High Evolutionary Potential Research Articles

The Spiral Model of Evolution: Stable Life Forms of Organisms and Unstable Life Forms of Cancers.

If one must prioritize among the vast array of contributing factors to cancer evolution, environmental-stress-mediated chromosome instability (CIN) should easily surpass individual gene mutations. CIN leads to the emergence of genomically unstable life forms, enabling them to grow dominantly within the stable life form of the host. In contrast, stochastic gene mutations play a role in aiding the growth of the cancer population, with their importance depending on the initial emergence of the new system. Furthermore, many specific gene mutations among the many available can perform this function, decreasing the clinical value of any specific gene mutation. Since these unstable life forms can respond to treatment differently than stable ones, cancer often escapes from drug treatment by forming new systems, which leads to problems during the treatment for patients. To understand how diverse factors impact CIN-mediated macroevolution and genome integrity-ensured microevolution, the concept of two-phased cancer evolution is used to reconcile some major characteristics of cancer, such as bioenergetic, unicellular, and multicellular evolution. Specifically, the spiral of life function model is proposed, which integrates major historical evolutionary innovations and conservation with information management. Unlike normal organismal evolution in the microevolutionary phase, where a given species occupies a specific location within the spiral, cancer populations are highly heterogenous at multiple levels, including epigenetic levels. Individual cells occupy different levels and positions within the spiral, leading to supersystems of mixed cellular populations that exhibit both macro and microevolution. This analysis, utilizing karyotype to define the genetic networks of the cellular system and CIN to determine the instability of the system, as well as considering gene mutation and epigenetics as modifiers of the system for information amplification and usage, explores the high evolutionary potential of cancer. It provides a new, unified understanding of cancer as a supersystem, encouraging efforts to leverage the dynamics of CIN to develop improved treatment options. Moreover, it offers a historically contingent model for organismal evolution that reconciles the roles of both evolutionary innovation and conservation through macroevolution and microevolution, respectively.

Diversity and Genetic Structure of a Natural Population of Mauritia flexuosa L. f. in APA-Pandeiros, Using Microsatellite Markers

Genetic diversity is essential to ensure that species maintain high adaptive evolutionary potential to resist environmental stochasticity. Thus, this research aimed to estimate the genetic diversity and structure of a natural population of Mauritia flexuosa and its stages, using five microsatellite primers. DNA was extracted from leaves collected from individuals of the three classes (G1-adult, G2-juvenile and G3-regenerant). Genetic diversity estimates indicated an average of 7.8 alleles/locus and lower observed heterozygosity (Ho) than expected heterozygosity (He) in the population (0.272-0.395 and 0.275-0.401, respectively). The Shannon Index (I) indicated moderate genotypic diversity and richness in the analyzed population, and exclusive alleles were found at the different stages. Also found were a lower population index (FST = 0.019) and a higher individual fixation index (FIS = 0.169). Classes G1 and G2 exhibited greater genetic similarity to each other than to G3, which had more distant genetic characteristics. These results revealed lower genetic diversity among regenerating (G3) individuals and greater genetic diversity among adults (G1). Immediate strategies for in situ and ex situ genetic conservation of M. flexuosa are essential to preserve its genetic variability and assist future programs for the improvement.

Cleaner Fish Do Not Impact the Pigmentation of Salmon Lice (Lepeophtheirus salmonis) in Commercial Aquaculture Cages

Salmon lice are one of the biggest challenges to sustainable salmonid aquaculture. The species display high evolutionary potential, which is evident by its development of resistance to numerous chemical compounds used for delousing. In response to this, salmon farms now use non-chemical delousing methods to minimize the damage done by salmon lice, including heavy reliance on cleaner fish. Anecdotal reports from farmers and fish health personnel in areas where cleaner fish are used have suggested that salmon lice are becoming less pigmented, potentially making them harder for cleaner fish to visually detect. This experiment investigated changes in the pigmentation of salmon lice in relation to the use of cleaner fish, louse stage and sex, temperature, preferred salmon swimming depth, daylength, and salinity. Salmon lice were sampled from snorkel cages on a commercial salmon farm where three cages were stocked with farmed lumpfish and ballan wrasse, and three cages were without cleaner fish. Water temperature, salinity, and depth were recorded using a conductivity, temperature, and depth recorder. Pigmentation was measured via photographic analysis of individual lice. Although louse pigmentation varied considerably throughout the experiment, using cleaner fish throughout a single production cycle did not reduce average louse pigmentation compared to control cages. On average, male lice were significantly darker pigmented than females, but otherwise there were no patterns in louse pigmentation in relation to life stage, salinity, temperature, or daylength. Salmon lice exhibit a high degree of evolvability and have become resistant to every chemical removal treatment developed thus far. The present data suggest that, with the densities and species of cleaner fish commonly used in commercial salmon production, there is not strong directional selection on louse pigmentation. Lice, at least with regard to visual appearance, are not likely to adapt in a way which reduces cleaner fish efficacy anytime soon.

The Impatiens Downy Mildew Epidemic in the United States Is Caused by New, Introgressed Lineages of Plasmopara destructor with Prominent Genotypic Diversity and High Evolutionary Potential.

Impatiens downy mildew (IDM) caused by Plasmopara destructor is currently the primary constraint on the production and use of impatiens (Impatiens walleriana) as bedding plants worldwide. Downy mildew has been documented since the 1880s from wild-grown Impatiens spp. but epidemic outbreaks of the disease affecting the commercially grown, ornamental I. walleriana were only reported for the first time in 2003 in the United Kingdom and in 2004 in the United States. Here, we assess the genetic diversity, level of differentiation, and population structure from 623 samples associated with current and preepidemic IDM outbreaks, by genotyping the samples with simple sequence repeat markers. P. destructor population structure following the emergence of IDM in the United States is subdivided into four genetic lineages characterized by high genetic diversity, mixed reproduction mode, inbreeding, and an excess of heterozygosity. P. destructor genotypes are significantly differentiated from preepidemic IDM samples from hosts other than I. walleriana but no geographical or temporal subdivision is evident. P. destructor samples from different Impatiens spp. show significant but very low levels of differentiation in the analysis of molecular variance test that did not hold in discriminant analysis of principal components analyses. The same was observed between samples of P. destructor and P. velutina recovered from I. walleriana. The finding of shared genotypes in samples from different countries and lack of differentiation among U.S. and Costa Rican samples indicate the occurrence of international movement of the pathogen. Our study provides the first high-resolution analysis of the diversity of P. destructor populations and the IDM epidemic that may be instrumental for disease management and breeding efforts.

Large-scale population survey of Leptosphaeria maculans in France highlights both on-going breakdowns and potentially effective resistance genes in oilseed rape.

Leptosphaeria maculans, the cause of stem canker of oilseed rape, develops gene-for-gene interactions with its host and shows a high evolutionary potential to 'break down' novel resistance genes (R, Rlm) deployed in cultivars over large areas. For optimal management of R genes, updated knowledge of the population structure of the pathogen is needed. In France, large-scale surveys have been done at 10-year intervals since 2000. Here we report the characterization of a large L. maculans population collected in France in 2019-2020. A total of 844 isolates were collected from 11 sites in ten French departments and were phenotyped for their virulence against nine Brassica napus R genes. All isolates were virulent toward Rlm2 and Rlm9. Very few isolates were avirulent on Rlm1 (1.8%) and Rlm4 (0.6%). Avirulent isolates toward Rlm7 ('AvrLm7') varied from 67% to 11.3%, depending on the site sampled, illustrating the ongoing breakdown of Rlm7. The decrease of AvrLm7 isolates (29.2% at the national level) compared to the 2010 survey (96.5%) was accompanied by an increase of avirulent isolates on Rlm3 (0% in 2010; 54% in 2019-2020). However, virulent isolates on both Rlm3 and Rlm7, previously rarely detected, were found in all sites with a frequency of 17.3%. Finally, most or all isolates were avirulent on Rlm11 (96.1%), LepR2 (RlmS, 99.8%), and Rlm6 (100%), suggesting these three genes still effectively control the disease. These data will help guide strategies for breeding and deploying resistant oilseed rape varieties against L. maculans in France. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Head Shape Heritability in the Hungarian Meadow Viper Vipera ursinii rakosiensis.

Understanding heritability patterns in functionally relevant traits is a cornerstone for evaluating their evolutionary potential and their role in local adaptation. In this study, we investigated patterns of heritability in the head shape of the Hungarian meadow viper (Vipera ursinii rakosiensis). To this end, we used geometric morphometric data from 12 families composed of 8 mothers, 6 fathers and 221 offspring, bred in captivity at the Hungarian Meadow Viper Conservation Centre (Hungary). We separately evaluated maternal and paternal contributions to the offspring phenotype, in addition to additive genetic effects, all determined using a mixed animal model. Our results indicate a strong genetic and maternal contribution to head shape variations. In contrast, the paternal effects-which are rarely evaluated in wild-ranging species-as well as residual environmental variance, were minimal. Overall, our results indicate a high evolutionary potential for head shape in the Hungarian meadow viper, which suggests a strong contribution of this ecologically important trait in shaping the ability of this endangered species to adapt to changing conditions and/or habitats. Furthermore, our results suggest that maternal phenotypes should be carefully considered when designing captive breeding parental pairs for reinforcing the adaptive capacity of threatened populations, whereas the paternal phenotypes seem less relevant.

Genotype-environment associations across spatial scales reveal the importance of putative adaptive genetic variation in divergence.

Identifying areas of high evolutionary potential is a judicious strategy for developing conservation priorities in the face of environmental change. For wide‐ranging species occupying heterogeneous environments, the evolutionary forces that shape distinct populations can vary spatially. Here, we investigate patterns of genomic variation and genotype–environment associations in the hermit thrush (Catharus guttatus), a North American songbird, at broad (across the breeding range) and narrow spatial scales (at a hybrid zone). We begin by building a genoscape or map of genetic variation across the breeding range and find five distinct genetic clusters within the species, with the greatest variation occurring in the western portion of the range. Genotype–environment association analyses indicate higher allelic turnover in the west than in the east, with measures of temperature surfacing as key predictors of putative adaptive genomic variation rangewide. Since broad patterns detected across a species' range represent the aggregate of many locally adapted populations, we investigate whether our broadscale analysis is consistent with a finer scale analysis. We find that top rangewide temperature‐associated loci vary in their clinal patterns (e.g., steep clines vs. fixed allele frequencies) across a hybrid zone in British Columbia, suggesting that the environmental predictors and the associated candidate loci identified in the rangewide analysis are of variable importance in this particular region. However, two candidate loci exhibit strong concordance with the temperature gradient in British Columbia, suggesting a potential role for temperature‐related barriers to gene flow and/or temperature‐driven ecological selection in maintaining putative local adaptation. This study demonstrates how patterns identified at the broad (macrogeographic) scale can be validated by investigating genotype–environment correlations at the local (microgeographic) scale. Furthermore, our results highlight the importance of considering the spatial distribution of putative adaptive variation when assessing population‐level sensitivity to climate change and other stressors.

Nasopharyngeal Carcinoma Progression: Accumulating Genomic Instability and Persistent Epstein-Barr Virus Infection.

Genomic instability facilitates the evolution of cells, tissues, organs, and species. The progression of human malignancies can be regarded as the accumulation of genomic instability, which confers a high evolutionary potential for tumor cells to adapt to continuous changes in the tumor microenvironment. Nasopharyngeal carcinoma (NPC) is a head-and-neck squamous-cell carcinoma closely associated with Epstein–Barr virus (EBV) infection. NPC progression is driven by a combination of accumulated genomic instability and persistent EBV infection. Here, we present a review of the key characteristics of genomic instability in NPC and the profound implications of EBV infection. We further discuss the significance of profiling genomic instability for the assessment of disease progression and treatment efficacy, as well as the opportunities and challenges of targeted therapies for NPC based on its unique genomic instability.

Population Genomics Reveals Population Structure and Mating-Type Loci in Marssonina brunnea.

Marssonina brunnea is an important fungal pathogen of poplar trees. We collected 32 M. brunnea f.sp. multigermtubi (MbMu) and three M. brunnea f.sp. monogermtubi (MbMo) isolates from four poplar species in three Chinese regions and performed genome resequencing. An annotation of SNPs of MbMu indicated that the SNPs potentially have a functional effect on 69.2% of the predicted genes. Using the SNP dataset of nonredundant isolates, a structure and principal component analysis revealed that MbMu and MbMo belong to two genetically distinct populations. By contrast, subpopulation structures could not be found among MbMu isolates. A neighbor-net analysis and a homoplasy index test provided evidence of recombination among MbMu isolates. The short distance (109–174 bp) of linkage disequilibrium half-decay supported the presence of a high level of recombination in the MbMu population. The genetic architectures of the MAT loci of MbMu and MbMo were revealed by searching genome assemblies or by homology-based cloning, and a BLAST search verified each isolate carrying one of the two opposite MAT loci. This study revealed that the MbMu population contains a wide range of functional variants, shows high-frequency recombination, and exhibits heterothallic mating systems, indicating high evolutionary potential and a resultant threat to poplar plantations.

Genome-Wide Association Analyses Track Genomic Regions for Resistance to Ascochyta rabiei in Australian Chickpea Breeding Germplasm.

Ascochyta blight (AB), caused by a necrotrophic fungus, Ascochyta rabiei (syn. Phoma rabiei) has the potential to destroy the chickpea industry worldwide, due to limited sources of genetic resistance in the cultivated gene pool, high evolutionary potential of the pathogen and challenges with integrated disease management. Therefore, the deployment of stable genetic resistance in new cultivars could provide an effective disease control strategy. To investigate the genetic basis of AB resistance, genotyping-by-sequencing based DArTseq-single nucleotide polymorphism (SNP) marker data along with phenotypic data of 251 advanced breeding lines and chickpea cultivars were used to perform genome-wide association (GWAS) analysis. Host resistance was evaluated seven weeks after sowing using two highly aggressive single spore isolates (F17191-1 and TR9571) of A. rabiei. GWAS analyses based on single-locus and multi-locus mixed models and haplotyping trend regression identified twenty-six genomic regions on Ca1, Ca4, and Ca6 that showed significant association with resistance to AB. Two haplotype blocks (HB) on chromosome Ca1; HB5 (992178–1108145 bp), and HB8 (1886221–1976301 bp) were associated with resistance against both isolates. Nine HB on the chromosome, Ca4, spanning a large genomic region (14.9–56.6 Mbp) were also associated with resistance, confirming the role of this chromosome in providing resistance to AB. Furthermore, trait-marker associations in two F3 derived populations for resistance to TR9571 isolate at the seedling stage under glasshouse conditions were also validated. Eighty-nine significantly associated SNPs were located within candidate genes, including genes encoding for serine/threonine-protein kinase, Myb protein, quinone oxidoreductase, and calmodulin-binding protein all of which are implicated in disease resistance. Taken together, this study identifies valuable sources of genetic resistance, SNP markers and candidate genes underlying genomic regions associated with AB resistance which may enable chickpea breeding programs to make genetic gains via marker-assisted/genomic selection strategies.

Genetic Characteristics and Metabolic Interactions between Pseudocercospora fijiensis and Banana: Progress toward Controlling Black Sigatoka.

The international importance of banana and severity of black Sigatoka disease have led to extensive investigations into the genetic characteristics and metabolic interactions between the Dothideomycete Pseudocercospora fijiensis and its banana host. P. fijiensis was shown to have a greatly expanded genome compared to other Dothideomycetes, due to the proliferation of retrotransposons. Genome analysis suggests the presence of dispensable chromosomes that may aid in fungal adaptation as well as pathogenicity. Genomic research has led to the characterization of genes and metabolic pathways involved in pathogenicity, including: secondary metabolism genes such as PKS10-2, genes for mitogen-activated protein kinases such as Fus3 and Slt2, and genes for cell wall proteins such as glucosyl phosphatidylinositol (GPI) and glycophospholipid surface (Gas) proteins. Studies conducted on resistance mechanisms in banana have documented the role of jasmonic acid and ethylene pathways. With the development of banana transformation protocols, strategies for engineering resistance include transgenes expressing antimicrobial peptides or hydrolytic enzymes as well as host-induced gene silencing (HIGS) targeting pathogenicity genes. Pseudocercospora fijiensis has been identified as having high evolutionary potential, given its large genome size, ability to reproduce both sexually and asexually, and long-distance spore dispersal. Thus, multiple control measures are needed for the sustainable control of black Sigatoka disease.

Chikungunya virus: Molecular epidemiology of nonstructural proteins in Pakistan.

Chikungunya virus (CHIKV) is considered a public health problem due to its rapid spread and high morbidity. In 2016–2017 an outbreak of CHIKV was occurred in Pakistan but the data regarding the genomic diversity of CHIKV was not reported. Hence, the current study aimed to determine the genetic diversity of CHIKVs in Pakistan. A cross sectional study was carried out using sera of infected CHIKV patients (n = 1549) during the outbreak in Pakistan (2016–2018). Nucleotide sequencing of non-structural genes of CHIKV from eight isolates were performed followed by phylogenetic analysis using Bayesian method. Phylogenetic analysis suggested that the Pakistani CHIKV strains belonged to Indian Ocean Lineage (IOL) of genotype ECSA and C1.3a clade. Furthermore, the Pakistani isolates showed several key mutations (nsP2-H130Y, nsP2-E145D, nsP4-S55N and nsP4- R85G) corresponding to mutations reported in 2016 Indian strains of CHIKV. The molecular analysis revealed high evolutionary potential of CHIKV strains as well as better understanding of enhanced virulence and pathogenesis of this outbreak. The study highlights the need to continue surveillance in order to understand viral diversity over time and to devise preventive measures to limit diseases transmission in the region.

First Report of Hemileia vastatrix (Coffee Leaf Rust) Physiological Races Emergent in Coffee Germplasm Collections in the Coffee-Cropping Regions of China.

Coffee leaf rust (CLR), caused by the obligate biotrophic fungus Hemileia vastatrix (Hv), is a devastating disease worldwide leading to severe reductions in yield and economic losses in coffee plantations, especially of Coffea arabica L. (Talhinhas et al. 2017). The frequent emergence of new Hv races is a major constraint on coffee production due to continuous exertion of selective pressure on the pathogen from pathogen-resistant cultivars under the coevolutionary 'arms race' (Silva et al. 2018). More than 50 physiological races of Hv have been described globally (Várzea & Marques 2005), while at least 16 Hv races have been detected in China (Bai et al. 2018; Zhang et al. 2014; Chen et al. 1998). Coffee is an important cash crop in China (Yan et al. 2019). Most of the coffee germplasm collections in China are in the main coffee-cropping regions, although documentation on the prevalent Hv races is lacking. A total of 57 CLR samples (each sample contained multi leaves with 20-30 pustules of coffee rust) were collected from 4 germplasm fields situated in the main coffee-cropping regions during the high seasonal incidence of CLR in 2018-2019: Field 1, Coffee Germplasm Collection of Malipo County, Wenshan (23°11' N, 104°55' E, 550 m); Field 2, Coffee Germplasm Collection I in Puer (22°47'45″ N, 100°58'59″ E, 1320 m); Field 3, Coffee Germplasm Collection II in Puer (22°37'36″ N, 100°59'50″ E, 1010 m); and Field 4, Coffee Germplasm Collection in Ruili (24°01' N, 97°51' E, 1260 m). Urediniospores were recovered on susceptible genotypes 849/1 Matari and 19/1 Cantura and tested on a set of coffee differentials at the CIFC (Oeiras, Portugal) following standard race-typing procedure described by D' Oliveirar & Rodiagues (1961). The coffee trees where the rusts isolated were used to verify virulence and avirulence. The infection type criteria determining virulence and avirulence based on the classification standards for disease resistance (D' Oliveirar, 1954-57). Twenty-seven pure-cultured Hv isolates were derived from single rust pustules taken from distinct sample groups. The predominant race XXXVII (v2,5,6,7,9) was present in Field 1, 2, and 3 at high frequency (74.04%) separately derived from the genotypes CATUAÍ, Arabica-Catimor Derivates, T2, CCC 24, Typica, T8667 Catimor HW 26/5 (F2) and Sarchimor. Race XXXIV (v2,5,7,9) was detected in Field 4 (3.70%). Races XXXVII and XXXIV had emerged in China during 2011-2015 (Bai et al. 2017 & 2018). A new race (v2,5,6,7) (7.41%) was isolated from the host DTART 316 and was able to infect the differentiators of physiologic Groups D, E, R, 4, 6, and a. Based on its pathological and genetic characteristics, Hv with high evolutionary potential has inevitably overcome the resistance of released coffee cultivars with increase virulence, thereby adapting to new hosts (Silva et al. 2018; Talhinhas et al. 2017; Zambolim 2016; McCook & Vandermeer 2015). The results obtained in this work corroborate the evidence that the emergence of new Hv races occurs preferentially at germplasm fields since the multi-selection pressures from various hosts. Our findings are of considerable importance given the potential of the coffee germplasm collections in coffee regions to promote evolution of new races. The continued emergence of new Hv races places the current commercial cultivars at risk from a loss of resistance. Monitoring the occurrence, dissemination, distribution, and pathogenicity of new races is essential for targeted resistance breeding and CLR control.

The genetic drivers for the successful invasive potential of a generalist bird, the House crow

What kind of genetic structure helps the rapid range expansion of the invasive species is fundamental to understand spread of invasion. The House crow (Corvus splendens), an ecological generalist, having a large native and introduced distribution range, is a good study model to investigate the genetic structure and adaptations underpinning the evolutionary potential for successful biological invasion. Thirteen mainland and one island native population from the Indian subcontinent were studied using four nuclear introns and mitochondrial genome to determine the phylogeographic structure and demographic history. A large, panmictic long-term expanding native population dating from the last glacial period (~ 30,000 ya) was inferred leading to great genetic diversity across the whole native range. The thirteen mitochondrial encoded proteins, directly involved in the energy supplying pathway, could underlie metabolic adaptations during range expansion under diverse climate conditions. Therefore, to investigate the molecular selection on these genes in native and introduced ranges, five previously studied introduced populations from Southeast Asia and Africa were included. The native populations originating from hot arid and humid tropical areas exhibited the signatures of positive selection on four codons located in three genes (ND5, Cytb and COX2), suggesting these may have evolved under environmental stresses in those regions. Our findings demonstrated the native range population as the reservoir of the species’ genetic diversity, mitogenomic patterns of the introduced populations related to native range of species and no varaints could be associated with climate in introduced range. Thus,inferred that the pre-adapted standing genetic variations evolved during dispersion over the native range are the predominant source of the high evolutionary potential and contribute to the successful invasion history. These findings will help to predict the future introduced range of the House crow.

The Durability of Quantitative Host Resistance and Variability in Pathogen Virulence in the Interaction Between European Grapevine Cultivars and Plasmopara viticola

European grapevine, Vitis vinifera, carries no major resistances against Plasmopara viticola, the causal agent of grapevine downy mildew. The introgression of quantitative trait loci conferring resistance to P. viticola (Rpv) from American and Asian donor species has resulted in a range of resistant cultivars. In light of the perennial nature of grapevine and the high evolutionary potential of P. viticola, the durability of this quantitative resistance is an important challenge. Durability of host resistance and variability in pathogen virulence may be evaluated by describing interactions between pathogen isolates and grapevine cultivars in terms of Rpv loci. A set of 16 cultivars carrying different combinations of Rpv loci, was challenged with five P. viticola isolates, obtained from susceptible or Rpv3.1+V. vinifera cultivars. Based on the severity of sporulation, different host and pathogen phenotypes might be distinguished, which could be related to the presence of different Rpv loci. The hormonal responses before and during some interactions were compared to assess the resistance mechanisms underlying Rpv3.1, Rpv10, and Rpv12 and the infection mechanisms of the different isolates. This paper reports on the strength of some of the commonly used Rpv loci, single or stacked. The isolates derived from Rpv3.1+ hosts, GREPv1 and GPHPv1, were able to sporulate intensely on cultivars carrying Rpv3.1, without triggering necrosis. Moreover, Rpv10 was not able to efficiently halt the development of the Rpv3.1-breaking isolate GPHPv1. Cultivars carrying Rpv12, however, were resistant to all five P. viticola isolates. Phytohormones might be implicated in the basal resistance against this pathogen, but during the early defense response, no significant hormonal responses to the isolates were observed. The isolate-specificity of the Rpv3- and Rpv10-mediated resistance suggests that these loci do not result in the most sustainable resistance. Furthermore, the isolate-specific behavior of the pathogen emphasizes the need for a characterization system for P. viticola. A standardized phenotyping assay may be used to determine P. viticola pathogen phenotypes or measure the durability, strength, and isolate-specificity of the host quantitative resistances. The characterization of both components of the pathosystem may lead to an increased understanding of the resistance mechanisms, beneficial for a durable deployment of resistance genes.

Septoria Nodorum Blotch of Wheat: Disease Management and Resistance Breeding in the Face of Shifting Disease Dynamics and a Changing Environment.

The fungus Parastagonospora nodorum is a narrow host range necrotrophic fungal pathogen that causes Septoria nodorum blotch (SNB) of cereals, most notably wheat (Triticum aestivum). Although commonly observed on wheat seedlings, P. nodorum infection has the greatest effect on the adult crop. It results in leaf blotch, which limits photosynthesis and thus crop growth and yield. It can also affect the wheat ear, resulting in glume blotch, which directly affects grain quality. Reports of P. nodorum fungicide resistance, the increasing use of reduced tillage agronomic practices, and high evolutionary potential of the pathogen, combined with changes in climate and agricultural environments, mean that genetic resistance to SNB remains a high priority in many regions of wheat cultivation. In this review, we summarize current information on P. nodorum population structure and its implication for improved SNB management. We then review recent advances in the genetics of host resistance to P. nodorum and the necrotrophic effectors it secretes during infection, integrating the genomic positions of these genetic loci by using the recently released wheat reference genome assembly. Finally, we discuss the genetic and genomic tools now available for SNB resistance breeding and consider future opportunities and challenges in crop health management by using the wheat-P. nodorum interaction as a model.

Spatial pattern of genetic diversity in field populations of Fusarium incarnatum-equiseti species complex.

Fusarium is associated with a number of wilt, blight, scab, and rot diseases in a range of economically important staple food crops worldwide. An assessment of the genetic structure and population stratification of Fusarium incarnatum‐equiseti species complex (FIESC) pathogen populations is important to understand the evolutionary potential of such populations in adapting to environmental change. Based on intersimple sequence repeat polymerase chain reaction (ISSR‐PCR), it was found that the pathogen population was structured into three genetic clusters for which genetic differentiation was higher within than among populations. There was high intrapopulation genetic diversity for population 1 (94.63%) which consisted largely of isolates collected from North Trinidad. Populations 2 and 3 had a low level of admixture among the populations based on overall population differentiation. Population 1 accounted for the highest amount of genetic variation (95.82%) followed by populations 2 and 3. Population stratification was reflected in the dendrogram topology, which consisted of three main genetic clusters and which coincided with the outcome of Bayesian and PCoA analyses. The populations were isolated by distance, and Voronoi tessellations indicated physical or structural barriers to gene flow which contributed to restricted admixture between two of three populations. These findings suggest a high evolutionary potential for this FIESC pathogen population, the implications of which directly affect disease management strategies.

The potential for cleaner fish-driven evolution in the salmon louse Lepeophtheirus salmonis: Genetic or environmental control of pigmentation?

The parasitic salmon louse represents one of the biggest challenges to environmentally sustainable salmonid aquaculture across the globe. This species also displays a high evolutionary potential, as demonstrated by its rapid development of resistance to delousing chemicals. In response, farms now use a range of non‐chemical delousing methods, including cleaner fish that eat lice from salmon. Anecdotal reports suggest that in regions where cleaner fish are extensively used on farms, lice have begun to appear less pigmented and therefore putatively less visible to cleaner fish. However, it remains an open question whether these observations reflect a plastic (environmental) or adaptive (genetic) response. To investigate this, we developed a pigment scoring system and conducted complimentary experiments which collectively demonstrate that, a) louse pigmentation is strongly influenced by environmental conditions, most likely light, and b) the presence of modest but significant differences in pigmentation between two strains of lice reared under identical conditions. Based on these data, we conclude that pigmentation in the salmon louse is strongly influenced by environmental conditions, yet there are also indications of underlying genetic control. Therefore, lice could display both plastic and adaptive responses to extensive cleaner fish usage where visual appearance is likely to influence survival of lice.

Parallel Evolution of Enhanced Biofilm Formation and Phage-Resistance in Pseudomonas aeruginosa during Adaptation Process in Spatially Heterogeneous Environments

An opportunistic pathogen Pseudomonas aeruginosa has a versatile phenotype and high evolutionary potential to adapt to various natural habitats. As the organism normally lives in spatially heterogeneous and polymicrobial environments from open fields to the inside of hosts, adaptation to abiotic (spatial heterogeneity) and biotic factors (interspecies interactions) is a key process to proliferate. However, our knowledge about the adaptation process of P. aeruginosa in spatially heterogeneous environments associated with other species is limited. We show herein that the evolutionary dynamics of P. aeruginosa PAO1 in spatially heterogeneous environments with Staphylococcus aureus known to coexist in vivo is dictated by two distinct core evolutionary trajectories: (i) the increase of biofilm formation and (ii) the resistance to infection by a filamentous phage which is retained in the PAO1 genome. Hyperbiofilm and/or pili-deficient phage-resistant variants were frequently selected in the laboratory evolution experiment, indicating that these are key adaptive traits under spatially structured conditions. On the other hand, the presence of S. aureus had only a marginal effect on the emergence and maintenance of these variants. These results show key adaptive traits of P. aeruginosa and indicate the strong selection pressure conferred by spatial heterogeneity, which might overwhelm the effect of interspecies interactions.

Population genetic dynamics of dengue vectors Aedes aegypti and Aedes albopictus in Sri Lanka: baseline study for designing Wolbachia control method

Dengue is an arboviral disease transmitted principally by two vectors Aedes aegypti and Aedes albopictus. In the absence of a successful prophylaxis or treatment, the disease control relies solely on vector control. Therefore, the knowledge on vector population genetics can play an important role in designing efficient vector control strategies especially during the release of Wolbachia transinfected mosquitoes. As such, we investigated the population genetic structure of Ae. aegypti and Ae. albopictus in Sri Lanka covering seven (Colombo, Gampaha, Kalutara, Galle, Jaffna, Mullathivu and Kilinochchi) dengue endemic regions using six microsatellite markers specific for each species to provide baseline data to implement Wolbachia control method. According to the results, both species revealed small but significant population structure. The genetic structure observed for Ae. albopictus populations was more subtle compared to that of Ae. aegypti reflecting their comparatively high geneflow over long distances. Evidence for possible multiple invasions towards the northern part of the country from the southern Ae. albopictus populations facilitated by increased human activity and urbanization were also apparent. On the contrary, the dispersal of Ae. aegypti was observed to be more restricted especially between north and south parts of the country. The genetic diversity and effective population number was also greater for Ae. albopictus compared to Ae. aegypti indicating their relatively higher evolutionary potential and adaptability. As a whole, our study suggests that the scheduled dengue control measurers using Wolbachia infected mosquitoes need to cover both vector species based on their species specific geneflow patterns to yield an effective dengue control.