Genetic drift in an infinite population. The pseudohitchhiking model

Selected substitutions at one locus can induce stochastic dynamics that resemble genetic drift at a closely linked neutral locus. The pseudohitchhiking model is a one-locus model that approximates these effects and can be used to describe the major consequences of linked selection. As the changes in neutral allele frequencies when hitchhiking are rapid, diffusion theory is not appropriate for studying neutral dynamics. A stationary distribution and some results on substitution processes are presented that use the theory of continuous-time Markov processes with discontinuous sample paths. The coalescent of the pseudohitchhiking model is shown to have a random number of branches at each node, which leads to a frequency spectrum that is different from that of the equilibrium neutral model. If genetic draft, the name given to these induced stochastic effects, is a more important stochastic force than genetic drift, then a number of paradoxes that have plagued population genetics disappear.     

Determinants of web spider species diversity: Vegetation structural diversity vs. prey availability

Summary The hypotheses that vegetation structural diversity and prey availability determine alpha diversity were examined for scrub- and meadow-inhabiting web spider species assemblages along elevational gradients in Costa Rica and California. Prey availabilities were estimated by sticky trap catches, using only the orders and size classes of insects actually captured by the spiders. The measured component of vegetation structural diversity was the maximum tip height in 20 cm increments from 0 to 2.0 m. Spider species diversity and vegetation tip height diversity were both expressed by the Inverse Simpson Index. Web spider species diversity is highly significantly correlated with vegetation tip height diversity. Prey availability is not a significant predictor of web spider species diversity in these habitats.U.S. Department of Agriculture, Biological Control of Insects Research Laboratory, Agriculture Research Service, Columbia, MO 65205, USA     

FXR1, an autosomal homolog of the fragile X mental retardation gene.

Fragile X mental retardation syndrome, the most common cause of hereditary mental retardation, is directly associated with the FMR1 gene at Xq27.3. FMR1 encodes an RNA binding protein and the syndrome results from lack of expression of FMR1 or expression of a mutant protein that is impaired in RNA binding. We found a novel gene, FXR1, that is highly homologous to FMR1 and located on chromosome 12 at 12q13. FXR1 encodes a protein which, like FMR1, contains two KH domains and is highly conserved in vertebrates. The 3' untranslated regions (3'UTRs) of the human and Xenopus laevis FXR1 mRNAs are strikingly conserved (approximately 90% identity), suggesting conservation of an important function. The KH domains of FXR1 and FMR1 are almost identical, and the two proteins have similar RNA binding properties in vitro. However, FXR1 and FMR1 have very different carboxy-termini. FXR1 and FMR1 are expressed in many tissues, and both proteins, which are cytoplasmic, can be expressed in the same cells. Interestingly, cells from a fragile X patient that do not have any detectable FMR1 express normal levels of FXR1. These findings demonstrate that FMR1 and FXR1 are members of a gene family and suggest a biological role for FXR1 that is related to that of FMR1.     

X chromosome regulation of autosomal gene expression in bovine blastocysts

Although X chromosome inactivation in female mammals evolved to balance the expression of X chromosome and autosomal genes in the two sexes, female embryos pass through developmental stages in which both X chromosomes are active in somatic cells. Bovine blastocysts show higher expression of many X genes in XX than XY embryos, suggesting that X inactivation is not complete. Here, we reanalyzed bovine blastocyst microarray expression data from a network perspective with a focus on interactions between X chromosome and autosomal genes. Whereas male-to-female ratios of expression of autosomal genes were distributed around a mean of 1, X chromosome genes were clearly shifted towards higher expression in females. We generated gene coexpression networks and identified a major module of genes with correlated gene expression that includes female-biased X genes and sexually dimorphic autosomal genes for which the sexual dimorphism is likely driven by the X genes. In this module, expression of X chromosome genes correlates with autosome genes, more than the expression of autosomal genes with each other. Our study identifies correlated patterns of autosomal and X-linked genes that are likely influenced by the sexual imbalance of X gene expression when X inactivation is inefficient.     

Nucleotide diversity in Silene latifolia autosomal and sex-linked genes

The plant Silene latifolia has separate sexes and sex chromosomes, and is of interest for studying the early stages of sex chromosome evolution, especially the evolution of non-recombining regions on the Y chromosome. Hitch-hiking processes associated with ongoing genetic degeneration of the non-recombining Y chromosome are predicted to reduce Y-linked genes'' effective population sizes, and S. latifolia Y-linked genes indeed have lower diversity than X-linked ones. We tested whether this represents a true diversity reduction on the Y, versus the alternative possibility, elevated diversity at X-linked genes, by collecting new data on nucleotide diversity for autosomal genes, which had previously been little studied. We find clear evidence that Y-linked genes have reduced diversity. However, another alternative explanation for a low Y effective size is a high variance in male reproductive success. Autosomal genes should then also have lower diversity than expected, relative to the X, but this is not found in our loci. Taking into account the higher mutation rate of Y-linked genes, their low sequence diversity indicates a strong effect of within-population hitch-hiking on the Y chromosome.     

Arthropod diversity of exotic vs. native Robinia species in northern Arizona

1 Arthropods were collected on native locust, Robinia neomexicana A. Gray, and exotic Robinia pseudoacacia L. in northern Arizona over a 2‐year period to determine the number of arthropod species and number of individuals present. 2 More arthropod species were found on the native (251) than on the exotic Robinia (174). 3 Greater species diversity was likewise found on the native than the exotic. The five most numerous insects collected each year accounted for 81% to 91% of the total number collected on the exotic and native Robinia in 1997 and 1998. Only 12 species occurred on both the native and exotic Robinia in both years. 4 These findings are discussed in the context of using exotic trees in plantations and ecological theory regarding rates of arthropod species accumulation on exotic hosts.     

A model of onshore-offshore change in faunal diversity

Onshore-offshore patterns of faunal change occurred at many taxonomic scales during the Paleozoic Era, ranging from replacement of the Cambrian evolutionary fauna by the Paleozoic fauna to the environmental expansion of many orders and classes. A simple mathematical model is constructed to investigate such change. The environmental gradient across the marine shelf-slope is treated as a linear array of discrete habitats, each of which holds a set number of species, as observed in the fossil record. During any interval of time, some portion of the species in each habitat becomes extinct by background processes, with rates of extinction varying among both clades and habitats, as also observed in the record. After extinction, species are replaced from within the habitat and from immediately adjacent habitats, with proportions dependent on surviving species. This model leads to the prediction that extinction-resistant clades will always diversify at the expense of extinction-prone clades. But if extinction intensity is highest in nearshore habitats, extinction-resistant clades will expand preferentially in the onshore direction, build up diversity there, and then diversify outward toward the offshore. Thus, onshore-offshore patterns of diversification may be the expectation for faunal change quite independently of whether or not clades originate onshore. When the model is parameterized for Paleozoic trilobites and brachiopods, numerical solutions exhibit both a pattern of faunal change and a time span for diversification similar to that seen in the fossil record. They also generate structure similar to that seen in global diversification, including logistic patterns of growth, declining origination but constant extinction within clades through time, and declining overall extinction across clades through time.     

A loss-of-function model for cystogenesis in human autosomal dominant polycystic kidney disease type 2.

Autosomal dominant polycystic kidney disease (ADPKD) is genetically heterogeneous, with at least three chromosomal loci (PKD1, PKD2, and PKD3) that account for the disease. Mutations in the PKD2 gene, on the long arm of chromosome 4, are expected to be responsible for approximately 15% of cases of ADPKD. Although ADPKD is a systemic disease, it shows a focal expression, because <1% of nephrons become cystic. A feasible explanation for the focal nature of events in PKD1, proposed on the basis of the two-hit theory, suggests that cystogenesis results from the inactivation of the normal copy of the PKD1 gene by a second somatic mutation. The aim of this study is to demonstrate that somatic mutations are present in renal cysts from a PKD2 kidney. We have studied 30 renal cysts from a patient with PKD2 in which the germline mutation was shown to be a deletion that encompassed most of the disease gene. Loss-of-heterozygosity (LOH) studies showed loss of the wild-type allele in 10% of cysts. Screening of six exons of the gene by SSCP detected eight different somatic mutations, all of them expected to produce truncated proteins. Overall, >/=37% of the cysts studied presented somatic mutations. No LOH for the PKD1 gene or locus D3S1478 were observed in those cysts, which demonstrates that somatic alterations are specific. We have identified second-hit mutations in human PKD2 cysts, which suggests that this mechanism could be a crucial event in the development of cystogenesis in human ADPKD-type 2.     

Segregation analysis of autosomal fragile sites in three families with the fragile X chromosome.

Fragile sites on chromosomes 9, at 9p21, 10, at 10q25 and 12, at 12q24, were found in the lymphocytes of some members of three families during the study for detection of a fragile X chromosome. The sites were found to be heritable and folato-sensitive. The genetic implications of these results are discussed.     

A note on the essential parameters of the two-allele autosomal locus model

A resolution of the parameter problem for the two-allele autosomal locus (TAAL) model has been presented. It was shown that three are four essential parameters which describe the model, by examination of the joint probability for sibs with specified parental phenotypes. This equation together with previously derived prevalence relationships uniquely specifices all parameters of the model except for the singular case VA = 0.     

The NZB X SWR model of lupus nephritis. II. Autoantibodies deposited in renal lesions show a distinctive and restricted idiotypic diversity

The F1 progeny (SNF1) derived from crossing autoimmune NZB with normal SWR mice uniformly develop lethal glomerulonephritis in marked contrast to the NZB parents. In the preceding paper we found qualitative and idiotypic differences between the anti-DNA antibodies produced by the SNF1 mice and their NZB parents. We identified two clusters of interrelated cross-reactive idiotypic (CRI) families among the SNF1-derived autoantibodies. Here we analyzed the idiotypic profile of the broad spectrum of immunoglobulins deposited in the nephritic kidneys of SNF1 mice and found a restricted idiotypic diversity. To establish that the autoantibody idiotypes detected in the renal lesions were not there as a result of nonspecific trapping, five separate batches of kidney eluates obtained from 100 SNF1 kidneys were analyzed. Both during early and late stages of nephritis, the predominant and consistent idiotypic markers of antibodies in the renal lesion of SNF1 mice were those shared by the two clusters of anti-DNA CRI families. We have termed these nephritogenic idiotypic markers collectively as idiotypes-lupus nephritis-SNF1 or IdLNF1. The Id564 family that encompasses a set of SNF1-derived highly cationic anti-DNA antibodies bearing the normal SWR parent's allotype was more prominently represented in the SNF1 kidneys with early nephritis. Although cationic antibodies were prevalent, the IdLNF1 markers were present on both cationic and anionic or neutral antibodies in the renal lesions of SNF1 mice, and the Ig allotypes of both parents were equally represented in those nephritogenic antibodies. The IdLNF1 positive family of antibodies were also found in high levels in the sera of old SNF1 mice, but they could not be detected in the sera of NZB or SWR mice, nor were they present in the immunoglobulins deposited in the kidneys of rare old NZB mice. The results suggest that select families of nephritogenic idiotypes that are dormant in the autoimmune NZB and the normal SWR parents become expressed in the SNF1 progeny due to genetic and immunoregulatory defects.     

Genetic diversity in diploid vs. tetraploid Rorippa amphibia (Brassicaceae)

The frequency of polyploidy increases with latitude in the Northern Hemisphere, especially in deglaciated, recently colonized areas. The cause or causes of this pattern are largely unknown, but a greater genetic diversity of individual polyploid plants due to a doubled genome and/or a hybrid origin is seen as a likely factor underlying selective advantages related to life in extreme climates and/or colonization ability. A history of colonization in itself, as well as a recent origin, and possibly a limited number of polyploidization events would all predict less genetic diversity in polyploids than in diploids. The null hypothesis of higher gene diversity in polyploids has to date hardly been quantified and is here tested in self-incompatible Rorippa amphibia (Brassicaceae). The species occurs in diploid and tetraploid forms and displays clear geographical polyploidy in Europe. On the basis of eight microsatellite loci it can be concluded that the level of gene diversity is higher in tetraploids than in diploids, to an extent that is expected under neutral evolution when taking into account the larger effective population size in the doubled cytotype. There is thus no evidence for reduced genetic diversity in the tetraploids. The evidence presented here may mean that the tetraploids' origin is not recent, has not been affected by bottlenecks and/or that tetraploids were formed multiple times while an effect of introgression may also play a role.     

Identifying the source of species invasions: sampling intensity vs. genetic diversity

Population geneticists and community ecologists have long recognized the importance of sampling design for uncovering patterns of diversity within and among populations and in communities. Invasion ecologists increasingly have utilized phylogeographical patterns of mitochondrial or chloroplast DNA sequence variation to link introduced populations with putative source populations. However, many studies have ignored lessons from population genetics and community ecology and are vulnerable to sampling errors owing to insufficient field collections. A review of published invasion studies that utilized mitochondrial or chloroplast DNA markers reveals that insufficient sampling could strongly influence results and interpretations. Sixty per cent of studies sampled an average of less than six individuals per source population, vs. only 45% for introduced populations. Typically, far fewer introduced than source populations were surveyed, although they were sampled more intensively. Simulations based on published data forming a comprehensive mtDNA haplotype data set highlight and quantify the impact of the number of individuals surveyed per source population and number of putative source populations surveyed for accurate assignment of introduced individuals. Errors associated with sampling a low number of individuals are most acute when rare source haplotypes are dominant or fixed in the introduced population. Accuracy of assignment of introduced individuals is also directly related to the number of source populations surveyed and to the degree of genetic differentiation among them ( F _ST). Incorrect interpretations resulting from sampling errors can be avoided if sampling design is considered before field collections are made.     

A spider diversity model for the Caucasus Ecoregion

Precise information on spatial patterns of species richness and endemic species distribution is important for effective species conservation. In the Caucasus Ecoregion such information is virtually non-existent for invertebrate taxa. Using occurrence data from a large database we calculated species distribution models with the GARP algorithm for 471 spider species to visualize the diversity distribution of spider species in this region. Overall species diversity was highest in mountain forests of the North Caucasus, east-central Georgia, the southern slopes of the eastern Great Caucasus and south-east Azerbaijan. A regression tree analysis Chi squared automatic interaction detector method revealed the mean temperature of the driest quarter and precipitation parameters to be the main environmental factors shaping these patterns. Diversity of endemic species was correlated with overall species diversity but hotspots of endemic species (10+ percent of all species) exists in high-mountain areas, suggesting post-glacial speciation events in the high mountains as the main sources of high endemism in Caucasus. Further information on the spatial distribution of species diversity of invertebrate taxa in the Caucasus Ecoregion is needed to improve conservation efforts in this biodiversity hotspot.     

Aspermia,associated with a presumably balanced X/autosomal translocation

Summary A new case of X/autosome translocation in a male patient is described. Azoospermia and Klinefelter like stigmata can be explained as a consequence of the balanced translocation, or by disturbed X-chromosomal inactivation during spermiogenesis.

---

Zusammenfassung Es wird über einen neuen Fall einer X/Autosom-Translokation beim Mann berichtet. Azoospermie und Klinefelter-ähnliche Stigmata können unmittelbar auf die balancierte Translokation zurückgeführt werden oder Folge einer durch die Translokation gestörten X-chromosomalen Inaktivierung während der Spermiogenese sein.

     

Genetic diversity vs geographic distribution of five congeneric caddisflies

We compared the genetic structure and diversity offive Cheumatopsyche (Trichoptera:Hydropsychidae) species from Upper Three Runs Creek inSouth Carolina to analyze the relationship betweengenetic variability and potential gene flow (i.e.,geographic distribution) in a group of loticmacroinvertebrates. Among these species is an endemicto the stream (Cheumatopsyche richardsoni), asoutheastern U.S.A. endemic (C. edista), andthree widely distributed species (C. pasella,C. pettiti, and C. pinaca). Usingcellulose acetate plates, we reliably scored 19presumptive allozyme loci for each species. C. richardsoni and C. pettiti were the leastgenetically variable taxa, C. pasella and C. pinaca the most, and C. edista fell inbetween. Therefore, unless this C. pettitipopulation is not representative of the species ingeneral, the genetic diversity of C. richardsoniand C. edista fall within the range exhibited byother congeners. In turn, each species’ geneticdiversity is evidently not correlated to its relativegeographic distribution. Four species (all but C. pettiti) had moderate to high proportions ofpolymorphic loci in Hardy-Weinberg disequilibria, thecause of which is likely one of three factors: (1) eachspecies experiences disruptive selection, (2) weinadvertently sampled adults from more than onegenetically distinct stream population, or (3) eachspecies is divided into partially reproductivelyisolated subpopulations within the stream. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic diversity in a seed production population vs. natural populations of Sitka Spruce

Isozyme analysis was applied to estimate the level of variation and the genetic structure of a seed-production population (i.e., seed orchard) and 10 range-wide natural populations of Sitka spruce (Picea sitchensis (Bong.) Carr.). Gene diversity and heterozygosity estimates were comparatively high in both the seed orchard and the natural populations studied. The seed orchard population showed a significantly higher number of alleles per locus and percentage of polymorphic loci. Though not significant, mean heterozygosity of the seed orchard was higher than that observed for all natural populations. Genetic distance analysis indicated that the seed-orchard population was genetically similar to three natural populations from which the parent trees were selected. Parent trees sampling breadth has been identified as the major cause for the observed increased level. The impact of recurrent selection and seed orchard biology and management on maintaining the genetic diversity is discussed.