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Lychee pepper spot, a field disease affecting lychee fruit skin, pedicels and petioles, is caused by Colletotrichum siamense, a fungal pathogen within the gloeosporioides species complex. Members of Colletotrichum from the gloeosporioides species complex and occasionally those from the acutatum species complex also cause postharvest anthracnose of lychee. Pepper spot was first described in Australia many years after anthracnose on lychee was first described, giving rise to the hypothesis that a novel species or strain within the gloeosporioides species complex causes pepper spot. In the present study, 19 isolates of Colletotrichum spp., collected from pepper spot and anthracnose symptoms on lychee fruit, representing 13 different genotypes across five species, were inoculated onto lychee fruit in the field or on detached fruit in the laboratory, to understand more about their pathogenic diversity. We found that symptoms were specific to genotype of the pathogen, as three genetically similar isolates of C. siamense consistently caused pepper spot and anthracnose, whilst other isolates caused anthracnose only. Cross‐inoculation studies on detached fruit of lychee, banana, avocado and mango also provided some evidence of host specialization in isolates of C. siamense infecting lychee in Australia. Our experiments provided further evidence that detached fruit assays cannot be used as a reliable proxy for field inoculation studies. This research confirms that C. siamense is a causal agent of both lychee pepper spot and lychee anthracnose in Australia, and Colletotrichum alienum and Colletotrichum queenslandicum are reported as causal agents of anthracnose of lychee for the first time. [ABSTRACT FROM AUTHOR]

Host specialization plays a critical role in the ecology and evolution of plant–microbe symbiosis. Theory predicts that host specialization is associated with microbial genome streamlining and is influenced by the abundance of host species, both of which can vary across latitudes, leading to a latitudinal gradient in host specificity. Here, we quantified the host specificity and composition of plant–bacteria symbioses on leaves across 329 tree species spanning a latitudinal gradient. Our analysis revealed a predominance of host‐specialized leaf bacteria. The degree of host specificity was negatively correlated with bacterial genome size and the local abundance of host plants. Additionally, we found an increased host specificity at lower latitudes, aligning with the high prevalence of small bacterial genomes and rare host species in the tropics. These findings underscore the importance of genome streamlining and host abundance in the evolution of host specificity in plant‐associated bacteria along the latitudinal gradient. [ABSTRACT FROM AUTHOR]

Divergent host specialization by phytophagous insects is often detected as local adaptation and is thought to have played an important role in their diversification even within an ecological specialist. The phytophagous ladybird beetle Henosepilachna niponica Lewis (Coleoptera: Coccinellidae) predominantly depends on thistles (Cirsium spp., Asteraceae). The distribution of H. niponica occupies multiple areas dominated by different thistle species. This implies the possibility of the occurrence of host‐associated divergent specialization of H. niponica. In this study, we investigated the pattern of host‐use ability of three allopatric H. niponica populations (Aomori, Iwate, and Yamagata) on three thistle species – Cirsium alpicola Nakai, Cirsium nipponicum (Maxim.) Makino, and Cirsium tonense Nakai – under laboratory conditions. The results displayed asymmetric local adaptation by the beetles. The adults and larvae of the Aomori population showed sufficient acceptance and performance on C. nipponicum and C. tonense, the hosts of the Iwate and Yamagata populations, respectively. On the other hand, the Iwate and Yamagata populations fed small amounts of and performed poorly on C. alpicola, the host of the Aomori population. In contrast, the adults from all the populations clearly preferred feeding on C. nipponicum or C. tonense to C. alpicola. We concluded that the small but significant population differentiation and asymmetric local adaptation by beetles to congeneric host plant species could be a sign of the earliest stage of population divergence by divergent natural selection, given that these divergences will act as 'immigrant inviability' and 'habitat isolation' at least asymmetrically when these populations come into contact. [ABSTRACT FROM AUTHOR]

Simple Summary: The host plants and the symbiotic relationship between bacteria and herbivorous insects play important roles in the population differentiation of phytophagous insects. However, current studies have paid limited attention to the connection between host-related differentiation and symbiotic bacterial communities in phytophagous insects. This study constructed phylogenetic trees using 58 Aphis odinae samples collected from different host plants and analyzed the symbiotic bacterial communities of samples from five commonly occurring host plants. The results indicate a partial correlation between differentiation related to host plants and the symbiotic bacterial communities in A. odinae, providing insights into the microevolutionary process between bacterial symbionts and insects. Host plants play a vital role in insect population differentiation, while symbiotic associations between bacteria and insects are ubiquitous in nature. However, existing studies have given limited attention to the connection between host-related differentiation and symbiotic bacterial communities in phytophagous insects. In this study, we collected 58 samples of Aphis odinae from different host plants in southern China and constructed phylogenetic trees to investigate their differentiation in relation to host plants. We also selected aphid samples from the five most preferred host plants and analyzed their symbiotic bacterial composition using Illumina sequencing of the V3–V4 hypervariable region of the 16S rRNA gene. The phylogeny and symbiotic bacterial community structure of A. odinae populations on different host plants showed that samples from Triadica sebifera (Euphorbiaceae) had a consistent presence of Wolbachia as the predominant secondary symbiont and suggested the possibility of undergoing differentiation. Conversely, although differentiation was observed in samples from Rhus chinensis (Anacardiaceae), no consistent presence of predominant secondary symbionts was found. Additionally, the samples from Heptapleurum heptaphyllum (Araliaceae) consistently carried Serratia, but no host differentiation was evident. In summary, this study reveals a partial correspondence between symbiotic bacterial communities and host-related differentiation in A. odinae. The findings contribute to our understanding of the microevolutionary influencing the macroevolutionary relationships between bacterial symbionts and phytophagous insects. The identification of specific symbionts associated with host-related differentiation provides valuable insights into the intricate dynamics of insect-bacteria interactions. [ABSTRACT FROM AUTHOR]

We reconstruct the phylogeny of the most speciose genus of cuckoo bees, genus Nomada Scopoli, 1770, using 221 species from throughout its distribution, yet with a strong emphasis on the West Palearctic. For phylogenetic reconstruction, we sequenced ultraconserved elements, allowing robust phylogenetic estimates with both concatenation and coalescent-based methods. By integrating extensive information on Nomada host records, we study macroevolutionary patterns of host associations, transitions, and phylogenetic conservatism. Using Bayesian divergence time estimates, we assess the historical biogeography of the genus, focusing on the West Palearctic. Our results show that Nomada likely originated in the Eastern Mediterranean and Near Eastern region, and likely expanded its range to a near-global distribution from there. We recovered long-standing phylogenetic conservatism in the host usage of Nomada and provided strong statistical evidence for an ancestral host association with Andrena and its most recent common ancestor. However, host transitions occurred multiple times independently in the natural history of Nomada , and species of the genus are brood parasites in at least 5 genera and 4 different families of bees in the Old World. At last, we systematically revise the taxonomy of the Old World Nomada by integrating morphological study with our well-supported phylogenetic estimates. We re-establish the genus Acanthonomada Schwarz, 1966, stat. res. as a distinct, second genus in the tribe Nomadini. We recognize 13 subgenera for Nomada , 9 of which are described as new: Afronomada Straka and Bossert, subgen. nov. Colliculla Straka, subgen. nov. Gestamen Straka, subgen. nov. Hungias Straka, subgen. nov. Mininomada Straka, subgen. nov. Nomacolla Straka, subgen. nov. Nomonosa Straka, subgen. nov. Plumada Straka, subgen. nov. and Profuga Straka, subgen. nov. Aside from the subgenus Nomada s.s. we reinstitute 3 previously synonymized subgenera: Heminomada Cockerell, 1902, stat. res. Holonomada Robertson, 1903, stat. res. and Hypochrotaenia Holmberg, 1886 stat. res. A total of 15 subgeneric names are formally synonymized with the newly established subgeneric concepts. [ABSTRACT FROM AUTHOR]

The biological control of weeds requires the successful introduction and establishment of natural enemies into other regions, to reduce population densities of target species. Potential biocontrol agents are sought in the native region of target weed and should be highly specialized. The gall‐inducing fly Eutreta xanthochaeta Aldrich (Diptera: Tephritidae) is native to Mexico and has been brought into other regions of the world – such as Hawaii (USA), South Africa, and Australia – for the biological control of Lantana camara L. (Verbanaceae), although this not always proved to be successful. Here we investigate the trophic interactions of this fly species with two host plants inhabiting in sympatry, L. camara and Lippia myriocephala Schltdl. & Cham. (Verbenaceae), evaluating its preference through infestation rates, the gall distribution in the plant architecture, as well as the indirect impact upon production of inflorescences affecting the reproductive capacity of the plants. We found that the fly was not monophagous in its native range, and under natural conditions it preferred the wild host L. myriocephala in the presence of L. camara. Moreover, we found that gall formation was linked to changes in the host architecture along with the potential for reproduction, leading to increased terminal buds and a reduction in the inflorescences produced on the twigs where galls develop. Lantana camara consists of both horticultural hybrids and wild varieties resulting in unresolved taxonomic ambiguities. Hence, there may be adaptive limitations of this fly to distinct geographic races or climatic conditions in the various regions, which needs further investigation. [ABSTRACT FROM AUTHOR]

Simple Summary: Aphids are generally dietary specialists, colonizing a specific plant or a group of closely related plants, but a few species are generalists, colonizing hundreds of hosts across multiple plant families. In these generalist aphids, host-specialized lineages or host-specialized biotypes are often observed in nature. This is the case for the cotton-melon aphid, Aphis gossypii Glover. When introduced to alternative hosts, the host-specialized biotypes show poor fitness and may even die within a few days. The underlying mechanisms of aphid host specialization remain unknown until now. We hypothesized that host-specialized biotypes express biotype-specific salivary effectors or elicitors that determine the compatibility of aphid-plant interactions. In this research, we described three strategies to identify biotype-specific effectors in two host-specialized biotypes of A. gossypii, a biotype specialized in Malvaceae and another in Cucurbitaceae. The strategy of combining transcriptome and proteome has the highest efficiency, obtaining less than one dozen effector candidates, and we strongly recommend this strategy to identify biotype-specific effectors in aphids and other sap-sucking insects. Polyphagous aphids often consist of host-specialized biotypes that perform poorly in non-native hosts. The underlying mechanisms remain unknown. Host-specialized biotypes may express biotype-specific salivary effectors or elicitors that determine aphid hosts. Here, we tried three strategies to identify possible effectors in Malvaceae- (MA) and Cucurbitaceae-specialized (CU) biotypes of the cotton-melon aphid Aphis gossypii Glover. The whole-aphid RNA-seq identified 765 differentially expressed genes (DEGs), and 139 of them were possible effectors; aphid-head RNA-seq identified 523 DEGs were identified, and 98 of them were possible effectors. The homologous genes of published aphid effectors were not differentially expressed between CU and MA. Next, quantitative proteomic analyses of saliva identified 177 possible proteins, and 44 of them were different proteins. However, none of the genes of the 44 proteins were differentially expressed, reflecting the discrepancy between transcriptome and proteome data. Finally, we searched for DEGs of the 177 salivary proteins in the aphid-head transcriptomes, and the salivary proteins with expression differences were regarded as effector candidates. Through this strategy, 11 effector candidates were identified, and their expression differences were all confirmed by RT-qPCR. The combinatorial analysis has great potential to identify biotype-specific effector candidates in aphids and other sap-sucking insects. [ABSTRACT FROM AUTHOR]

In the era of growing antimicrobial resistance, a threat affecting humans, endangering animals, as well as livelihoods and food security worldwide, we wanted to find possible explanations for its continuous spread from a new perspective. The ubiquity of resistance genes requires a One Health approach to finding the explanations for continuous AMR spread. The natural transformability of Campylobacter jejuni, its high incidence of infections, and emerging resistance worldwide inspired us to choose C. jejuni ST-21CC to be our pathogen for analyzing its contribution and connection to the cycle of AMR dissemination. ST-21CC is known as a generalist among humans and broilers, the most prevalent lineage worldwide, but it is rarely found in wild birds. Emerging in wild birds, genetic relatedness and similar resistance profiles were expected. We analyzed 23 Croatian C. jejuni strains belonging specifically to ST-21CC from humans, broilers, and wild birds. The genomic data obtained through whole genome sequencing and phenotypic susceptibility data of strains were compared. Our findings suggest high fluoroquinolone resistance in ST-21CC strains, with more diverse genetic backgrounds in wild birds. Intriguing were three isolates of ST-822 (from human and storks), sharing a similar genetic fingerprint. [ABSTRACT FROM AUTHOR]

Abstract Background Rhizosphere fungi play an important role in plant community dynamics and biogeochemical cycling. While the drivers of fungal community assembly have been studied in varied ecosystems, it is still unclear how these processes function for rhizosphere soil fungi in temperate forests. Furthermore, it is unknown whether the relative contributions of important determinants remain consistent or vary across fungal ecological guilds. This study used high-throughput next-generation sequencing to characterize the fungal communities of 247 rhizosphere soil samples from 19 tree species in a temperate forest within Northeast China. We aimed to investigate how three important determinants in temperate forests (host tree species, neighbouring plant communities, and edaphic properties) influence the community assembly of fungal functional guilds in the rhizosphere soil of trees. Results We found that host tree species contributed more to plant pathogens’ community composition than ectomycorrhizal fungi, and plant pathogens consistently showed higher host specialization than ectomycorrhizal fungi. Saprotrophs also showed high host specialization, which was mediated by the tree species’ effect on rhizosphere soil pH. Although neighboring plant communities contributed remarkably to richness of all fungal guilds, this effect on fungal composition varied across functional guilds, with stronger effect for biotrophic guilds (plant pathogens and ectomycorrhizal fungi) than for non-biotrophic guild (saprotrophs). Neighboring plant communities shaped the ectomycorrhizal community composition strongly in all samples regardless of host trees’ mycorrhizal type, whereas edaphic properties were the most important drivers for this guild in samples from only ectomycorrhizal-associated trees. Edaphic properties played an important role in shaping ectomycorrhizal and saprotrophic fungal compositions, indicating the importance of edaphic properties on the fungal functional guilds associated with the absorption and decomposition of nutrients. Conclusions These results demonstrated that rhizosphere soil fungal community assembly determinants varied across fungal guilds, reflecting their different ecological functions in temperate forest ecosystems.

Abstract Molecular epidemiology studies are essential to refine our understanding of migrations of phytopathogenic bacteria, the major determining factor in their emergence, and to understand the factors that shape their population structure. Microsatellite and minisatellite typing are useful techniques for deciphering the population structure of Xanthomonas citri pv. citri, the causal agent of Asiatic citrus canker. This paper presents a molecular epidemiology study, which has improved our understanding of the history of the pathogen's introductions into the Arabian Peninsula, since it was first reported in the 1980s. An unexpectedly high genetic diversity of the pathogen was revealed. The four distinct genetic lineages within X. citri pv. citri, which have been reported throughout the world, were identified in the Arabian Peninsula, most likely as the result of multiple introductions. No copper‐resistant X. citri pv. citri strains were identified. The pathogen's population structure on Mexican lime (their shared host species) was closely examined in two countries, Saudi Arabia and Yemen. We highlighted the marked prevalence of specialist pathotype A* strains in both countries, which suggests that specialist strains of X. citri pv. citri may perform better than generalist strains when they occur concomitantly in this environment. Subclade 4.2 was the prevailing lineage identified. Several analyses (genetic structure deciphered by discriminant analysis of principal components, RST‐based genetic differentiation, geographic structure) congruently suggested the role of human activities in the pathogen's spread. We discuss the implications of these results on the management of Asiatic citrus canker in the region.

Host plants play a vital role in insect population differentiation, while symbiotic associations between bacteria and insects are ubiquitous in nature. However, existing studies have given limited attention to the connection between host-related differentiation and symbiotic bacterial communities in phytophagous insects. In this study, we collected 58 samples of Aphis odinae from different host plants in southern China and constructed phylogenetic trees to investigate their differentiation in relation to host plants. We also selected aphid samples from the five most preferred host plants and analyzed their symbiotic bacterial composition using Illumina sequencing of the V3–V4 hypervariable region of the 16S rRNA gene. The phylogeny and symbiotic bacterial community structure of A. odinae populations on different host plants showed that samples from Triadica sebifera (Euphorbiaceae) had a consistent presence of Wolbachia as the predominant secondary symbiont and suggested the possibility of undergoing differentiation. Conversely, although differentiation was observed in samples from Rhus chinensis (Anacardiaceae), no consistent presence of predominant secondary symbionts was found. Additionally, the samples from Heptapleurum heptaphyllum (Araliaceae) consistently carried Serratia, but no host differentiation was evident. In summary, this study reveals a partial correspondence between symbiotic bacterial communities and host-related differentiation in A. odinae. The findings contribute to our understanding of the microevolutionary influencing the macroevolutionary relationships between bacterial symbionts and phytophagous insects. The identification of specific symbionts associated with host-related differentiation provides valuable insights into the intricate dynamics of insect-bacteria interactions.

Abstract Background Host range is a fundamental trait to understand the ecological and evolutionary dynamics of symbionts. Increasing host specificity is expected to be accompanied with specialization in different symbiont traits. We tested this specificity-specialization association in a large group of 16 ant-associated silverfish species by linking their level of host specificity to their degree of behavioural integration into the colony and to their accuracy of chemically imitating the host’s recognition system, i.e. the cuticular hydrocarbon (CHC) profile. Results As expected, facultative associates and host generalists (targeting multiple unrelated ants) tend to avoid the host, whereas host-specialists (typically restricted to Messor ants) were bolder, approached the host and allowed inspection. Generalists and host specialists regularly followed a host worker, unlike the other silverfish. Host aggression was extremely high toward non-ant-associated silverfish and modest to low in ant-associated groups. Surprisingly, the degree of chemical deception was not linked to host specificity as most silverfish, including facultative ant associates, imitated the host’s CHC profile. Messor specialists retained the same CHC profile as the host after moulting, in contrast to a host generalist, suggesting an active production of the cues (chemical mimicry). Host generalist and facultative associates flexibly copied the highly different CHC profiles of alternative host species, pointing at passive acquisition (chemical camouflage) of the host’s odour. Conclusions Overall, we found that behaviour that seems to facilitate the integration in the host colony was more pronounced in host specialist silverfish. Chemical deception, however, was employed by all ant-associated species, irrespective of their degree of host specificity.

BackgroundPowdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley (Hordeum vulgare).ResultsThe near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs). We found largely retained genome synteny and gene repertoires, yet detected copy number variation (CNV) of secretion signal peptide-containing protein-coding genes (SPs) and locally disrupted synteny blocks. Genes coding for sequence-related SPs are often locally clustered, but neither the SPs nor the TEs reside preferentially in genomic regions with unique features. Extended comparative analysis with different host-specific B. graminis formae speciales revealed the existence of a core suite of SPs, but also isolate-specific SP sets as well as congruence of SP CNV and phylogenetic relationship. We further detected evidence for a recent, lineage-specific expansion of TEs in the Bgh genome.ConclusionsThe characteristics of the Bgh genome (largely retained synteny, CNV of SP genes, recently proliferated TEs and a lack of significant compartmentalization) are consistent with a "one-speed" genome that differs in its architecture and (co-)evolutionary pattern from the "two-speed" genomes reported for several other filamentous phytopathogens.

The cotton aphid, Aphis gossypii Glover, is a species of polyphagous aphid with many biotypes, and its host transfer has always been the focus of research on the control of cotton aphid. An important factor affecting aphid specialization is the nutritional association with microbial symbionts that provide the host with nutrients lacking in the diet. We analyzed the microbial composition and biodiversity of reared on zucchini for 10 generations (T1–T10) and cotton as a control (CK), by high-throughput Illumina sequencing of 16S ribosomal RNA genes. The findings showed that the change in plant hosts decreased the richness and variety of microbial species. Regardless of whether the plant host is altered or not, Proteobacteria and Firmicutes are the predominate phyla in cotton-specialized aphid. Additionally, cotton-specialized aphids that live in zucchini had considerably lower relative abundances of non-dominant phyla (Bacteroidetes) than cotton hosts. At the genus level the dominant communities were Buchnera, Acinetobacter, and Arsenophonus. The relative abundance of Buchnera was significantly higher in aphids reared on zucchini than those on cotton, whereas the opposite was observed for Acinetobacter, as well as for some non-dominant communities (Stenotrophomonas, Pseudomons, Flavobacterium, Novosphingobium). Collectively, this study clarifies the dynamic changes of symbiotic bacteria in cotton-specialized aphids reared on zucchini for multiple generations. Among them, Buchnera is crucial for the cotton-specialized aphid to get nutrients during the transfer of the host and has a favorable impact on the colonization of cotton-specialized aphid populations on zucchini hosts. It not only enriches our understanding of the relationship between the bacterial microbiota of aphids and their adaptability to new hosts, zucchini, but also expands the current body of research on the mechanisms underlying the host shifting ability of cotton-specialized aphids.

Background: Rhizosphere fungi play an important role in plant community dynamics and biogeochemical cycling. While the drivers of fungal community assembly have been studied in varied ecosystems, it is still unclear how these processes function for rhizosphere soil fungi in temperate forests. Furthermore, it is unknown whether the relative contributions of important determinants remain consistent or vary across fungal ecological guilds. This study used high-throughput next-generation sequencing to characterize the fungal communities of 247 rhizosphere soil samples from 19 tree species in a temperate forest within Northeast China. We aimed to investigate how three important determinants in temperate forests (host tree species, neighbouring plant communities, and edaphic properties) influence the community assembly of fungal functional guilds in the rhizosphere soil of trees. Results: We found that host tree species contributed more to plant pathogens' community composition than ectomycorrhizal fungi, and plant pathogens consistently showed higher host specialization than ectomycorrhizal fungi. Saprotrophs also showed high host specialization, which was mediated by the tree species' effect on rhizosphere soil pH. Although neighboring plant communities contributed remarkably to richness of all fungal guilds, this effect on fungal composition varied across functional guilds, with stronger effect for biotrophic guilds (plant pathogens and ectomycorrhizal fungi) than for non-biotrophic guild (saprotrophs). Neighboring plant communities shaped the ectomycorrhizal community composition strongly in all samples regardless of host trees' mycorrhizal type, whereas edaphic properties were the most important drivers for this guild in samples from only ectomycorrhizal-associated trees. Edaphic properties played an important role in shaping ectomycorrhizal and saprotrophic fungal compositions, indicating the importance of edaphic properties on the fungal functional guilds associated with the absorption and decomposition of nutrients. Conclusions: These results demonstrated that rhizosphere soil fungal community assembly determinants varied across fungal guilds, reflecting their different ecological functions in temperate forest ecosystems. [ABSTRACT FROM AUTHOR]

Polyphagous aphids often consist of host-specialized biotypes that perform poorly in non-native hosts. The underlying mechanisms remain unknown. Host-specialized biotypes may express biotype-specific salivary effectors or elicitors that determine aphid hosts. Here, we tried three strategies to identify possible effectors in Malvaceae- (MA) and Cucurbitaceae-specialized (CU) biotypes of the cotton-melon aphid Aphis gossypii Glover. The whole-aphid RNA-seq identified 765 differentially expressed genes (DEGs), and 139 of them were possible effectors; aphid-head RNA-seq identified 523 DEGs were identified, and 98 of them were possible effectors. The homologous genes of published aphid effectors were not differentially expressed between CU and MA. Next, quantitative proteomic analyses of saliva identified 177 possible proteins, and 44 of them were different proteins. However, none of the genes of the 44 proteins were differentially expressed, reflecting the discrepancy between transcriptome and proteome data. Finally, we searched for DEGs of the 177 salivary proteins in the aphid-head transcriptomes, and the salivary proteins with expression differences were regarded as effector candidates. Through this strategy, 11 effector candidates were identified, and their expression differences were all confirmed by RT-qPCR. The combinatorial analysis has great potential to identify biotype-specific effector candidates in aphids and other sap-sucking insects.

Drosophila sechellia is an island endemic host specialist that has evolved to consume the toxic fruit of Morinda citrifolia, also known as noni fruit. Recent studies by our group and others have examined genome-wide gene expression responses of fruit flies to individual highly abundant compounds found in noni responsible for the fruit's unique chemistry and toxicity. In order to relate these reductionist experiments to the gene expression responses to feeding on noni fruit itself, we fed rotten noni fruit to adult female D. sechellia and performed RNA-sequencing. Combining the reductionist and more wholistic approaches, we have identified candidate genes that may contribute to each individual compound and those that play a more general role in response to the fruit as a whole. Using the compound specific and general responses, we used transcription factor prediction analyses to identify the regulatory networks and specific regulators involved in the responses to each compound and the fruit itself. The identified genes and regulators represent the possible genetic mechanisms and biochemical pathways that contribute to toxin resistance and noni specialization in D. sechellia. [ABSTRACT FROM AUTHOR]

Molecular epidemiology studies are essential to refine our understanding of migrations of phytopathogenic bacteria, the major determining factor in their emergence, and to understand the factors that shape their population structure. Microsatellite and minisatellite typing are useful techniques for deciphering the population structure of Xanthomonas citri pv. citri, the causal agent of Asiatic citrus canker. This paper presents a molecular epidemiology study, which has improved our understanding of the history of the pathogen's introductions into the Arabian Peninsula, since it was first reported in the 1980s. An unexpectedly high genetic diversity of the pathogen was revealed. The four distinct genetic lineages within X. citri pv. citri, which have been reported throughout the world, were identified in the Arabian Peninsula, most likely as the result of multiple introductions. No copper‐resistant X. citri pv. citri strains were identified. The pathogen's population structure on Mexican lime (their shared host species) was closely examined in two countries, Saudi Arabia and Yemen. We highlighted the marked prevalence of specialist pathotype A* strains in both countries, which suggests that specialist strains of X. citri pv. citri may perform better than generalist strains when they occur concomitantly in this environment. Subclade 4.2 was the prevailing lineage identified. Several analyses (genetic structure deciphered by discriminant analysis of principal components, RST‐based genetic differentiation, geographic structure) congruently suggested the role of human activities in the pathogen's spread. We discuss the implications of these results on the management of Asiatic citrus canker in the region. [ABSTRACT FROM AUTHOR]

Fern‐feeding insects have not received much attention because ferns have been considered herbivore‐resistant plants. However, ferns are attacked by herbivorous insects, including specialized spore feeders. For a better understanding of host specialization, we investigated the effect of experimentally transferred larvae of a spore‐feeding moth, Stathmopoda sp. (Lepidoptera: Stathmopodidae), from its original fern host Amauropelta linkiana (C. Presl) Pic. Serm., to three closely related species [Amauropelta rudis (Kunze) Pic. Serm, Amauropelta oligocarpa (Humb. & Bonpl. ex Willd.) Pic. Serm., and Amauropelta resinifera (Desv.) Pic. Serm.], and one alien fern species, Macrothelypteris torresiana (Gaudich.) Ching (all Thelypteridaceae). After experimental host‐plant transfer, we measured spore consumption of the larvae, and the survival and duration of each developmental stage. Once larvae were transferred to alternative hosts, they were still able to complete their life cycle, but consumed more spores, required more time to reach the adult stage, and had lower survival rates than on their original host, or even skipped the fifth instar on alternative hosts. Thus, our results suggested a strong adaptation of this moth species on its original host plant. We discuss some traits of experimental hosts, as the spores may contain fewer nutrients, or higher concentrations of toxic agents for larval development, thus restricting successful host‐plant switching. Further studies to measure the frequency and successful colonization of alternative hosts in nature are needed, by assessing variation in the chemical composition of spores between original and alternative hosts. [ABSTRACT FROM AUTHOR]

The English grain aphid, Sitobion avenae, is a significant agricultural pest affecting wheat, barley, and oats. In Chile, the most prevalent and persistent clone (superclone) of S. avenae harbors the facultative endosymbiont bacterium Regiella insecticola. To determine the role of this bacterium in the reproductive success of this superclone, the presence of R. insecticola was manipulated to assess its impact on (1) the reproductive performance of this clone on two host plant species (wheat and barley), (2) the production of winged morphs, (3) changes in the insects' proteomic profiles, and (4) the root/shoot ratio of plant. It was found that the reproductive performance of this S. avenae superclone varied across host plants, depending on the presence of the facultative bacterial endosymbiont. Aphids infected with R. insecticola showed higher reproductive success on wheat, while the opposite effect was observed on barley. Aphid biomass was greater when infected with R. insecticola, particularly on barley. Additionally, aphids harboring R. insecticola exhibited a higher proportion of winged individuals on both host plants. Protein regulation in aphids on wheat was lower compared to those on barley. A higher root/shoot biomass ratio was observed in wheat plants compared to barley when infested by R. insecticola-infected aphid. Thus, R. insecticola significantly influences the reproductive performance and proteomic profile of a S. avenae superclone, with these effects shaped by the host plant. This suggests that the interaction between the host plant and the facultative endosymbiont contributes to the ecological success of this superclone., (© 2024 Wiley Periodicals LLC.)

In the era of growing antimicrobial resistance, a threat affecting humans, endangering animals, as well as livelihoods and food security worldwide, we wanted to find possible explanations for its continuous spread from a new perspective. The ubiquity of resistance genes requires a One Health approach to finding the explanations for continuous AMR spread. The natural transformability of Campylobacter jejuni, its high incidence of infections, and emerging resistance worldwide inspired us to choose C. jejuni ST-21CC to be our pathogen for analyzing its contribution and connection to the cycle of AMR dissemination. ST-21CC is known as a generalist among humans and broilers, the most prevalent lineage worldwide, but it is rarely found in wild birds. Emerging in wild birds, genetic relatedness and similar resistance profiles were expected. We analyzed 23 Croatian C. jejuni strains belonging specifically to ST-21CC from humans, broilers, and wild birds. The genomic data obtained through whole genome sequencing and phenotypic susceptibility data of strains were compared. Our findings suggest high fluoroquinolone resistance in ST-21CC strains, with more diverse genetic backgrounds in wild birds. Intriguing were three isolates of ST-822 (from human and storks), sharing a similar genetic fingerprint.

We analysed a phylogenomic dataset comprising 730 terminal taxa and >160,000 nucleotide positions obtained using anchored hybrid enrichment of genomic DNA for a sample of deltocephaline leafhoppers and outgroups. Maximum likelihood analyses of concatenated nucleotide and amino acid sequences as well as coalescent gene tree analysis, yielded well‐resolved phylogenetic estimates that were highly congruent with most branches receiving maximum support. Some topological incongruence occurs among the trees resulting from different analyses, mainly distributed among very short branches at intermediate levels in the phylogeny, pertaining to relationships among some tribes and multi‐tribe lineages restricted to particular continents. Coalescent gene tree analysis revealed extensive gene tree conflict at these nodes, suggesting that certain relationships may remain difficult to resolve consistently even with genome‐scale datasets and dense taxon sampling. Ancestral character state reconstruction of feeding preference indicates that grass specialization has been acquired three or fewer times in some highly diverse but relatively derived lineages. Molecular divergence time estimation suggests that the earliest divergences in the subfamily occurred during the Cretaceous but that most modern tribes did not appear until after the Cretaceous–Palaeogene boundary and that grass specialist lineages generally diversified and spread at the same time as grasslands were becoming widespread globally. These analyses also show a high level of global biogeographic structure, with several large lineages of primarily arboreal deltocephalines restricted to particular regions or continents and long‐distance dispersal among continents occurring primarily among grass‐specialist lineages. The results represent a major improvement over previous analyses of this diverse subfamily, which were based on 152 or fewer taxa and data from morphology and partial sequences of two genes. [ABSTRACT FROM AUTHOR]

Background: Host range is a fundamental trait to understand the ecological and evolutionary dynamics of symbionts. Increasing host specificity is expected to be accompanied with specialization in different symbiont traits. We tested this specificity-specialization association in a large group of 16 ant-associated silverfish species by linking their level of host specificity to their degree of behavioural integration into the colony and to their accuracy of chemically imitating the host's recognition system, i.e. the cuticular hydrocarbon (CHC) profile. Results: As expected, facultative associates and host generalists (targeting multiple unrelated ants) tend to avoid the host, whereas host-specialists (typically restricted to Messor ants) were bolder, approached the host and allowed inspection. Generalists and host specialists regularly followed a host worker, unlike the other silverfish. Host aggression was extremely high toward non-ant-associated silverfish and modest to low in ant-associated groups. Surprisingly, the degree of chemical deception was not linked to host specificity as most silverfish, including facultative ant associates, imitated the host's CHC profile. Messor specialists retained the same CHC profile as the host after moulting, in contrast to a host generalist, suggesting an active production of the cues (chemical mimicry). Host generalist and facultative associates flexibly copied the highly different CHC profiles of alternative host species, pointing at passive acquisition (chemical camouflage) of the host's odour. Conclusions: Overall, we found that behaviour that seems to facilitate the integration in the host colony was more pronounced in host specialist silverfish. Chemical deception, however, was employed by all ant-associated species, irrespective of their degree of host specificity. [ABSTRACT FROM AUTHOR]

The specialization and distribution of pathogens among species has substantial impact on disease spread, especially when reservoir hosts can maintain high pathogen densities or select for increased pathogen virulence. Theory predicts that optimal within-host growth rate will vary among host genotypes/species and therefore that pathogens infecting multiple hosts should experience different selection pressures depending on the host environment in which they are found. This should be true for pathogens with broad host ranges, but also those experiencing opportunistic infections on novel hosts or that spill over among host populations. There is very little empirical data, however, regarding how adaptation to one host might directly influence infectivity and growth on another. We took an experimental evolution approach to examine short-term adaptation of the plant pathogen, Pseudomonas syringae pathovar tomato, to its native tomato host compared with an alternative host, Arabidopsis, in either the presence or absence of bacteriophages. After four serial passages (20 days of selection in planta), we measured bacterial growth of selected lines in leaves of either the focal or alternative host. We found that passage through Arabidopsis led to greater within-host bacterial densities in both hosts than did passage through tomato. Whole genome resequencing of evolved isolates identified numerous single nucleotide polymorphisms based on our novel draft assembly for strain PT23. However, there was no clear pattern of clustering among plant selection lines at the genetic level despite the phenotypic differences observed. Together, the results emphasize that previous host associations can influence the within-host growth rate of pathogens.

Abstract Negative interspecific mating interactions, known as reproductive interference, can hamper species coexistence in a local patch and promote niche partitioning or geographical segregation of closely related species. Conspecific sperm precedence (CSP), which occurs when females that have mated with both conspecific and heterospecific males preferentially use conspecific sperm for fertilization, might contribute to species coexistence by mitigating the costs of interspecific mating and hybridization. We discussed whether two species exhibiting CSP can coexist in a local environment in the presence of reproductive interference. First, using a behaviorally explicit mathematical model, we demonstrated that two species characterized by negative mating interactions are unlikely to coexist because the costs of reproductive interference, such as loss of mating opportunity with conspecific partners, are inevitably incurred when individuals of both species are present. Second, we experimentally examined differences in mating activity and preference in two Harmonia ladybird species known to exhibit CSP. These behavioral differences may lead to local extinction of H. yedoensis because of reproductive interference by H. axyridis. This prediction is consistent with field observations that H. axyridis uses various food sources and habitats whereas H. yedoensis is confined to a less preferred prey item and a pine tree habitat. Finally, by a comparative approach, we observed that niche partitioning or parapatric distribution, but not sympatric coexistence in the same habitat, is maintained between species with CSP belonging to a wide range of taxa, including vertebrates and invertebrates living in aquatic or terrestrial environments. Taken together, it is possible that reproductive interference may destabilize local coexistence even in closely related species that exhibit CSP.

Abstract Genetic diversity within pathogen populations is critically important for predicting pathogen evolution, disease outcomes and prevalence. However, we lack a good understanding of the processes maintaining genetic variation and constraints on pathogen life‐history evolution. Here, we analysed interactions between 12 wheat host genotypes and 145 strains of Zymoseptoria tritici from five global populations to investigate the evolution and maintenance of variation in pathogen virulence and reproduction. We found a strong positive correlation between virulence (amount of leaf necrosis) and reproduction (pycnidia density within lesions), with substantial variation in both traits maintained within populations. On average, highly virulent isolates exhibited higher reproduction, which might increase transmission potential in agricultural fields planted to homogeneous hosts at a high density. We further showed that pathogen strains with a narrow host range (i.e. specialists) for reproduction were on average less virulent, and those with a broader host range (i.e. generalists) were on average less fecund on a given specific host. These costs associated with adaptation to different host genotypes might constrain the emergence of generalists by disrupting the directional evolution of virulence and fecundity. We conclude that selection favouring pathogen strains that are virulent across diverse hosts, coupled with selection that maximizes fecundity on specific hosts, may explain the maintenance of these pathogenicity traits within and among populations.

Changes in life history traits are often considered speciation triggers and can have dramatic effects on the evolutionary history of a lineage. Here, we examine the consequences of changes in two life history traits, host‐type and phoresy, in the hypermetamorphic blister beetles, Meloidae. Subfamilies Nemognathinae and Meloinae exhibit a complex life cycle involving multiple metamorphoses and parasitoidism. Most genera and tribes are bee‐parasitoids, and include phoretic or nonphoretic species, while two tribes feed on grasshopper eggs. These different life strategies are coupled with striking differences in species richness among clades. We generated a mitogenomic phylogeny for Nemognathinae and Meloinae, confirming the monophyly of these two clades, and used the dated phylogeny to explore the association between diversification rates and changes in host specificity and phoresy, using state‐dependent speciation and extinction (SSE) models that include the effect of hidden traits. To account for the low taxon sampling, we implemented a phylogenetic‐taxonomic approach based on birth‐death simulations, and used a Bayesian framework to integrate parameter and phylogenetic uncertainty. Results show that the ancestral hypermetamorphic Meloidae was a nonphoretic bee‐parasitoid, and that transitions towards a phoretic bee‐parasitoid and grasshopper parasitoidism occurred multiple times. Nonphoretic bee‐parasitoid lineages exhibit significantly higher relative extinction and lower diversification rates than phoretic bee‐and grasshopper‐parasitoids, but no significant differences were found between the latter two strategies. This suggests that Orthopteran host shifts and phoresy contributed jointly to the evolutionary success of the parasitoid meloidae. We also demonstrate that SSE models can be used to identify hidden traits coevolving with the focal trait in driving a lineage's diversification dynamics. [ABSTRACT FROM AUTHOR]

Drosophila sechellia is a dietary specialist endemic to the Seychelles islands that has evolved to consume the fruit of Morinda citrifolia. When ripe, the fruit of M. citrifolia contains octanoic acid and hexanoic acid, two medium-chain fatty acid volatiles that deter and are toxic to generalist insects. Drosophila sechellia has evolved resistance to these volatiles allowing it to feed almost exclusively on this host plant. The genetic basis of octanoic acid resistance has been the focus of multiple recent studies, but the mechanisms that govern hexanoic acid resistance in D. sechellia remain unknown. To understand how D. sechellia has evolved to specialize on M. citrifolia fruit and avoid the toxic effects of hexanoic acid, we exposed adult D. sechellia, D. melanogaster and D. simulans to hexanoic acid and performed RNA sequencing comparing their transcriptional responses to identify D. sechellia specific responses. Our analysis identified many more genes responding transcriptionally to hexanoic acid in the susceptible generalist species than in the specialist D. sechellia. Interrogation of the sets of differentially expressed genes showed that generalists regulated the expression of many genes involved in metabolism and detoxification whereas the specialist primarily downregulated genes involved in the innate immunity. Using these data, we have identified interesting candidate genes that may be critically important in aspects of adaptation to their food source that contains high concentrations of HA. Understanding how gene expression evolves during dietary specialization is crucial for our understanding of how ecological communities are built and how evolution shapes trophic interactions. [ABSTRACT FROM AUTHOR]

Insect host–parasitoid interactions abound in nature and are characterized by a high degree of host specialization. In addition to their behavioral and immune defenses, many host species rely on heritable bacterial endosymbionts for defense against parasitoids. Studies on aphids and flies show that resistance conferred by symbionts can be very strong and highly specific, possibly as a result of variation in symbiont-produced toxins. I argue that defensive symbionts are therefore an important source of diversifying selection, promoting the evolution of host specialization by parasitoids. This is likely to affect the structure of host–parasitoid food webs. I consider potential changes in terms of food web complexity, although the nature of these effects will also be influenced by whether maternally transmitted symbionts have some capacity for lateral transfer. This is discussed in the light of available evidence for horizontal transmission routes. Finally, I propose that defensive mutualisms other than microbial endosymbionts may also exert diversifying selection on insect parasitoids. [ABSTRACT FROM AUTHOR]

Many fungal plant pathogens encompass multiple populations specialized on different plant species. Understanding the factors underlying pathogen adaptation to their hosts is a major challenge of evolutionary microbiology, and it should help to prevent the emergence of new specialized pathogens on novel hosts. Previous studies have shown that French populations of the gray mold pathogen Botrytis cinerea parasitizing tomato and grapevine are differentiated from each other, and have higher aggressiveness on their host of origin than on other hosts, indicating some degree of host specialization in this polyphagous pathogen. Here, we aimed at identifying the genomic features underlying the specialization of B. cinerea populations to tomato and grapevine. Based on whole genome sequences of 32 isolates, we confirmed the subdivision of B. cinerea pathogens into two genetic clusters on grapevine and another, single cluster on tomato. Levels of genetic variation in the different clusters were similar, suggesting that the tomato-specific cluster has not recently emerged following a bottleneck. Using genome scans for selective sweeps and divergent selection, tests of positive selection based on polymorphism and divergence at synonymous and nonsynonymous sites, and analyses of presence and absence variation, we identified several candidate genes that represent possible determinants of host specialization in the tomatoassociated population. This work deepens our understanding of the genomic changes underlying the specialization of fungal pathogen populations. [ABSTRACT FROM AUTHOR]

Abstract Background Hybridization is a central mechanism in evolution, producing new species or introducing important genetic variation into existing species. In plant-pathogenic fungi, adaptation and specialization to exploit a host species are key determinants of evolutionary success. Here, we performed experimental crosses between the two pathogenic Microbotryum species, M. lychnidis-dioicae and M. silenes-acaulis that are specialized to different hosts. The resulting offspring were analyzed on phenotypic and genomic levels to describe genomic characteristics of hybrid offspring and genetic factors likely involved in host-specialization. Results Genomic analyses of interspecific fungal hybrids revealed that individuals were most viable if the majority of loci were inherited from one species. Interestingly, species-specific loci were strictly controlled by the species’ origin of the mating type locus. Moreover we detected signs of crossing over and chromosome duplications in the genomes of the analyzed hybrids. In Microbotryum, mitochondrial DNA was found to be uniparentally inherited from the a2 mating type. Genome comparison revealed that most gene families are shared and the majority of genes are conserved between the two species, indicating very similar biological features, including infection and pathogenicity processes. Moreover, we detected 211 candidate genes that were retained under host-driven selection of backcrossed lines. These genes and might therefore either play a crucial role in host specialization or be linked to genes that are essential for specialization. Conclusion The combination of genome analyses with experimental selection and hybridization is a promising way to investigate host-pathogen interactions. This study manifests genetic factors of host specialization that are required for successful biotrophic infection of the post-zygotic stage, but also demonstrates the strong influence of intra-genomic conflicts or instabilities on the viability of hybrids in the haploid host-independent stage.

Drylands comprise over 41% of all terrestrial surface area and are home to approximately 35.5% of the world's population; however, both free-living and parasitic fauna of these regions remain relatively understudied. Yet, the very conditions that make these regions challenging to study – extreme environmental conditions and low population density for various organisms – also make them potentially untapped natural laboratories for examining eco-evolutionary relationships between hosts and parasites. Adaptations and ecological patterns illustrated by desert parasite communities can serve as exemplars within the extremes regarding the evolution of virulence, breadth of host spectra, and lifecycle strategies. This review provides relevant examples for each of these three topics using parasites from dryland regions in order to encourage future empirical tests of hypotheses regarding parasite ecology and evolution within dryland ecosystems and stimulate wider investigation into the parasitofauna of arid regions in general. As global climate changes and anthropogenic disturbance increases, desertification is a growing problem which has been labeled as a threat to global health. Thus, deserts not only provide useful natural laboratories in which to study parasite transmission but understanding parasite transmission within these habitats becomes increasingly important as larger, likely highly resource insecure, populations are projected to live on the margins of desert regions in the future.

Abstract Background To understand the genetic mechanisms of insect herbivory, the transcriptional response of insects feeding on different host plant species has to be studied. Here, we generated gene expression data of the generalist herbivore Spodoptera exigua (Hübner) feeding on three selected host plant species and a control (artificial diet). The host plant species used in this study –cabbage (Brassica oleracea), maize (Zea mays) and tobacco (Nicotiana tabacum)- are members of different plant families that each employ specific defence mechanisms and toxins. Results Spodoptera exigua larvae had a higher growth rate, indicator for herbivore success, when feeding on Z. mays compared to larvae feeding on B. oleracea or N. tabacum. Larvae feeding on the different host plant species showed divergent transcriptional responses. We identified shared and unique gene expression patterns dependent of the host plant species the larvae fed on. Unique gene expression patterns, containing uniquely upregulated transcripts including specific detoxification genes, were found for larvae feeding on either B. oleracea or N. tabacum. No diet-specific gene cluster was identified for larvae feeding on the host for which larvae showed optimal herbivore success, Z. mays, or artificial diet. In contrast, for larvae feeding on hosts for which they showed low herbivore success, specific diet-dependent gene clusters were identified. Functional annotation of these clusters indicates that S. exigua larvae deploy particular host plant-specific genes for digestion and detoxification. Conclusions The lack of a host plant-specific gene activity for larvae feeding on Z. mays and the artificial diet suggest a general and non-specific gene activity for host plants with optimal herbivore success. Whereas the finding of specific gene clusters containing particular digestion and detoxifying genes expressed in larvae feeding on B. oleracea and N. tabacum, with low herbivore success, imply a host plant-specific gene activity for larvae feeding on host plants with suboptimal herbivore success. This observation leads to the conclusion that a polyphagous herbivore is able to feed on a large variation of host plants due to the flexibility and diversity of genes involved in digestion and detoxification that are deployed in response to particular host plant species.

Fitness responses to environment can shape species distributions, though opposing eco‐evolutionary processes can obscure environmental effects. For example, host specificity influences parasite dynamics, but is unclear how adaptation of parasites to local host communities may scale up to continental distributions. Here, we develop a macroecological framework to determine how host community structure affects the distribution of specialist and generalist populations of Striga hermonthica, an African parasitic plant of cereal crops. Combining data from global crop production and parasite experimental trials, we find that parasites perform best on the host species that is most common in their location of origin. Moreover, niche model contrasts predict parasite specialization on two hosts that evolved alongside Striga during domestication (pearl millet and sorghum), indicating that specialist parasites may be most likely to occur where host niches differ most in multivariate environmental space. Our study demonstrates that patterns of parasite local adaptation to host communities can emerge at continental scales and that differential environmental tolerances of hosts indirectly shape the distribution of specialist and generalist parasites. By predicting spatial dynamics of parasite specialization versus generalization directly from environmental data, our approach may help inform current and future management of pests and disease. [ABSTRACT FROM AUTHOR]

Campylobacter spp. are the most frequent agent of human gastroenteritis worldwide, and the spread of multidrug-resistant strains makes the clinical treatment difficult. The current study presents the resistome analysis of 39,798 Campylobacter jejuni and 11,920 Campylobacter coli genomes available in public repositories. Determinants of resistance to β-lactams (Be) and tetracyclines (Te) were the most frequent for both species, with resistance to quinolones (Qu) as the third most important on C. jejuni and to aminoglycosides (Am) on C. coli. Moreover, resistance to Te, Qu, and Am was frequently found in co-occurrence with resistance to other antibiotic families. Geographical differences on clonal complexes distribution were found for C. jejuni and on resistome genotypes for both C. jejuni and C. coli species. Attending to the resistome patterns by isolation source, three main clusters of genomes were found on C. jejuni genomes at antimicrobial resistance gene level. The first cluster was formed by genomes from human, food production animals (e.g., sheep, cow, and chicken), and food (e.g., dairy products) isolates. The higher incidence of tet(O), associated with tetracycline resistance, and the gyrA (T86I) single-nucleotide polymorphism (SNP), associated with quinolone resistance, among genomes from this cluster could be due to the intense use of these antibiotics in veterinary and human clinical settings. Similarly, a high incidence of tet(O) genes of C. coli genomes from pig, cow, and turkey was found. Moreover, the cluster based on resistome patterns formed by C. jejuni and C. coli genomes of human, turkey, and chicken origin is in agreement with previous observations reporting chicken or poultry-related environments as the main source of human campylobacteriosis infections. Most clonal complexes (CCs) associated with chicken host specialization (e.g., ST-354, ST-573, ST-464, and ST-446) were the CCs with the highest prevalence of determinants of resistance to Be, Qu, and Te. Finally, a clear trend toward an increase in the occurrence of Te and Qu resistance determinants on C. jejuni, linked to the spread of the co-occurrence of the blaOXA–61 and tet(O)-tet(O/W/O) genes and the gyrA (T86I) SNP, was found from 2001 to date in Europe.

Campylobacter spp. are the most frequent agent of human gastroenteritis worldwide, and the spread of multidrug-resistant strains makes the clinical treatment difficult. The current study presents the resistome analysis of 39,798 Campylobacter jejuni and 11,920 Campylobacter coli genomes available in public repositories. Determinants of resistance to β-lactams (Be) and tetracyclines (Te) were the most frequent for both species, with resistance to quinolones (Qu) as the third most important on C. jejuni and to aminoglycosides (Am) on C. coli. Moreover, resistance to Te, Qu, and Am was frequently found in co-occurrence with resistance to other antibiotic families. Geographical differences on clonal complexes distribution were found for C. jejuni and on resistome genotypes for both C. jejuni and C. coli species. Attending to the resistome patterns by isolation source, three main clusters of genomes were found on C. jejuni genomes at antimicrobial resistance gene level. The first cluster was formed by genomes from human, food production animals (e.g., sheep, cow, and chicken), and food (e.g., dairy products) isolates. The higher incidence of tet(O) , associated with tetracycline resistance, and the gyrA (T86I) single-nucleotide polymorphism (SNP), associated with quinolone resistance, among genomes from this cluster could be due to the intense use of these antibiotics in veterinary and human clinical settings. Similarly, a high incidence of tet(O) genes of C. coli genomes from pig, cow, and turkey was found. Moreover, the cluster based on resistome patterns formed by C. jejuni and C. coli genomes of human, turkey, and chicken origin is in agreement with previous observations reporting chicken or poultry-related environments as the main source of human campylobacteriosis infections. Most clonal complexes (CCs) associated with chicken host specialization (e.g., ST-354, ST-573, ST-464, and ST-446) were the CCs with the highest prevalence of determinants of resistance to Be, Qu, and Te. Finally, a clear trend toward an increase in the occurrence of Te and Qu resistance determinants on C. jejuni , linked to the spread of the co-occurrence of the bla OXA– 61 and tet(O)-tet(O/W/O) genes and the gyrA (T86I) SNP, was found from 2001 to date in Europe. [ABSTRACT FROM AUTHOR]

Chemical defenses, repellents, and attractants are important shapers of species interactions. Chemical attractants could contribute to the divergence of coevolving plant-insect interactions, if pollinators are especially responsive to signals from the local plant species. We experimentally investigated patterns of daily floral scent production in three Lithophragma species (Saxifragaceae) that are geographically isolated and tested how scent divergence affects attraction of their major pollinator-the floral parasitic moth Greya politella (Prodoxidae). These moths oviposit through the corolla while simultaneously pollinating the flower with pollen adhering to the abdomen. The complex and species-specific floral scent profiles were emitted in higher amounts during the day, when these day-flying moths are active. There was minimal divergence found in petal color, which is another potential floral attractant. Female moths responded most strongly to scent from their local host species in olfactometer bioassays, and were more likely to oviposit in, and thereby pollinate, their local host species in no-choice trials. The results suggest that floral scent is an important attractant in this interaction. Local specialization in the pollinator response to a highly specific plant chemistry, thus, has the potential to contribute importantly to patterns of interaction specificity among coevolving plants and highly specialized pollinators.

Abstract Successful geographic range expansion by parasites and parasitoids may also require host range expansion. Thus, the evolutionary advantages of host specialization may trade off against the ability to exploit new host species encountered in new geographic regions. Here, we use molecular techniques and confirmed host records to examine biogeography, population divergence, and host flexibility of the parasitoid fly, Ormia ochracea (Bigot). Gravid females of this fly find their cricket hosts acoustically by eavesdropping on male cricket calling songs; these songs vary greatly among the known host species of crickets. Using both nuclear and mitochondrial genetic markers, we (a) describe the geographical distribution and subdivision of genetic variation in O. ochracea from across the continental United States, the Mexican states of Sonora and Oaxaca, and populations introduced to Hawaii; (b) demonstrate that the distribution of genetic variation among fly populations is consistent with a single widespread species with regional host specialization, rather than locally differentiated cryptic species; (c) identify the more‐probable source populations for the flies introduced to the Hawaiian islands; (d) examine genetic variation and substructure within Hawaii; (e) show that among‐population geographic, genetic, and host song distances are all correlated; and (f) discuss specialization and lability in host‐finding behavior in light of the diversity of cricket songs serving as host cues in different geographically separate populations.

Abstract Plant–soil feedbacks (PSFs) drive plant community diversity via interactions between plants and soil microbes. However, we know little about how frequently PSFs affect plants at the seed stage, and the compositional shifts in fungi that accompany PSFs on germination. We conducted a pairwise PSF experiment to test whether seed germination was differentially impacted by conspecific versus heterospecific soils for seven grassland species. We used metagenomics to characterize shifts in fungal community composition in soils conditioned by each plant species. To investigate whether changes in the abundance of certain fungal taxa were associated with multiple PSFs, we assigned taxonomy to soil fungi and identified putative pathogens that were significantly more abundant in soils conditioned by plant species that experienced negative or positive PSFs. We observed negative, positive, and neutral PSFs on seed germination. Although conspecific and heterospecific soils for pairs with significant PSFs contained host‐specialized soil fungal communities, soils with specialized microbial communities did not always lead to PSFs. The identity of host‐specialized pathogens, that is, taxa uniquely present or significantly more abundant in soils conditioned by plant species experiencing negative PSFs, overlapped among plant species, while putative pathogens within a single host plant species differed depending on the identity of the heterospecific plant partner. Finally, the magnitude of feedback on germination was not related to the degree of fungal community differentiation between species pairs involved in negative PSFs. Synthesis. Our findings reveal the potential importance of PSFs at the seed stage. Although plant species developed specialized fungal communities in rhizosphere soil, pathogens were not strictly host‐specific and varied not just between plant species, but according to the identity of plant partner. These results illustrate the complexity of microbe‐mediated interactions between plants at different life stages that next‐generation sequencing can begin to unravel.

Fomitopsis pinicola is a common brown-rot fungal species found in northern hemisphere. It grows on many different gymnosperm and angiosperm trees. Recent studies show that it is a species complex; three species from North America and one species from Europe have been recognized in this complex. In the current study, six new species in the Fomitopsis pinicola complex were discovered from East Asia, based on morphological characters and phylogenetic analyses inferred from the sequence data of the internal transcribed spacer (ITS) regions, the second subunit of RNA polymerase II (RPB2), and the translation elongation factor 1-α gene (TEF). Detailed descriptions of the six new species are provided. Our results also indicates that species of the F. pinicola complex from East Asia usually have limited distribution areas and host specialization.

Fomitopsis pinicola is a common brown-rot fungal species found in northern hemisphere. It grows on many different gymnosperm and angiosperm trees. Recent studies show that it is a species complex; three species from North America and one species from Europe have been recognized in this complex. In the current study, six new species in the Fomitopsis pinicola complex were discovered from East Asia, based on morphological characters and phylogenetic analyses inferred from the sequence data of the internal transcribed spacer (ITS) regions, the second subunit of RNA polymerase II (RPB2), and the translation elongation factor 1-α gene (TEF). Detailed descriptions of the six new species are provided. Our results also indicates that species of the F. pinicola complex from East Asia usually have limited distribution areas and host specialization. [ABSTRACT FROM AUTHOR]

Negative interspecific mating interactions, known as reproductive interference, can hamper species coexistence in a local patch and promote niche partitioning or geographical segregation of closely related species. Conspecific sperm precedence (CSP), which occurs when females that have mated with both conspecific and heterospecific males preferentially use conspecific sperm for fertilization, might contribute to species coexistence by mitigating the costs of interspecific mating and hybridization. We discussed whether two species exhibiting CSP can coexist in a local environment in the presence of reproductive interference. First, using a behaviorally explicit mathematical model, we demonstrated that two species characterized by negative mating interactions are unlikely to coexist because the costs of reproductive interference, such as loss of mating opportunity with conspecific partners, are inevitably incurred when individuals of both species are present. Second, we experimentally examined differences in mating activity and preference in two Harmonia ladybird species known to exhibit CSP. These behavioral differences may lead to local extinction of H. yedoensis because of reproductive interference by H. axyridis. This prediction is consistent with field observations that H. axyridis uses various food sources and habitats whereas H. yedoensis is confined to a less preferred prey item and a pine tree habitat. Finally, by a comparative approach, we observed that niche partitioning or parapatric distribution, but not sympatric coexistence in the same habitat, is maintained between species with CSP belonging to a wide range of taxa, including vertebrates and invertebrates living in aquatic or terrestrial environments. Taken together, it is possible that reproductive interference may destabilize local coexistence even in closely related species that exhibit CSP. [ABSTRACT FROM AUTHOR]

Genetic diversity within pathogen populations is critically important for predicting pathogen evolution, disease outcomes and prevalence. However, we lack a good understanding of the processes maintaining genetic variation and constraints on pathogen life‐history evolution. Here, we analysed interactions between 12 wheat host genotypes and 145 strains of Zymoseptoria tritici from five global populations to investigate the evolution and maintenance of variation in pathogen virulence and reproduction. We found a strong positive correlation between virulence (amount of leaf necrosis) and reproduction (pycnidia density within lesions), with substantial variation in both traits maintained within populations. On average, highly virulent isolates exhibited higher reproduction, which might increase transmission potential in agricultural fields planted to homogeneous hosts at a high density. We further showed that pathogen strains with a narrow host range (i.e. specialists) for reproduction were on average less virulent, and those with a broader host range (i.e. generalists) were on average less fecund on a given specific host. These costs associated with adaptation to different host genotypes might constrain the emergence of generalists by disrupting the directional evolution of virulence and fecundity. We conclude that selection favouring pathogen strains that are virulent across diverse hosts, coupled with selection that maximizes fecundity on specific hosts, may explain the maintenance of these pathogenicity traits within and among populations. [ABSTRACT FROM AUTHOR]

Botrytis cinerea, the grey mould agent, is one of the most important pathogens of grapevine, due to the great yield losses caused and the economic costs related to disease control. Ground cover plants are assumed to have a role in the complex epidemiology of the pathogen, even if no information on the genetic variability of the strains is available. In this study, a molecular epidemiology approach, based on the comparative analysis of the nucleotide sequences of multiple genes (ITS1‐ITS2, G3PDH, NEP1, NEP2, BC‐hch, and sdhB), was used to evaluate whether B. cinerea isolated from herbaceous species contributes to grey mould diffusion on grapevines. From 330 samples collected in two vineyards in Lombardy, Italy, 63 B. cinerea strains were isolated from tissues of grapevine with symptoms (50 strains) and spontaneous ground cover plants (13 strains). Capsella bursa‐pastoris, Cardamine impatiens, Lamium purpureum, and Crepis tectorum were identified as novel B. cinerea hosts. Sequence analysis and phylogeny showed that the same genotypes were present on both grapevines and herbaceous plants, with no fitness (estimated from growth and sporulation on potato dextrose agar) or pathogenicity (on grapevine leaves and berries, and tomato leaves) penalties. This confirms that ground cover plants can be a source of inoculum for B. cinerea on grapevine. Moreover, phylogenetic analysis of the BC‐hch gene allowed the identification of two genetically distinct clusters, characterized by vegetative incompatibility and different distributions of the mating types, fitness, and pathogenicity. Therefore, B. cinerea seems to be composed of two diverging subpopulations that do not differ for host specialization. [ABSTRACT FROM AUTHOR]

Herbivorous insects are among the most successful radiations of life. However, we know little about the processes underpinning the evolution of herbivory. We examined the evolution of herbivory in the fly, Scaptomyza flava, whose larvae are leaf miners on species of Brassicaceae, including the widely studied reference plant, Arabidopsis thaliana (Arabidopsis). Scaptomyza flava is phylogenetically nested within the paraphyletic genus Drosophila, and the whole genome sequences available for 12 species of Drosophila facilitated phylogenetic analysis and assembly of a transcriptome for S. flava. A time-calibrated phylogeny indicated that leaf mining in Scaptomyza evolved between 6 and 16 million years ago. Feeding assays showed that biosynthesis of glucosinolates, the major class of antiherbivore chemical defense compounds in mustard leaves, was upregulated by S. flava larval feeding. The presence of glucosinolates in wild-type (WT) Arabidopsis plants reduced S. flava larval weight gain and increased egg-adult development time relative to flies reared in glucosinolate knockout (GKO) plants. An analysis of gene expression differences in 5-day-old larvae reared on WT versus GKO plants showed a total of 341 transcripts that were differentially regulated by glucosinolate uptake in larval S. flava. Of these, approximately a third corresponded to homologs of Drosophila melanogaster genes associated with starvation, dietary toxin-, heat-, oxidation-, and aging-related stress. The upregulated transcripts exhibited elevated rates of protein evolution compared with unregulated transcripts. The remaining differentially regulated transcripts also contained a higher proportion of novel genes than the unregulated transcripts. Thus, the transition to herbivory in Scaptomyza appears to be coupled with the evolution of novel genes and the co-option of conserved stress-related genes.

Studying the pollen preferences of introduced bees allows us to investigate how species use host-plants when establishing in new environments. Osmia cornifrons is a solitary bee introduced into North America from East Asia for pollination of Rosaceae crops such as apples and cherries. We investigated whether O. cornifrons (i) more frequently collected pollen from host-plant species they coevolved with from their geographic origin, or (ii) prefer host-plant species of specific plant taxa independent of origin. To address this question, using pollen metabarcoding, we examined the identity and relative abundance of pollen in larval provisions from nests located in different landscapes with varying abundance of East-Asian and non-Asian plant species. Our results show that O. cornifrons collected more pollen from plant species from their native range. Plants in the family Rosaceae were their most preferred pollen hosts, but they differentially collected species native to East Asia, Europe, or North America depending on the landscape. Our results suggest that while O. cornifrons frequently collect pollen of East-Asian origin, the collection of pollen from novel species within their phylogenetic familial affinities is common and can facilitate pollinator establishment. This phylogenetic preference highlights the effectiveness of O. cornifrons as crop pollinators of a variety of Rosaceae crops from different geographic origins. Our results imply that globalization of non-native plant species may ease the naturalization of their coevolved pollinators outside of their native range.

Abstract The aim of this study was to explore the diversity of ectoparasitic fungi (Ascomycota, Laboulbeniales) that use bat flies (Diptera, Hippoboscoidea) as hosts. Bat flies themselves live as ectoparasites on the fur and wing membranes of bats (Mammalia, Chiroptera); hence this is a tripartite parasite system. Here, we collected bats, bat flies, and Laboulbeniales, and conducted phylogenetic analyses of Laboulbeniales to contrast morphology with ribosomal sequence data. Parasitism of bat flies by Laboulbeniales arose at least three times independently, once in the Eastern Hemisphere (Arthrorhynchus) and twice in the Western Hemisphere (Gloeandromyces, Nycteromyces). We hypothesize that the genera Arthrorhynchus and Nycteromyces evolved independently from lineages of ectoparasites of true bugs (Hemiptera). We assessed phylogenetic diversity of the genus Gloeandromyces by considering the LSU rDNA region. Phenotypic plasticity and position‐induced morphological adaptations go hand in hand. Different morphotypes belong to the same phylogenetic species. Two species, G. pageanus and G. streblae, show divergence by host utilization. In our assessment of coevolution, we only observe congruence between the Old World clades of bat flies and Laboulbeniales. The other associations are the result of the roosting ecology of the bat hosts. This study has considerably increased our knowledge about bats and their associated ectoparasites and shown the necessity of including molecular data in Laboulbeniales taxonomy.

Abstract Background The majority of wood decomposing fungi are mushroom-forming Agaricomycetes, which exhibit two main modes of plant cell wall decomposition: white rot, in which all plant cell wall components are degraded, including lignin, and brown rot, in which lignin is modified but not appreciably removed. Previous studies suggested that brown rot fungi tend to be specialists of gymnosperm hosts and that brown rot promotes gymnosperm specialization. However, these hypotheses were based on analyses of limited datasets of Agaricomycetes. Overcoming this limitation, we used a phylogeny with 1157 species integrating available sequences, assembled decay mode characters from the literature, and coded host specialization using the newly developed R package, rusda. Results We found that most brown rot fungi are generalists or gymnosperm specialists, whereas most white rot fungi are angiosperm specialists. A six-state model of the evolution of host specialization revealed high transition rates between generalism and specialization in both decay modes. However, while white rot lineages switched most frequently to angiosperm specialists, brown rot lineages switched most frequently to generalism. A time-calibrated phylogeny revealed that Agaricomycetes is older than the flowering plants but many of the large clades originated after the diversification of the angiosperms in the Cretaceous. Conclusions Our results challenge the current view that brown rot fungi are primarily gymnosperm specialists and reveal intensive white rot specialization to angiosperm hosts. We thus suggest that brown rot associated convergent loss of lignocellulose degrading enzymes was correlated with host generalism, rather than gymnosperm specialism. A likelihood model of host specialization evolution together with a time-calibrated phylogeny further suggests that the rise of the angiosperms opened a new mega-niche for wood-decay fungi, which was exploited particularly well by white rot lineages.