Theoretical Analysis of Principal Components in an Umbrella Model of Intraspecific Evolution

Principal component analysis (PCA) is one of the most frequently-used approach to describe population structure from multilocus genotype data. Regarding geographic range expansions of modern humans, interpretations of PCA have, however, been questioned, as there is uncertainty about the wave-like patterns that have been observed in principal components. It has indeed been argued that wave-like patterns are mathematical artifacts that arise generally when PCA is applied to data in which genetic differentiation increases with geographic distance. Here, we present an alternative theory for the observation of wave-like patterns in PCA. We study a coalescent model -- the umbrella model -- for the diffusion of genetic variants. The model is based on a hierarchy of splits from an ancestral population without any particular geographical structure. In the umbrella model, splits occur almost continuously in time, giving birth to small daughter populations at a regular pace. Our results provide detailed mathematical descriptions of eigenvalues and eigenvectors for the PCA of sampled genomic sequences under the model. Removing variants uniquely represented in the sample, the PCA eigenvectors are defined as cosine functions of increasing periodicity, reproducing wave-like patterns observed in equilibrium isolation-by-distance models. Including rare variants in the analysis, the eigenvectors corresponding to the largest eigenvalues exhibit complex wave shapes. The accuracy of our predictions is further investigated with coalescent simulations. Our analysis supports the hypothesis that highly structured wave-like patterns could arise from genetic drift only, and may not always be artificial outcomes of spatially structured data. Genomic data related to the peopling of the Americas are reanalyzed in the light of our new theory.

Seasonal Prevalence and Novel Multilocus Genotypes of Giardia duodenalis in Yaks (Bos grunniens) in Qinghai Province, Western China

Background: Giardia duodenalis is an important opportunistic zoonotic intestinal protozoon, which could parasitize yaks. However, a few studies have been conducted on the seasonal infection of G. duodenalis in yaks in China. Methods: Overall, 1,027 fecal samples were collected from yaks of two age groups in seven cities of Qinghai Province, China at four seasons between May 2016 and Sep 2017. The prevalence and assemblages were analyzed by nested PCR and multilocus sequence typing (MLST). Results: The overall prevalence of G. duodenalis was 2.04% (21/1027) based on triose phosphate isomease (tpi) locus. No significant differences in prevalence of the organism in yaks were found among different sampling areas. Additionally, same result was also presented in different seasons. However, there was statistically significant difference between young yaks within 6 months (8.33%, 4/48) and adult yaks over 6 months (1.73%, 17/979). The assemblage A recognized as a zoonotic assemblage (n=3) was found in yaks (>6 months) from Xining, while assemblage E (n=18) was detected from yaks in six cities. There were 5, 2 and 3 G. duodenalis subtypes detected positive at the tpi, the β-giardin (bg), and the glutamate dehydrogenase (gdh) loci, with 2, 2 and 3 novel subtypes, respectively. Three samples were successfully sequenced at all three loci, forming 1 assemblages A multilocus genotype (MLG) and 2 assemblages E MLGs, not reported. Conclusion: This study indicated a zoonotic potential of G. duodenalis in yaks from Qinghai Province and provides basic information about the epidemiology of G. duodenalis.

Multilocus Genotyping of ‘Candidatus Phytoplasma solani’ Associated with Rubbery Taproot Disease of Sugar Beet in the Pannonian Plain

Rubbery taproot disease of sugar beet (RTD), associated with ‘Candidatus Phytoplasma solani’, appeared in 2020 on an epidemic scale in northern Serbia and southern Slovakia, situated at opposite edges of the Pannonian Plain. In the affected locations where the disease was assessed, symptomatic sugar beets were analysed for phytoplasma infection. Additionally, multilocus sequence analyses of ‘Ca. P. solani’ strains on epidemiologically informative marker genes (tuf, stamp and vmp1) were performed. Symptomatic sugar beets from other countries of the Pannonian Plain (Croatia, Hungary and Austria), one sample from Germany, and red beets from Serbia were included in the analyses. ‘Ca. P. solani’ was detected in sugar beet in all assessed countries, as well as in red beet. Molecular analyses revealed the high genetic variability of ‘Ca. P. solani’ with the presence of all four tuf-types (a, b1, b2 and d), 14 stamp genotypes (seven new) and five vmp1 profiles (one new). The most common multilocus genotype in Serbia, Slovakia, Croatia, and Hungary was dSTOLg (tuf-d/STOL/V2-TA). It was dominant on sites with epidemic RTD outbreaks in the Pannonian Plain and in several sugar beet fields with non-epidemic RTD occurrence suggesting the prevalence of a particular epidemiological pathway during the epidemic’s phases.

Host Dependent and Geographical Structuring of Citrus Canker Bacteria at Peshawar, Pakistan

Citrus canker disease, caused by Xanthomonas axonopodis pv. Citri (Xac) induces huge losses to citrus, particularly in nurseries. This study assessed the level of genetic diversity and divergence in Xac population prevalent in district Peshawar on various host species, based on isolates collected from different fruit nurseries of Peshawar. Surveillance resulted in collection of 80 samples, out of which 50 bacterial samples were isolated. Genotyping of the isolates using RAPD markers amplified 35 scorable loci with an average of 8.7 loci per primers and level of polymorphism was 100%, i.e., almost all of the isolates genotyped had a different multilocus genotype. The loci GLA-031000 was recorded with the highest gene diversity (0.51) followed by GLB-05_1000 and GLA-03_1100 (0.49). The maximum diversity index (0.50) was recorded for loci GLA-031000, followed by GLB-051000 and GLA-03_1100 (0.48). A high diversity was observed across all locations, with the range of genotypic diversity from 0.778 (detected at Malakandair) to 0.955 (detected at Hayatabad and Tarnab). Divergence between samples collected from different locations was limited as revealed by the PCA, PCoA, phylogenetic tree and network analyses. Samples originated from various hosts also revealed a high diversity across host types with the minimum genotype diversity observed for Eureka Lemon (0.750) and the maximum for sweet lemon (0.966). The divergence for samples collected on various citrus host types was absent. The very small linkage disequilibrium (0.006–0.159) reflected on the potential recombination in the population, which must have direct implications to disease management and resistance exploitation. © 2021 Friends Science Publishers

Prevalence and multi-locus genotyping of Giardia duodenalis in rabbits from Shaanxi province in northwestern China

Giardia duodenalis is an important parasite with veterinary and public health significance worldwide. The presence and zoonotic assemblages of G. duodenalis have previously been reported in rabbits. In this study, to understand the infection status of G. duodenalis in rabbits from Shaanxi province, a total of 537 fecal samples were collected from two breeds of rabbits in four age groups (<30 days, 31–90 days, 91–200 days and >200 days) from four geographical origins (Fengxiang, Yangling, Tongchuan, and Shanyang). The presence of G. duodenalis in these samples was assessed using molecular assays based on beta-giardin (bg). The glutamate dehydrogenase (gdh) and triosephosphate isomerase (tpi) loci were then amplified in the bg-positive samples for multi-locus genotype (MLG) analysis. The total prevalence of G. duodenalis in these rabbits was 3.54% (19/537). Giardia duodenalis infection was found in both breeds of rabbits, and in all farms and age groups, but with no statistically significant differences related to these factors (p > 0.05). Two assemblages, including B and E, were identified, with the former the predominant assemblage detected in both breeds, and in all age groups and farms. Sequence analysis revealed 2 (named as rbg1-2), 1 (named as rtpi1), and 2 (named as rgdh1-2) haplotypes at the gene loci of bg, tpi, and gdh, respectively, forming a multilocus genotype (MLG) of assemblage B (rbg1, rtpi1, and rgdh1). These findings reveal the significant zoonotic potential and genetic diversity of G. duodenalis in rabbits in Shaanxi Province, PR China.

Evidence of sexual reproduction events in the dagger nematode Xiphinema index in grapevine resistance experiments under controlled conditions

The dagger nematode Xiphinema index has a major economic impact due to its transmission of Grapevine fanleaf virus (GFLV) to grapevines. This vector nematode, which was introduced into Western countries from the Middle East together with the domesticated grapevine, mostly reproduces by meiotic parthenogenesis, but microsatellite multilocus genotype (MLG) analysis has revealed the occurrence of rare sexual reproduction events in field conditions. In a previous six-year study under controlled conditions, we evaluated the durability of resistance (R) to X. index in accessions derived from a muscadine R source and reference accessions. In this previous study, we used an equal-proportion mixture of four lines (from Spain, Italy, Greece and Iran) representative of X. index diversity as the inoculum, and we collected random samples in three-, four-, five- and six-year-old vines. Here, we genotyped the individuals from these samples using MLG technique, and we analyzed the changes in line frequency and the occurrence of sexual reproduction events between lines over time. The nematode lines differed in aggressiveness and hybrids between lines were detected at a low, but apparently increasing rate. Hybridization events were recovered in all accessions, regardless of resistance status and propagation type. Finally, our data provide the first evidence of sexual reproduction in the nematode X. index under controlled conditions.

Genomic basis of drought resistance in Fagus sylvatica

In the course of global climate change, central Europe is experiencing more frequent and prolonged periods of drought. These drought events have severe and detrimental impacts on the forest ecosystem. The drought years 2018 and 2019 affected European beeches (Fagus sylvatica L.) in noticeably different ways: even in the same local stand, badly drought damaged trees immediately neighboured apparently healthy trees. This led to the hypothesis that the genotype rather than the environment was responsible for this conspicuous pattern. We used this natural experiment to study the genomic basis of drought resistance in a Pool-GWAS approach. Contrasting the extreme phenotypes, we identified 106 significantly associated SNPs throughout the genome. The majority of affected genes was previously implicated in drought reaction in other plant species. Most observed non-synonymous changes led either to a substantial functional amino acid exchange or a stop-codon. A SNP-assay with 70 informative loci allowed the successful prediction of drought phenotype from the multilocus genotype in 98.6% in a validation sample of 92 trees with Linear Discriminant Analysis. Drought resistance in European beech appeared to be a moderately polygenic trait that should nevertheless respond well to natural selection, selective management, and breeding. The widespread distribution of drought resistance across natural beech populations represents an important argument for maintaining genetic diversity in dynamic forest ecosystems. The results from this study could therefore contribute to harness beech wood forests against ongoing climate change.

Identification of resistant clones of Eurasian (Myriophyllum spicatum) and hybrid (Myriophyllum spicatum × Myriophyllum sibiricum) watermilfoil to an operational rate of fluridone

Genetic assays to identify herbicide-resistant plants are a promising tool to reduce herbicide failures. However, the genetic basis of herbicide resistance is frequently unknown. In clonal weed species, DNA fingerprinting could be a useful tool to identify known resistant versus susceptible genets (clones) that occur in multiple locations, without an immediate need for understanding the genetic mutation(s) conferring resistance. Eurasian watermilfoil (Myriophyllum spicatum L.) and hybrids with native northern watermilfoil (Myriophyllum spicatum × Myriophyllum sibiricum Kom.) are mostly clonal invasive aquatic plants, and the same clones can be found in multiple waterbodies. Previously, a clone was confirmed as resistant to the commonly used herbicide fluridone, and a recent genetic survey in Michigan identified this genotype (MG-237) in at least seven other lakes. We hypothesized that MG-237 collected from different lakes would also exhibit fluridone resistance. However, MG-237 may have accumulated resistance mutations at different times during its spread across Michigan, resulting in fluridone-resistant and fluridone-susceptible MG-237 clones distributed in different lakes. We used a herbicide assay to test the response of several accessions, including MG-237 accessions from multiple lakes, to the Michigan operational rate of 6 µg L−1 fluridone. We found that all accessions of MG-237 exhibited resistance to 6 µg L−1 fluridone. A second genotype (MG-377) was also resistant to 6 µg L−1 fluridone. The rest of the accessions were found to be significantly injured by 6 µg L−1 fluridone. Our results suggest that 6 µg L−1 fluridone would not effectively control waterbodies dominated by MG-237 or MG-377, whereas waterbodies dominated by the other genotypes in our study would likely be controlled. Although more studies are needed to identify the variation in sensitivity of the accessions tested here and the genetic basis of fluridone resistance in Myriophyllum, our results suggest that multilocus genotype data may be an effective tool to identify and track herbicide-resistant genotypes of Myriophyllum in the short term.