Population genetic structure of a common host predicts the spread of white‐nose syndrome,an emerging infectious disease in bats

Landscape complexity influences patterns of animal dispersal, which in turn may affect both gene flow and the spread of pathogens. White‐nose syndrome (WNS) is an introduced fungal disease that has spread rapidly throughout eastern North America, causing massive mortality in bat populations. We tested for a relationship between the population genetic structure of the most common host, the little brown myotis (Myotis lucifugus), and the geographic spread of WNS to date by evaluating logistic regression models of WNS risk among hibernating colonies in eastern North America. We hypothesized that risk of WNS to susceptible host colonies should increase with both geographic proximity and genetic similarity, reflecting historical connectivity, to infected colonies. Consistent with this hypothesis, inclusion of genetic distance between infected and susceptible colonies significantly improved models of disease spread, capturing heterogeneity in the spatial expansion of WNS despite low levels of genetic differentiation among eastern populations. Expanding our genetic analysis to the continental range of little brown myotis reveals strongly contrasting patterns of population structure between eastern and western North America. Genetic structure increases markedly moving westward into the northern Great Plains, beyond the current distribution of WNS. In western North America, genetic differentiation of geographically proximate populations often exceeds levels observed across the entire eastern region, suggesting infrequent and/or locally restricted dispersal, and thus relatively limited opportunities for pathogen introduction in western North America. Taken together, our analyses suggest a possibly slower future rate of spread of the WNS pathogen, at least as mediated by little brown myotis.     

Pathogens manipulate the preference of vectors,slowing disease spread in a multi‐host system

The spread of vector‐borne pathogens depends on a complex set of interactions among pathogen, vector, and host. In single‐host systems, pathogens can induce changes in vector preferences for infected vs. healthy hosts. Yet it is unclear if pathogens also induce changes in vector preference among host species, and how changes in vector behaviour alter the ecological dynamics of disease spread. Here, we couple multi‐host preference experiments with a novel model of vector preference general to both single and multi‐host communities. We show that viruliferous aphids exhibit strong preferences for healthy and long‐lived hosts. Coupling experimental results with modelling to account for preference leads to a strong decrease in overall pathogen spread through multi‐host communities due to non‐random sorting of viruliferous vectors between preferred and non‐preferred host species. Our results demonstrate the importance of the interplay between vector behaviour and host diversity as a key mechanism in the spread of vectored‐diseases.     

Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew,Plasmopara viticola

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Significant deviations from Hardy-Weinberg equilibrium caused by low levels of microsatellite genotyping errors

Microsatellite genotyping from samples with varying quality can result in an uneven distribution of errors. Previous studies reporting error rates have focused on estimating the effects of both randomly distributed and locus‐specific errors. Sample‐specific errors, however, can also significantly affect results in population studies despite a large sample size. From two studies including six microsatellite markers genotyped from 272 sperm whale DNA samples, and 33 microsatellites genotyped from 213 bowhead whales, we investigated the effects of sample‐ and locus‐specific errors on calculations of Hardy–Weinberg equilibrium. The results of a jackknife analysis in these two studies identified seven individuals that were highly influential on estimates of Hardy–Weinberg equilibrium for six different markers. In each case, the influential individual was homozygous for a rare allele. Our results demonstrate that Hardy–Weinberg P values are very sensitive to homozygosity in rare alleles for single individuals, and that > 50% of these cases involved genotype errors likely due to low sample quality. This raises the possibility that even small, normal levels of laboratory errors can result in an overestimate of the degree to which markers are out of Hardy–Weinberg equilibrium and hence overestimate population structure. To avoid such bias, we recommend routine identification of influential individuals and multiple replications of those samples.     

Prominent genetic structure across native and introduced ranges of Pluchea indica,a mangrove associate,as revealed by microsatellite markers

阔苞菊(Pluchea indica)是一种红树林伴生植物,以其在原产地的药用特性和部分引入地的入侵性而闻名。本研究旨在评估阔苞菊在其分布范围内遗传变异的地理分布,确定影响其遗传结构的因素,并利用这些信息对阔苞菊在原产地和引入地的保护和管理策略提出建议。 我们以来自阔苞菊原产地(亚洲)和引入地(美国)的31个种群共348个个体的15个核微卫星位点数据对阔苞菊的遗传多样性和种群结构进行了评估。在大尺度范围以及局部区域两种空间尺度上对阔苞菊遗传变异的空间格局进行了探讨,并验证了以下假说：地理距离和自然地理屏障将影响种群结构并在空间尺度上产生不同程度的分化。研究结果表明,与所研究区域内的其它红树林物种的遗传多样性参数相比, 我们发现阔苞菊在种群水平上具有相对较高的遗传多样性以及在物种水平上具有明显的遗传分化。大多数阔苞菊种群显示杂合子缺失, 这主要是由于近交和有限的基因流所导致。在较大空间尺度上进行的种群结构分析显示,该物种自然分布范围内存在两个主要遗传谱系,中国的种群与印度尼西亚、马来西亚、新加坡、泰国、柬埔寨和菲律宾的种群分别属于不同的谱系,而美国的种群可能来自于中国的谱系。 此外,在局部区域范围内也同样检测到种群之间的遗传分化。大部分阔苞菊种群所表现出的遗传瓶颈效应强调了其具有本地灭绝的风险。基于上述研究结果,我们建议采用原位保护策略对阔苞菊进行管理,并开展对优先保护种群的保护行动以维持遗传多样性。     

Clonal diversity,clonal persistence and rapid taxon replacement in natural populations of species and hybrids of the Daphnia longispina complex

Hybridization is common among cyclical parthenogens, especially in zooplankton species assemblages of the genus Daphnia. To explore hybridization dynamics and the extent of clonal diversity in the Daphnia longispina complex, we analysed population structure in eight permanent lakes. Based on 15 microsatellite loci, three major taxonomic units emerged: two species, D. galeata and D. longispina and their F1 hybrids, supported by factorial correspondence analysis and two Bayesian methods. At the same time, the detection of backcross classes differed between methods. Mean clonal diversity was lowest in the F1 hybrids, as expected from the high rate of asexual reproduction. Within taxa, replicated genotypes were of clonal origin, but clonal lineages persisted in subsequent years in only one of three resampled lakes. In another lake, the taxon composition changed from being dominated by hybrids to complete dominance by one parental taxon. Such a year‐to‐year taxon replacement has not been reported for the D. longispina complex before. Our data on this hybrid complex illustrate that high‐resolution genotyping is essential for the understanding of ecological and evolutionary outcomes of hybridization in partially clonal taxa.     

Genetic structure in large, continuous mammal populations: the example of brown bears in northwestern Eurasia

Knowledge of population structure and genetic diversity and the spatio-temporal demographic processes affecting populations is crucial for effective wildlife preservation, yet these factors are still poorly understood for organisms with large continuous ranges. Available population genetic data reveal that widespread mammals have for the most part only been carefully studied at the local population scale, which is insufficient for understanding population processes at larger scales. Here, we provide data on population structure, genetic diversity and gene flow in a brown bear population inhabiting the large territory of northwestern Eurasia. Analysis of 17 microsatellite loci indicated significant population substructure, consisting of four genetic groups. While three genetic clusters were confined to small geographical areas-located in Estonia, southern Finland and Leningrad oblast, Russia-the fourth cluster spanned a very large area broadly falling between northern Finland and the Arkhangelsk and Kirov oblasts of Russia. Thus, the data indicate a complex pattern where a fraction of the population exhibits large-scale gene flow that is unparalleled by other wild mammals studied to date, while the remainder of the population appears to have been structured by a combination of demographic history and landscape barriers. These results based on nuclear data are generally in good agreement with evidence previously derived using mitochondrial markers, and taken together, these markers provide complementary information about female-specific and population-level processes. Moreover, this study conveys information about spatial processes occurring over multiple generations that cannot be readily gained using other approaches, e.g. telemetry.     

Micro‐ and macrospatial scale analyses illustrates mixed mating strategies and extensive geneflow in populations of an invasive haploid pathogen

Sexual reproduction in fungi involves either a single individual (selfing) or two individuals (outcrossing). To investigate the roles that these two strategies play in the establishment of an invasive alien pathogen, the Eucalyptus leaf‐infecting fungus, Teratosphaeria (Mycosphaerella) nubilosa was studied. Specifically, the genetic diversity of the pathogen was investigated at micro and macrospatial scales. Interestingly, while data obtained at microspatial scales show clearly that selfing is the main reproductive strategy, at macrospatial scales the population genetic structure was consistent with a genetically outcrossing organism. Additional analyses were performed to explore these apparently discordant results at different spatial scales and to quantify the contribution of selfing vs. outcrossing to the genotypic diversity. The results clearly show that the fungus has a mixed mating strategy. While selfing is the predominant form of mating, outcrosses must have occurred in the pathogen that increased the genotypic diversity of the fungus over time. This mating strategy, coupled with the high levels of geneflow between distant populations of the pathogen, has created an even distribution of maximum diversity from the smallest (leaf) to largest scales (>500 km), which will make breeding for resistance difficult. These data illustrate the evolutionary potential and danger of the introduction of multiple genotypes of a potentially outcrossing pathogen, especially when it has a high dispersal potential.     

Biology, herbivory, and host specificity of Antiblemma leucocyma (Lepidoptera: Noctuidae) on Miconia calvescens DC. (Melastomataceae) in Brazil

Miconia calvescens DC. (Melastomataceae) is an invasive tree considered one of the greatest threats to natural ecosystems of Hawaii and other Pacific islands. The potential for using the defoliator Antiblemma leucocyma (Lepidoptera: Noctuidae) as a biological control agent of M. calvescens was evaluated in the native habitat of the insect in Brazil. Impact assessment in the field showed that 37.2% of leaves presented damage by A. leucocyma, and among damaged leaves, 1.5-51.9% of the leaf area (16.3% on average) was affected. Damage was found in young to fully expanded leaves (28-915 cm² in area). Individual A. leucocyma developing as third through sixth instars in the laboratory consumed an average of 1348 cm² of M. calvescens leaf material in about 11 days. Populations of A. leucocyma in the field were heavily impacted (up to 83% parasitism) by a braconid parasitoid. Observations in the field and single- and two-host choice tests in the laboratory indicated that A. leucocyma has a narrow host range restricted to M. calvescens. Usefulness of this herbivore for biological control in Hawaii appears low, however, because of its probable susceptibility to generalist parasitoids.     

Extensive spatial genetic structure revealed by AFLP but not SSR molecular markers in the wind-pollinated tree, Fagus sylvatica

Studies of fine-scale spatial genetic structure (SGS) in wind-pollinated trees have shown that SGS is generally weak and extends over relatively short distances (less than 30-40 m) from individual trees. However, recent simulations have shown that detection of SGS is heavily dependent on both the choice of molecular markers and the strategy used to sample the studied population. Published studies may not always have used sufficient markers and/or individuals for the accurate estimation of SGS. To assess the extent of SGS within a population of the wind-pollinated tree Fagus sylvatica, we genotyped 200 trees at six microsatellite or simple sequence repeat (SSR) loci and 250 amplified fragment length polymorphisms (AFLP) and conducted spatial analyses of pairwise kinship coefficients. We re-sampled our data set over individuals and over loci to determine the effect of reducing the sample size and number of loci used for SGS estimation. We found that SGS estimated from AFLP markers extended nearly four times further than has been estimated before using other molecular markers in this species, indicating a persistent effect of restricted gene flow at small spatial scales. However, our SSR-based estimate was in agreement with other published studies. Spatial genetic structure in F. sylvatica and similar wind-pollinated trees may therefore be substantially larger than has been estimated previously. Although 100-150 AFLP loci and 150-200 individuals appear sufficient for adequately estimating SGS in our analysis, 150-200 individuals and six SSR loci may still be too few to provide a good estimation of SGS in this species.     

Cost‐effective development of highly polymorphic microsatellite in Japanese quail facilitated by next‐generation sequencing

Next‐generation sequencing technologies permit rapid and cost‐effective identification of numerous putative microsatellite loci. Here, from the genome sequences of Japanese quail, we developed microsatellite markers containing dinucleotide repeats and employed these for characterisation of genetic diversity and population structure. A total of 385 individuals from 12 experimental and one wild‐derived Japanese quail lines were genotyped with newly developed autosomal markers. The maximum number of alleles, expected heterozygosity and polymorphic information content (PIC) per locus were 10, 0.80 and 0.77 respectively. Approximately half of the markers were highly informative (PIC ≥ 0.50). The mean number of alleles per locus and observed heterozygosity within a line were in the range of 1.3–4.1 and 0.11–0.53 respectively. Compared with the wild‐derived line, genetic diversity levels were low in the experimental lines. Genetic differentiation (F_ST) between all pairs of the lines ranged from 0.13 to 0.83. Genetic clustering analyses based on multilocus genotypes of individuals showed that most individuals formed clearly defined clusters corresponding to the origins of the lines. These results suggest that Japanese quail experimental lines are highly structured. Microsatellite markers developed in this study may be effective for future genetic studies of Japanese quail.     

Host-related genetic differentiation in the anther smut fungus Microbotryum violaceum in sympatric, parapatric and allopatric populations of two host species Silene latifolia and S. dioica

We investigated genetic diversity in West European populations of the fungal pathogen Microbotryum violaceum in sympatric, parapatric and allopatric populations of the host species Silene latifolia and S. dioica, using four polymorphic microsatellite loci. In allopatric host populations, the fungus was highly differentiated by host species, exhibiting high values of F(ST) and R(ST), and revealed clear and distinct host races. In sympatric and parapatric populations we found significant population differentiation as well, except for one sympatric population in which the two host species grew truly intermingled. The mean number of alleles per locus for isolates from each of the host species was significantly higher in sympatric/parapatric than in allopatric populations. This suggests that either gene flow between host races in sympatry, or in case of less neutral loci, selection in a more heterogeneous host environment can increase the level of genetic variation in each of the demes. The observed pattern of host-related genetic differentiation among these geographically spread populations suggest a long-term divergence between these host races. In sympatric host populations, both host races presumably come in secondary contact, and host-specific alleles are exchanged depending on the amount of fungal gene flow.     

The effect on Orchestia hurleyi (Amphipoda: Talitridae) of a whitey disease caused by Bacillus subtilis

Abstract

Field observations made over 10 years suggested that a bacterial disease of adults of the terrestrial amphipod Orchestia hurleyi Duncan, caused by Bacillus subtilis, is progressing southwards down the eastern side of New Zealand's South Island. As the disease spread, amphipod density appeared to decline and population age structure became truncated. In the vicinity of Dunedin and further south the amphipods are still disease-free. Signs of the disease are a progressive weakening and wasting. The animal cannot jump, and its speed of walking is reduced. Its body becomes opaque white instead of the normal translucent reddish-brown. Diseased females do not brood. There is no evidence that diseased animals moult. Death is caused by general wasting or by predators. The disease-causing organism was isolated, and healthy amphipods were re-infected from the isolate. Signs of the disease were apparent within 7 days of inoculation. The presence of the disease-causing organism in the haemocoel causes host defences to be mobilised, as shown by elevated haemocyte counts (4512 mm^?3, cf. 300 mm^?3 in healthy, disease-free adults), but as the disease progresses the animal's defences are overcome, and haemocyte counts fall to an average of 784 mm^?3 during the later stages of disease. The blood of terminally diseased amphipods is thick and creamy white, packed with motile bacterial cells, and few (if any) haemocytes are present in the circulation. Two populations were studied, one disease-free (at Dunedin) and the other heavily diseased (at Christchurch). The incidence of disease (as measured by a performance test) was about 30%r in Christchurch adults. The disease-causing strain of B. subtilis was found on the body surface of almost all adults in the diseased population. It is possible that the bacterium gains entry to the haemocoel through wounds suffered during ecdysis, conflict, or predator attack. The main differences shown by the diseased population relative to the disease-free population were: lower average density (992 m^?2, cf. 1677 m^?2); lower maximum density (3104 m^?2, cf. 9971 m^?2); smaller average size, with fewer adult instars; a smaller proportion of females brooding in each instar; and much lower egg production. The brood size/mother age relationship was the same for both populations — number of eggs in brood = -4.9 + 0.64(instar number of mother)—because in the diseased population only healthy females breed. Lower egg production in the diseased population reflects the smaller proportion of healthy females, and the number of broods per female is lower since life expectancy is much less. A computer model based on Leslie matrices was used to simulate the ecological effects of the disease. It gave predictions which conformed with the observed population features with respect to age structure and density.     

Tricholoma matsutake in a natural Pinus densiflora forest: correspondence between above- and below-ground genets, association with multiple host trees and alteration of existing ectomycorrhizal communities

Tricholoma matsutake (matsutake) is an ectomycorrhizal (ECM) fungus that produces economically important mushrooms in Japan. Here, we use microsatellite markers to identify genets of matsutake sporocarps and below-ground ECM tips, as well as associated host genotypes of Pinus densiflora. We also studied ECM fungal community structure inside, beneath and outside the matsutake fairy rings, using morphological and internal transcribed spacer (ITS) polymorphism analysis. Based on sporocarp samples, one to four genets were found within each fairy ring, and no genetic differentiation among six sites was detected. Matsutake ECM tips were only found beneath fairy rings and corresponded with the genotypes of the above-ground sporocarps. We detected nine below-ground matsutake genets, all of which colonized multiple pine trees (three to seven trees per genet). The ECM fungal community beneath fairy rings was species-poor and significantly differed from those inside and outside the fairy rings. We conclude that matsutake genets occasionally establish from basidiospores and expand on the root systems of multiple host trees. Although matsutake mycelia suppress other ECM fungi during expansion, most of them may recover after the passage of the fairy rings.     

Phylogeography of Biomphalaria glabrata and B. pfeifferi, important intermediate hosts of Schistosoma mansoni in the New and Old World tropics

The historical phylogeography of the two most important intermediate host species of the human blood fluke Schistosoma mansoni, B. glabrata in the New World, and B. pfeifferi in the Old World, was investigated using partial 16S and ND1 sequences from the mitochondrial genome. Nuclear sequences of an actin intron and internal transcribed spacer (ITS)-1 were also obtained, but they were uninformative for the relationships among populations. Phylogenetic analyses based on mtDNA revealed six well-differentiated clades within B. glabrata: the Greater Antilles, Venezuela and the Lesser Antilles, and four geographically overlapping Brazilian clades. Application of a Biomphalaria-specific mutation rate gives an estimate of the early Pleistocene for their divergence. The Brazilian clades were inferred to be the result of fragmentation, due possibly to climate oscillations, with subsequent range expansion producing the overlapping ranges. Within the Venezuela and Lesser Antilles clade, lineages from each of these areas were estimated to have separated approximately 740 000 years ago. Compared to B. glabrata, mitochondrial sequences of B. pfeifferi are about 4x lower in diversity, reflecting a much younger age for the species, with the most recent common ancestor of all haplotypes estimated to have existed 880 000 years ago. The oldest B. pfeifferi haplotypes occurred in southern Africa, suggesting it may have been a refugium during dry periods. A recent range expansion was inferred for eastern Africa less than 100 000 years ago. Several putative species and subspecies, B. arabica, B. gaudi, B. rhodesiensis and B. stanleyi, are shown to be undifferentiated from other B. pfeifferi populations.     

Clonal diversity of a lizard malaria parasite, Plasmodium mexicanum, in its vertebrate host, the western fence lizard: role of variation in transmission intensity over time and space

Within the vertebrate host, infections of a malaria parasite (Plasmodium) could include a single genotype of cells (single-clone infections) or two to several genotypes (multiclone infections). Clonal diversity of infection plays an important role in the biology of the parasite, including its life history, virulence, and transmission. We determined the clonal diversity of Plasmodium mexicanum, a lizard malaria parasite at a study region in northern California, using variable microsatellite markers, the first such study for any malaria parasite of lizards or birds (the most common hosts for Plasmodium species). Multiclonal infections are common (50-88% of infections among samples), and measures of genetic diversity for the metapopulation (expected heterozygosity, number of alleles per locus, allele length variation, and effective population size) all indicated a substantial overall genetic diversity. Comparing years with high prevalence (1996-1998 = 25-32% lizards infected), and years with low prevalence (2001-2005 = 6-12%) found fewer alleles in samples taken from the low-prevalence years, but no reduction in overall diversity (H = 0.64-0.90 among loci). In most cases, rare alleles appeared to be lost as prevalence declined. For sites chronically experiencing low transmission intensity (prevalence approximately 1%), overall diversity was also high (H = 0.79-0.91), but there were fewer multiclonal infections. Theory predicts an apparent excess in expected heterozygosity follows a genetic bottleneck. Evidence for such a distortion in genetic diversity was observed after the drop in parasite prevalence under the infinite alleles mutation model but not for the stepwise mutation model. The results are similar to those reported for the human malaria parasite, Plasmodium falciparum, worldwide, and support the conclusion that malaria parasites maintain high genetic diversity in host populations despite the potential for loss in alleles during the transmission cycle or during periods/locations when transmission intensity is low.     

陕棉抗病种质及其衍生品种的遗传多样性与群体结构研究

通过72个分布于棉花全基因组的SSR标记,对54份陕棉抗病种质及其衍生品种的遗传多样性与群体结构进行了分析。结果表明:(1)54份陕棉种质间的遗传相似系数在0.733 3~0.987 2之间,其中材料间相似系数≤0.90的占11.1%,相似系数≥0.95的占55.6%,相似系数在0.90~0.95的占33.3%。(2)72个SSR标记等位基因变异的多态性信息含量(PIC值)在0.04~0.68,平均为0.33。(3)基于遗传距离的UPGMA聚类分析显示,在遗传相似系数为0.877时将54个品种分为5类,第Ⅰ类44个品种,第Ⅲ类7个品种,第Ⅱ、Ⅳ、Ⅴ类各1个品种。(4)基于数学模型的聚类和群体结构分析显示,54份种质归属于4个组群。研究认为,54份材料间遗传相似系数较大,遗传基础比较狭窄,多样性很低。