Snapshot of DNA methylation changes associated with hybridization in Xenopus

Hybridization often results in dramatic genome reconfigurations including epigenetic changes that control gene expression. Here we survey methylation patterns of interspecific Xenopus F1 hybrids relative to parental species X. laevis and X. muelleri, using methyl-sensitive amplification polymorphisms (MSAPs). Out of a total of 546 MSAP markers, 364 were effective in elucidating the difference in methylation patterns between the hybrids and the parental species. Principal coordinate analysis of methylated fragments revealed four distinct clusters with the two parental species separate from hybrid males and females. On average, hybrids were characterized by a higher proportion (70.6%) of methylated fragments compared with the parental species (64.5%), and this difference was consistent with previously observed disruptions of hybrid transcriptomes. The proportion of methylated fragments did not correlate with variation in genome size, as measured with flow cytometry. The levels of methylation in sterile hybrid males (73.8%) were higher than in fertile hybrid females (68.6%), but this difference was not statistically significant. A total of 76 methylated fragments (20.9%) were hybrid-unique, presumably originating from methylation alterations in hybrid genomes.

Sensory Components of Behavioral Isolation Between Zimbabwe and Cosmopolitan Drosophila Melanogaster

Successful reproduction requires males and females from the same species to recognize and prefer each other over individuals of other species. Mate recognition is mediated through the sensory systems, and one way speciation can occur is through behavioral isolation via sensory cues.Drosophila melanogasterfemales from central Africa (the "Zimbabwe" morph) prefer to mate with Zimbabwe males over males from otherDrosophilastrains ("Cosmopolitan" strains). Cosmopolitan females typically show little or no preference towards Cosmopolitan males. We hypothesize that alterations in one or more cues detected by the sensory system underlie the mating preferences of Zimbabwe females. Here, we investigate the relative contributions of three sensory factors (olfaction, vision, and hearing) to female mating preference using a number of Zimbabwe strains. Our findings suggest that auditory and visual cues are the most critical to this mate choice preference phenomenon. These results elucidate plausible mechanisms underlying incipient speciation inDrosophila.

The acylphosphatase (Acyp) alleles associate with male hybrid sterility in Drosophila

Hybrid defects are believed to result from genetic incompatibilities between genes that have evolved in separate parental lineages. These genetic dysfunctions on the hybrid genomic background, also known as Dobzhansky-Muller incompatibilities, can be an incipient signature of speciation, and as such - a subject of active research. Here we present evidence that Acyp locus (CG16870) that encodes acylphosphatase, a small enzyme that catalyzes the hydrolysis of acylphosphates and participates in ion transport across biological membranes, is involved in genetic incompatibilities leading to male sterility in hybrids between Drosophila simulans and D. mauritiana. There is a strong association between Acyp alleles (genotype) and the sterility/fertility pattern (phenotype), as well as between the phenotype, the genotype and its transcriptional activity. Allele-specific expression in hybrids heterozygous for Acyp suggests a cis-type regulation of this gene, where an allele from one of the parental species (D. simulans) is consistently overexpressed.

Testis-derived microRNA profiles of African clawed frogs (Xenopus) and their sterile hybrids

Gene regulation was long predicted to play a vital role in speciation and species divergence. Only recently with the advent of new technologies, however, has it been possible to address the question of the relative contributions of different mechanisms of gene expression to the evolution of phenotypic diversity. Here we broaden the question and ask whether microRNAs, a large class of small regulatory RNAs, play a role in reproductive isolation between species by contributing to hybrid male sterility. MicroRNAs from the testes of clawed frogs (Xenopus) were extracted and the expression profiles of sterile hybrids were compared with males of a parental species. Hybrid testes were largely microRNA-depleted relative to those of nonhybrids, and this pattern was validated with quantitative RT-PCR. A number of candidate differential microRNAs from this study have previously been described as testis-specific in the mouse, suggesting that microRNA structural conservation may be associated with functional retention.

Physiological sex predicts hybrid sterility regardless of genotype

Reproductive isolation between biological species is characterized by Haldane's rule, which states that the heterogametic sex (XY or ZW) suffers the most dysfunctional effects of hybridization. It has been hypothesized that, in addition to X-linked recessive genes, Haldane's rule also reflects the faster evolution of genes related to male reproduction (faster-male evolution). We used sex-reversed hybrid Xenopus to test faster-male evolution by examining the fertility of sex-reversed individuals with the genotype of the inverse phenotypic sex. Hybrid males are sterile and hybrid females are fertile irrespective of their genotypic sex. Gene expression profiles match these adult phenotypes, and our results demonstrate that faster-male evolution is the most likely mechanism producing hybrid male sterility.

Sterility and gene expression in hybrid males of Xenopus laevis and X. muelleri

BACKGROUND

Reproductive isolation is a defining characteristic of populations that represent unique biological species, yet we know very little about the gene expression basis for reproductive isolation. The advent of powerful molecular biology tools provides the ability to identify genes involved in reproductive isolation and focuses attention on the molecular mechanisms that separate biological species. Herein we quantify the sterility pattern of hybrid males in African Clawed Frogs (Xenopus) and apply microarray analysis of the expression pattern found in testes to identify genes that are misexpressed in hybrid males relative to their two parental species (Xenopus laevis and X. muelleri).

METHODOLOGY/PRINCIPAL FINDINGS

Phenotypic characteristics of spermatogenesis in sterile male hybrids (X. laevis x X. muelleri) were examined using a novel sperm assay that allowed quantification of live, dead, and undifferentiated sperm cells, the number of motile vs. immotile sperm, and sperm morphology. Hybrids exhibited a dramatically lower abundance of mature sperm relative to the parental species. Hybrid spermatozoa were larger in size and accompanied by numerous undifferentiated sperm cells. Microarray analysis of gene expression in testes was combined with a correction for sequence divergence derived from genomic hybridizations to identify candidate genes involved in the sterility phenotype. Analysis of the transcriptome revealed a striking asymmetric pattern of misexpression. There were only about 140 genes misexpressed in hybrids compared to X. laevis but nearly 4,000 genes misexpressed in hybrids compared to X. muelleri.

CONCLUSIONS/SIGNIFICANCE

Our results provide an important correlation between phenotypic characteristics of sperm and gene expression in sterile hybrid males. The broad pattern of gene misexpression suggests intriguing mechanisms creating the dominance pattern of the X. laevis genome in hybrids. These findings significantly contribute to growing evidence for allelic dominance in hybrids and have implications for the mechanism of species differentiation at the transcriptome level.

Gene expression polymorphism inDrosophilapopulations

Although changes in gene expression have long been recognized as critical to evolutionary processes, the extent of natural polymorphism in gene expression has yet to be assessed, thus opening a new area of active research. We present microarray and quantitative real-time polymerase chain reaction (RT-PCR) data from Cosmopolitan and Zimbabwe morphs of Drosophila melanogaster. These morphs provide a useful model for investigations into the incipient stages of speciation because Zimbabwe females tend to preferentially mate with their own males and discriminate against Cosmopolitan males, while Cosmopolitan females mate indiscriminately. We analysed expression profiles from heads of mated and nonmated females and identified 45 candidate genes whose expression levels were associated with the behavioural morphs and were modified by mating. Genes with altered transcription levels were randomly distributed across the genome and fell into diverse categories of biological activities. Several candidate genes, such as desaturase2 and Odorant receptor 63a, were additionally subjected to quantitative RT-PCR analysis. Notably, desaturase2, which has been invoked to play a role in sexual isolation between Cosmopolitan and Zimbabwe D. melanogaster/races/strains and predicted to be translational-inactive in Cosmopolitan due to a major deletion, was found to be up-regulated in Zimbabwe and down-regulated, but still expressed, in Cosmopolitan.

RNA world - the dark matter of evolutionary genomics

For a long time, molecular evolutionary biologists have been focused on DNA and proteins, whereas RNA has lived in the shadow of its famous chemical cousins as a mere intermediary. Although this perspective has begun to change since genome-wide transcriptional profiling was successfully extended to evolutionary biology, it still echoes in evolutionary literature. In this mini-review, new developments of RNA biochemistry and transcriptomics are brought to the attention of evolutionary biologists. In particular, the unexpected abundance and functional significance of noncoding RNAs is briefly reviewed. Noncoding RNAs control a remarkable range of biological pathways and processes, all with obvious fitness consequences, such as initiation of translation, mRNA abundance, transposon jumping, chromosome architecture, stem cell maintenance, development of brain and muscles, insulin secretion, cancerogenesis and plant resistance to viral infections.

Sex-biased gene expression in a ZW sex determination system

Studies of the transcriptome have shown that a substantial fraction of interspecific differences in gene expression is the result of sex-biased gene expression. These results suggest that sex-dependent selection may be an important force in generating differences between species but to date all studies have focused on Drosophila. We examined a sample of the transcriptome in the gonads of two species of Xenopus to provide an additional test of how sex-biased gene expression may contribute to differences in gene expression between species. In contrast to Drosophila, Xenopus provides an example of a ZW system with morphologically indistinguishable sex chromosomes. About 81% of the transcriptome was differentially expressed between X. laevis and X. muelleri and there were more genes that were male-biased compared to the number of genes that were female-biased or non-sex-biased. While there were more genes up-regulated in males of Xenopus, the largest magnitude difference in expression between species occurred in female-biased genes, and male-biased genes were proportionally more abundant for the smallest changes in expression between species. Our results suggest that more genes have a role in the function of the testis compared to the ovary and female-biased genes play a principle role in expression divergence between species. These results differ from those in the Drosophila XY system in that more female-biased genes had >4-fold difference of expression between species than male-biased genes, suggesting that ZW sex chromosomes may facilitate enhanced gene expression divergence between species.

Adaptive differentiation of thermotolerance in Drosophila along a microclimatic gradient

We examined whether a remarkable occurrence - the physiological evolution of two Drosophila melanogaster populations, despite a spatial separation of only 100-400 m, was idiosyncratic and temporary, or persisted over multiple years. We ascertained the high-temperature tolerance of Drosophila descended from populations on the north-facing slope (NFS) and south-facing slope (SFS) of 'Evolution Canyon' (Lower Nahal Oren, Mt Carmel, Israel), which were collected in 1997, 1999, and 2000. Results for these Drosophila uniformly resembled other studies in many respects: an inverse relationship between survival and heat-shock temperature, male-female differences in thermotolerance, and inducible thermotolerance. Importantly, for all years of collection, SFS flies consistently exceeded NFS flies in basal and inducible thermotolerance after diverse heat shocks, with and without thermal pretreatment, and whether isofemale lines, synthetic populations, or inbred lines were compared. Inbred lines, however, had lower thermotolerance than outbred lines. Several nonexclusive processes may explain the evolution of such physiological differentiation.

Association of misexpression with sterility in hybrids of Drosophila simulansand D. mauritiana

Recent studies have identified genes associated with hybrid sterility and other hybrid dysfunctions, but the consequences of introgressions of these "speciation genes" are often poorly understood. Previously, we identified a panel of genes that are underexpressed in sterile male hybrids of Drosophila simulans and D. mauritiana relative to pure species. Here, we build on this reverse-genetics approach to demonstrate that the underexpression of at least five of these genes in hybrids is associated with hybrid sterility and that these five genes are coordinately regulated. We map one upstream regulator of these genes to a region previously shown to harbor one or more factors causing hybrid sterility. Finally, we show that the genes underexpressed in hybrids are often highly conserved, as might be predicted for downstream targets of the genetic changes that cause hybrid sterility. This approach integrates forward genetics with reverse genetics to show a proximate consequence of the introgression of particular hybrid sterility-conferring regions between species: underexpression of genes necessary for normal spermatogenesis.

Characterization of a male-predominant antisense transcript underexpressed in hybrids of Drosophila pseudoobscura and D. persimilis

Characterizing genes that are misregulated in hybrids may elucidate the genetic basis of hybrid sterility or other hybrid dysfunctions that contribute to speciation. Previously, a small segment of a male-predominant transcript that is underexpressed in adult male hybrids of Drosophila pseudoobscura and D. persimilis relative to pure species was identified in a differential display screen. Here, we obtained the full sequence of this 1330-bp transcript and determined that it is an antisense message with high sequence similarity to the D. melanogaster TRAP100 gene, part of the Mediator protein complex that regulates transcriptional initiation during development. Both the sense and the antisense messages are transcribed in D. pseudoobscura, but only the sense message (TRAP100) is transcribed in D. melanogaster complex species. Unlike the antisense message, the sense message is transcribed similarly in D. pseudoobscura males and females and in hybrids of D. pseudoobscura and D. persimilis. The high sequence similarity between distantly related species suggests that the sense message is functionally constrained within the genus. We speculate that the antisense transcript may have evolved a role in male-specific post-transcriptional regulation of TRAP100 in the D. pseudoobscura lineage and that its underexpression in sterile hybrid males may cause an overproduction of TRAP100 protein, possibly yielding deleterious effects.

Genome-wide patterns of expression in Drosophila pure species and hybrid males

One of the most fundamental questions for understanding the origin of species is why genes that function to cause fertility in a pure-species genetic background fail to produce fertility in a hybrid genetic background. A related question is why the sex that is most often sterile or inviable in hybrids is the heterogametic (usually male) sex. In this survey, we have examined the extent and nature of differences in gene expression between fertile adult males of two Drosophila species and sterile hybrid males produced from crosses between these species. Using oligonucleotide microarrays and real-time quantitative polymerase chain reaction, we have identified and confirmed that differences in gene expression exist between pure species and hybrid males, and many of these differences are quantitative rather than qualitative. Furthermore, genes that are expressed primarily or exclusively in males, including several involved in spermatogenesis, are disproportionately misexpressed in hybrids, suggesting a possible genetic cause for their sterility.

Modification of heat-shock gene expression in Drosophila melanogaster populations via transposable elements

We report multiple cases in which disruption of hsp70 regulatory regions by transposable element (TE) insertions underlies natural variation in expression of the stress-inducible molecular chaperone Hsp70 in Drosophila melanogaster. Three D. melanogaster populations from different continents are polymorphic for jockey or P element insertions in the promoter of the hsp70Ba gene. All three TE insertions are within the same 87-bp region of hsp70Ba promoter, and we suggest that the distinctive promoter architecture of hsp genes may make them vulnerable to TE insertions. Each of the TE insertions reduces Hsp70 levels, and RNase protection assays demonstrate that such insertions can reduce transcription of the hsp70Ba gene. In addition, the TEs alter two measures of organismal fitness, inducible thermotolerance and female reproductive success. Thus, transposition can create quantitative genetic variation in gene expression within populations, on which natural selection can act.

Evolvability of Hsp70 expression under artificial election for inducible thermotolerance in independent populations of Drosophila melanogaster

To test whether expression of the inducible heat-shock protein Hsp70 increases under selection for inducible thermotolerance in Drosophila melanogaster, we performed artificial selection on replicate sets of Drosophila lines founded from two independent populations. Selection entailed pretreatment at 36 degrees C to induce thermotolerance and Hsp70 expression, followed by a more severe heat shock, whose temperature varied between sexes and among generations to achieve 50% mortality. Inducible thermotolerance increased slowly and continuously in selected lines and was 37%-50% greater than in controls after 10-11 generations. Lines founded from the two populations differed in their coevolution of Hsp70 expression. In lines founded from Evolution Canyon, Israel, Hsp70 level initially increased and thereafter was unchanged; replicate lines exhibited two temporal patterns of response to selection. In lines founded from Australia, Hsp70 levels increased throughout selection. In both cases, however, the increase in Hsp70 level averaged only 15%, suggesting that pleiotropy in Hsp70 function constrains evolutionary increase in its expression.

Genetic evidence for adaptation-driven incipient speciation of Drosophila melanogaster along a microclimatic contrast in "Evolution Canyon," Israel

Substantial genetic differentiation, as great as among species, exists between populations of Drosophila melanogaster inhabiting opposite slopes of a small canyon. Previous work has shown that prezygotic sexual isolation and numerous differences in stress-related phenotypes have evolved between D. melanogaster populations in "Evolution Canyon," Israel, in which slopes 100-400 m apart differ dramatically in aridity, solar radiation, and associated vegetation. Because the canyon's width is well within flies' dispersal capabilities, we examined genetic changes associated with local adaptation and incipient speciation in the absence of geographical isolation. Here we report remarkable genetic differentiation of microsatellites and divergence in the regulatory region of hsp70Ba which encodes the major inducible heat shock protein of Drosophila, in the two populations. Additionally, an analysis of microsatellites suggests a limited exchange of migrants and lack of recent population bottlenecks. We hypothesize that adaptation to the contrasting microclimates overwhelms gene flow and is responsible for the genetic and phenotypic divergence between the populations.

Nonrandom mating in Drosophila melanogaster laboratory populations derived from closely adjacent ecologically contrasting slopes at "Evolution Canyon"

Ecological differentiation of natural populations of Drosophila melanogaster, Drosophila simulans, and another drosophilid, Zaprionus tuberculatus, in "Evolution Canyon," Mount Carmel, Israel, is well established. The fitness complex of D. melanogaster includes oviposition temperature preferences, tolerance to high temperature, drought stress and starvation, and different longevity patterns. This remarkable differentiation has evolved despite small interslope distances (only 100-400 m), within easy dispersal distance. The differences between populations are those expected from genetic adaptation to local microclimates. How such differentiation could evolve and be maintained despite the likelihood of genetic exchange between populations is a challenging question. We hypothesized that interslope microclimatic differences caused strong differential selection for stress tolerance, accompanied by behavioral differentiation (habitat choice and reduced migration rate), reinforced by sexual isolation. Here we report highly significant mate choice by flies from different slopes of the canyon, with preference for sexual partners originating from the same slope. No preferences were found when the sexual partners belonged to different isofemale lines from the same slope.

Expression of the heat-shock protein HSP70 in Drosophila buzzatii lines selected for thermal resistance

The level of HSP70 expression induced by a non-lethal high temperature was examined in lines selected for increased thermal resistance and in corresponding control lines of Drosophila buzzatii, in order to test if selection for high temperature resistance leads to an increased level of HSP70 expression. The lines used were selected for up to 64 generations either as adults or through all larval stages. In adult selection lines, hard selection was implemented every second generation after mild heat hardening. In larval selection lines, larvae were exposed each generation to laboratory "natural" selection. Generally lines selected as adults showed a higher HSP70 expression than did controls, both in third instar larvae and in adults. A strong negative response to selection of HSP70 expression was found in all lines that were selected at cycling temperatures during larval development. The results suggests that a trade off between heat resistance in form of HSP70 expression and fecundity/fertility are responsible for the level of HSP70 expression. The effect of the different methods of selection on HSP70 expression suggests that heat resistance constitutes more than one trait.

High-temperature stress and the evolution of thermal resistance in Drosophila

The evolution of thermal resistance and acclimation is reviewed at the population level using populations and isofemale lines of Drosophila buzzatii and D. melanogaster originating from different climatic regions. In general, ample genetic variation for thermal resistance was found within and among populations. A rough correlation between the climate of origin and thermal resistance was apparent. Acclimation at a non-lethal temperature led to a significant increase in survival after heat shock, and recurrent acclimation events generally increased survival even further. Acclimation effects lasted over several days, but this effect decreased gradually with time since acclimation. Protein studies showed that the concentration of Hsp70 in adult flies is greatly increased by acclimation and thereafter gradually decreases with time. For populations with relatively high survival at one life stage, survival often was low at other life stages. Furthermore, selection on different life stages showed that a selection response in one life stage did not necessarily result in a correlated response in another. These observations indicate that different mechanisms or genes at least in part are responsible for or are expressed at different developmental stages. Selection for increased resistance was successful despite low heritabilities for the trait. Survival and fertility were compared between acclimated and non-acclimated flies, and a cost of expressing the "heat shock response" was identified in that increased survival after acclimation was accompanied by reduced fertility. The relative costs increased under nutritional stress. Metabolic rate was genetically variable but did not correlate with temperature resistance. The more resistant lines, however, often had shorter developmental time. Inbreeding reduced thermal stress tolerance of adult flies, but it did not reduce tolerance of embryos that possibly are exposed to strong natural selection for thermal stress resistance. In general, inbreeding may reduce stress resistance, and thus multiple stressful events may account for increased inbreeding depression in harsh environments.

Perception of parental sex guilt and sexual behavior and arousal of college students

The present study examined the relationship between perceptions of parental sex guilt and the sexual arousability and sexual activity of 63 single male and 89 single female undergraduates. The results indicate that the same sex parent is perceived as more influential in determining the sex guilt of the child whereas the perceived sex guilt of the mother may have more influence on the sexual arousability of the son and the sexual activity of the daughter.