BIOL 115 Lecture Notes - Lecture 5: Allopatric Speciation, Reproductive Isolation, Population Bottleneck

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19 Sep 2017

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If we say that tortoises have a maximum of two offspring in their lifetime. We can assume that natural selection would favor the fatter tortoises. However, this is only true if we assume that tortoises breed when they are old. If living longer means it is more likely that you will produce offspring, then natural selection will favor that. Individuals have to express a genotype as a phenotype for selection to work. There has to be phenotypic variation (that is heritable) for selection to act on. Females benefit directly by choosing a male with a certain phenotype. We have one individual who is a choosy individual and that individual has a preference for pink. This preference arises for one of several reasons: One way that this could arise is because of direct benefits (pink individuals have less parasites) Doesn(cid:495)t explain why the preference arises, but does explain how you can get crazy.

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In the passages below, Darwin and Wallace both clearly define what a species is based on their observations of the natural world. They then provide explanations for how new species arise.

Excerpt from âThe Origin of Species and Genera (S322: 1880), January 1880 issue of Nineteenth Century,â by Alfred R. Wallace ... A species may be defined as a group of individuals of animals or plants which breed together freely and reproduce their like; whence it follows that all the individuals of a species, now living or which have lived, have descended from a few common ancestors, or perhaps from a single pair. Thus all horses, whether Shetland ponies, racers, or cart-horses, form one species, because they freely breed together, and are known to have all descended from a common stock. By the same test the common ass, the kiang, the quagga, and the zebra, are each shown to be distinct species; for though sometimes two of these species will breed together, they do not do so freely, they do not reproduce their like but an intermediate form called a mule, and these mules are not capable of reproducing their kind, as are the offspring of any pairs of a single species.

Excerpt from âOn the Origin of Species,â by Charles Darwin, 1859 ... So with natural species, if we look to forms very distinct, for instance to the horse and tapir, we have no reason to suppose that links ever existed directly intermediate between them, but between each and an unknown common parent. The common parent will have had in its whole organisation much general resemblance to the tapir and to the horse; but in some points of structure may have differed considerably from both, even perhaps more than they differ from each other. Hence in all such cases, we should be unable to recognise the parent-form of any two or more species, even if we closely compared the structure of the parent with that of its modified descendants, unless at the same time we had a nearly perfect chain of the intermediate links. ...

ï¿¼ï¿¼Excerpt from On the Origin of Species, Chapter 4, by Charles Darwin, 1859 ... On the view that each species has been independently created, I can see no explanation of this great fact in the classification of all organic beings; but, to the best of my judgment, it is explained through inheritance and the complex action of natural selection, entailing extinction and divergence of character, as we have seen illustrated in the diagram. ...

Question: From all these readings, is there evidence that both Darwin and Wallace independently formulated the theory of evolution by natural selection? Support your answer.

Recently I have found myself in a discussion with a guy thatisn't a creationist, but denies evolution. He cites several studiesthat show problems like this one, but I do not have the knowledgeto refute it properly. Whats the problem with the following:

One problem is that population genetics shows us evolutiondestroys functional sequences much faster than it creates them inany large-genome animal with low reproductive rates, becausedeleterious mutations arrive faster than selection can remove them.This would include just about all mammals, reptiles, and birds--anyof our would-be ancestors over the last 300m years.

Specifically, humans get 60 to 160 mutations per generation,10-20+% of our genome is sensitive to substitution, and this givesus 6-32 deleterious mutations per offspring (most slight). Evenwith the low estimate of 6, every child is less fit than theirparents and natural (or even artificial) selection can only choosethe least degenerate each generation. For every generation where amutation can be selected, random mutations destroy 5-32+ previouslyselected. Beneficial mutations like lactose tolerance (a jammedswitch) take 1000s of years to appear and fixate.

If you know the genome size, mutation rate, and reproductiverate, you can calculate at what rate deleterious mutations arrivefaster than they can be removed:

"It has been estimated that there are as many as 100 newmutations in the genome of each individual human. If even a smallfraction of these mutations are deleterious and removed byselection, it is difficult to explain how human populations couldhave survived. If the effects of mutations act in a multiplicativemanner, the proportion of individuals that become selectivelyeliminated from the population (proportion of `genetic deaths') is1-e^-U, where U is the deleterious mutation rate per diploid, so ahigh rate of deleterious mutation (U>>1) is paradoxical in aspecies with a low reproductive rate." High genomic deleteriousmutation rates in hominids, (Nature, 1999)

They worry about a deleterious rate of U much greater than 1 asbeing prohibitively high and we're talking about it being 6-32+,since we now know the functional genome is much larger than wethought it was in 1999. Taking their Poisson probabilitydistribution and using U=6, that means 1-e^-6 = 99.752% of thepopulation will have to be selected away each generation for onelucky enough to have no deleterious mutations. For two to surviveand maintain constant population size that would require on average806 offspring per female--impossible for most mammals, birds, andreptiles. Actually much more since natural selection is notomnisciently efficient.

For years we have been able to analyze the fossils of extincthumans like those of Neanderthals. Their bones gave us clues to howthey looked, how they lived, and how they might be related to us.In the last few years, we have been able to get a better view intothese extinct species and their relationship to our species. Thanksto next generation genomic sequencing technologies, we have beenable to obtain genetic data on Neanderthals, Denisovans and othersthat have allowed us to make direct comparisons between our speciesand theirs. In addition, we have been able to observe the presenceof DNA from these extinct species within our own genomes which tellus that we had kids with these now extinct humans.

If we take Neanderthal DNA as an example, we find that we share99.5 percent of our DNA with them. Which means that we andNeanderthals were separated from each other for more than 500,000years. This also means that we were genetically similar enough tobe able to have offspring with each other. We see evidence of thisgenetic introgression between us and Neanderthals when we look atour DNA. Interestingly, if we obtain one thousand DNA samples fromGrossmont College students, we estimate that we would be able toextract at least 20% of the Neanderthal genome from them. Thismeans that 20% of our collective nucleotide sequences are sharedwith Neanderthals but this doesnât mean that 20% of our genes areNeanderthal specific genes. Of the twenty-one thousand genes thatNeanderthals had, only a few dozen of their genes survive withinour genome. The same holds true for Denisovans. What is moreinteresting is that older versions of ourselves have a tendency tohave higher levels of DNA from extinct humans compared toourselves. In other words, over the course of thousands of years wehave been slowly weeding out the DNA of the other humans from ourgenome in favor of our genes.

One basic question that we might like to ask is why have we beenlosing Neanderthal and Denisovan genes over time? Also, why do westill have a significant amount of DNA segments that donât seem tobe going anywhere? The answer to this has to do with selection.

The answer to the first part of the question has to do with thefact that we were not fully genetically compatible with the otherhuman species to begin with. Basically, to have had Neanderthal orDenisovan genes in the past meant that an individual's level offitness was reduced. To get rid of their genes in favor of our ownwould mean that the relative fitness of individuals would increaseovertime.

The answer to the second question has to do with the fact thatDNA segments from Neanderthals and Denisovans that did not code forproteins remained because there was little selective pressureagainst them. As far as genes are concerned, the only Neanderthaland Denisovan genes that remain only exist because they had aselective advantage or at least have been neutral to ourspecies.

DNA segments that that were neutral or that had a selectiveadvantage, whether genes or not, simply remained because they wereadvantages or there was little selective pressure against them.

Your task for this week is to look for information about oneNeanderthal or Denisovan gene that survive within our species andto tell me what function that gene has and how that gene mayincrease the fitness of modern human populations.

In your post, discussONE Neanderthal orDenisovan gene that is currently found within our species.
- Tell us about the gene and its function. Explain what it doesfor us. (Make sure you give a citation.)
- Explain in your own words any possible advantages that yourNeanderthal or Denisovan gene might have. Make sure you give ininformed opinion that is grounded in your research.

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BIOL 115 Lecture Notes - Lecture 5: Allopatric Speciation, Reproductive Isolation, Population Bottleneck

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