Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference

Updated description of Diospyrosdussaudii Lecomte (Ebenaceae), with lectotypification and notes on its distribution

Diospyrosdussaudii is a poorly known species and previous descriptions lacked details about its female flowers and fruits. The species had not been recorded since type collections were made in 1913. As a result of our Diospyros research in Thailand, new specimens and data are now available for this species. In this study, we provide an updated morphological description, illustrations, lectotypification and a distribution map. The species was previously reported to be endemic to Laos; as such, the occurrences in Thailand greatly expand the distribution of the species. In addition, we analysed the phylogenetic relationships between D.dussaudii and other Diospyros species from Southeast Asia and other regions, using DNA sequence data from eight plastid regions. Our phylogenetic analyses indicate that D.dussaudii is closely related to D.castanea, D.dasyphylla and D.insidiosa. Their taxonomic affinities are discussed.

Lembosia mimusopis sp. nov. from Thailand

A novel species Lembosia mimusopis is introduced with evidence from morpho-molecular characterization. It was collected from the leaves of Mimusops elengi in Chiang Rai Province, Thailand. The new species is unique in having a mucilaginous sheath surrounding its immature ascospores. LSU sequence analyses phylogenetically support separation of this species from other Lembosia species.

Mutualistic interaction of native Serratia marcescens UENF-22GI with Trichoderma longibrachiatum UENF-F476 boosting seedling growth of tomato and papaya

A plethora of bacteria-fungal interactions occur on the extended fungal hyphae network in soil. The mycosphere of saprophytic fungi can serve as a bacterial niche boosting their survival, dispersion, and activity. Such ecological concepts can be converted to bioproducts for sustainable agriculture. Accordingly, we tested the hypothesis that the well-characterised beneficial bacterium Serratia marcescens UENF-22GI can enhance plant growth-promoting properties when combined with Trichoderma longibrachiatum UENF-F476. The cultural and cell interactions demonstrated S. marcescens and T. longibrachiatum mutual compatibility. Bacteria cells were able to attach, forming aggregates to biofilms and migrating through the fungal hyphae network. Long-distance bacterial migration through growing hyphae was confirmed using a two-compartment Petri dishes assay. Fungal inoculation increased the bacteria survival rates into the vermicompost substrate over the experimental time. Also, in vitro indolic compound, phosphorus, and zinc solubilisation bacteria activities increased in the presence of the fungus. In line with the ecophysiological bacteria fitness, the bacterium-fungal combination boosted tomato and papaya plantlet growth when applied into the plant substrate under nursery conditions. Mutualistic interaction between mycosphere-colonizing bacterium S. marcescens UENF-22GI and the saprotrophic fungi T. longibrachiatum UENF-F467 increased the ecological fitness of the bacteria alongside with beneficial potential for plant growth. A proper combination and delivery of mutual compatible beneficial bacteria-fungal represent an open avenue for microbial-based products for the biological enrichment of plant substrates in agricultural systems.

Relative time constraints improve molecular dating

Dating the tree of life is central to understanding the evolution of life on Earth. Molecular clocks calibrated with fossils represent the state of the art for inferring the ages of major groups. Yet, other information on the timing of species diversification can be used to date the tree of life. For example, horizontal gene transfer events and ancient coevolutionary interactions such as (endo)symbioses occur between contemporaneous species and thus can imply temporal relationships between two nodes in a phylogeny. Temporal constraints from these alternative sources can be particularly helpful when the geological record is sparse, for example, for microorganisms, which represent the majority of extant and extinct biodiversity. Here, we present a new method to combine fossil calibrations and relative age constraints to estimate chronograms. We provide an implementation of relative age constraints in RevBayes that can be combined in a modular manner with the wide range of molecular dating methods available in the software. We use both realistic simulations and empirical datasets of 40 Cyanobacteria and 62 Archaea to evaluate our method. We show that the combination of relative age constraints with fossil calibrations significantly improves the estimation of node ages. [Archaea, Bayesian analysis, cyanobacteria, dating, endosymbiosis, lateral gene transfer, MCMC, molecular clock, phylogenetic dating, relaxed molecular clock, revbayes, tree of life.]

Morphological and Phylogenetic Appraisal of Novel and Extant Taxa of Stictidaceae from Northern Thailand

Stictidaceae comprises taxa with diverse lifestyles. Many species in this family are drought resistant and important for studying fungal adaptation and evolution. Stictidaceae comprises 32 genera, but many of them have been neglected for decades due to the lack of field collections and molecular data. In this study, we introduce a new species Fitzroyomyces hyaloseptisporus and a new combination Fitzroyomycespandanicola. We also provide additional morphological and molecular data for Ostropomyces pruinosellus and O. thailandicus based on new collections isolated from an unidentified woody dicotyledonous host in Chiang Rai, Thailand. Taxonomic conclusions are made with the aid of morphological evidence and phylogenetic analysis of combined LSU, ITS and mtSSU sequence data. Characteristics such as the shape and septation of ascospores and conidia as well as lifestyles among genera of Stictidaceae are discussed.

The Archean origin of oxygenic photosynthesis and extant cyanobacterial lineages

The record of the coevolution of oxygenic phototrophs and the environment is preserved in three forms: genomes of modern organisms, diverse geochemical signals of surface oxidation and diagnostic Proterozoic microfossils. When calibrated by fossils, genomic data form the basis of molecular clock analyses. However, different interpretations of the geochemical record, fossil calibrations and evolutionary models produce a wide range of age estimates that are often conflicting. Here, we show that multiple interpretations of the cyanobacterial fossil record are consistent with an Archean origin of crown-group Cyanobacteria. We further show that incorporating relative dating information from horizontal gene transfers greatly improves the precision of these age estimates, by both providing a novel empirical criterion for selecting evolutionary models, and increasing the stringency of sampling of posterior age estimates. Independent of any geochemical evidence or hypotheses, these results support oxygenic photosynthesis evolving at least several hundred million years before the Great Oxygenation Event (GOE), a rapid diversification of major cyanobacterial lineages around the time of the GOE, and a post-Cryogenian origin of extant marine picocyanobacterial diversity.

High molecular diversity and divergent subpopulations of the begomovirus cnidoscolus mosaic leaf deformation virus associated with Cnidoscolus urens

Begomoviruses have circular, single-stranded DNA genomes encapsidated into twinned quasi-icosahedral particles and are transmitted by whiteflies of the Bemisia tabaci sibling group. Begomoviruses infect cultivated and non-cultivated plants, causing great losses in economically important crops worldwide. To better understand the genetic diversity of begomoviruses infecting the non-cultivated host Cnidoscolus urens, leaf samples exhibiting virus-like symptoms were collected in different localities in the state of Alagoas, Brazil, during 2015 and 2016. Forty-two complete DNA-A sequences were cloned and sequenced by the Sanger method. Based on nucleotide sequence comparisons, the 42 new isolates were identified as the bipartite begomovirus cnidoscolus mosaic leaf deformation virus (CnMLDV). The CnMLDV isolates were clustered in two phylogenetic groups (clusters I and II) corresponding to their sampling areas, and the high value of Wright's F fixation index observed for the DNA-A sequences suggests population structuring. At least seven independent intraspecies recombination events were predicted among CnMLDV isolates, with recombination breakpoints located in the common region (CR) and in the CP and Rep genes. Also, a high per site nucleotide diversity (π) was observed for CnMLDV isolates, with CP being significantly more variable than Rep. Despite the high genetic variability, strong negative or purifying selection was identified as the main selective force acting upon CP and Rep.

Sequencing and characterization of an L-asparaginase gene from a new species of Penicillium section Citrina isolated from Cerrado

The enzyme L-asparaginase (L-ASNase) is used in the treatment of Acute Lymphoblastic Leukemia. The preparations of this enzyme for clinical use are derived from bacterial sources and its use is associated with serious adverse reactions. In this context, it is important to find new sources of L-ASNase. In this work, the Placket-Burman Experimental Design (PBD) was used to determine the influence of the variables on the L-ASNase production then it was followed by a 2^8-4 Factorial Fractional Design (FFD). The results obtained from PBD have shown a range of L-ASNase activity, from 0.47 to 1.77 U/gcell and the results obtained from FFD have showed a range of L-ASNase activity, from 1.10 to 2.36 U/gcell. L-proline and ammonium sulfate were identified as of significant positive variables on this production enzyme by Penicillium cerradense sp. nov. The precise identification of this new species was confirmed by morphological characteristics and sequence comparisons of the nuclear 18S-5.8S-28S partial nrDNA including the ITS1 and ITS2 regions, RNA polymerase II, β-tubulin and calmodulin genomic regions. The genetic sequence coding for the L-ASNase was obtained after carrying out a full genome sequencing. The L-ASNase expressed by P. cerradense sp. nov may have promising antineoplastic properties.

A Taxonomic Appraisal of Bambusicolous Fungi in Occultibambusaceae (Pleosporales, Dothideomycetes) with New Collections from Yunnan Province, China

During our ongoing studies of bambusicolous fungi in southwest China and Thailand, three saprobic pleosporalean taxa were discovered on bamboos in Yunnan Province of China. Occultibambusa hongheensis and Seriascoma bambusae spp. nov. are introduced based on morphological characteristics coupled with multi-locus phylogenetic analyses of combined LSU, SSU, TEF1-α, RPB2 and ITS sequence data. Occultibambusa kunmingensis is also reported from a terrestrial habitat for the first time. Comprehensive descriptions, color photo plates of micromorphology, and a phylogenetic tree showing the placements of these three taxa are provided. In addition, synopsis tables of Occultibambusa and Seriascoma with morphological features are also provided.

Proposal to recognise the tribes Adinobotryeae and Glycyrrhizeae (Leguminosae subfamily Papilionoideae) based on chloroplast phylogenomic evidence

Within the legume family, the taxonomic status of subtribe Glycyrrhizinae of tribe Galegeae and of the genus Adinobotrys has been re-assessed. Based on genome skimming data, we conducted phylogenomic analyses of the inverted repeat-lacking clade within subfamily Papilionoideae. The results support the sister relationship between Glycyrrhizeae and Adinobotrys. Glycyrrhizeae is resurrected based on Glycyrrhiza and Glycyrrhizopsis, and a new tribe, Adinobotryeae, is proposed to accommodate Adinobotrys.

Species diversification in the lowlands of mid-latitude South America: Turnera sidoides subsp. carnea as a case study

The lowlands of mid-latitude South America comprise complex temperate ecoregions characterized by a unique biodiversity. However, the processes responsible for shaping its species diversity are still largely unknown. Turnera sidoides subsp. carnea is a variable subspecies occurring in the lowlands of northeastern Argentina and Uruguay, extending to southern Paraguay and Brazil. It constitutes a good model to perform evolutionary studies. Here we used an integrative approach to understand the process of diversification within this subspecies and to increase the knowledge concerning patterns and processes responsible for shaping the species diversity in the temperate lowlands of South America. The results provided strong evidences that this subspecies is an autopolyploid complex per se, being in an active process of intrasubspecific diversification. Morphological and genetic data show that the diversity of T. sidoides subsp. carnea is in congruence with the great past and present abiotic and biotic variability of the mid-latitude South American lowlands. The evolutionary history of this subspecies is consistent with past fragmentation and allopatric differentiation at diploid level. Geographic isolation and local adaptation would have promoted strong morphological, ecological, and genetic differentiation, resulting in two morphotypes and different genetic groups indicative of incipient speciation.

Morphological and phylogenetic appraisal of Ophioceras (Ophioceraceae, Magnaporthales)

Ophioceras is accommodated in the monotypic family Ophioceraceae (Magnaporthales, Sordariomycetes), and the genus is delimited based on molecular data. During an ongoing survey of bambusicolous fungi in southwest China, we collected a submerged decaying branch of bamboo from Sichuan Province, China and an Ophioceras species occurring on this substrate was observed and isolated. An Ophioceras taxon was delimited based on morphological characteristics and combined LSU, RPB1 and ITS sequence analyses and is described as Ophioceras sichuanense sp. nov. The species formed a well-supported clade basal to Ophioceras (100% ML, 1.00 PP). Based on the updated phylogenetic tree of Magnaporthales, Ceratosphaerella castillensis (generic type) and C. rhizomorpha formed a clade within Ophioceras and morphologically resemble Ophioceras. Therefore, Ceratosphaerella is synonymized under Ophioceras. The phylogenetic relationships of Ophioceras are discussed in relation to morphological similarities of genera in Magnaporthales. The generic circumscription of Ophioceras is emended.

Novel saprobic Hermatomyces species (Hermatomycetaceae, Pleosporales) from China (Yunnan Province) and Thailand

During our survey of the diversity of woody litter fungi in China and Thailand, three Hermatomyces species were collected from dead woody twigs of Dipterocarpus sp. (Dipterocarpaceae) and Ehretiaacuminata (Boraginaceae). Both morphology and multigene analyses revealed two taxa as new species (Hermatomycesturbinatus and H.jinghaensis) and the remaining collections as new records of H.sphaericus. Hermatomycesturbinatus is characterized by 1) dimorphic conidia, having circular to oval lenticular conidia and 2) turbinate conidia consisting of two columns with two septa composed of 2–3 cells in each column. Hermatomycesjinghaensis is characterized by dimorphic conidia, having circular to oval lenticular conidia and clavate or subcylindrical to cylindrical conidia and consisting of one or two columns with 6–8 cells in each column. Phylogenetic analyses of combined LSU, ITS, tub2, tef1-α and rpb2 sequence data supports the placement of these new taxa within Hermatomycetaceae with high statistical support.

Biodiversity of Lignicolous Freshwater Hyphomycetes from China and Thailand and Description of Sixteen Species

Freshwater hyphomycetes are a highly diverse group of fungi with a worldwide distribution and have been mostly reported from tropical and subtropical regions. During investigations of freshwater fungi from the Greater Mekong subregion in China and Thailand, sixteen freshwater hyphomycetes (three of them belong to the class Dothideomycetes while thirteen belong to the class Sordariomycetes) were collected. Based on morphology and multi-gene phylogenetic analyses, Neospadicoides thailandica, Pseudodactylaria aquatica, Sporidesmium nujiangense, Tetraploa thailandica, Vamsapriyaaquatica and Wongia fusiformis are described as new species; Aquapteridospora bambusinum is proposed as a new combination; Acrodictys liputii, Chloridium gonytrichii, Pseudoberkleasmium chiangmaiense, Pleomonodictys capensis, Sporidesmium aturbinatum and Vamsapriya indica are reported as new country records; and Sporidesmium tropicale, Sporoschisma chiangraiense and Sporoschisma longicatenatum are introduced as three new collections. In addition, a checklist of freshwater fungi from China over the last five years is also provided.

Magalhães P. Filamentous Fungi Producing l-Asparaginase with Low Glutaminase Activity Isolated from Brazilian Savanna Soil

l-asparaginase is an enzyme used as treatment for acute lymphoblastic leukemia (ALL) due to its ability to hydrolyze l-asparagine, an essential amino acid synthesized by normal cells unlike neoplastic cells. The adverse effects of l-asparaginase formulations are associated with its glutaminase activity and bacterial origin; therefore, it is important to find new sources of l-asparaginase-producing eukaryotic microorganisms with low glutaminase activity. This work evaluated the biotechnological potential of filamentous fungi isolated from Brazilian Savanna soil and plants for l-asparaginase production. Thirty-nine isolates were screened for enzyme production using the plate assay, followed by measuring enzymatic activity in cells after submerged fermentation. The variables influencing l-asparaginase production were evaluated using Plackett-Burman design. Cell disruption methods were evaluated for l-asparaginase release. Penicillium sizovae 2DSST1 and Fusarium proliferatum DCFS10 showed the highest l-asparaginase activity levels and the lowest glutaminase activity levels. Penicillium sizovae l-asparaginase was repressed by carbon sources, whereas higher carbon concentrations enhanced l-asparaginase by F. proliferatum. Maximum enzyme productivity, specific enzyme yield and the biomass conversion factor in the enzyme increased after Plackett-Burman design. Freeze-grinding released 5-fold more l-asparaginase from cells than sonication. This study shows two species, which have not yet been reported, as sources of l-asparaginase with possible reduced immunogenicity for ALL therapy.

Monilochaetes pteridophytophila (Australiascaceae, Glomerellales), a new fungus from tree fern

Background

During taxonomic and phylogenetic studies of fungi on pteridophytes in Thailand, Monilochaetes pteridophytophila sp. nov. was collected from the frond stalks of a tree fern (Alsophila costularis, Cyatheaceae). The new species is introduced, based on evidence from morphology and phylogenetic analyses of a concatenated dataset of LSU, ITS, SSU and RPB2 sequences.

New information

Monilochaetes pteridophytophila differs from extant species of Monilochaetes in having darker conidiophores with fewer septae (1-4-septate). Monilochaetes pteridophytophila forms a distinct clade, basal from other species of Monilochaetes in Australiascaceae. A detailed description and illustrations of the new species are provided. We also provided a synopsis of accepted species of Monilochaetes.

An Update on Trichoderma Mitogenomes: Complete De Novo Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma harzianum (Hypocreales, Sordariomycetes), an Ex-Neotype Strain CBS 226.95, and Tracing the Evolutionary Divergences of Mitogenomes in Trichoderma

Members of the genus Trichoderma (Hypocreales), widely used as biofungicides, biofertilizers, and as model fungi for the industrial production of CAZymes, have actively been studied for the applications of their biological functions. Recently, the study of the nuclear genomes of Trichoderma has expanded in the directions of adaptation and evolution to gain a better understanding of their ecological traits. However, Trichoderma's mitochondria have received much less attention despite mitochondria being the most necessary element for sustaining cell life. In this study, a mitogenome of the fungus Trichoderma harzianum CBS 226.95 was assembled de novo. A 27,632 bp circular DNA molecule was revealed with specific features, such as the intronless of all core PCGs, one homing endonuclease, and a putative overlapping tRNA, on a closer phylogenetic relationship with T. reesei among hypocrealean fungi. Interestingly, the mitogenome of T. harzianum CBS 226.95 was predicted to have evolved earlier than those of other Trichoderma species and also assumed with a selection pressure in the cox3. Considering the bioavailability, both for the ex-neotype strain of the T. harzianum species complex and the most globally representative commercial fungal biocontrol agent, our results on the T. harzianum CBS 226.95 mitogenome provide crucial information which will be helpful criteria in future studies on Trichoderma.

Properties of Markov Chain Monte Carlo Performance across Many Empirical Alignments

Nearly all current Bayesian phylogenetic applications rely on Markov chain Monte Carlo (MCMC) methods to approximate the posterior distribution for trees and other parameters of the model. These approximations are only reliable if Markov chains adequately converge and sample from the joint posterior distribution. Although several studies of phylogenetic MCMC convergence exist, these have focused on simulated data sets or select empirical examples. Therefore, much that is considered common knowledge about MCMC in empirical systems derives from a relatively small family of analyses under ideal conditions. To address this, we present an overview of commonly applied phylogenetic MCMC diagnostics and an assessment of patterns of these diagnostics across more than 18,000 empirical analyses. Many analyses appeared to perform well and failures in convergence were most likely to be detected using the average standard deviation of split frequencies, a diagnostic that compares topologies among independent chains. Different diagnostics yielded different information about failed convergence, demonstrating that multiple diagnostics must be employed to reliably detect problems. The number of taxa and average branch lengths in analyses have clear impacts on MCMC performance, with more taxa and shorter branches leading to more difficult convergence. We show that the usage of models that include both Γ-distributed among-site rate variation and a proportion of invariable sites is not broadly problematic for MCMC convergence but is also unnecessary. Changes to heating and the usage of model-averaged substitution models can both offer improved convergence in some cases, but neither are a panacea.

A simple method for the cultivation of the "unculturable" asterinaceous fungi (Asterinales/Dothideomycetes)

Although asterinaceous fungi have been studied for many years, all previous attempts to isolate, cultivate, and propagate these fungi in vitro have failed. This paper provides the first reports of in vitro isolation of representative strains of species belonging to five fungi from different genera belonging to Asterinales. To confirm if the sequences of DNA obtained from the mycelia are the same obtained in the direct extraction, a phylogenetic analysis of nuc LSU rDNA was performed. This paper reports for the first time the success of in vitro culturing of asterinaceous fungi using the ascospores ejection technique, opening perspectives of studies of genetics, physiology, among other aspects of the biology for this very understudied group of fungi.

Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model

Genome sequencing projects routinely generate haploid consensus sequences from diploid genomes, which are effectively chimeric sequences with the phase at heterozygous sites resolved at random. The impact of phasing errors on phylogenomic analyses under the multispecies coalescent (MSC) model is largely unknown. Here, we conduct a computer simulation to evaluate the performance of four phase-resolution strategies (the true phase resolution, the diploid analytical integration algorithm which averages over all phase resolutions, computational phase resolution using the program PHASE, and random resolution) on estimation of the species tree and evolutionary parameters in analysis of multilocus genomic data under the MSC model. We found that species tree estimation is robust to phasing errors when species divergences were much older than average coalescent times but may be affected by phasing errors when the species tree is shallow. Estimation of parameters under the MSC model with and without introgression is affected by phasing errors. In particular, random phase resolution causes serious overestimation of population sizes for modern species and biased estimation of cross-species introgression probability. In general, the impact of phasing errors is greater when the mutation rate is higher, the data include more samples per species, and the species tree is shallower with recent divergences. Use of phased sequences inferred by the PHASE program produced small biases in parameter estimates. We analyze two real data sets, one of East Asian brown frogs and another of Rocky Mountains chipmunks, to demonstrate that heterozygote phase-resolution strategies have similar impacts on practical data analyses. We suggest that genome sequencing projects should produce unphased diploid genotype sequences if fully phased data are too challenging to generate, and avoid haploid consensus sequences, which have heterozygous sites phased at random. In case the analytical integration algorithm is computationally unfeasible, computational phasing prior to population genomic analyses is an acceptable alternative. [BPP; introgression; multispecies coalescent; phase; species tree.]

Phylogenomic framework of the IRLC legumes (Leguminosae subfamily Papilionoideae) and intercontinental biogeography of tribe Wisterieae

The inverted repeat-lacking clade (IRLC) is one of the most derived clades within the subfamily Papilionoideae of the legume family, and includes various economically important plants, e.g., chickpeas, peas, liquorice, and the largest genus of angiosperms, Astragalus. Tribe Wisterieae is one of the earliest diverged groups of the IRLC, and its generic delimitation and spatiotemporal diversification needs further clarifications. Based on genome skimming data, we herein reconstruct the phylogenomic framework of the IRLC, and infer the inter-generic relationships and historical biogeography of Wisterieae. We redefine tribe Caraganeae to contain Caragana only, and tribe Astragaleae is reduced to the Erophaca-Astragalean clade. The chloroplast capture scenario was hypothesized as the most plausible explanation of the topological incongruences between the chloroplast CDSs and nuclear ribosomal DNA trees in both the Glycyrrhizinae-Adinobotrys-Wisterieae clade and the Chesneyeae-Caraganeae-Hedysareae clade. A new name, Caragana lidou L. Duan & Z.Y. Chang, is proposed within Caraganeae. Thirteen genera are herein supported within Wisterieae, including a new genus, Villosocallerya L. Duan, J. Compton & Schrire, segregated from Callerya. Our biogeographic analyses suggest that Wisterieae originated in the late Eocene and its most recent common ancestor (MRCA) was distributed in continental southeastern Asia. Lineages of Wisterieae remained in the ancestral area from the early Oligocene to the early Miocene. By the middle Miocene, Whitfordiodendron and the MRCA of Callerya-Kanburia-Villosocallerya Clade became disjunct between the Sunda area and continental southeastern Asia, respectively; the MRCA of Wisteria migrated to North America via the Bering land bridge. The ancestor of Austrocallerya and Padbruggea migrated to the Wallacea-Oceania area, which split in the early Pliocene. In the Pleistocene, Wisteria brachybotrys, W. floribunda and Wisteriopsis japonica reached Japan, and Callerya cinerea dispersed to South Asia. This study provides a solid phylogenomic for further evolutionary/biogeographic/systematic investigations on the ecologically diverse and economically important IRLC legumes.

The Hidden Diversity of Diatrypaceous Fungi in China

In this study, we investigated the diversity of diatrypaceous fungi from six regions in China based on morpho-molecular analyses of combined ITS and tub2 gene regions. We accept 23 genera in Diatrypaceae with 18 genera involved in the phylogram, and the other five genera are lacking living materials with sequences data. Eleven species included in four genera (viz. Allocryptovalsa, Diatrype, Diatrypella, and Eutypella) have been isolated from seven host species, of which nine novel species (viz. Allocryptovalsa castaneae, A. castaneicola, Diatrype betulae, D. castaneicola, D. quercicola, Diatrypella betulae, Da. betulicola, Da. hubeiensis, and Da. shennongensis), a known species of Diatrypella favacea, and a new record of Eutypella citricola from the host genus Morus are included. Current results show the high diversity of Diatrypaceae which are wood-inhabiting fungi in China.

Reappraisal of Immotthia in Dictyosporiaceae, Pleosporales: Introducing Immotthia bambusae sp. nov. and Pseudocyclothyriella clematidis comb. et gen. nov. Based on Morphology and Phylogeny

Immotthia is a poorly known genus, and currently, no DNA sequence data are available to ascertain its proper phylogenetic placement and evolutionary relationships with other bitunicate fungi. To date, there are only two species accepted in the genus. During our ongoing research study of bambusicolous fungi in southwest China and Thailand, a fungus associated with stromata of Hypoxylon sp. was found on dead bamboo culms in Loei Province, Thailand. Preliminary morphological identification revealed that the fungal collection belongs to Immotthia. A novel species, Immotthia bambusae, is introduced herein based on a comparison of morphological characteristics with the type specimen of I. hypoxylon (≡ Amphisphaeria hypoxylon Ellis and Everh.), a synonym of I. atrograna (Cooke and Ellis) M. E. Barr. Phylogenetic analyses of a concatenated ITS, LSU, SSU, and TEF1-α DNA sequence matrix showed that Immotthia belongs to Dictyosporiaceae, Pleosporales. Despite I. bambusae strains constituting a supported subclade, they are nested with the genus Pseudocoleophoma. Pseudocoleophoma clematidis is morphologically different from all other Pseudocoleophoma species, while its conidial characteristics are similar to Cyclothyriella. Multigene phylogenetic analyses showed that P. clematidis formed a clade basal to Immotthia, separated from Pseudocoleophoma with strong statistical support. Therefore, we introduce a monotypic genus, Pseudocyclothyriella Phukhams. and Phookamsak, gen. nov. to accommodate the single species, Pseudocyclothyriella clematidis (Phukhams. and K. D. Hyde) Phukhams. and Phookamsak, comb. nov. Detailed descriptions, color micrographs, and phylogenetic trees to show the placement of the new taxa are provided. In addition, an updated taxonomic treatment of the genera Immotthia and Pseudocyclothyriella is also provided based on the study of the type materials and phylogeny generated from DNA sequence data.

Evolution and insights into the structure and function of the DedA superfamily containing TMEM41B and VMP1

TMEM41B and VMP1 are endoplasmic reticulum (ER)-localizing multi-spanning membrane proteins required for ER-related cellular processes such as autophagosome formation, lipid droplet homeostasis and lipoprotein secretion in eukaryotes. Both proteins have a VTT domain, which is similar to the DedA domain found in bacterial DedA family proteins. However, the molecular function and structure of the DedA and VTT domains (collectively referred to as DedA domains) and the evolutionary relationships among the DedA domain-containing proteins are largely unknown. Here, we conduct a remote homology search and identify a new clade consisting mainly of bacterial proteins of unknown function that are members of the Pfam family PF06695. Phylogenetic analysis reveals that the TMEM41, VMP1, DedA and PF06695 families form a superfamily with a common origin, which we term the DedA superfamily. Coevolution-based structural prediction suggests that the DedA domain contains two reentrant loops facing each other in the membrane. This topology is biochemically verified by the substituted cysteine accessibility method. The predicted structure is topologically similar to that of the substrate-binding region of Na+-coupled glutamate transporter solute carrier 1 (SLC1) proteins. A potential ion-coupled transport function of the DedA superfamily proteins is discussed. This article has an associated First Person interview with the joint first authors of the paper.

Taxonomy and Phylogeny of Rust Fungi on Hamamelidaceae

Hamamelidaceae is composed of woody plant taxa of important economic value; however, reports on diseases affecting these plants are rare. Three kinds of rusts were studied, of which the first one is characterized by catenulate spores in peridiate columnar sori on Sycopsis sinensis, the second one produces two-celled pedicellate teliospores in pulvinate sori on S. sinensis and Corylopsis spp., and the last one produces aeciospores in cup-shaped aecia on Hamamelis spp. Phylogenetic analyses indicated that the three species belong to the same genus in Pucciniaceae. The first fungus is distinct in teliospore morphology, producing one-celled catenulate spores in peridiate columnar sori and molecular phylogeny from species of other genera. Thus, it is described herein as a new genus and species Novopuccinia sycopsis-sinensis in Pucciniaceae. The latter two species were reported as Puccinia corylopsidis and Aecidium hamamelidis, respectively. However, phylogenetic analysis using ITS and 28S genes has revealed that these are closely related to the new genus and species. By combining host, distribution, and evolutionary hypothesis of rust fungi with endocyclic life cycle, these are reclassified as N. corylopsidis and N. hamamelidis. Taxonomic descriptions, illustrations, and a key to rust fungal species occurring in Hamamelidaceae in Asia are provided.

Morpho-molecular characterization of Discosia ravennica sp. nov. and a new host record for Sporocadus rosigena

Collections of fungal samples from two dead leaf specimens from Italy were subjected to morphological examination and phylogenetic analyses. Two coelomycetous taxa belonging to two different genera in Xylariomycetidae, Sordariomycetes, namely Discosia and Sporocadus, were identified. The Discosia taxon is revealed as a new species and is herein introduced as Discosia ravennica sp. nov. while the Sporocadus taxon is identified as Sporocadus rosigena. Multi-locus phylogeny based on DNA sequence data of the large subunit (LSU) and internal transcribed spacer (ITS) of nuclear ribosomal genes, β-tubulin (β-tub) and RNA polymerase II second largest subunit (rpb2) showed that D. ravennica is related to D. neofraxinea but it forms an independent lineage that supports its new species status. The new taxon also differs from other Discosia species by its unilocular to bilocular, superficial and applanate conidiomata with basal stroma composed of cells of textura angularis, elongate-ampulliform conidiogenous cells and conidia smaller in size. Sporocadus rosigena is here reported as a new host record from Quercus ilex from Italy. Descriptions, illustrations and molecular data for both species are provided in this paper.

Adaptive radiation and speciation in Rhipicephalus ticks: A medley of novel hosts, nested predator-prey food webs, off-host periods and dispersal along temperature variation gradients

Rhipicephalus are a species-diverse genus of ticks, mainly distributed in the Afrotropics with some species in the Palearctic and Oriental regions. Current taxonomic consensus comprise nine informal species groups/lineages based on immature morphology. This work integrates biogeographic, ecological and molecular lines of evidence to better understand Rhipicephalus evolution. Phylogenetic analysis based on four genes (12S, 16S, 28S-D2 and COI) recovered five distinct clades with nine descendant clades that are generally congruent with current taxonomy, with some exceptions. Historical biogeography is inferred from molecular divergence times, ancestral distribution areas, host-use and climate niches of four phylogenetically significant bioclimatic variables (isothermality, annual, seasonal and diurnal temperature range). Novel hosts enabled host-linked dispersal events into new environments, and ticks exploited new hosts through nested predator-prey connections in food webs. Diversification was further induced by climate niche partitioning along gradients in temperature range during off-host periods. Ancestral climate niche estimates corroborated dispersal events by indicating hypothetical ancestors moved into environments with different annual and seasonal temperature ranges along latitudinal gradients. Host size for immature and adult life stages was important for dispersal and subsequent diversification rates. Clades that utilise large, mobile hosts (ungulates and carnivores) early in development have wider geographic ranges but slower diversification rates, and those utilising small, less mobile hosts (rodents, lagomorphs and afroinsectivores) early in development have smaller ranges but higher diversification rates. These findings suggest diversification is driven by a complex set of factors linked to both host-associations (host size, ranges and mobility) and climate niche partitioning along annual and seasonal temperature range gradients that vary with latitude. Moreover, competitive interactions can reinforce these processes and drive speciation. Off-host periods facilitate adaptive radiation by enabling host switches along nested predator-prey connections in food webs, but at the cost of environmental exposure that partitions niches among dispersing progenitors, disrupting geneflow and driving diversification. As such, the evolution and ecological niches of Rhipicephalus are characterised by trade-offs between on- and off-host periods, and these trade-offs interact with nested predator-prey connections in food webs, host-use at different life stages, as well as gradients in annual and seasonal temperature ranges to drive adaptive radiation and speciation.

Stachybotrys musae sp. nov., S. microsporus, and Memnoniella levispora (Stachybotryaceae, Hypocreales) Found on Bananas in China and Thailand

A study was conducted to investigate saprobic fungal niches of Stachybotryaceae (Hypocreales) associated with leaves of Musa (banana) in China and Thailand. Three hyphomycetous taxa were collected during the dry season of 2018 and 2019. After a careful phenotypic characterization (both macro- and microscopically) and a phylogenetic tree reconstruction using a concatenated sequence dataset of internal transcribed spacer (ITS), calmodulin (cmdA), RNA polymerase II second largest subunit (rpb2), β-tubulin (tub2), and the translation elongation factor 1-alpha (tef1) gene regions, we report three species of Stachybotryaceae. Stachybotrys musae is introduced as a novel taxon from Yunnan, China, while S.microsporus is reported from Chiang Rai Province in Thailand on Musa. In addition, Memnoniella levispora is also reported from China for the first time.

Additions to the Genus Arthrinium (Apiosporaceae) From Bamboos in China

Arthrinium has a widespread distribution occurring in various substrates (e.g., air, soil debris, plants, lichens, marine algae and even human tissues). It is characterized by the basauxic conidiogenesis in the asexual morph, with apiospores in the sexual morph. In this study, seventeen isolates of Arthrinium were collected in China. Based on their morphology and phylogenetic characterization, four new species (A. biseriale, A. cyclobalanopsidis, A. gelatinosum, and A. septatum) are described and seven known species (A. arundinis, A. garethjonesii, A. guizhouense, A. hydei, A. neosubglobosa, A. phyllostachium and A. psedoparenchymaticum) are identified, of which the sexual morph of three species (A. guizhouense, A. phyllostachium and A. psedoparenchymaticum) and asexual morph of A. garethjonesii are reported for the first time. The detailed descriptions, illustrations and comparisons with related taxa of these new collections are provided. Phylogenetic analyses of combined ITS, LSU, TUB2, and TEF sequence data support their placements in the genus Arthrinium and justify the new species establishments and identifications of known species.

Felsenstein Phylogenetic Likelihood

In 1981, the Journal of Molecular Evolution (JME) published an article entitled "Evolutionary trees from DNA sequences: A maximum likelihood approach" by Joseph (Joe) Felsenstein (J Mol Evol 17:368-376, 1981). This groundbreaking work laid the foundation for the emerging field of statistical phylogenetics, providing a tractable way of finding maximum likelihood (ML) estimates of evolutionary trees from DNA sequence data. This paper is the second most cited (more than 9000 citations) in JME after Kimura's (J Mol Evol 16:111-120, 1980) seminal paper on a model of nucleotide substitution (with nearly 20,000 citations). On the occasion of the 50th anniversary of JME, we elaborate on the significance of Felsenstein's ML approach to estimating phylogenetic trees.

Testing the utility of alternative metrics of branch support to address the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei: Pelagiaria)

The use of high-throughput sequencing technologies to produce genome-scale datasets was expected to settle some long-standing controversies across the Tree of Life, particularly in areas where short branches occur at deep timescales. Instead, these datasets have often yielded many well-supported but conflicting topologies, and highly variable gene-tree distributions. A variety of branch-support metrics beyond the nonparametric bootstrap are now available to assess how robust a phylogenetic hypothesis may be, as well as new methods to quantify gene-tree discordance. We applied multiple branch support metrics to an ancient group of marine fishes (Teleostei: Pelagiaria) whose interfamilial relationships have proven difficult to resolve due to a rapid accumulation of lineages very early in its history. We analyzed hundreds of loci including published UCE data and newly generated exonic data along with their flanking regions to represent all 16 extant families for more than 150 out of 284 valid species in the group. Branch support was lower for interfamilial relationships (except the SH-like aLRT and aBayes methods) regardless of the type of marker used. Several nodes that were highly supported with bootstrap had very low site and gene-tree concordance, revealing underlying conflict. Despite this conflict, we were able to identify four consistent interfamilial clades, each comprised of two or three families. Combining exons with their flanking regions also produced increased branch lengths in the deep branches of the pelagiarian tree. Our results demonstrate the limitations of employing current metrics of branch support and species-tree estimation when assessing the confidence of ancient evolutionary radiations and emphasize the necessity to embrace alternative measurements to explore phylogenetic uncertainty and discordance in phylogenomic datasets.

Novel taxa and species diversity of Cordyceps sensu lato (Hypocreales, Ascomycota) developing on wireworms (Elateroidea and Tenebrionoidea, Coleoptera)

Species of Cordyceps sensu lato (Hypocreales, Sordariomycetes) have always attracted much scientific attention for their abundant species diversity, important medicinal values and biological control applications. The insect superfamilies Elateroidea and Tenebrionoidea are two large groups of Coleoptera and their larvae are generally called wireworms. Most wireworms inhabit humid soil or fallen wood and are often infected with Cordyceps s.l. However, the species diversity of Cordyceps s.l. on Elateroidea and Tenebrionoidea is poorly known. In the present work, we summarise taxonomic information of 63 Cordyceps s.l. species that have been reported as pathogens of wireworms. We review their hosts and geographic distributions and provide taxonomic notes for species. Of those, 60 fungal species are accepted as natural pathogens of wireworms and three species (Cordycepsmilitaris, Ophiocordycepsferruginosa and O.variabilis) are excluded. Two new species, O.borealis from Russia (Primorsky Krai) and O.spicatus from China (Guizhou), are described and compared with their closest allies. Polycephalomycesformosus is also described because it is reported as a pathogen of wireworms for the first time. Phylogeny was reconstructed from a combined dataset, comprising SSU, LSU and TEF1-α gene sequences. The results, presented in this study, support the establishment of the new species and confirm the identification of P.formosus.

Paraeutypella guizhouensis gen. et sp. nov. and Diatrypella longiasca sp. nov. (Diatrypaceae) from China

Background

In this study, we introduce a novel genus, Paraeutypella, of the family Diatrypaceae comprising three species viz. Paraeutypellaguizhouensis sp. nov. and P.citricola (basionym: Eutypellacitricola) and P.vitis (basionym: Sphaeriavitis). Diatrypellalongiasca sp. nov. is also introduced, which forms a distinct clade in Diatrypella sensu stricto. The discovery of this new genus will contribute to expanding the knowledge and taxonomic framework of Diatrypaceae (Xylariales).

New information

Generic delimitations in Diatrypaceae are unsettled because the phylogeny has yet to be resolved using extensive taxon sampling and sequencing of ex-type cultures. During an investigation of xylarialean fungi, we collected eutypella-like fungi which is distinct from Eutypella sensu stricto in our phylogenetic analyses (ITS and β-tubulin), thus, introduced as Paraeutypellaguizhouensis gen. et sp. nov.. Paraeutypella is characterised by having 4–25 perithecia in a stroma each with 3–6 sulcate, long ostiolar necks. Paraeutypellacitricola comb. nov. (basionym: Eutypellacitricola) is introduced on Acer sp. from China. Diatrypellalongiasca sp. nov. is introduced as a new species in Diatrypella sensu stricto. which has 2–5 ascomata per stroma and long ascospores, unusual when compared to other Diatrypella species and distinct phylogenetically.

Phytophthora theobromicola sp. nov.: A New Species Causing Black Pod Disease on Cacao in Brazil

Black pod disease, caused by Phytophthora species, is among the main limiting factors of cacao (Theobroma cacao L.) production. High incidence levels of black pod disease have been reported in Brazil, being induced by Phytophthora capsici, Phytophthora citrophthora, Phytophthora heveae, and Phytophthora palmivora. To assess the diversity of Phytophthora species affecting cacao in Brazil, 40 new isolates were obtained from cacao pods exhibiting symptoms of black pod disease collected in different smallholder farms in 2017. Further, ten cacao-infecting isolates morphologically identified as P. citrophthora and P. palmivora were molecularly characterized. The genomic regions beta-tubulin, elongation factor 1 alpha, heat shock protein 90, and internal transcribed spacer, and the mitochondrially encoded cytochrome c oxidase I and II genes were PCR-amplified and Sanger-sequenced from the cacao-infecting Phytophthora isolates. The morphological characterization and evaluation of the mycelial growth rates for the Phytophthora isolates were performed in vitro. Based on the molecular analysis and morphological comparisons, 19 isolates were identified as P. palmivora (clade 4). Interestingly, 31 isolates grouped together in the phylogenetic tree and were placed apart from previously known species in Phytophthora clade 2. Therefore, these isolates are considered as a new species herein referred to as Phytophthora theobromicola sp. nov., which produced papillate, semipapillate, and persistent sporangia on simple sporangiophores. The P. palmivora isolates were identified as A1 mating type by pairing each isolate with known A1 and A2 tester strains of P. capsici, but no oogonia/antheridia were observed when P. theobromicola was paired with the different tester strains. The P. theobromicola and P. citrophthora isolates showed higher mycelial growth rates, when compared to P. palmivora, on different media at 10, 15, and 20°C, but similar values were observed when grown on clarified CA media at 25 and 30°C. The pathogenicity tests carried out on pods of four cacao clones (CCN51, PS1319, Cepec2004, and CP49) showed significant variability among the isolates of both Phytophthora species, with P. theobromicola inducing higher rates of necrotic lesion expansion, when compared to P. palmivora. Here, two Phytophthora species were found associated with black pod disease in the state of Bahia, Brazil, and the previously undescribed P. theobromicola seems to be prevalent in field conditions. This is the first report of P. theobromicola on T. cacao. Also, these findings are crucial to improve the disease control strategies, and for the development of cacao materials genetically resistant to Phytophthora.

Assessment of Cytospora Isolates From Conifer Cankers in China, With the Descriptions of Four New Cytospora Species

Cytospora species are widely distributed and often occur as endophytes, saprobes or phytopathogens. They primarily cause canker and dieback diseases of woody host plants, leading to the growth weakness or death of host plants, thereby causing significant economic and ecological losses. In order to reveal the diversity of Cytospora species associated with canker and dieback diseases of coniferous trees in China, we assessed 11 Cytospora spp. represented by 28 fungal strains from symptomatic branches or twigs of coniferous trees, i.e., Juniperus procumbens, J. przewalskii, Picea crassifolia, Pinus armandii, P. bungeana, Platycladus orientalis in China. Through morphological observations and multilocus phylogeny of ITS, LSU, act, rpb2, tef1-α, and tub2 gene sequences, we focused on four novel Cytospora species (C. albodisca, C. discostoma, C. donglingensis, and C. verrucosa) associated with Platycladus orientalis. This study represented the first attempt to clarify the taxonomy of Cytospora species associated with canker and dieback symptoms of coniferous trees in China.

Discovery of novel fungal species and pathogens on bat carcasses in a cave in Yunnan Province, China

Virulent infectious fungal diseases, in natural and managed landscapes, are increasing. Fungal diseases in humans, animals and plants have caused die-off and extinction events and have become a threat to food security. A caving expedition in Yunnan Province, China, revealed two bat carcasses covered in fungal mycelia. Eleven fungal isolates were obtained from these bat carcasses, and morphological observations and multigene phylogenetic analyses revealed they were Fusarium incarnatum, Mucor hiemalis and Trichoderma harzianum and four new species, Mortierella rhinolophicola, M. multispora, M. yunnanensis and Neocosmospora pallidimors. One of the more alarming findings is that a number of infections related to Neocosmospora, previously associated with human and animal mycotoxicoses, are reported to be increasing, and here we present a new species from this genus, isolated from dead bats. Due to the ecosystem services provided by bats, and the close relationship between bats and humans, future research should focus on the impacts and significance of N. pallidimors to human and animal health, examining its pathogenicity and secondary metabolites. Taxonomic descriptions, color images of the habitat, in situ samples, microstructures and cultures are presented. SEM photographs of microstructures and phylogenetic trees showing the placement of new and known species are also provided.

Spectral neighbor joining for reconstruction of latent tree Models

A common assumption in multiple scientific applications is that the distribution of observed data can be modeled by a latent tree graphical model. An important example is phylogenetics, where the tree models the evolutionary lineages of a set of observed organisms. Given a set of independent realizations of the random variables at the leaves of the tree, a key challenge is to infer the underlying tree topology. In this work we develop Spectral Neighbor Joining (SNJ), a novel method to recover the structure of latent tree graphical models. Given a matrix that contains a measure of similarity between all pairs of observed variables, SNJ computes a spectral measure of cohesion between groups of observed variables. We prove that SNJ is consistent, and derive a sufficient condition for correct tree recovery from an estimated similarity matrix. Combining this condition with a concentration of measure result on the similarity matrix, we bound the number of samples required to recover the tree with high probability. We illustrate via extensive simulations that in comparison to several other reconstruction methods, SNJ requires fewer samples to accurately recover trees with a large number of leaves or long edges.

Morpho-phylogenetic evidence reveals new species in Rhytismataceae (Rhytismatales, Leotiomycetes, Ascomycota) from Guizhou Province, China

Karst formations represent a unique eco-environment. Research in the microfungi inhabiting this area is limited. During an ongoing survey of ascomycetous microfungi from karst terrains in Guizhou Province, China, we discovered four new species, which are introduced here as Hypodermaparalinderae, Terrierakarsti, T.meitanensis and T.sigmoideospora placed in Rhytismataceae, based on phylogenetic analyses and morphological characters. Molecular analyses, based on concatenated LSU-ITS-mtSSU sequence data, were used to infer phylogenetic affinities. Detail descriptions and comprehensive illustrations of these new taxa are provided and relationships with the allied species are discussed, based on comparative morphology and molecular data.

The Asymptotic Behavior of Bootstrap Support Values in Molecular Phylogenetics

The phylogenetic bootstrap is the most commonly used method for assessing statistical confidence in estimated phylogenies by non-Bayesian methods such as maximum parsimony and maximum likelihood (ML). It is observed that bootstrap support tends to be high in large genomic data sets whether or not the inferred trees and clades are correct. Here, we study the asymptotic behavior of bootstrap support for the ML tree in large data sets when the competing phylogenetic trees are equally right or equally wrong. We consider phylogenetic reconstruction as a problem of statistical model selection when the compared models are nonnested and misspecified. The bootstrap is found to have qualitatively different dynamics from Bayesian inference and does not exhibit the polarized behavior of posterior model probabilities, consistent with the empirical observation that the bootstrap is more conservative than Bayesian probabilities. Nevertheless, bootstrap support similarly shows fluctuations among large data sets, with no convergence to a point value, when the compared models are equally right or equally wrong. Thus, in large data sets strong support for wrong trees or models is likely to occur. Our analysis provides a partial explanation for the high bootstrap support values for incorrect clades observed in empirical data analysis. [Bootstrap; model selection; star-tree paradox; support value.].

The insights into the evolutionary history of Translucidithyrium: based on a newly-discovered species

During the field studies, a Translucidithyrium-like taxon was collected in Xishuangbanna of Yunnan Province, during an investigation into the diversity of microfungi in the southwest of China. Morphological observations and phylogenetic analysis of combined LSU and ITS sequences revealed that the new taxon is a member of the genus Translucidithyrium and it is distinct from other species. Therefore, Translucidithyriumchinensesp. nov. is introduced here. The Maximum Clade Credibility (MCC) tree from LSU rDNA of Translucidithyrium and related species indicated the divergence time of existing and new species of Translucidithyrium was crown age at 16 (4–33) Mya. Combining the estimated divergence time, paleoecology and plate tectonic movements with the corresponding geological time scale, we proposed a hypothesis that the speciation (estimated divergence time) of T.chinense was earlier than T.thailandicum. Our findings provided new insights into the species of Translucidithyrium about ecological adaptation and speciation in two separate areas.

The insights into the evolutionary history of Translucidithyrium: based on a newly-discovered species

During the field studies, a Translucidithyrium-like taxon was collected in Xishuangbanna of Yunnan Province, during an investigation into the diversity of microfungi in the southwest of China. Morphological observations and phylogenetic analysis of combined LSU and ITS sequences revealed that the new taxon is a member of the genus Translucidithyrium and it is distinct from other species. Therefore, Translucidithyrium chinensesp. nov. is introduced here. The Maximum Clade Credibility (MCC) tree from LSU rDNA of Translucidithyrium and related species indicated the divergence time of existing and new species of Translucidithyrium was crown age at 16 (4–33) Mya. Combining the estimated divergence time, paleoecology and plate tectonic movements with the corresponding geological time scale, we proposed a hypothesis that the speciation (estimated divergence time) of T. chinense was earlier than T. thailandicum. Our findings provided new insights into the species of Translucidithyrium about ecological adaptation and speciation in two separate areas.

Analysis of Adaptive Evolution and Coevolution of rbcL Gene in the Genus Hildenbrandia (Rhodophyta)

The adaptive evolution and coevolution of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene in the genus Hildenbrandia were studied based on phylogenetic tree construction and the physicochemical properties and the secondary structures of protein encoded by rbcL (Rubisco large subunit) were analyzed. The amino acids compositions and grand average of hydropathicity of freshwater H. rivularis and marine H. rubra were similar. Rubisco large subunit of Hildenbrandia was hydrophilic and the secondary structure was primarily composed of α-helixes and β-sheets, revealing the relatively stable structure of this protein. The predicted phosphorylation sites in H. rivularis and H. rubra were 33 and 36, respectively. No positive selection sites were detected in the genus Hildenbrandia, implying that rbcL gene evolved either neutrally or under purifying selection. A total of 41 coevolutionary groups were detected in the Rubisco large subunit of Hildenbrandia and the coevolving sites are in closer proximity in 3-dimensional structure of the protein. Despite the long evolutionary history, rbcL gene in genus Hildenbrandia under different environments is rather conservative.

Analysis of Adaptive Evolution and Coevolution of rbcL Gene in the Genus Galdieria (Rhodophyta)

To research the adaptive evolution and coevolution of the rbcL gene in the genus Galdieria, 36 sequences were selected. The bioinformatics of proteins encoded by rbcL genes of Galdieria were analyzed, and phylogenetic trees were constructed by the maximum-likelihood method. Then, adaptive evolution and coevolution were analyzed. The phylogenetic tree showed that the inner groups were clustered into four branches, in which the sequences of Galdieria maxima were divided into two small branches, and the posterior probability of each branch is above 94.9%. Eleven reliable positive selection sites were detected in the branched-site model, indicating that the rbcL protein-coding gene of Galdieria underwent adaptive evolution to adapt to extreme environments. Site 269 F is located in the loop 6 domain, while sites 272 D and 273 W are located in the 6-helix structure. Many coevolution pairs were detected, which were closely related to the hydrophobic and molecular weight correlation values of amino acids. The results are helpful to research the evolution process of freshwater red algae, to explore the changes of its essential genes and protein functions to adapt to different environmental pressures, and to understand the close relationship between amino acids in proteins and the molecular mechanism of evolution.