You are collaborating with a group of archeologists to reconstruct the history o

Question

You are collaborating with a group of archeologists to reconstruct the history of cattle domestication. Your archeologist colleagues tell you that cattle were already domesticated by 9000 years ago, as evidenced by the appearance of pottery fragments containing traces of milk. However, it is not clear from archeological records when the domestication began, or how large the cattle herds were in the first few millennia after domestication. As a biologist, you are familiar with genetic drift and coalescence so you know that effective population size and the time to last common ancestor can be estimated from the patterns of contemporary genetic diversity. You sequence the coding sequence of a milk protein gene from many cows belonging to different breeds on several continents. From these sequences, you estimate that the effective population size of cattle is 100,000, and all present-day alleles coalesce 600,000 years ago. You realize that this is inconsistent with archeological data (no milk pottery is observed until 9,000 years ago) as well as with our knowledge of human evolution (modern humans evolved only 100,000 years ago). To get more genetic data, you sequence the upstream non-coding sequence of the same gene. When you analyze these sequences, they indicate an effective population size of 5,000 and coalescence time of 3,000 years ago. Given this obvious contradiction between two parts of the same gene, you decide to get more independent data by sequencing the mitochondrial genome and several neutrally evolving nuclear genes. The mtDNA produces the same estimate of population size and coalescence time as the upstream non-coding region of the milk protein gene, while the nuclear genes give you the same estimate as the protein-coding portion of the milk gene. You must now propose evolutionary scenarios that could explain your observations.

1 (1 point). The current number of cattle on the planet is approximately 1.3 billion, yet all estimates of the effective population size are much lower. List several factors that could contribute to this mismatch.

Explanation / Answer

Although it is clear that selection is pervasive in humans and other organisms, the relative importance of positive and negative selection is still debated. Much of the natural selection acting on genomes may be negative selection acting to remove new deleterious mutations. Most exons in protein-coding regions are highly conserved between species, because many potential mutations would disrupt protein function. Therefore, the conservation of genic regions provides evidence of past negative selection and provides an important route to genome annotation. Similar evidence for conservation and negative selection in non-coding regions provides the basis for an important approach for detecting functional elements, such as microRNAs. 70–75% of amino-acid altering mutations are affected by moderate or strong negative selection. Importantly, however, much of this selection might act at the level of gametogenesis, on mature gametes or during early development. Mutations that are strongly deleterious will be quickly eliminated by natural selection, and only mutations that have, at worst, a mildly negative fitness effect will be observed as segregating in the population. Much attention has focused on this type of selection because it provides the footprints of evolutionary adaptation at the molecular level. Identifying genomic regions that have been influenced by positive selection provides a key to understanding the processes that lead to differences among species and a subset of heritable phenotypic differences within species. For example, we can learn much about the biological basis of the evolution of modern humans by studying how positive selection has affected the human genome over the past few hundred thousand years. In general, positive selection is relevant when we seek to understand species-specific adaptations or processes that relate to dynamic interactions between the organism and its environment. the genome on the human lineage leading from the ancestor of human and chimpanzees to modern humans18–20. In general, these studies have identified genes involved in immune-related functions, spermatogenesis, olfaction and sensory perception, and have highlighted several other functional gene categories with an increased likelihood of having experienced positive selection. Genes in these categories are likely to be involved in direct interactions with the environment, and will be under selective pressure in the face of environmental change. In particular, genes involved in dynamic competitive or co-evolutionary interactions are expected to experience more positive selection. A prime example of this is immunity and defence-related genes, which are involved in dynamic interactions with pathogens. As a category, these genes have experienced by far the most positive selection in humans and other organisms18–20.

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