Habitat and Host Indicate Lineage Identity in Colletotrichum gloeosporioides s.l. from Wild and Agricultural Landscapes in North America

Understanding the factors that drive the evolution of pathogenic fungi is central to revealing the mechanisms of virulence and host preference, as well as developing effective disease control measures. Prerequisite to these pursuits is the accurate delimitation of species boundaries. Colletotrichum gloeosporioides s.l. is a species complex of plant pathogens and endophytic fungi for which reliable species recognition has only recently become possible through a multi-locus phylogenetic approach. By adopting an intensive regional sampling strategy encompassing multiple hosts within and beyond agricultural zones associated with cranberry (Vaccinium macrocarpon Aiton), we have integrated North America strains of Colletotrichum gloeosporioides s.l. from these habitats into a broader phylogenetic framework. We delimit species on the basis of genealogical concordance phylogenetic species recognition (GCPSR) and quantitatively assess the monophyly of delimited species at each of four nuclear loci and in the combined data set with the genealogical sorting index (gsi). Our analysis resolved two principal lineages within the species complex. Strains isolated from cranberry and sympatric host plants are distributed across both of these lineages and belong to seven distinct species or terminal clades. Strains isolated from V. macrocarpon in commercial cranberry beds belong to four species, three of which are described here as new. Another species, C. rhexiae Ellis & Everh., is epitypified. Intensive regional sampling has revealed a combination of factors, including the host species from which a strain has been isolated, the host organ of origin, and the habitat of the host species, as useful indicators of species identity in the sampled regions. We have identified three broadly distributed temperate species, C. fructivorum, C. rhexiae, and C. nupharicola, that could be useful for understanding the microevolutionary forces that may lead to species divergence in this important complex of endophytes and plant pathogens

Predicting Species Boundaries and Assessing Undescribed Diversity in , an Obligate Lung Symbiont

Far more biodiversity exists in Fungi than has been described, or could be described in several lifetimes, given current rates of species discovery. Although this problem is widespread taxonomically, our knowledge of animal-associated fungi is especially lacking. Fungi in the genus are obligate inhabitants of mammal lungs, and they have been detected in a phylogenetically diverse array of species representing many major mammal lineages. The hypothesis that cospeciate with their mammalian hosts suggests that thousands of species may exist, potentially equal to the number of mammal species. However, only six species have been described, and the true correspondence of diversity to host species boundaries is unclear. Here, we use molecular species delimitation to estimate the boundaries of species sampled from 55 mammal species representing eight orders. Our results suggest that species often colonize several closely related mammals, especially those in the same genus. Using the newly estimated ratio of fungal to host diversity, we estimate ≈4600 to 6250 species inhabit the 6495 currently recognized extant mammal species. Additionally, we review the literature and find that only 240 (~3.7%) mammal species have been screened for , and many detected lineages are not represented by any genetic data. Although crude, our findings challenge the dominant perspective of strict specificity of to their mammal hosts and highlight an abundance of undescribed diversity

Will the application of biocontrol fungi disrupt predation of Acanthococcus lagerstroemiae by coccinellids?

Insect predators are the most important natural enemies of the crapemyrtle bark scale (CMBS) in the USA. Mycopesticides (biocontrol fungi) are considered an IPM tool to increase CMBS mortality; however, their impacts on CMBS predators are unknown. The objectives of this study were to assess the abundance and diversity of CMBS natural enemies in Louisiana; evaluate the impacts of mycopesticides on survival of CMBS predators by life stage; and determine if entomopathogenic spores delivered to crapemyrtles are transferred to predators under field conditions. The mycopesticides Ancora® (Isaria fumosorosea PFR97), BioCeres® (Beauveria bassiana ANT-03), and BotaniGard® (B. bassiana GHA) were tested against the coccinellids Chilocorus spp. and Hyperaspis bigeminata under laboratory and field conditions. Adults and larvae of the coccinellids were treated with each mycopesticide and survival recorded over a 14-day period. The most common natural enemies on CMBS infested trees were the coccinellids Chilocorus cacti, C. stigma, and Hyperaspis bigeminata (Coleoptera: Coccinellidae). In laboratory bioassays BotaniGard® reduced survival of adults and larvae of both genera by at least 57%. BioCeres® reduced the survival of Chilocorus spp. adults by 40% and Ancora® reduced survival of H. bigeminata larvae by 69%. Under field conditions, CMBS infestations were sprayed with the mycopesticides and coccinellids were collected every other day for a two-week period. Spores of the applied mycopesticides were recovered from the coccinellids; however, it is not known if infection occurred in the field trial or spores were delivered to CMBS infestations by the coccinellids. We conclude that mycopesticides negatively impacted the survival of coccinellids in laboratory trials, and coccinellids can transport pathogen spores under field conditions

Why species delimitation matters for fungal ecology: Colletotrichum diversity on wild and cultivated cashew in Brazil

Anthracnose is one of the most important plant diseases globally, occurring on a wide range of cultivated and wild host species. This study aimed to identify the Colletotrichum species associated with cashew anthracnose in Brazil, determine their phylogenetic relationships and geographical distribution, and provide some insight into the factors that may be influencing community composition. Colletotrichum isolates collected from symptomatic leaves, stems, inflorescences, and fruit of cultivated and wild cashew, across four Brazilian biomes, were identified as Colletotrichum chrysophilum, Colletotrichum fragariae, Colletotrichum fructicola, Colletotrichum gloeosporioides sensu stricto, Colletotrichum queenslandicum, Colletotrichum siamense and Colletotrichum tropicale. Colletotrichum siamense was the most dominant species. The greatest species richness was associated with cultivated cashew; leaves harbored more species than the other organs; the Atlantic Forest encompassed more species than the other biomes; and Pernambuco was the most species-rich location. However, accounting for the relative abundance of Colletotrichum species and differences in sample size across strata, the interpretation of which community is most diverse depends on how species are delimited. The present study provides valuable information about the Colletotrichum/cashew pathosystem, sheds light on the causal agents identification,and highlights the impact that species delimitation can have on ecological studies of fungi

Draft Genome Sequence of cf. , a Causal Agent of Cercospora Leaf Blight on Soybean

cf. is an ascomycete fungal pathogen that infects various plants, including important agricultural commodities, such as soybean. Here, we report the first draft genome sequence and assembly of this pathogen

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Untangling the influences of unmodeled evolutionary processes on phylogenetic signal in a forensically important HIV-1 transmission cluster

Stochastic models of sequence evolution have been developed to reflect many biologically important processes, allowing for accurate phylogenetic reconstruction when an appropriate model is selected. However, commonly used models do not incorporate several potentially important biological processes. Spurious phylogenetic inference may result if these processes play an important role in the evolution of a dataset yet are not incorporated into assumed models. Few studies have attempted to assess the relative importance of multiple processes in producing spurious inferences. The application of phylogenetic methods to infer the source of HIV-1 transmission clusters depends upon accurate phylogenetic results, yet there are several relevant unmodeled biological processes (e.g., recombination and convergence) that may cause complications. Here, through analyses of HIV-1 env sequences from a small, forensically important transmission cluster, we tease apart the impact of these processes and present evidence suggesting that convergent evolution and high rates of insertions and deletions (causing alignment uncertainty) led to spurious phylogenetic signal with forensic relevance. Previous analyses show paraphyly of HIV-1 lineages sampled from an individual who, based on non-phylogenetic evidence, had never acted as a source of infection for others in this transmission cluster. If true, this pattern calls into question assumptions underlying phylogenetic approaches to source and recipient identification. By systematically assessing the contribution of different unmodeled processes, we demonstrate that removal of sites likely influenced by strong positive selection both reduces the alignment-wide signal supporting paraphyly of viruses sampled from this individual and eliminates support for the effects of recombination. Additionally, the removal of ambiguously aligned sites alters strongly supported relationships among viruses sampled from different individuals. These observations highlight the need to jointly consider multiple unmodeled evolutionary processes and motivate a phylogenomic perspective when inferring viral transmission histories. © 2014 Elsevier Inc