A Neo-Sex Chromosome That Drives Postzygotic Sex Determination in the Hessian Fly (Mayetiola destructor)

Two nonoverlapping autosomal inversions defined unusual neo-sex chromosomes in the Hessian fly (Mayetiola destructor). Like other neo-sex chromosomes, these were normally heterozygous, present only in one sex, and suppressed recombination around a sex-determining master switch. Their unusual properties originated from the anomalous Hessian fly sex determination system in which postzygotic chromosome elimination is used to establish the sex-determining karyotypes. This system permitted the evolution of a master switch (Chromosome maintenance, Cm) that acts maternally. All of the offspring of females that carry Cm-associated neo-sex chromosomes attain a female-determining somatic karyotype and develop as females. Thus, the chromosomes act as maternal effect neo-W''s, or W-prime (W′) chromosomes, where ZW′ females mate with ZZ males to engender female-producing (ZW′) and male-producing (ZZ) females in equal numbers. Genetic mapping and physical mapping identified the inversions. Their distribution was determined in nine populations. Experimental matings established the association of the inversions with Cm and measured their recombination suppression. The inversions are the functional equivalent of the sciarid X-prime chromosomes. We speculate that W′ chromosomes exist in a variety of species that produce unisexual broods.SEX chromosomes are usually classified as X, Y, Z, or W on the basis of their pattern of segregation and the gender of the heterogametic sex (Ohno 1967). However, when chromosome-based sex determination occurs postzygotically, the same nomenclature confounds important distinctions and may hide interesting evolutionary phenomena. The Hessian fly (Mayetiola destructor), a gall midge (Diptera: Cecidomyiidae) and an important insect pest of wheat, presents an excellent example (Stuart and Hatchett 1988, 1991). In this insect, all of the female gametes and all of the male gametes have the same number of X chromosomes (Figure 1A); no heterogametic sex exists. Nevertheless, Hessian fly sex determination is chromosome based; postzygotic chromosome elimination produces different X chromosome to autosome ratios in somatic cells (male A1A2X1X2/A1A2OO and female A1A2X1X2/A1A2X1X2, where A1 and A2 are the autosomes, X1 and X2 are the X chromosomes, and the paternally derived chromosomes follow the slash) (Stuart and Hatchett 1991; Marin and Baker 1998). Thus, Hessian fly “X” chromosomes are defined by their haploid condition in males, rather than by their segregation in the gametes.Open in a separate windowFigure 1.—Chromosome behavior and sex determination in the Hessian fly. (A) Syngamy (1) establishes the germ-line chromosome constitution: ∼32 maternally derived E chromosomes (represented as a single white chromosome) and both maternally derived (black) and paternally derived (gray) autosomes and X chromosomes. During embryogenesis, while the E chromosomes are eliminated, the paternally derived X chromosomes are either retained (2) or excluded (3) from the presumptive somatic cells. When the paternally derived X chromosomes are retained (2), a female-determining karyotype is established. When they are eliminated (3), a male-determining karyotype is established. Thelygenic mothers carry Cm (white arrow), which conditions all of their offspring to retain the X chromosomes. Recombination occurs during oogenesis (4). All ova contain a full complement of E chromosomes and a haploid complement of autosomes and X chromosomes. Chromosome elimination occurs during spermatogenesis (5). Sperm contain only the maternally derived autosomes and X chromosomes. (B) The segregation of Cm (white dot) on a Hessian fly autosome among monogenic families. Thelygenic females produce broods composed of equal numbers of thelygenic (Cm/−) and arrhenogenic (−/−) females (box 1). Arrhenogenic females produce males (box 2). (C) Matings between monogenic and amphigenic families. Cm (white dot) is dominant to the amphigenic-derived chromosomes (gray dot) and generates all-female offspring (box 3). Amphigenic-derived chromosomes are dominant to the arrhenogenic-derived chromosomes (no dot) and generate offspring of both sexes (box 4).An autosomal, dominant, genetic factor called Chromosome maintenance (Cm) complicates Hessian fly sex determination further (Stuart and Hatchett 1991). Cm has a maternal effect that acts upstream of X chromosome elimination during embryogenesis (Figure 1A). It prevents X chromosome elimination so that all of the offspring of Cm-bearing mothers obtain a female-determining karyotype. Cm-bearing females produce only female offspring and are therefore thelygenic. The absence of Cm usually has the opposite effect; all of the offspring of most Cm-lacking females obtain a male-determining karyotype. These Cm-lacking females produce only male offspring and are therefore arrhenogenic. Like a sex-determining master switch, Cm is usually heterozygous and present in only one sex (Figure 1B). Thus, thelygenic females (Cm/−) are “heterogametic,” as their Cm-containing gametes and Cm-lacking gametes produce thelygenic (Cm/−) and arrhenogenic (−/−) females in a 1:1 ratio. Collectively, thelygenic and arrhenogenic females are called monogenic because they produce unisexual families. However, some Hessian fly females produce broods of both sexes and are called amphigenic. No mating barrier between monogenic and amphigenic families exists (Figure 1C), but amphigenic females have always been found in lower abundance (Painter 1930; Gallun et al. 1961; Stuart and Hatchett 1991). In experimental matings, the inheritance of maternal phenotype was consistent with the segregation of three Cm alleles (Figure 1C): a dominant thelygenic allele, a hypomorphic amphigenic allele, and a null arrhenogenic allele (Stuart and Hatchett 1991).Here we report the genetic and physical mapping of Cm on Hessian fly autosome 1 (A1). Two nonoverlapping inversions were identified that segregated perfectly with Cm. The most distal inversion was present in all thelygenic females examined. The more proximal inversion extended recombination suppression. These observations suggested that successive inversions evolved to suppress recombination around Cm after it arose. The inversions therefore appear to have evolved in response to the forces that shaped vertebrate Y and W chromosomes (Charlesworth 1996; Graves and Shetty 2001; Rice and Chippindale 2001; Carvalho and Clark 2005). We therefore believe the inversion-bearing chromosomes may be classified as maternal effect neo-W''s.     

The Genetics of Postmating,Prezygotic Reproductive Isolation Between Drosophila virilis and D. americana

Many studies have demonstrated the rapid diversification of reproductive genes that function after mating but before fertilization. This process might lead to the evolution of postmating, prezygotic barriers between species. Here, I investigate the phenotypic and genetic basis of postmating, prezygotic isolation between two closely related species of Drosophila, Drosophila virilis and D. americana. I show that a strong barrier to interspecific fertilization results in a 99% reduction in progeny production. A genetic interaction among maternal and paternal alleles at only a few loci prevents the fertilization of D. virilis females by D. americana males. These loci are autosomal and isolation acts recessively; the fertilization incompatibility is caused by at least two loci in the maternal D. virilis parent in combination with at least three loci in the paternal D. americana parent. These findings, together with results from classical experiments, suggest that male–female coevolution within D. americana may have driven postmating, prezygotic isolation between species.AN understanding of speciation requires insight into the origins and mechanisms of reproductive isolation. Divergent selection on traits that facilitate mating or fertilization might eventually lead to incompatibilities between males and females of incipient species. In animals, it has long been recognized that sexual selection can promote the evolution of specialized courtship rituals or elaborate phenotypic displays to attract mates (Darwin 1871). Similarly, sexual selection can be a powerful evolutionary force during or after mating by affecting the many biochemical, physiological, and morphological mechanisms involved in fertilization (Eberhard 1996). Postmating reproductive traits might also be subject to sexually antagonistic coevolution, whereby a difference in the reproductive interests of males and females leads to an evolutionary arms race between the sexes (Rice 1996). Just as divergent sexual selection on mate signals and preferences might give rise to premating (sexual) isolation (reviewed in Ritchie 2007), postcopulatory sexual selection and sexual conflict might promote the evolution of postmating barriers to fertilization or hybrid incompatibilities (Howard 1999; Wu and Davis 1993). Indeed, these evolutionary forces have apparently led to competitive gametic isolation (Price 1997; Price et al. 2000; Fishman et al. 2008) and sperm–egg incompatibilities (Galindo et al. 2003). Moreover, because sexual selection and antagonistic coevolution can act rapidly (Fisher 1930; Rice 1996), they might be particularly important in the early stages of speciation.In diverse animal taxa, sexual selection and/or sexual conflict are thought to drive rapid evolution of a variety of postmating reproductive traits, including male genital morphology (Eberhard 1996), length of sperm and female sperm-storage organs (Pitnick et al. 1997; Miller and Pitnick 2002), ejaculate composition (e.g., Swanson et al. 2001a; Dorus et al. 2004), female reproductive tract proteins (e.g., Lawniczak and Begun 2007; Kelleher et al. 2007), and gamete recognition molecules (e.g., Wyckoff et al. 2000; Swanson et al. 2001b). In recent years, many studies have also documented strong signatures of positive selection in the rapid evolution of reproductive genes (e.g., Haerty et al. 2007; Turner et al. 2008; reviewed in Swanson and Vacquier 2002; Clark et al. 2006). For internally fertilizing species, coevolution between the female reproductive tract and the male ejaculate is particularly dynamic (Pitnick et al. 2007). For example, in Drosophila, hundreds of nonsperm seminal fluid proteins are transferred during mating, including many fast-evolving accessory gland proteins (ACPs) (Swanson et al. 2001a; Wagstaff and Begun 2005). As expected, there is evidence for coordinated evolution of female reproductive tract genes, which also show elevated rates of evolution in Drosophila (Panhuis and Swanson 2006; Prokupek et al. 2008). But what are the consequences of such rapid rates of diversification? How many of these fast-evolving reproductive genes contribute to isolating barriers? Major progress toward addressing these questions would require identifying and characterizing individual loci that cause postmating, prezygotic isolation.A large body of classical work suggests that the Drosophila virilis species group might represent an ideal model for studying the genetics of reproductive isolation (Patterson and Stone 1952); and importantly, the D. virilis genome sequence is now available. There is also evidence that postmating, prezygotic isolation may be significant among D. virilis and the closely related North American species, D. americana and D. novamexicana. Patterson et al. (1942) describe reproductive isolation due to “gamete mortality” in reciprocal crosses between D. virilis and D. americana. In later studies, these authors discovered that very few eggs from interspecific crosses become fertilized or hatch and speculate that sperm become “immobilized in the reproductive tract of the alien female” (Patterson and Stone 1952). Moreover, a recent study has found a similar problem with fertilization in crosses between D. americana and D. novamexicana (Y. Ahmed and B. McAllister, personal communication). Consistent with the evolution of these interspecific barriers, male and female reproductive tract proteins have been shown to evolve rapidly in the D. virilis species group (Civetta and Singh 1995; Haerty et al. 2007). In addition, females of both D. virilis and D. americana produce a large opaque vaginal mass in response to mating (the “insemination reaction”; Wheeler 1947), which almost certainly reflects an evolutionary history of interaction between the female reproductive tract and male ejaculate (Knowles and Markow 2001).Despite the potential importance of postmating, prezygotic isolation in D. virilis group divergence, almost nothing is known about its genetic architecture. On the basis of the results from their crosses between D. virilis and D. americana, Patterson et al. (1942) infer that postmating isolation involves recessive autosomal genes. However, their experiments often cannot distinguish between the effects of the apparent fertilization incompatibility and premating isolation, the latter also being strong between D. americana females and D. virilis males (Stalker 1942). Their genetic mapping studies were also crude.In this study, I have two main objectives. First, I characterize the phenotypic basis of postmating isolation between D. virilis and D. americana. To do so, I perform a series of crosses within and between species. I find that low F₁ hybrid production between D. virilis and D. americana is due primarily to a reduction in interspecific fertilization; females presented with heterospecific males almost always become inseminated, but very few eggs are fertilized. Second, I perform a detailed genetic analysis of the fertilization incompatibility between D. virilis females and D. americana males. Using the D. virilis genome assembly, I developed molecular markers targeted to genomic regions of interest for high-resolution genetic mapping of both the maternal and paternal components of isolation. This study is a first step toward understanding the genetic and evolutionary mechanisms of postmating, prezygotic reproductive isolation in Drosophila.     

Nested Association Mapping for Identification of Functional Markers

Identification of functional markers (FMs) provides information about the genetic architecture underlying complex traits. An approach that combines the strengths of linkage and association mapping, referred to as nested association mapping (NAM), has been proposed to identify FMs in many plant species. The ability to identify and resolve FMs for complex traits depends upon a number of factors including frequency of FM alleles, magnitudes of their genetic effects, disequilibrium among functional and nonfunctional markers, statistical analysis methods, and mating design. The statistical characteristics of power, accuracy, and precision to identify FMs with a NAM population were investigated using three simulation studies. The simulated data sets utilized publicly available genetic sequences and simulated FMs were identified using least-squares variable selection methods. Results indicate that FMs with simple additive genetic effects that contribute at least 5% to the phenotypic variability in at least five segregating families of a NAM population consisting of recombinant inbred progeny derived from 28 matings with a single reference inbred will have adequate power to accurately and precisely identify FMs. This resolution and power are possible even for genetic architectures consisting of disequilibrium among multiple functional and nonfunctional markers in the same genomic region, although the resolution of FMs will deteriorate rapidly if more than two FMs are tightly linked within the same amplicon. Finally, nested mating designs involving several reference parents will have a greater likelihood of resolving FMs than single reference designs.THE primary purpose for identifying functional markers (FMs) associated with complex traits in plant species is to provide molecular genetic information underlying variability upon which both artificial and natural selection are based. FMs are defined as polymorphic sites within genomes that causally affect phenotypic trait variability (Andersen and Lubberstedt 2003). This definition is a pragmatic recognition that phenotypic variability can be due to genomic variability located outside of open reading frames. Forward genetics approaches to associate naturally occurring structural genomic variants with phenotypic variability can be broadly categorized as (1) linkage mapping, also referred to as quantitative trait locus (QTL) mapping, (2) association genetic mapping, also known as linkage disequilibrium (LD) mapping, and (3) designs that combine linkage and LD mapping.The third approach based on the concept of combining LD with QTL mapping is a natural extension of the multifamily QTL approach and has been referred as joint linkage and linkage disequilibrium mapping (JLLDM) (Xiong and Jin 2000; Farnir et al. 2002; Wu et al. 2002; Perez-Enciso 2003; Jung et al. 2005) in samples from natural populations. The combined approach also has been applied to designed mapping families sampled from plant breeding populations (Xu 1998a; Jannink and Jansen 2000; Jannink and Wu 2003; Jansen et al. 2003). A special case of designed mapping families that are interconnected, known as nested association mapping (NAM), was proposed by Yu et al. (2008). As originally proposed, a NAM population consists of multiple families of recombinant inbred lines (RILs) derived from multiple inbred lines crossed to a single reference inbred line. Implicitly, genomic information is composed of high-density genotypes of parental inbred lines and low-density genotypes from segregating progeny. If the segregating progeny are RILs or doubled haploid lines (DHLs), then the genomic information can be “immortalized” for associations with phenotypes obtained through long-term longitudinal studies (Nordborg and Weigel 2008).A NAM population consisting of 25 families with 200 RILs for each family has been developed and released as a genetic resource for identification of FMs in maize (Yu et al. 2008). Other publicly available NAM populations are being developed for several species including Arabidopsis thaliana (Buckler and Gore 2007), barley (R. Wise, personal communication), sorghum (J. Yu, personal communication), and soybean (B. Diers, personal communication).The power, accuracy, and precision of identifying FMs in experimental NAM populations have not been investigated for complex genetic architectures. These statistical properties depend upon a number of factors including the following:

1. Data analysis method: Some methods are more powerful than others; however, experimental biologists prefer methods implemented in existing software packages. Are least-squares methods sufficiently powerful to identify FMs in established and developing NAM populations?
2. Frequency of functional markers and magnitudes of genetic effects: Development of a NAM population will change the allele frequencies of the FM relative to the reference population from which the lines are sampled. How will allele frequency and magnitude of genetic effects in a typical NAM population affect the ability to identify FMs?
3. Disequilibrium among functional and nonfunctional markers: Disequilibrium may exist among alleles within subpopulations even when there is no physical basis for genetic linkage. To what extent can the NAM design address consequences of gametic disequilibrium (population structure) in the reference population?
4. Multiple FMs in the same genomic region: If multiple FMs are physically located in the same genomic region, will equilibrium among the parental lines enable resolution of multiple FMs?
5. Mating design: An appropriate mating design can maximize the number of families that are informative for FMs. Will multiple-reference mating designs improve the probability of identifying FMs?

These five questions were addressed.     

Anecdotal,Historical and Critical Commentaries on Genetics: Personal Reflections on the Origins and Emergence of Recombinant DNA Technology

The ability to identify genetic markers in nonmodel systems has allowed geneticists to construct linkage maps for a diversity of species, and the sex-determining locus is often among the first to be mapped. Sex determination is an important area of study in developmental and evolutionary biology, as well as ecology. Its importance for organisms might suggest that sex determination is highly conserved. However, genetic studies have shown that sex determination mechanisms, and the genes involved, are surprisingly labile. We review studies using genetic mapping and phylogenetic inferences, which can help reveal evolutionary pattern within this lability and potentially identify the changes that have occurred among different sex determination systems. We define some of the terminology, particularly where confusion arises in writing about such a diverse range of organisms, and highlight some major differences between plants and animals, and some important similarities. We stress the importance of studying taxa suitable for testing hypotheses, and the need for phylogenetic studies directed to taxa where the patterns of changes can be most reliably inferred, if the ultimate goal of testing hypotheses regarding the selective forces that have led to changes in such an essential trait is to become feasible.THE ever-increasing accessibility of genetic markers is allowing sex-determining regions to be genetically mapped in a growing number of nonmodel organisms. There are several reasons for studying sex determination. In animals, gonadal differences are often accompanied by striking somatic secondary sexual dimorphisms, which are interesting in an evolutionary context (Shine 1989; Badyaev 2002). In plants, females and males often differ in flower morphology and abundance (Dawson and Geber 1998), and, although sex differences are often minor outside the flowers (or inflorescences), they do exist (Dawson and Geber 1998; Eppley and Wenk 2001). The genetic control of these phenotypes is a fundamental biological process, and studying sex determination pathways is important in animal developmental biology (Adams and McLaren 2002; Pinyopich et al. 2003), including genetic pathway evolution (Wilkins 1995; Williams and Carroll 2009).Until recently, sex determination was generally studied by testing for genetic control vs. partial or complete environmental influences. Genetic systems were examined cytologically to determine the level of heteromorphism between the sex chromosomes and to identify whether females or males are heterogametic (see the comprehensive review in Bull 1983). Male heterogametic systems, referred to as XY, were also tested to identify whether the Y chromosome carries a male-determining gene, as in almost all therian mammals and most dioecious plants so far studied, or whether sex is determined through X–autosome balance, as in Drosophila and Caenorhabditis elegans (Haag 2005). For female heterogametic (ZW) species, analogous tests were used to identify how femaleness is determined.Until recently, sex-determining genes and regions could be genetically mapped in only a few model species, but now that molecular genetic markers can be developed in nonmodel species, new information is becoming available about how genetic sex determination (GSD) mechanisms have changed during evolutionary history. It has long been known from genetic mapping in model systems, including mammals, and (more recently) birds, that sex chromosomes often have large nonrecombining regions (Bull 1983; Charlesworth 1991; Charlesworth et al. 2005). However, in other organisms, nonrecombining regions are not always large and may sometimes be absent. The evolution of sexual reproduction and recombination have been the focus of many years of discussion in evolutionary biology (Otto 2009), and studies of sex chromosomes are important for understanding why recombination is often lost, and elucidating the evolutionary consequences of recombination suppression (Charlesworth 1996; Otto and Barton 1997; Barton and Charlesworth 1998). The adaptation of genes on the sex chromosomes is also interesting, because this location affects the outcome of sex-specific selection pressures (Rice 1984; Charlesworth et al. 1987; Vicoso and Charlesworth 2006; Mank 2009a). Finally, the mechanism of sex determination can affect sex ratios (West and Sheldon 2002; Dorken and Pannell 2008; West 2009) and is therefore significant in evolutionary ecology.Sex determination is also relevant in applied biology. In many domesticated animals, one sex may be of greatest economic interest to farmers and breeders. Modern meat production is largely based on males, including industrial production of chicken, cattle, and many fish, whereas females are the sex required for milk (cattle) and egg (chicken) production. Similarly, a few crop plants are dioecious, and, in some of these, the crop is produced by females (e.g., grapes, dates, and papaya), while in other species the sexes differ in characteristics such as fiber or chemical content. Because immature birds, fish, and plants have no obvious phenotypic sex differences, maximizing agricultural returns often requires genetically sexing juveniles. Mapping sex determination is an important first step toward identifying the sex-determining genes or finding other sex-specific markers to develop molecular sexing methods.In this review, we first summarize recent developments in genetic mapping of sex determination, concentrating on nonmodel plants and animals with genetic sex determination. We show how this information can be useful for understanding the evolution of sex determination and sex chromosomes and identify some important unanswered questions.     

Estimating Breeding Values With Molecular Relatedness and Reconstructed Pedigrees in Natural Mating Populations of Common Sole,Solea Solea

Captive populations where natural mating in groups is used to obtain offspring typically yield unbalanced population structures with highly skewed parental contributions and unknown pedigrees. Consequently, for genetic parameter estimation, relationships need to be reconstructed or estimated using DNA marker data. With missing parents and natural mating groups, commonly used pedigree reconstruction methods are not accurate and lead to loss of data. Relatedness estimators, however, infer relationships between all animals sampled. In this study, we compared a pedigree relatedness method and a relatedness estimator (“molecular relatedness”) method using accuracy of estimated breeding values. A commercial data set of common sole, Solea solea, with 51 parents and 1953 offspring (“full data set”) was used. Due to missing parents, for 1338 offspring, a pedigree could be reconstructed with 10 microsatellite markers (“reduced data set”). Cross-validation of both methods using the reduced data set showed an accuracy of estimated breeding values of 0.54 with pedigree reconstruction and 0.55 with molecular relatedness. Accuracy of estimated breeding values increased to 0.60 when applying molecular relatedness to the full data set. Our results indicate that pedigree reconstruction and molecular relatedness predict breeding values equally well in a population with skewed contributions to families. This is probably due to the presence of few large full-sib families. However, unlike methods with pedigree reconstruction, molecular relatedness methods ensure availability of all genotyped selection candidates, which results in higher accuracy of breeding value estimation.To estimate genetic parameters, additive genetic relationships between individuals are inferred from known pedigrees (Falconer and Mackay 1996; Lynch and Walsh 1997). However, in natural populations (Ritland 2000; Thomas et al. 2002) and in captive species where natural mating in groups is used to obtain offspring (Brown et al. 2005; Fessehaye et al. 2006; Blonk et al. 2009) pedigrees are reconstructed. In these populations there is no control on mating structure, and typically unbalanced population structures with highly skewed parental contributions are obtained (Bekkevold et al. 2002; Brown et al. 2005; Fessehaye et al. 2006; Blonk et al. 2009). To reconstruct pedigrees, parental allocation methods are often used (Marshall et al. 1998; Avise et al. 2002; Duchesne et al. 2002). These methods require that all parents be known. For situations where parental information is not available, numerous DNA-marker-based methods for estimating molecular relatedness have been developed (Lynch 1988; Queller and Goodnight 1989; Ritland 2000; Toro et al. 2002). These relatedness estimators determine relationship values between individuals on a continuous scale. Evaluation of relatedness estimators within real and simulated data in both plants and animals (e.g., see Van de Casteele et al. 2001 ; Milligan 2003; Oliehoek et al. 2006; Rodríguez-Ramilo et al. 2007; Bink et al. 2008) has generally focused on bias and sampling error of estimated genetic variances or relatedness values. Relatively little attention has been paid to their efficiency for estimation of breeding values.Two types of relatedness estimators are currently available: method-of-moments estimators and maximum-likelihood estimators. Method-of-moments estimators (e.g., Queller and Goodnight 1989; Li et al. 1993; Ritland 1996; Lynch and Ritland 1999; Toro et al. 2002) determine relationships while calculating sharing of alleles between pairs in different ways. A variant of method-of-moments estimators is the transformation of continuous relatedness values to categorical genealogical relationships using “explicit pedigree reconstruction” (Fernández and Toro 2006) or thresholds (Rodríguez-Ramilo et al. 2007). However, correlations of transformed coancestries with known genealogical coancestries are low (Rodríguez-Ramilo et al. 2007). Several studies have compared different method-of-moments estimators but none revealed one single best estimator (Van de Casteele et al. 2001; Oliehoek et al. 2006; Rodríguez-Ramilo et al. 2007; Bink et al. 2008).Maximum-likelihood (ML) approaches classify animals into a limited number of relationship classes (Mousseau et al. 1998; Thomas et al. 2002; Wang 2004; Herbinger et al. 2006; Anderson and Weir 2007). For each pair a likelihood to fall into a possible relatedness class (e.g., full sib vs. unrelated) is calculated given its genotype and phenotype. ML techniques combined with a Markov chain Monte Carlo approach reconstruct groups with specific relationships jointly and are therefore more efficient than other ML approaches. To minimize standard errors, all discussed ML methods require balanced population structures, large sibling groups, and a large variance of relatedness (Thomas et al. 2002; Wang 2004; Anderson and Weir 2007). Therefore, these methods may not be suitable for natural mating systems.Unlike parental allocation methods, a benefit from relatedness estimators is that essentially all selection candidates are maintained for breeding value estimation, even with missing parents. The question is, however, whether such relatedness estimators also give accurate breeding values to perform selection.In this study, we test suitability of a relatedness estimator to obtain breeding values in a population of common sole, Solea solea (n = 1953) obtained by natural mating. First, we estimate breeding values using pedigree relatedness of animals for which a pedigree could be reconstructed (using parental allocation). This data set (n = 1338) is further referred to as “reduced data set.” We compare results with estimated breeding values using a simple but robust method-of-moments relatedness estimator: “molecular relatedness” (Toro et al. 2002, 2003). Next, we estimate breeding values using molecular relatedness in the full data set (n = 1953). Results show that accuracies of estimated breeding values obtained with molecular relatedness and pedigree relatedness are comparable. Accuracy increases when breeding values are estimated with molecular relatedness in the full data set. This implies that a molecular relatedness estimator can be used to estimate breeding values in captive natural mating populations.     

Gorilla Mothers Also Matter! New Insights on Social Transmission in Gorillas (Gorilla gorilla gorilla) in Captivity

The present paper describes two distinct behaviors relating to food processing and communication that were observed in a community of five separately housed groups of lowland gorillas (Gorilla gorilla gorilla) in captivity during two study periods one decade apart: (1) a food processing technique to separate wheat from chaff, the so-called puff-blowing technique; and (2) a male display used to attract the attention of visitors, the so-called throw-kiss-display. We investigated (a) whether the behaviors were transmitted within the respective groups; and if yes, (b) their possible mode of transmission. Our results showed that only the food processing technique spread from three to twenty-one individuals during the ten-year period, whereas the communicative display died out completely. The main transmission mode of the puff-blowing technique was the mother-offspring dyad: offspring of puff-blowing mothers showed the behavior, while the offspring of non- puff-blowing mothers did not. These results strongly support the role mothers play in the acquisition of novel skills and vertical social transmission. Furthermore, they suggest that behaviors, which provide a direct benefit to individuals, have a high chance of social transmission while the loss of benefits can result in the extinction of behaviors.     

Sex-Linked Inheritance in Macaque Monkeys: Implications for Effective Population Size and Dispersal to Sulawesi

Sex-specific differences in dispersal, survival, reproductive success, and natural selection differentially affect the effective population size (N_e) of genomic regions with different modes of inheritance such as sex chromosomes and mitochondrial DNA. In papionin monkeys (macaques, baboons, geladas, mandrills, drills, and mangabeys), for example, these factors are expected to reduce N_e of paternally inherited portions of the genome compared to maternally inherited portions. To explore this further, we quantified relative N_e of autosomal DNA, X and Y chromosomes, and mitochondrial DNA using molecular polymorphism and divergence information from pigtail macaque monkeys (Macaca nemestrina). Consistent with demographic expectations, we found that N_e of the Y is lower than expected from a Wright–Fisher idealized population with an equal proportion of males and females, whereas N_e of mitochondrial DNA is higher. However, N_e of 11 loci on the X chromosome was lower than expected, a finding that could be explained by pervasive hitchhiking effects on this chromosome. We evaluated the fit of these data to various models involving natural selection or sex-biased demography. Significant support was recovered for natural selection acting on the Y chromosome. A demographic model with a skewed sex ratio was more likely than one with sex-biased migration and explained the data about as well as an ideal model without sex-biased demography. We then incorporated these results into an evaluation of macaque divergence and migration on Borneo and Sulawesi islands. One X-linked locus was not monophyletic on Sulawesi, but multilocus data analyzed in a coalescent framework failed to reject a model without migration between these islands after both were colonized.THE effective size of a population (N_e) determines the relative impact of genetic drift and natural selection on mutations with mild effects on fitness (Charlesworth 2009). Differences in N_e are hypothesized to affect virtually every aspect of genome evolution, including rates of molecular evolution, abundance of introns and transposable elements, and persistence of duplicate genes, and this has important implications for the evolution of complexity via both adaptive and degenerative processes (Lynch 2007). Of relevance are not only the number of different individuals in a population, but also the number of copies of a gene within each individual. In diploid species with separate sexes, sex chromosomes and mitochondrial DNA (mtDNA) differ in copy number from autosomal DNA (aDNA): both sexes have two alleles at autosomal loci whereas in species with male heterogamy, males have one X and one Y chromosome, females have two Xs, and a female/male pair has effectively only one copy of mtDNA due to maternal inheritance. Sex-specific differences in demographic parameters such as migration, adult sex ratio, and variance in reproductive success also affect relative copy number and associated levels of neutral polymorphism at mtDNA, aDNA, the X chromosome (xDNA), and the Y chromosome (yDNA) (Hedrick 2007).The effective population size is the number of individuals in a Wright–Fisher idealized population (Fisher 1930; Wright 1931) that have the same magnitude of genetic drift as an observed population, where ideal individuals are diploid, and have discrete (nonoverlapping) generations, constant population size, and random mating. N_e can be quantified in terms of variance in allele frequency over generations (variance N_e) or variance in inbreeding over time (inbreeding N_e). If population size is constant with random mating, these approaches for quantifying N_e produce identical results (Kimura and Crow 1963; Whitlock and Barton 1997). At mutation–drift equilibrium with an equal number of males and females and a Poisson distributed number of offspring with a mean of two offspring per individual, N_e-aDNA and N_e-xDNA are expected to be four and three times as large, respectively, as N_e-yDNA and N_e-mtDNA; we refer to this as the “ideal expectation with an equal proportion of males and females.”Demography can alter relationships between N_e of different parts of the genome. For example, extreme skew in adult sex ratio can cause N_e of uniparentally inherited portions of the genome to exceed N_e of biparentally inherited portions (Figure 1A; Nunney 1993; Caballero 1994; Hoelzer 1997; Hedrick 2007). With a skewed sex ratio, the more common sex has a higher variance in reproductive success than the rare one, and this causes the overall variance in reproductive success to increase as the sex-ratio bias increases (Nunney 1993). Sex-biased dispersal such as female philopatry also alters relationships between N_e-aDNA, N_e-xDNA, N_e-yDNA, and N_e-mtDNA (Figure 1B), causing N_e of portions of the genome that disperse less to increase (Nei and Takahata 1993; Hoelzer 1997; Wang and Caballero 1999).Open in a separate windowFigure 1.—N_e of aDNA, xDNA, mtDNA, and yDNA as a function of (A) sex ratio skew and (B) the probability of female dispersal. In B, a finite island model of subdivided populations of constant size is assumed with a population size of 10,000 individuals, 10 subpopulations, and a male probability of migration equal to 0.1.At least five factors related to natural selection also can cause the relative N_e of aDNA, xDNA, yDNA, and mtDNA to depart from expectations: (1) very low or absent recombination in mtDNA and a portion of yDNA, (2) haploidy of mtDNA and yDNA, (3) hemizygosity of xDNA in males, (4) sexual selection and differences in gene content, and (5) differences in the rate and variance of mutation. “Selective sweeps” in which an advantageous mutation is fixed by natural selection, reduces N_e of linked sites (Maynard Smith and Haigh 1974) and this can affect the entire mitochondrial genome and nonrecombining portion of the Y chromosome. Nonrecombining portions of yDNA and mtDNA are also affected by stochastic loss of alleles containing the fewest deleterious mutations (“Muller''s ratchet”; Muller 1964; Felsenstein 1974), which results in a gradual decline of fitness of these chromosomes over time. N_e of nonrecombining DNA is further reduced by elimination of variation linked to substantially deleterious mutations (“background selection”; Charlesworth et al. 1993), by interference between linked polymorphisms that impedes fixation of advantageous alleles and extinction of deleterious ones (the “Hill–Robertson effect”; Hill and Robertson 1966; McVean and Charlesworth 2000), and by increased frequency of deleterious mutations linked to advantageous ones during a selective sweep (“genetic hitchhiking”; Rice 1987). Hemizygous X-linked and haploid Y-linked loci in males and mtDNA loci in both sexes are more vulnerable to recessive deleterious mutations because they are not masked by a second allele (Otto and Goldstein 1992). Hemizygosity on the X chromosome can also increase the rate of selective sweeps when advantageous mutations are recessive (Charlesworth et al. 1987). Similarly, these loci are also susceptible to recessive species incompatibilities—a factor that at least partially accounts for Haldane''s rule for hybrid sterility (Haldane 1922; Orr 1997). Sexual selection differentially influences the probability of fixation of mutations depending on mode of inheritance (Wade and Shuster 2004), especially mutations with antagonistic fitness effects between the sexes (Gibson et al. 2002). Additionally, the rate of evolution of animal mtDNA is much higher than aDNA, xDNA, and yDNA (Haag-Liautard et al. 2008) and this presumably contributes to variation in the frequency of nonneutral mutations in different parts of the genome.Differences among N_e of mtDNA, yDNA, xDNA, and aDNA are thought to be particularly pronounced in papionin monkeys (macaques, baboons, geladas, mandrills, drills, and mangabeys). These monkeys have a highly sex-biased adult demography; females form stable philopatric groups of close relatives, whereas males generally change social groups and disperse more widely (Dittus 1975). Often adult sex ratio of papionins is female biased (Dittus 1975; Melnick and Pearl 1987; O''Brien and Kinnard 1997; Okamoto and Matsumura 2001), and males have higher variance in reproductive success than females (Dittus 1975; de Ruiter et al. 1992; Keane et al. 1997; Van Noordwijk and Van Schaik 2002; Widdig et al. 2004). These sex differences predict strong population subdivision of mtDNA with little or no subdivision of aDNA, deep mtDNA coalescence times, and frequent mtDNA paraphyly among species, and discordant genealogical relationships between mtDNA and yDNA—and this has been observed in multiple studies (Melnick and Pearl 1987; Melnick 1988; Melnick and Hoelzer 1992; Melnick et al. 1993; Hoelzer et al. 1994; Evans et al. 1999, 2001, 2003; Tosi et al. 2000, 2002, 2003; Newman et al. 2004). Female philopatry and obligate male migration is a common social system in mammals (Greenwood 1980; Dobson 1982; Johnson 1986), though less so in humans (Seielstad et al. 1998), and molecular variation provides an effective tool for exploring the impact of natural selection and demography on aDNA, the sex chromosomes, and mtDNA (Nachman 1997; Bachtrog and Charlesworth 2002; Stone et al. 2002; Berlin and Ellegren 2004; Hellborg and Ellegren 2004; Wilder et al. 2004; Hammer et al. 2008).We explored the genetic effects of demography and linked selection in structuring sequence polymorphism of a papionin monkey—the macaques—at two levels. We first tested whether levels of polymorphism in aDNA, xDNA, yDNA, and mtDNA in a Bornean population of the pigtail macaque, Macaca nemestrina, match expectations under scenarios involving natural selection and also whether the data might be explained by simple demographic models with sex-specific dispersal or a biased sex ratio. We then explored demography on a larger, inter-island scale by estimating the time of divergence between macaques on Borneo and Sulawesi islands and by testing for evidence of ongoing migration between these islands.     

Mating-System Variation,Demographic History and Patterns of Nucleotide Diversity in the Tristylous Plant Eichhornia paniculata

Inbreeding in highly selfing populations reduces effective size and, combined with demographic conditions associated with selfing, this can erode genetic diversity and increase population differentiation. Here we investigate the role that variation in mating patterns and demographic history play in shaping the distribution of nucleotide variation within and among populations of the annual neotropical colonizing plant Eichhornia paniculata, a species with wide variation in selfing rates. We sequenced 10 EST-derived nuclear loci in 225 individuals from 25 populations sampled from much of the geographic range and used coalescent simulations to investigate demographic history. Highly selfing populations exhibited moderate reductions in diversity but there was no significant difference in variation between outcrossing and mixed mating populations. Population size interacted strongly with mating system and explained more of the variation in diversity within populations. Bayesian structure analysis revealed strong regional clustering and selfing populations were highly differentiated on the basis of an analysis of F_st. There was no evidence for a significant loss of within-locus linkage disequilibrium within populations, but regional samples revealed greater breakdown in Brazil than in selfing populations from the Caribbean. Coalescent simulations indicate a moderate bottleneck associated with colonization of the Caribbean from Brazil ∼125,000 years before the present. Our results suggest that the recent multiple origins of selfing in E. paniculata from diverse outcrossing populations result in higher diversity than expected under long-term equilibrium.THE rate of self-fertilization in hermaphrodite organisms is expected to affect a number of important features of population genetic structure and diversity. Most directly, homozygosity increases as a function of the selfing rate and thus reduces the effective population size (N_e), up to twofold with complete selfing (Pollak 1987; Charlesworth et al. 1993; Nordborg 2000). Further, because of increased homozygosity, crossing over rarely occurs between heterozygous sites, thus increasing linkage disequilibrium (LD). Higher LD causes stronger hitchhiking effects such as selective sweeps, background selection, and Hill–Robertson interference, all of which are expected to further reduce the amount of neutral genetic variation within populations (reviewed in Charlesworth and Wright 2001).Population genetic processes resulting from inbreeding may be further augmented by demographic and life-history characteristics associated with the selfing habit. In particular, selfing populations can be founded by single individuals, resulting in striking reductions in diversity as a result of genetic bottlenecks and reproductive isolation. The capacity for uniparental reproduction gives many selfers prolific colonizing ability and the capacity to establish after long-distance dispersal, especially in comparison with obligate outcrossers (Baker 1955; Pannell and Barrett 1998). The colonization–extinction dynamics typical of many selfing species and limited pollen-mediated gene flow also increase differentiation among populations, resulting in considerable population subdivision (Hamrick and Godt 1990, 1996; Schoen and Brown 1991). Although the total amounts of among-population variation may be less affected by these processes (Pannell and Charlesworth 1999; Ingvarsson 2002), the demographic and life-history characteristics of many selfing species are likely to result in nonequilibrium conditions occurring in selfing populations.In many taxa where selfing has evolved it may be of relatively recent origin (Schoen et al. 1997; Takebayashi and Morrell 2001; Foxe et al. 2009; Guo et al. 2009). Where selfing has recently established, demographic forces associated with colonization may be as important as the mating system per se in structuring patterns of diversity. For example, if selfing originates through the establishment of a small number of founders, we would expect a sharp reduction in diversity relative to the outcrossing progenitor and a strong signature of a genetic bottleneck. In contrast, if selfing has evolved recently through the spread of genetic modifiers of small effect, newly established populations may retain significant amounts of ancestral polymorphism from their outcrossing progenitors. In this latter case populations may retain considerably more variation than expected under long-term equilibrium predictions.Molecular evidence for reduced nucleotide diversity and greater differentiation among populations of selfing taxa compared to populations of related outcrossing taxa has been reported from Leavenworthia (Liu et al. 1998, 1999), Arabidopsis (Savolainen et al. 2000; Wright et al. 2002), Solanum (Baudry et al. 2001), Mimulus (Sweigart and Willis 2003), Amsinckia (Perusse and Schoen 2004), and Caenorhabditis (Graustein et al. 2002; Cutter et al. 2006; Cutter 2008). In each case the reduction in diversity was more severe than the twofold reduction predicted for selfing populations at equilibrium. This indicates that factors in addition to the mating system are reducing diversity, but it has been difficult to uncouple the relative importance of genetic hitchhiking from the ecology and demographic history of selfing taxa. This challenge parallels similar difficulties in efforts to distinguish selective from demographic explanations in population genetic studies of Drosophila (Haddrill et al. 2005; Ometto et al. 2005; Thornton and Andolfatto 2006; Jensen et al. 2008). However, in many plant populations, especially those with annual life histories and small structured populations, demographic processes may play a more prominent role in causing reduced diversity than increased hitchhiking associated with selfing.Molecular population genetic studies of selfing in plants have generally focused on either small samples from a large number of populations (e.g., Sweigart and Willis 2003; Nordborg et al. 2005) or relatively large within-population samples from a small number of populations (e.g., Baudry et al. 2001). Ideally, a deeper sampling both within and among populations combined with independent ecological and historical information is required to improve understanding of the interplay of demographic and selective factors. Here we address these issues by examining patterns of nucleotide diversity within a large sample of populations of Eichhornia paniculata (Pontederiaceae), an annual species for which there is considerable ecological and demographic information (reviewed in Barrett and Husband 1997).E. paniculata occurs primarily in northeastern (N.E.) Brazil and the Caribbean islands of Cuba and Jamaica. Various lines of evidence suggest that Brazil is the original source region for Caribbean populations (reviewed in Barrett et al. 2009). Populations of E. paniculata exhibit striking mating-system diversity, ranging from predominantly outcrossing to those that are highly selfing (outcrossing rate, t = 0.002–0.96; n = 54 populations) (Barrett and Husband 1990; Barrett et al. 1992). Variation in mating system is associated with the evolutionary breakdown of the species'' tristylous genetic polymorphism and the spread and fixation of selfing variants capable of autonomous self-pollination (Barrett et al. 1989). Populations of E. paniculata are characterized by three morph structures: trimorphic with long-, mid-, and short-styled morphs (hereafter L-, M-, and S-morphs); dimorphic, with two floral morphs, most commonly the L- and M-morphs; and monomorphic, primarily composed of selfing variants of the M-morph. The morph structure and presence of selfing variants within populations explain ∼60% of the variation in outcrossing rates among populations (Barrett and Husband 1990). Trimorphic populations are largely outcrossing, dimorphic populations display mixed mating, and monomorphic populations are highly selfing. Patterns of allozyme variation indicate a reduction in diversity with increased selfing rates and greater among-population differentiation (Glover and Barrett 1987; Barrett and Husband 1990; Husband and Barrett 1993). Finally, studies of the inheritance of mating-system modifiers (Fenster and Barrett 1994; Vallejo-Marín and Barrett 2009) in combination with allozyme (Husband and Barrett 1993) and molecular evidence (Barrett et al. 2009) indicate that the transition from outcrossing to selfing in E. paniculata has occurred on multiple occasions.The goal of our study was to investigate the relation between mating-system variation and neutral molecular diversity for a large sample of E. paniculata populations encompassing most of the geographical range. This was accomplished by collecting multilocus nucleotide sequence data from 225 individuals sampled from 25 populations including trimorphic, dimorphic, and monomorphic populations. Because it has been previously demonstrated that this sequence of morph structures is strongly associated with increasing rates of self-fertilization (see Barrett and Husband 1990), we predicted a decrease in neutral diversity and increases in F_st and linkage disequilibrium from floral trimorphism to monomorphism. This extensive population-level sampling across a wide range of selfing rates allowed us to investigate the relative importance of mating system, geography, and current population size in structuring genetic variation. We also applied the approaches of Bayesian clustering (Pritchard et al. 2000; Falush et al. 2003; Gao et al. 2007) and divergence population genetics (Wakeley and Hey 1997; Hey and Nielsen 2004; Becquet and Przeworski 2007) to investigate the demographic history of E. paniculata and to provide a framework for understanding island colonization and the transition from outcrossing to selfing.     

Age Structure,Changing Demography and Effective Population Size in Atlantic Salmon (Salmo salar)

Effective population size (N_e) is a central evolutionary concept, but its genetic estimation can be significantly complicated by age structure. Here we investigate N_e in Atlantic salmon (Salmo salar) populations that have undergone changes in demography and population dynamics, applying four different genetic estimators. For this purpose we use genetic data (14 microsatellite markers) from archived scale samples collected between 1951 and 2004. Through life table simulations we assess the genetic consequences of life history variation on N_e. Although variation in reproductive contribution by mature parr affects age structure, we find that its effect on N_e estimation may be relatively minor. A comparison of estimator models suggests that even low iteroparity may upwardly bias N_e estimates when ignored (semelparity assumed) and should thus empirically be accounted for. Our results indicate that N_e may have changed over time in relatively small populations, but otherwise remained stable. Our ability to detect changes in N_e in larger populations was, however, likely hindered by sampling limitations. An evaluation of N_e estimates in a demographic context suggests that life history diversity, density-dependent factors, and metapopulation dynamics may all affect the genetic stability of these populations.THE effective size of a population (N_e) is an evolutionary parameter that can be informative on the strength of stochastic evolutionary processes, the relevance of which relative to deterministic forces has been debated for decades (e.g., Lande 1988). Stochastic forces include environmental, demographic, and genetic components, the latter two of which are thought to be more prominent at reduced population size, with potentially detrimental consequences for average individual fitness and population persistence (Newman and Pilson 1997; Saccheri et al. 1998; Frankham 2005). The quantification of N_e in conservation programs is thus frequently advocated (e.g., Luikart and Cornuet 1998; Schwartz et al. 2007), although gene flow deserves equal consideration given its countering effects on genetic stochasticity (Frankham et al. 2003; Palstra and Ruzzante 2008).Effective population size is determined mainly by the lifetime reproductive success of individuals in a population (Wright 1938; Felsenstein 1971). Variance in reproductive success, sex ratio, and population size fluctuations can reduce N_e below census population size (Frankham 1995). Given the difficulty in directly estimating N_e through quantification of these demographic factors (reviewed by Caballero 1994), efforts have been directed at inferring N_e indirectly through measurement of its genetic consequences (see Leberg 2005, Wang 2005, and Palstra and Ruzzante 2008 for reviews). Studies employing this approach have quantified historical levels of genetic diversity and genetic threats to population persistence (e.g., Nielsen et al. 1999b; Miller and Waits 2003; Johnson et al. 2004). N_e has been extensively studied in (commercially important) fish species, due to the common availability of collections of archived samples that facilitate genetic estimation using the temporal method (e.g., Hauser et al. 2002; Shrimpton and Heath 2003; Gomez-Uchida and Banks 2006; Saillant and Gold 2006).Most models relating N_e to a population''s genetic behavior make simplifying assumptions regarding population dynamics. Chiefly among these is the assumption of discrete generations, frequently violated in practice given that most natural populations are age structured with overlapping generations. Here, theoretical predictions still apply, provided that population size and age structure are constant (Felsenstein 1971; Hill 1972). Ignored age structure can introduce bias into temporal genetic methods for the estimation of N_e, especially for samples separated by time spans that are short relative to generation interval (Jorde and Ryman 1995; Waples and Yokota 2007; Palstra and Ruzzante 2008). Moreover, estimation methods that do account for age structure (e.g., Jorde and Ryman 1995) still assume this structure to be constant. Population dynamics will, however, likely be altered as population size changes, thus making precise quantifications of the genetic consequences of acute population declines difficult (Nunney 1993; Engen et al. 2005; Waples and Yokota 2007). This problem may be particularly relevant when declines are driven by anthropogenic impacts, such as selective harvesting regimes, that can affect age structure and N_e simultaneously (Ryman et al. 1981; Allendorf et al. 2008). Demographic changes thus have broad conservation implications, as they can affect a population''s sensitivity to environmental stochasticity and years of poor recruitment (Warner and Chesson 1985; Ellner and Hairston 1994; Gaggiotti and Vetter 1999). Consequently, although there is an urgent need to elucidate the genetic consequences of population declines, relatively little is understood about the behavior of N_e when population dynamics change (but see Engen et al. 2005, 2007).Here we focus on age structure and N_e in Atlantic salmon (Salmo salar) river populations in Newfoundland and Labrador. The freshwater habitat in this part of the species'' distribution range is relatively pristine (Parrish et al. 1998), yet Atlantic salmon in this area have experienced demographic declines, associated with a commercial marine fishery, characterized by high exploitation rates (40–80% of anadromous runs; Dempson et al. 2001). A fishery moratorium was declared in 1992, with rivers displaying differential recovery patterns since then (Dempson et al. 2004b), suggesting a geographically variable impact of deterministic and stochastic factors, possibly including genetics. An evaluation of those genetic consequences thus requires accounting for potential changes in population dynamics as well as in life history. Life history in Atlantic salmon can be highly versatile (Fleming 1996; Hutchings and Jones 1998; Fleming and Reynolds 2004), as exemplified by the high variation in age-at-maturity displayed among and within populations (Hutchings and Jones 1998), partly reflecting high phenotypic plasticity (Hutchings 2004). This diversity is particularly evident in the reproductive biology of males, which can mature as parr during juvenile freshwater stages (Jones and King 1952; Fleming and Reynolds 2004) and/or at various ages as anadromous individuals, when returning to spawn in freshwater from ocean migration. Variability in life history strategies is further augmented by iteroparity, which can be viewed as a bet-hedging strategy to deal with environmental uncertainty (e.g., Orzack and Tuljapurkar 1989; Fleming and Reynolds 2004). Life history diversity and plasticity may allow salmonid fish populations to alter and optimize their life history under changing demography and population dynamics, potentially acting to stabilize N_e. Reduced variance in individual reproductive success at low breeder abundance (genetic compensation) will achieve similar effects and might be a realistic aspect of salmonid breeding systems (Ardren and Kapuscinski 2003; Fraser et al. 2007b). Little is currently known about the relationships between life history plasticity, demographic change and N_e, partly due to scarcity of the multivariate data required for these analyses.Our objective in this article is twofold. First, we use demographic data for rivers in Newfoundland to quantify how life history variation influences age structure in Atlantic salmon and hence N_e and its empirical estimation from genetic data. We find that variation in reproductive contribution by mature parr has a much smaller effect on the estimation of N_e than is often assumed. Second, we use temporal genetic data to estimate N_e and quantify the genetic consequences of demographic changes. We attempt to account for potential sources of bias, associated with (changes in) age structure and life history, by using four different analytical models to estimate N_e: a single-sample estimator using the linkage disequilibrium method (Hill 1981), the temporal model assuming discrete generations (Nei and Tajima 1981; Waples 1989), and two temporal models for species with overlapping generations (Waples 1990a,b; Jorde and Ryman 1995) that differ principally in assumptions regarding iteroparity. A comparison of results from these different estimators suggests that iteroparity may often warrant analytical consideration, even when it is presumably low. Although sometimes limited by statistical power, a quantification and comparison of temporal changes in N_e among river populations suggests a more prominent impact of demographic changes on N_e in relatively small river populations.     

Epigenetic Inheritance and the Missing Heritability Problem

Epigenetic phenomena, and in particular heritable epigenetic changes, or transgenerational effects, are the subject of much discussion in the current literature. This article presents a model of transgenerational epigenetic inheritance and explores the effect of epigenetic inheritance on the risk and recurrence risk of a complex disease. The model assumes that epigenetic modifications of the genome are gained and lost at specified rates and that each modification contributes multiplicatively to disease risk. The potentially high rate of loss of epigenetic modifications causes the probability of identity in state in close relatives to be smaller than is implied by their relatedness. As a consequence, the recurrence risk to close relatives is reduced. Although epigenetic modifications may contribute substantially to average risk, they will not contribute much to recurrence risk and heritability unless they persist on average for many generations. If they do persist for long times, they are equivalent to mutations and hence are likely to be in linkage disequilibrium with SNPs surveyed in genomewide association studies. Thus epigenetic modifications are a potential solution to the problem of missing causality of complex diseases but not to the problem of missing heritability. The model highlights the need for empirical estimates of the persistence times of heritable epialleles.THE modern definition of epigenetics is the study of heritable changes in gene expression that are not caused by changes in DNA sequence (Richards 2006; Bird 2007; Bossdorf et al. 2008). Epigenetic effects include methylation of the cytosine residue in DNA and the modification of chromatin proteins that package DNA (Youngson and Whitelaw 2008). Although this definition of epigenetics includes inheritance during both mitosis and meiosis, I am concerned in this article only with epigenetic changes that are transmitted to offspring, what has been called “transgenerational epigenetic inheritance” (Morgan and Whitelaw 2008; Youngson and Whitelaw 2008). The modern definition of epigenetics arose from the original definition of Waddington (1957; Holliday and Pugh 1975).The possibility of nongenetic inherited effects on phenotype has excited great interest among both evolutionary biologists and human geneticists because it provides an additional mechanism of inherited variability and one that is not detectable in genomic surveys of sequence variation. Inherited epigenetic changes have been proposed as an explanation for the “missing heritability,” meaning inherited causes of risk of complex genetic diseases that have not yet been identified in genomewide association studies (GWAS) (Maher 2008; McCarthy and Hirschhorn 2008). Inherited epigenetic changes that contribute to disease risk would not be detectable in GWAS but may contribute to average risk and to similarities among relatives.In this article, I present a simple model of the inheritance of epigenetic changes. The goal is to quantify the potential contribution they can make to average risk and recurrence risk. The model is developed in a standard population genetics framework and can be regarded as a generalization of previous multilocus models of complex diseases, particularly that of Risch (1990).I assume that epigenetic effects are caused by the presence or the absence of epigenetic modifications of specific chromosomal locations. Bird (2007), Haig (2007), Richards (2008), and others have emphasized that, although epigenetic changes differ in many ways from mutations, their transmission to offspring is the same as the transmission of mutations, except for the possibility that they might be spontaneously lost. If the gain and loss of epigenetic changes are controlled by a locus elsewhere in the genome, as modeled by Bjornsson et al. (2004), then the resulting phenotypic effects are attributable to variation at that locus (Richards 2006; Johannes et al. 2008). The epigenetic changes are simply the mechanism by which that locus affects phenotype. If, however, the appearance of an epigenetic change at a location in the genome is not attributable to any particular locus or loci, then the phenotypic effects of the presence or the absence of an epigenetic change are attributable to the genomic location itself. That is the case I am concerned with here.I begin by introducing the basic model of a randomly mating population and extend standard genetic theory to the case of epigenetic inheritance. Then I consider nonequilibrium populations in which environmental changes cause an increase in the rate of gain of epigenetic changes.     

A High Frequency of Beneficial Mutations Across Multiple Fitness Components in Saccharomyces cerevisiae

Mutation-accumulation experiments are widely used to estimate parameters of spontaneous mutations affecting fitness. In many experiments only one component of fitness is measured. In a previous study involving the diploid yeast Saccharomyces cerevisiae, we measured the growth rate of 151 mutation-accumulation lines to estimate parameters of mutation. We found that an unexpectedly high frequency of fitness-altering mutations was beneficial. Here, we build upon our previous work by examining sporulation efficiency, spore viability, and haploid growth rate and find that these components of fitness also show a high frequency of beneficial mutations. We also examine whether mutation-acycumulation (MA) lines show any evidence of pleiotropy among accumulated mutations and find that, for most, there is none. However, MA lines that have zero fitness (i.e., lethality) for any one fitness component do show evidence for pleiotropy among accumulated mutations. We also report estimates of other parameters of mutation based on each component of fitness.ADAPTATION can occur from standing genetic variation or from newly arising mutations. The relative importance of these two sources of adaptive mutations is affected by a variety of factors, including those that alter standing levels of genetic variation (see Barrett and Schluter 2008) and those that generate new mutations. Predicting how quickly a population will adapt and the type of beneficial mutations that will fuel that adaptation requires estimates of the additive genetic variance in fitness and of the beneficial mutation rate and the distribution of beneficial effects. While additive genetic variance for fitness has been estimated in a variety of organisms (Mousseau and Roff 1987), the beneficial mutation rate and the distribution of beneficial effects have only been estimated in a few studies (Shaw et al. 2002; Joseph and Hall 2004; Perfeito et al. 2007; Dickinson 2008; Hall et al. 2008). Surprisingly, these studies estimate that between 6 (Joseph and Hall 2004) and 50% (Shaw et al. 2002) of fitness-altering mutations are beneficial. In contrast, most mutation-accumulation (MA) experiments identify few, if any, beneficial mutations. Such wildly different estimates have even been generated from studies of the same species in similar environments (Zeyl and Devisser 2001; Joseph and Hall 2004; Dickinson 2008; Hall et al. 2008). If these estimates are correct, then they would suggest that the genotypes used in these experiments have vastly different evolutionary potential with respect to their capacity to exhibit rapid adaptation from new mutations.A more likely scenario is that much of the variation in estimates of the beneficial mutation rate is due to methodological differences between studies. One possibility is the fitness component being analyzed. The beneficial mutation rate may be under- or overestimated if the fitness component is under stabilizing selection or subject to antagonistic pleiotropy. Analyses of mutation-accumulation data typically assume that selection is directional. As a result, analyses of phenotypes under stabilizing selection may falsely conclude that mutations that increase a phenotype are beneficial and mutations that lower values are deleterious (see Keightley and Lynch''s 2003 criticism of Shaw et al. 2002). Alternatively, the beneficial mutation rate may be over- (or under) estimated if mutations increase fitness in regard to one component, but lower fitness in regard to lifetime fitness or another fitness component (i.e., antagonistic pleiotropy). Here, we explore these possibilities by investigating whether the high beneficial mutation rates estimated from our previous experiments are specific to the fitness component that we examined.In two previous studies we accumulated mutations in 152 yeast, MA lines and used measures of their effects on diploid growth rate to estimate parameters of beneficial and deleterious mutations. In the first study we estimated that 6% of mutations accumulated during the first 1012 generations of accumulation improved diploid growth (Joseph and Hall 2004). To determine whether this high beneficial mutation rate was due to sampling error, we passaged the lines for an additional 1050 generations and found that 13% of mutations improved diploid growth (Hall et al. 2008). Similarly, another yeast MA experiment (Dickinson 2008) estimated an uncorrected frequency of beneficial mutations of 25%, although correction for within-colony selection reduces this estimate by approximately half. Together, these studies indicate that a substantial proportion of mutations accumulated in these yeast MA lines are beneficial for a single fitness component and that this observation cannot be explained by the chance sampling of a few beneficial mutations.In this study we return to our yeast MA lines (Joseph and Hall 2004) and examine whether the high beneficial mutation rate that we estimated after 1012 generations is an artifact of the fitness component that we examined. To test this hypothesis we examined whether our MA lines carry mutations that are beneficial across multiple fitness components: diploid growth, sporulation efficiency, spore viability, and haploid growth rate. If our previous results are due to us analyzing a fitness component that is either subject to stabilizing selection or antagonistic pleiotropy, then mutations accumulated in our lines will be conditionally beneficial and analyses of additional fitness components would yield different estimates of the beneficial mutation rate. We found that three of the four fitness components yield high estimates of the beneficial mutation rate. This suggests that multiple MA lines have accumulated beneficial mutations and that the high beneficial mutation rate that we previously estimated is not an artifact of the fitness component that we examined.Measuring multiple components of fitness also allowed us to examine the pleiotropic effects of beneficial and deleterious mutations. In general, we found that mutations altering one component of fitness have little effect on other components. However, lethal mutations were typically pleiotropic.

Conclusions:

We find that for three of four fitness components examined, a high frequency of spontaneous, fitness-altering mutations in diploid yeast is beneficial. Further, we do not detect pleiotropy of small-effect mutations, while lethal mutations show high levels of pleiotropy. In most cases, pleiotropy is positive. Two lines show evidence of antagonistic pleiotropy, indicating trade-offs, although heterozygote advantage cannot be ruled out.     

Identification of Selection Signatures in Cattle Breeds Selected for Dairy Production

Genetic correlations are expected to be high among functionally related traits and lower between groups of traits with distinct functions (e.g., reproductive vs. resource-acquisition traits). Here, we explore the quantitative-genetic and QTL architecture of floral organ sizes, vegetative traits, and life history in a set of Brassica rapa recombinant inbred lines within and across field and greenhouse environments. Floral organ lengths were strongly positively correlated within both environments, and analysis of standardized G-matrices indicates that the structure of genetic correlations is ∼80% conserved across environments. Consistent with these correlations, we detected a total of 19 and 21 additive-effect floral QTL in the field and the greenhouse, respectively, and individual QTL typically affected multiple organ types. Interestingly, QTL × QTL epistasis also appeared to contribute to observed genetic correlations; i.e., interactions between two QTL had similar effects on filament length and two estimates of petal size. Although floral and nonfloral traits are hypothesized to be genetically decoupled, correlations between floral organ size and both vegetative and life-history traits were highly significant in the greenhouse; G-matrices of floral and vegetative traits as well as floral and life-history traits differed across environments. Correspondingly, many QTL (45% of those mapped in the greenhouse) showed environmental interactions, including approximately even numbers of floral and nonfloral QTL. Most instances of QTL × QTL epistasis for floral traits were environment dependent.EVOLUTIONARY responses to selection are dependent on genetic architecture. The proportion of phenotypic variation with a heritable genetic basis affects the response to selection, as does the structure of genetic correlations among selected traits. For example, an evolutionary response will be constrained if selection favors an increase in the value of two traits that are negatively correlated; i.e., a negative correlation is antagonistic to the joint vector of selection. Alternatively, if the vector of selection is parallel to the genetic correlation, then trait covariation is reinforcing and the population mean may more rapidly approach favored trait values (Etterson and Shaw 2001; Merilä and Björklund 2004). One measure of genetic architecture is the G-matrix (Lynch and Walsh 1998), which is composed of genetic variances (diagonal matrix elements) and genetic covariances among traits (off-diagonal matrix elements). G-matrices have been shown to vary across environments (Donohue et al. 2000; Conner et al. 2003; Brock and Weinig 2007), indicating that the molecular-genetic underpinnings of matrix elements (e.g., identity and/or relative effect of additive and epistatic loci, degree of pleiotropy, etc.) and the traits'' evolutionary potential vary across environments. Few studies, however, have related matrix and QTL architectures; and, therefore, the molecular-genetic underpinnings of quantitative-genetic estimates remain unclear (but see Gardner and Latta 2007; Kelly 2009).In angiosperms, covariances between floral whorls (e.g., petal and stamen length) are frequently positive among functionally related traits. These positive correlations can arise from pollinator-mediated (or pollination-mediated) selection for specific allometric relationships among floral traits and ensuing linkage disequilibrium (LD) among causal loci (Berg 1959, 1960; also referred to as phenotypic integration, see Pigliucci 2003; Klingenberg 2008). For example, in outcrossing species, male fitness may be more dependent on the frequency and efficiency of pollinator visitation than female fitness (Bell 1985; but see Hodgins and Barrett 2008). Anther placement relative to the corolla opening can affect the efficiency of pollen dissemination (Conner and Via 1993; Morgan and Conner 2001); in addition, comparative work indicates that petal–stamen length correlations are stronger than stamen–pistil length correlations in outcrossers, whereas species that reproduce via autogamous selfing show the opposite pattern (Ushimaru and Nakata 2002). Alternatively, strong floral integration could be attributed to the developmental hypothesis that genetic correlations arise due to pleiotropic genes coregulating floral whorls (Herrera 2001; Herrera et al. 2002). Strong correlations resulting from linkage disequilibrium or from developmentally based pleiotropy may constrain the evolution of novel reproductive morphologies when biotic or abiotic factors (and selection) change (Cheverud 1984; Clark 1987; Smith and Rausher 2008; Agrawal and Stinchcombe 2009).Similar to genetic covariances among floral traits, covariances between floral and nonfloral traits could also alter the evolutionary response of reproductive traits. In contrast to hypotheses regarding the adaptive significance of floral-trait integration, genetic correlations between floral and nonfloral traits (e.g., vegetative or phenological traits) are hypothesized to be disadvantageous (Berg 1960). More specifically, floral allometry may be shaped by selection for reproductive success, as described above, whereas vegetative morphology is shaped primarily by selection to optimize other functions, such as light capture. If floral and nonfloral traits have a common genetic basis, then selection on phenological or morphological traits may result in maladaptive expression of floral organ size. As a result, functionally integrated floral traits are predicted to be genetically decoupled from vegetative and phenological traits (Berg 1960).QTL mapping provides a powerful tool to explore the genetic architecture of evolutionarily important traits. The QTL architecture of interspecific floral traits has been explored in diverse systems (Bradshaw et al. 1995; Fishman et al. 2002; Goodwillie et al. 2006; Bouck et al. 2007; Moyle 2007); however, insight into the molecular genetic basis of intraspecific floral variation comes almost exclusively from Arabidopsis thaliana (Juenger et al. 2000, 2005) and Mimulus guttatus (Hall et al. 2006). Floral traits in these intraspecific crosses are polygenic with a majority of detected QTL being of small to moderate effect size. Consistent with other quantitative-genetic studies (reviewed in Ashman and Majetic 2006), floral traits in A. thaliana and M. guttatus mapping populations exhibited moderate to high genetic correlations. In both systems, mapped QTL often affected multiple floral traits. In the few cases where QTL underlying intraspecific floral morphology have been evaluated, only a single growth environment was used; estimation of floral quantitative genetics across environments and subsequent comparison with the QTL architecture underlying observed across-environment patterns are lacking.Using a segregating progeny of Brassica rapa (recombinant inbred lines, RILs) and a small sample of crop and wild accessions, we examine the quantitative-genetic and QTL architecture of floral traits under field and greenhouse environments. Specifically, we address the following questions: (1) Does this RIL population express significant genetic (co)variation for floral traits when growing in the field or greenhouse? (2) Is there significant genetic variation for vegetative traits and days to flowering in field and greenhouse environments, and is there evidence for genetic correlations between floral and nonfloral traits? (3) Does the genetic architecture of floral and nonfloral traits, as measured by the G-matrix, differ across environments? (4) What is the number and effect size of additive and epistatic QTL in field and greenhouse environments? (5) What is the relationship between mapped QTL and quantitative genetic estimates of trait (co)variation within and between floral and nonfloral traits? And (6) what is the relationship between the quantitative-genetic architecture of floral traits in the RILs vs. in the accessions?     

Paternal Leakage and Heteroplasmy of Mitochondrial Genomes in Silene vulgaris: Evidence From Experimental Crosses

The inheritance of mitochondrial genetic (mtDNA) markers in the gynodioecious plant Silene vulgaris was studied using a series of controlled crosses between parents of known mtDNA genotype followed by quantitative PCR assays of offspring genotype. Overall, ∼2.5% of offspring derived from crosses between individuals that were homoplasmic for different mtDNA marker genotypes showed evidence of paternal leakage. When the source population of the pollen donor was considered, however, population-specific rates of leakage varied significantly around this value, ranging from 10.3% to zero. When leakage did occur, the paternal contribution ranged from 0.5% in some offspring (i.e., biparental inheritance resulting in a low level of heteroplasmy) to 100% in others. Crosses between mothers known to be heteroplasmic for one of the markers and homoplasmic fathers showed that once heteroplasmy enters a maternal lineage it is retained by ∼17% of offspring in the next generation, but lost from the others. The results are discussed with regard to previous studies of heteroplasmy in open-pollinated natural populations of S. vulgaris and with regard to the potential impact of mitochondrial paternal leakage and heteroplasmy on both the evolution of the mitochondrial genome and the evolution of gynodioecy.MATERNAL inheritance of the mitochondrial genome seems to be the usual case in angiosperms, with only occasional reports of paternal leakage (Birky 2001). The mode of inheritance has several interesting consequences for the evolution of the plant mitochondrial genome and plant mating systems. One is that maternal inheritance contributes to homoplasmy, or within-individual genetic homogeneity, in that it precludes the mixing of mitochondrial genomes of differing origin at the time of fertilization. Homoplasmy is further enforced by repeated sampling events associated with the transmission of a finite number of mitochondria from mother to daughter cells during mitotic or meiotic events (Birky 2001). This within-individual genetic drift is sometimes known as vegetative sorting (McCauley and Olson 2008). Paternal leakage would allow the possibility of mitochondrial heteroplasmy (within-individual cytoplasmic genetic diversity) when it leads to some degree of biparental inheritance. With homoplasmy the mitochondrial genome evolves as an effectively asexual lineage. While intra- or intermolecular recombination associated with repeat sequences often found in noncoding regions of plant mitochondrial genomes can result in structural rearrangements (Mackenzie and McIntosh 1999), there is limited opportunity for such events to generate novel genotypic combinations. Heteroplasmy enhances the possibility that recombination can occur between divergent genomes and generate novel genotypes.A second consequence of the mode of inheritance concerns the evolution of gynodioecy or the co-occurrence of female and hermaphrodite individuals. This phenomenon is often ascribed to the interaction between mitochondrial genes that confer cytoplasmic male sterility (CMS) and nuclear genes, known as restorers, that counteract the effects of CMS and restore male function (Frank 1989), a topic that continues to be the object of much study by plant evolutionary biologists (McCauley and Bailey 2009). The evolutionary dynamics of these interactions are usually evaluated on the basis of the assumption of pure maternal inheritance of mitochondrial genes. This maximizes the potential for genetic conflict between a CMS gene and its restorers, since a difference in the mode of inheritance between the mitochondrial and nuclear genomes results in a difference in their respective currency of fitness. With paternal leakage, pollen production is no longer unimportant for the fitness of the mitochondrial genes carried by a hermaphrodite (Wade and McCauley 2005).Recently there has been increased appreciation of the potential role of paternal leakage and heteroplasmy in the evolution of the mitochondrial genomes of a broad array of eukaryotes (Kmiec et al. 2006; White et al. 2008). This includes studies of the plant genus Silene, which have provided evidence of at least occasional paternal transmission of mitochondria in several species, as well as mitochondrial heteroplasmy. Observations supporting the possibility of mitochondrial paternal leakage and heteroplasmy in the genus Silene are especially intriguing given the occurrence of gynodioecy in this genus. Evidence of paternal leakage comes primarily from two types of observation. First are observations of mitochondrial genotypes that most likely result from intra- or intergenic recombination (see studies by Städler and Delph 2002 for S. acaulis and McCauley et al. 2005; Houliston and Olson 2006; and McCauley and Ellis 2008 for S. vulgaris). Second, direct evidence of heteroplasmy in S. vulgaris comes from studies that utilize real time quantitative PCR (q-PCR) to quantify the within-individual diversity of mitochondrial marker genes (Welch et al. 2006; Pearl et al. 2009). The likelihood that heteroplasmy is due to paternal leakage in S. vulgaris was inferred from observations by Pearl et al. (2009) of heteroplasmic offspring of open-pollinated homoplasmic mothers. A second observation by Pearl et al. (2009) bears on the inheritance of heteroplasmy. Heteroplasmic mothers were more likely than homoplasmic mothers to produce heteroplasmic offspring, but this heteroplasmy was also lost between generations in many cases, in keeping with the theory of vegetative sorting.One interesting result from Welch et al. (2006) and Pearl et al. (2009) is that incidents of heteroplasmy and apparent leakage do not seem to be evenly distributed among the natural populations from which samples were taken. Most of the heteroplasmic individuals documented by Welch et al. (2006) were from just one of the three populations studied. Similarly, while the apparent leakage rate observed by Pearl et al. (2009) was ∼8% when all 14 study populations are considered together, if the rate is calculated on a population-by-population basis, it exceeds 10% in 3 of them and is zero in 3 others (see their Supplementary Table 2). Population-to-population variation in the rate of leakage might suggest that variable environmental conditions influence leakage or that any genetic variation that influences the traits that determine mode of inheritance is geographically structured.Much of the current evidence for mitochondrial paternal leakage in Silene is indirect in that it is derived from observations of apparent recombinant genotypes or of heteroplasmy. While this evidence is compelling, alternate explanations, such as mutational hotspots within the genes under study, are at least possible. Even the evidence of leakage presented by Pearl et al. (2009) was based on mother–offspring comparisons of individuals collected from natural populations, in which the pollen donor was unknown. Though some evidence for paternal leakage and heteroplasmy reported in McCauley et al. (2005) comes from controlled crosses of S. vulgaris, those crosses were few in number and any incidents of heteroplasmy were based on qualitative observations rather than the q-PCR method used more recently. Thus, it would be valuable to conduct a large number of controlled crosses between S. vulgaris individuals of known mitochondrial genotype to assay directly the rate and magnitude of paternal leakage and any resulting heteroplasmy and also to assay the degree to which heteroplasmy is transmitted between generations. Taken together, this information would allow one to begin to ask, not only about the origins of mitochondrial heteroplasmy in Silene, but also about the degree to which the frequency of mitochondrial heteroplasmy in natural populations results from gains through paternal leakage vs. loss from vegetative sorting. Furthermore, since the among-population heterogeneity in levels of heteroplasmy and leakage summarized above could be due to either real differences between populations in factors promoting these phenomena or simply ascertainment bias associated with differences between populations in the level of polymorphism of the q-PCR markers, it would be valuable to test for a population effect in an experimental setting.Here we present comparisons of parent and offspring mitochondrial genotypes obtained by q-PCR following three types of controlled crosses in which either (1) the two parents are homoplasmic for different alleles of a marker gene, (2) both parents are homoplasmic for the same allele, or (3) the maternal parent is heteroplasmic. In the first cross type any contribution of the pollen donor to the offspring mitochondrial genotype would be detectable. This quantifies the likelihood of leakage. Knowing the natural population from which the pollen donor and pollen recipient trace their respective ancestry allows investigation of the possibility of a population effect without the confounding effects of varying levels of marker polymorphism present in field studies. In the second cross type, any observed mother–offspring difference would most likely be due to error of some sort (or the unlikely possibility of mutation at the SNP that defines the marker). Thus, these crosses act as a control by estimating the experimental error rate. The third type of cross measures the frequency with which heteroplasmy is transmitted maternally to offspring or is lost. Taken together this study represents what is, to our knowledge, the first attempt to combine experimental crosses and q-PCR methodology to examine mitochondrial genome inheritance and heteroplasmy in a plant species; important information given that it is not yet clear how widespread mitochondrial leakage and heteroplasmy are in the genus Silene, in other gynodioecious species, or in other species of plants in general.     

Infertility and Male Mating Behavior Deficits Associated With Pde1c in Drosophila melanogaster

Pde1c is a calcium/calmodulin-regulated, dual-specificity cyclic nucleotide phosphodiesterase. We have used a transposon insertion line to investigate the physiological function of Pde1c in Drosophila melanogaster and to show that the insertion leads to male sterility and male mating behavior defects that include reduced copulation rates. Sterility appears to be primarily due to elimination of sperm from the female reproductive system. The male mating behavior defects were fully rescued by expression of exogenous Pde1c under the control of either a Pde1c or a pan-neuronal promoter, whereas the sterility could be only partially rescued by expression of exogenous Pde1c under the control of these promoters. We also show that Pde1c has a male-specific expression pattern in the CNS with an increased number of Pde1c-expressing neurons in the abdominal ganglion in males.THE cyclic nucleotides, cyclic AMP (cAMP) and cyclic GMP (cGMP), have been known for many years to regulate a wide variety of physiological processes in all animals (e.g., Siegel et al. 1994). Similarly, there is a large body of research focused on an understanding of the structure and regulation of the enzymes that synthesize cAMP and cGMP, the adenylyl and guanylyl cyclases, respectively. Although the concentrations of cyclic nucleotides within a cell are regulated by both their synthesis and their degradation, less attention has been devoted to the function and regulation of the enzymes that break down cyclic nucleotides, the phosphodiesterases (PDEs).Mammals have >20 genes that code for cyclic nucleotide PDEs, which have been subdivided into 11 families on the basis of their sequences, substrate specificities, and regulatory properties (Conti and Beavo 2007). Insects also have a wide variety of PDEs with Drosophila melanogaster containing 6 genes that code for cyclic nucleotide PDEs (Morton and Hudson 2002; Day et al. 2005). On the basis of their sequence similarity to the mammalian PDEs, these 6 genes have been classified into 6 of the 11 families: Pde1c, Pde4, Pde6, Pde8, Pde9, and Pde11 (Day et al. 2005). When their biochemical properties have been investigated, they match well with other members of the same family (Day et al. 2005).Despite the importance of cyclic nucleotides in insect physiology, only one of the Drosophila PDEs has been associated with a mutant phenotype. This gene, Pde4, also known as dunce, was one of the first learning and memory mutants discovered (Byers et al. 1981; Davis et al. 1995). In this study, we have investigated the phenotypes associated with reduced expression of Pde1c, a PDE that has dual specificity for both cAMP and cGMP and that is stimulated in the presence of calcium and calmodulin (Day et al. 2005). Here we show that Pde1c is required for male fertility and male mating behavior. Male sterility appears to be primarily due to females rejecting sperm or failing to store the sperm from mutant males.     

Introgression of Drosophila simulans Nuclear Pore Protein 160 in Drosophila melanogaster Alone Does Not Cause Inviability but Does Cause Female Sterility

We have been analyzing genes for reproductive isolation by replacing Drosophila melanogaster genes with homologs from Drosophila simulans by interspecific backcrossing. Among the introgressions established, we found that a segment of the left arm of chromosome 2, Int(2L)S, carried recessive genes for hybrid sterility and inviability. That nuclear pore protein 160 (Nup160) in the introgression region is involved in hybrid inviability, as suggested by others, was confirmed by the present analysis. Male hybrids carrying an X chromosome of D. melanogaster were not rescued by the Lethal hybrid rescue (Lhr) mutation when the D. simulans Nup160 allele was made homozygous or hemizygous. Furthermore, we uniquely found that Nup160 is also responsible for hybrid sterility. Females were sterile when D. simulans Nup160 was made homozygous or hemizygous in the D. melanogaster genetic background. Genetic analyses indicated that the D. simulans Nup160 introgression into D. melanogaster was sufficient to cause female sterility but that other autosomal genes of D. simulans were also necessary to cause lethality. The involvement of Nup160 in hybrid inviability and female sterility was confirmed by transgene experiment.INVESTIGATING the genetic bases of reproductive isolation is important for understanding speciation (Sawamura and Tomaru 2002; Coyne and Orr 2004; Wu and Ting 2004; Noor and Feder 2006; Presgraves 2010). In fact, continued interest in this issue has led to the isolation of several genes that are responsible for hybrid sterility and inviability in Drosophila (Ting et al. 1998; Barbash et al. 2003; Presgraves et al. 2003; Brideau et al. 2006; Masly et al. 2006; Phadnis and Orr 2009; Prigent et al. 2009; Tang and Presgraves 2009). Drosophila melanogaster and Drosophila simulans are the best pair for such genetic analyses (Sturtevant 1920). Hybrid male lethality in the cross between D. melanogaster females and D. simulans males is caused by incompatibility involving chromatin-binding proteins (Barbash et al. 2003; Brideau et al. 2006), and hybrid female lethality in the reciprocal cross is caused by incompatibility between a maternally supplied factor and a repetitive satellite DNA (Sawamura et al. 1993a; Sawamura and Yamamoto 1997; Ferree and Barbash 2009). Furthermore, individuals with the genotype equivalent to the backcrossed generation exhibit different incompatibilities (Pontecorvo 1943; Presgraves 2003), two components of which have been identified (Presgraves et al. 2003; Tang and Presgraves 2009). Because of the discovery of rescuing mutations that prevent hybrid inviability and sterility (Watanabe 1979; Hutter and Ashburner 1987; Sawamura et al. 1993a,b; Davis et al. 1996; Barbash and Ashburner 2003), chromosome segments from D. simulans can be introgressed into the D. melanogaster genome (Sawamura et al. 2000; Masly et al. 2006). For example, introgression of the D. simulans chromosome 4 or Y into D. melanogaster results in male sterility (Muller and Pontecorvo 1940; Orr 1992), and the recessive sterility by the chromosome 4 introgression is attributed to an interspecific gene transposition between chromosomes (Masly et al. 2006).The other successful introgressions of this type are the tip and the middle regions of the left arm of chromosome 2, Int(2L)D and Int(2L)S, respectively (Sawamura et al. 2000). Both female and male Int(2L)S homozygotes are sterile (Figure 1A), and the recessive sterility genes have been mapped with recombination and complementation assays against deficiencies. The male sterility genes are polygenic and interact epistatically with each other (Sawamura and Yamamoto 2004; Sawamura et al. 2004b), but the female sterility gene has been mapped to a 170-kb region containing only 20 open reading frames (ORFs) (Sawamura et al. 2004a). Interestingly, Int(2L)S also carries a recessive lethal gene whose effect is detected only in a specific genotype (Figure 1B). Lethality in hybrid males from the cross between D. melanogaster females and D. simulans males is rescued by the Lethal hybrid rescue (Lhr) mutation in D. simulans (Watanabe 1979), but the hybrid males cannot be rescued if they carry the introgression, presumably because of incompatibility between an X-linked gene(s) of D. melanogaster and a homozygous D. simulans gene in the Int(2L)S region (Sawamura 2000). Because the female sterility gene and the lethal gene were not separated by recombination, Sawamura et al. (2004a) suggested that female sterility and lethality may be a consequence of the pleiotropic effects of a single gene.Open in a separate windowFigure 1.—Viability and fertility of flies with various genotypes. (A) Females and males that are heterozygous or homozygous for the D. simulans introgression Int(2L)S (Int) in the D. melanogaster genetic background. (B) Four genotypic classes from the cross between introgression heterozygote [Int(2L)S/CyO] females and D. simulans Lethal hybrid rescue (Lhr) males. (C) Four genotypic classes from the cross between D. melanogaster females with a deficiency (Df) [Df(2L)/CyO] and D. simulans Lhr males. Open chromosome regions are from D. melanogaster, and shaded ones are from D. simulans.Because the hybrid lethal gene on Int(2L)S is recessive, the gene can be mapped by deficiencies instead of using introgression (Figure 1C) (Sawamura 2000; Sawamura et al. 2004a). In fact, hybrid males carrying a deficiency encompassing this region (hemizygous for the D. simulans genes) and the D. melanogaster X chromosome are lethal even if they carry the hybrid rescue mutation (see also Presgraves 2003). Tang and Presgraves (2009) subsequently narrowed down this region with multiple deficiencies and identified the hybrid lethal gene with a complementation test and transformation. We confirmed their conclusion and report our data here. In the transformation experiment, we used the natural promoter of the gene, instead of overexpressing the gene (Tang and Presgraves 2009), and we directly indicated, for the first time, that the hybrid lethal gene is also responsible for the female sterility of introgression homozygotes. The D. simulans allele of the gene seems to be nonfunctional on the genetic background of D. melanogaster. Moreover, our results indicated that this gene and chromosome X of D. melanogaster are not sufficient to explain the inviability and that another autosomal gene(s) in D. simulans is required.     

Bayesian Inference of Genetic Parameters Based on Conditional Decompositions of Multivariate Normal Distributions

It is widely recognized that the mixed linear model is an important tool for parameter estimation in the analysis of complex pedigrees, which includes both pedigree and genomic information, and where mutually dependent genetic factors are often assumed to follow multivariate normal distributions of high dimension. We have developed a Bayesian statistical method based on the decomposition of the multivariate normal prior distribution into products of conditional univariate distributions. This procedure permits computationally demanding genetic evaluations of complex pedigrees, within the user-friendly computer package WinBUGS. To demonstrate and evaluate the flexibility of the method, we analyzed two example pedigrees: a large noninbred pedigree of Scots pine (Pinus sylvestris L.) that includes additive and dominance polygenic relationships and a simulated pedigree where genomic relationships have been calculated on the basis of a dense marker map. The analysis showed that our method was fast and provided accurate estimates and that it should therefore be a helpful tool for estimating genetic parameters of complex pedigrees quickly and reliably.MUCH effort in genetics has been devoted to revealing the underlying genetic architecture of quantitative or complex traits. Traditionally, the polygenic model has been used extensively to estimate genetic variances and breeding values of natural and breeding populations, where an infinite number of genes is assumed to code for the trait of interest (Bulmer 1971; Falconer and Mackay 1996). The genetic variance of a quantitative trait can be decomposed into an additive part that corresponds to the effects of individual alleles and a part that is nonadditive because of interactions between alleles. Attention has generally been focused on the estimation of additive genetic variance (and heritability), since additive variation is directly proportional to the response of selection via the breeder''s equation (Falconer and Mackay 1996, Chap. 11). However, to estimate additive genetic variation and heritability accurately, it can be important to identify potential nonadditive sources in genetic evaluations (Misztal 1997; Ovaskainen et al. 2008; Waldmann et al. 2008), especially if the pedigree being analyzed contains a large proportion of full-sibs and clones, as these in particular give rise to nonadditive genetic relationships (Lynch and Walsh 1998, pp. 145). The polygenic model using pedigree and phenotypic information, i.e., the animal model (Henderson 1984), has been the model of choice for estimating genetic parameters in breeding and natural populations (Abney et al. 2000; Sorensen and Gianola 2002; O′Hara et al. 2008).Recent breakthroughs in molecular techniques have made it possible to create genome-wide, single nucleotide polymorphism (SNP) maps. These maps have helped to uncover a vast amount of new loci responsible for trait expression and have provided general insights into the genetic architecture of quantitative traits (e.g., Valdar et al. 2006; Visscher 2008; Flint and Mackay 2009). These insights can help when calculating disease risks in humans, when attempting to increase the yield from breeding programs, and when estimating relatedness in conservation programs. High-density SNPs of many species of importance to science and agriculture can now be scored quickly and relatively cheaply, for example, in mice (Valdar et al. 2006), chickens (Muir et al. 2008), and dairy cattle (VanRaden et al. 2009).In the analysis of populations of breeding stock, the inclusion of dense marker data has improved the predictive ability (i.e., reliability) of genetic evaluations compared to the traditional phenotype model, both in simulations (Meuwissen et al. 2001; Calus et al. 2008; Hayes et al. 2009) and when using real data (Legarra et al. 2008; VanRaden et al. 2009; González-Recio et al. 2009). Meuwissen et al. (2001) suggested that the effect of all markers should first be estimated, and then summed, to obtain genomic estimated breeding values (GEBVs). An alternative procedure, where all markers are used to compute the genomic relationship matrix (in place of the additive polygenic relationship matrix) has also been suggested (e.g., Villanueva et al. 2005; VanRaden 2008; Hayes et al. 2009); this matrix is then incorporated into the statistical analysis to estimate GEBVs. A comparison of both procedures (VanRaden 2008) yielded similar estimates of GEBVs in cases where the effect of an individual allele was small. In addition, if not all pedigree members have marker information, a combined relationship matrix derived from both genotyped and ungenotyped individuals could be computed; this has been shown to increase the accuracy of GEBVs (Legarra et al. 2009; Misztal et al. 2009). Another plausible option to incorporate marker information is to use low-density SNP panels within families and to trace the effect of SNPs from high-density genotyped ancestors, as suggested by Habier et al. (2009) and Weigel et al. (2009). However, fast and powerful computer algorithms, which can use the marker information as efficiently as possible in the analysis of quantitative traits, are needed to obtain accurate GEBVs from genome-wide marker data.This study describes the development of an efficient Bayesian method for incorporating general relationships into the genetic evaluation procedure. The method is based on expressing the multivariate normal prior distribution as a product of one-dimensional normal distributions, each conditioned on the descending variables. When evaluating the genetic parameters of natural and breeding populations, high-dimensional distributions are often used as prior distributions of various genetic effects, such as the additive polygenic effect (Wang et al. 1993), multivariate additive polygenic effects (Van Tassell and Van Vleck 1996), and quantitative trait loci (QTL) effects via the identical-by-decent matrix (Yi and Xu 2000). A Bayesian framework is adopted to obtain posterior distributions of all unknown parameters, estimated by using Markov chain Monte Carlo (MCMC) sampling algorithms in the software package WinBUGS (Lunn et al. 2000, 2009). By performing prior calculations in the form of the factorized product of simple univariate conditional distributions, the computational time of the MCMC estimation procedure is reduced considerably. This feature permits rapid inference for both the polygenic model and the genomic relationship model. Moreover, the decomposition allows for inbreeding of varying degree, since the correct genetic covariance structure can be inferred into the analysis. In this article, we test the method on two previously published pedigree data sets: phenotype data from a large pedigree of Scots pine, incorporation of information on both additive and dominance genetic relationships (Waldmann et al. 2008); and genomic information obtained from a genome-wide scan of a simulated animal population (Lund et al. 2009).     

Reproductive Isolation in Hybrid Mice Due to Spermatogenesis Defects at Three Meiotic Stages

Early in the process of speciation, reproductive failures occur in hybrid animals between genetically diverged populations. The sterile hybrid animals are often males in mammals and they exhibit spermatogenic disruptions, resulting in decreased number and/or malformation of mature sperms. Despite the generality of this phenomenon, comparative study of phenotypes in hybrid males from various crosses has not been done, and therefore the comprehensive genetic basis of the disruption is still elusive. In this study, we characterized the spermatogenic phenotype especially during meiosis in four different cases of reproductive isolation: B6-ChrX^MSM, PGN-ChrX^MSM, (B6 × Mus musculus musculus-NJL/Ms) F₁, and (B6 × Mus spretus) F₁. The first two are consomic strains, both bearing the X chromosome of M. m. molossinus; in B6-ChrX^MSM, the genetic background is the laboratory strain C57BL/6J (predominantly M. m. domesticus), while in PGN-ChrX^MSM the background is the PGN2/Ms strain purely derived from wild M. m. domesticus. The last two cases are F₁ hybrids between mouse subspecies or species. Each of the hybrid males exhibited cell-cycle arrest and/or apoptosis at either one or two of three distinct meiotic stages: premeiotic stage, zygotene-to-pachytene stage of prophase I, and metaphase I. This study shows that the sterility in hybrid males is caused by spermatogenic disruptions at multiple stages, suggesting that the responsible genes function in different cellular processes. Furthermore, the stages with disruptions are not correlated with the genetic distance between the respective parental strains.WHEN animals from genetically diverged populations hybridize, complete or partial sterility is often observed in the F₁ hybrids or in their descendants. This phenomenon belonging to postzygotic reproductive isolation accelerates irreversible genetic divergence by preventing free gene flow across the two diverging populations, and thereby plays a pivotal role in speciation. Sexual dimorphism is a general feature of reproductive isolation (Wu and Davis 1993; Laurie 1997; Orr 1997; Kulathinal and Singh 2008). In mammals, impairment is much more severe in males than in females, and in general the heterogametic sex is more sensitive to interspecific and intersubspecific genetic incompatibility. This phenomenon is well known as Haldane''s rule (Haldane 1922; Laurie 1997; Orr 1997).In many animals, the reproductive isolation is caused by spermatogenic disruptions characterized by reduced number of germ cells and small testis size. These animals include Drosophila (Joly et al. 1997), stickleback fish Pungitius (Takahashi et al. 2005), caviomorph rodent Thrichomys (Borodin et al. 2006), house musk shrew Suncus (Borodin et al. 1998), wallaby Petrogale (Close et al. 1996), and genus Mus (Forejt and Iványi 1974; Matsuda et al. 1992; Hale et al. 1993; Yoshiki et al. 1993; Kaku et al. 1995; Gregorová and Forejt 2000; Elliott et al. 2001, 2004; Good et al. 2008). Although reproductive isolation by spermatogenic impairment is a well-known phenomenon, its underlying genetic mechanism and molecular basis have remained elusive. The Dobzhansky–Muller model, which infers that hybrid sterility or inviability is caused by deleterious epistatic interactions between nuclear genes derived from their respective parent species or subspecies (Dobzhansky 1936; Muller 1942), is widely accepted in animals and plants and is also applicable to the sterility of hybrid animals in F₂ or backcross generations, so-called hybrid breakdown, in which the genes causing postzygotic reproductive isolation are partially recessive (Orr 2005).The genetic incompatibility between house mouse subspecies is an ideal animal model for studying the early stage of speciation. Two subspecies of mouse, Mus musculus domesticus and M. m. musculus, diverged from their common ancestor 0.3–1.0 MYA (Yonekawa et al. 1980; Moriwaki 1994; Bonhomme and Guénet 1996; Boursot et al. 1996; Din et al. 1996). M. m. domesticus ranges across western Europe and the Middle East, whereas M. m. musculus ranges throughout eastern Europe and northern Asia (Bonhomme and Guénet 1996). The two subspecies meet in a narrow hybrid zone, which is most likely maintained by a balance between dispersal and selection against hybrids (Hunt and Selander 1973; Bonhomme and Guénet 1996; Payseur et al. 2004). M. m. domesticus also displays reproductive isolation from the Japanese wild mouse, M. m. molossinus, which originated from hybridization of M. m. castaneus and M. m. musculus and its nuclear genome is predominantly derived from M. m. musculus (Yonekawa et al. 1980, 1988; Moriwaki 1994; Sakai et al. 2005). To investigate the reproductive isolation between M. m. domesticus and M. m. molossinus, we previously constructed a consomic strain B6-ChrX^MSM (Oka et al. 2004). This strain has the X chromosome from the MSM/Ms strain, which is derived from M. m. molossinus, in the genetic background of the laboratory strain C57BL/6J (B6), which is predominantly derived from M. m. domesticus (Moriwaki 1994). F₁ hybrid animals between B6 and MSM/Ms strains are fully fertile. On the contrary, B6-ChrX^MSM shows male-specific sterility characterized by a reduced sperm number and dysfunction of the sperm, including abnormal morphology and low motility, indicating that B6-ChrX^MSM is a model of hybrid breakdown in animals (Oka et al. 2004, 2007). Our previous study indicated that the abnormal morphology of the sperm head results from the genetic incompatibility between MSM/Ms-derived X-linked genes and B6 genes on autosomes including chromosomes 1 and 11 (Oka et al. 2007).In this study, to understand the genetic mechanism of reproductive isolation in mice, we first undertook in-depth characterization of phenotype for each B6-ChrX^MSM male especially during meiosis. Meiosis is a special cell division that produces four haploid cells after one round of chromosome replication and two rounds of chromosome segregation. During meiosis, homologous chromosomes pair, synapse, undergo crossing over, and achieve bipolar attachment to the spindle to segregate one set of chromosomes to each daughter cell. Homologous recombination is initiated during the leptotene stage of meiotic prophase I with the formation of DNA double-strand breaks (DSBs), which are repaired immediately during the zygotene stage or after crossing over of homologous chromosomes during the pachytene stage (Roeder 1997; Tarsounas and Moens 2001).During the first wave of spermatogenesis, most mitotic spermatogonia in the B6-ChrX^MSM testes fail to initiate meiotic DNA replication. Some proportion of those spermatogonia that enter into meiosis are again arrested and eliminated by apoptosis at the pachytene stage, resulting in the production of a small number of sperms. We extended the same analysis to three other cases of reproductive isolation. Another consomic strain PGN-ChrX^MSM has an MSM/Ms-derived X chromosome in the genetic background of the PGN2/Ms strain derived from wild mice (M. m. domesticus). PGN-ChrX^MSM males produce a small number of dysfunctional sperms as was the case with B6-ChrX^MSM males, but the former males show apoptosis mainly at metaphase of meiosis I. Furthermore, we examined F₁ hybrid males from intersubspecific cross of (B6 × M. m. musculus-NJL/Ms) and interspecific cross of (B6 × M. spretus). These F₁ hybrid males exhibited apoptosis at metaphase I and at the zygotene-to-pachytene stage of prophase I. As a whole, the postzygotic reproductive isolation in mice is caused by disruptions at a minimum of three different spermatogenic stages.     

Phenotypic Consequences of Aneuploidy in Arabidopsis thaliana

Aneuploid cells are characterized by incomplete chromosome sets. The resulting imbalance in gene dosage has phenotypic consequences that are specific to each karyotype. Even in the case of Down syndrome, the most viable and studied form of human aneuploidy, the mechanisms underlying the connected phenotypes remain mostly unclear. Because of their tolerance to aneuploidy, plants provide a powerful system for a genome-wide investigation of aneuploid syndromes, an approach that is not feasible in animal systems. Indeed, in many plant species, populations of aneuploid individuals can be easily obtained from triploid individuals. We phenotyped a population of Arabidopsis thaliana aneuploid individuals containing 25 different karyotypes. Even in this highly heterogeneous population, we demonstrate that certain traits are strongly associated with the dosage of specific chromosome types and that chromosomal effects can be additive. Further, we identified subtle developmental phenotypes expressed in the diploid progeny of aneuploid parent(s) but not in euploid controls from diploid lineages. These results indicate long-term phenotypic consequences of aneuploidy that can persist after chromosomal balance has been restored. We verified the diploid nature of these individuals by whole-genome sequencing and discuss the possibility that trans-generational phenotypic effects stem from epigenetic modifications passed from aneuploid parents to their diploid progeny.THE genome of aneuploid individuals contains incomplete chromosome sets. The balance between chromosome types, and the genes they encode, is compromised, resulting in altered expression of many genes, including genes with dosage-sensitive effects on phenotypes. In humans, only a few types of aneuploid karyotypes are viable (Hassold and Hunt 2001), highlighting the deleterious effect of chromosome imbalance. The most commonly known viable form of aneuploidy in humans is Down syndrome, which results from a trisomy of chromosome 21 in an otherwise diploid background. Down syndrome patients exhibit many specific phenotypes, sometimes visible only in a subset of patients (Antonarakis et al. 2004). For phenotypes found in all Down syndrome patients, the penetrance of each phenotype varies between patients (Antonarakis et al. 2004). Despite the increasing amount of information available about the human genome and the availability of a mouse model for Down syndrome (O''Doherty et al. 2005), the genes responsible for most of the phenotypes associated with Down syndrome are still unknown (Patterson 2007; Korbel et al. 2009; Patterson 2009). Recently, detailed phenotypic analyses of as many as 30 aneuploid patients have allowed the identification of susceptibility regions for several specific phenotypes (Patterson 2007, 2009; Korbel et al. 2009; Lyle et al. 2009), but the specific genes remain to be identified. Understanding the physiology of aneuploidy is not only relevant to those individuals with aneuploid genomes but also to understanding cancer since most cancerous cells are aneuploid (Matzke et al. 2003; Pihan and Doxsey 2003; Storchova and Pellman 2004; Holland and Cleveland 2009; Williams and Amon 2009) or the consequences of copy number variation and dosage sensitivity (Dear 2009; Henrichsen et al. 2009).Plants are more tolerant of aneuploidy than animals (Matzke et al. 2003) for reasons that remain unclear. Since the discovery of the Datura trisomic “chromosome mutants” by Blakeslee (1921, 1922), viable trisomics of each chromosome type have been described in numerous species. Trisomics exhibit phenotypes specific to the identity of the triplicated chromosome (Blakeslee 1922; Khush 1973; Koornneef and Van der Veen 1983; Singh 2003). More complex aneuploids, i.e., individuals carrying more than one additional chromosome, can be viable as well and have been observed in many plants species, especially among the progeny of triploid individuals (McClintock 1929; Levan 1942; Johnsson 1945; Khush 1973). Some species appear to be more tolerant of complex aneuploidies than others, suggesting a genetic basis for aneuploidy tolerance (Satina and Blakeslee 1938; Khush 1973; Ramsey and Schemske 2002; Henry et al. 2009). Aneuploid individuals frequently appear spontaneously within polyploid plant populations, presumably due to a failure to equally partition the multiple chromosome sets at meiosis (Randolph 1935; Doyle 1986). These aneuploids exhibit few or subtle phenotypic abnormalities and can often compete with their euploid progenitors (Ramsey and Schemske 1998). Plants therefore provide an excellent opportunity for a genome-wide investigation of aneuploid syndromes: sample size is not limited, phenotypes can be described and assessed in detail, and plant aneuploid populations provide a complex mixture of viable karyotypes.In this article, we report our investigation of the relationship between phenotype and karyotype in populations of aneuploid Arabidopsis thaliana plants. All simple trisomics of A. thaliana have been previously isolated and phenotypically characterized (Steinitz-Sears 1962; Lee-Chen and Steinitz-Sears 1967; Steinitz-Sears and Lee-Chen 1970; Koornneef and Van der Veen 1983), demonstrating that they are tolerated in A. thaliana. We previously reported that aneuploid swarms—populations of aneuploid individuals of varying aneuploid karyotypes—could be obtained from the progeny of triploid A. thaliana individuals (Henry et al. 2005, 2009). Using a combination of a quantitative PCR-based method and flow cytometry, we were able to derive the full aneuploid karyotype of each of these individuals (Henry et al. 2006). We further crossed triploid A. thaliana to diploid or tetraploid individuals and demonstrated that at least 44 of the 60 possible aneuploid karyotypes that could result from these crosses (aneuploid individuals carrying between 11 and 19 chromosomes) were viable and successfully produced adult plants. Taken together, these populations and methods make it possible to explore the basis of aneuploid syndromes in A. thaliana. In this study, we were able to phenotypically characterize at least one individual from 25 different aneuploid karyotypes falling between diploidy and tetraploidy. We demonstrated that specific phenotypes are affected by the dosage of specific chromosome types. The effect of the dosage of specific chromosome types on traits was additive and could be used to predict the observed phenotype. The availability of multiple generations of aneuploid and euploid individuals allowed us to investigate potential long-term effects of aneuploidy as well as parent-of-origin effects on aneuploid phenotypes.