cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12312440
title: Evolutionary relationships among <i>Massospora</i> spp. (Entomophthorales), obligate pathogens of cicadas

description: The fungal genus <i>Massospora</i> (Zoopagomycota: Entomophthorales) includes more than a dozen obligate, sexually transmissible pathogenic species that infect cicadas (Hemiptera) worldwide. At least two species are known to produce psychoactive compounds during infection, which has garnered considerable interest for this enigmatic genus. As with many Entomophthorales, the evolutionary relationships and host associations of <i>Massospora</i> spp. are not well understood. The acquisition of <i>M. diceroproctae</i> from Arizona, <i>M. tettigatis</i> from Chile, and <i>M. platypediae</i> from California and Colorado provided an opportunity to conduct molecular phylogenetic analyses and morphological studies to investigate whether these fungi represent a monophyletic group and delimit species boundaries. In a three-locus phylogenetic analysis including the D1–D2 domains of the nuclear 28S rRNA gene (28S), elongation factor 1 alpha-like (<i>EFL</i>), and beta-tubulin (<i>BTUB</i>), <i>Massospora</i> was resolved in a strongly supported monophyletic group containing four well-supported genealogically exclusive lineages, based on two of three methods of phylogenetic inference. There was incongruence among the single-gene trees: two methods of phylogenetic inference recovered trees with either the same topology as the three-gene concatenated tree (<i>EFL</i>) or a basal polytomy (28S, <i>BTUB</i>). <i>Massospora levispora</i> and <i>M. platypediae</i> isolates formed a single lineage in all analyses and are synonymized here as <i>M. levispora. Massospora diceroproctae</i> was sister to <i>M. cicadina</i> in all three single-gene trees and on an extremely long branch relative to the other <i>Massospora</i>, and even the outgroup taxa, which may reflect an accelerated rate of molecular evolution and/or incomplete taxon sampling. The results of the morphological study presented here indicate that spore measurements may not be phylogenetically or diagnostically informative. Despite recent advances in understanding the ecology of <i>Massospora</i>, much about its host range and diversity remains unexplored. The emerging phylogenetic framework can provide a foundation for exploring coevolutionary relationships with cicada hosts and the evolution of behavior-altering compounds.
DOI: 10.6084/m9.figshare.12312440.v1
title: Evolutionary relationships among <i>Massospora</i> spp. (Entomophthorales), obligate pathogens of cicadas

description: The fungal genus <i>Massospora</i> (Zoopagomycota: Entomophthorales) includes more than a dozen obligate, sexually transmissible pathogenic species that infect cicadas (Hemiptera) worldwide. At least two species are known to produce psychoactive compounds during infection, which has garnered considerable interest for this enigmatic genus. As with many Entomophthorales, the evolutionary relationships and host associations of <i>Massospora</i> spp. are not well understood. The acquisition of <i>M. diceroproctae</i> from Arizona, <i>M. tettigatis</i> from Chile, and <i>M. platypediae</i> from California and Colorado provided an opportunity to conduct molecular phylogenetic analyses and morphological studies to investigate whether these fungi represent a monophyletic group and delimit species boundaries. In a three-locus phylogenetic analysis including the D1–D2 domains of the nuclear 28S rRNA gene (28S), elongation factor 1 alpha-like (<i>EFL</i>), and beta-tubulin (<i>BTUB</i>), <i>Massospora</i> was resolved in a strongly supported monophyletic group containing four well-supported genealogically exclusive lineages, based on two of three methods of phylogenetic inference. There was incongruence among the single-gene trees: two methods of phylogenetic inference recovered trees with either the same topology as the three-gene concatenated tree (<i>EFL</i>) or a basal polytomy (28S, <i>BTUB</i>). <i>Massospora levispora</i> and <i>M. platypediae</i> isolates formed a single lineage in all analyses and are synonymized here as <i>M. levispora. Massospora diceroproctae</i> was sister to <i>M. cicadina</i> in all three single-gene trees and on an extremely long branch relative to the other <i>Massospora</i>, and even the outgroup taxa, which may reflect an accelerated rate of molecular evolution and/or incomplete taxon sampling. The results of the morphological study presented here indicate that spore measurements may not be phylogenetically or diagnostically informative. Despite recent advances in understanding the ecology of <i>Massospora</i>, much about its host range and diversity remains unexplored. The emerging phylogenetic framework can provide a foundation for exploring coevolutionary relationships with cicada hosts and the evolution of behavior-altering compounds.
DOI: 10.6084/m9.figshare.12848625.v1
title: Seven new species of <i>Graphilbum</i> from conifers in Norway, Poland, and Russia

description: During surveys of insect-associated mycobiomes in Norway, Poland, and Russia, isolates with affinity to <i>Graphilbum</i> (Ophiostomatales, Ascomycota) were recovered. In this study, eight known <i>Graphilbum</i> species as well as the newly collected isolates were compared based on morphology and DNA sequence data for four gene regions. The results revealed seven new species, described here as <i>G. acuminatum, G. carpaticum, G. curvidentis, G. furuicola, G. gorcense, G. interstitiale</i>, and <i>G. sexdentatum</i>. In addition to these species, <i>G. crescericum</i> and <i>G. sparsum</i> were commonly found in Norway. All new species were recovered from conifers in association with bark beetles, cerambycid beetles, and weevils and were morphologically similar, predominantly with pesotum-like asexual morphs. Where sexual morphs were present, these were small ascomata with short necks and rod-shaped ascospores having hyaline sheaths. The results suggest that <i>Graphilbum</i> species are common members of the Ophiostomatales in conifer ecosystems.
DOI: 10.6084/m9.figshare.12919324
title: Hysterangium bonobo: A newly described truffle species that is eaten by bonobos in the Democratic Republic of Congo

description: Many animals have been shown to eat fungi and most truffle-like fungi depend on animals for spore dispersal via mycophagy. Although these interactions are widespread, they are understudied in many habitats. In this study, we show that bonobos (<i>Pan paniscus</i>) forage and feed on an undescribed truffle species in the rainforests of the Democratic Republic of Congo. Based on morphological and molecular assessment of collections, we show that the species eaten by bonobos is a previously undescribed taxon described here as <i>Hysterangium bonobo</i>. This species is known in the local Bantu language (Bongando) as simbokilo and is used for baiting traps to catch several species of small mammals. Our findings highlight the need for further research into mycophagy and systematics of sequestrate fungi in Africa.
DOI: 10.6084/m9.figshare.12919324.v1
title: Hysterangium bonobo: A newly described truffle species that is eaten by bonobos in the Democratic Republic of Congo

description: Many animals have been shown to eat fungi and most truffle-like fungi depend on animals for spore dispersal via mycophagy. Although these interactions are widespread, they are understudied in many habitats. In this study, we show that bonobos (<i>Pan paniscus</i>) forage and feed on an undescribed truffle species in the rainforests of the Democratic Republic of Congo. Based on morphological and molecular assessment of collections, we show that the species eaten by bonobos is a previously undescribed taxon described here as <i>Hysterangium bonobo</i>. This species is known in the local Bantu language (Bongando) as simbokilo and is used for baiting traps to catch several species of small mammals. Our findings highlight the need for further research into mycophagy and systematics of sequestrate fungi in Africa.
DOI: 10.6084/m9.figshare.12848625
title: Seven new species of <i>Graphilbum</i> from conifers in Norway, Poland, and Russia

description: During surveys of insect-associated mycobiomes in Norway, Poland, and Russia, isolates with affinity to <i>Graphilbum</i> (Ophiostomatales, Ascomycota) were recovered. In this study, eight known <i>Graphilbum</i> species as well as the newly collected isolates were compared based on morphology and DNA sequence data for four gene regions. The results revealed seven new species, described here as <i>G. acuminatum, G. carpaticum, G. curvidentis, G. furuicola, G. gorcense, G. interstitiale</i>, and <i>G. sexdentatum</i>. In addition to these species, <i>G. crescericum</i> and <i>G. sparsum</i> were commonly found in Norway. All new species were recovered from conifers in association with bark beetles, cerambycid beetles, and weevils and were morphologically similar, predominantly with pesotum-like asexual morphs. Where sexual morphs were present, these were small ascomata with short necks and rod-shaped ascospores having hyaline sheaths. The results suggest that <i>Graphilbum</i> species are common members of the Ophiostomatales in conifer ecosystems.
DOI: 10.6084/m9.figshare.12848640
title: <i>Ophiocordyceps desmidiospora</i>, a basal lineage within the “Zombie-Ant Fungi” clade

description: The genus <i>Ophiocordyceps</i> contains the most diverse assemblage of fungi that attack ants worldwide and are remarkably well adapted to the specific ecologies of their hosts. <i>Desmidiospora myrmecophila</i> Thaxt. is closely related to other ant-pathogenic species within <i>Ophiocordyceps</i>, possibly specific to queens, but the sheer infrequency of encounters and previously unsuccessful attempts to culture this fungus has precluded any meaningful assessment until now. A new record of <i>Desmidiospora myrmecophila</i> from Louisiana was found infecting a foundress <i>Camponotus pennsylvanicus</i> queen, the same host species favored by the more common and ubiquitous ant-pathogenic <i>Ophiocordyceps unilateralis</i> clade found in the same geographic locality. To evaluate a long-held assumption that these fungi represent synanamorphs of a single species, we sampled our <i>Desmidiospora</i> specimen along with the local <i>O. unilateralis</i> population for molecular comparison. We are able to present for the first time the in vitro characteristics and morphology of <i>Desmidiospora myrmecophila</i>, as well as a phylogenetic context for this fungus based on combined molecular analysis of representative members of the Ophiocordycipitaceae. Our results place the <i>Desmidiospora myrmecophila</i> lineage within the genus <i>Ophiocordyceps</i>, with a basal affiliation to the <i>Ophiocordyceps unilateralis</i> core clade; thus, in accordance to the “One Fungus–One Name” (1F1N) rule, we propose a new synonym to suppress <i>Desmidiospora</i> in protection of <i>Ophiocordyceps</i>, i.e., <i>O. desmidiospora</i>. These results further implicate this species as an important and quintessential example of cryptic diversity among an already taxonomically diverse and ecologically important group of fungi.
DOI: 10.6084/m9.figshare.12848634
title: Four mycangium types and four genera of ambrosia fungi suggest a complex history of fungus farming in the ambrosia beetle tribe Xyloterini

description: Ambrosia beetles farm fungal cultivars (ambrosia fungi) and carry propagules of the fungal mutualists in storage organs called mycangia, which occur in various body parts and vary greatly in size and complexity. The evolution of ambrosia fungi is closely tied to the evolution and development of the mycangia that carry them. The understudied ambrosia beetle tribe Xyloterini included lineages with uncharacterized ambrosia fungi and mycangia, which presented an opportunity to test whether developments of different mycangium types in a single ambrosia beetle lineage correspond with concomitant diversity in their fungal mutualists. We collected representatives of all three Xyloterini genera (<i>Trypodendron, Indocryphalus</i>, and <i>Xyloterinus politus</i>) and characterized their ambrosia fungi in pure culture and by DNA sequencing. The prothoracic mycangia of seven <i>Trypodendron</i> species all yielded <i>Phialophoropsis</i> (Microascales) ambrosia fungi, including three new species, although these relationships were not all species specific. <i>Indocryphalus</i> mycangia are characterized for the first time in the Asian <i>I. pubipennis</i>. They comprise triangular prothoracic cavities substantially smaller than those of <i>Trypodendron</i> and unexpectedly carry an undescribed species of <i>Toshionella</i> (Microascales), which are otherwise ambrosia fungi of Asian <i>Scolytoplatypus</i> (Scolytoplatypodini). <i>Xyloterinus politus</i> has two different mycangia, each with a different ambrosia fungus: <i>Raffaelea</i> cf. <i>canadensis</i> RNC5 (Ophiostomatales) in oral mycangia of both sexes and <i>Kaarikia abrahamsonii</i> (Sordariomycetes, genus incertae sedis with affinity for Distoseptisporaceae), a new genus and species unrelated to other known ambrosia fungi, in shallow prothoracic mycangia of females. In addition to their highly adapted mycangial mutualists, <i>Trypodendron</i> and <i>X. politus</i> harbor a surprising diversity of facultative symbionts in their galleries, including <i>Raffaelea</i>. A diversity of ambrosia fungi and mycangia suggest multiple ancestral cultivar captures or switches in the history of tribe Xyloterini, each associated with unique adaptations in mycangium anatomy. This further supports the theory that developments of novel mycangium types are critical events in the evolution of ambrosia beetles and their coadapted fungal mutualists.
DOI: 10.6084/m9.figshare.12848634.v1
title: Four mycangium types and four genera of ambrosia fungi suggest a complex history of fungus farming in the ambrosia beetle tribe Xyloterini

description: Ambrosia beetles farm fungal cultivars (ambrosia fungi) and carry propagules of the fungal mutualists in storage organs called mycangia, which occur in various body parts and vary greatly in size and complexity. The evolution of ambrosia fungi is closely tied to the evolution and development of the mycangia that carry them. The understudied ambrosia beetle tribe Xyloterini included lineages with uncharacterized ambrosia fungi and mycangia, which presented an opportunity to test whether developments of different mycangium types in a single ambrosia beetle lineage correspond with concomitant diversity in their fungal mutualists. We collected representatives of all three Xyloterini genera (<i>Trypodendron, Indocryphalus</i>, and <i>Xyloterinus politus</i>) and characterized their ambrosia fungi in pure culture and by DNA sequencing. The prothoracic mycangia of seven <i>Trypodendron</i> species all yielded <i>Phialophoropsis</i> (Microascales) ambrosia fungi, including three new species, although these relationships were not all species specific. <i>Indocryphalus</i> mycangia are characterized for the first time in the Asian <i>I. pubipennis</i>. They comprise triangular prothoracic cavities substantially smaller than those of <i>Trypodendron</i> and unexpectedly carry an undescribed species of <i>Toshionella</i> (Microascales), which are otherwise ambrosia fungi of Asian <i>Scolytoplatypus</i> (Scolytoplatypodini). <i>Xyloterinus politus</i> has two different mycangia, each with a different ambrosia fungus: <i>Raffaelea</i> cf. <i>canadensis</i> RNC5 (Ophiostomatales) in oral mycangia of both sexes and <i>Kaarikia abrahamsonii</i> (Sordariomycetes, genus incertae sedis with affinity for Distoseptisporaceae), a new genus and species unrelated to other known ambrosia fungi, in shallow prothoracic mycangia of females. In addition to their highly adapted mycangial mutualists, <i>Trypodendron</i> and <i>X. politus</i> harbor a surprising diversity of facultative symbionts in their galleries, including <i>Raffaelea</i>. A diversity of ambrosia fungi and mycangia suggest multiple ancestral cultivar captures or switches in the history of tribe Xyloterini, each associated with unique adaptations in mycangium anatomy. This further supports the theory that developments of novel mycangium types are critical events in the evolution of ambrosia beetles and their coadapted fungal mutualists.
DOI: 10.6084/m9.figshare.12848640.v1
title: <i>Ophiocordyceps desmidiospora</i>, a basal lineage within the “Zombie-Ant Fungi” clade

description: The genus <i>Ophiocordyceps</i> contains the most diverse assemblage of fungi that attack ants worldwide and are remarkably well adapted to the specific ecologies of their hosts. <i>Desmidiospora myrmecophila</i> Thaxt. is closely related to other ant-pathogenic species within <i>Ophiocordyceps</i>, possibly specific to queens, but the sheer infrequency of encounters and previously unsuccessful attempts to culture this fungus has precluded any meaningful assessment until now. A new record of <i>Desmidiospora myrmecophila</i> from Louisiana was found infecting a foundress <i>Camponotus pennsylvanicus</i> queen, the same host species favored by the more common and ubiquitous ant-pathogenic <i>Ophiocordyceps unilateralis</i> clade found in the same geographic locality. To evaluate a long-held assumption that these fungi represent synanamorphs of a single species, we sampled our <i>Desmidiospora</i> specimen along with the local <i>O. unilateralis</i> population for molecular comparison. We are able to present for the first time the in vitro characteristics and morphology of <i>Desmidiospora myrmecophila</i>, as well as a phylogenetic context for this fungus based on combined molecular analysis of representative members of the Ophiocordycipitaceae. Our results place the <i>Desmidiospora myrmecophila</i> lineage within the genus <i>Ophiocordyceps</i>, with a basal affiliation to the <i>Ophiocordyceps unilateralis</i> core clade; thus, in accordance to the “One Fungus–One Name” (1F1N) rule, we propose a new synonym to suppress <i>Desmidiospora</i> in protection of <i>Ophiocordyceps</i>, i.e., <i>O. desmidiospora</i>. These results further implicate this species as an important and quintessential example of cryptic diversity among an already taxonomically diverse and ecologically important group of fungi.
DOI: 10.6084/m9.figshare.4572697.v1
title: Conditional Spectral Analysis of Replicated Multiple Time Series with Application to Nocturnal Physiology

description: This article considers the problem of analyzing associations between power spectra of multiple time series and cross-sectional outcomes when data are observed from multiple subjects. The motivating application comes from sleep medicine, where researchers are able to non-invasively record physiological time series signals during sleep. The frequency patterns of these signals, which can be quantified through the power spectrum, contain interpretable information about biological processes. An important problem in sleep research is drawing connections between power spectra of time series signals and clinical characteristics; these connections are key to understanding biological pathways through which sleep affects, and can be treated to improve, health. Such analyses are challenging as they must overcome the complicated structure of a power spectrum from multiple time series as a complex positive-definite matrix-valued function. This article proposes a new approach to such analyses based on a tensor-product spline model of Cholesky components of outcome-dependent power spectra. The approach flexibly models power spectra as nonparametric functions of frequency and outcome while preserving geometric constraints. Formulated in a fully Bayesian framework, a Whittle likelihood based Markov chain Monte Carlo (MCMC) algorithm is developed for automated model fitting and for conducting inference on associations between outcomes and spectral measures. The method is used to analyze data from a study of sleep in older adults and uncovers new insights into how stress and arousal are connected to the amount of time one spends in bed. Supplementary material for this article are available online.
DOI: 10.6084/m9.figshare.4876799.v2
title: A Probabilistic Record Linkage Model for Survival Data

description: In the absence of a unique identifier, combining information from multiple files relies on partially identifying variables (e.g., gender, initials). With a record linkage procedure, these variables are used to distinguish record pairs that belong together (matches) from record pairs that do not belong together (nonmatches). Generally, the combined strength of the partially identifying variables is too low causing imperfect linkage; some true nonmatches are identified as match and, on the other hand, some true matches as nonmatch. To avoid bias in further analyses, it is necessary to correct for imperfect linkage. In this article, pregnancy data from the Perinatal Registry of the Netherlands were used to estimate the associations between the (baseline) characteristics from the first delivery and the time to a second delivery. Because of privacy regulations, no unique identifier was available to determine which pregnancies belonged to the same woman. To deal with imperfect linkage in a time-to-event setting, where we have a file with baseline characteristics and a file with event times, we developed a joint model in which the record linkage procedure and the time-to-event analysis are performed simultaneously. R code and example data are available as online supplemental material.
DOI: 10.6084/m9.figshare.5829639.v1
title: PLEMT: A Novel Pseudolikelihood-Based EM Test for Homogeneity in Generalized Exponential Tilt Mixture Models

description: Motivated by analyses of DNA methylation data, we propose a semiparametric mixture model, namely, the generalized exponential tilt mixture model, to account for heterogeneity between differentially methylated and nondifferentially methylated subjects in the cancer group, and capture the differences in higher order moments (e.g., mean and variance) between subjects in cancer and normal groups. A pairwise pseudolikelihood is constructed to eliminate the unknown nuisance function. To circumvent boundary and nonidentifiability problems as in parametric mixture models, we modify the pseudolikelihood by adding a penalty function. In addition, the test with simple asymptotic distribution has computational advantages compared with permutation-based test for high-dimensional genetic or epigenetic data. We propose a pseudolikelihood-based expectation–maximization test, and show the proposed test follows a simple chi-squared limiting distribution. Simulation studies show that the proposed test controls Type I errors well and has better power compared to several current tests. In particular, the proposed test outperforms the commonly used tests under all simulation settings considered, especially when there are variance differences between two groups. The proposed test is applied to a real dataset to identify differentially methylated sites between ovarian cancer subjects and normal subjects. Supplementary materials for this article are available online.