look at punnett squares now? I’ve heard of them…
Jacinta: Well it might help. They were named after a bloke called Punnett back in 1905, the early days of Mendelian genetics. They’re neat little tables, that can start to get quite complicated, for determining the genotypes of offspring, when you breed dominant with recessive, heterozygous with homozygous and so on. It’s useful for simple genotypes, but when genotypes are multifactorial, as they often are, other methods are obviously required.
Canto: Okay, that’s more than enough to absorb for now.
Jacinta: I think, since we’ve started with Mendel, we might do a historical account. Or maybe not….
References
https://www.google.com/search?client=safari&rls=en&q=alleles&ie=UTF-8&oe=UTF-8
https://byjus.com/biology/mendel-laws-of-inheritance/
https://www.yourgenome.org/facts/what-is-meiosis