Introduction

Traditional studies of evolutionary relationships among living organisms (phylogenetics) relied predominantly on comparisons of morphological characters. However, phylo-genetic studies have increasingly benefited from additional inputs from molecular genetics. Reconstruction of evolutionary relationships among mammals provides a prime example of such benefits, and the broad outlines of the phylogenetic tree of mammals have now been convincingly established. For instance, it has proved possible to identify four major clusters (superorders) of placental mammals: (1) Afrotheria—elephants, manatees, hyraxes, tenrecs, golden moles, elephant shrews, and the aardvark; (2) Xenarthra—sloths, anteaters, and armadillos; (3) Euarchontoglires—rodents, lagomorphs, primates, dermopterans, and tree shrews; (4) Laurasiatheria— artiodactyls (including cetaceans), perissodactyls, carnivores, pangolins, bats, and most insectivores ("eulipotyphlans": hedgehogs, shrews, and moles).

All phylogenetic reconstructions based on molecular data depend on studies of the genetic material DNA or of proteins, whose synthesis is governed by individual DNA sequences. The primary components of the double-stranded DNA molecule are nucleotide bases, sugar groups, and phosphate groups. There are four nucleotide bases (adenine, cy-tosine, guanine, and thymine), and specific chemical bonds between pairs of these (adenine with thymine; cytosine with guanine) provide the backbone for DNA's double helix structure. These specific bonds between pairs of bases also ensure that, if one strand is separated, the missing strand will be faithfully replicated. Because the basic unit in the double-stranded DNA molecule is hence a bonded pair of bases (one base in each strand), the length of a DNA sequence is measured in base pairs (bp). The sequence of nucleotide bases in the DNA molecule provides the basis for protein synthesis through the genetic code, with a group of three bases ("triplet") in the DNA sequence corresponding to one amino acid in the protein sequence. Protein sequences hence depend directly upon DNA sequences, and a score of different amino acids are combined into chains of specific composition through translation of sequences of nucleotide bases in DNA, assisted by two kinds of RNA (messenger RNA and transfer RNAs). However, the original simple concept of "one gene, one protein" has needed modification. One major reason for this is that a

DNA sequence corresponding to a particular protein sequence often contains non-coding regions (introns) between the coding regions (exons). Only the exons are ultimately reflected in the amino acid sequence of the corresponding protein. Furthermore, the products of individual DNA sequences can be spliced together to produce a protein.

Both DNA sequences and protein sequences are particularly suitable for phylogenetic reconstruction because they consist of relatively simple components arranged in linear series (nucleotide bases and amino acids, respectively) that can be easily compared between species. Initially, comparisons between species were based on laborious step-by-step determination of the amino acid sequences of proteins, as there was no straightforward technique for studying DNA sequences themselves. The first phylogenetic trees derived from molecular genetics were therefore based on amino acid sequences of proteins, and relatively few species were included in comparisons because of the time-consuming procedure involved in protein sequencing. At first, it was also technically very difficult to determine DNA sequences. However, a major breakthrough came with development of the capacity for generating large quantities of individual DNA sequences through amplification using the polymerase chain reaction (PCR). This opened the way to relatively straightforward and rapid direct determination of DNA sequences, and heralded the transition from studies of gene products (proteins) to studies of the genes themselves (DNA sequences). In fact, because it became easier and faster to determine DNA sequences directly, a protein sequence is now commonly inferred from the DNA sequence of the corresponding gene rather than from sequencing of the protein.

It is important to note that there are two different sets of genetic material (genomes) in mammalian cells, as in animals generally. The primary genome is contained in the chromosomes in the nucleus (nuclear DNA), but each mitochondrion in the cell cytoplasm also contains a number of copies of a separate small genome (mitochondrial DNA). As several mitochondria are present in each cell, there are numerous copies of the mitochondrial genome, whereas there is only one nuclear genome per cell. However, the basic structure of DNA is the same for nuclear DNA (nDNA) and mitochondrial DNA (mtDNA), with chains of nucleotide bases, although mtDNA is organized in a ring whereas nDNA exists as lin ear sequences within chromosomes. The mitochondrion is a respiratory power plant found in all organisms with a cell nucleus (eukaryotes). It is, in fact, derived from a free-living bacterium that took up residence in the cell cytoplasm in an ancestral eukaryote more than a billion years ago, in an arrangement that was of mutual benefit (symbiosis). Originally, the mitochondrial genome contained many more genes than are now present in mammals, whose mitichondria retain only a small number of protein-coding genes that are all connected with respiration.

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