Sex determination and evolution of unisexuality in the Conchostraca

Field collected or laboratory-reared samples of 60 species of conchostracans (representing all extant genera) indicate that males and females are equally common in most species. Deviations from this pattern occur in four lineages.Cyzicus andLeptestheria each include at least one unisexual species; many species of Limnadiinae are either unisexual or characterized by female-biased sex ratios; and Cyclestheriidae are either unisexual or express males in the later generations of their life cycles. Laboratory studies indicate that species with sex ratios near unity are gonochoric (obligately sexual), whereas females in species with female-biased sex ratios are capable of both outcrossing and selfing modes of reproduction. Phylogenetic analysis of patterns of reproduction suggest that sexual reproduction is the primitive condition. Genetic analysis of sexual species indicate that gender is determined by one or a few genetic factors and that the male-determining allele is recessive. The inheritance of gender in androdioecious species (where females are capable of self-fertilization) is similar to that in sexual species. Androdioecy is likely to be the intermediate stage between obligately sexual reproduction and unisexuality in the Limnadiinae. The phylogenetic distribution of sex ratio variation suggests that unisexuality in Cyzicidae, Leptestheriidae, and Cyclestheriidae has arisen independently of that in the Limnadiinae and that these cases have evolved by different evolutionary pathways.     

Reproductive isolation and genetic differentiation in North American species of Triops (Crustacea: Branchiopoda: Notostraca)

Electrophoretic analysis of 31 populations, ranging from California to Kansas, indicates that the North American tadpole shrimp Triops longicaudatus (LeConte) is actually a mixture of at least two reproductively isolated species. In the central United States, the predominant species is T. longicaudatus, which is found typically in ephemeral prairie pools. In the southwestern United States, the predominant species is Triops newberryi (Packard), which characteristically inhabits large playa pools. The two species coexist occasionally and in sympatric situations they are reproductively isolated from each other. The two species are genetically distinct at a level greater than is typical of conspecific populations. These genetic differences are correlated with subtle morphological differences and profound differences in reproductive biology. Both species represent complexes of bisexual and unisexual populations. Bisexual populations of T. longicaudatus are usually composed of males and females in approximately equal frequencies; bisexual populations of T. newberryi are composed of males in low frequencies and self-compatible hermaphrodites. Unisexual populations of both species apparently consist entirely of self-compatible hermaphrodites. This revised version was published online in August 2006 with corrections to the Cover Date.     

Social heterosis and the maintenance of genetic diversity at the genome level

Social heterosis is when individuals in groups or neighbourhoods receive a mutualistic benefit from across‐individual genetic diversity. Although it can be a viable evolutionary mechanism to maintain allelic diversity at a given locus, its efficacy at maintaining genome‐wide diversity is in question when multiple loci are being simultaneously selected. Therefore, we modelled social heterosis in a population of haploid genomes of two‐ or three‐linked loci. With such linkages, social heterosis decreases gametic diversity, but maintains allelic diversity. Genomes tend to survive as complimentary pairs, with alternate alleles at each locus (e.g. the pair AbC and aBc). The outcomes of selection appear similar to fitness epistasis but are novel in the sense that phenotypic interactions occur across rather than within individuals. The model’s results strongly suggest that strong linkage across gene loci actually increases the probability that social heterosis maintains significant genetic diversity at the level of the genome.     

Implications of life-history transitions on the population genetic structure of the toxigenic marine dinoflagellate Alexandrium tamarense

Genotypic or phenotypic markers for characterization of natural populations of marine microalgae have typically addressed questions regarding differentiation among populations, usually with reference to a single or few clonal isolates. Based upon a large number of contemporaneous isolates from the same geographical population of the toxigenic species Alexandrium tamarense from the North Sea, we uncovered significant genetic substructure and low but significant multilocus linkage disequilibrium (LD) within the planktonic population. Between the alternative molecular genotyping approaches, only amplified fragment length polymorphism (AFLP) revealed cryptic genetic population substructure by Bayesian clustering, whereas microsatellite markers failed to yield concordant patterns. Both markers, however, gave evidence for genetic differentiation of population subgroups as defined by AFLP. A considerable portion of multilocus LD could be attributed to population subdivision. The remaining LD within population subgroups is interpreted as an indicator of frequency shifts of clonal lineages during vegetative growth of planktonic populations. Phenotypic characters such as cellular content and composition of neurotoxins associated with paralytic shellfish poisoning (PSP) and allelochemical properties may contribute to intra- or inter-annual differentiation of planktonic populations, if clonal lineages that express these characters are selectively favoured. Nevertheless, significant phenotypic differentiation for these characters among the genetically differentiated subgroups was only detected for PSP toxin content in two of the four population subgroups. By integrating the analysis of phenotypic and genotypic characteristics, we developed a conceptual population genetic model to explain the importance of life-cycle dynamics and transitions in the evolutionary ecology of these dinoflagellates.     

Phylogeography of Haplotypes of Five Microsatellites Located in a Low-recombination Region of the X Chromosome: Studies Worldwide and in Brazilian Populations

We studied five microsatellites (DXS995, DXS8076, DXS8114, DXS1002 and DXS1050) located in a region of very low recombination rate in the long arm of the human X chromosome (Xq13.3–Xq21.3). No recombination was seen in 291 meioses in CEPH families. To test whether haplotypes composed of the five microsatellites could differentiate among distinct human continental populations, we studied an international panel containing 72 males from Africa, Europe, Asia and the America. Haplotypic diversity was very high within these groups and no haplotypes were shared among them. This led to the hope that we might be able to identify continent-specific lineages. However, in a median joining network there was no clear discrimination of the different continental groups. We then tested whether we could identify X chromosomal lineages from different continental origins in Brazilians. We typed 180 white Brazilians from four different geographical regions and examined their proportions of haplotype sharing with Africans, Asians, Europeans and Amerindians. No phylogeographical patterns emerged from the data. Moreover, there were several instances of the same haplotype being shared by many (and in one instance all) groups, suggesting that recombination might be occurring. We thus studied pairwise the level of linkage disequilibrium (LD) between the microsatellites. No detectable linkage disequilibrium between the most external loci DXS995 and DXS1050 was observed. Thus, even though recombination may be absent on short time spans, as seen in the CEPH pedigrees, on a long term basis it occurs often enough to dissipate all linkage disequilibrium. On the other hand, we observed very strong linkage disequilibrium between the pairs DXS995/DXS8076 and DXS1002/DXS8114, raising the possibility of resequencing the segment between them to identify single nucleotide polymorphisms (SNPs) in their intervals. The combination of X-linked microsatellites and SNPs in strong linkage disequilibrium might provide a powerful new tool to investigate human demographic history.     

Follicle duct cell ultrastructure and eggshell formation in Triops cancriformis (crustacea,notostraca)

Electron microscopy of the cells of the follicle duct of Triops cancriformis shows that the follicular ducts are lined by a single-layered epithelium which also produces the eggshell material. The cytoplasm is rich in rough endoplasmic reticulum that synthesizes the eggshell material which subsequently aggregates into preformed vacuoles. Newly formed spheres of eggshell material are then excreted into the lumen. At the end of vitellogenesis the oocytes descend toward the longitudinal oviduct and pass through the eggshell material which fills the follicle ducts. The production of the eggshell and its chemical composition in some Phyllopoda are compared. The paper discusses the relationship between the eggshell construction and the reproductive biology of the population.     

Short-term consequences of reproductive mode variation on the genetic architecture of energy metabolism and life-history traits in the pea aphid

Cyclically parthenogenetic animals such as aphids are able alternating sexual and asexual reproduction during its life cycle, and represent good models for studying short-term evolutionary consequences of sex. In aphids, different morphs, whether sexual or asexual, winged or wingless, are produced in response to specific environmental cues. The production of these morphs could imply a differential energy investment between the two reproductive phases (i.e., sexual and asexual), which can also be interpreted in terms of changes in genetic variation and/or trade-offs between the associated traits. In this study we compared the G-matrices of energy metabolism, life-history traits and morph production in 10 clonal lineages (genotypes) of the pea aphid, Acyrthosiphon pisum, during both sexual and asexual phases. The heritabilities (broad-sense) were significant for almost all traits in both phases; however the only significant genetic correlation we found was a positive correlation between resting metabolic rate and production of winged parthenogenetic females during the asexual phase. These results suggest the pea aphid shows some lineage specialization in terms of energy costs, but a higher specialization in the production of the different morphs (e.g., winged parthenogenetic females). Moreover, the production of winged females during the asexual phase appears to be more costly than wingless females. Finally, the structures of genetic variance-covariance matrices differed between both phases. These differences were mainly due to the correlation between resting metabolic rate and winged parthenogenetic females in the asexual phase. This structural difference would be indicating that energy allocation rules changes between phases, emphasizing the dispersion role of asexual morphs.     

The extent of linkage disequilibrium in a large cattle population of western Africa and its consequences for association studies

Several previous studies concluded that linkage disequilibrium (LD) in livestock populations from developed countries originated from the impact of strong selection. Here, we assessed the extent of LD in a cattle population from western Africa that was bred in an extensive farming system. The analyses were performed on 363 individuals in a Bos indicus x Bos taurus population using 42 microsatellite markers on BTA04, BTA07 and BTA13. A high level of expected heterozygosity (0.71), a high mean number of alleles per locus (9.7) and a mild shift in Hardy-Weinberg equilibrium were found. Linkage disequilibrium extended over shorter distances than what has been observed in cattle from developed countries. Effective population size was assessed using two methods; both methods produced large values: 1388 when considering heterozygosity (assuming a mutation rate of 10(-3)) and 2344 when considering LD on whole linkage groups (assuming a constant population size over generations). However, analysing the decay of LD as a function of marker spacing indicated a decreasing trend in effective population size over generations. This decrease could be explained by increasing selective pressure and/or by an admixture process. Finally, LD extended over small distances, which suggested that whole-genome scans will require a large number of markers. However, association studies using such populations will be effective.     

Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

Extensive phenotypic variation is a common feature among village chickens found throughout much of the developing world, and in traditional chicken breeds that have been artificially selected for traits such as plumage variety. We present here an assessment of traditional and village chicken populations, for fine mapping of Mendelian traits using genome-wide single-nucleotide polymorphism (SNP) genotyping while providing information on their genetic structure and diversity. Bayesian clustering analysis reveals two main genetic backgrounds in traditional breeds, Kenyan, Ethiopian and Chilean village chickens. Analysis of linkage disequilibrium (LD) reveals useful LD (r(2) ≥ 0.3) in both traditional and village chickens at pairwise marker distances of ~10 Kb; while haplotype block analysis indicates a median block size of 11-12 Kb. Association mapping yielded refined mapping intervals for duplex comb (Gga 2:38.55-38.89 Mb) and rose comb (Gga 7:18.41-22.09 Mb) phenotypes in traditional breeds. Combined mapping information from traditional breeds and Chilean village chicken allows the oocyan phenotype to be fine mapped to two small regions (Gga 1:67.25-67.28 Mb, Gga 1:67.28-67.32 Mb) totalling ~75 Kb. Mapping the unmapped earlobe pigmentation phenotype supports previous findings that the trait is sex-linked and polygenic. A critical assessment of the number of SNPs required to map simple traits indicate that between 90 and 110K SNPs are required for full genome-wide analysis of haplotype block structure/ancestry, and for association mapping in both traditional and village chickens. Our results demonstrate the importance and uniqueness of phenotypic diversity and genetic structure of traditional chicken breeds for fine-scale mapping of Mendelian traits in the species, with village chicken populations providing further opportunities to enhance mapping resolutions.     

High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland

Nucleotide polymorphism at 12 nuclear loci was studied in Scots pine populations across an environmental gradient in Scotland, to evaluate the impacts of demographic history and selection on genetic diversity. At eight loci, diversity patterns were compared between Scottish and continental European populations. At these loci, a similar level of diversity (θ_sil=∼0.01) was found in Scottish vs mainland European populations, contrary to expectations for recent colonization, however, less rapid decay of linkage disequilibrium was observed in the former (ρ=0.0086±0.0009, ρ=0.0245±0.0022, respectively). Scottish populations also showed a deficit of rare nucleotide variants (multi-locus Tajima''s D=0.316 vs D=−0.379) and differed significantly from mainland populations in allelic frequency and/or haplotype structure at several loci. Within Scotland, western populations showed slightly reduced nucleotide diversity (π_tot=0.0068) compared with those from the south and east (0.0079 and 0.0083, respectively) and about three times higher recombination to diversity ratio (ρ/θ=0.71 vs 0.15 and 0.18, respectively). By comparison with results from coalescent simulations, the observed allelic frequency spectrum in the western populations was compatible with a relatively recent bottleneck (0.00175 × 4N_e generations) that reduced the population to about 2% of the present size. However, heterogeneity in the allelic frequency distribution among geographical regions in Scotland suggests that subsequent admixture of populations with different demographic histories may also have played a role.     

Estimating the minimum rate of genetic transformation in bacteria

Extensive data from multilocus electrophoresis are available for many bacterial populations. In some cases, for example Neisseria gonorrhoeae, these data are consistent with the population being in linkage equilibrium. This raises the following question. What frequency of transformation, or other means of genetic recombination, is needed, relative to mutation, to produce apparent panmixis? Simulation of a finite-population model suggests that, if transformation is at least twenty times as frequent as mutation, the population structure will be indistinguishable from a panmictic one, using the best available data sets. That is, relatively infrequent transformation is sufficient to produce approximate linkage equilibrium.     

Sex chromosome evolution in the clam shrimp,Eulimnadia texana

Chromosomes that determine sex are predicted to evolve differently than autosomes: a lack of recombination on one of the two sex chromosomes is predicted to allow an accumulation of deleterious alleles that eventually leads to reduced functionality and potential physical degradation of the nonrecombining chromosome. Because these changes should occur at an elevated evolutionary rate, it is difficult to find appropriate species in which to test these evolutionary predictions. The unique genetic sex‐determining mechanism of the crustacean Eulimnadia texana prevents major chromosome degeneration because of expression of both ‘proto‐sex’ (i.e. early stage of development) chromosomes in homozygous form (ZZ and WW). Herein, we exploit this unique genetic system to examine the predicted accumulation of deleterious alleles by comparing both homogametic sexual types to their heterogametic counterpart. We report differences in crossing over in a sex‐linked region in the ZW hermaphrodites (～ 3%) relative to the ZZ males (～ 21%), indicative of cross‐over suppression in the ZW hermaphrodites. Additionally, we report that both ZZ and WW genotypes have reduced fitness relative to ZW hermaphrodites, which is consistent with the prediction of harboured recessive mutations embedded on both the Z and the W chromosomes. These results suggest that the proto‐sex chromosomes in E. texana accumulate recessive deleterious alleles. We hypothesize that recessive deleterious alleles of large effect cannot accumulate because of expression in both ZZ and WW individuals, keeping both chromosomes from losing significant function.     

Widespread genetic linkage of mating signals and preferences in the Hawaiian cricket Laupala

The evolution of novel sexual communication systems is integral to the process of speciation, as it discourages gene flow between incipient species. Physical linkage between genes underlying male-female communication (i.e. sexual signals and preferences for them) facilitates both rapid and coordinated divergence of sexual communication systems between populations and reduces recombination in the face of occasional hybridization between diverging populations. Despite these ramifications of the genetic architecture of sexual communication for sexual selection and speciation, few studies have examined this relationship empirically. Previous studies of the closely related Hawaiian crickets Laupala paranigra and Laupala kohalensis have indirectly suggested that many of the genes underlying the difference in pulse rate of male song are physically linked with genes underlying the difference in female preference for pulse rate. Using marker-assisted introgression, we moved 'slow pulse rate' alleles from L. paranigra at five known quantitative trait loci (QTL) underlying male pulse rate into the 'fast pulse rate' genetic background of L. kohalensis and assessed the effect of these loci on female preference. An astounding four out of five song QTL predicted the preferences of female fourth-generation backcrosses, providing direct evidence for the extensive genetic linkage of song and preference in one of the fastest diversifying genera currently known.     

SHEsis, a powerful software platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci

In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses of linkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large number of samples has been sought for long. In order to achieve the goal of obtaining meaningful results directly from raw data,we developed a robust and user-friendly software platform with a series of tools for analysis in association study with high efficiency. The platform has been well evaluated by several sets of real data.     

Characterization of the genetic diversity, structure and admixture of British chicken breeds

The characterization of livestock genetic diversity can inform breed conservation initiatives. The genetic diversity and genetic structure were assessed in 685 individual genotypes sampled from 24 British chicken breeds. A total of 239 alleles were found across 30 microsatellite loci with a mean number of 7.97 alleles per locus. The breeds were highly differentiated, with an average F(ST) of 0.25, similar to that of European chicken breeds. The genetic diversity in British chicken breeds was comparable to that found in European chicken breeds, with an average number of alleles per locus of 3.59, ranging from 2.00 in Spanish to 4.40 in Maran, and an average expected heterozygosity of 0.49, ranging from 0.20 in Spanish to 0.62 in Araucana. However, the majority of breeds were not in Hardy-Weinberg Equilibrium, as indicated by heterozygote deficiency in the majority of breeds (average F(IS) of 0.20), with an average observed heterozygote frequency of 0.39, ranging from 0.15 in Spanish to 0.49 in Cochin. Individual-based clustering analyses revealed that most individuals clustered to breed origin. However, genetic subdivisions occurred in several breeds, and this was predominantly associated with flock supplier and occasionally by morphological type. The deficit of heterozygotes was likely owing to a Wahlund effect caused by sampling from different flocks, implying structure within breeds. It is proposed that gene flow amongst flocks within breeds should be enhanced to maintain the current levels of genetic diversity. Additionally, certain breeds had low levels of both genetic diversity and uniqueness. Consideration is required for the conservation and preservation of these potentially vulnerable breeds.     

Linkage disequilibrium for different scales and applications

Assessing the patterns of linkage disequilibrium (LD) has become an important issue in both evolutionary biology and medical genetics since the rapid accumulation of densely spaced DNA sequence variation data in several organisms. LD deals with the correlation of genetic variation at two or more loci or sites in the genome within a given population. There are a variety of LD measures which range from traditional pairwise LD measures such as D' or r2 to entropy-based multi-locus measures or haplotype-specific approaches. Understanding the evolutionary forces (in particular recombination) that generate the observed variation of LD patterns across genomic regions is addressed by model-based LD analysis. Marker type and its allelic composition also influence the observed LD pattern, microsatellites having a greater power to detect LD in population isolates than SNPs. This review aims to explain basic LD measures and their application properties.     

Positive relationships between genetic diversity and abundance in fishes

Molecular markers, such as mitochondrial DNA and microsatellite loci, are widely studied to assess population genetics and phylogeography; however, the selective neutrality of these markers is increasingly being questioned. Given the importance of molecular markers in fisheries science and conservation, we evaluated the neutrality of both mtDNA and microsatellite loci through their associations with population size. We surveyed mtDNA and microsatellite data from the primary literature and determined whether genetic diversity increased with abundance across a total of 105 marine and freshwater fishes, with both global fisheries catch data and body size as proxies for abundance (with an additional 57 species for which only body size data were assessed). We found that microsatellite data generally yielded higher associations with abundance than mtDNA data, and within mtDNA analyses, number of haplotypes and haplotype diversity were more strongly associated with abundance than nucleotide diversity, particularly for freshwater fishes. We compared genetic diversity between freshwater and marine fishes and found that marine fishes had higher values of all measures of genetic diversity than freshwater fishes. Results for both mtDNA and microsatellites generally conformed to neutral expectations, although weaker relationships were often found between mtDNA nucleotide diversity and ‘abundance’ compared to any other genetic statistic. We speculate that this is because of historical events unrelated to natural selection, although a role for selection cannot be ruled out.     

Temporal dynamics of genotypic diversity reveal strong clonal selection in the aphid Myzus persicae

Parthenogenetic organisms often harbour substantial genotypic diversity. This diversity may be the result of recurrent formations of new clones, or it may be maintained by environmental heterogeneity acting on ecological differences among clones. In aphids, both processes may be important because obligate and cyclical parthenogens can form mixed populations. Using microsatellites, I analysed the temporal dynamics of clonal diversity in such a population of the aphid Myzus persicae over a 1-year period. The frequency distribution of clonal genotypes was very skewed, with many rare and few common clones. The relative frequencies of common clones underwent strong and rapid changes indicative of intense clonal selection. Differences in their host associations suggest that these shifts may partly be caused by changes in the abundance of annual host plants. Other selective factors of potential importance are also discussed. New, sexually produced genotypes made a minor contribution to clonal diversity, consistent with the observed heterozygote excess characteristic of predominantly asexual populations in M. persicae.     

Fluctuating Selection,Egg Banks and Population Genetic Structure in Cyclically Parthenogenetic Species

Associations between neutral genetic markers and genes under selection have been suggested to explain the population genetic structure of neutral genes in cyclically parthenogenetic freshwater invertebrates. A simulation model was constructed in order to analyse the extrapolated consequences of observed fluctuations in genotype frequencies in Daphnia, in the presence of egg banks. When of sufficient depth and magnitude, egg banks in combination with fluctuating selection were shown to maintain genetic variation within populations indefinitely. The level of equilibrium diversity increased with the depth and magnitude of the banks, and with intensity of selection. The same threshold was responsible for genetic differentiation between populations, which was independent of migration rate, and which was attained very rapidly following initial Hardy–Weinberg equilibrium. In the absence of selection, egg banks increased the effective size of local populations, thereby decreasing genetic differentiation at migration-drift equilibrium. These results suggest that egg banks are crucial to the genetic structure in the presence of fluctuating selective pressures, but more data are needed if this knowledge is to be used in an improved general understanding of the genetic structure of cyclically parthenogenetic species.     

Extremely low effective population sizes, genetic structuring and reduced genetic diversity in a threatened bumblebee species, Bombus sylvarum (Hymenoptera: Apidae)

Habitat fragmentation may severely affect survival of social insect populations as the number of nests per population, not the number of individuals, represents population size, hence they may be particularly prone to loss of genetic diversity. Erosion of genetic diversity may be particularly significant among social Hymenoptera such as bumblebees (Bombus spp.), as this group may be susceptible to diploid male production, a suggested direct cost of inbreeding. Here, for the first time, we assess genetic diversity and population structuring of a threatened bumblebee species (Bombus sylvarum) which exists in highly fragmented habitat (rather than oceanic) islands. Effective population sizes, estimated from identified sisterhoods, were very low (range 21-72) suggesting that isolated populations will be vulnerable to loss of genetic variation through drift. Evidence of significant genetic structuring between populations (theta = 0.084) was found, but evidence of a bottleneck was detected in only one population. Comparison across highly fragmented UK populations and a continental population (where this species is more widespread) revealed significant differences in allelic richness attributable to a high degree of genetic diversity in the continental population. While not directly related to population size, this is perhaps explained by the high degree of isolation between UK populations relative to continental populations. We suggest that populations now existing on isolated habitat islands were probably linked by stepping-stone populations prior to recent habitat loss.