|MadSci Network: Molecular Biology|
This is a very interesting question. Let me begin with some of the current estimates of what is in the human genome, and how much of it is useless. If you compare the human genome to the genome of other organisms, it is possible to see what percentage of the human genome is conserved between the two species. In comparison to mouse, which diverged from human about 70 million years ago, about 5% of the sequence is conserved, meaning that there are fewer changes than one would expect over that amount of time if changes had no effect. About 3% of the conserved sequence is known coding sequence (part of the gene that codes for the amino acids of a protein sequence). Here is an overview of one of the key mouse sequencing papers: http://www.bio-itworld.com/archive/021003/paperview.html The citation is: Mouse Genome Sequencing Consortium. "Initial sequencing and comparative analysis of the mouse genome." Nature 420, 520-562 (2002). Full text available at: www.nature.com/nature/mousegenome Here you will find that most mouse genes (at least 99%) have a human counterpart, and about 99% of mouse genes have a human counterpart. Most of the rest of the human genome, the 95% that is not conserved from mouse to human, is repetitive "junk" DNA. These sequences are mobile genetic elements that expanded explosively at several distinct times in human evolution. We know this because after the repeated elements expand to occupy a larger percentage of the human genome, the individual copies mutate at a fairly constant rate over time. This means that repeats that are divergent in sequence are old, and repeats that are highly similar duplicated recently. Your question implies that we can identify squid genes in the human genome that are no longer used by humans. A more accurate way to look at the problem is that there are a set of genes in common between humans and squids. There is a continuous chain of living individuals extending back to the common ancestor of humans and squids. Both organisms, for example, use a contractile apparatus consisting of actin and myosin to make their muscles work. The human and squid proteins differ in their sequence because the sequences in both lineages have diverged since these two species diverged. If you were to look at all of the proteins expressed in gills, you would find a set of proteins common to cell types in the rest of the squid. There is not a single gene that says, "make a gill." Complex structures like hands, gills, eyes, and other organs form in response to the expression of an array of regulatory genes that act during development. Gills are an interesting example, because the gill arches of fish have become the bones of our inner ear. Here is a quote from Developmental Biology by Scott F. Gilbert. You can see this online at: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=dbio.TOC&depth=2 __________ "One of the most celebrated cases of embryonic homology is that of the fish gill cartilage, the reptilian jaw, and the mammalian middle ear (reviewed in Gould 1990). First, the gill arches of jawless (agnathan) fishes became modified to form the jaw of the jawed fishes. In the jawless fishes, a series of gills opened behind the jawless mouth. When the gill slits became supported by cartilaginous elements, the first set of these gill supports surrounded the mouth to form the jaw. There is ample evidence that jaws are modified gill supports. First, both these sets of bones are made from neural crest cells. (Most other bones come from mesodermal tissue.) Second, both structures form from upper and lower bars that bend forward and are hinged in the middle. Third, the jaw musculature seems to be homologous to the original gill support musculature. Thus, the vertebrate jaw appears to be homologous to the gill arches of jawless fishes. But the story does not end here. The upper portion of the second embryonic arch supporting the gill became the hyomandibular bone of jawed fishes. This element supports the skull and links the jaw to the cranium (Figure 1.14A). As vertebrates came up onto land, they had a new problem: how to hear in a medium as thin as air. The hyomandibular bone happens to be near the otic (ear) capsule, and bony material is excellent for transmitting sound. Thus, while still functioning as a cranial brace, the hyomandibular bone of the first amphibians also began functioning as a sound transducer (Clack 1989). As the terrestrial vertebrates altered their locomotion, jaw structure, and posture, the cranium became firmly attached to the rest of the skull and did not need the hyomandibular brace. The hyomandibular bone then seems to have become specialized into the stapes bone of the middle ear. What had been this bone's secondary function became its primary function. The original jaw bones changed also. The first embryonic arch generates the jaw apparatus. In amphibians, reptiles, and birds, the posterior portion of this cartilage forms the quadrate bone of the upper jaw and the articular bone of the lower jaw. These bones connect to each other and are responsible for articulating the upper and lower jaws. However, in mammals, this articulation occurs at another region (the dentary and squamosal bones), thereby 'freeing' these bony elements to acquire new functions. The quadrate bone of the reptilian upper jaw evolved into the mammalian incus bone of the middle ear, and the articular bone of the reptile's lower jaw has become our malleus. This latter process was first described by Reichert in 1837, when he observed in the pig embryo that the mandible (jawbone) ossifies on the side of Meckel's cartilage, while the posterior region of Meckel's cartilage ossifies, detaches from the rest of the cartilage, and enters the region of the middle ear to become the malleus (Figure 1.14B,C). Thus, the middle ear bones of the mammal are homologous to the posterior lower jaw of the reptile and to the gill arches of agnathan fishes. Chapter 22 will detail more recent information concerning the relationship of development to evolution." ________ If genes are not expressed in the human genome, they do not survive intact over evolutionary time, because they accumulate mutations in the absence of selection. If there were squid genes in the human genome that could be "activated," it is likely that the accumulated mutations would result in a truncated gene product (3 of the 64 codons are "stop") with many changes in its sequence. See also the MGI Glossary: http://www.informatics.jax.org/mgihome//other/glossary.shtml Yours, Paul Szauter Mouse Genome Informatics
Try the links in the MadSci Library for more information on Molecular Biology.