Coccidioides immitis and C. posadasii , the causative agents of coccidioidomycosis, are dimorphic fungal pathogens, which grow as hyphae in the saprobic phase in the environment and as spherules in the parasitic phase in the mammalian host. In this study, we use comparative transcriptomics to identify gene expression differences between the saprobic and parasitic growth phases. We prepared Illumina mRNA sequencing libraries for saprobic-phase hyphae and parasitic-phase spherules in vitro for C. immitis isolate RS and C. posadasii isolate C735 in biological triplicate. Of 9,910 total predicted genes in Coccidioides , we observed 1,298 genes up-regulated in the saprobic phase of both C. immitis and C. posadasii and 1,880 genes up-regulated in the parasitic phase of both species. Comparing the saprobic and parasitic growth phases, we observed considerable differential expression of cell surface-associated genes, particularly chitin-related genes. We also observed differential expression of several virulence factors previously identified in Coccidioides and other dimorphic fungal pathogens. These included alpha (1,3) glucan synthase, SOWgp, and several genes in the urease pathway. Furthermore, we observed differential expression in many genes predicted to be under positive selection in two recent Coccidioides comparative genomics studies. These results highlight a number of genes that may be crucial to dimorphic phase-switching and virulence in Coccidioides . These observations will impact priorities for future genetics-based studies in Coccidioides and provide context for studies in other fungal pathogens.

Abstract. Ecologists and evolutionary biologists perceive the ecological niche as a multidimensional relationship between an organism and its environment. Yet, we know little about the degree to which multiple niche axes evolve in concert across various spatial scales to explain differences in distribution patterns and habitat specialization among lineages. Here we used contemporary phylogenetic approaches to analyze the evolution of species' distributions across multiple spatial scales in Lasthenia, a young and ecologically diverse plant clade largely occurring within the California Floristic Province, USA. Lasthenia species and subspecies range from widely distributed taxa that occupy a diversity of habitat types to locally restricted habitat endemics, including several lineages that are strongly associated with isolated ephemeral wetlands called vernal pools. We quantified the niche of Lasthenia species and subspecies at three different spatial scales: the range-wide climate niche, the habitat niche, and the within-habitat depth niche for those taxa occupying vernal pools. We incorporated phylogenetic uncertainty into our analyses by reanalyzing previously described DNA sequences in a Bayesian context and conducting all subsequent comparative analyses over the resulting posterior distribution of ultrametric phylogenetic trees. Using a biogeographic approach for ancestral habitat reconstruction, we estimated that Lasthenia lineages have undergone up to four independent transitions from strictly terrestrial habitats to a niche that incorporates semiaquatic habitats, and one of these transitions led to the subsequent proliferation of vernal pool species and subspecies. We found that the local niche axis, corresponding to the depth distribution of taxa within pools, was more phylogenetically conserved than the large-scale axes representing climatic associations. Furthermore, we did not find evidence that niche breadth estimates along different axes were consistently correlated, indicating that ecological specialization may be specific to certain niche axes rather than an overall characteristic of a species.

BackgroundGene duplication is a source of evolutionary innovation and can contribute to the divergence of lineages; however, the relative importance of this process remains to be determined. The explosive divergence of the African cichlid adaptive radiations provides both a model for studying the general role of gene duplication in the divergence of lineages and also an exciting foray into the identification of genomic features that underlie the dramatic phenotypic and ecological diversification in this particular lineage. We present the first genome-wide study of gene duplication in African cichlid fishes, identifying gene duplicates in three species belonging to the Lake Malawi adaptive radiation (Metriaclima estherae, Protomelas similis, Rhamphochromis “chilingali”) and one closely related species from a non-radiated riverine lineage (Astatotilapia tweddlei).ResultsUsing Astatotilapia burtoni as reference, microarray comparative genomic hybridization analysis of 5689 genes reveals 134 duplicated genes among the four cichlid species tested. Between 51 and 55 genes were identified as duplicated in each of the three species from the Lake Malawi radiation, representing a 38%–49% increase in number of duplicated genes relative to the non-radiated lineage (37 genes). Duplicated genes include several that are involved in immune response, ATP metabolism and detoxification.ConclusionsThese results contribute to our understanding of the abundance and type of gene duplicates present in cichlid fish lineages. The duplicated genes identified in this study provide candidates for the analysis of functional relevance with regard to phenotype and divergence. Comparative sequence analysis of gene duplicates can address the role of positive selection and adaptive evolution by gene duplication, while further study across the phylogenetic range of cichlid radiations (and more generally in other adaptive radiations) will determine whether the patterns of gene duplication seen in this study consistently accompany rapid radiation.

Results presented here indicate the utility of our new microsatellite primers in ongoing and future studies concerning population genetics and gene flow in C. roderickii, as well as the potential applicability of these primers in similar studies on other Ceanothus species.