C. Van Oosterhout

Inbreeding depression and genetic load of sexually selected traits: how the guppy lost its spots

Abstract To date, few studies have investigated the effects of inbreeding on sexually selected traits, although inbreeding depression on such traits can play an important role in the evolution and ecology of wild populations. Sexually selected traits such as ornamentation and courtship behaviour may not be primary fitness characters, but selection and dominance coefficients of their mutations will resemble those of traits under natural selection. Strong directional selection, for instance, through female mate‐choice, purges all but the most recessive deleterious mutations, and the remaining dominance variation will result in inbreeding depression once populations undergo bottlenecks. We analysed the effects of inbreeding on sexually selected traits (colour pattern and courtship behaviour) in the male guppy, Poecilia reticulata, from Trinidad, and found a significant decline in the frequency of mating behaviour and colour spots. Such effects occurred although the genetic basis of these traits, many of which are Y‐linked and hemizygous, would be expected to leave relatively little scope for inbreeding depression. Findings suggest that these sexually selected traits could reflect the genetic condition or health of males, and thus may be informative mate‐cue characters for female choice as suggested by the ‘good genes’ model.

Population genetic analysis of microsatellite variation of guppies (Poecilia reticulata) in Trinidad and Tobago: evidence for a dynamic source-sink metapopulation structure, founder events and population bottlenecks

Riverine fish populations are traditionally considered to be highly structured and subject to strong genetic drift. Here, we use microsatellites to analyse the population structure of the guppy (Poecilia reticulata), focussing on the headwater floodplain area of the Caroni drainage in Trinidad. We also analyse the population genetics of guppies in the Northern Drainage in Trinidad, a habitat characterized by rivers flowing directly into the sea, and a small isolated population in Tobago. Upland Caroni populations are highly differentiated and display low levels of genetic diversity. However, we found no evidence to suggest that these upland populations experienced recent population crashes and the populations appear to approach mutation–drift equilibrium. Dominant downstream migration over both short‐ and long‐time frames has a strong impact on the population genetics of lowland Caroni populations. This drainage system could be considered a source–sink metapopulation, with the tributary furthest downstream representing a ‘super sink’, receiving immigrants from rivers upstream in the drainage. Moreover, the effective population size in the lowlands is surprisingly low in comparison with the apparently large census population sizes.

Rapid loss of MHC class II variation in a bottlenecked population is explained by drift and loss of copy number variation.

Population bottlenecks may reduce genetic variation and potentially increase the risk of extinction. Here, we present the first study to use historic samples to analyse loss of variation at the major histocompatibility complex (MHC), which plays a central role in vertebrate disease resistance. Balancing selection acts on the MHC and could moderate the loss of variation expected from drift; however, in a Wisconsin population of greater prairie‐chickens (Tympanuchus cupido), the number of MHC class II B alleles per individual declined by 44% following a population bottleneck, compared to a loss of only 8% at microsatellites. Simulations indicate that drift likely reduced MHC variation at the population level, as well as within individuals by reducing the number of gene copies per individual or by fixing the same alleles across multiple loci. These multiple effects of genetic drift on MHC variation could have important implications for immunity and fitness.

Evolution of MHC class IIB in the genome of wild and ornamental guppies, Poecilia reticulata

This is the first study to quantify genomic sequence variation of the major histocompatibility complex (MHC) in wild and ornamental guppies, Poecilia reticulata. We sequenced 196–219 bp of exon 2 MHC class IIB (DAB) in 56 wild Trinidadian guppies and 14 ornamental strain guppies. Each of two natural populations possessed high allelic richness (15–16 alleles), whereas only three or fewer DAB alleles were amplified from ornamental guppies. The disparity in allelic richness between wild and ornamental fish cannot be fully explained by fixation of alleles by inbreeding, nor by the presence of non-amplified sequences (ie null alleles). Rather, we suggest that the same allele is fixed at duplicated MHC DAB loci owing to gene conversion. Alternatively, the number of loci in the ornamental strains has contracted during >100 generations in captivity, a hypothesis consistent with the accordion model of MHC evolution. We furthermore analysed the substitution patterns by making pairwise comparisons of sequence variation at the putative peptide binding region (PBR). The rate of non-synonymous substitutions (dN) only marginally exceeded synonymous substitutions (dS) in PBR codons. Highly diverged sequences showed no evidence for diversifying selection, possibly because synonymous substitutions have accumulated since their divergence. Also, the substitution pattern of similar alleles did not show evidence for diversifying selection, plausibly because advantageous non-synonymous substitutions have not yet accumulated. Intermediately diverged sequences showed the highest relative rate of non-synonymous substitutions, with dN/dS>14 in some pairwise comparisons. Consequently, a curvilinear relationship was observed between the dN/dS ratio and the level of sequence divergence.

Gyrodactylus pictae n. sp. (Monogenea: Gyrodactylidae) from the Trinidadian swamp guppy Poecilia picta Regan, with a discussion on species of Gyrodactylus von Nordmann, 1832 and their poeciliid hosts

Gyrodactylus pictae n. sp. is recorded from Poecilia picta in heterospecific shoals with the guppy P.␣reticulata in Northern Trinidad. G. pictae is morphologically similar to G. turnbulli Harris, 1986, but the hamuli and marginal hooks are slightly smaller and more gracile. The toe and the point of the marginal hook have a distinctly different shape, providing the best morphological characters for distinguishing the two species. The rDNA ITS1 and ITS2 sequences differ from those of G. turnbulli (the closest relative) by >5, suggesting that these two taxa are not sibling species. The origin of the two species on poeciliids of the subgenus Micropoecilia is discussed, and it is suggested that this may represent a case of host–parasite co-evolution.

Solutions for PCR, cloning and sequencing errors in population genetic analysis

PCR and sequencing artefacts can seriously bias population genetic analyses, particularly of populations with low genetic variation such as endangered vertebrate populations. Here, we estimate the error rates, discuss their population genetics implications, and propose a simple detection method that helps to reduce the risk of accepting such errors. We study the major histocompatibility complex (MHC) class IIB of guppies, Poecilia reticulata and find that PCR base misincorporations inflate the apparent sequence diversity. When analysing neutral genes, such bias can inflate estimates of effective population size. Previously suggested protocols for identifying genuine alleles are unlikely to exclude all sequencing errors, or they ignore genuine sequence diversity. We present a novel and statistically robust method that reduces the likelihood of accepting PCR artefacts as genuine alleles, and which minimises the necessity of repeated genotyping. Our method identifies sequences that are unlikely to be a PCR artefact, and which need to be independently confirmed through additional PCR of the same template DNA. The proposed methods are recommended particularly for population genetic studies that involve multi-template DNA and in studies on genes with low genetic diversity.

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.

Experimental infections with the tropical monogenean, Gyrodactylus bullatarudis: Potential invader or experimental fluke?

Introduced exotic species have the potential to spread their associated parasites to native species which can be catastrophic if these hosts are immunologically naïve to the novel parasite. The guppy (Poecilia reticulata) has been disseminated worldwide outside of its native habitat and therefore could be an important source of infection to native fish species. Its parasite fauna is dominated by the ectoparasitic monogeneans, Gyrodactylus turnbulli and Gyrodactylus bullatarudis. The current study tested the host specificity of G. bullatarudis by experimentally infecting a range of isolated fish hosts, including temperate species. Surprisingly, the parasite was capable of establishing and reproducing, for several days, on the three-spined stickleback when transferred directly to this host. We also established that G. bullatarudis could be transmitted under aquarium conditions at both 25 degrees C and 15 degrees C. At the higher temperature, the parasite was even capable of reproducing on this atypical host. The implications of these findings are discussed in terms of host specificity, host switching and climate change.

On the Ecology and Host Relationships of Acanthogyrus (Acanthosentis) tilapiae (Acanthocephala: Quadrigyridae) from Cichlids in Lake Malawi

Abstract About 2,000 specimens of the quadrigyrid acanthocephalan Acanthogyrus (Acanthosentis) tilapiae (Baylis, 1948) were collected from 9 species of cichlid fish hosts (Cichlidae: Perciformes) in 7 different sites in Lake Malawi, Africa, during September 2005. New host records are noted in 5 species, Labeotropheus trewavasae (Fryer), Melanochromis vermivorus (Trewavas), Nimbochromis polystigma (Regan), Tropheops microstoma (Trewavas), and Rhamphochromis sp. (Regan). High prevalence of A. tilapiae was observed in all host species analyzed. The parasite manages to infect its cichlid hosts, despite their distinct trophic specializations. Nevertheless, significant variation in parasite load was detected between sympatrically occurring rock-dwelling (mbuna) cichlids, with Pseudotropheus zebra (Boulenger) showing the most heavy infections. In addition, significant variation in parasite burden was detected between sampling locations, but host gender and weight did not explain significant variation in the numbers of A. tilapiae individuals. Differential exposure to parasites and host susceptibility may explain the marked variation in parasite abundance among cichlid hosts. Worms appear to be recruited in the summer, develop and mature through the winter, and reproduce sexually in late winter and spring.

Transposons in the MHC: The Yin and Yang of the vertebrate immune system

R ecent research on transposable elements (TEs) in the major histocompatibility complex (MHC) proposed that TEs may play an adaptive evolutionary role in the vertebrate immune system (Doxiadis et al., 2008). Here, I argue that although transposons will undoubtedly affect the evolution of the MHC, their increased density in this region may be an evolutionary inevitability, given the genomic architecture of these genes. The MHC is an evolutionary innovation of the jawed vertebrates in their race against organismal parasites; however, functional epistasis and high gene diversity of this multigene family may have rendered the MHC prone to the onslaught of genomic parasites. Transposons are genomic parasites that exploit their host’s resources for their own reproduction and they seem to have the upper hand in the coevolutionary arms race by their potential to out-replicate the host genomes in which they reside (Jordan et al., 2003). Indeed, TEs constitute a large proportion of the vertebrate genome, and on average more than 40% of the mammalian genome consists of these parasitic elements (Margulies et al., 2005). TEs are often deleterious to their host and can disrupt coding regions of the genome, induce recombination between copies of the repeats and affect the splicing of the targeted genes (van de Lagemaat et al., 2006). However, just as any other mutation, TEs do provide genetic variation that is the substrate for natural selection. This variation might be crucial to some gene regions, particularly to the MHC, as according to the Red Queen’s hypothesis, the immune system of the vertebrate host is involved in a coevolutionary arms race with fast-evolving organismal parasites. Although severely detrimental and lethal TEs are likely to be purged from the gene pool by natural selection, some TEs have been ‘domesticated’ by their hosts (Miller et al., 1999). These TEs may have gained a regulatory role (van de Lagemaat et al., 2003), or have become part of a gene (Feschotte and Pritham, 2007). Currently, the paradigm is that TEs are not merely ‘selfish elements’, but that they can play a constructive role in adaptive evolution. The potential functional role of TEs or TE-derived sequences can be inferred from their nucleotide sequence conservation (Lowe et al., 2007), the donation of TE sequences in promoter regions (Jordan et al., 2003) and the lower than expected rate of TE interruption by other newer transposons (Abrusán et al., 2008). Furthermore, TEs have a non-random distribution throughout the genome, and they show an increased density in the MHC in a wide range of vertebrates. Recently, Doxiadis et al. (2008) showed that the polarity of TEs—whether they are oriented in sense or antisense— affects the stability of the MHC gene region. Sense-oriented TEs are able to promote gene duplications and deletions by gene-conversion-like events, and thus form novel region configurations. In contrast, antisense-oriented retroelements seem to promote evolutionary stability, possibly by reducing the recombination rate with other MHC haplotypes (Doxiadis et al., 2008). The equilibrium frequency of TEs will, however, not only be determined by natural selection, but also by other evolutionary forces; for example, the transposition activity of the transposon (that is, the ‘mutation rate’), random genetic drift and the recombination rate. The interaction between these evolutionary forces, as well as the epidemiology of transposons within host genomes, will govern the population genetics and dynamics of TEs. Given that the effective population size of most vertebrates is relatively small, genetic drift may play an equal, if not more important, role than natural selection in the population genetics of vertebrate TEs. In addition, differences in the recombination rate may also explain the variation in density of TEs across the vertebrate genome. Recently, van Oosterhout (2009) proposed a new theory of MHC evolution, coined Associative Balancing Complex (ABC) evolution, which may explain why the density of TEs is relatively high in this genomic region. Although traditional theories of balancing selection were developed for single genes, ABC evolution takes into account the effect of epistasis and high MHC gene diversity. Functional epistasis between the immune genes reduces the effective rate of recombination in some areas of the MHC (Stenzel et al., 2004; Gregersen et al., 2006). These so-called haploblocks are characterized by strong linkage disequilibrium, and the low recombination rate reduces the efficacy of purifying selection (Haddrill et al., 2007). TEs and other deleterious mutations can become fixed in all copies of a particular haploblock in a process analogous to Muller’s (1932) Ratchet. They can accumulate as a ‘sheltered load’ (Stone, 2004) when they are recessive so that their effects are not expressed in heterozygote condition. The high gene diversity (heterozygosity) and linkage disequilibrium in the MHC region thus facilitate the accumulation of recessive deleterious mutations and TEs. This may explain why there are over 100 heritable diseases associated with the human MHC (the human leukocyte antigen) (de Bakker et al., 2006), and why these genetic polymorphisms are not removed by natural selection (van Oosterhout, 2009). In the MHC, purifying selection is considerably less efficient than in many places elsewhere in the genome, which means that in their wake, transposons have made the human MHC into a hotbed of heritable diseases and disorders. In summary, some TEs in the MHC may confer selective advantages, for example, by suppressing recombination, promoting gene duplications and deletions (Doxiadis et al., 2008), and by reinforcing epistasis and balancing selection on the immune genes (van Oosterhout, 2009). Similar to point mutations, TEs provide important genetic variation for selection, but according to the ‘nearly neutral theory’, the majority of the polymorphisms that are present in the population will have a nearly neutral or slightly detrimental effect on fitness (Hughes, 2007). Transposons simply seem to have targeted the MHC because the genomic features that have made this immune gene family such an efficient defence against Heredity (2009) 103, 190–191 & 2009 Macmillan Publishers Limited All rights reserved 0018-067X/09