Multigene Phylogeny Research Articles

Gelidiorariphycus gen. nov. (Gelidiales, Rhodophyta): a rare genus found in the Americas

ABSTRACT DNA sequence analyses have demonstrated that Gelidium as currently circumscribed is not monophyletic and has three distinctive lineages: Gelidium sensu stricto that includes the generitype Gelidium corneum, the Capreolia group, and another lineage that includes two distinct clades formed by species from the eastern Pacific and western Atlantic Oceans. A new genus of small gelidioid algae, Gelidiorariphycus, is described to accommodate one of the clades in this latter lineage. Four species (Gelidiorariphycus loratus, G. gahunbooi, G. stipitatus and G. sungminbooi) segregated into this genus in single- and multi-gene phylogenies. Gelidiorariphycus is sister to a clade formed by an unidentified eastern Pacific species and Gelidium lingulatum. These clades are closely related to a clade formed by Gelidiophycus and the Capreolia group. All four Gelidiorariphycus species were morphologically similar with small thalli that have simple and distally flattened erect axes. Fertile tetrasporophytes were found to have sori with sterile margins that are acutely tapered, which may be morphologically distinctive, but determining this requires additional study. These species were rare, with only one or two samples of each collected despite Gelidiales surveys having been done in the areas where they are known. They were mainly found growing on shallow subtidal rocky shores, but a G. gahunbooi specimen was also collected at more than 30 m depth. Their small size and preference for subtidal habitats may explain the small number of specimens collected. The recognition of this new genus is a further step in the establishment of a natural classification system for genera within the Gelidiaceae.

Multigene phylogeny and haplotype analysis reveals predominance of oomycetous fungus, Phytophthora meadii (McRae) associated with fruit rot disease of arecanut in India

An oomycetous fungus Phytophthora causing fruit rot is the most devastating disease of arecanut in different agro-climatic zones of Karnataka with varied climatic profiles. The main aim of this investigation was to characterize the geo-distant Phytophthora populations infecting arecanut using robust morphological, multi-gene phylogeny and haplotype analysis. A total of 48 geo-distant fruit rot infected samples were collected during the South-West monsoon of 2017–19. Pure culture of the suspected pathogen was isolated from the infected nuts and pathogenic ability was confirmed and characterized. Colony morphology revealed typical whitish mycelium with stellate or petalloid pattern and appearance with torulose hyphae. Sporangia were caducous, semipapillate or papillate, globose, ellipsoid or ovoid-obpyriform in shape and sporangiophores were irregularly branched or simple sympodial in nature. Subsequent multi-gene phylogeny (ITS, β-tub, TEF-1α and Cox-II) and sequence analysis confirmed the identity of oomycete as Phytophthora meadii which is predominant across the regions studied. We identified 49 haplotypes representing the higher haplotype diversity with varying relative haplotype frequency. Comprehensive study confirmed the existence of substantial variability among geo-distant populations (n = 48) of P. meadii. The knowledge on population dynamics of the pathogen causing fruit rot of arecanut generated from this investigation would aid in developing appropriate disease management strategies to curtail its further occurrence and spread in arecanut ecosystem.

Ancient Tethyan Vicariance and Long-Distance Dispersal Drive Global Diversification and Cryptic Speciation in the Red Seaweed Pterocladiella.

We investigated the globally distributed red algal genus Pterocladiella, comprising 24 described species, many of which are economically important sources of agar and agarose. We used DNA-based species delimitation approaches, phylogenetic, and historical biogeographical analyses to uncover cryptic diversity and infer the drivers of biogeographic patterns. We delimited 43 species in Pterocladiella, of which 19 are undescribed. Our multigene time-calibrated phylogeny and ancestral area reconstruction indicated that Pterocladiella most likely originated during the Early Cretaceous in the Tethys Sea. Ancient Tethyan vicariance and long-distance dispersal have shaped current distribution patterns. The ancestor of Eastern Pacific species likely arose before the formation of the formidable Eastern Pacific Barrier—a first confirmation using molecular data in red algae. Divergences of Northeast and Southeast Pacific species have been driven by the Central American Seaway barrier, which, paradoxically, served as a dispersal pathway for Atlantic species. Both long- and short-distance dispersal scenarios are supported by genetic relationships within cosmopolitan species based on haplotype analysis. Asymmetrical distributions and the predominance of peripatry and sympatry between sister species suggest the importance of budding speciation in Pterocladiella. Our study highlights the underestimation of global diversity in these crucial components of coastal ecosystems and provides evidence for the complex evolution of current species distributions.

New species of Cercosporoid on Mango in Thailand

Fungi in Cercospora and Pseudocercospora are commonly known as cercosporoid fungi. In the current study, a cercosporoid fungus was isolated from Mangifera indica from Chiang Mai, Thailand. The isolate was identifi ed as Pseudocercospora mangiferae sp. nov. based on morphology and ITS, act, tef1-α and rpb2 multigene phylogeny. Further, this is the fi rst report of a Pseudocercospora species on M. indica in Thailand.

Evolution and Biogeography of Freshwater Snails of the Genus Bulinus (Gastropoda) in Afromontane Extreme Environments

Mountains are considered island-like systems often characterized by exceptional biodiversity and endemism. There are many highly isolated mountain ranges in Africa that collectively have been called the Afromontane archipelago. Freshwater snails of the genus Bulinus are composed of many veterinary and biomedical important species. These intermediate hosts for schistosomiasis parasites are wide spread and some of the species are considered to be highly adapted to very harsh environmental conditions such as droughts or low temperatures. However, the extent to which the Bulinus have adapted to live in high-altitudes and factors influencing these range shifts are not well investigated. In this study, we analyzed pan-African Bulinus species from various habitats across different altitudinal ranges, focusing on the high mountains or “sky islands” to examine how the contemporary climate and historical geological factors affect species distributions and evolutionary processes. Using a fossil-calibrated multigene phylogeny composed of two mitochondrial genes (cox1, 16S) and two nuclear genes (ITS2 and H3), we tested: 1) how often and when extreme altitudes were colonized, 2) what are the biogeographical affinities and degree of isolation of high-altitude species, 3) which lineages diversified and evolved endemism in the Afromontane environments, and 4) whether the Afromontane regions represent “sky islands”. Bayesian phylogenetic inference employing a fossil-calibrated molecular clock resulted in a strongly supported phylogeny resolving the relationships between the four Bulinus groups. High-altitude colonization exists exclusively within the Bulinus truncatus/tropicus complex. Several independent colonization events occurred in the Pliocene and Pleistocene throughout Africa, mostly from nearby regions of the respective mountain ranges. Most species evolved in low to mid-altitudinal ranges. Endemism is pronounced in the Ethiopian Highlands and those of Kenya and Lesotho. A previously unknown species was found at an extreme altitude (∼4,000 m a.s.l.) on Mt. Elgon/Uganda extending the formerly known altitudinal maximum of the genus by roughly 900 m. The endemic species has already diverged in the Pliocene (∼4 myr) and is currently characterized by low genetic diversity. There is further cryptic diversity in mountain ranges of Lesotho. Our findings are discussed in a biogeographical, conservation and biomedical context.

Morphology and Phylogeny of a new species Pseudocercospora rauvolfiicola on medicinal plant Rauvolfia serpentina from Sonebhadra Forest, Uttar Pradesh, India

A new species of Pseudocercospora is discovered causing foliar disease on the medicinal plant Rauvolfia serpentina (Apocynaceae) from India. The new species is described and illustrated on the morphology of asexual-morphs, growth characters and multigene phylogeny. Morphologically, new species has similar characters with allied species in Pseudocercospora but differs in having catenate and branched conidia. Phylogenetic analysis using combined LSU, ITS, ACT and TEF1α data supports the isolate to be a new species of Pseudocercospora (Capnodiales, Mycosphaerellaceae).

Ecological and Phenotypic Diversification after a Continental Invasion in Neotropical Freshwater Stingrays.

Habitat transitions are key potential explanations for why some lineages have diversified and others have not-from Anolis lizards to Darwin's finches. The ecological ramifications of marine-to-freshwater transitions for fishes suggest evolutionary contingency: some lineages maintain their ancestral niches in novel habitats (niche conservatism), whereas others alter their ecological role. However, few studies have considered phenotypic, ecological, and lineage diversification concurrently to explore this issue. Here, we investigated the macroevolutionary history of the taxonomically and ecologically diverse Neotropical freshwater river rays (subfamily Potamotrygoninae), which invaded and diversified in the Amazon and other South American rivers during the late Oligocene to early Miocene. We generated a time-calibrated, multi-gene phylogeny for Potamotrygoninae and reconstructed evolutionary patterns of diet specialization. We measured functional morphological traits relevant for feeding and used comparative phylogenetic methods to examine how feeding morphology diversified over time. Potamotrygonine trophic and phenotypic diversity are evenly partitioned (non-overlapping) among internal clades for most of their history, until 20-16 mya, when more recent diversification suggests increasing overlap among phenotypes. Specialized piscivores (Heliotrygon and Paratrygon) evolved early in the history of freshwater stingrays, while later trophic specialization (molluscivory, insectivory, and crustacivory) evolved in the genus Potamotrygon. Potamotrygonins demonstrate ecological niche lability in diets and feeding apparatus; however, diversification has mostly been a gradual process through time. We suggest that competition is unlikely to have limited the potamotrygonine invasion and diversification in South America.

A revision of the wilsoni species group in the millipede genus Nannaria Chamberlin, 1918 (Diplopoda, Polydesmida, Xystodesmidae).

Although many new species of the millipede genus Nannaria Chamberlin, 1918 have been known from museum collections for over half a century, a systematic revision has not been undertaken until recently. There are two species groups in the genus: the minor species group and the wilsoni species group. In this study, the wilsoni species group was investigated. Specimens were collected from throughout its distribution in the Appalachian Mountains of the eastern United States and used for a multi-gene molecular phylogeny. The phylogenetic tree recovered Nannaria and the two species groups as monophyletic, with Oenomaeapulchella as its sister group. Seventeen new species were described, bringing the composition of the wilsoni species group to 24 species, more than tripling its known diversity, and increasing the total number of described Nannaria species to 78. The genus now has the greatest number of species in the family Xystodesmidae. Museum holdings of Nannaria were catalogued, and a total of 1,835 records used to produce a distribution map of the species group. Live photographs, illustrations of diagnostic characters, ecological notes, and conservation statuses are given. The wilsoni species group is restricted to the Appalachian region, unlike the widely-distributed minor species group (known throughout eastern North America), and has a distinct gap in its distribution in northeastern Tennessee and adjacent northwestern North Carolina. The wilsoni species group seems to be adapted to mesic microhabitats in middle to high elevation forests in eastern North America. New species are expected to be discovered in the southern Appalachian Mountains.

Nuclear and Mitochondrial SSU rRNA Genes Reveal Hidden Diversity of Haptophrya Endosymbionts in Freshwater Planarians and Challenge Their Traditional Classification in Astomatia.

Like many other aquatic animals, freshwater planarians have also become partners of symbiotic ciliates from the class Oligohymenophorea. In the present study, we explored the hidden diversity and addressed the questionable systematic position of mouthless obligatory gut endosymbionts of freshwater planarians, using the nuclear and mitochondrial SSU rRNA genes. Although all isolated ciliates morphologically corresponded to a single species, molecular analyses suggested the existence of three genetically distinct entities: Haptophrya planariarum, Haptophrya dugesiarum nov. spec., and Haptophrya schmidtearum nov. spec. The two former species share the same planarian host, which indicates a speciation model involving one duplication event without host switching. Such a diversification pattern was recognized also in astome ciliates inhabiting megascolecid and glossoscolecid earthworms. The present multi-gene phylogenies along with the secondary structure of the mitochondrial 16S rRNA molecule, however, challenge the traditional classification of Haptophrya within the subclass Astomatia. Haptophrya very likely evolved from an orphan scuticociliate lineage by the loss of oral apparatus and by the transformation of the thigmotactic field into an adhesive sucker. Since astomy evolved multiple times independently within the Oligohymenophorea, the loss of cell mouth cannot be used as a sole argument for the assignment of Haptophrya to the Astomatia anymore.

Multigene phylogeny of blister beetles (Coleoptera, Meloidae) reveals extensive polyphyly of the tribe Lyttini and allows redefining its boundaries

AbstractMeloidae is a beetle family with about 3000 species divided into three subfamilies and 16 tribes. Included is the tribe Lyttini containing 33 genera and about 400 species. However, the boundaries of Lyttini have proved hard to define since the systematics of this tribe have repeatedly changed. In this study, we investigated the phylogeny of Lyttini and tested for its monophyly based on a comprehensive molecular dataset of mitochondrial (COI and 16S) and nuclear (CAD and 28S) genes including 57 genera and 385 species representing most of the tribes of Meloidae. Further phylogenetic analyses were performed on a reduced taxon set (51 genera and 135 species covering 60% of the generic diversity of Lyttini) in order to maximize the number of loci and minimize missing data. Phylogenetic results strongly supported the monophyly of most of the tribes of the subfamily Meloinae, apart from Lyttini, which is split into 11 phylogenetically distinct lineages scattered throughout the tree. Based on these results, we restrict the tribe Lyttini to the genera Alosimus Mulsant, Lydus Dejan, Lytta Fabricius, Muzimes Mulsant & Rey and Oenas Latreille, all exclusive to the Holarctic region. The relationships among the remaining genera previously included in Lyttini and the other 10 lineages representing ‘non‐Lyttini’ tribes remain to be clarified. This study also provides a number of nomenclatural acts [including Pseudolytta n. stat.; Lytta (Taurilytta) n. subgen.; Lytta (Teratolytta) n.stat.; Mimovesperus resurrected; Denierella = Epicauta n.syn.; Psalydolytta = Epicauta n. syn.] and working hypotheses for future investigations on the systematics of Meloidae.

Multigene phylogeny reveals the ribbed shell morphotypes in the land snail genus Sarika (Eupulmonata: Ariophantidae), with description of two new species from Thailand and Myanmar

Abstract The speciose land snail genus Sarika is widely distributed throughout mainland Southeast Asia. This genus is generally recognized by a smooth and polished shell. However, we recognize four species with a ribbed shell surface (S. siamensis, S. theodori, S. costabilis sp. nov., and S. costata sp. nov.) exhibiting genital characters similar to those of Sarika s.s. and so a rearrangement in the systematics of the genus is suggested. Here, we analysed these four ribbed shell species together with Sarika s.s. by a combined morphological and molecular approach to species delineation, the latter based on both mitochondrial (coi and 16S) and nuclear (28S) markers. Our molecular phylogeny affirms the monophyly of the genus Sarika including both smooth and ribbed shell morphotypes that is statistically well supported. The ribbed shell morphotype in the land snail genus Sarika is also well defined in terms of diagnostic morpho-anatomical characters that can be divided into two species groups. The S. costata species group consists of only one species, S. costata sp. nov., while the S. siamensis species group comprises S. siamensis, S. theodori and S. costabilis sp. nov. These findings provide a solid basis for the systematics of family Ariophantidae.

Taxonomy, phylogeny and identification of Chaetomiaceae with emphasis on thermophilic species.

Chaetomiaceae comprises phenotypically diverse species, which impact biotechnology, the indoor environment and human health. Recent studies showed that most of the traditionally defined genera in Chaetomiaceae are highly polyphyletic. Many of these morphology-based genera, such as Chaetomium, Thielavia and Humicola, have been redefined using multigene phylogenetic analysis combined with morphology; however, a comprehensive taxonomic overview of the family is lacking. In addition, the phylogenetic relationship of thermophilic Chaetomiaceae species with non-thermophilic taxa in the family is largely unclear due to limited taxon sampling in previous studies. In this study, we provide an up-to-date overview on the taxonomy and phylogeny of genera and species belonging to Chaetomiaceae, including an extensive taxon sampling of thermophiles. A multigene phylogenetic analysis based on the ITS (internal transcribed spacers 1 and 2 including the 5.8S nrDNA), LSU (D1/D2 domains of the 28S nrDNA), rpb2 (partial RNA polymerase II second largest subunit gene) and tub2 (β-tubulin gene) sequences was performed on 345 strains representing Chaetomiaceae and 58 strains of other families in Sordariales. Divergence times based on the multi-gene phylogeny were estimated as aid to determine the genera in the family. Genera were delimited following the criteria that a genus must be a statistically well-supported monophyletic clade in both the multigene phylogeny and molecular dating analysis, fall within a divergence time of over 27 million years ago, and be supported by ecological preference or phenotypic traits. Based on the results of the phylogeny and molecular dating analyses, combined with morphological characters and temperature-growth characteristics, 50 genera and 275 species are accepted in Chaetomiaceae. Among them, six new genera, six new species, 45 new combinations and three new names are proposed. The results demonstrate that the thermophilic species fall into seven genera (Melanocarpus, Mycothermus, Remersonia, Thermocarpiscus gen. nov., Thermochaetoides gen. nov., Thermothelomyces and Thermothielavioides). These genera cluster in six separate lineages, suggesting that thermophiles independently evolved at least six times within the family. A list of accepted genera and species in Chaetomiaceae, together with information on their MycoBank numbers, living ex-type strains and GenBank accession numbers to ITS, LSU, rpb2 and tub2 sequences is provided. Furthermore, we provide suggestions how to describe and identify Chaetomiaceae species.

Multi-locus phylogeny unmasks hidden species within the specialised spider-parasitic fungus, Gibellula (Hypocreales, Cordycipitaceae) in Thailand.

Over 80 species of hypocrealean fungi are reported as pathogens of spiders and harvestmen. Among these fungi, the genus Gibellula is highly regarded as a specialised spider-killer that has never been reported to infect other arthropods. While more than 20 species of Gibellula are known, few attempts to identify the infected spiders have been made despite the fact that the host specificity can help identify the fungal species. Here, we morphologically describe and illustrate eight new species of Gibellula and three new records from Thailand of known species along with the multi-gene phylogeny that clearly showed the segregation among the proposed species. Examination of the Gibellula-infected spider hosts identified Oxyopidae, Uloboridae and, for the first time, the ant-mimicking genus Myrmarachne. Taxonomic novelties: New species: Gibellula brevistipitata Kuephadungphan, Tasanathai & Luangsa-ard, G. longicaudata Tasanathai, Kuephadungphan & Luangsa-ard, G. longispora Kuephadungphan & Luangsa-ard, G. nigelii Kuephadungphan, Tasanathai & Luangsa-ard, G. parvula Kuephadungphan, Tasanathai & Luangsa-ard, G. pilosa Kuephadungphan, Tasanathai & Luangsa-ard, G. solita Kuephadungphan, Tasanathai & Luangsa-ard, G. trimorpha Tasanathai, Khonsanit, Kuephadungphan & Luangsa-ard. Citation: Kuephadungphan W, Petcharad B, Tasanathai K, Thanakitpipattana D, Kobmoo N, Khonsanit A, Samson RA, Luangsa-ard JJ (2022). Multi-locus phylogeny unmasks hidden species within the specialised spider-parasitic fungus, Gibellula (Hypocreales, Cordycipitaceae) in Thailand. Studies in Mycology 101: 245-286. doi: 10.3114/sim.2022.101.04.

An enigmatic interstitial trichomycterine catfish from south-eastern Brazil found at about 1000 km away from its sister group (Siluriformes: Trichomycteridae)

During recent field studies in the upper Rio Paraná basin, south-eastern Brazil, a small undescribed trichomycterine catfish with interstitial habits was found. The combination of morphological character states exhibited by this species did not allow placement to any genus from eastern South America. A multigene phylogeny here performed strongly supported the new taxon as sister to Scleronema. Due to the confusing generic classification of the Trichomycterinae, the new taxon is formally placed in a new subgenus of Scleronema (Plesioscleronema subgen. nov.), instead of in a new monotypic genus. The inclusion of the new taxon in Scleronema implicated in a review of generic diagnostic morphological characters. Two apomorphic character states were found to be useful to diagnose Scleronema in this broader sense: presence of a skin flap on the posterior margin of the opercle and a unique frontal bone morphology. Scleronema auromaculatum spec. nov. differs from other trichomycterines by a unique morphology of the area involving the postero-dorsal portion of the quadrate and the adjacent region of the hyomandibula, the uroneural separated by the dorsal hypural plate by an interspace, and a widened hemal spine of the preural centre 2. The about 1000 km gap between the area where the new species was collected and the nearest collecting site of its sister group is probably a consequence of both anthropic environmental degradation and the specialised interstitial habits in this fish group, making it difficult to be found in ichthyological inventories.

Global diversity and systematics of Hymenochaetaceae with poroid hymenophore

Taxonomy and phylogeny of poroid Hymenochaetaceae based on the most comprehensive phylogenetic analyses are presented. A phylogeny based on a combined dataset of ITS and nLSU sequences for accepted genera of Hymenochaetaceae was analyzed and two or multigene phylogenies for most species of ten large genera including Coltricia, Fomitiporella, Fomitiporia, Fulvifomes, Fuscoporia, Inonotus, Phylloporia, Porodaedalea, Sanghuangporus and Tropicoporus, were carried out. Based on samples from 37 countries of five continents, seven new genera, Meganotus, Neophellinus, Nothonotus, Pachynotus, Perenninotus, Pseudophylloporia and Rigidonotus, are introduced, 37 new species, Coltricia tibetica, Fomitiporella crassa, F. queenslandica, Fomitiporia eucalypti, F. gatesii, F. ovoidospora, Fulvifomes azonatus, F. caligoporus, F. costaricense, F. floridanus, F. jouzaii, F. nakasoneae, F. subindicus, Fuscoporia sinuosa, F. submurina, Inonotus subradiatus, I. vietnamensis, Neomensularia castanopsidis, Pachynotus punctatus, Phellinus cuspidatus, P. subellipsoideus, Phylloporia minutissima, P. tabernaemontanae, Porodaedalea occidentiamericana, P. orientoamericana, P. qilianensis, P. schrenkianae, Pseudophylloporia australiana, Sanghuangporus australianus, S. lagerstroemiae, Tropicoporus angustisulcatus, T. hainanicus, T. lineatus, T. minus, T. ravidus, T. substratificans and T. tenuis, are described, and 108 new combinations are proposed. In addition, one illegitimate name and two invalid names are renamed, and Coltricia and Coltriciella were synonymized. The taxonomic relevance and limits of the new taxa are discussed. Photos and illustrations for 37 new species are presented, and a full description for each new species is given. Eventually, this study recognizes 672 species in 34 genera and provides a modern treatment of the poroid Hymenochaetaceae in the world. A key to the accepted poroid genera of Hymenochaetaceae is provided, and identification keys to the accepted species of 32 poroid genera worldwide are given. A synopsis description of each species is included in these keys.

Multigene Phylogeny Reveals Endophytic Xylariales Novelties from Dendrobium Species from Southwestern China and Northern Thailand.

Xylariales are common endophytes of Dendrobium. However, xylarialean species resolution remains difficult without sequence data and poor sporulation on artificial media and asexual descriptions for only several species and old type material. The surface-sterilized and morph-molecular methods were used for fungal isolation and identification. A total of forty-seven strains were identified as twenty-three species belonging to Apiosporaceae, Hypoxylaceae, Induratiaceae, and Xylariaceae. Five new species—Annulohypoxylon moniliformis, Apiospora dendrobii, Hypoxylon endophyticum, H. officinalis and Nemania dendrobii were discovered. Three tentative new species were speculated in Xylaria. Thirteen known fungal species from Hypoxylon, Nemania, Nigrospora, and Xylaria were also identified. Another two strains were only identified at the genus and family level (Induratia sp., Hypoxylaceae sp.). This study recorded 12 new hosts for xylarialean endophytes. This is the first report of Xylariales species as endophytes from Dendrobium aurantiacum var. denneanum, D. cariniferum, D. harveyanum, D. hercoglossum, D. moniliforme, and D. moschatum. Dendrobium is associated with abundant xylarialean taxa, especially species of Hypoxylon and Xylaria. We recommend the use of oat agar with low concentrations to induce sporulation of Xylaria strains.

Using RDNA sequences to define dinoflagellate species

Dinoflagellate species are traditionally defined using morphological characters, but molecular evidence accumulated over the past several decades indicates many morphologically-based descriptions are inaccurate. This recognition led to an increasing reliance on DNA sequence data, particularly rDNA gene segments, in defining species. The validity of this approach assumes the divergence in rDNA or other selected genes parallels speciation events. Another concern is whether single gene rDNA phylogenies by themselves are adequate for delineating species or if multigene phylogenies are required instead. Currently, few studies have directly assessed the relative utility of multigene versus rDNA-based phylogenies for distinguishing species. To address this, the current study examined D1-D3 and ITS/5.8S rDNA gene regions, a multi-gene phylogeny, and morphological characters in Gambierdiscus and other related dinoflagellate genera to determine if they produce congruent phylogenies and identify the same species. Data for the analyses were obtained from previous sequencing efforts and publicly available dinoflagellate transcriptomic libraries as well from the additional nine well-characterized Gambierdiscus species transcriptomic libraries generated in this study. The D1-D3 and ITS/5.8S phylogenies successfully identified the described Gambierdiscus and Alexandrium species. Additionally, the data showed that the D1-D3 and multigene phylogenies were equally capable of identifying the same species. The multigene phylogenies, however, showed different relationships among species and are likely to prove more accurate at determining phylogenetic relationships above the species level. These data indicated that D1-D3 and ITS/5.8S rDNA region phylogenies are generally successful for identifying species of Gambierdiscus, and likely those of other dinoflagellates. To assess how broadly general this finding is likely to be, rDNA molecular phylogenies from over 473 manuscripts representing 232 genera and 863 described species of dinoflagellates were reviewed. Results showed the D1-D3 rDNA and ITS phylogenies in combination are capable of identifying 97% of dinoflagellate species including all the species belonging to the genera Alexandrium, Ostreopsis and Gambierdiscus, although it should be noted that multi-gene phylogenies are preferred for inferring relationships among these species. A protocol is presented for determining when D1-D3, confirmed by ITS/5.8S rDNA sequence data, would take precedence over morphological features when describing new dinoflagellate species. This protocol addresses situations such as: a) when a new species is both morphologically and molecularly distinct from other known species; b) when a new species and closely related species are morphologically indistinguishable, but genetically distinct; and c) how to handle potentially cryptic species and cases where morphotypes are clearly distinct but have the same rDNA sequence. The protocol also addresses other molecular, morphological, and genetic approaches required to resolve species boundaries in the small minority of species where the D1-D3/ITS region phylogenies fail.

Multi-Gene Phylogeny of the Ciliate Genus Trachelostyla (Ciliophora, Hypotrichia), With Integrative Description of Two Species, Trachelostyla multinucleata Spec. nov. and T. pediculiformis (Cohn, 1866).

Many hypotrich genera, including Trachelostyla, are taxonomically challenging and in a need of integrative revision. Using morphological data, molecular phylogenetic analyses, and internal transcribed spacer 2 (ITS2) secondary structures, we attempt to cast more light on species relationships within the genus Trachelostyla. The present multifaceted approach reveals that (1) a large-sized species with numerous macronuclear nodules, isolated from sandy littoral sediments in southern China, is new to science and is endowed here with a name, T. multinucleata spec. nov.; (2) two other Chinese populations previously identified as T. pediculiformis represent undescribed species; and (3) multigene phylogeny is more robust than single-gene trees, recovering the monophyly of the genus Trachelostyla with high bootstrap frequency. Additionally, ITS2 secondary structures and the presence of compensatory base changes in helices A and B indicate the presence of four distinct taxa within the molecularly studied members of the genus Trachelostyla. Molecular data are more suitable for delimitation of Trachelostyla species than morphological characters as interspecific pairwise genetic distances of small subunit (18S) rDNA, ITS1-5.8S-ITS2, and large subunit (28S) rDNA sequences do not overlap, whereas ranges of multiple morphometric features might transcend species boundaries.

A Polyphasic Approach Reveals Novel Genotypes and Updates the Genetic Structure of the Banana Fusarium Wilt Pathogen.

Fusarium oxysporum f. sp. cubense (Foc) is a soil-borne fungus that causes Fusarium wilt, a destructive plant disease that has resulted in devastating economic losses to banana production worldwide. The fungus has a complex evolutionary history and taxonomic repute and consists of three pathogenic races and at least 24 vegetative compatibility groups (VCGs). Surveys conducted in Asia, Africa, the Sultanate of Oman and Mauritius encountered isolates of F. oxysporum pathogenic to banana that were not compatible to any of the known Foc VCGs. Genetic relatedness between the undescribed and known Foc VCGs were determined using a multi-gene phylogeny and diversity array technology (DArT) sequencing. The presence of putative effector genes, the secreted in xylem (SIX) genes, were also determined. Fourteen novel Foc VCGs and 17 single-member VCGs were identified. The multi-gene tree was congruent with the DArT-seq phylogeny and divided the novel VCGs into three clades. Clustering analysis of the DArT-seq data supported the separation of Foc isolates into eight distinct clusters, with the suite of SIX genes mostly conserved within these clusters. Results from this study indicates that Foc is more diverse than hitherto assumed.

Morpho-Molecular Characterization of Five Novel Taxa in Parabambusicolaceae (Massarineae, Pleosporales) from Yunnan, China.

Parabambusicolaceae is a well-studied family in Massarineae, Pleosporales, comprising nine genera and approximately 16 species. The family was introduced to accommodate saprobic bambusicola-like species in both freshwater and terrestrial environments that mostly occur on bamboos and grasses but are also found on different host substrates. In the present study, we surveyed and collected ascomycetes from bamboo and submerged grass across Yunnan Province, China. A biphasic approach based on morphological characteristics and multigene phylogeny demonstrated five new taxa in Parabambusicolaceae. A novel genus Scolecohyalosporium is introduced as a monotypic genus to accommodate S. submersum sp. nov., collected from dead culms of grass submerged in a freshwater stream. The genus is unique in forming filiform ascospores, which differ from other known genera in Parabambusicolaceae. Multigene phylogeny showed that the genus has a close relationship with Multiseptospora. Moreover, the novel monotypic genus Neomultiseptospora, isolated from bamboo, was introduced to accommodate N. yunnanensis sp. nov. Neomultiseptospora yunnanensis formed a separated branch basal to Scolecohyalosporium submersum and Multiseptospora thailandica with high support (100% ML, 1.00 PP). Furthermore, the newly introduced species, Parabambusicola hongheensis sp. nov. was also isolated from bamboo in terrestrial habitats. Parabambusicola hongheensis clustered with the other three described Parabambusicola species and has a close relationship with P. bambusina with significant support (88% ML, 1.00 PP). Parabambusicola hongheensis was reported as the fourth species in this genus. Detailed description, illustration, and updated phylogeny of Parabambusicolaceae were provided.