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Lecture 12

LECTURE 12 - Part 1 - translated audio to words

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John Stinchcombe

LECTURE 12 – BIO220 – Audio to Words Translation for first half… So, what I want to talk about for this lecture falls under the broad category of ecological and evolutionary genomics. And what this field is trying to do is to take an ecological or an evolutionary perspective to both understand patterns of genomic variation or patterns of DNA variation, but also to use our information, that we can get from understanding DNA and genome sequences, to understand ecological and evolutionary phenomena. So, for example, chimpanzees and humans... so this is outdated, Matt Deymond is no longer the sexiest… so, these individuals share 99% of their DNA sequence. These 3 are in a zoo, he's on a magazine cover. Why is that? This is the fundamental genetic code that's specifying proteins, amino acids, the functioning of our bodies… we have 98-99% identical. We want to understand, how is it, that with the same material, we can get dramatically different phenotypes out of evolution. So these are some of the things we are going to talk about. So, just as a reminder, you all remember from BIO120, that differences in ecology are creating natural selection in all the time out there in the environment. Genetics is ensuring transmission across generations. And so, as a consequence, offspring resemble their parents. You put these two things together, of natural selection and genetics, and you get evolution. What we want to do, is use our knowledge of genetic principles to understand ecological and evolutionary phenomena. And then, the flip side of the coin is also true. We want to use our knowledge of behaviour and ecology to deduce the mechanisms out in nature that are producing patterns in genetic data. So those are the two sides of the coin of ecological genetics that we're going to focus on. So, we put up, onto Portal, some review slides. Some of them are just definitions of key terms. Some of them are slides from BIO120 on issues related to heterozygosity, the polymorphism, what forces maintain genetic variation in populations and so on. Please review it. I'm going to assume that that was BIO120, you guys all got As in that course… you completely call it to memory, right? *evil maniacal laugh* Okay, well, everything you're going to need is either on the slides or in the review material. So, want to understand modern topics, natural selection and it's effect on the genome, and we're going to try to apply these to real world problems, in particular, to agriculture, to harvested populations, and to conservation of endangered species. So, the first point to think of, is that our genomes are really mosaics. So we all have genetic material that we receive from our mother and from our father, and as a consequence of this, the total amount of DNA we have is our genome. Some of this is mitochondrial. Mitochondrial DNA… and in plants, this is in the chloroplasts. This is due to the endosymbiosis of prokaryotic bacteria way back in the origin of eukaryotes. And these organelles, inside cells, have their own genomes, and their own DNA. And, all population members are going to be getting mitochondrial DNA, or in the case of plants, chloroplast DNA. We have sex chromosomes… so, in humans this is the x/y system. Where humans, fruit flies, and so on… where females have 2XXs, males have an X and a Y. For birds, butterflies and moths, this is reversed… where the homogametic sex has two what are called "Z" chromosomes, and females are the heterogametic sex… so they have a W chromosome and a Z chromosome. And then there are the autosomes. Now, the autosomes are all the other chromosomes besides the sex chromosomes. We receive one copy from each of our parents. But the autosomes themselves, we can break up into two areas. The first area are areas of high recombination, where there's lots of crossing over during the formation of gametes. The other area would be areas of low recombination. So, a classic example of this would be areas near the centromeres or telomeres of chromosomes. These areas have reduced recombination. So, as we've broken down, the total amount of DNA present in all of our cells… you see that it's not just one giant amalgamation, that there's some structure to it. And in particular, there are a few key aspects of it. In that, mitochondrial DNA in particular, is inherited maternally. So, when a sperm and an egg fuse, a sperm is providing pretty much nothing but DNA to the egg. The egg has its own haploid set of chromosomes. But all of the cytoplasm, where all the mitochondria are, are maternally provided. And so, mitochondrial DNA is maternally inherited, while the rest of these are inherited from both of the sexes. And these will have dramatically different effects on their evolutionary dynamics and what we can learn about evolution from studying genetic markers, in these different regions of the genome. So, let's see here… they have different modes of transmission… I just mentioned that… some of them are uniparentally inherited. So, we get the mitochondria from the mother, for males they get the Y chromosome only from the father. Others are biparental. Some of these aspects of the chromosome, a contingent that we have of the genome, are only present in half the population. A classic example of this is the Y chromosome. Or, in the case of birds... and moths and butterflies... the W chromosome. And, one thing to remember, in particular about recombination, is that, when there are areas of low recombination, you have whole chunks of chromosomes that will be inherited together. In contrast, when you have areas of high recombination, where there's lots of crossing over during the formation of gametes, then those areas of the chromosome are going to be inherited almost independently. So how do we use these? So, if we look at biparentally inherited genetic markers, we can infer the contributions of both parents. Or, we can look at mitochondrial DNA that will track the contribution of maternal lineages. Or Y chromosomes to track the contribution of paternal lineages. And so if you combine them, we're going to understand both evolution, and also we can apply some of our knowledge of ecology and behavior. So, let me give you an example of how this has really transformed a lot of studies in ecology and evolution. In elephants, they're composed of natal groups where females live… females are sort of the dominant parts of the social hierarchy… young live with the group that they were born into. And there are usually 2-20. And, they're composed only of mature females and juveniles. The males, when they hit adolescence…
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