Saprolegnia parasitica zoospore activity and host survival indicates isolate variation in host preference

The ubiquitous freshwater pathogen Saprolegnia parasitica has long been considered a true generalist, capable of infecting a wide range of fish species. It remains unclear, however, whether different isolates of this pathogen, obtained from distinct geographic locations and host species, display differences in host preference. To assess this, the current study examined the induced zoospore encystment responses of four S. parasitica isolates towards the skin of four fish species. While three of the isolates displayed ‘specialist’ responses, one appeared to be more of a ‘generalist’. In vivo challenge infections involving salmon and sea trout with the ‘generalist’ (salmon isolate EA001) and a ‘specialist’ (sea trout isolate EA016) pathogen, however, did not support the in vitro findings, with no apparent host preference reflected in infection outcomes. Survival of sea trout and salmon though was significantly different following a challenge infection with the sea trout (EA016) isolate. These results indicate that while S. parasitica isolates can be considered true generalists, they may target hosts to which they have been more frequently exposed (potential local adaptation). Understanding host preference of this pathogen could aid our understanding of infection epidemics and help with the development of fish management procedures.     

Population differentiation in an annual legume: local adaptation

Abstract. Studies of many plants species have demonstrated adaptive genetic differentiation to local environmental conditions. Typically these studies are conducted to evaluate adaptation to contrasting environments. As a consequence, although local adaptation has been frequently demonstrated, we have little information as to the spatial scale of adaptive evolution. We evaluated adaptive differentiation between populations of the annual legume Chamaecrista fasciculata using a replicated common-garden design. Study sites were established in three field locations that are home to native populations of C. fasciculata . Each location was planted for two years with seed from the population native to the study site (home population) and populations located six distances (0.1-2000 km) from each site (transplanted populations). Seeds were planted into the study sites with minimum disturbance to determine the scale of local adaptation, as measured by a home-site fitness advantage, for five fitness components: germination, survival, vegetative biomass, fruit production, and the number of fruit produced per seed planted (an estimate of cumulative fitness). For all characters there was little evidence for local adaptation, except at the furthest spatial scales. Patterns of adaptive differentiation were fairly consistent in two of the three sites, but varied between years. Little genetic variation was expressed at the third site. These results, combined with previous estimates of limited gene flow, suggest that metapopulation processes and temporal environmental variation act together to reduce local adaptation, except over long distances.     

Interspecific and intraspecific variation in the performance of three pest aphid species on five grain legume hosts

The suitability of five grain legume species (narrow-leafed lupin, chickpea, faba bean, field pea, lentil) as hosts for three aphid species (green peach aphid, cowpea aphid, bluegreen aphid) was evaluated by measuring the mean relative growth rate (MRGR) and survivorship of nymphs over a 5 day period. For each aphid species, intraspecific (interclonal) variation was also determined by independently measuring the performance of 30 clones collected from a variety of hosts and from different parts of the Western Australia (WA) wheatbelt. The suitability of the grain legumes varied among aphid species. Chickpea was not a suitable host for any of the aphids tested. Averaged over all clones, lentil and faba bean were the most suitable hosts for cowpea aphid, and narrow-leafed lupin was the most suitable host for green peach aphid. Field pea was a suitable host for all three species, but only at a suboptimal level. Cowpea aphid showed the greatest amount of intraspecific variation, with significant variation in MRGR among clones on all hosts except chickpea and significant variation in survivorship on chickpea and lupin. For green peach aphid, there was significant variation in MRGR among clones on field pea and lupin, but in survivorship on lupin only. Bluegreen aphid clones showed significant variation only for MRGR on faba bean and lupin. There were positive correlations in performance of green peach aphid clones on faba bean and lentil, and of cowpea aphid clones on faba bean and lentil. Bluegreen aphid clones showed a negative correlation in performance on field pea and faba bean. These results show the importance of screening cultivars against a wide variety of aphid clones when assessing aphid susceptibility in breeding programmes. The implications of these results on the adaptability of parthenogenetic aphids are discussed.     

A resource budget model to explain intraspecific variation in mast reproductive dynamics

Rowan, Sorbus aucuparia L., exhibits conspicuous geographic variation in its inter-annual patterns of reproduction across southern Norway. Along the southern west coast, trees flower and produce clusters of succulent berries every other year, while in the east, trees mast every 3 years. We investigate two hypotheses for this variation: local adaptation to environmental conditions that favors different reproductive schedules at different locations or variation arising from single stereotyped reproductive strategy in the face of a geographic variation in productivity. To assess the theoretical plausibility of each of these hypotheses, we develop a refined resource budget model for mast reproduction. The refined model assumes that there is a lower bound on the amount of resource that may be allocated to reproduction, which allows the prediction of the relation between reproductive schedules and productivity. From the analysis of the model, we find that the observed geographic transition in rowan mast is caused if either productivity in the east is lower than that in the west or if plants in the eastern populations have evolved to pause reproduction until energy reserves are replenished to higher levels. The prediction by the productivity gradient hypothesis match with the empirical finding that the productivity is, in fact, likely to be lower in the east than the west, although we lack empirical data to test the likelihood of the local adaptation hypothesis. There is a need for experimental studies to clarify the validity of the local adaptation hypothesis. Akiko Satake is the recipient of the 11th Denzaburo Miyadi Award.     

Host adaptation and host-parasite co-evolution in Cryptosporidium: implications for taxonomy and public health

To assess the genetic diversity and evolution of Cryptosporidium parasites, the partial ssrRNA, actin, and 70 kDa heat shock protein (HSP70) genes of 15 new Cryptosporidium parasites were sequenced. Sequence data were analysed together with those previously obtained from other Cryptosporidium parasites (10 Cryptosporidium spp. and eight Cryptosporidium genotypes). Results of this multi-locus genetic characterisation indicate that host adaptation is a general phenomenon in the genus Cryptosporidium, because specific genotypes were usually associated with specific groups of animals. On the other hand, host–parasite co-evolution is also common in Cryptosporidium, as closely related hosts usually had related Cryptosporidium parasites. Results of phylogenetic analyses suggest that the Cryptosporidium parvum bovine genotype and Cryptosporidium meleagridis were originally parasites of rodents and mammals, respectively, but have subsequently expanded their host ranges to include humans. Understanding the evolution of Cryptosporidium species is important not only for clarification of the taxonomy of the parasites but also for assessment of the public health significance of Cryptosporidium parasites from animals.     

Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops

Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possible, and the complexity of the evolutionary process of local adaptation means that plant studies are set to move to the genome level, and account for the interaction of genes under selection in systems-level approaches. This way we can understand how plants adapted during the expansion of agriculture across many latitudes with rapidity.     

Evolutionary adaptation to host plants in a laboratory population of the phytophagous mite Tetranychus urticae Koch

Summary For evolutionary expansion of host range to occur in an herbivore population, genetic variation in ability to survive on and/or accept new hosts must be present. To determine whether a population of the phytophagous mite Tetranychus urticae contained such variation, I established lines from the population on two hosts on which mites initially showed both high juvenile mortality and low acceptance, tomato and broccoli. In less than ten generations, mites from the line kept on each host showed both lower mortality and greater acceptance on it than mites from a control line kept on lima bean, a favorable host for T. urticae. Host acceptance was measured by the proportion of mites attempting to disperse from leaves of the host. The line kept on tomato but not the one kept on broccoli also increased in development rate on its host. These results and those of a similar previous experiment on cucumber indicate that T. urticae populations can adapt to a diversity of initially unfavorable hosts. T. urticae populations therefore should be able to respond to temporal and spatial variation in host availability by adapting to the most abundant hosts.     

Locking life-cycles onto seasons: Circle-map models of population dynamics and local adaptation

We have formulated a model describing the timing of maturity and reproduction in briefly semelparous organisms whose development rate is primarily controlled by environmental factors. The model is expressed as a circle-map relating time of year at maturation in successive generations. The properties of this map enable us to determine the degree of synchrony to be expected between the life-cycles of members of a population exposed to a regular seasonal environment. We have proved that organisms with a life-history composed of a contiguous series of stages, all with development driven by the same seasonal function, cannot phase-lock their life-cycles to the seasons. However if the organism exhibits facultative diapause induced by a critical time/critical development mechanism of the type proposed by Norling (1984a,b,c) then it will always succeed in phase-locking to a perfectly periodic driving function. Within the context of this circle-map model we have examined population extinctions caused by attempting to over-winter in an inappropriate life-history stage, or by attempting to reproduce at a time of year when this is impossible. We have shown that the possibility of such extinctions limits both the shortness of the post-critical stage, and the lateness of the critical time. We have examined the fitness of persistent cohorts as a function of critical time and development. We find that if the post-critical stage is riskier than the pre-critical then natural selection favors a short post-critical stage and a late critical time; the limitation of this process being dependent on the proportion of the growing season over which successful reproduction is possible. We have determined the variation with life-cycle length (and hence latitude or altitude) of the maturation pattern corresponding to optimal life-history parameters. We find that for organisms which can mature only over a small part of the growing season the majority of any latitudinal gradient exhibits a unimodal maturation pattern. Organisms which can mature and reproduce over the majority of the growing season exhibit more complex patterns, but still exhibit substantial ranges of latitude over which unimodal or bimodal patterns are optimal.     

Crossing the threshold: gene flow,dominance and the critical level of standing genetic variation required for adaptation to novel environments

Genetic architecture plays an important role in the process of adaptation to novel environments. One example is the role of allelic dominance, where advantageous recessive mutations have a lower probability of fixation than advantageous dominant mutations. This classic observation, termed ‘Haldane's sieve’, has been well explored theoretically for single isolated populations adapting to new selective regimes. However, the role of dominance is less well understood for peripheral populations adapting to novel environments in the face of recurrent and maladaptive gene flow. Here, we use a combination of analytical approximations and individual‐based simulations to explore how dominance influences the likelihood of adaptation to novel peripheral environments. We demonstrate that in the face of recurrent maladaptive gene flow, recessive alleles can fuel adaptation only when their frequency exceeds a critical threshold within the ancestral range.     

Patch dynamics ofGlaucopsyche lygdamus (Lycaenidae): correlations between butterfly density and host species diversity

Glaucopsyche lygdamus egg densities were surveyed over a 2000-m section of Gold Creek and at 30 different isolated patches in the Gold Basin drainage in Colorado. Host plant numbers and diversity were quantified, as well as other variables potentially influencing butterfly population size, such as patch size and isolation. Egg densities correlated significantly only with measures of host species diversity. Patches consisting of a single host species, no matter how large, did not support high butterfly densities, but patches of multiple, equitably distributed host species did. The most likely explantation, in light of oviposition preference and larval performance data accumulated for this butterfly species, is that host species diversity is necessary for the persistence ofG. lygdamus populations, because alternative host species buffer population losses during poor or unusual years. The dependence of both ovipositing butterflies and developing larvae on the ephemeral, young, host plant flowers make the butterfly especially vulnerable to year-to-year variation in host plant availability and quality.     

Dispersal in a parasitic worm and its two hosts: consequence for local adaptation

Characterizing host and parasite population genetic structure and estimating gene flow among populations is essential for understanding coevolutionary interactions between hosts and parasites. We examined the population genetic structure of the trematode Schistosoma mansoni and its two host species (the definitive host Rattus rattus and the intermediate host Biomphalaria glabrata) using microsatellite markers. Parasites were sampled from rats. The study was conducted in five sites of the Guadeloupe Island, Lesser Antilles. Mollusks display a pattern of isolation by distance whereas such a pattern is not found neither in schistosomes nor in rats. The comparison of the distribution of genetic variability in S. mansoni and its two host species strongly suggests that migration of parasites is principally determined by that of the vertebrate host in the marshy focus of Guadeloupe. However, the comparison between genetic differentiation values in schistosomes and rats suggests that the efficacy of the schistosome rat-mediated dispersal between transmission sites is lower than expected given the prevalence, parasitic load and migration rate of rats among sites. This could notably suggest that rat migration rate could be negatively correlated to the age or the infection status of individuals. Models made about the evolution of local adaptation in function of the dispersal rates of hosts and parasites suggest that rats and mollusks should be locally adapted to their parasites.     

Evolutionary variations on a theme: host plant specialization in five geographical populations of the leaf beetle Chrysomela lapponica

The ancestral host plants of Chrysomela lapponica are Salicaceae rich in salicylic glycosides (SGs), which serve as precursors for larval chemical defensive secretions. Nevertheless, some populations have shifted to plants poor in SGs or even lacking these compounds. To study whether this shift is accompanied by adaptations to novel SG-poor host plants, we reared C. lapponica larvae from five geographical populations on host plants with high (Salix myrsinifolia) or low (S. caprea) SG content. Individuals from two populations (Finland and Kola region in Russia) associated in nature with SG-rich S. myrsinifolia showed higher survival and shorter developmental time on native host species than on foreign SG-poor S. caprea, thus demonstrating local adaptations to their ancestral SG-rich host plant. Individuals from a Belarus population associated in nature with SG-poor S. caprea showed higher survival on this species than on foreign SG-rich S. myrsinifolia, thus demonstrating local adaptation to the novel SG-poor host. On the other hand, individuals from two other populations associated in nature with SG-poor plants (Baikal and Ural region) performed equally well on both SG-rich S. myrsinifolia and SG-poor S. caprea in our rearing experiments, thus showing no local adaptation to a specific SG-host type, but rather a wide feeding niche including several Salicaceae species of different SG-type. Our results suggest that diet breadth of C. lapponica is a local phenomenon, and that adaptation strategies to novel host plants may differ between populations of a single leaf beetle species.     

Genome‐wide signature of local adaptation linked to variable CpG methylation in oak populations

It has long been known that adaptive evolution can occur through genetic mutations in DNA sequence, but it is unclear whether adaptive evolution can occur through analogous epigenetic mechanisms, such as through DNA methylation. If epigenetic variation contributes directly to evolution, species under threat of disease, invasive competition, climate change or other stresses would have greater stores of variation from which to draw. We looked for evidence of natural selection acting on variably methylated DNA sites using population genomic analysis across three climatologically distinct populations of valley oaks. We found patterns of genetic and epigenetic differentiations that indicate local adaptation is operating on large portions of the oak genome. While CHG methyl polymorphisms are not playing a significant role and would make poor targets for natural selection, our findings suggest that CpG methyl polymorphisms as a whole are involved in local adaptation, either directly or through linkage to regions under selection.     

Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses

In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments.     

Population history and genomic signatures for high-altitude adaptation in Tibetan pigs

Background

The Tibetan pig is one of domestic animals indigenous to the Qinghai-Tibet Plateau. Several geographically isolated pig populations are distributed throughout the Plateau. It remained an open question if these populations have experienced different demographic histories and have evolved independent adaptive loci for the harsh environment of the Plateau. To address these questions, we herein investigated ~ 40,000 genetic variants across the pig genome in a broad panel of 678 individuals from 5 Tibetan geographic populations and 34 lowland breeds.

Results

Using a series of population genetic analyses, we show that Tibetan pig populations have marked genetic differentiations. Tibetan pigs appear to be 3 independent populations corresponding to the Tibetan, Gansu and Sichuan & Yunnan locations. Each population is more genetically similar to its geographic neighbors than to any of the other Tibetan populations. By applying a locus-specific branch length test, we identified both population-specific and -shared candidate genes under selection in Tibetan pigs. These genes, such as PLA2G12A, RGCC, C9ORF3, GRIN2B, GRID1 and EPAS1, are involved in high-altitude physiology including angiogenesis, pulmonary hypertension, oxygen intake, defense response and erythropoiesis. A majority of these genes have not been implicated in previous studies of highlanders and high-altitude animals.

Conclusion

Tibetan pig populations have experienced substantial genetic differentiation. Historically, Tibetan pigs likely had admixture with neighboring lowland breeds. During the long history of colonization in the Plateau, Tibetan pigs have developed a complex biological adaptation mechanism that could be different from that of Tibetans and other animals. Different Tibetan pig populations appear to have both distinct and convergent adaptive loci for the harsh environment of the Plateau.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-834) contains supplementary material, which is available to authorized users.     

8种常绿阔叶树木的叶结构特点及其对光照变化的适应性分析

通过对8种常绿阔叶树种和对照种(香樟)的叶结构特征比较,分析它们对光照变化的适应特性。结果显示,由于植物类群系统演化的非同步性,常绿阔叶树种对光照变化的适应方式各有不同,各具特点,需要按各自特点加以分析。比较而言,同科树种的可比性较强。按叶结构特点及其群落等资料综合分析,浙江桂(Cinnamomum chekiangense)和冬青(Ilex purpurea)表现为喜光,灰毛含笑(Michelia foveolata var．cinerascens)其次;大叶冬青(Ilex latifolia)和红茴香(Illicium henryi)表现为耐荫;乐东拟单性木兰(Parameria lotungensis)、云南拟单性木兰(Parameria yunnanensis)等其它种类为中性树种。该研究结果对预测常绿阔叶树种在园林中的合理配植有指导意义。     

Testing limits to adaptation along altitudinal gradients in rainforest Drosophila

Given that evolution can generate rapid and dramatic shifts in the ecological tolerance of a species, what prevents populations adapting to expand into new habitat at the edge of their distributions? Recent population genetic models have focused on the relative costs and benefits of migration between populations. On the one hand, migration may limit adaptive divergence by preventing local populations from matching their local selective optima. On the other hand, migration may also contribute to the genetic variance necessary to allow populations to track these changing optima. Empirical evidence for these contrasting effects of gene flow in natural situations are lacking, largely because it remains difficult to acquire. Here, we develop a way to explore theoretical models by estimating genetic divergence in traits that confer stress resistance along similar ecological gradients in rainforest Drosophila. This approach allows testing for the coupling of clinal divergence with local density, and the effects of genetic variance and the rate of change of the optimum on the response to selection. In support of a swamping effect of migration on phenotypic divergence, our data show no evidence for a cline in stress-related traits where the altitudinal gradient is steep, but significant clinal divergence where it is shallow. However, where clinal divergence is detected, sites showing trait means closer to the presumed local optimum have more genetic variation than sites with trait means distant from their local optimum. This pattern suggests that gene flow also aids a sustained response to selection.     

Interspecific antagonism and virulence in hosts exposed to two parasite species

Co-infection of host organisms by multiple parasite species has evolutionary consequences for all participants in the symbiosis. In this study, we co-exposed aquatic-snails (Biomphalaria glabrata) to two of their trematode parasites, Schistosoma mansoni and Echinostoma caproni. In co-exposed snails, E. caproni prevalence was 63% compared to only 23% for S. mansoni. Co-exposed E. caproni-infected snails exhibited reduced fecundity, higher mortality, and higher parasite reproduction (higher virulence) compared to hosts exposed to echinostomes alone. Conversely, co-exposed S. mansoni-infected snails released fewer parasites and produced greater numbers of eggs compared to hosts exposed to S. mansoni alone. These results suggest that co-exposure not only influences the establishment (presence or absence) of particular parasite species, but also impacts host life history, parasite reproduction, and the virulence of the interaction.     

Interspecific and intraspecific variation in resistance to ichthyophthiriasis among poeciliid and goodeid fishes

A study was undertaken on genetic variation in resistance to infection by Ichthyophthirius multifiliis in two goodeid ( Ameca splendens and Ilyodon xantusi ) and two poeciliid species ( Xiphophorus maculatus and Xiphophorus variatus ), and among four strains of X. maculatus (red, red wagtail, yellow comet tail, blue). Analysis of infection data was performed with a generalized linear interactive modelling package (GLIM). Partitioning of the variation was such that the minimal variation attributable to each of several factors was computed. Size of fish, parasite isolate, temperature/tank effects, and various interactions all affect infection levels. Removal of these effects allowed the identification of highly significant differences in both inter- and intraspecific variation in resistance. Three distinct groups of fish were identified in terms of their resistance. Species recently derived from wild populations (the two goodeids) were more susceptible than the two poeciliid species which have a much longer history of domestication. The blue strain of X. maculatus had significantly higher resistance than the other three strains.     

Interspecific genetics of speciation phenotypes: song and preference coevolution in Hawaiian crickets

Understanding the genetic architecture of traits involved in premating isolation between recently diverged lineages can provide valuable insight regarding the mode and tempo of speciation. The repeated coevolution of male courtship song and female preference across the species radiation of Laupala crickets presents an unusual opportunity to compare the genetic basis of divergence across independent evolutionary histories. Previous studies of one pair of species revealed a polygenic basis (including a significant X chromosome contribution) to quantitative differences in male song and female acoustic preference. Here, we studied interspecific crosses between two phenotypically less-diverged species that represents a phylogenetically independent occurrence of intersexual signalling evolution. We found patterns consistent with an additive polygenic basis to differentiation in both song and preference (n(E) = 5.3 and 5.1 genetic factors, respectively), and estimate a moderate contribution of the X chromosome (7.6%) of similar magnitude to that observed for Laupala species with nearly twice the phenotypic divergence. Together, these findings suggest a similar genetic architecture underlying the repeated evolution of sexual characters in this genus and provide a counterexample to prevailing theory predicting an association between early lineage divergence and sex-linked 'major genes'.