Genetics

doi: 10.1093/genetics/181.1.vpmid: N/A

We are pleased to introduce Adam Wilkins as the new Perspectives Editor of Genetics. Adam, a long-time GSA member, brings many years of experience and insight, having had a very successful 24-year run as the Editor of BioEssays. He brings to our pages a crisp, clear, incisive writing and editorial style. Adam earned his Ph.D. in Jon Gallant's lab in the Genetics Department at the University of Washington. He was a post-doctoral fellow at MIT (with Ethan Signer) and the University of Wisconsin (with Bill Dove). Prior to joining BioEssays in 1984, he was on the faculty of Massey University in Palmerston North, New Zealand. Adam authored The Evolution of Developmental Pathways (Sinauer Associates, 2002) and Genetic Analysis of Animal Development (John Wiley & Sons, 1986 and 1993), and he was co-editor of Molecular Evolution (Jones & Bartlett, 1984) and Molecular Model Systems in the Lepidoptera (Cambridge University Press, 1995). Adam will carry the Perspectives torch that Jim Crow and Bill Dove ignited in 1987 and kept burning brightly all this time. The Perspectives articles are an important part of our journal—for many readers they are a must read—and we are grateful to Jim and Bill for enriching our journal and our intellectual environment with such skill and dedication. Adam would like to learn what readers wish to see in the Perspectives section. Please send your suggestions to Adam at [email protected]. We are fortunate to have been able to recruit someone with such experience, expertise, and enthusiasm. Thank you for joining our editorial team, Adam! Mark Johnston, Editor-in-Chief Tracey DePellegrin Connelly, Executive Editor © Genetics 2009 This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

doi: 10.1093/genetics/181.1.nppmid: N/A

Molecular population genetics and evolution of Drosophila meiosis genes, pp. 177–185 Jennifer A. Anderson, William D. Gilliland and Charles H. Langley Even though meiosis is virtually universal in eukaryotes, a significant fraction of genes involved in the process are lineage-specific. These investigators survey polymorphism and divergence of 33 meiosis-related genes in Drosophila melanogaster and Drosophila simulans. A number of intriguing differences in patterns of polymorphism and divergence between the two species are evident, affording an opportunity to investigate phenotypic effects associated with polymorphisms and recently fixed sibling–species differences. Pds1p is required for meiotic recombination and prophase I progression in Saccharomyces cerevisiae, pp. 65–79 Katrina F. Cooper, Michael J. Mallory, Vincent Guacci, Katherine Lowe and Randy Strich The metaphase–anaphase transition of mitosis is triggered by the destruction of Pds1, which leads to the removal of the cohesin that holds replicated sister chromatids together. Cells without Pds1 survive, but they are sick and often aneuploid. These authors find, to their surprise, that Pds1 is required for meiosis, where its role is to protect Mcd1p from degradation. LINE-like retrotransposition in Saccharomyces cerevisiae, pp. 301–311 Chun Dong, Russell T. Poulter and Jeffrey S. Han How was a third of the human genome made? Much of the DNA in our genome is the result of LINE element retrotransposition. This process is poorly understood, in part due to the difficulty studying these highly repetitive DNA elements. These authors reengineer a LINE element and introduce it into the LINE-free model organism Saccharomyces cerevisiae, where it appears to faithfully transpose. The vast experimental resources provided by budding yeast are sure to advance our understanding of LINE retrotransposition. Drosophila and vertebrate casein kinase Iδ exhibits evolutionary conservation of circadian function, pp. 139–152 Jin-Yuan Fan, Fabian Preuss, Michael J. Muskus, Edward S. Bjes and Jeffrey L. Price Casein kinase Iδ plays many roles in many different cellular processes in many organisms. It is essential for circadian rhythms such as the sleep/wake cycle. This article reports that the properties of the fly and vertebrate casein kinases Iδ are similar. Remarkably, alterations in mammalian CKIs that lead to shortening of the circadian period have the same effect when expressed in flies. This is due to an alteration of the frequency of cycling of phosphorylation of its substrate protein PER, a central regulator of circadian rhythms. Thus, the mechanism of the sleep/wake cycle is remarkably similar in flies and mammals. Population genetic inference from resequencing data, pp. 187–197 Rong Jiang, Simon Tavaré and Paul Marjoram Ultralow-cost sequencing technologies are increasingly available. They generate a large number of quite short sequence reads that often incompletely cover the genomic region of interest. These authors modeled data produced by these technologies and describe the degree of genome coverage required for successful population genetic inference from such data. Drosophila PCH2 is required for a pachytene checkpoint that monitors double-strand-break-independent events leading to meiotic crossover formation, pp. 39–51 Eric F. Joyce and Kim S. McKim The proper repair of DNA double-strand breaks during meiotic prophase generates crossovers that ensure proper meiotic segregation. This is controlled at two checkpoints: one monitors repair of the double-strand breaks, the other—the PCH2-dependent pathway—has been thought to respond to a defect in synaptonemal complex (SC) formation. These investigators find that the PCH2-dependent checkpoint in Drosophila is activated in the absence of defects in SC formation. They propose that there is a “crossover checkpoint” that detects problems in the process of forming crossovers. The classical nuclear localization signal receptor, importin-α, is required for efficient transition through the G1/S stage of the cell cycle in Saccharomyces cerevisiae, pp. 105–118 Kanika F. Pulliam, Milo B. Fasken, Laura M. McLane, John V. Pulliam and Anita H. Corbett Eukaryotic cells use their compartments to great effect. In the case described in this article, eukaryotic cells regulate steps in the cell cycle by regulating import of proteins into the nucleus. The authors find that the protein import pathway is required for yeast cells to replicate their DNA: when it is blocked, progress through the cell cycle stops. The researchers identify three import factors that are mislocalized to the cytoplasm when that happens, identifying some targets of this mode of regulation. Simple telomeres in a simple animal: Absence of subtelomeric repeat regions in the placozoan Trichoplax adhaerens, pp. 323–325 Hugh M. Robertson The subtelomeric DNA sequences of most animal chromosomes are similar between chromosomes, presumably reflecting their concerted evolution. The roles of subtelomeric sequences are unclear. Robertson reports that Trichoplax adhaerens, the sole named species of the animal phylum Placozoa, has an extremely simple body plan and also extremely simple telomeres: each of eleven telomeres has 1.5–13 kb of unique sequence between the simple telomeric repeats and the first gene. Formation and longevity of chimeric and duplicate genes in Drosophila melanogaster, pp. 313–322 Rebekah L. Rogers, Trevor Bedford and Daniel L. Hartl Duplicate genes are well known to be a major source of novel genetic material, but the contribution of chimeric genes to evolutionary novelty has been largely overlooked. These authors identify 14 chimeric genes in Drosophila melanogaster and explain how they formed. They also model duplicate and chimeric gene dynamics, assessing rates of their formation, loss, and preservation. An appreciable number of chimeric genes are preserved 1 every 6.3 million years, indicating that chimeras contribute significantly to genome content. Curing of yeast [URE3] prion by the Hsp40 cochaperone Ydj1p is mediated by Hsp70, pp. 129–137 Deepak Sharma, Robert F. Stanley and Daniel C. Masison Yeast prions are highly ordered protein aggregates that propagate by purloining the soluble form of the same protein, prodding it to misfold similarly as it joins the aggregate. Hsp40 chaperones promote protein folding and prevent protein aggregation by regulating Hsp70. Overexpressing Hsp40 “cures” yeast of [URE3] prions. This article presents the surprising finding that Hsp40 dimerization, substrate binding, membrane localization, and ability to transfer substrate to Hsp70 are dispensable for its curing function. Only the domain required for regulating Hsp70 activity is sufficient for curing. Thus, Hsp40 cures prion disease indirectly by regulating Hsp70. Loss of the mitochondrial nucleoid protein, Abf2p, destabilizes repetitive DNA in the yeast mitochondrial genome, pp. 331–334 Rey A. Sia, Stephanie Carrol, Lidza Kalifa, Christine Hochmuth and Elaine A. Sia Deletions of repetitive DNA of the mitochondria are associated with human cancer and aging. This article describes the role of the Abf2p, an abundant mitochondrial nucleoid-associated protein of yeast that has been called the “mitochondrial histone,” in avoiding this fate. Loss of Abf2p, the ortholog of human mTFA, results in increased rates of frameshift mutations and recombination between direct repeats in the mitochondrial genome, but does not affect point mutation rates. © Genetics 2009 This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Johnston, Mark

doi: 10.1534/genetics.108.100255pmid: N/A

IT is a tremendous honor to be appointed the 16th editor-in-chief of Genetics. I pledge to do my best to live up to my colleagues' high expectations. The responsibility is great: this journal, the first American “periodical record bearing on heredity and variation” carries a long tradition of excellence and a stellar list of editors (from Curt Stern and Jim Crow to David Stadler and Beth Jones) and authors (from Beadle and Muller and McClintock to Hartwell and Horvitz and Fire). We are all—editors, authors, readers—stewards of this grand legacy. Let's work together to take this flagship of our field to even greater heights. This will require agility, foresight, and innovation because scientific publishing is rife with challenge. The push for open access stresses our ability to cover the expense of publishing a journal. We rely on subscriptions (mostly from institutions) to subsidize our costs, but if our content is free, why would anyone subscribe? If we embrace full open access, we will have to charge authors more (much more) to publish in our journal. At the same time, because of the intense interest in a journal's “impact” (measured to four significant figures!) and the proliferation of journals, we must redouble our efforts (thereby increasing our expenses) to make our journal and its content visible. We will simply have to work harder and more creatively to meet these challenges. I think our biggest challenge is the perception that a few journals—which are not run, as this one is, by practicing scientists—are the preferred venue for your best work. Journals such as Genetics, which are sponsored by scientific societies and managed and edited by peers of the authors, should be the first choice for your submissions. I find it strange that they are not; we will simply have to work harder to make it so. And we must do this on a shoestring budget: our margin is razor thin, and we have no large publishing house or well-endowed foundation to carry us. We have already taken steps to meet these challenges. Over the past 2 years, under the leadership of Suzanne Sandmeyer and the Board of Senior Editors that she chaired, both the print and the online journal were given a new, contemporary look. We redesigned the cover to include color images and provide a modern, visually appealing (and, we somewhat sheepishly admit, glossy) mien. We created a new journal website that provides a clean aspect and intuitive search and navigation, with the spotlight appropriately on content. We organized articles by topic, reflecting the integrated nature of modern genetics research. And, under the guidance of Reviews Editor Allan Spradling, we began publishing reviews of topics of special interest to geneticists. These have been excellent. I urge you to take a look. And please send Allan ([email protected]) your suggestions for future topics and authors. Genetics has enjoyed unprecedented growth in the number of submitted manuscripts and thus in the size of its editorial board. During the past year, our 80 associate editors have deftly handled peer review of more than 2000 submitted manuscripts. These associate editors—each the authors' peer—manage the review and decide if a manuscript should be accepted for publication. Such a sizable editorial board calls for a degree of structure to efficiently handle manuscripts and to maintain uniform standards. In response to this need, early last year the late Editor-in-Chief Beth Jones initiated significant changes in the journal's editorial procedures, and we have continued to implement Beth's vision. We recruited eight senior editors to help set policies and determine the direction and scope of the journal. They are now collaborating with groups of associate editors, organized around the journal's topical areas, to set and maintain our standards. These senior editors, like the associate editors, are leading geneticists, each an active, practicing scientist, who is therefore eminently qualified to judge the contributions of their peers. We have the best editorial team in the business. It is a privilege to work with them. I am confident you can entrust your best work to our editors. We are pleased to report another development: Adam Wilkins, longtime editor of the journal BioEssays, recently agreed to become the editor of the popular Perspectives section of the journal. Founded 20 years ago by Jim Crow and Bill Dove under the aegis of Editor-in-Chief John (Jan) Drake, Perspectives articles are a must read for many in our audience. We are grateful to Jim and Bill for their outstanding—and selfless—efforts to enrich our journal and our intellectual environment. Adam has some exciting ideas for this part of the journal, and we look forward to watching (and helping) the Perspectives evolve. Please let Adam know what kinds of articles you would like to read ([email protected]). Other changes are in the offing. We are revisiting our policies and procedures—as we must in this highly competitive, rapidly changing scientific publishing environment. Please see the journal scope statement that accompanies this editorial. We welcome—solicit, actually—your input and ideas. One change we are glad that we did not have to make is that of the managing editor position. Those of you who have published in or reviewed for the journal know well the skills of Managing Editor Tracey DePellegrin Connelly. Under Tracey's direction, we are undertaking efforts to increase the distribution, visibility, usage, and effectiveness of our journal. Accordingly, Tracey has been promoted to the position of Executive Editor. Please join me and our editorial team in carrying the torch of Genetics that was lit back in 1916 by the founders of our field. We have an extraordinary legacy to protect and build upon. Please help us do that by continuing to support Genetics. Genetics Scope Statement The journal Genetics, published by The Genetics Society of America, publishes high quality, original research presenting novel findings on a range of topics bearing on heredity and variation. These topics include population and evolutionary genetics, complex traits, developmental and behavioral genetics, cellular genetics, gene expression, genome integrity and transmission, and genome and systems biology. The journal also publishes Reviews, Perspectives articles on current and historical issues in genetics, and articles on genetics education. Genetics is a peer-edited journal—all editorial decisions are made by the authors' peers—with a tradition of rigorous peer review. Full documentation of the data presented and compelling evidence for the conclusions drawn are required. Each submitted manuscript is assigned to an Associate Editor, a peer of the authors who manages the review process and decides if the manuscript is acceptable for publication in Genetics. A manuscript may be rejected without review if the editors judge it to be outside the scope of the journal. A manuscript will also be returned without being reviewed if it does not follow the Genetics style guide or if improper grammar or syntax precludes its proper scientific review. Criteria for Publication the study is of interest to a wide range of genetics and genomics investigators the results presented provide strong support for the conclusions reached the conclusions provide new insights into a biological process or the study demonstrates novel and creative approaches to an important biological problem or the manuscript describes development of new resources, methods, technologies, or tools of interest to a wide range of geneticists. © Genetics 2009 This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) © Genetics 2009

Wilkins, Adam S; Holliday, Robin

doi: 10.1534/genetics.108.099762pmid: 19139151

Anecdotal, Historical and Critical Commentaries on Genetics Edited by James F. Crow and William F. Dove … if there is one event in the whole evolutionary sequence at which my own mind lets my awe still overcome my instinct to analyse, and where I might concede that there may be a difficulty in seeing a Darwinian gradualism hold sway throughout almost all, it is this event—the initiation of meiosis. W. J. Hamilton (1999, p. 419) THE origins of meiosis in early eukaryotic history have never been satisfactorily explained. Since the reduction-division process in meiosis is essential for sexual life cycles, discussion of the origins of meiosis has been closely tied to debates about the evolutionary value of sex itself and the selective pressures for its maintenance. Yet the cytological events involved in the origins of meiosis are as puzzling as the question of selective pressures. While meiosis almost certainly evolved from mitosis, it has not one but four novel steps: the pairing of homologous chromosomes, the occurrence of extensive recombination between non-sister chromatids during pairing, the suppression of sister-chromatid separation during the first meiotic division, and the absence of chromosome replication during the second meiotic division. This complexity presents a challenge to any Darwinian explanation of meiotic origins. While the simultaneous creation of these new features in one step seems impossible, their step-by-step acquisition via selection of separate mutations seems highly problematic, given that the entire sequence is required for reliable production of haploid chromosome sets. Both Maynard Smith (1978) and Hamilton (1999) regarded the origins of meiosis as one of the most difficult evolutionary problems. In this Perspectives article, we present a hypothesis of the origins of meiosis that encompasses both the cytological novelties and the selective forces that might have favored them. We first present the reasons for thinking that the initial step involved a key innovation, that of extensive homolog pairing (synapsis), and then discuss how the other three distinctive properties can be accounted for. We next ask what selective pressures might have favored the acquisition of homolog synapsis. The conclusion is surprising: the initial function of chromosome pairing was to limit, not enhance, recombination. Finally, we review the evidence that much of the molecular machinery required for the initial forms of homolog pairing probably existed in proto-eukaryote unicellular forms prior to the evolution of meiosis and therefore could have been readily “recruited” for the new role. Some experimental tests of the hypothesis are proposed. IDENTIFYING A KEY STEP IN THE EVOLUTION OF MEIOSIS FROM MITOSIS In the evolution of the eukaryotes, it can be assumed that the earliest eukaryotic species were single-cell haploid forms, possessing just a single set of chromosomes, and that they propagated by mitosis. While many of the simplest contemporary eukaryotes, namely protists and fungi, exhibit the mitotic propagation of both haploid and diploid states, diploidy is almost certainly a derived state. In principle, the very first diploid cells could have first arisen either by cell fusion or by endomitosis. Hurst and Nurse (1991) have argued that the first diploids probably arose via rare endomitotic errors rather than by cell fusion. Yet, since non-sexual cell and nuclear fusions can occur independently of sex (“parasexuality”), either route to early diploid states is possible. In this view, the formation of occasional diploid cells predated regular sexual life cycles in eukaryotes. The origins of mitosis itself in the first eukaryotes are, of course, of high interest. The fact that mitosis is a universal eukaryotic property suggests that it arose at the base of the eukaryotic tree. A key point is that there are prokaryotic homologs of all the key molecules employed in eukaryotic mitosis (see reviews by Hirano 2005 and Erickson 2007). These include the actins, required for daughter cell separation in eukaryotes; the tubulins, required in eukaryotes for the mitotic spindle and movement of chromosomes; and the molecules required for chromosome condensation and sister-chromatid cohesion, members of the so-called structural maintenance of chromosomes (SMC) family. The prokaryotic members of the tubulin family are the FtsZ genes, which were first discovered in Escherichia coli but later found in many prokaryotic species, while similarly, the homologs of the SMC proteins are found throughout the eubacterial and archaebacterial kingdoms. It is not difficult to imagine that members of the actin-related, FtsZ, and SMC gene families could have been evolutionarily recruited for use in the first primitive forms of mitosis; the latter must have involved a switch from membrane-based to spindle-based attachment points for segregating sister chromosomes. The evolution of meiosis, however, poses problems of a different order. The crucial but reasonable deduction, based on both cytology and genetics, is that meiosis evolved from mitosis (Cavalier-Smith 1981; Simchen and Hugerat 1993). While the various similarities between the two forms of cell division argue for a close evolutionary relationship between them, the greater complexity of meiosis indicates that it is the derived process. Furthermore, while mitosis is universal in eukaryotic species, meiosis is merely ubiquitous, consistent with its loss in some eukaryotic lineages. Comparative evidence suggests that meiosis appeared early in eukaryotic cell history (Ramesh et al. 2005; Schurko and Logsdon 2008), and its high degree of similarity in different taxonomic groups suggests that it arose only once (Hamilton 1999; Ramesh et al. 2005). As noted above and summarized in Table 1, the cytological events specific to meiosis are the following: (1) the acquisition of homolog pairing (and its concomitant, homolog separation), (2) the occurrence of efficient intergenic recombination between homologs during pairing, (3) the suppression of sister-chromatid separation in the first division, and (4) the absence of S phase at the start of the second division. TABLE 1 Comparison of mitotic and meiotic stages Mitotic stage . Result . Meiotic stage . Result . S phase Chromatid duplication S phase, I Chromatid duplication; DNA breaks introduced Prophase Chromosome condensation Prophase, I Chromosome condensation; homolog pairing, recombination Metaphase Chromosome alignment in center of spindle body Metaphase, I Alignment of homologs in center of spindle body Anaphase Centromere splitting; chromatids separated Anaphase, I Separation of homologs with independent assortment; centromere splitting suppressed Telophase Chromatid decondensation; two daughter nuclei with mother-cell ploidy, single-chromatid chromosomes Telophase, I Partial or complete chromatid decondensation; two haploid nuclei with replicated chromatids Prophase, II No S phase; chromosome condensation Metaphase, II Alignment of replicated chromatids Anaphase, II Centromere splitting; separation of chromatids Telophase, II Chromatid decondensation; four haploid nuclei, single-chromatid chromosomes Mitotic stage . Result . Meiotic stage . Result . S phase Chromatid duplication S phase, I Chromatid duplication; DNA breaks introduced Prophase Chromosome condensation Prophase, I Chromosome condensation; homolog pairing, recombination Metaphase Chromosome alignment in center of spindle body Metaphase, I Alignment of homologs in center of spindle body Anaphase Centromere splitting; chromatids separated Anaphase, I Separation of homologs with independent assortment; centromere splitting suppressed Telophase Chromatid decondensation; two daughter nuclei with mother-cell ploidy, single-chromatid chromosomes Telophase, I Partial or complete chromatid decondensation; two haploid nuclei with replicated chromatids Prophase, II No S phase; chromosome condensation Metaphase, II Alignment of replicated chromatids Anaphase, II Centromere splitting; separation of chromatids Telophase, II Chromatid decondensation; four haploid nuclei, single-chromatid chromosomes The four novel properties of meiosis are indicated by italics. Open in new tab TABLE 1 Comparison of mitotic and meiotic stages Mitotic stage . Result . Meiotic stage . Result . S phase Chromatid duplication S phase, I Chromatid duplication; DNA breaks introduced Prophase Chromosome condensation Prophase, I Chromosome condensation; homolog pairing, recombination Metaphase Chromosome alignment in center of spindle body Metaphase, I Alignment of homologs in center of spindle body Anaphase Centromere splitting; chromatids separated Anaphase, I Separation of homologs with independent assortment; centromere splitting suppressed Telophase Chromatid decondensation; two daughter nuclei with mother-cell ploidy, single-chromatid chromosomes Telophase, I Partial or complete chromatid decondensation; two haploid nuclei with replicated chromatids Prophase, II No S phase; chromosome condensation Metaphase, II Alignment of replicated chromatids Anaphase, II Centromere splitting; separation of chromatids Telophase, II Chromatid decondensation; four haploid nuclei, single-chromatid chromosomes Mitotic stage . Result . Meiotic stage . Result . S phase Chromatid duplication S phase, I Chromatid duplication; DNA breaks introduced Prophase Chromosome condensation Prophase, I Chromosome condensation; homolog pairing, recombination Metaphase Chromosome alignment in center of spindle body Metaphase, I Alignment of homologs in center of spindle body Anaphase Centromere splitting; chromatids separated Anaphase, I Separation of homologs with independent assortment; centromere splitting suppressed Telophase Chromatid decondensation; two daughter nuclei with mother-cell ploidy, single-chromatid chromosomes Telophase, I Partial or complete chromatid decondensation; two haploid nuclei with replicated chromatids Prophase, II No S phase; chromosome condensation Metaphase, II Alignment of replicated chromatids Anaphase, II Centromere splitting; separation of chromatids Telophase, II Chromatid decondensation; four haploid nuclei, single-chromatid chromosomes The four novel properties of meiosis are indicated by italics. Open in new tab Most of the attention of evolutionary geneticists has focused on the second step—extensive genetic recombination during pairing—and its significance as a generator of genetic diversity (Fisher 1930; Muller 1932; Maynard Smith 1978; Crow 1988). Yet, while genetic recombination is a key feature of meiosis, it is not unique to this process. Recombinational capacity is found throughout the prokaryotes and therefore must considerably predate eukaryotes and, therefore, meiosis (Levin 1988; Cavalier-Smith 2002; Marcon and Moens 2005). Accordingly, the original proto-eukaryote cells must also have possessed the enzymatic machinery for recombination. In particular, a crucial set of molecules for genetic recombination, the recA family of proteins, is utilized for recombination in both prokaryotes and eukaryotes (Aboussekhra et al. 1992; Shinohara et al. 1992). Furthermore, within eukaryotes, genetic recombination is not restricted to meiosis. Diploid somatic cells of fungi, plants, and animals undergo chromosomal crossing over, the phenomenon known as “mitotic recombination.” There are, however, three significant contrasts between meiotic and mitotic recombination. First, mitotic recombination between homologs takes place at a very much lower frequency than in meiosis. Second, while crossing over between sister chromatids in mitotic cells is fairly frequent (as seen with physical labeling techniques), meiosis is structured to promote crossing over between non-sister chromatids. Third, as found in yeast cells, mitotic recombination is mediated efficiently by either of two recA homologs, rad51 and Dmc1, while meiotic exchange between homologs requires Dmc1 specifically (reviewed in Neale and Keeney 2006). If mitosis preceded meiosis in evolution, it seems equally likely that mitotic recombination preceded meiotic recombination. In thinking about the origins of meiosis, a point of interest is that meiosis as it exists is not the simplest conceivable process for producing haploid cells from diploid cells. In principle, premeiotic DNA replication would not be necessary. The unreplicated chromosomes would simply pair with each other with or without recombination and would move to opposite poles to produce just two haploid nuclei. The whole process would be accomplished in one division, not two. This hypothetical sequence of events, “one-step meiosis” (Cavalier-Smith 1981; Archetti 2004), differs from the normal “two-step” meiosis in involving (1) the active suppression of DNA synthesis and (2) the pairing of homologous but unreplicated chromosomes prior to metaphase. Although one-step meiosis would achieve the same results as actual meiosis, it is hard to imagine how both properties could have arisen readily and simultaneously from mitosis. In contrast, consider meiosis as it actually occurs. It begins with an S phase, which may differ in certain features from the normal mitotic S phase (Stern and Hotta 1977), yielding chromosomes that each consists of a pair of sister chromatids. This is followed by pairing of homologous chromosomes along their entire length (synapsis), a state that is visibly obvious in most eukaryotic species as the chromosomes condense. In this phase, homologous non-sister chromatids recombine with each other, sometimes only once, but more often at several sites along their length. After recombination, the chromosomes condense further and the paired homologs become aligned on the metaphase plate. There are already two kinetochores to which the chromatids are attached but, in contrast to mitosis, the kinetochores do not split in this first meiotic division: the homologs simply separate to opposite poles. This absence of kinetochore fission in the first meiotic division (MI) reflects a difference in the molecular mechanics of centromere–microtubule attachment, a consequence of the geometry of sister-chromatid placement when homologs are paired. In contrast to the “bi-orientation” of sister chromatids to opposite poles in mitosis, both sister chromatids of each paired chromosome in metaphase I are attached to spindle fibers running to the same pole (“mono-orientation”) (reviewed in Hauf and Watanabe 2004). When the two sets of chromosomes produced by MI are enclosed within nuclei, they are already replicated. So these nuclei are in effect the equivalent of the G2 state of the mitotic cycle. The absence of replication in the second meiotic division (MII) presumably follows from the same mechanism that prevents further rounds of replication in the G2 phase of cells preparing for mitosis, namely the absence of binding of one or more of the “licensing factors” (e.g., the Mcm 2–7 proteins) at replication origins through their removal during S phase (reviewed in Blow and Dutta 2005). Although the precise mechanism is not known, it seems likely that sister-chromatid separation at the centromeres generates a signal that begins the process of “replication licensing.” In the absence of that molecular transition, at the end of meiosis I, the chromatids cannot undergo a new round of replication. Whatever the mechanism is that inhibits a second S phase, prophase of meiosis II consists simply of chromosome condensation. It, in turn, is followed by metaphase II and then by anaphase II, in which the sister chromatids are separated and segregated to opposite poles, yielding two haploid nuclei with single (nonreplicated) chromatids. The separation of sister chromatids in meiosis II involves molecular players and processes similar to those involved in sister-chromatid separation in mitosis (reviewed in Rivera and Losada 2006). Altogether, the second division produces a tetrad of products from each initial meiotic I nucleus, and each of these final daughter nuclei possesses one (haploid) unreplicated genome. Thus, and perhaps counterintuitively, the evolution of two-step meiosis requires fewer new events than the seemingly simpler one-step process. Indeed, it actually necessitates only one, namely the synapsis of homologous chromosomes, each consisting of two sister chromatids, with the rest of the sequence following in the known pattern of mitosis for replicated chromosomes. Archetti (2004) has produced an argument, which is based on considerations of selection pressures, as to why the simpler hypothetical path of one-step meiosis is such a rarity, if it exists at all. In contrast, our argument is based on the known facts of cytology and molecular biology. Our key proposition, therefore, is that the origin of meiosis involved the evolution of stable genomewide synapsis, lasting into metaphase, and the insertion of this step into the mitotic cycle. Such pairing at first might appear to be a striking novelty. Yet, widespread pairing of homologs in somatic (nonmeiotic) cells has been found both in Drosophila (McKee 2004) and in yeast (Burgess et al. 1999). Such somatic pairing differs from meiotic synapsis in three respects: (1) it is not as extensive (McKee 2004); (2) it does not lead to the levels of genetic recombination seen in meiosis; and (3) it terminates in either interphase or prophase, allowing each chromosome to proceed to the metaphase plate independently of its homolog. Nevertheless, if such homolog pairing in mitotic cells is an ancestral eukaryotic property, then the origins of meiotic synapsis need have involved only its temporal extension into metaphase and more intimate or extensive apposition of homologs, especially at the kinetochores. Meiotic synapsis would thus be a modification of an already existing property, not a wholly novel one. As argued above, the absence of sister-chromatid separation at the end of meiosis I would reflect the altered geometry of microtubule attachment, when homolog kinetochores are paired, while the absence of S phase in meiosis II would be a consequence of the absence of sister-chromatid separation. The remaining distinctive feature of meiosis, namely high recombination levels during chromosome pairing, can be seen as a property that evolved later (see below). Our proposal that a key innovation converted a mitotic cycle into a meiotic one is not the first suggestion of its kind. Cavalier-Smith (2002) argued that suppression of kinetochore splitting in MI was the key innovation in meiosis. This event, however, comes after homolog pairing, which clearly is a novelty. Furthermore, as noted above, the absence of kinetochore splitting directly reflects the difference in sister-chromatid orientation with respect to the poles between MI and MII (Hauf and Watanabe 2004). This, in turn, reflects the inherent structural-geometric differences in microtubule attachment between paired and unpaired chromosomes at the level of individual chromosomes (Paliulis and Nicklas 2000). In Table 2, we compare the stages of mitosis and meiosis in terms of our hypothesis. TABLE 2 Relationship of key meiotic stages to mitotic stages Meiotic stage . Relationship to mitosis . Modification . Novelty . S phase, meiosis I Comparable to mitotic S phasea X Prophase I Homolog pairing X Metaphase II Comparable to mitotic metaphaseb X Anaphase I Comparable to mitotic anaphaseb X Prophase II (no S phase) Comparable to mitotic G2 statec X Metaphase II Essentially mitotic metaphased X Anaphase II Essentially mitotic anaphased X Telophase II Essentially mitotic telophased X Meiotic stage . Relationship to mitosis . Modification . Novelty . S phase, meiosis I Comparable to mitotic S phasea X Prophase I Homolog pairing X Metaphase II Comparable to mitotic metaphaseb X Anaphase I Comparable to mitotic anaphaseb X Prophase II (no S phase) Comparable to mitotic G2 statec X Metaphase II Essentially mitotic metaphased X Anaphase II Essentially mitotic anaphased X Telophase II Essentially mitotic telophased X a DNA breaks introduced during replication; almost certainly part of later meiotic evolution. b With the difference that it is replicated chromosomes that are first aligned at metaphase, then separated at anaphase. c In that the chromosomes are “unlicensed” and hence refractory to replication. d The mechanics are the same; the only difference is in the number of chromosomes (one-half) relative to mitosis. Open in new tab TABLE 2 Relationship of key meiotic stages to mitotic stages Meiotic stage . Relationship to mitosis . Modification . Novelty . S phase, meiosis I Comparable to mitotic S phasea X Prophase I Homolog pairing X Metaphase II Comparable to mitotic metaphaseb X Anaphase I Comparable to mitotic anaphaseb X Prophase II (no S phase) Comparable to mitotic G2 statec X Metaphase II Essentially mitotic metaphased X Anaphase II Essentially mitotic anaphased X Telophase II Essentially mitotic telophased X Meiotic stage . Relationship to mitosis . Modification . Novelty . S phase, meiosis I Comparable to mitotic S phasea X Prophase I Homolog pairing X Metaphase II Comparable to mitotic metaphaseb X Anaphase I Comparable to mitotic anaphaseb X Prophase II (no S phase) Comparable to mitotic G2 statec X Metaphase II Essentially mitotic metaphased X Anaphase II Essentially mitotic anaphased X Telophase II Essentially mitotic telophased X a DNA breaks introduced during replication; almost certainly part of later meiotic evolution. b With the difference that it is replicated chromosomes that are first aligned at metaphase, then separated at anaphase. c In that the chromosomes are “unlicensed” and hence refractory to replication. d The mechanics are the same; the only difference is in the number of chromosomes (one-half) relative to mitosis. Open in new tab SELECTION PRESSURES TO FOSTER HOMOLOGOUS CHROMOSOME PAIRING The conclusion that meioisis originated with the insertion of homolog synapsis into the mitotic cycle immediately raises two questions. The first concerns the nature of the selective pressures for this new chromosomal behavior and the second concerns the molecular requirements for this novel cytological feature. In this section, we discuss the possible selective pressures; in the molecular side of the scenario, we approach the molecular aspects. A cardinal feature of contemporary meiosis is its association with high levels of intergenic recombination. The selective benefits are twofold: such recombination helps reduce unfavorable gene combinations and promotes new favorable ones. Correspondingly, most thinking about the evolution of meiosis has focused on the selection pressures to foster the elimination of harmful gene combinations and to promote beneficial ones (Fisher 1930; Muller 1932; Maynard Smith 1978; Crow, 1988). From this standpoint, any selection for homolog synapsis would actually have involved selection for improved efficiency of genetic recombination mediated by such pairing. Nevertheless, the view that the benefits of intergenic recombination were a prime selective force for the origins of meiosis has always been problematical. Although the arguments are often constructed in terms of the immediate benefits to offspring (see review by Ghiselin 1988), the explanation implicitly invokes an element of group selection with respect to future benefits for the population. Yet natural selection cannot operate with foresight. Hence, whatever initial benefits chromosome pairing in proto-eukaryotes may have conveyed, they would have had to have been more immediate than the promotion of intergenic recombination. An alternative view is that the initial benefit of meiosis was enhanced repair of DNA damage via recombination (Bernstein 1977; Bernstein et al. 1988). The need for efficient DNA repair is a basic and ancient requirement of living cells, as shown by its ubiquity among prokaryotic cells, and originally served to protect early cells from incoming solar UV irradiation and other DNA-damaging agents, as well as desiccation. Furthermore, recombination of homologous sequences provides an efficient mode of DNA repair. In E. coli cells, for example, inactivation of either of the key recombination functions, recA or the recBC enzyme, greatly increases lethality upon exposure to UV irradiation, despite the presence of other DNA repair systems (Clark 1971; Smith 2004). The argument for DNA repair as the primary (initial) benefit of meiosis implies that the existing forms of DNA repair were borderline insufficient for the needs of the earliest eukaryotic cells. Prokaryotes, however, are endowed with a rich assortment of DNA repair capacities, including inducible recombinational repair (Levin 1988; Cavalier-Smith 2002; Marcon and Moens 2005), and the existence of abundant prokaryotic life in the harsh conditions of Archean seas (Knoll 2003), well before eukaryotic cells existed, suggests that DNA repair capacities must have sufficed to cope with the kinds of DNA damage associated with that environment. Especially in light of cellular capacities to upregulate recombinational repair and the highly efficient repair of double-strand breaks (DSBs) utilizing sister chromatids in mitotic cells (Argueso et al. 2008), the argument that meiosis was necessary for extra repair capacity does not seem compelling. If, however, the two standard hypotheses about selection pressures for meiosis are inadequate, then another explanation is needed. If the deduction that homolog synapsis was the key initial event in the origin of meiosis, one has to ask just what such pairing yields. The answer is “accurate alignment” and that may be the key to the puzzle: accurate alignment should promote not only recombination but also recombination between fully matched long sequences. We propose, in effect, that homolog synapsis was selected because it promotes fidelity of recombination, thus reducing the chances of ectopic pairing and consequent ectopic recombination. Genomewide homolog pairing would help to ensure that only identical regions (not diverged homologous ones at different chromosomal locations) would recombine. As in the DNA repair hypothesis, the selective benefits would be immediate but the proposed advantage would be radically different: instead of the restoration of wild-type DNA sequences following damage (as in the DNA repair hypothesis), the selective benefit of the new process would be the prevention of recombination-generated damage. Our suggestion is directly related to the argument that recombination, particularly in multi-chromosomal cells, can have deleterious effects and is regulated tightly to minimize them (Bernstein et al. 1988). There is, in fact, some direct experimental evidence for this proposition. Holliday et al. (1976) presented an extensive analysis of DNA repair-defective mutants in a gene that they designated rec-1 in the fungus Ustilago maydis. The phenotype of these mutants, however, is more complex than a simple repair deficiency. The strains exhibited (1) 20% nonviable cells, (2) elevated rates of mitotic recombination, (3) defective meiosis in crosses between differently marked strains with formation of aneuploid and nonviable meiotic products, and (4) considerable heterogeneity in diploid but not in haploid colonies. This complex phenotype is most simply interpreted as an abnormality in the regulation or control of recombination manifested in both mitosis and meiosis. The heterogeneity of diploid rec-1 strains is probably due to abnormal genetic events generated by recombination and leading to unbalanced genomes. In effect, the wild-type strain keeps recombination in check and failure to do so leads to errors in transmission of the genetic material. That recombinogenic enzymes are normally kept to low levels of activity is shown by another study. The recA homolog RAD51 in the ciliate Tetrahymena thermophila is normally present at a low level of activity, but upon exposure of the cells to either UV or methyl methanesulfonate (Campbell and Romero 1998), its levels increase dramatically, presumably to facilitate recombinational repair in the highly polyploid macronucleus. This finding suggests that the activities of the recA enzymes, rather than homolog pairing, can be the rate-limiting steps for recombination. A further finding that supports the general proposition that recombination has to be tightly regulated, presumably to prevent deleterious defects, comes from an analysis by Lynch (2005). Plotting the results of many studies that measured recombination frequency per unit length of DNA as a function of genome size, he finds that there is an exponential decrease in genome size with an approximate slope of −1 (see Figure 2 in Lynch 2005). Such a distribution is the strong signature of a process that has to be kept in check. If one of the hazards of excess recombination is recombining the “wrong” sequences, then the greater the nuclear concentration of partially related sequences, the greater the probability of recombinational errors following ectopic pairing should be. Indeed, chromosome aberrations produced by induced DSBs occur preferentially at repetitive sequences in the genome (Argueso et al. 2008). It is probable that growing genome size and complexity, a key feature of eukaryotic evolution (Cavalier-Smith 1978), would have increased the opportunities for recombination events between such paralogous (repetitive) sequences at different chromosomal locations. The consequences would include deletions, duplications, and inversions in intrachromosomal recombination and translocations and dicentric chromosomes from interchromosomal exchanges. Other things being equal, the number of defects would be expected to increase exponentially as a function of the increase in repetitive sequences throughout the genome. Such alterations would reduce the fidelity of genome transmission, and hence the fraction of viable cells in any clonal lineage. In contrast, homolog synapsis prior to recombination should substantially reduce this burden of recombination-induced damage. It does not eliminate it, however. Recombinational errors occur in meiosis, even between fully homologous sequences, as first shown by the deletion-duplication phenomenon of the Bar and Suprabar mutations in Drosophila (Sturtevant 1925). The recent demonstrations of ubiquitous copy number variation (CNV) in mice, chimpanzees, and humans (Li et al. 2004; Adams et al. 2005; Perry et al. 2006; Redon et al. 2006) has revealed just how common such recombination errors are, even with presumably full pairing of homologs in meiosis. The key point, however, is that, in the absence of accurate extensive pairing, such errors take place even more frequently. For example, the male-specific region of the Y chromosome, which has no pairing partner on the X, seems to have accumulated a huge stock of permanent duplications and palindromes, as a result of recombinational errors between its own sequences (Rozen et al. 2003; Skaletsky et al. 2003). Similarly, imperfectly paired “homeologous” sequences within a haploid strain derived from the allopolyploid species Brassica napus undergo far more recombination-mediated exchange between such related but nonhomologous sequences than in the parent strain (Nicholas et al. 2007). A reasonable inference from all such findings is that, in early eukaryotic cell evolution, any trend toward increased genome size via the addition of new repetitive sequences would have increased the frequency of recombinational errors between such sequences. There is a second way, however, in which recombination, prior to the advent of meiosis, might have been harmful. Imagine that recombination in a diploid cell can take place at any point in the cell cycle but that resolution of recombination events is not always instantaneous. Such unresolved recombination events at the time of chromosome separation in anaphase would produce uncompleted chromosome separations, leading to either chromosome fragmentation or nondisjunction. The larger the genome size and the greater the number of chromosomes, the greater the chances of such events. It has been shown in E. coli that unresolved recombination events can indeed block chromosome segregation, leading to the production of filamentous cells (Ishioka et al. 1998). In contemporary eukaryotic cells, such events are avoided through the use of DNA damage checkpoints, which halt chromosome separations until repair is achieved. Proto-eukaryotic cells, however, might have lacked such checkpoints, just as contemporary prokaryotic cells seem to lack replication-completion checkpoints (Bendich 2007), and might have been vulnerable to such chromosome disjunction errors. Diploid cells in early (proto-) eukaryotes would thus have faced a dilemma. They would have required efficient recombinational repair for survival but would have needed to avoid the potential concomitants of such repair, namely recombinational errors between nonidentical sequences or unresolved recombinational events at the time of mitosis. What sort of events or process could have helped these cells to navigate between the Scylla of unrepaired DNA and the Charybdis of recombinationally induced errors? Any process that both promotes accurate DNA sequence alignment and restricts recombination to a distinct period prior to the separation of chromosomes would help to resolve this dilemma. This is precisely what meiotic pairing of homologs achieves. Such pairing should promote accurate homology searches, thereby reducing the number of additions or deletions that a more random DNA search procedure would generate. At the same time, concentration of recombination events to a period that precedes chromosome segregation, as occurs in homolog synapsis, would promote the maintenance of genomic integrity through the reduction of chromosomal disjunctional events and hence the fidelity of genome transmission. To sum up, we propose that the selection pressures for homolog synapsis and the origins of meiosis were to improve recombinational accuracy and to restrict it to a safe interval, while retaining its short-term (repair) benefits. A cell lineage that had evolved this capability for diploid cells would be less error-prone in transmitting its genetic material. Subsequent optimizing mutations could have included those that enhanced recombination enzyme activities during the chromosome pairing period and reduced them outside this interval, as seen in normal mitotic cells. By our hypothesis, the reduction-division process, restoring the haploid state, would have occurred automatically. In effect, the proposed initial sequence of events need not have involved the union of sex cells but instead a “parasexual” process, as discussed below. THE MOLECULAR SIDE OF THE SCENARIO Even if the puzzle of meiotic origins is largely reduced to explaining the evolution of stable post-prophase homolog synapsis, the precise molecular foundations of that process remain obscure. The molecular and cytological complexity of the pairing process in present-day species (Kleckner 2006) at first seems to preclude the origination of synapsis via one or two mutational steps, although the evolution of meiosis-specific rec8 cohesins from a preexisting cohesin (Parisi et al. 1999) was undoubtedly a crucial element. Other cytogenetic features such as synaptonemal complexes and the requirement for recombination to promote normal chromosome disjunction could well have evolved subsequently. Initially, pairing in simple diploid cells, perhaps containing just one or two homolog pairs, might have involved fewer components and steps. In principle, the molecular evolution of a new cohesin molecule that specifically promoted homolog pairing might have provided the crucial trigger for meiosis. In contemporary yeast cells, the cohesin protein rec8 is maintained specifically at centromeres and the adjoining regions during normal synapsis of homologs and is essential for synapsis; its absence leads to the loss of reduction division and the occurrence of sister-chromatid separation (equational division) in MI (Watanabe and Nurse 1999; Hauf and Watanabe 2004). Alternatively, it is possible that homolog synapsis was initially produced by elevated rates of chromosome breaking and joining, mediated by homologous sequence annealing, and promoted by existing cohesins. Although synapsis of homologs does not require DSBs in all contemporary organisms (Joyce and Kim 2007) and might not have been involved in the earliest forms of synapsis, in proto-eukaryotes with a small number of chromosomes, such recombination induction might, in principle, have sufficed to initiate homolog pairing. Whatever the trigger for the origins of synapsis, the resulting opportunity for repair and recombination might have permitted these lineages to repress non-damage-induced recombinational repair at other times, thus concentrating such repair in one discrete period. Although the origins of homolog synapsis can never be known with certainty, it is striking how much of the molecular machinery that it brings into play is conserved between prokaryotes and eukaryotes and between mitosis and meiosis. In particular, the involvement of recA-family recombination enzymes and their enrichment in present-day eukaryotes at the sites of “recombination nodules” during meiosis (Bishop 1994; Tarsounas et al. 1999) is evidence of the evolutionary continuity between prokaryotic and eukaryotic recombination. The molecular evolution of Dmc1 was clearly a key step in promoting interhomolog recombination, but as a member of the recA gene family, its origins are not problematical. Strikingly, a number of the SMC family proteins, in particular the condensins and the cohesins, play similar roles in controlling sister-chromatid behavior in both meiosis and mitosis (reviewed in Haering and Nasmyth 2003). Finally, as noted earlier, the molecular machinery for centromere splitting is shared between mitosis and meiosis II. These molecules include a serine/threonine phosphatase, PP2A, and one of its substrates, the kinetichore-associated protein Shugoshin (reviewed in Rivera and Losado 2006). In sum, it appears that most of the molecular components required for the evolution of homolog pairing and recombination between homologs were present in one form or another in the earliest premeiotic proto-eukaryotic cells. LINKING PARASEXUAL REDUCTION DIVISION TO SEXUAL REPRODUCTION The discussion so far has neglected one crucial element: the fact that meiosis is intimately linked to sexual reproduction. Indeed, cycles of sexual reproduction would be impossible without the reduction division that takes place in meiosis. Our hypothesis, however, links the evolutionary advent of homolog pairing to diploidization events that may have occurred independently of sex-cell fusion. Such diploidization events, followed by recombination and reduction division to regenerate haploid states, are termed “parasexual cycles.” Parasexual sexual cycles were first described in fungi (Pontecorvo 1959) and fungal parasexual cycles remain the best characterized, but they are also known in the cellular slime molds and in tetraploid cancer cells where the reduction of ploidy is from tetraploidy to diploidy (Rajaraman et al. 2005). We propose, therefore, that homolog synapsis and the concomitant reduction of diploid states originated in some form of parasexual cycle in the early proto-eukaryote lineage and that the functional relationship between diploidization via sex-cell union and meiosis was a subsequent evolutionary event. In this view, some form of “parameiosis” (Becker and Castro-Prado 2006)—a reduction division of some higher ploidy to a lower level without a preceding sex-cell fusion—preceded true meiosis in evolution. The possibility of such an evolutionary dissociation between early diploidization events (and their concomitant reduction/division sequels) and meiosis is consistent with the fact that, developmentally, diploidization and meiosis can be uncoupled. In many unicellular eukaryotes, haploid sex-cell fusion leads promptly to nuclear fusion, which immediately triggers meiosis, thus regenerating the haploid state. In contrast, in more complex, multicellular eukaryotes, meiosis is greatly delayed following the initial fusion of sex cells, taking place much later in the life cycle, during gametogenesis. Clearly, different signals in different organisms trigger the onset of meiosis and the particular one(s) employed reflect the organism's evolutionary history. The idea presents a way of cutting the Gordian knot posed by the difficulty of accounting for the simultaneous origins of sex and meiosis in evolution. In effect, some form of reduction division could have preceded both true meiosis and the first systems of sex-cell union in early (unicellular) eukaryotes, as also suggested by Hurst and Nurse (1991). TESTING THE HYPOTHESIS There is, of course, no direct way to test the basic hypothesis presented here since the cells in which meiosis first originated existed well over 1 billion years ago and this progenitor lineage undoubtedly vanished long ago. Nevertheless, the hypothesis makes two strong experimental predictions. The first is that, if extensive homolog pairing could be induced in the prophase of diploid mitotic cells, it could trigger a meiotic-like sequence of two cell divisions. In principle, this might be achievable in transgenic yeast cells by the induction of rec8 and Dmc1 activities. A positive result would provide strong support for the hypothesis. A negative result, however, would be less informative, given the possibility that modern cells have evolved properties that make the original behavior less automatic. The second prediction is that inducing high recombination activities in either diploid mitotic cells or hyperrecombination events in meiotic cells should promote more recombinational errors, with consequent declines in cell progeny viability. Furthermore, the number of such events should increase dramatically as a function of the number of chromosomes per haploid set, the ploidy level, and the number of induced recombination events per nucleus. In particular, it should be possible to engineer diploid and tetraploid yeast strains with inducible rad51 and/or Dmc1 constructs. To test this possibility, one could then induce excess activities of these genes in various stages of the mitotic cell cycle or in meiosis I. The prediction is that CNVs or aneuploid variants, having reduced fitness, should be induced and that tetraploid strains should have even more than diploids. In yeast strains genetically crippled in their DNA damage checkpoints, such excess recombination events in somatic cells should lead to additional chromosomal nondisjunction or chromosomal breakage events. It is possible, however, that induction of recombination enzymes would be insufficient to induce extra recombination events, although the Tetrahymena results of Campbell and Romero (1998) suggest otherwise. In this case, very mild conditions promoting a low level of chromosome breakage should be included, either by very low level nonlethal X ray or by enzymatically induced DSBs. The latter have been shown to recruit cohesin to those sites, promoting sister-chromatid pairing in diploid yeast cells (Strom et al. 2004). Indeed, even a few DSBs trigger enhanced genomewide sister-chromatid cohesion (Strom et al. 2007; Unal et al. 2007). Our hypothesis predicts that such treatment should produce more CNVs and various rearrangements in polyploid yeast strains than in diploid strains. Results of this kind would support the proposition that there were strong selection pressures to limit ectopic recombination and promote the accuracy of recombination. CONCLUSIONS The evolutionary origins of meiosis have been a matter of intense debate for decades and are intimately connected to the controversy about the biological value of sexual reproduction itself, which dates from the 19th century (Ghiselin 1988). Yet the predominant focus in this literature has been on the nature of the putative selection pressures rather than on the actual cytological changes involved. Furthermore, much of the discussion has been about the maintenance of sex (and meiosis) rather than its origins, particularly in animals (Maynard Smith 1978; Hamilton 1999; Archipova and Meselson 2004), a group of organisms that arose long after meiosis originated. For the origins of meiosis, one must consider the earliest eukaryotic-like cells and their probable environment (Archetti 2004; Marcon and Moens 2005; Holliday 2006). Here, we have argued that the origins of meiosis from mitosis initially involved only one new step, namely homolog synapsis. Two of the other unusual features of meiosis are prefigured in mitosis and would have been brought into play as consequences of the existing regulatory features of mitosis while the remaining one (extensive recombination) could have evolved later. We further propose that the selective pressures for acquiring extensive homolog pairing capacity in early eukaryotes were to localize and restrict recombination, minimizing ectopic recombination and thus reducing duplications and deletions and larger aneuploid changes. (Extensive synapsis would also have probably simultaneously promoted genetic recombination but primarily among the “right” sequences.) A similar general conclusion from a consideration of cancer cells has been proposed by Heng (2007). Our brief comparative survey of the molecular machinery needed for the evolution of meiosis from mitosis suggests that much of it could have been recruited for use in meiosis via appropriate point mutations. Other features of meiosis, such as synaptonemal complexes and the requirement for recombination to ensure chromosome disjunction, would have been secondarily evolved properties. A schematic summary of our evolutionary scenario is shown in Figure 1. Figure 1.— Open in new tabDownload slide Schematic of our hypothesis, which is shown as a time line of events in the evolution of meiosis. Thick arrows indicate long-term events (evolutionary timescale or multi-generation) while the thin arrow for the proposed parameiosis process indicates an immediate consequence and event. Figure 1.— Open in new tabDownload slide Schematic of our hypothesis, which is shown as a time line of events in the evolution of meiosis. Thick arrows indicate long-term events (evolutionary timescale or multi-generation) while the thin arrow for the proposed parameiosis process indicates an immediate consequence and event. Our hypothesis in no way contradicts the idea that meiosis serves to promote intergenic recombination, thereby providing new variation for selection to act upon. Indeed, one of us has proposed that the advantages of increased intergenic recombination were important in the early establishment of eukaryotic cells competing for niches with prokaryotic cells (Holliday 2006). We argue here, however, that this benefit of meiosis did not provide the initial selective pressure for its origins. Although our idea differs from traditional thinking about the advantages of meiosis, it is consistent with the known facts, and its central premise—that recombination has to be limited in extent to ensure the fidelity of the transmission of the genetic complement—is testable. Acknowledgements We thank Francisco Ayala, James F. Crow, and William Holloman for their comments on an early draft of this article and Michael Lynch and two anonymous referees for helpful comments on the original submitted version. We are also grateful to Richard D'Ari and Arthur Lesk for alerting us, respectively, to the results of Ishioka et al. (1998) and the analysis of Lynch (2005). References Aboussekhra, A., R. Chanet, A. Adijir and F. Fabre, 1992 Semidominant suppressors of Srs2 helicase mutations of Saccharomyces cerevisiae map in the RAD51 gene, whose sequence predicts a protein with similarities to prokaryotic RecA proteins. Mol. Cell. Biol. 12: 3224 –3234. Crossref Search ADS PubMed Adams, D. J., E. T. Dermitzkis, T. Cox, J. Smith, R. Davies et al., 2005 Complex haplotypes, copy number polymorphisms and coding variation in two recently diverged mouse strains. Nat. Genet. 37: 532 –536. Crossref Search ADS PubMed Archetti, M. ( 2004 ) Loss of complementation and the logic of two-step meiosis. J. Evol. Biol. 17: 1098 –1105. Crossref Search ADS PubMed Archipova, I., and M. Meselson, 2004 Deleterious transposable elements and the extinction of asexuals. BioEssays 27: 76 –85. Argueso, J. L., J. Westmoreland, P. A. Mieczkowski, M. Gawal, T. D. Petes et al., 2008 Double-strand breaks associated with repetitive DNA can reshape the genome. Proc. Natl. Acad. Sci. USA 105: 11845 –11850. Crossref Search ADS Becker, T. C., and M. A. de Castro-Prado, 2006 Parasexuality in asexual development mutants of Aspergillus nidulans. Biol. Res. 39: 297 –305. PubMed Bendich, A., 2007 The size and form of chromosomes are constant in the nucleus, but highly variable in bacteria, mitochondria and chloroplasts. BioEssays 29: 474 –483. Crossref Search ADS PubMed Bernstein, H., 1977 Germ line recombination may be primarily a manifestation of DNA repair processes. J. Theor. Biol. 69: 371 –380. Crossref Search ADS PubMed Bernstein, H., F. A. Hopf and R. E. Michod, 1988 Is meiotic recombination an adaptation for repairing DNA, producing genetic variation, or both?, pp. 139–160 in The Evolution of Sex: An Examination of Current Ideas, edited by R. E. Michod and B. R. Levin. Sinauer Associates, Sunderland, MA. Bishop, D. K., 1994 RecA homologs Dmc1 and Rad51 interact to form multiple nuclear complexes prior to meiotic chromosome synapsis. Cell 79: 1081 –1092. Crossref Search ADS PubMed Blow, J. J., and A. Dutta, 2005 Preventing re-replication of chromosomal DNA. Nat. Rev. Genet. 6: 476 –486. Crossref Search ADS Burgess, S. M., N. Kleckner and B. M. Weiner, 1999 Somatic pairing of homologs in budding yeast: existence and modulation. Genes Dev. 13: 1627 –1641. Crossref Search ADS PubMed Campbell, C. C., and D. P. Romero, 1998 Identification and characterization of the RAD51 gene from the ciliate Tetrahymena thermophila. Nucleic Acids Res. 26: 3165 –3172. Crossref Search ADS PubMed Cavalier-Smith, T., 1978 Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA c–value paradox. J. Cell Sci. 34: 247 –278. PubMed Cavalier-Smith, T., 1981 The origin and early evolution of the eukaryotic cell, pp. 33–84 in Molecular and Cellular Aspects of Microbial Evolution, edited by M. J. Carlile, J. F. Collins and B. E. B. Moseley, Society of General Microbiology Symposium 32. Cambridge University Press, Cambridge, UK. Cavalier-Smith, T., 2002 Origins of the machinery of recombination and sex. Heredity 88: 125 –141. Crossref Search ADS PubMed Clark, A. J., 1971 Toward a metabolic interpretation of genetic recombination of E. coli and its phage. Annu. Rev. Microbiol. 25: 437 –464. Crossref Search ADS PubMed Crow, J. F., 1988 The importance of recombination, pp. 56–73 in The Evolution of Sex: An Examination of Current Ideas, edited by R. E. Michod and B. R. Levin. Sinauer Associates, Sunderland, MA. Erickson, H. P., 2007 Evolution of the cytoskeleton. BioEssays 29: 668 –677. Crossref Search ADS PubMed Fisher, R. A., 1930 The Genetical Theory of Natural Selection. Clarendon Press, Oxford. Ghiselin, M. T., 1988 The evolution of sex: a history of competing points of view, pp. 7–23 in The Evolution of Sex: An Examination of Current Ideas, edited by R. E. Michod and B. R. Levin. Sinauer Associates, Sunderland, MA. Haering, C. H., and K. Nasmyth, 2003 Building and breaking bridges between sister chromatids. BioEssays 25: 1178 –1191. Crossref Search ADS PubMed Hamilton, W. J., 1999 Narrow Roads to Gene Land: Evolution of Sex, Vol. 2. Oxford University Press, Oxford. Hauf, S., and Y. Watanabe, 2004 Kinetochore orientation in mitosis and meiosis. Cell 119: 317 –327. Crossref Search ADS PubMed Heng, H., 2007 Evolution of altered karyotypes by sexual reproduction preserves species identity. Genome 50: 517 –524. Crossref Search ADS PubMed Hirano, T., 2005 SMC proteins and chromosome mechanics: from bacteria to humans. Philos. Trans. R. Soc. Lond. B Biol. Sci. 360: 507 –514. Crossref Search ADS PubMed Holliday, R., 2006 Meiosis and sex: potent weapons in the competition between early eukaryotes and prokaryotes. BioEssays 28: 1123 –1125. Crossref Search ADS PubMed Holliday, R., R. E. Halliwell, M. W. Evans and V. Rowell, 1976 Genetic characterization of rec1, a mutant of Ustilago maydis defective in repair and recombination. Genet. Res. 27: 413 –453. Crossref Search ADS PubMed Hurst, L., and P. Nurse, 1991 A note on the evolution of meiosis. J. Theor. Biol. 150: 561 –563. Crossref Search ADS PubMed Ishioka, K., A. Fukuoh, H. Iwasaki, A. Nakata and H. Shinagawa, 1998 Abortive recombination in Escherichia coli ruv mutants blocks chromosome partitioning. Genes Cells 3: 209 –220. Crossref Search ADS PubMed Joyce, E. F., and K. S. Kim, 2007 When specialized sites are important for synapsis and the distribution of crossovers. BioEssays 29: 217 –226. Crossref Search ADS PubMed Kleckner, N., 2006 Chiasma formation: chromatin/axis interplay and the role(s) of the synaptonemal complex. Chromosoma 115: 175 –194. Crossref Search ADS PubMed Knoll, A. H., 2003 Life on a Young Planet. Princeton University Press, Princeton, NJ. Levin, B. R., 1988 The evolution of sex in bacteria, pp. 194–211 in The Evolution of Sex: An Examination of Current Ideas, edited by R. E. Michod and B. R. Levin. Sinauer Associates, Sunderland, MA. Li, J., T. Jiang, J. H. Mao, A. Balmain, L. Peterson et al., 2004 Genomic segmental polymorphisms in inbred mouse strains. Nat. Genet. 36: 952 –954. Crossref Search ADS PubMed Lynch, M., 2005 The origins of eukaryotic gene structure. Mol. Biol. Evol. 23: 450 –468. PubMed Marcon, E., and P. B. Moens, 2005 The evolution of meiosis: recruitment and modification of somatic DNA-repair proteins. BioEssays 27: 795 –808. Crossref Search ADS PubMed Maynard Smith, J., 1978 The Evolution of Sex. Cambridge University Press, Cambridge, UK. McKee, B. D, 2004 Homologous pairing and chromosome dynamics in meiosis and mitosis. Biochim. Biophys. Acta 1677: 165 –180. Crossref Search ADS PubMed Muller, H. J., 1932 Some genetic aspects of sex. Am. Nat. 66: 118 –138. Crossref Search ADS Neale, M. J., and S. Keeney, 2006 Clarifying the mechanics of DNA strand exchange in meiotic recombination. Nature 442: 153 –158. Crossref Search ADS PubMed Nicholas, S. D., G. Mignon, F. Eber, O. Corinton, H. Monod et al., 2007 Homeologous recombination plays a major role in chromosome rearrangements that occur during meiosis of Brassica napus haploids. Genetics 175: 487 –503. Crossref Search ADS PubMed Paliulis, L. V., and R. B. Nicklas, 2000 The reduction of chromosome number in meiosis is determined by properties built into the chromosomes. J. Cell Biol. 150: 1223 –1232. Crossref Search ADS PubMed Parisi, S., M. J. McKay, M. Molnar, M. A. Thompson, P. J. Van Der Speck et al., 1999 Rec8p, a meiotic recombination and sister chromatid cohesion phosphoprotein of the Rad21p family, conserved from fission yeast to humans. Mol. Cell. Biol. 19: 3515 –3528. Crossref Search ADS PubMed Perry, G. H., J. Tchinda, S. D. McGrath, J. Zhang, S. R. Picker et al., 2006 Hotspots for copy number variation in chimpanzees and humans. Proc. Natl. Acad. Sci. USA 103: 8006 –8011. Crossref Search ADS Pontecorvo, G., 1959 Trends in Genetic Analysis. Columbia University Press, New York. Rajaraman, R., M. M. Rajaraman, S. R. Rajaraman and D. L. Guernsey, 2005 Neosis—a paradigm of self-renewal in cancer. Cell. Biol. Int. 29: 1084 –1097. Crossref Search ADS PubMed Ramesh, M. A., S. B. Malik and J. M. Logsdon, Jr., 2005 A phylogenomic inventory of meiotic genes: evidence for sex in Giardia and an early eukaryotic origin of meiosis. Curr. Biol. 15: 185 –191. PubMed Redon, R., S. Ishikawa, K. R. Fitch, L. Feuk, G. H. Perry et al., 2006 Global variation in copy number in the human genome. Nature 444: 444 –454. Crossref Search ADS PubMed Rivera, T., and A. Losado, 2006 Shogoshin and PP2A, shared duties at the centromere. BioEssays 28: 775 –779. Crossref Search ADS PubMed Rozen, S., H. Skaletsky, J. D. Marszalek, P. J. Minx and H. S. Cordum, 2003 Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423: 873 –876. Crossref Search ADS PubMed Schurko, A. M., and J. M. Logsdon, Jr., 2008 Using a meiotic toolkit to investigate ancient asexual “scandals” and the evolution of sex. BioEssays 30: 579 –589. Crossref Search ADS PubMed Shinohara, A., H. Ogawa, T. Ogawa and A Shinohara, 1992 Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like protein. Cell 69: 457 –470. Crossref Search ADS PubMed Simchen, G., and Y. Hugerat, 1993 What determines whether chromosomes segregate reductionally or equationally in meiosis? BioEssays 15: 1 –8. Crossref Search ADS PubMed Skaletsky, H., Y. Kuroda-Kawaguchi, P. J. Minx, H. S. Cordum and L. Hillier, 2003 The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423: 825 –837. Crossref Search ADS PubMed Smith, K. C., 2004 Recombinational DNA repair: the ignored repair systems. BioEssays 26: 1322 –1326. Crossref Search ADS PubMed Stern, H., and Y. Hotta, 1977 Biochemistry of meiosis. Philos. Trans. R. Soc. Lond. B Biol. Sci. 277: 277 –294. Crossref Search ADS PubMed Strom, L., L. B. Lindros, K. Shirahige and C. Sjogren, 2004 Postreplicative recruitment of cohesin to double-strand breaks is required for DNA repair. Mol. Cell 16: 1003 –1015. Crossref Search ADS PubMed Strom, L., C. Carlsson, H. B. Lindroos, S. Wedahl, Y. Katou et al., 2007 Postreplicative formation of cohesion is required for repair and is induced by a single DNA break. Science 317: 242 –245. Crossref Search ADS PubMed Sturtevant, A. H., 1925 The effects of unequal crossing over at the Bar locus in Drosophila. Genetics 10: 117 –147. Crossref Search ADS PubMed Tarsounas, M., T. Morita, R. E. Pearlman and P. B. Moens, 1999 RAD51 and DMC1 form mixed complexes prior to meiotic chromosome synapsis. J. Cell Biol. 147: 207 –220. Crossref Search ADS PubMed Unal, E., J. M. Heidinger-Pauli and D. Koshland, 2007 DNA double-strand breaks trigger genome-wide sister-chromatid cohesion through Eco1 (Ctf7). Science 317: 245 –248. Crossref Search ADS PubMed Watanabe, Y., and P. Nurse, 1999 Cohesin Rec8 is required for reductional chromosome segregation at meiosis. Nature 400: 461 –464. Crossref Search ADS PubMed © Genetics 2009 This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Dymond, Jessica S; Scheifele, Lisa Z; Richardson, Sarah; Lee, Pablo; Chandrasegaran, Srinivasan; Bader, Joel S; Boeke, Jef D

doi: 10.1534/genetics.108.096784pmid: 19015540

A major challenge in undergraduate life science curricula is the continual evaluation and development of courses that reflect the constantly shifting face of contemporary biological research. Synthetic biology offers an excellent framework within which students may participate in cutting-edge interdisciplinary research and is therefore an attractive addition to the undergraduate biology curriculum. This new discipline offers the promise of a deeper understanding of gene function, gene order, and chromosome structure through the de novo synthesis of genetic information, much as synthetic approaches informed organic chemistry. While considerable progress has been achieved in the synthesis of entire viral and prokaryotic genomes, fabrication of eukaryotic genomes requires synthesis on a scale that is orders of magnitude higher. These high-throughput but labor-intensive projects serve as an ideal way to introduce undergraduates to hands-on synthetic biology research. We are pursuing synthesis of Saccharomyces cerevisiae chromosomes in an undergraduate laboratory setting, the Build-a-Genome course, thereby exposing students to the engineering of biology on a genomewide scale while focusing on a limited region of the genome. A synthetic chromosome III sequence was designed, ordered from commercial suppliers in the form of oligonucleotides, and subsequently assembled by students into ∼750-bp fragments. Once trained in assembly of such DNA “building blocks” by PCR, the students accomplish high-yield gene synthesis, becoming not only technically proficient but also constructively critical and capable of adapting their protocols as independent researchers. Regular “lab meeting” sessions help prepare them for future roles in laboratory science.

Goodson-Gregg, Nathan; De Stasio, Elizabeth A

doi: 10.1534/genetics.108.095588pmid: 19015544

While many institutions use a version of the Ames test in the undergraduate genetics laboratory, students typically are not exposed to techniques or procedures beyond qualitative analysis of phenotypic reversion, thereby seriously limiting the scope of learning. We have extended the Ames test to include both quantitative analysis of reversion frequency and molecular analysis of revertant gene sequences. By giving students a role in designing their quantitative methods and analyses, students practice and apply quantitative skills. To help students connect classical and molecular genetic concepts and techniques, we report here procedures for characterizing the molecular lesions that confer a revertant phenotype. We suggest undertaking reversion of both missense and frameshift mutants to allow a more sophisticated molecular genetic analysis. These modifications and additions broaden the educational content of the traditional Ames test teaching laboratory, while simultaneously enhancing students' skills in experimental design, quantitative analysis, and data interpretation.

Flibotte, Stephane; Edgley, Mark L; Maydan, Jason; Taylor, Jon; Zapf, Rick; Waterston, Robert; Moerman, Donald G

doi: 10.1534/genetics.108.096487pmid: 18957702

We have developed a significantly improved and simplified method for high-resolution mapping of phenotypic traits in Caenorhabditis elegans using a combination of single nucleotide polymorphisms (SNPs) and oligo array comparative genome hybridization (array CGH). We designed a custom oligonucleotide array using a subset of confirmed SNPs between the canonical wild-type Bristol strain N2 and the Hawaiian isolate CB4856, populated with densely overlapping 50-mer probes corresponding to both N2 and CB4856 SNP sequences. Using this method a mutation can be mapped to a resolution of ∼200 kb in a single genetic cross. Six mutations representing each of the C. elegans chromosomes were detected unambiguously and at high resolution using genomic DNA from populations derived from as few as 100 homozygous mutant segregants of mutant N2/CB4856 heterozygotes. Our method completely dispenses with the PCR, restriction digest, and gel analysis of standard SNP mapping and should be easy to extend to any organism with interbreeding strains. This method will be particularly powerful when applied to difficult or hard-to-map low-penetrance phenotypes. It should also be possible to map polygenic traits using this method.

Joyce, Eric F; McKim, Kim S

doi: 10.1534/genetics.108.093112pmid: 18957704

During meiosis, programmed DNA double-strand breaks (DSBs) are repaired to create at least one crossover per chromosome arm. Crossovers mature into chiasmata, which hold and orient the homologous chromosomes on the meiotic spindle to ensure proper segregation at meiosis I. This process is usually monitored by one or more checkpoints that ensure that DSBs are repaired prior to the meiotic divisions. We show here that mutations in Drosophila genes required to process DSBs into crossovers delay two important steps in meiotic progression: a chromatin-remodeling process associated with DSB formation and the final steps of oocyte selection. Consistent with the hypothesis that a checkpoint has been activated, the delays in meiotic progression are suppressed by a mutation in the Drosophila homolog of pch2. The PCH2-dependent delays also require proteins thought to regulate the number and distribution of crossovers, suggesting that this checkpoint monitors events leading to crossover formation. Surprisingly, two lines of evidence suggest that the PCH2-dependent checkpoint does not reflect the accumulation of unprocessed recombination intermediates: the delays in meiotic progression do not depend on DSB formation or on mei-41, the Drosophila ATR homolog, which is required for the checkpoint response to unrepaired DSBs. We propose that the sites and/or conditions required to promote crossovers are established independently of DSB formation early in meiotic prophase. Furthermore, the PCH2-dependent checkpoint is activated by these events and pachytene progression is delayed until the DSB repair complexes required to generate crossovers are assembled. Interestingly, PCH2-dependent delays in prophase may allow additional crossovers to form.

Paré, Adam C; Dean, Derek M; Ewer, John

doi: 10.1534/genetics.108.094193pmid: 18984572

We used P-element transposase-mediated “male recombination” between two P elements in trans to create genetic deletions that removed a number of loci, including the gene encoding the neuropeptide crustacean cardioactive peptide (CCAP). Two classes of recombinant chromosomes were produced. Approximately one-quarter were viable when homozygous or hemizygous, whereas the remaining lines caused homozygous and hemizygous lethality. Preliminary analyses using PCR and CCAP immunohistochemistry suggested that, whereas the DNA of the viable lines was largely intact, most lethal lines contained chromosomal deletions that were roughly bounded by the insertion sites of the two P elements used. Southern blot analyses of select lethal lines showed that the DNA flanking the deletion was indeed grossly intact whereas the intervening DNA could not be detected. Sequencing across the deletion in three of these lethal lines identified a single line bearing intact genomic DNA on either side of the deletion separated by 30 bp of P-element DNA. The method described here suggests a simple procedure for creating deletions with defined end points. Importantly, it can use preexisting P-element insertion strains and does not rely on the use of transposable elements that are engineered to cause specific DNA rearrangements.

Cooper, Katrina F; Mallory, Michael J; Guacci, Vincent; Lowe, Katherine; Strich, Randy

doi: 10.1534/genetics.108.095513pmid: 19001291

Sister-chromatid separation at the metaphase–anaphase transition is regulated by a proteolytic cascade. Destruction of the securin Pds1p liberates the Esp1p separase, which ultimately targets the mitotic cohesin Mcd1p/Scc1p for destruction. Pds1p stabilization by the spindle or DNA damage checkpoints prevents sister-chromatid separation while mutants lacking PDS1 (pds1Δ) are temperature sensitive for growth due to elevated chromosome loss. This report examined the role of the budding yeast Pds1p in meiotic progression using genetic, cytological, and biochemical assays. Similar to its mitotic function, Pds1p destruction is required for metaphase I–anaphase I transition. However, even at the permissive temperature for growth, pds1Δ mutants arrest with prophase I spindle and nuclear characteristics. This arrest was partially suppressed by preventing recombination initiation or by inactivating a subset of recombination checkpoint components. Further studies revealed that Pds1p is required for recombination in both double-strand-break formation and synaptonemal complex assembly. Although deleting PDS1 did not affect the degradation of the meiotic cohesin Rec8p, Mcd1p was precociously destroyed as cells entered the meiotic program. This role is meiosis specific as Mcd1p destruction is not altered in vegetative pds1Δ cultures. These results define a previously undescribed role for Pds1p in cohesin maintenance, recombination, and meiotic progression.