Well-supported Monophyletic Clade Research Articles

Evolutionary unraveling: new insights into the Persicaria amphibia complex

The Persicaria amphibia complex exhibits significant morphological variation depending on its habitat, existing in either aquatic or terrestrial forms. Traditionally, four distinct elements have been recognized based on morphological features along with their distinct geographical distributions. Recent studies suggest that the Asian element may be genetically distinct from the European and American elements. However, a comprehensive study on the genetic differentiation among all four elements remains lacking. This study aimed to leverage whole plastid genome sequences and ITS2 haplotypes to comprehensively assess the genomic diversity within the P. amphibia complex. Notably, we included multiple individuals from New York State to resolve the ongoing debate regarding the taxonomic status of two American elements – whether they represent a single species or distinct entities. Our analysis revealed a well-supported monophyletic clade encompassing all four elements, endorsing their own section, Amphibia. Notably, the terrestrial form of the American element is sister to all other elements, suggesting it deserves its own species status. This reinstates its historical name, P. coccinea, separating it from the broader P. amphibia. Furthermore, distinct compositions of the ITS2 haplotypes differentiated the four elements, although the European element should be further investigated with more sampling. The most intriguing discovery is the identification of putative hybrids between the two American elements. In one population out of four putative hybrid populations, all three entities – the two parent species and their hybrid offspring – thrive together, showcasing a fascinating microcosm of ongoing evolutionary processes. Unraveling the intricate genetic tapestry within each American species and their hybrid populations remains a compelling next step. By delving deeper into their genetic makeup, we can gain a richer understanding of their evolutionary trajectories and the intricacies of their interactions. Finally, it is estimated that the two species of sect. Amphibia diverged approximately 4.02 million years ago during the Pliocene epoch, when there was a significant global cooling and drying trend.

Agaricus cervinoculus sp. nov. (Agaricaceae), a new wild edible mushroom from Mexico

In Mexico, there are 55 wild species of Agaricus representing approximately 10 % of the world’s diversity of the genus. 22 species of these wild mushrooms are traditionally consumed. The lack of keys for the identification of Mexican species, the difficulties in recognizing distinctive morphological characters and the need for comprehensive studies in some sections of the genus, makes it difficult to distinguish species complexes. The edible species known locally as “ojo de venado” was previously identified as A. sylvaticus in Mexico. Our phylogenetic analyses revealed that this ethnotaxon, which is sold in the markets of Xalapa (Veracruz, Mexico), includes at least two species of A. sect. Subrutilescentes. One of them, Agaricus cervinoculus, is described as a new species. A full description, photographs and comparisons to other similar species are provided. This new species constitutes a well-supported monophyletic clade, sister to the “A. subrutilescens” group.

Effects of color variation and physiological state on ascidian microbiomes.

Ascidians, known for their color variation, host species-specific microbial symbiont communities. Some ascidians can also transition into a nonfiltering (resting) physiological state. Recent studies suggest that the microbial symbiont communities may vary across different physiological states and color morphs of the host. The colonial ascidian, Polyclinum constellatum, which exhibits several color morphs in the Caribbean Sea, periodically ceases its filtering activity. To investigate if color variation in P. constellatum is indicative of sibling speciation, we sequenced fragments of the ribosomal 18S rRNA and the mitochondrial cytochrome oxidase subunit I genes. Additionally, we sequenced a fragment of the 16S rRNA gene to characterize the microbial communities of two common color morphs (red and green) in colonies that were either actively filtering (active) or nonfiltering (resting). Phylogenetic analyses of both ascidian genes resulted in well-supported monophyletic clades encompassing all color variants of P. constellatum. Interestingly, no significant differences were observed among the microbial communities of the green and red morphs, suggesting that color variation in this species is a result of intraspecific variation. However, the host's physiological state significantly influenced the microbial community structure. Nonfiltering (resting) colonies hosted higher relative abundances of Kiloniella (Alphaproteobacteria) and Fangia (Gammaproteobacteria), while filtering colonies hosted more Reugeria (Alphaproteobacteria) and Endozoicomonas (Gammaproteobacteria). This study demonstrates that microbial symbiont communities serve as reliable indicators of the taxonomic state of their host and are strongly influenced by the host's feeding condition.

Amesuviridae: a new family of plant-infecting viruses in the phylum Cressdnaviricota, realm Monodnaviria.

The phylum Cressdnaviricota comprises viruses with single-stranded, circular DNA genomes that encode an HUH-type endonuclease (known as Rep). The phylum includes two classes, eight orders, and 11 families. Here, we report the creation of a twelfth family in the order Mulpavirales, class Arfiviricetes of the phylum Cressdnaviricota. The family Amesuviridae comprises viruses that infect plants and is divided into two genera: Temfrudevirus, including the species Temfrudevirus temperatum (with temperate fruit decay-associated virus as a member), and Yermavirus, including the species Yermavirus ilicis (with yerba mate-associated circular DNA virus as a member). Both viruses encode Rep proteins with HUH endonuclease and SH3 superfamily helicase domains. Phylogenetic analysis indicates that the replicative module of amesuviruses constitutes a well-supported monophyletic clade related to Rep proteins from viruses in the order Mulpavirales. Furthermore, both viruses encode a single capsid protein (CP) related to geminivirus CPs. Phylogenetic incongruence between the replicative and structural modules of amesuviruses suggests a chimeric origin resulting from remote recombination events between ancestral mulpavirales and geminivirids. The creation of the family Amesuviridae has been ratified by the International Committee on Taxonomy of Viruses (ICTV).

Phylogenetic Position of the Genus Manunema (Nematoda, Plectida, Leptolaimidae)

During an investigation of a natural sandy beach on Jeju Island, South Korea, a species of marine nematode belonging to the rare genus Manunema was discovered and is now being reported. Up until now, no molecular sequences of this genus have been available, and its position within the nematode system has been a subject of dispute. Currently, Manunema is classified within the order Plectida, either as the only genus of the family Peresianidae in the superfamily Haliplectoidea or directly as a genus of the family Leptolaimidae. Here, we report on the discovery of Manunema cf. proboscidis Gerlach, 1957, which was found off Jeju Island, South Korea. We also conduct an in-depth investigation of its peculiar morphology, with a particular focus on the reproductive system type observed within the species. Additionally, we examine the phylogenetic relationship of the genus using 18S rRNA sequences. Partial mtCOI, nearly complete sequences of the 18S ribosomal RNA gene as well as a partial 28S (D2–D3 region) gene are provided. Morphologically, the presence of tubular precloacal supplements (shared by superfamily Leptolaimoidea and not Haliplectoidea) and antidromously reflected ovaries of females in Manunema (shared by the order Plectida and not Desmoscolecida) may have taxonomic significance. Our phylogenetic trees based on 18S rRNA also reflected this, including Manunema in a well-supported monophyletic clade of the family Leptolaimidae.

(2953) Proposal to conserve the name Absconditella against Geisleria (Ascomycota: Lecanoromycetes)

(2953) Absconditella Vězda in Preslia 37: 238. 1965, nom. cons. prop. Typus: A. sphagnorum Vězda & Poelt (=) Geisleria Nitschke in Rabenhorst, Lich. Eur. Exs. No. 574. Oct 1861, nom. rej. prop. Typus: G. sychnogonioides Nitschke Vězda (in Preslia 37: 238. 1965) introduced a new genus of lichenized fungi, Absconditella (Stictidaceae, Ostropales, Lecanoromycetes, Ascomycota) with A. sphagnorum Vězda & Poelt as the type to accommodate species having minute, urceolate (apothecioid) ascomata with a non-amyloid hymenium and without a dark pigment, simple and indistinctly septate paraphyses, asci with a distinct non-amyloid tholus and chlorococcoid algae as a photobiont. At least 12 additional species have been described (Vězda, l.c. 1965; Vězda & Vivant in Folia Geobot. Phytotax. 10: 205. 1975; Döbbeler & Poelt in Herzogia 4: 364. 1977; Vězda & Pišút in Nova Hedwigia 40: 342, 344. 1985 [“1984”]; Søchting & al. in Biblioth. Lichenol. 88: 613. 2004; Spribille & al. in Bryologist 112: 111. 2009; Kondratyuk & al. in Acta Bot. Hung. 55: 277. 2013; Van den Boom & al. in Phytotaxa 238: 272. 2015; Cáceres & Aptroot in Bryologist 119: 254. 2016; Kalb & Aptroot in Bryologist 121: 57, 60. 2018) and four have been transferred from other genera (Vězda, l.c. 1965: 241, 244; Rossman in Mycotaxon 8: 505. 1979; Hawksworth & al. in Lichenologist 12: 106. 1980). The genus is cosmopolitan, and most species are sporadically collected due to their small size and probably ephemeral nature. The name Geisleria was introduced by Nitschke (in Rabenhorst, Lich. Eur. Exs. No. 574. 1861) for a single species, G. sychnogonioides Nitschke. Three more species were described later, one of which, G. alpina Servít (in Blumea 7: 594. 1954), appeared to be a parasymbiont on Polyblastia albida Arnold (Swinscow in Lichenologist 3: 418. 1967); another, G. jamesii Swinscow (l.c.: 420), was reassigned to Swinscowia S.H. Jiang, Lücking & Sérus. (Hongsanan & al. in Fungal Diversity 10: 139. 2020); and the third, G. xylophila Vězda (in Folia Geobot. Phytotax. 5: 312. 1970), is still known only by the type specimen. For a long time, the type of ascomata has been one of the main characteristics to delimit higher taxa in Ascomycetes. The ascomata of Geisleria are enclosed, perithecium-like with a narrow pore, and therefore G. sychnogonioides has been referred to pyrenocarpous families such as Verrucariaceae in Eurotiomycetes (Stizenberger in Ber. Thätigk. St. Gallischen Naturwiss. Ges. 22: 502. 1882) or Strigulaceae in Dothideomycetes (Harris, Taxon. Revis. Arthopyrenia [Ph.D. thesis, Michigan State University, U.S.A.]: 145. 1975; Roux & Sérusiaux in Biblioth. Lichenol. 90: 89–90. 2004). The relationships of Geisleria with other lichenized genera remained disputable until Aptroot & al. (in Lichenologist 46: 115–128. 2014) showed that Geisleria is sister to the type of the generic name Absconditella, forming a highly supported clade within Stictidaceae. Due to the small sample size, the authors (Aptroot & al., l.c.) only discussed the need for taxonomic re-arrangements but did not perform them. The most recent study on the lichenized genus Absconditella with more species and specimens included (Suija & Van den Boom in Mycol. Progr., in press) confirmed Aptroot & al.'s results as Geisleria was nested within Absconditella, forming a well-supported monophyletic clade. In contrast to Geisleria, the ascomata of Absconditella are cup-shaped with an exposed spore-bearing layer (apothecia). Aptroot & al. (l.c.) examined the type material of G. sychnogonioides and revealed that the ascomata of this species are still typical apothecia but the disc is only narrowly exposed, leaving the impression of enclosed fruit-bodies. The microscopical examination of additional materials by Suija & Van den Boom (l.c.) confirmed their statement. Following the principle of priority (Art. 11.3), we should adopt the earlier generic name Geisleria over Absconditella. However, the recognition and application of the older name would necessitate the introduction of 15 new combinations. Therefore, we propose to conserve the more widely used name Absconditella against Geisleria. AS, https://orcid.org/0000-0003-3784-9414 PvdB, https://orcid.org//0000-0002-1929-2088

Disentangling cryptic species in Parastenocarididae (Copepoda: Harpacticoida) with an integrative approach: the case of Stammericaris similior sp. nov. and Stammericaris destillans Bruno & Cottarelli 2017.

Stammericaris similior sp. nov. is described combining light microscopy, scanning electron microscopy, and genetic barcoding. The new species was collected from rimstone pools in Scrivilleri Cave, a cave in Sicily with so far unexplored microcrustacean fauna. The new species is particularly interesting because it is morphologically very similar to Stammericaris destillans, an epikarstic parastenocaridid endemic to a different Sicilian cave; however, the phylogenetic analysis based on the mitochondrial COI gene of sixteen parastenocaridids shows that these two Stammericaris are two distinct species, with an uncorrected p-distance of 22.9, and the sequences of Stammericaris similior sp. nov. cluster together in a well-supported monophyletic clade, with two different haplotypes. To our knowledge, the presence of different species of almost identical morphology had not been recorded before for the genus Stammericaris. The integrated molecular and morphological analysis, the latter conducted with the support of SEM, allows disentangling the affinities of the new species and identifying a few distinctive characters: the males of the new species are characterized by the caudal rami shorter than the anal somite; the morphology of the P3, which is thin and slightly arched, with three proximal spinules on exp-1; the peculiar structure of the P4 enp; the P4 basis ornamented with two spinules of different length, the one closest to the endopod being the shortest one, and a half-moon shaped lamella. The new species differs from S. destillans for its larger size, the presence of: three spinules, instead of two, on the P3 exp-1; the half-moon shaped lamella on the P4 basis; a row of spinules along the inner margin of P4 exp-1. We also provide data on the ecology and distribution of the new species, a list of the other copepod species collected, and a dichotomic key for the males of all species presently assigned to the genus.

Hepatozoon Miller, 1908 parasites in the Colubridae snakes Clelia clelia (Daudin, 1803) and Drymarchon corais (Boie, 1827) from the Eastern Amazonia

Based on the genetic, morphological, and morphometric data of blood gamonts, we identified Hepatozoon parasites in colubrid snakes sampled in the Eastern Amazon region. Hepatozoon trigeminum was detected in the mussurana snake Clelia clelia and exhibited wide and elongated gamonts (mean dimensions: 14.25±0.65 × 4.31±0.43 μm) with an evident parasitophorous vacuole. Hepatozoon odwyerae sp. nov. was described in the indigo snake Drymarchon corais, whose gamonts have elongated and thin bodies (mean dimensions: 13.41±0.79 × 3.72±0.35 μm) with one end more tapered than the other. Phylogenetic analyses, based on the amplification of a 441 bp fragment of the 18S rRNA gene, revealed that the novel sequences of Hepatozoon spp. from our study were closely related to hemogregarine lineages found in lizards and snakes from Brazil, forming a well-supported monophyletic clade with them. The present study provides the first species description of Hepatoozon in D. corais and a new record of a host species for C. clelia using the integrated taxonomic data. We also highlight the importance of further investigations into the diversity of Hepatozoon in snakes, a rich but underestimated group of parasites, especially in the Amazonian biome.

Dolioletta advena sp. nov., a New Species of Doliolid (Tunicata, Thaliacea) from the Adriatic Sea

The Adriatic Sea, as a part of Mediterranean, is one of the best investigated areas in the world regarding zooplankton. Nevertheless, in the last decade four new species of gelatinous zooplankton were described from the Adriatic Sea. Whether these species are newcomers or they were simply overlooked is still under investigations. Here we provide a description of a new species of Doliolida from the genus Dolioletta, Dolioletta advena sp. nov., found in the Adriatic Sea in August 2021, in a period of high sea temperatures and salinities, suggesting its thermal predilection. Its blastozooids dominated the studied doliolid blastozooid communities in the South Adriatic, except in the 50–100 m depth layer at a coastal Lokrum station. Blastozooids of D. advena sp. nov. possess unique morphological features which easily distinguish it from other doliolid species: the most prominent feature being the curved digestive tract where the intestine does not form a tight coil as in other Dolioletta species. The placement of this species in the genus Dolioletta is corroborated by COI phylogenetic analysis which showed that D. advena sp. nov. forms a well-supported monophyletic clade with Dolioletta gegenbauri (81% bootstrap support). In addition to D. advena sp. nov. COI sequence, we provide COI sequences of five doliolid and one pyrosomatid species, which will greatly improve the availability of thaliacean sequences for metabarcoding studies. The origin of D. advena sp. nov. is unknown, but given the fact that doliolids are well investigated in the Mediterranean Sea, it is likely that it arrived with sea currents either through the Suez Canal or the Strait of Gibraltar. Future investigations will confirm or reject this hypothesis.

Taxonomic study of polymorphic basidiomycetous fungi Sirobasidium and Sirotrema: Sirobasidium apiculatum sp. nov., Phaeotremella translucens comb. nov. and rediscovery of Sirobasidium japonicum in Japan.

Species in the genera Sirobasidium and Sirotrema (Tremellales, Tremellomycetes, Agaricomycotina, Basidiomycota) have been described based solely on the morphology of teleomorph, and many of them lack both isolates of anamorphic yeast state and nucleotide sequence data. Strains of Sirotrema translucens and Sirobasidium japonicum were established for the first time from basidiocarps collected in Japan. Also, an undescribed species in the genus Sirobasidium was isolated. Sirobasidium sp. was characterized by its apiculate epibasidia and 2-celled basidia divided by a longitudinal septum, which is a unique combination of characteristics in the genus. Although the phylogenetic placement of Sb. japonicum within the Tremellales was not resolved in our analysis, Sirobasidium sp. formed a well-supported monophyletic clade with Sb. magnum and Fibulobasidium spp., and Sirotrema translucens was located in the genus Phaeotremella. Mating experiments using single-basidiospore strains showed that Sb. japonicum produced basidia, epibasidia, and basidiospores on a nutrient-poor medium, and the life cycle was successfully completed in controlled conditions. In conclusion, we propose Sirobasidium apiculatum sp. nov. and Phaeotremella translucens comb. nov.

Plenodomus species infecting oilseed rape in Russia

The Phoma disease (Phoma stem canker, black leg, Phoma leaf spot) is one of the most harmful diseases of oilseed rape and other Brassicaceae in the world, particularly in Russia. The causal agents of this disease are Plenodomus biglobosus and Plenodomus lingam. Since 2005, a number subclades have been described within P. biglobosus and P. lingam (2 and 7, respectively). These subclades can be identified by multilocus sequence analysis. So far, biodiversity and geographic distribution of Plenodomus spp. infecting oilseed rape in Russia, have not been comprehensively analyzed. For this study, as many as 18 Plenodomus spp. isolates were obtained from the samples of stem canker and leaf spot of oilseed rape from four regions of Russia in 2004–2021. The aims of this study were to identify the isolates by phylogenetic analyses inferred from 3 gene sequences: nuclear ribosomal internal transcribed spacer, actin, and β-tubulin, and to assess pathogenicity of the isolates. The phylogenetic reconstructions revealed two well-supported monophyletic clades corresponding to the two species of the genus Plenodomus., P. lingam ‘brassicae’ and P. biglobosus ‘brassicae’.This paper provides robust phylogeny of the Plenodomus spp. clade, accompanied with the detailed description of morphological features of both species, and results of pathogenicity tests.

Comparative Plastome Analyses of Ephedra przewalskii and E. monosperma (Ephedraceae)

Ephedra species were erect, branching shrubs found in desert or arid regions worldwide as the source of ephedrine alkaloids. In this study, the complete chloroplast genome of Ephedra przewalskii and E. monosperma on the Qinghai-Tibet Plateau were sequenced, assembled, and annotated. Compared with the other four published Ephedra species, the chloroplast genomes of Ephedra species were highly conservative, with a quadripartite structure. The length of the chloroplast genome was 109,569 bp in E. przewalskii with 36.6% GC and 109,604 bp in E. monosperma with 36.6% GC. We detected 118 genes in both Ephedra species, including 73 PCGs, 37 tRNA genes, and eight rRNA genes. Among them, the ndh family genes were lost, which could be used to study the phylogeny and genetic diversity of the genus Ephedra, combined with multiple highly variable intergenic spacer (IGS) regions. Codon usage preference of Ephedra species was weak. The ratio of non-synonymous substitutions and synonymous substitutions was low, showing that the PCGs of Ephedra may be under the pressure of purifying selection. ML and BI analysis showed similar phylogenetic topologies. Ephedra species clustered together in a well-supported monophyletic clade. E. przewalskii and E. monosperma were not gathered in one clade, consistent with the classification system by Flora of China. This study reveals differences in the chloroplast genomes of Ephedra, providing valuable and abundant data for the phylogenetic analysis and species identification of Ephedra.

Molecular, morphological and chemical variation of the Usnea pectinata aggregate from Tanzania, São Tomé and Príncipe

AbstractThis study investigated the molecular, chemical and morphological variation in the Usnea pectinata aggregate using 42 specimens, 22 from Tanzania and 20 from São Tomé and Príncipe. A total of 31 sequences (13 ITS, 13 nuLSU and 5 RPB1) were generated. The results are presented in two phylogenies: first a three-markers ‘backbone’ phylogeny for the U. pectinata aggregate, where six distinct, strongly supported subclades indicate considerable genetic variation in the dataset; and second, an ITS phylogeny with 47 terminals along with a mapping of morphological and chemistry data. Several well-supported monophyletic clades were recovered in both phylogenies and these may well represent separate species in the complex referred to here as the U. pectinata aggregate. Three morphotypes characterized by axis pigmentation and four by branch shape were noted. Six chemotypes were observed.

The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK.

The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organization as Alpha. Originating in early autumn but discovered in December 2020, it spread rapidly and caused large waves of infections worldwide. The Alpha variant is notable for being defined by a long ancestral phylogenetic branch with an increased evolutionary rate, along which only two sequences have been sampled. Alpha genomes comprise a well-supported monophyletic clade within which the evolutionary rate is typical of SARS-CoV-2. The Alpha epidemic continued to grow despite the continued restrictions on social mixing across the UK and the imposition of new restrictions, in particular, the English national lockdown in November 2020. While these interventions succeeded in reducing the absolute number of cases, the impact of these non-pharmaceutical interventions was predominantly to drive the decline of the SARS-CoV-2 lineages that preceded Alpha. We investigate the only two sampled sequences that fall on the branch ancestral to Alpha. We find that one is likely to be a true intermediate sequence, providing information about the order of mutational events that led to Alpha. We explore alternate hypotheses that can explain how Alpha acquired a large number of mutations yet remained largely unobserved in a region of high genomic surveillance: an under-sampled geographical location, a non-human animal population, or a chronically infected individual. We conclude that the latter provides the best explanation of the observed behaviour and dynamics of the variant, although the individual need not be immunocompromised, as persistently infected immunocompetent hosts also display a higher within-host rate of evolution. Finally, we compare the ancestral branches and mutation profiles of other VOCs and find that Delta appears to be an outlier both in terms of the genomic locations of its defining mutations and a lack of the rapid evolutionary rate on its ancestral branch. As new variants, such as Omicron, continue to evolve (potentially through similar mechanisms), it remains important to investigate the origins of other variants to identify ways to potentially disrupt their evolution and emergence.

Resolving the phylogenetic relationship betweenParmotrema crinitumandParmotrema perlatumpopulations

AbstractThe widespread speciesParmotrema crinitum(Ach.) M. Choisy andParmotrema perlatum(Huds.) M. Choisy are mainly distinguished by their reproductive strategies. WhileP. crinitumpropagates by isidia,P. perlatumproduces soredia. In this study, we aim to evaluate the phylogenetic relationship between both species and to critically examine their species boundaries. To this purpose, 46 samples belonging toP. crinitumandP. perlatumwere used in our analysis, including 22 for which we studied the morphology and chemistry, before extracting their DNA. We used 35 sequences of the internal transcribed spacer region of nuclear ribosomal DNA (ITS) ofParmotrema perlatumfrom Europe and Africa (20 of which were newly generated), and 11 ofParmotrema crinitumfrom Europe, North America and North Africa (two newly generated). Additionally, 28 sequences of several species fromParmotremawere included in the ITS dataset. The ITS data matrix was analyzed using different approaches, such as traditional phylogeny (maximum likelihood and Bayesian analyses), genetic distances, automatic barcode gap discovery (ABGD) and the coalescent-based method poisson tree processes (PTP), in order to test congruence among results. Our results indicate that all samples referred toP. crinitumandP. perlatumnested in a well-supported monophyletic clade, but phylogenetic relationships among them remain unresolved. Delimitations inferred from PTP, ABGD and genetic distance analyses were comparable and suggested thatP. crinitumandP. perlatumbelong to the same lineage. Interestingly, two samples ofP. perlatumseparate in a different monophyletic clade, which is supported as a different lineage by all the analyses.

Molecular identification of helminth parasites of the Heterakidae and Ascarididae families of free-ranging chickens from selected rural communities of KwaZulu-Natal province of South Africa

Free-range chickens are predisposed to diverse parasitic infections during scavenging. Accurate identification of these parasites using morphological characters has been a challenge. Therefore, this study aimed to identify nematodes from the Heterakidae and Ascarididae family infecting free-ranging chickens from KwaZulu-Natal province of South Africa using a combination of morphological and molecular techniques. Forty-two free-ranging adult indigenous chickens were purchased from randomly selected households in Shongweni (n=12), Umzinto (n=10), Gingindlovu (n=10) and Ozwathini (n=10) rural villages and examined for nematodes of the Heterakidae and Ascarididae family. Collected specimen were identified morphologically and confirmed using mitochondrial and nuclear ribosomal markers. Results showed that Ascaridia galli was common, occurring at all sampling locations with an overall prevalence of 58.3%, while Heterakis gallinarum and H. beramporia occurred in three locations. Ascaridia galli had high prevalence in Shongweni (58.3%), followed by Gingindlovu (40%), Ozwathini (20%) and Umzinto (10%). Heterakis gallinarum infection was prevalent in three locations, with an overall prevalence of 90% in Gingindlovu, 80% in Ozwathini and 58.3 % in Shongweni. Heterakis gallinarum and H. beramporia were not recorded in Umzinto. Heterakis beramporia was recorded in low prevalence in Gingindlovu (20%), Ozwathini (10%) and Shongweni (8.3%) villages. Mixed infections of A. galli and H. gallinarum were recorded in Gingindlovu, Ozwathini and Shongweni, and H. gallinarum and H. beramporia in Gingindlovu. Molecular analysis confirmed identification of A. galli, and further showed close relationship with the GenBank-derived South African isolates. Haplotype network further confirmed their ancestral history, where all South African A. galli isolates formed five novel haplotypes corresponding with the structure of the phylogenetic tree. Similar structure was observed with Heterakis isolates, where analysis of the cox1 gene showed that H. gallinarum formed a well-supported monophyletic clade with other Heterakis species. The ITS marker identified three specimens from Gingindlovu, Ozwathini and Shongweni as H. beramporia, which formed strongly supported sister clade to H. indica and this is the first report confirming the occurrence of H. beramporia in South Africa.

Diaporthe species infecting sunflower (Helianthus annuus) in Russia, with the description of two new species

ABSTRACT Phomopsis stem canker is economically important sunflower disease that caused by multiple Diaporthe species. Recent investigations resulted in the resolution that there are at least 13 Diaporthe species that can infect sunflower. A comprehensive analysis of the biodiversity and geographic distribution of Diaporthe species in Russia, particularly those that infect sunflower, has not been undertaken. For this study, 16 Diaporthe isolates were obtained from samples of stem canker and visually healthy seeds of Helianthus annuus from northwestern, central European, southern European Russia, North Caucasus, and the Urals in 2016–2019. The aim of this study was to identify these Diaporthe isolates based on morphology and sequence analyses of the nuclear ribosomal internal transcribed spacer (ITS) region, partial calmodulin (cal), DNA-lyase (apn2), histone H3 (his3), translation elongation factor-1α gene (tef1), and ß-tubulin (tub2) genes. The phylogenetic reconstruction revealed well-supported monophyletic clades corresponding to six Diaporthe species: D. eres, D. gulyae, D. helianthi, and D. phaseolorum. Two new species were described: Diaporthe monetii sp. nov. and Diaporthe vangoghii sp. nov. The isolates of D. gulyae and D. phaseolorum collected represent the first records of these species in Russia.

The complete chloroplast genome of Ficus pumila, a functional plant in East Asia

Ficus pumila L. is a climbing fig commonly used as an ornamental plant. In this study, we sequenced and assembled the complete chloroplast genome of F. pumila. The complete chloroplast genome of F. pumila is 160,248 bp in length which includes a pair of inverted repeats (IRs) of 25,871 bp separated by a large single-copy (LSC) region of 88,405 bp and a small single-copy (SSC) region of 20,101 bp. The overall guanine–cytosine (GC) content of F. pumila cp genome is 35.98%, while the corresponding values of LSC, SSC, and IR sequences are 33.65, 29.05, and 42.65%, respectively. The phylogenetic tree was shown to be consistent with the traditional morphology-based taxonomy of Moraceae. Five plants from the genus Ficus formed a well-supported monophyletic clade with 100% bootstrap value, and F. pumila is closely related to F. hirta, F. carica, and F. racemosa, with a support value of 97%. The complete chloroplast of F. pumila contributes to the growing number of chloroplast genomes for phylogenetic and evolutionary studies in Moraceae.

Molecular and morphological analyses clarify species delimitation in section Costatae and reveal Betula buggsii sp. nov. (sect. Costatae, Betulaceae) in China.

Delineating closely related and morphologically similar species is difficult. Here, we integrate morphology, genetics, ploidy and geography to resolve species and subspecies boundaries in four trees of section Costatae (genus Betula): Betula ashburneri, B. costata, B. ermanii and B. utilis, as well as multiple subspecies and polyploid races. We genotyped 371 individuals (20-133 per species) from 51 populations at 15 microsatellite markers, as well as a subset of individuals, using restriction-site associated DNA sequencing and nuclear internal transcribed spacers. We determined the ploidy level of eight individuals using flow cytometry and characterized leaf variation for a subset of 109 individuals by morphometric analysis. Integration of multiple lines of evidence suggested a series of revisions to the taxonomy of section Costatae. Betula costata and B. ermanii were found to be valid. Molecular and leaf morphology analyses revealed little differentiation between diploid B. albosinensis and some samples of B. utilis ssp. utilis. By contrast, other B. utilis ssp. utilis samples and ssp. albosinensis formed a morphological continuum but differed based on genetics. Specifically, B. utilis ssp. albosinensis was divided into two groups with group I genetically similar to B. utilis ssp. utilis and group II, a distinct cluster, proposed as the new diploid species Betula buggsii sp. nov. Phylogenomic analysis based on 2285 620 single nucleotide polymorphisms identified a well-supported monophyletic clade of B. buggsii. Morphologically, B. buggsii is characterized by elongated lenticels and a distinct pattern of bark peeling and may be geographically restricted to the Qinling-Daba Mountains. Our integrated approach identifies six taxa within section Costatae: B. ashburneri, B. buggsii, B. costata, B. utilis ssp. utilis, B. utilis ssp. albosinensis and B. ermanii. Our research demonstrates the value of an integrative approach using morphological, geographical, genetic and ploidy-level data for species delineation.

Western Atlantic invasion of sun corals: incongruence between morphology and genetic delimitation among morphotypes in the genus Tubastraea

The scleractinian corals of the genus Tubastraea Lesson, 1830 are currently globally dispersed and even so still present a confused taxonomy due to the overlap of morphological characters between the species. In this study, we investigate Tubastraea species previously found in the western Atlantic, based on the molecular marker (ITS gene) and morphology, to determine the accuracy of their descriptions. We identified three morphotypes from Brazil which were genetically delimited into two species: Tubastraea coccinea (Morphotypes I and II) and Tubastraea sp. (Morphotype III). Although morphotype I has morphological patterns of Tubastraea aurea (Quoy & Gaimard, 1833) there was no molecular divergence to support the species differentiation and continue to be recognized as a morphological variant of T. coccinea. The third morphotype is both morphologically and genetically distinct from T. coccinea and is also not representative of the species Tubastraea tagusensis Wells, 1982 despite earlier descriptions describing T. tagusensis in Brazil. Morphotype III exhibited distinct morphological characteristics among the other morphotypes, mainly due to greater polyp projection. In addition, it has fusions between septa, a characteristic that differentiates it from T. tagusensis. Nevertheless, molecular phylogenetic analyses showed that Brazilian Tubastraea fell into two well-supported monophyletic clades, and samples collected in the United States overlapped in both clades. Florida samples exhibited fewer morphotypes and showed greater genetic diversity, presenting haplotypes in four other internal clades. This study highlights the need for an integrative approach to conduct a deeper species delimitation of Tubastraea, essential for managing bioinvasion events by sun corals.