Simple repetitive sequences are associated with differentiation of the sex chromosomes in the guppy fish

Summary Hybridization of restriction enzymedigested genomic guppy (Poecilia reticulata, Poeciliidae) DNA with the oligonucleotide probe (GACA)₄ revealed a male-specific simple tandem repeat locus, which defines the Y chromosome in outbred populations. The related (GATA)₄ probe identifies certain males with the red color phenotype. In contrast only in two out of eight laboratory guppy strains was the typical (GACA)₄ band observed. By specific staining of the constitutive heterochromatin one pair of chromosomes could also be identified as the sex chromosomes, confirming the XX/XY mechanism of sex determination. All males exhibit Y chromosomes with a large region of telomeric heterochromatin. Hybridization in situ with nonradioactively labeled oligonucleotide probes localized the (GACA)_n repeats to this heterochromatic portion. Together these results may be regarded as a recent paradigm for the differentiation of heteromorphic sex chromosomes from a pair of autosomes during the course of evolution. According to the fish model system, this may have happened in several independent consecutive steps.     

Geographic variation in multiple paternity within natural populations of the guppy (Poecilia reticulata)

Mating can increase an individual''s risk of mortality by predation. In response to predation hazards, males in some species court females less often, but alternatively engage in coerced copulations more frequently and females become less selective. Such predator-mediated shifts in mating tactics may result in higher levels of multiple inseminations in females and, thus, in greater frequencies of females with broods of mixed paternity. We tested this hypothesis using two polymorphic microsatellite loci to estimate conservatively multiple paternity in broods of female guppies (Poecilia reticulata) originating from ten natural populations that have evolved under different fish predation regimes in Trinidad. The frequency of broods that were multiply sired was significantly greater on average in populations experiencing high predation pressure compared to populations experiencing a relatively low predation risk. These results suggest that the intensity of male sperm competition covaries geographically with predation pressure in this species and that the local risk of predation mediates the opportunity for sexual selection within populations.     

Divergent selection for opsin gene variation in guppy (Poecilia reticulata) populations of Trinidad and Tobago

The guppy is known to exhibit remarkable interindividual variations in spectral sensitivity of middle to long wavelength-sensitive (M/LWS) cone photoreceptor cells. The guppy has four M/LWS-type opsin genes (LWS-1, LWS-2, LWS-3 and LWS-4) that are considered to be responsible for this sensory variation. However, the allelic variation of the opsin genes, particularly in terms of their absorption spectrum, has not been explored in wild populations. Thus, we examined nucleotide variations in the four M/LWS opsin genes as well as blue-sensitive SWS2-B and ultraviolet-sensitive SWS1 opsin genes for comparison and seven non-opsin nuclear loci as reference genes in 10 guppy populations from various light environments in Trinidad and Tobago. For the first time, we discovered a potential spectral variation (180 Ser/Ala) in LWS-1 that differed at an amino acid site known to affect the absorption spectra of opsins. Based on a coalescent simulation of the nucleotide variation of the reference genes, we showed that the interpopulation genetic differentiation of two opsin genes was significantly larger than the neutral expectation. Furthermore, this genetic differentiation was significantly related to differences in dissolved oxygen (DO) level, and it was not explained by the spatial distance between populations. The DO levels are correlated with eutrophication that possibly affects the color of aquatic environments. These results suggest that the population diversity of opsin genes is significantly driven by natural selection and that the guppy could adapt to various light environments through color vision changes.     

Primers for 12 polymorphic microsatellite DNA loci from the guppy (Poecilia reticulata)

Twelve polymorphic microsatellite DNA loci were isolated from genomic guppy DNA. We assessed the level of genetic diversity for these loci using individuals from five native Trinidadian populations. All the loci were polymorphic although there were considerable differences among loci and populations in allele frequencies. Within populations, the number of alleles ranged from 1 to 22 and observed heterozygosities ranged from 0.000 to 0.990. Allele frequencies differed substantially between populations suggesting divergence.     

Isolation and characterization of 43 microsatellite DNA markers for guppy (Poecilia reticulata)

Thirty‐nine polymorphic microsatellite DNA markers were isolated from the guppy (Poecilia reticulata) genomic library. All of the loci showed moderate allelic variation ranging from two to seven alleles, with observed heterozygosities from 0.000 to 0.938. The microsatellite DNA markers isolated will be available for use in analysis of quantitative trait loci in breeding programmes and for population genetic studies on experimental fish.     

Reasons for the invasive success of a guppy (Poecilia reticulata) population in Trinidad

The introduction of non-native species into new habitats poses a major threat to native populations. Of particular interest, though often overlooked, are introductions of populations that are not fully reproductively isolated from native individuals and can hybridize with them. To address this important topic we used different approaches in a multi-pronged study, combining the effects of mate choice, shoaling behaviour and genetics. Here we present evidence that behavioural traits such as shoaling and mate choice can promote population mixing if individuals do not distinguish between native and foreign conspecifics. We examined this in the context of two guppy (Poecilia reticulata) populations that have been subject to an introduction and subsequent population mixing event in Trinidad. The introduction of Guanapo River guppies into the Turure River more than 50 years ago led to a marked reduction of the original genotype. In our experiments, female guppies did not distinguish between shoaling partners when given the choice between native and foreign individuals. Introduced fish are therefore likely to benefit from the protection of a shoal and will improve their survival chances as a result. The additional finding that male guppies do not discriminate between females on the basis of origin will further increase the process of population mixing, especially if males encounter mixed shoals. In a mesocosm experiment, in which the native and foreign populations were allowed to mate freely, we found, as expected on the basis of these behavioural interactions, that the distribution of offspring genotypes could be predicted from the proportions of the two types of founding fish. This result suggests that stochastic and environmental processes have reinforced the biological ones to bring about the genetic dominance of the invading population in the Turure River. Re-sampling the Turure for genetic analysis using SNP markers confirmed the population mixing process and showed that it is an on-going process in this river and has led to the nearly complete disappearance of the original genotype.     

Marked genetic divergence revealed by allozymes among populations of the guppy Poecilia reticulata (Poeciliidae), in Trinidad

Populations of the guppy Poecilia reticulata from six locations in N. Trinidad were examined by starch gel electrophoresis to estimate their degree of genetic divergence. Variability at seven enzyme-coding loci demonstrated that populations differed markedly in allele frequencies with some allelic substitution between sites (for 23 loci, Nei's mean genetic identity, Ī ranged from 0.869–1.00; the coefficient of gene differentiation, G _ST= 0.086; and the absolute differentiation between populations, _m= 0.044). There was a good correspondence between degree of physical isolation and extent of genetic differentiation, as exemplified by the partitioning of gene diversity (Nei's gene diversity analysis = 66% between river basins; 32% within river basins; 2% within rivers), though there was considerable variability in the contribution of individual loci. Most populations were in Hardy-Weinberg equilibrium, and any significant deviations were due exclusively to heterozygote deficiencies. The patterns of population differentiation are discussed in relation to probable past geological and historical events, and present-day evolutionary forces. Notable among these are previous continental land connections, periodic immigration from N.E. South America, and post-colonization events including differential predation, sexual selection, apparent restricted vagility and small effective population sizes.     

Evidence for the wide distribution of repetitive DNA sequences in the genusStreptomyces

Summary Repeated DNA sequences were detected as rapidly reannealing sequences in the chromosomal DNA of 13 out of 14Streptomyces species using either hypochromicity measurements or hydroxyapatite chromatography. These sequences made up between approximately 4% and 11% of the total DNA of these species; only inStreptomyces rimosus were repeated DNA sequences not detected. The repeated sequences fall into a number of distinct percentage G+C (%G+C) classes, many being of rather low %G+C. Analytical density ultracentrifugation of the DNA of these species indicated satellite bands of low %G+C, and high-resolution thermal denaturation profiles indicated the presence of blocks of DNA of low G+C content too. No such satellite band could be found inStreptomyces coelicolor and no low-%G+C DNA could be detected in its thermal denaturation profile. The possible relationship of this repeated DNA, an unusual occurrence in a procaryote, to genetic instability and genetic control mechanisms inStreptomyces is discussed.     

Heterozygosity and orange coloration are associated in the guppy (Poecilia reticulata)

The good‐genes‐as‐heterozygosity hypothesis predicts that more elaborate male sexual ornaments are associated with higher levels of heterozygosity. Recent theoretical work suggests that such associations are likely to arise in finite, structured populations. We investigated the correlation between multilocus heterozygosity (MLH), which was estimated using 13 microsatellite loci, and male coloration in a wild population of guppies (Poecilia reticulata), a model species in sexual selection research. We found that MLH was a significant predictor of the relative area of orange spots, a trait that is subject to strong female preference in this species. Neither the relative area of black spots nor the number of black or orange spots was significantly correlated with MLH. We found no statistical support for local effects (i.e. strong effects of heterozygosity at specific markers), which suggests that relative orange spots area reflects genome‐wide heterozygosity.     

Sperm transfer through forced matings and its evolutionary implications in natural guppy (Poecilia reticulata ) populations

In species in which individuals alternate between mating strategies, males may respond to elevated predation risk by switching from conspicuous courtship displays to less risky or more profitable sneaky mating attempts. As a consequence, in such species female choice is likely to be undermined more frequently in relatively dangerous localities. We tested this prediction using the guppy, a species of fish in which individual males alternate between courtship (solicited) and forced (unsolicited) copulations according to prevailing levels of predation. We collected females at late stages of gestation from four high- and four low-predation populations in Trinidad and examined them for the presence of sperm in their gonoducts. Due to the patterns of sperm storage in guppies, sperm found in the gonoducts of such late-cycle females can only arise from unsolicited copulations. We anticipated that because female guppies are subject to greater sexual harassment in the form of forced mating attempts in high-risk localities, a higher proportion of females in these populations would contain sperm in their gonoducts arising from recent unsolicited copulations. Contrary to this prediction, only one of the four paired comparisons (from the Quaré River) revealed a significant difference in the proportion of females recently inseminated through forced copulations. The paired comparisons for the remaining three rivers revealed no significant differences in the proportion of females with recoverable sperm in their gonoducts. However, overall, we found that 44.5% (±4.3 SE) of females had sperm in their gonoduct arising from sneaky mating, a figure three times higher than previously reported for this species. We discuss these findings in relation to recent predictions concerning the strength of sexual selection in natural populations.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 78 , 605–612.     

Identification of C-genome chromosomes involved in intergenomic translocations in Avena sativa L., using cloned repetitive DNA sequences

Four anonymous non-coding sequences were isolated from an Avena strigosa (A genome) genomic library and subsequently characterized. These sequences, designated As14, As121, As93 and As111, were 639, 730, 668, and 619 bp long respectively, and showed different patterns of distribution in diploid and polyploid Avena species. Southern hybridization showed that sequences with homology to sequences As14 and As121 were dispersed throughout the genome of diploid (A genome), tetraploid (AC genomes) and hexaploid (ACD genomes) Avena species but were absent in the C-genome diploid species. In contrast, sequences homologous to sequences As93 and As111 were found in diploid (A and C genomes), tetraploid (AC genomes) and hexaploid (ACD genomes) species. The chromosomal locations of the 4 sequences in hexaploid oat species were determined by fluorescent in situ hybridization and found to be distributed over the length of the 28 chromosomes (except in the telomeric regions) of the A and D genomes. Furthermore, 2 C-genome chromosome pairs with the As14 sequence, and 4 with As121, were discovered to beinvolved in intergenomic translocations. These chromosomes were identified as 1C, 2C, 4C and 16C by combining the As14 or As121 sequences with two ribosomal sequences and a C-genome-specific sequence as probes in fluorescence in situ hybridization. These sequences offer new tools for analyzing possible intergenomic translocations in other hexaploid oat species. Received: 8 April 1999 / Accepted: 30 July 1999     

Geographical variation in allometry in the guppy (Poecilia reticulata)

Variation in static allometry, the power relationship between character size and body size among individuals at similar developmental stages, remains poorly understood. We tested whether predation or other ecological factors could affect static allometry by comparing the allometry between the caudal fin length and the body length in adult male guppies (Poecilia reticulata) among populations from different geographical areas, exposed to different predation pressures. Neither the allometric slopes nor the allometric elevations (intercept at constant slope) changed with predation pressure. However, populations from the Northern Range in Trinidad showed allometry with similar slopes but lower intercepts than populations from the Caroni and the Oropouche drainages. Because most of these populations are exposed to predation by the prawn Macrobrachium crenulatum, we speculated that the specific selection pressures exerted by this predator generated this change in relative caudal fin size, although effects of other environmental factors could not be ruled out. This study further suggests that the allometric elevation is more variable than the allometric slope.     

Development of 51 genomic microsatellite DNA markers of guppy (Poecilia reticulata) and their application in closely related species

Fifty‐one microsatellite DNA markers of guppy (Poecilia reticulata) were developed. All of the markers detected moderate allelic variation. The number of alleles for each locus ranged from two to 10. Observed and expected heterozygosities varied from 0.10 to 0.63 and from 0.23 to 0.77, respectively. Three additional fish species of family Poeciliidae were used for the cross‐species amplification of these markers. It was found that only four to 16 markers detected polymorphism in these three fish species.     

Ultraviolet vision and mate choice in the guppy (Poecilia reticulata)

Ultraviolet (UV) vision is well documented for many speciesof vertebrates. UV cues are known to be used in foraging, navigationand in mate choice. We conducted a series of behavioral experimentsto investigate the role of UV perception in mate choice inboth female and male guppies (Poecilia reticulata). In ourexperiments the visual appearance of potential mates was manipulatedusing either UV transmitting (UV+) or UV blocking (UV-) filters.Female guppies significantly preferred UV+ males. Male guppiestended to prefer UV- females, but their preferences were marginallynonsignificant. Further experiments investigating the roleof luminance, indicate that UV wavelengths are probably beingused for color discrimination rather than for detecting differencesin brightness. These experiments raise the possibility thatUV is used in mate assessment in different ways by male andfemale guppies. This may reflect the different strategies thatthe two sexes have in order to maximize reproductive success.To our knowledge, these are the first data showing that UVis used by any fish species in mate selection.     

Characterization of tetranucleotide microsatellite markers in guppy (Poecilia reticulata)

Ten tetranucleotide microsatellite loci are characterized for guppy, Poecilia reticulata, an important model species in the study of adaptation and mating systems. Loci were isolated following a microsatellite enrichment procedure using probe‐labelled magnetic beads. These microsatellites were designed for use in examining gene flow, reproductive isolation, and parentage within natural guppy populations.     

Abundance and polymorphism of simple repetitive DNA sequences in Bmssica napus L.

Summary The Brassica napus genome has been investigated by DNA fingerprinting with six synthetic oligonucleotide probes complementary to simple repetitive sequences, namely (GATA)₄, (GACA)₄, (GGAT)₄, (CA)₈, (CT)₈ and (GTG)₅. While all sequence motifs were found to be present in the B. napus genome, their organization and abundance varied considerably. Among the investigated probes, (GATA)₄ revealed the highest level of intraspecific polymorphism and distinguishes not only between cultivars but even between different individuals belonging to the same cultivar. In contrast, (GTG)₅, (GACA)₄ and (GGAT)₄ produced relatively homogeneous fingerprint patterns throughout different cultivars, while hybridization to (CT)₈ and (CA)₈ resulted in only a few weak bands superimposed on a smear. The isoschizomeric pair Hpa II and Msp I revealed the presence of methylated cytosines in the vicinity of (GATA)_m repeats. The applicability of simple repetitive sequence polymorphisms as molecular markers for Brassica species is discussed.     

Parallel evolution and vicariance in the guppy (Poecilia reticulata) over multiple spatial and temporal scales

Well-studied model systems present ideal opportunities to understand the relative roles of contemporary selection versus historical processes in determining population differentiation and speciation. Although guppy populations in Trinidad have been a model for studies of evolutionary ecology and sexual selection for more than 50 years, this work has been conducted with little understanding of the phylogenetic history of this species. We used variation in nuclear (X-src) and mitochondrial DNA (mtDNA) sequences to examine the phylogeographic history of Poecilia reticulata Peters (the guppy) across its entire natural range, and to test whether patterns of morphological divergence are a consequence of parallel evolution. Phylogenetic, nested clade, population genetic, and demographic analyses were conducted to investigate patterns of genetic structure at several temporal scales and are discussed in relation to vicariant events, such as tectonic activity and glacial cycles, shaping northeast South American river drainages. The mtDNA phylogeny defined five major lineages, each associated with one or more river drainages, and analysis of molecular variance also detected geographic structuring among these river drainages in an evolutionarily conserved nuclear (X-src) locus. Nested clade and other demographic analyses suggest that the eastern Venezuela/ western Trinidad region is likely the center of origin of P. reticulata. Mantel tests show that the divergence of morphological characters, known to differentiate on a local scale in response to natural and sexual selection pressures, is not associated with mtDNA genetic distance; however, TreeScan analysis identified several significant associations of these characters with the haplotype tree. Parallel upstream/downstream patterns of morphological adaptation in response to selection pressures reported in P. reticulata within Trinidad rivers appears to persist across the natural range. Our results together with previous studies suggest that, although morphological variation in P. reticulata is primarily attributed to selection, phylogeographic history may also play a role.     

A rapid screening technique for the detection of repeated DNA sequences in plant tissues

Summary DNA sequences cloned from nuclear and mitochondrial chromosomes have been used as hybridisation probes to distinguish different plant genotypes. The probes are hybridised to squashed segments of tissue e.g. root tips. The squash-dot method is rapid and suitable for screening large numbers of individual plants. One probe, specific for a rye repeated sequence family, enables rye chromosomes to be detected in wheat plants. A probe for ribosomal DNA enables plants with high or low numbers of ribosomal RNA genes to be distinguished. A maize mitochondrial DNA probe is used to distinguish plants with N, T or S cytoplasms.     

Population genomics of natural and experimental populations of guppies (Poecilia reticulata)

Convergent evolution represents one of the best lines of evidence for adaptation, but few cases of phenotypic convergence are understood at the genetic level. Guppies inhabiting the Northern Mountain Range of Trinidad provide a classic example of phenotypic convergent evolution, where adaptation to low or high predation environments has been found for a variety of traits. A major advantage of this system is the possibility of long‐term experimental studies in nature, including transplantation from high to low predation sites. We used genome scans of guppies from three natural high and low predation populations and from two experimentally established populations and their sources to examine whether phenotypic convergent evolution leaves footprints at the genome level. We used population‐genetic modelling approaches to reconstruct the demographic history and migration among sampled populations. Naturally colonized low predation populations had signatures of increased effective population size since colonization, while introduction populations had signatures of decreased effective population size. Only a small number of regions across the genome had signatures of selection in all natural populations. However, the two experimental populations shared many genomic regions under apparent selection, more than expected by chance. This overlap coupled with a population decrease since introduction provides evidence for convergent selection occurring in the two introduced populations. The lack of genetic convergence in the natural populations suggests that convergent evolution is lacking in these populations or that the effects of selection become difficult to detect after a long‐time period.