Biology subjects

Matute, D. R.

Publications and source records attributed to Matute, D. R..

At least 19 recordsLinked to original sources

bioRxiv2026

Long-read sequencing reveals genomic landscape of structural variants in a major disease vector

The southern house mosquito Culex quinquefasciatus is a major disease vector for multiple arboviruses, including West Nile virus and St. Louis encephalitis virus. Insecticides are widely used to control Cx. quinquefasciatus populations, but resistant mosquitoes have emerged in numerous locations across the globe, including the United States. Much progress has been made in recent years in identifying insecticide resistance (IR) mutations in various pest species. In most species, these studies have focused primarily on SNPs as they are readily detectable. However, several genomic structural variants (SVs) have been experimentally shown to impact IR in Drosophila melanogaster, and structural variation has been observed in natural populations of vector species at a few genes that may be relevant to IR (e.g., cytochrome P450s). Because most population genomic data are derived from short sequencing reads, which fail to detect a large fraction of SVs, the contribution of structural variants to the evolution of IR and other adaptations in vector species is likely to be underestimated in the absence of long-read sequencing data. Here, we present the first genome-wide assessment of structural variants in Cx. quinquefasciatus from wild populations in Puerto Rico and Zambia using PacBio long-read sequencing. We constructed high-quality genome assemblies for each and found a total of 259,046 SVs which consisted predominantly of insertions and deletions. We found that 154,071 of these variants contained or overlapped genes. Of these SVs, 5,225 intersected IR genes and 56 of these were predicted to result in changes to downstream protein function. Several SVs predicted to severely impact protein-coding genes also coincided with signatures of selective sweeps, highlighting their possible role as targets of selection. Many of these variants would have gone undetected using short-read approaches, underscoring the importance of long-read sequencing for comprehensive population genetic analyses of adaptation to pesticides and other strong selective pressures, not only in insects but across the tree of life.

evolutionary biology↗

bioRxiv2026

Evolutionary rate correlations reveal long-term co-evolutionary interactions in Drosophila melanogaster

Co-evolution between genes can occur for a variety of reasons, including co-expression of genes, epistatic interactions between them, physical interactions of gene products and many others. Co-evolutionary partners of a gene are therefore of great interest in identifying potential factors that contribute to any phenotype of interest. State-of-the-art approaches to detect these interactions use correlations of evolutionary rates across a broader phylogeny, and so by necessity identify interactions only among genes that are present across long evolutionary time periods. This makes the methods unwieldy when interest lies in a single focal organism in which the genes of interest may have evolved in the recent evolutionary past. Here, we present a new approach to calculating evolutionary rate correlations which focuses on extracting maximum coverage for a single focal species, while retaining signals of co-evolution across large clades. We show how this approach is able to identify potential interactions even in highly studied species and highly studied genes, with a focus on the D. melanogaster sex-determiner, Sxl, using data from 72 species of Dipterans.

evolutionary biology↗

bioRxiv2026

Genome variation of Sporothrix schenckii and Sporothrix brasiliensis

Sporotrichosis, a subcutaneous mycosis caused by dimorphic fungi of the Sporothrix genus, has become a major zoonotic epidemic in South America, primarily driven by Sporothrix brasiliensis. To elucidate the genomic basis of its emergence and antifungal adaptation, we analyzed whole-genome sequences from 94 Sporothrix isolates, integrating single-nucleotide polymorphism (SNP), copy number variation (CNV), and genome-wide association (GWAS) analyses. Comparative genomics revealed 610,242 SNPs within S. brasiliensis and 1,474,627 within S. schenckii, confirming a marked disparity in intraspecific diversity. Phylogenomic tree inference resolved six well-supported S. brasiliensis clades with limited internal divergence, reflecting recent population expansion, while S. schenckii displayed deep phylogeographic structure separating North and South American lineages. CNV profiling identified 158 affected genes in S. brasiliensis (60 gains, 98 losses) and 88 in S. schenckii (54 gains, 34 losses), concentrated near sub-telomeric regions. In S. brasiliensis, gains were enriched for kinases and intracellular trafficking functions, whereas losses involved genes related to translation and primary metabolism, suggesting regulatory reinforcement coupled with metabolic streamlining. A GWAS of itraconazole resistance identified 81 SNPs distributed across multiple scaffolds, with many located within genes related with transport, signaling, and redox balance, supporting a polygenic basis for azole response. Together, these results highlight distinct evolutionary strategies of closely related Sporothrix species and delineate the genomic changes associated with the emergence and drug tolerance of S. brasiliensis.

genomics↗

bioRxiv2026

Negative allometry of egg size among 29 species of drosophilid flies

The body size of adults and immature stages are fundamental animal traits that influence animal physiology, ecology, and range distribution. While the importance of egg size has been acknowledged as a proxy of parental investment in animals, little work has addressed the tempo and mode of evolution of egg size and shape. Here, we present a comparative study of this trait using a phylogeny based on genome-wide markers together with measurements of egg size and adult body size from 29 drosophilid species. Our analyses revisit the allometric relationship between egg size and body size and show that egg size scales negatively with respect to adult size, even after accounting for shared evolutionary history. In other words, larger species tend to produce proportionally smaller eggs. We also detect a moderate phylogenetic signal in both egg size and egg shape, indicating that closely related species resemble each other in these traits. Model comparisons show that the evolution of egg morphology in drosophilids is best described by gradual divergence through time driven by stochastic evolutionary change. This pattern contrasts with findings from other animal groups, including birds, cephalopods, and reptiles, where alternative evolutionary models better explain trait evolution. Together, these results suggest that the evolutionary dynamics shaping egg morphology in drosophilids differ from those operating in other major lineages and underscore the importance of comparative analyses of early developmental traits across taxa.

evolutionary biology↗

bioRxiv2026

An ancient gene duplication is implicated in virulence in the human pathogen, Histoplasma

Histoplasma spp. is a dimorphic fungal primary pathogen that infects people worldwide and frequently affects immunosuppressed patients. Previous studies have identified the AMY1 gene product, the -amylase Amy1p, as essential for -glucan production and virulence in Histoplasma capsulatum. We identified two new genes (AMY2 and AMY3) in the Histoplasma genome that encode putative -amylases and made mutants using CRISPR/Cas9 technology, followed by evaluation of their role in -glucan biosynthesis and virulence. We also searched for AMY gene copies in 19 fungal genomes with the goals of identifying orthologs for AMY2 and AMY3, and establishing how many AMY copies existed across different fungi. We found that the number and type of -amylases vary depending on the fungal species; that all -amylases related to Histoplasma Amy1p belong to the GH13_5 subfamily, and all orthologs related to Histoplasmas Amy2p and Amy3p belong to the GH13_1 subfamily. We performed phylogenetic analyses of the three paralogs and revealed that the Histoplasma AMY duplications are ancient. We further established Amy2 is an ortholog of Aspergillus niger AgtA, and Aspergillus nidulans AmyD, and that it is partially involved in Histoplasma -glucan biosynthesis and virulence, while Amy3p is an ortholog of Aspergillus flavus Amy1, and it is dispensable for -glucan biosynthesis and virulence.

microbiology↗

bioRxiv2026

Body size, wing area, and wing loading follow a pattern of trait conservatism in Drosophila

Wing loading is a metric of flight performance that captures the relationship between body mass and wing area and reflects how much weight each unit of wing surface supports during flight. Comparative studies have documented substantial differences in wing loading among individuals and across species. However, no study has evaluated the extent of this variation when species are reared under identical, controlled conditions. Here, we address that gap by measuring wing loading in 30 species of drosophilids raised in a common lab environment. We applied comparative phylogenetic methods to assess the extent to which the evolution of body mass, wing area, and wing loading is structured by shared ancestry. We find that wing area and body mass exhibit moderate phylogenetic signal, but wing loading does not. In addition, all three traits are best explained by a model of evolution in which most trait divergence occurs during speciation events. More conservative analyses provide no support for adaptive peaks in wing loading within drosophilids. Together, our results indicate that the evolutionary dynamics of wing loading in Drosophila differ from those described in birds and bats, and raise the question of whether similar patterns characterize other insect lineages.

evolutionary biology↗

bioRxiv2026

Two species of Aedes show altitudinal variation in temperature preference in the islands of the Gulf of Guinea

BackgroundTemperature choice is a vector trait that influences microhabitat selection and can have important implications for vector species, as it may affect how often vectors encounter hosts. Aedes aegypti and Ae. albopictus are disease vectors whose geographic ranges continue to expand each year. One aspect that remains largely understudied is the altitudinal range of these species and the extent of differences in thermal behavior between lowland and highland populations. MethodsI collected Ae. aegypti and Ae. albopictus on the islands of Bioko and Sao Tome. I compared the distribution of the two species along an altitudinal cline spanning 2,000 m of elevation. I then used live specimens to test temperature preference for both species in a laboratory thermocline. ResultsI report the distribution of these two species on the island of Bioko and show that the abundance of immature stages of both species follows a negative exponential decay with altitude. I compare this distribution with that observed on the neighboring island of Sao Tome, also in the Gulf of Guinea. Overall, the distribution patterns of the two species are similar, but models indicate a higher abundance at sea level in Sao Tome than in Bioko. I used specimens from this survey to study temperature preference under controlled conditions. I found no significant differences between species or between sexes; however, I detected an altitudinal cline in temperature preference, with high-elevation populations preferring cooler temperatures on both islands. ConclusionsThese results indicate the presence of phenotypic variation in a key trait--temperature choice--that may alter the likelihood of contact between these vectors and humans.

zoology↗

bioRxiv2025

Telomeric assemblies of Paracoccidioides genomes

Paracoccidioides is a genus of dimorphic fungal pathogens endemic to Latin America. We generated long-read de novo assemblies for 11 isolates representing four species of the brasiliensis complex (P. brasiliensis, P. americana, P. restrepiensis, P. venezuelensis) and P. lutzii. These include the first complete telomere-to-telomere assemblies for P. brasiliensis (Pb18) and P. americana (Pb03), each with five chromosomes. Comparative analyses revealed chromosomal fusion and fission events distinguishing P. brasiliensis and P. americana, and a 90 kb tandem duplication in P. americana containing siderophore biosynthesis genes (sid1, sid3, sid4), a cluster of putative virulence factors. Mitochondrial genomes showed conserved gene order but a phylogenetic topology inconsistent with the nuclear tree, suggesting mitochondrial introgression between P. lutzii and P. venezuelensis. RNA transposable elements were enriched near telomeres, correlated with genome size, and most abundant in P. lutzii. These assemblies provide key resources for understanding genome evolution and introgression in Paracoccidioides. SIGNIFICANCESpecies of Paracoccidioides cause paracoccidioidomycosis, a systemic mycosis that remains a major public health problem in Latin America. Despite their clinical importance, genome evolution across the genus is poorly understood owing to the lack of complete reference assemblies. Here, we present the first telomere-to-telomere reference genomes for P. brasiliensis and P. americana, enabling a comprehensive comparison of chromosomal structure across the genus. Our analyses reveal that the nuclear genome is highly dynamic and shaped by large-scale rearrangements and structural variants, including the duplication of a siderophore biosynthesis-related gene cluster linked to virulence. In contrast, the mitochondrial genome is structurally conserved but shows introgression between species, revealing hidden evolutionary exchange. Together, these genomic resources redefine our understanding of Paracoccidioides evolution and provide a foundation for advances in molecular diagnostics, epidemiological surveillance, and studies of fungal pathogenicity.

microbiology↗

bioRxiv2025

The contribution of transposable element insertions to genetic diversity in Aedes aegypti populations

Aedes aegypti is a vector of multiple tropical diseases. The main strategy to control transmission is insecticide-based population control. However, mosquito populations rapidly evolve resistance, possibly enabled by their high levels of genetic diversity. Genome-wide surveys of diversity in Ae. aegypti have focused on single nucleotide polymorphisms (SNPs), and although structural variants such as transposable element (TE) insertions have been implicated in insecticide resistance (IR) in Drosophila, these have not been thoroughly characterized in Aedes. Here, we evaluated the TE content in 122 Ae. aegypti genomes from six countries across Africa, North, and South America. We found that TEs contribute substantially to genetic diversity and reflect population structure broadly consistent with that seen in SNPs. Although most TEs insertions are rare, some were observed at higher frequencies, suggesting that a small subset of these may be beneficial. For example, we identified numerous TEs with large frequency differences across populations, consistent with the possibility that these are in haplotypes underlying local adaptation. Specifically, we found three TEs near genes that may be involved in metabolic insecticide resistance: CYP6P12, GSTD11 and GSTZ1. In Colombian samples, we also identified a TE insertion that is in negative linkage disequilibrium with several insecticide resistance mutations that form an intermediate-frequency haplotype in the VGSC gene region. These results suggest the possibility that, just as TEs have been implicated in adaptation in other animals such as Drosophila, they may play an important role in the evolution of resistance to control efforts in Aedes and other pests.

evolutionary biology↗

bioRxiv2025

Flight feathers evolve fastest near the tip of the wing

Form-function relationships are foundational to evolutionary biology, but we are only beginning to understand the mechanisms that link biomechanical function to morphological evolution. In bird wings, the pace of morphological evolution follows a gradient of aerodynamic force production along the wing, with the fastest rates experienced at the wingtip. We examined how this gradient has manifested in the evolution of the individual flight feathers that comprise the wing surface. Specifically, we studied whether the flight feathers show a pattern of allometric scaling with respect to avian body size, and if the allometric pattern varies along the wing. We also asked whether the pace of evolution of the primary flight feathers follows the same gradient pattern as the overall wing morphology, and if there is modularity within the feather series. We measured the lengths of each of the primary flight feathers from 509 wings representing 514 bird species and calculated morphological disparity and evolutionary rate for each feather in the primary sequence. We found that evolutionary rate and disparity increase significantly toward the wingtip. We also found evidence for modularity within the feather sequence, but we were unable to positively delineate those modules. Our study provides further evidence that the mechanical sensitivity of morphological traits predicts their evolution, with highly sensitive features biased toward higher rates, and that it scales across multiple levels of anatomical organization.

evolutionary biology↗

bioRxiv2025

Sex differentiation, divergence, and introgression in the leishmaniasis vector Lutzomyia longipalpis

An estimated one billion people are at risk of acquiring the disease leishmaniasis annually. This disease, among others, is transmitted to humans via sandfly vectors of the family Psychodidae. In the Neotropics, Lutzomyia longipalpis is one of the most common vectors of leishmaniasis, but little is known about its genetics and population structure, hampering control efforts. We generated sex-specific genome assemblies of Lu. longipalpis from Colombia, and examined population genomics of this species. We found that sex accounts for [~]11% of genome-wide variation, primarily driven by differentiation between the sexes in an XY sex chromosome. Analyses of transposable elements indicate that the size difference in the sex chromosome is driven by more transposable elements in the male chromosome. Further, we examined population genomics and structure across the South American continent. We identified significant genetic divergence between Colombian and Brazilian sandflies and population structure within Lu. longipalpis sensu lato samples collected from the same sites in Brazil. These results strongly suggest the presence of multiple, sympatric species within a cryptic species complex, concordant with other published phenotypic evidence. SIGNIFICANCELeishmaniasis has emerged as an important public health issue. Transmission occurs exclusively through Phlebotomine sandflies of the genera Lutzomyia and Phlebotomus, yet our ability to prevent its spread is constrained by limited knowledge of the biological and ecological factors that make these insects effective vectors. In this manuscript, we leverage whole-genome sequencing to investigate the evolutionary forces shaping genetic diversity in Lutzomyia longipalpis, a key vector of leishmaniasis.

genomics↗

bioRxiv2025

Mapping Histoplasma in Bats and Cave Ecosystems: Evidence from Midwestern Brazil

Caves serve as natural reservoirs for diverse microbial species due to their unique biotic and abiotic conditions. Histoplasma spp. is frequently associated with guano-enriched soil, low luminosity, and high humidity, particularly in Latin America, a region highly endemic for histoplasmosis. Despite the continents diverse biomes, local environmental and host distributions of Histoplasma remain poorly understood. To address this knowledge gap, we conducted a Histoplasma-specific quantitative PCR (qPCR) assay targeting the hc100 gene on guano samples from seven bat-inhabited caves and tissue samples from 74 bats of nine species in the Federal District of Brazil and surround-ing regions. We detected Histoplasma DNA in 16 of 80 soil samples (20%) and in 33 bats representing seven species. Among 222 tissue samples (74 lung, 74 spleen, 74 brain), 39 tested positive: 22 lung, 10 spleen, and 7 brain samples. Four bats had Histoplasma DNA in both lung and brain, and two in both lung and spleen. By mapping the presence of Histoplasma across sampled caves, we identified environmental hotspots of fungal prevalence, emphasizing the need for targeted surveillance. ImportanceOur study provides critical insights into the environmental and host distribution of Histoplasma spp. in Brazil, identifying caves with high fungal prevalence and demonstrating its presence in multiple bat species. These findings underscore the necessity of public health interventions to mitigate the risk of histoplasmosis among cave visitors in the region. Additionally, we highlight the utility of qPCR for detecting Histoplasma in environmental and biological samples, supporting future epidemiological research in Latin America.

microbiology↗

bioRxiv2025

A Novel Sarocladium spinificis Strain Suppresses Coccidioides posadasii Growth: Morphological and Genetic Perspectives

Sarocladium is a diverse fungal genus with implications in both plant and human diseases, exhibiting roles in pathogenicity, endophytism, and biocontrol. This study characterizes two Sarocladium spinificis strains, CA16 (CBS 144516) and CA18 (CBS 144517), isolated from patients initially suspected of having coccidioidomycosis. Morphological, phylogenetic, and genomic analyses confirmed their classification within the Sarocladium genus, closely related to S. spinificis. Both strains exhibited growth at 24{degrees}C and 37{degrees}C, with distinct morphological features. Comparative genomic analysis identified unique orthologous clusters and functional gene families associated with adaptability and potential pathogenicity. Notably, these strains demonstrated enhanced production of secreted proteins, CAZymes, and peptidases, highlighting metabolic versatility. Co-cultivation experiments revealed that S. spinificis strains CA16 and CA18 inhibited the growth of Coccidioides posadasii, suggesting competitive interactions and potential antifungal properties. These findings underscore the ecological and clinical significance of S. spinificis and its impact on microbial communities, advancing our understanding of its diversity, pathogenic potential, and antifungal capabilities. ImportanceAccurate identification and characterization of emerging fungal pathogens are essential for improving diagnosis and treatment. Sarocladium spinificis, though not widely recognized as a human pathogen, exhibits traits suggesting a potential role in opportunistic infections. This study provides the first detailed morphological, phylogenetic, and genomic characterization of clinical S. spinificis isolates, highlighting its ability to survive at body temperature and its antifungal resistance. Additionally, we demonstrate that these strains inhibit Coccidioides posadasii, the agent of Valley fever, suggesting ecological competition or antifungal properties. These findings contribute to understanding fungal interactions in clinical and environmental settings, with implications for fungal pathogenesis and antifungal strategies. By uncovering new aspects of S. spinificis biology, this work expands knowledge of Sarocladium species in human health and lays the foundation for future research on its ecological role, pathogenic potential, and therapeutic applications.

microbiology↗

bioRxiv2024

Phylogenetic and functional diversity among Drosophila-associated metagenome-assembled genomes

Host-associated microbial communities can mediate interactions between their hosts and biotic and abiotic environments. While much work has been done to document how microbiomes vary across species and environments, much less is known about the functional consequences of this variation. Here, we test for functional variation among drosophilid-associated bacteria by conducting Oxford Nanopore long-read sequencing and generating metagenome-assembled genomes (MAGs) from six species of drosophilid fly collected in association with anthropogenic environments in North America, Europe, and Africa. Using phylogenetic analyses, we find that drosophilid flies harbor a diverse microbiome that includes core members closely related to the genera Gilliamella, Orbus, Entomomonas, Dysgonomonas, and others. Comparisons with publicly available bacterial genomes show that many of these genera are associated with phylogenetically diverse insect gut microbiomes. Using functional annotations and predicted secondary metabolite biosynthetic gene clusters, we show that MAGs belonging to different bacterial orders and genera vary in gene content and predicted functions including metabolic capacity and how they respond to environmental stressors. Our results provide evidence that wild drosophilid flies harbor phylogenetically and functionally diverse microbial communities. These findings highlight a need to quantify the abundance and function of insect-associated bacteria from the genera Gilliamella, Orbus, Entomomonas, and others on the performance of their insect hosts across diverse environments.

genomics↗

bioRxiv2024

The comparative analysis of lineage-pair traits.

A powerful but poorly understood analysis in ecology and evolutionary biology is the comparative study of lineage-pair traits. "Lineage-pair traits" are characters like diet niche overlap and strength of reproductive isolation that are defined for pairs of lineages instead of individual taxa. Comparative tests for causal relationships among such variables have led to groundbreaking insights in several classic studies, but the statistical validity of these analyses has been unclear due to the complex dependency structure of the data. Specifically, lineage-pair datasets contain non-independent observations, but studies to-date have relied on untested workarounds for data dependency rather than direct models of linear-pair covariance, and the statistical consequences of non-independence have not been thoroughly explored. Here we consider how evolutionary relatedness among taxa translates into non-independence among taxonomic pairs. We develop models by which phylogenetic signal in an underlying character generates covariance among pairs in a lineage-pair trait. We incorporate the resulting lineage-pair covariance matrix into a modified version of phylogenetic generalized least squares and a new beta regression model suitable for bounded response variables. Both models outperform previous approaches in simulation tests. We re-analyze two empirical datasets and find dramatic improvements in model fit and, in the case of avian hybridization data, an even stronger relationship between pair age and RI than revealed by standard linear regression. We present a new tool, the R package phylopairs, to allow empiricists from a variety of biological fields to test relationships among pairwise-defined variables in a manner that is statistical robust and more straightforward to implement.

evolutionary biology↗

bioRxiv2024

Temperature affects conspecific and heterospecific mating rates in Drosophila

Behavioral mating choices and mating success are important factors in the development of reproductive isolation during speciation. Environmental conditions, especially temperature, can affect these key traits. Environmental conditions can vary across, and frequently delimit species geographic ranges. Pairing suboptimal conditions with relative rarity of conspecifics at range margins may set the stage for hybridization. Despite the importance of mating behaviors as a reproductive barrier, a general understanding of the interaction between behavioral choices and the environment is lacking, in part because systematic studies are rare. With this report, we begin to bridge that gap by providing evidence that temperature has a significant - but not consistent influence on mating choices and success, and thus on reproductive isolation in Drosophila. We studied mating propensity and success at four different temperatures among 14 Drosophila species in non-choice conspecific mating trials and in heterospecific trials among two Drosophila species triads that are known to regularly hybridize in the wild. We show that mating frequency varies significantly across a 10{degrees}C range (from 18{o}C to 28{o}C), both in 1:1 mating trials and in high-density en-masse trials, but that the effect of temperature is highly species-specific. We also show that mating frequency is consistently low and that temperature has a moderate effect in some heterospecific crosses. As conspecific mating propensity decreases outside of the optimal thermal range, while heterospecific matings remain constant, the proportion of heterospecific matings at suboptimal temperatures is relatively high. This result indicates that temperature can modulate behavioral choices that impose reproductive barriers and influence the rate of hybridization. More broadly, our results demonstrate that to truly understand how mating choice and reproductive isolation occur in nature, they need to be studied in an environmental context.

animal behavior and cognition↗

bioRxiv2024

Demographic history and the efficacy of selection in the globally invasive mosquito Aedes aegypti

Aedes aegypti is the main vector species of yellow fever, dengue, zika and chikungunya. The species is originally from Africa but has experienced a spectacular expansion in its geographic range to a large swath of the world, the demographic effects of which have remained largely understudied. In this report, we examine whole-genome sequences from 6 countries in Africa, North America, and South America to investigate the demographic history of the spread of Ae. aegypti into the Americas its impact on genomic diversity. In the Americas, we observe patterns of strong population structure consistent with relatively low (but probably non-zero) levels of gene flow but occasional long-range dispersal and/or recolonization events. We also find evidence that the colonization of the Americas has resulted in introduction bottlenecks. However, while each sampling location shows evidence of a past population contraction and subsequent recovery, our results suggest that the bottlenecks in America have led to a reduction in genetic diversity of only [~]35% relative to African populations, and the American samples have retained high levels of genetic diversity (expected heterozygosity of [~]0.02 at synonymous sites) and have experienced only a minor reduction in the efficacy of selection. These results evoke the image of an invasive species that has expanded its range with remarkable genetic resilience in the face of strong eradication pressure.

evolutionary biology↗

bioRxiv2024

Phenotypic characterization of cryptic species in the fungal pathogen Histoplasma

Histoplasmosis is an endemic mycosis that often presents as a respiratory infection in immunocompromised patients. Hundreds of thousands of new infections are reported annually around the world. The etiological agent of the disease, Histoplasma, is a dimorphic fungus commonly found in the soil where it grows as mycelia. Humans can become infected by Histoplasma through inhalation of its spores (conidia) or mycelial particles. The fungi transitions into the yeast phase in the lungs at 37{degrees}C. Once in the lungs, yeast cells reside and proliferate inside alveolar macrophages. We have previously described that Histoplasma is composed of at least five cryptic species that differ genetically, and assigned new names to the lineages. Here we evaluated multiple phenotypic characteristics of 12 strains from five phylogenetic species of Histoplasma to identify phenotypic traits that differentiate between these species: H. capsulatum sensu stricto, H. ohiense, H. mississippiense, H. suramericanum, and an African lineage. We report diagnostic traits for two species. The other three species can be identified by a combination of traits. Our results suggest that 1) there are significant phenotypic differences among the cryptic species of Histoplasma, and 2) that those differences can be used to positively distinguish those species in a clinical setting and for further study of the evolution of this fungal pathogen. IMPORTANCEIdentifying species boundaries is a critical component of evolutionary biology. Genome sequencing and the use of molecular markers have advanced our understanding of the evolutionary history of fungal pathogens, including Histoplasma, and have allowed for the identification of new species. This is especially important in organisms where morphological characteristics cannot be used for this purpose. In this study, we revise the taxonomic status of the four named species of the genus Histoplasma: H. capsulatum sensu stricto, H. ohiense, H. mississippiense, and H. suramericanum and propose the use of species-specific phenotypic traits to aid their identification when genome sequencing is not available. These results have implications not only for evolutionary study of Histoplasma, but also for clinicians, as the Histoplasma species could determine the outcome of disease and treatment needed.

microbiology↗