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Evolutionary Genetics and Common Ancestors

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How do species evolve from a common ancestor?

What are the differences between human, chimpanzee and their common ancestor, on the chromosome and genome levels?

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1. How do species evolve from a common ancestor?

What is a species? Members of one species do not normally interbreed with members of other species in nature. Sometimes, members of different species, such as lions and tigers, can interbreed if kept together in captivity. But in nature, geographic isolation and differences in behavior, such as choice of habitat, keep these sorts of closely related animal species apart. Similarly, closely related species of plants can sometimes be hybridized by horticulturists, but these hybrids are rarely found in nature. A species, then, is defined by science as a group of interbreeding or potentially interbreeding populations that is reproductively isolated from other such groups.

Interestingly, according to the evolution theory of existence, all species are related.

How? Just as the tree of life illustrates, all organisms, both living and extinct, are related. Every branch of the tree represents a species, and every fork separating one species from another represents the common ancestor shared by these species. While the tree's countless forks and far-reaching branches clearly show that relatedness among species varies greatly, it is also easy to see that every pair of species share a common ancestor from some point in evolutionary history. For example, scientists estimate that the common ancestor shared by humans and chimpanzees lived some 5 to 8 million years ago. Humans and bacteria obviously share a much more distant common ancestor, but our relationship to these single-celled organisms is no less real. Indeed, DNA analyses show that although humans share far more genetic material with our fellow primates than we do with single-celled organisms, we still have more than 200 genes in common with bacteria.

It is important to realize that describing organisms as relatives does not mean that one of those organisms is an ancestor of the other, or, for that matter, that any living species is the ancestor of any other living species. A person may be related to blood relatives, such as cousins, aunts, and uncles, because she shares with them one or more common ancestors, such as a grandparent, or great-grandparent. But those cousins, aunts, and uncles are not her ancestors. In the same way, humans and other living primates are related, but none of these living relatives is a human ancestor.

(Source: http://www.pbs.org/wgbh/evolution/library/05/index.html).

More information : History of hominoid taxonomy
The history of hominoid taxonomy is somewhat confusing and complex. The names of subgroups have changed their meaning over time as new evidence from fossil discoveries, anatomy comparisons and DNA sequences, has changed understanding of the relationships between hominoids. The story of the hominoid taxonomy is one of gradual demotion of humans from a special position in the taxonomy to being one branch among many. It also illustrates the growing influence of cladistics (the science of classifying living things by strict descent) on taxonomy.
As of 2005, there are eight extant genera of hominoids: Homo (humans), Pan (chimpanzees), Gorilla, Pongo (orangutans), and four genera of gibbons. The common ancestor is the Hominoidea:

However, DNA comparisons provide convincing evidence that within the subfamily Homininae, gorillas are the outgroup. This suggests that chimpanzees should be in Hominini along with humans. This classification was first proposed (though one rank lower) by M. Goodman et. al. in 1990.[4]
(Source: http://en.wikipedia.org/wiki/Common_Chimpanzee).

2. What are the differences between human, chimpanzee and their common ancestor, on the chromosome and genome levels?

Generally, what do genes have to do with evolution? Genes are the portions of an organism's DNA that carry the code responsible for building that organism in a very specific way. Genes -- and, thus, the traits they code for -- are passed from parent to offspring. From generation to generation, well-understood molecular mechanisms reshuffle, duplicate, and alter genes in a way that produces genetic variation. This variation is the raw material for evolution.
From an evolutionary perspective, it is true that all animals (and ultimately, all organisms) are related by descent from a common ancestor, and that because of this, we all share genes that are related to a certain extent. This degree of sharing is directly proportional to the relatedness of the animals in question. However, when you consider all animals as a group, I think that you will see that the specific differences involve more than simple rearrangements and recombinations. Many genes have been duplicated, completely deleted, or changed in their functions in radical ways. The collected DNA of an organism is called its genome. Genes are those sections of the genome which encode proteins. The human genome is made up of almost 3 billion nucleotide bases, but only on the order of 30 million of those bases (or around 1-2%) are used to code for protein products -- these 30 million or so bases make up our approximately 30,000 genes. It seems likely that species which are closely related to us (for example, Chimpanzees and Gorillas, with whom we supposedly (according to evolutionary theory) shared a common ancestor only ~6 million years ago) have a similar number of genes, which differ in their organization, nucleotide sequences, and the levels of their expression (http://www.madsci.org/posts/archives/jul2001/996378986.Ge.r.html).
Common Ancestor "walked on four legs": The great ape family was previously referred to as Pongidae, and humans (and fossil hominids) were omitted from it, but on grounds of relatedness there is no argument for doing this. Chimpanzees, gorillas, humans and orangutans are all more closely related to one another than any of these four genera are to the gibbons and siamangs. Awkwardly, however, the term "hominid" is still used with the specific meaning of extinct animals more closely related to humans than the other great apes (for example, australopithecines). It is now usual to use the subfamily Homininae to separate the hominids, in this narrow sense, from the extant non-human members of the family Hominidae. ...

Solution Summary

This solution explains how species evolve from a common ancestor and the chromosomal and genome differences between human, chimpanzee and their common ancestor. All references used are included.