Consider a piece of text, either this one that you are now reading or any other. Surely
        they are all pretty much alike, in so far as they are all run-on strings of characters. In
        this same sense, we can envision that all DNA strands are alike because all are monotonous
        polymers with the same general chemical makeup. Indeed, this is how we think of DNA when
        considering its basic function of inheritance, in which all parts of all chromosomes must
        be duplicated and then passed from one cell generation to the next. The capacity for
        inheritance is fundamentally a consequence of DNA's general molecular structure, and not of
        its sequence per se, as Watson and Crick (1953), and indeed Muller (1922) long before them,
        well appreciated. Muller did not know that genes are made of DNA, but he did realize that,
        whatever genes were made of, they must have a general capacity to replicate, regardless of
        the information they carry (Muller 1922).
        But sequence does matter when DNA fulfills its other, more directly functional role.
        When the DNA that makes up a gene is exposed and expressed, when a gene is serving its
        individual function, then the detailed sequence means all.
        So where does recombination (Box 1) fit in? Is recombination something that happens to
        DNA generally? Or does it happen to particular sequences? Bacteria have their chi (χ)
        sequence, which is a specific series of eight base pairs in the DNA of the bacterial
        chromosome that stimulate the action of proteins that bring about recombination (Eggleston
        and West 1997). Similarly, the immunoglobulin genes of mammals have recombination signal
        sequences that are involved in V-J joining—a kind of somatic recombination involving the
        joining of a variable gene segment and a joining segment to form an immunoglobulin gene
        (Krangel 2003). But does normal meiotic recombination depend on the local DNA sequence? In
        yeast, as well as mammals (mice and humans), the answer is partly yes, for it is clear that
        chromosomes have local recombination hotspots where crossing over is much more likely to
        occur than in other places on the chromosome. Recombination hotspots are local regions of
        chromosomes, on the order of one or two thousand base pairs of DNA (or less—their length is
        difficult to measure), in which recombination events tend to be concentrated. Often they
        are flanked by “coldspots,” regions of lower than average frequency of recombination
        (Lichten and Goldman 1995).
      
      
        Diverse Implications of Recombination Hotspots: The Study of Meiosis and the Mapping
        of Human Disease Alleles
        Recombination hotspots are of strong interest to at least two quite different groups of
        biologists. For geneticists and cell biologists who study meiosis, the existence of
        recombination hotspots offers a way to learn what other processes are associated with
        recombination. This is partly how we know that homologous crossovers in yeast and other
        eukaryotes are initiated by the cleavage of single chromosomes, called “double-strand
        breaks” (Box 1). It turns out that because of this causal linkage, the hotspots for
        doublestrand breaks and the hotspots for recombination are one and the same (Game et al.
        1989; Sun et al. 1989; Keeney et al. 1997; Lopes et al. 1999; Allers and Lichten 2001;
        Hunter 2003).
        For population geneticists, much of the interest in recombination hotspots comes from
        their possible effect on the patterns of DNA sequence variation along human chromosomes and
        from the possibility that these patterns could be used to map the position of alleles that
        cause disease. When multiple copies of the DNA sequence of a gene, or of a larger region of
        a chromosome, are aligned, they reveal the location and distribution of variation at
        individual nucleotide positions—single nucleotide polymorphisms (SNPs). Each particular
        sequence, or haplotype, will carry a configuration for the SNPs for that region (Figure 1).
        Investigators have long known that SNPs that are adjacent or near each other tend to be
        highly correlated in their pattern and to exhibit strong linkage disequilibrium (Box 1). It
        is this linkage disequilibrium that enables scientists to map the locations of mutations
        that cause heritable genetic diseases. If alleles that cause a disease have the same kind
        of linkage disequilibrium with nearby SNPs as SNPs generally have with each other, then one
        could search for genes with disease alleles by looking for a pattern of SNPs that is found
        only in people who have the disease. This general method for mapping disease alleles is
        called “association mapping,” and it is basically a search for linkage disequilibrium
        between disease alleles and other SNPs. Whether or not association mapping works depends on
        the actual patterns of linkage that occur among SNPs in human populations, and these
        patterns depend in turn on how much recombination has occurred in the past (as well as on
        other demographic and mutation processes).
        With the advent of larger human haplotype data sets, it has become clear that there are
        often fairly long regions with very high linkage disequilibrium (Daly et al. 2001; Patil et
        al. 2001; Gabriel et al. 2002). This pattern of variation has been characterized as
        occurring in “haplotype blocks,” which are apparent regions of low recombination (or high
        linkage disequilibrium). Figure 1 shows a hypothetical example of haplotype blocks among
        eight haplotypes for a series of SNPs found over a region of a chromosome. Given diverse
        evidence of recombination hotspots in humans, a much discussed question is whether
        recombination hotspots play a large role in the formation of the pattern of haplotype
        blocks (Wang et al. 2002; Innan et al. 2003; Phillips et al. 2003; Stumpf and Goldstein
        2003). The occurrence of haplotype blocks has inspired the HAPMAP project
        (http://www.hapmap.org/), which has the goal of identifying a subset of SNPs that capture
        most of the relevant linkage information in the human genome (IHC 2003). If one had a
        subset of all common SNPs, with one or two per haplotype block, then this subset would
        contain much of the available information for association mapping of disease alleles.
      
      
        The Evolution of Recombination and (Possibly) Recombination Hotspots
        Recombination is a nearly ubiquitous feature of genomes, and a great many theories have
        been put forward to explain why it would be evolutionarily advantageous for genes to
        regularly break with one another to join new genes (Barton and Charlesworth 1998). By and
        large these theories predict that recombination should occur more often where genes occur
        in higher concentration and that it should happen less often in areas of the genome where
        genes are spaced far apart. This expectation is roughly born out in the human genome, where
        recombination rates are higher in regions of the genome with higher gene density (Fullerton
        et al. 2001; Kong et al. 2002).
        To consider the possible evolutionary advantages of individual recombination hotspots,
        we can draw from theory on the evolution of recombination modifiers. In particular, recent
        population genetic theory has brought to light some fairly general circumstances for which
        mutations that raise recombination rates would be favored by natural selection (Barton
        1995; Otto and Barton 1997; Otto and Barton 2001; Otto and Lenormand 2002). The basic idea
        is that linkage disequilibrium can easily occur (for many reasons) between two (or more)
        polymorphic sites that are under selection. When this occurs, an allele that raises the
        recombination rate (and decreases the linkage disequilibrium) can cause selection to act
        more efficiently. If an allele that is under positive or negative selection always occurs
        with an allele at another locus that is also under selection (i.e., the two loci are in
        strong linkage disequilibrium), then selection cannot act on one locus independently of the
        second locus. As new, multilocus configurations of beneficial alleles are generated (by
        recombination) and increase in frequency by selection, the modifiers of recombination that
        caused the production of those beneficial configurations increase in frequency with them. A
        key piece of evidence supporting this kind of theory of the evolution of recombination is
        directional selection, like that which occurs in artificial selection experiments, which
        often generates a correlated elevation in recombination rates (Otto and Lenormand
        2002).
        Connecting these ideas about the evolution of recombination modifiers to the question of
        recombination hotspots, we come to the possibility that individual hotspots may have arisen
        as a byproduct of linkage disequilibrium between genes on either side of the hotspot that
        were under selection. This situation would create a kind of selection pressure favoring
        recombinant haplotypes and thus also favoring those chromosomes that happen to have a high
        recombination rate between the selected genes. If true, then we might expect local
        recombination rates (i.e., hotspots and coldspots for recombination) to fluctuate in
        location and intensity, in ways that would be hard to precisely predict without knowing
        what genes have been under selection and what patterns of linkage disequilibria there may
        have been.
        In this light, the paper by Ptak et al. (2004) in this issue of 
        PLoS Biology is especially interesting. They report that chimpanzees do
        not have a recombination hotspot in the TAP2 region where humans have a fairly well
        characterized recombination hotspot (Jeffreys and Neumann 2002). Ptak et al.'s is a
        statistical study of linkage disequilibrium in the TAP2 region of chimpanzees and humans,
        and is less direct than the sperm-typing study of Jeffreys and Neumann (2002). However the
        contrast in linkage patterns between humans and our closest relatives suggests that
        recombination hotspots can evolve fairly quickly.
      
      
        Functional Constraints on Recombination Hotspots
        As appealing as the recombination modifier theory of recombination hotspots may be,
        there is circumstantial evidence that argues against it and that suggests that
        recombination hotspots are not directly the byproduct of selection on alleles in linkage
        disequilibrium. Particularly important in this regard is that some wellstudied organisms
        (notably the worm 
        Caenorhabditis elegans and the fruitfly 
        Drosophila melanogaster ) have not shown evidence of
        recombination hotspots. If we compare these organisms with yeast and mammals, which do show
        hotspots, we gain some more insight into the factors affecting the evolution of
        hotspots.
        Recall that double-strand breaks are the sites where recombination is initiated during
        meiosis, and that this is true regardless of the presence of hotspots for both phenomena.
        Apparently it is the case in yeast and mammals that both recombination and double-strand
        breaks are also prerequisites for the proper formation of the synaptonemal complex (SC)
        (Figure 2) and thus for proper orientation of the spindle apparatus and accurate
        segregation of chromosomes during meiosis (Paques and Haber 1999; Lichten 2001; Hunter
        2003; Page and Hawley 2003). In contrast, neither double-strand breaks nor recombination
        appear to be required for the formation of the SC in 
        D. melanogaster or 
        C. elegans (Zickler and Kleckner 1999; MacQueen et al. 2002;
        McKim et al. 2002; Hunter 2003; Page and Hawley 2003). Double-strand breaks and
        recombination do indeed co-occur in these model organisms, and are required for proper
        chromosome segregation, but they occur after the formation of the SC. Both of these species
        have broad chromosomal regions where crossing over occurs at higher rates than others, but
        there have been no reports of local recombination hotspots.
        Recombination during meiosis seems to be required for proper chromosome segregation;
        however, in those organisms where recombination and double-strand-break hotspots occur,
        these phenomena are also required for proper formation of the SC. It is as if the
        recombination machinery has been partly co-opted for chromosome alignment in some
        eukaryotes more so than in others. The implication of these findings is that recombination
        hotspots are byproducts of other functional constraints associated with the recombination
        process. This does not rule out the evolutionary theory of recombination modifiers, or that
        the location and intensity of recombination hotspots may evolve rapidly, but it does
        suggest that we may not need to invoke the evolutionary modifier theory to explain the
        existence of recombination hotspots.
      
      
        Conclusions
        Recombination hotspots co-occur with double-strand-break hotspots in some eukaryotes,
        and together these phenomena appear to play an important role in the formation of the SC in
        those organisms. Given the limited phylogenetic occurrence of recombination hotspots (i.e.,
        their occurrence in some, but not all, species), general theories for the evolution of
        recombination may not be very helpful for understanding the existence of recombination
        hotspots. However, in those species where they do occur, it is quite possible that
        recombination hotspots do evolve in location and intensity. Furthermore, the presence of
        recombination hotspots in humans may have large effects on the length of local patterns of
        linkage disequilibrium (haplotype blocks) and thus on our ability to map disease alleles by
        their association with other markers.