Nuclear DNA

Surprisingly, only a small fraction of the nuclear DNA (nDNA) contained in chromosomes consists of gene sequences that code for production of proteins. It is estimated that less than 5% of human DNA consists of genes that code for approximately 30,000 different proteins. Much of the rest (95%) has no well-established function and is often labeled "junk DNA". A large part of this DNA consists of repetitive sequences that in some cases are present as many thousands of copies. Such DNA sequences that have been inserted into the genome are known as "retroposons", but their function remains essentially unknown.

Reconstruction of phylogenetic relationships using DNA sequences that code for protein sequences (or using the protein sequences themselves) hence involves only a small part of the nuclear genome. Nevertheless, there are many different nuclear genes available for analysis, and the sequence data set for mammals is increasing rapidly. Certainly, the potential total sequence information that can be obtained from the 30,000 protein-coding genes in the nuclear genome is vastly greater than that provided by the 13 protein-coding genes in the mitochondrial genome. As a general rule, the reliability of phylogenetic trees generated with molecular data increases both with the number of species included in comparisons and with the number of DNA sequences analyzed. However, there are some unresolved problems with the methods currently employed for reconstruction of trees using molecular data. Furthermore, there are practical limits to the quantity of data that can be effectively analyzed, so various short-cuts are necessary.

In addition to protein-coding DNA sequences, some categories of retroposons (inserted sequences) are becoming increasingly useful as tools for reconstructing phylogenetic relationships. This is particularly true of inserted sequences known as short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINEs), respectively.

The African elephant (Loxodonta africana) has been grouped into the Afrotheria cluster of placental mammals. (Photo by © Craig Lovell/ Corbis. Reproduced by permission.)

Four phylogenetic mammal trees have been established. The branch Laurasiatheria includes carnivores such as the gray wolf (Canis lupus). (Photo by Tom Brakefield/Bruce Coleman, Inc. Reproduced by permission.)

Because SINEs and LINEs apparently arise at random and occur widely throughout the genome, they are almost ideal derived characters. Given the vast array of DNA sequences in the nuclear genome, the probability of convergent evolution in the insertion of a SINE or LINE is exceedingly small. It is highly improbable that one of these sequences will be inserted at exactly the same site in the genome in two separate lineages. Secondly, because each insertion is a unique event that is unlikely to be reversed, SINEs and LINEs provide excellent markers for the recognition of groups of related organisms descended from ancestors possessing specific insertions. A very good example of the use of such evidence comes from discussion of the relationships between cetaceans (dolphins and whales) and artiodactyls (even-toed hoofed mammals). It has been accepted for some time that cetaceans are in some way related to artiodactyls. However, accumulating evidence from DNA sequences (both mtDNA and nDNA) indicated that cetaceans are, in fact, specifically related to hippopotamuses and thus nested within the artio-dactyl group. This interpretation conflicts with the standard interpretation of the morphological evidence, according to which cetaceans constitute the sister-group to all artiodactyls. Certain fossil forms (mesonychians) that were regarded as relatives of whales and dolphins lacked a characteristic double-pulley adaptation of the ankle joint that is found in all artiodactyls (and was most probably present in their common ancestor). It had therefore been concluded that cetaceans branched away before the emergence of ancestral artio-dactyls. This conflict of evidence was convincingly resolved by the discovery that cetaceans and hippopotamuses share a number of SINEs that are not found in any other mammals. Subsequently, early whale fossils possessing the typical ar-tiodactyl ankle joint were discovered. Hence, it is now well established that cetaceans and hippopotamuses are sister-groups and that mesonychians are not direct relatives of the cetaceans after all.

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