Fourth Clade Research Articles

Genetic diversity and species prevalence revealed by Mitochondrial COI- DNA sequence of thrips population in cotton

Aim: To elucidate the population genetic diversity and species prevalence of thrips on cotton. Methodology: Thrips species were identified utilizing both mitochondrial cytochrome oxidase subunit I (COI) sequence analysis and morphology-based keys. Results: Thrips palmi Karny, Thrips hawaiiensis (Morgan), Ayyaria chaetophora Karny, Scirtothrips dorsalis Hood and Rhipiphorothrips cruentatus Hood identified from collected samples. The distribution analysis revealed that T. palmi stands out as the most abundant and prevalent species, constituting a substantial majority (74%) and occupying a pervasive presence across most cotton-growing locations. The phylogenetic analysis, relying on COI sequences, clearly categorized these five species into four distinct major clades. T. hawaiiensis and R. cruentatus were placed within the first clade, while the second clade featured Scirtothrips dorsalis. The third clade comprised the abundant T. palmi, and the fourth clade accommodated A. chaetophora. Interpretation: The study highlighted genetic diversity of five species of thrips, accentuating the emergence of T. palmi as a dominant pest in cotton, an observation not previously reported. Key words: Cotton thrips, Genetic diversity, MtCOI, Phylogenetic analysis, Species prevalence

Global phylogenomic diversity of Brucella abortus: spread of a dominant lineage

Brucella abortus is a globally important zoonotic pathogen largely found in cattle hosts and is typically transmitted to humans through contaminated dairy products or contact with diseased animals. Despite the long, shared history of cattle and humans, little is known about how trade in cattle has spread this pathogen throughout the world. Whole genome sequencing provides unparalleled resolution to investigate the global evolutionary history of a bacterium such as B. abortus by providing phylogenetic resolution that has been unobtainable using other methods. We report on large-scale genome sequencing and analysis of B. abortus collected globally from cattle and 16 other hosts from 52 countries. We used single nucleotide polymorphisms (SNPs) to identify genetic variation in 1,074 B. abortus genomes and using maximum parsimony generated a phylogeny that identified four major clades. Two of these clades, clade A (median date 972 CE; 95% HPD, 781–1142 CE) and clade B (median date 150 BCE; 95% HPD, 515 BCE–164 CE), were exceptionally diverse for this species and are exclusively of African origin where provenance is known. The third clade, clade C (median date 949 CE; 95% HPD, 766–1102 CE), had most isolates coming from a broad swath of the Middle East, Europe, and Asia, also had relatively high diversity. Finally, the fourth major clade, clade D (median date 1467 CE; 95% HPD, 1367–1553 CE) comprises the large majority of genomes in a dominant but relatively monomorphic group that predominantly infects cattle in Europe and the Americas. These data are consistent with an African origin for B. abortus and a subsequent spread to the Middle East, Europe, and Asia, probably through the movement of infected cattle. We hypothesize that European arrival to the Americas starting in the 15th century introduced B. abortus from Western Europe through the introduction of a few common cattle breeds infected with strains from clade D. These data provide the foundation of a comprehensive global phylogeny of this important zoonotic pathogen that should be an important resource in human and veterinary epidemiology.

A radiation of Psylliodes flea beetles on Brassicaceae is associated with the evolution of specific detoxification enzymes.

Flea beetles of the genus Psylliodes have evolved specialized interactions with plant species belonging to several distantly related families, mainly Brassicaceae, Solanaceae, and Fagaceae. This diverse host use indicates that Psylliodes flea beetles are able to cope with different chemical defense metabolites, including glucosinolates, the characteristic defense metabolites of Brassicaceae. Here we investigated the evolution of host use and the emergence of a glucosinolate-specific detoxification mechanism in Psylliodes flea beetles. In phylogenetic analyses, Psylliodes species clustered into four major clades, three of which contained mainly species specialized on either Brassicaceae, Solanaceae, or Fagaceae. Most members of the fourth clade have broader host use, including Brassicaceae and Poaceae as major host plant families. Ancestral state reconstructions suggest that Psylliodes flea beetles were initially associated with Brassicaceae and then either shifted to Solanaceae or Fagaceae, or expanded their host repertoire to Poaceae. Despite a putative ancestral association with Brassicaceae, we found evidence that the evolution of glucosinolate-specific detoxification enzymes coincides with the radiation of Psylliodes on Brassicaceae, suggesting that these are not required for using Brassicaceae as hosts but could improve the efficiency of host use by specialized Psylliodes species.

Complex norovirus transmission dynamics at hospital wards revealed by deep sequencing.

Detailed knowledge regarding norovirus transmission within hospitals is limited. We investigated a norovirus hospital outbreak affecting 65 patients at five different wards. PCR showed that 61 (94%) of the patients were infected with genotype II.4 strains. Successful Ion Torrent deep sequencing of GII.4 positive samples from 59 patients followed by phylogenetic analysis revealed that all sequences but two clustered into four distinct clades. Two of the clades belonged to GII.4 Sydney 2012, while the other two belonged to GII.4 New Orleans 2009. One of the clades was predominant at two wards, while two clades were predominant at one ward each. The fourth clade was found in sporadic cases at several wards. Thus, at four out of five wards, variants from one clade were predominant. At one ward, a single clade accounted for all cases, while at three wards the predominant clade accounted for 60%-71% of cases. Analysis of quasispecies variation identified positions that could further discriminate between variants from separate wards. The results illustrate a complex transmission of healthcare-associated norovirus infections and show that sequencing can be used to discriminate between related and unrelated cases.

Unexpected ubiquity of heart-shaped scale morphotype in Centroplasthelida (Haptista): Ancestral trait or multiple acquisitions?

Centrohelids (Haptista: Centroplasthelida) are axopodial protists with a remarkable diversity of external siliceous scale morphologies. It is believed that the last common ancestor of centrohelids had a double layer of siliceous scales composed of plate scales closer to a cell surface and spine scales radiating outwards. The characteristic morphotype of spine scales with a heart-shaped base was once believed to be a unique feature of the genus Choanocystis, as it was defined by Siemensma and Roijackers (1988). Further research revealed that this morphology is present in different and sometimes distantly related lineages: Ozanamiidae, Meringosphaeridae, and Marophryidae. Here, we report the fourth clade, Pterocystidae, which is also revealed to contain representatives having this phenotype. Cernunnos gen. nov. is erected here to place Cernunnos uralica sp. nov., Cernunnos arctica sp. nov., Cernunnos america sp. nov., and Cernunnos antarctica Tikhonenkov et Mylnikov, 2010, Gerasimova comb. nov. C. uralica was studied with scanning electron microscopy and SSU rDNA sequencing. Molecular phylogenetic analysis placed it into marine environmental clade P within Pterocystida. The ubiquity of spine scales with heart-shaped bases could be an example of parallel evolution, but taking into account the considerable similarity it is likely an ancestral trait, acquired from the last common ancestor of centrohelids.

The Temnocephalidae (Platyhelminthes): molecular data illuminate the evolution of an ancient group of symbiotic flatworms

The Temnocephalidae sensu Van Steenkiste et al., 2021 is a diverse group of rhabdocoel flatworms that are ectosymbiotic mostly on freshwater crustaceans. The family is found on all inhabited continents except for N. America (north of Mexico) and Africa. Here, we explore the systematic implications of a molecular phylogeny inferred from partial sequences of the nuclear 18S and 28S ribosomal RNA genes. In agreement with previous views based on morphology, the earliest diverging group within the family was exemplified by the genus Scutariella (subfamily Scutariellinae) followed by the genus Didymorchis (Didymorchinae). The genus Dactylocephala from Madagascar, previously thought to be in the Temnocephalinae, then diverged as sister to the remaining temnocephalids. A new subfamily, Dactylocephalinae, is proposed to contain this genus. Remaining subfamilies were, in turn, Diceratocephalinae, Actinodactylellinae and Temnocephalinae. Further subdivision was apparent within the Temnocephalinae. One well-supported clade included the genera Temnohaswellia (eastern Australia and New Zealand), Temnomonticellia (Tasmania) and Temnocephala (South America). The widespread genus Temnosewellia (= Ts.) was not supported as monophyletic. One clade of Temnosewellia sensu lato included numerous species known primarily from crayfish of the genus Euastacus, found in eastern and south-eastern Australia. Two other clades circumscribed the taxa Ts. minor and Ts. dendyi. Identities and membership of these two clades are clouded by frequent misidentifications, the reasons for which are discussed here. A fourth clade of Temnosewellia s.l. included Ts. rouxi and other taxa from northern Australia and Asia (ranging at least from Japan to India). The diversity of temnocephalids in Australia, and especially in Asia, is greatly underappreciated. Some general comments are made about geographic distribution of temnocephalids, but detailed biogeographic analysis requires broader sampling. http://zoobank.org/urn:lsid:zoobank.org:pub:C8E6F83E-5A8E-4756-AAB9-1E65BBA7D9DE

Species richness under a vertebral stripe: integrative taxonomy uncovers three additional species of Pholidobolus lizards (Sauria, Squamata, Gymnophthalmidae) from the north-western Colombian Andes.

The systematic study of biodiversity underlies appropriate inference in most other fields of biological research, yet it remains hampered by disagreements on both theoretical and empirical issues such as the species concept and the operational diagnosis of a species. Both become particularly challenging in those lineages where morphological traits are evolutionarily constrained by their adaptive value. For instance, cryptic organisms often conserve or converge in their external appearance, which hinders the recognition of species boundaries. An integrative approach has been adopted to study microgeographic variation in the leaf-litter lizard Pholidobolusvertebralis and test three predictions derived from the evolutionary species concept. Molecular data provided unambiguous evidence of divergence among the three recovered new clades and a common evolutionary history for each of them. The broadly sympatric clades were indeed diagnosable from externally visible traits, such as head scales, adult size, and sexually dimorphic ventral colouration. Also, they barely overlapped on the phenotypic space that summarised 39 morphometric and meristic traits. These clades are described as three species and an available name is suggested for a recovered fourth clade. The geographic distribution of the new and proximate species suggests a role for elevation on evolutionary divergence; it also raises interesting questions on the speciation pattern of an otherwise underestimated cryptic lineage.

Comparative Genomics of Lentilactobacillus parabuchneri isolated from dairy, KEM complex, Makgeolli, and Saliva Microbiomes

BackgroundLentilactobacillus parabuchneri is of particular concern in fermented food bioprocessing due to causing unwanted gas formation, cracks, and off-flavor in fermented dairy foods. This species is also a known culprit of histamine poisonings because of decarboxylating histidine to histamine in ripening cheese. Twenty-eight genomes in NCBI GenBank were evaluated via comparative analysis to determine genomic diversity within this species and identify potential avenues for reducing health associated risks and economic losses in the food industry caused by these organisms.ResultCore genome-based phylogenetic analysis revealed four distinct major clades. Eight dairy isolates, two strains from an unknown source, and a saliva isolate formed the first clade. Three out of five strains clustered on clade 2 belonged to dairy, and the remaining two strains were isolated from the makgeolli and Korean effective microorganisms (KEM) complex. The third and fourth clade members were isolated from Tete de Moine and dairy-associated niches, respectively. Whole genome analysis on twenty-eight genomes showed ~ 40% of all CDS were conserved across entire strains proposing a considerable diversity among L. parabuchneri strains analyzed. After assigning CDS to their corresponding function, ~ 79% of all strains were predicted to carry putative intact prophages, and ~ 43% of the strains harbored at least one plasmid; however, all the strains were predicted to encode genomic island, insertion sequence, and CRISPR-Cas system. A type I-E CRISPR-Cas subgroup was identified in all the strains, with the exception of DSM15352, which carried a type II-A CRISPR-Cas system. Twenty strains were predicted to encode histidine decarboxylase gene cluster that belongs to not only dairy but also saliva, KEM complex, and unknown source. No bacteriocin-encoding gene(s) or antibiotic resistome was found in any of the L. parabuchneri strains screened.ConclusionThe findings of the present work provide in-depth knowledge of the genomics of L. parabuchneri by comparing twenty-eight genomes available to date. For example, the hdc gene cluster was generally reported in cheese isolates; however, our findings in the current work indicated that it could also be encoded in those strains isolated from saliva, KEM complex, and unknown source. We think prophages are critical mobile elements of L. parabuchneri genomes that could pave the way for developing novel tools to reduce the occurrence of this unwanted species in the food industry.

Analyses of morphological and molecular characteristics of Telotylenchinae from Iran point at the validity of the genera Bitylenchus and Sauertylenchus.

To investigate relationships within the subfamily Telotylenchinae, more than 500 soil samples were collected from various natural and agricultural habitats in several localities of Iran. Individuals of seven known species, including Bitylenchus dubius, B. parvus, B. serranus, Sauertylenchus maximus, Tylenchorhynchus clarus, T. microconus and Trophurus ussuriensis, were recovered and characterized based on morphological and morphometric characters. Furthermore, phylogenetic relationships within representatives of the subfamily Telotylenchinae were explored using 13 sequences from the D2-D3 expansion regions of 28S ribosomal (r) DNA and 13 sequences for the partial 18S rDNA genes obtained in the present study. Analyses based on the relatively conserved 18S rDNA gene underlined the polyphyletic status of Tylenchorhynchus sensu lato, as three clusters representing Tylenchorhynchus, Bitylenchus and Sauertylenchus were well separated, and interspersed by, e.g., representatives of the Macrotrophurinae. Analysis of the more variable D2-D3 28S rDNA sequences suggested at least four clades within the subfamily Telotylenchinae: two clades dominated by Tylenchorhynchus species; a third clade harbouring representatives of Sauertylenchus, Bitylenchus, and Paratrophurus in distinct but unresolved branches;and a fourth clade dominated by Trophurus species. Although no molecular information was available from a number of genera that were originally gathered under Tylenchorhynchus sensu lato, we concluded that both Bitylenchus and Sauertylenchus should be seen as valid Telotylenchinae genera related to, but distinct from Tylenchorhynchus.

Pliocene-Pleistocene dispersal bring along low inter species diversity between Vimba species based on multilocus analysis

This study investigates phylogenetic and phylogeographic relationships of Vimba species using mitochondrial cytochrome b (cyt b) (1023 bp) and cytochrome c oxidase subunit I (COI) barcoding region (652 bp) genes. Ninety-one samples from 36 populations for the cyt b gene and 67 samples from 20 populations for the COI were analyzed. We identified 29 haplotypes and calculated overall haplotype diversity as Hd: 0.907 ± 0.015 for cyt b. We also identified 13 COI haplotypes and calculated overall haplotype diversity as 0.826 ± 0.026 for this marker. The phylogenetic analysis of Vimba species reveals the presence of four clades, based on concatenated cyt b and COI sequences. The first and second clade consist of Vimba vimba Western lineage, and Vimba vimba Caspian lineage, while the third and fourth clade consist of Vimba mirabilis and Vimba melanops. Based on haplotype network analyses and phylogeographic inferences, the Vimba genus is monophyletic, and its species dispersed in the Pleistocene era.

A dated molecular phylogeny and biogeographical analysis reveals the evolutionary history of the trans-pacifically disjunct tropical tree genus Ormosia (Fabaceae)

The papilionoid legume genus Ormosia (Fabaceae) comprises about 150 species of trees and exhibits a striking disjunct geographical distribution between the New World- and Asian and Australasian wet tropics and subtropics. Modern classifications of Ormosia are not grounded on a well-substantiated phylogenetic hypothesis and have been limited to just portions of the geographical range of the genus. The lack of an evolutionarily-based foundation for systematic studies has hindered taxonomic work on the genus and prevented the testing of biogeographical hypotheses related to the origin of the Old World/New World disjunction and the individual dispersal histories within both areas. Here, we present the most comprehensively sampled molecular phylogeny of Ormosia to date, based on analysis of both nuclear (ITS) and plastid (matK and trnL–F) DNA sequences from 82 species of the genus. Phylogenetically-based divergence times and ancestral range estimations are employed to test hypotheses related to the biogeographical history of the genus. We find strong support for the monophyly of Ormosia and the grouping of all sampled Asian species of the genus into two comparably sized clades, one of which is sister to another large clade containing all sampled New World species. Within the New World clade, additional resolution supports the grouping of most species into three mutually exclusive subordinate clades. The remaining New World species form a fourth well-supported clade in the analyses of plastid sequences, but that result is contradicted by the analysis of ITS. With few exceptions the supported clades have not been previously recognized as taxonomic groups. The biogeographical analysis suggests that Ormosia originated in continental Asia and dispersed to the New World in the Oligocene or early Miocene via long-distance trans-oceanic dispersal. We reject the hypothesis that the inter-hemispheric disjunction in Ormosia resulted from fragmentation of a more continuous “Boreotropical” distribution since the dispersal post-dates Eocene climatic maxima. Both of the Old World clades appear to have originated in mainland Asia and subsequently dispersed into the Malay Archipelago and beyond, at least two lineages dispersing across Wallace’s Line as far as the Solomon Islands and northeastern Australia. In the New World, the major clades all originated in Amazonia. Dispersal from Amazonia into peripheral areas in Central America, the Caribbean, and Extra-Amazonian Brazil occurred multiple times over varying time scales, the earliest beginning in the late Miocene. In a few cases, these dispersals were followed by local diversification, but not by reverse migration back to Amazonia. Within each of the two main areas of distribution, multiple modest bouts of oceanic dispersal were required to achieve the modern distributions.

Asian Admixture in European Echinococcus multilocularis Populations: New Data From Poland Comparing EmsB Microsatellite Analyses and Mitochondrial Sequencing.

The cestode Echinococcus multilocularis is the causative agent of a severe zoonotic disease: alveolar echinococcosis (AE). The parasite is distributed over a vast area in northern Eurasia and North America, but the impact of AE on human health is highly uneven between different regions. One hypothetical reason for this difference in virulence may be the genetic structure of E. multilocularis which—based on mitochondrial sequences and EmsB microsatellite profiles—forms four distinct clades. These clades correspond approximately to their continents of origin: Asia, Europe, and North America, with a fourth clade apparently restricted to Mongolia and neighboring regions, even though this clade has not yet been described by EmsB genotyping. However, there are various records of genetic variants from the “wrong” region, e.g., “European” haplotypes in Western Canada, which may be the result of introduction or natural migration of host animals. One such example, prompting this study, is the recent record of an “Asian” mitochondrial haplotype in worms from foxes in Poland. At the time, this could not be confirmed by EmsB microsatellite analysis, a method that has proven to possess greater discriminatory power with the E. multilocularis nuclear genome than sequencing of mitochondrial markers. Therefore, worms collected from foxes in Poland were examined both by EmsB analysis and sequencing of the full mitochondrial cox1 gene in order to allocate the samples to the European or Asian cluster. Based on EmsB analyses of 349 worms from 97 Polish red foxes, 92% of the worms clearly showed “European-type” EmsB profiles, but 27 worms (8%) from seven foxes showed profiles that clustered with samples of Asian origin. According to cox1 sequences, a total of 18 worms from 8 foxes belonged to the Asian cluster of haplotypes. The two methods did not fully agree: only 13 worms from three foxes belonged to Asian clusters by both EmsB and cox1, whereas 18 worms from nine foxes belonged to different clusters, according to each marker. Cross-fertilization between worms of Asian origin and those from the European Polish population may explain these conflicting results. The presence of clearly Asian elements in the Polish E. multilocularis population could be the result of introduction of E. multilocularis with host animals (e.g., domestic dogs), or the migration of foxes. In the absence of genetic data from eastern European countries, especially those bordering Poland, it cannot be concluded whether this Asian admixture is typical for a larger area toward central/eastern Europe, or the Polish parasite population is the western extreme of a gradient where both European and Asian elements mingle. Further studies are needed on this subject, preferably using both mitochondrial sequencing and EmsB microsatellite analysis.

The genome of a Bacteroidetes inhabitant of the human gut encodes a structurally distinct enoyl-acyl carrier protein reductase (FabI)

Enoyl-acyl carrier protein reductase (FabI) catalyzes a rate-controlling step in bacterial fatty-acid synthesis and is a target for antibacterial drug development. A phylogenetic analysis shows that FabIs fall into four divergent clades. Members of clades 1-3 have been structurally and biochemically characterized, but the fourth clade, found in members of phylum Bacteroidetes, is uncharacterized. Here, we identified the unique structure and conformational changes that distinguish clade 4 FabIs. Alistipes finegoldii is a prototypical Bacteroidetes inhabitant of the gut microbiome. We found that A. finegoldii FabI (AfFabI) displays cooperative kinetics and uses NADH as a cofactor, and its crystal structure at 1.72 Å resolution showed that it adopts a Rossmann fold as do other characterized FabIs. It also disclosed a carboxyl-terminal extension that forms a helix-helix interaction that links the protomers as a unique feature of AfFabI. An AfFabI·NADH crystal structure at 1.86 Å resolution revealed that this feature undergoes a large conformational change to participate in covering the NADH-binding pocket and establishing the water channels that connect the active site to the central water well. Progressive deletion of these interactions led to catalytically compromised proteins that fail to bind NADH. This unique conformational change imparted a distinct shape to the AfFabI active site that renders it refractory to a FabI drug that targets clade 1 and 3 pathogens. We conclude that the clade 4 FabI, found in the Bacteroidetes inhabitants of the gut, have several structural features and conformational transitions that distinguish them from other bacterial FabIs.

Living on the edge: comparative phylogeography and phylogenetics of Oreohelix land snails at their range edge in Western Canada

BackgroundThe biodiversity and distributions of terrestrial snails at local and regional scales are influenced by their low vagility and microhabitat specificity. The accessibility of large-bodied species and their characteristically high levels of genetic polymorphism make them excellent ecological and evolutionary models for studies on the phylogeography, phylogenetics, and conservation of organisms in fragmented populations. This study aims to elucidate the biodiversity, systematics, and distributions of genetic lineages within the genus Oreohelix at the northern and western periphery of their range.ResultsWe found four mitochondrial clades, three of which are putative subspecies of Oreohelix subrudis. One clade was geographically widespread, occurring within numerous sites in Cypress Hills and in the Rocky Mountains, a second was geographically restricted to the Rocky Mountains in Alberta, and a third was restricted to the Cypress Hills region. A fourth clade was the small-bodied species, O. cooperi. ITS2 sequence and screening data revealed three genetic clusters, of which one was O. cooperi. Cluster 1 contained most individuals in COI clade X and some from clade B and cluster 2 was predominantly made up of individuals from COI clades B and B′ and a few from clade X. ITS2 alleles were shared in a narrow contact zone between two COI clades, suggestive of hybridization between the two.ConclusionsA sky island known as Cypress Hills, in southeastern Alberta, Canada, is a biodiversity hotspot for terrestrial land snails in the genus Oreohelix. The observed phylogeographic patterns likely reflect reproductive isolation during the Last Glacial Maximum, followed by secondary contact due to passive, long-range dispersal resulting from low vagility, local adaptation, and complex glacial history.

Introduction The 41–43 species of birds-of-paradise (Paradisaeidae) (Beehler & Pratt 2016; Gill & Donsker 2019) are renowned for their exquisite beauty and plumage, and their diversity of extraordinary courtship displays (Gilliard 1969; Cooper & Forshaw 1977; Coates 1990; Frith & Frith 2009; Laman & Scholes 2012; Ligon et al. 2018). Males of the majority of birds-of-paradise (35–37 species) are presumed

Introduction The 41–43 species of birds-of-paradise (Paradisaeidae) (Beehler & Pratt 2016; Gill & Donsker 2019) are renowned for their exquisite beauty and plumage, and their diversity of extraordinary courtship displays (Gilliard 1969; Cooper & Forshaw 1977; Coates 1990; Frith & Frith 2009; Laman & Scholes 2012; Ligon et al. 2018). Males of the majority of birds-of-paradise (35–37 species) are presumed

Taxonomy and systematics of Hyaloscyphaceae and Arachnopezizaceae.

The circumscription and composition of the Hyaloscyphaceae are controversial and based on poorly sampled or unsupported phylogenies. The generic limits within the hyaloscyphoid fungi are also very poorly understood. To address this issue, a robust five-gene Bayesian phylogeny (LSU, RPB1, RPB2, TEF-1α, mtSSU; 5521 bp) with a focus on the core group of Hyaloscyphaceae and Arachnopezizaceae is presented here, with comparative morphological and histochemical characters. A wide representative sampling of Hyaloscypha supports it as monophyletic and shows H. aureliella (subgenus Eupezizella) to be a strongly supported sister taxon. Reinforced by distinguishing morphological features, Eupezizella is here recognised as a separate genus, comprising E. aureliella, E. britannica, E. roseoguttata and E. nipponica (previously treated in Hyaloscypha). In a sister group to the Hyaloscypha-Eupezizella clade a new genus, Mimicoscypha, is created for three seldom collected and poorly understood species, M. lacrimiformis, M. mimica (nom. nov.) and M. paludosa, previously treated in Phialina, Hyaloscypha and Eriopezia, respectively. The Arachnopezizaceae is polyphyletic, because Arachnoscypha forms a monophyletic group with Polydesmia pruinosa, distant to Arachnopeziza and Eriopezia; in addition, Arachnopeziza variepilosa represents an early diverging lineage in Hyaloscyphaceae s.str. The hyphae originating from the base of the apothecia in Arachnoscypha are considered anchoring hyphae (vs a subiculum) and Arachnoscypha is excluded from Arachnopezizaceae. A new genus, Resinoscypha, is established to accommodate Arachnopeziza variepilosa and A. monoseptata, originally described in Protounguicularia. Mimicoscypha and Resinoscypha are distinguished among hyaloscyphoid fungi by long tapering multiseptate hairs that are not dextrinoid or glassy, in combination with ectal excipulum cells with deep amyloid nodules. Unique to Resinoscypha is cyanophilous resinous content in the hairs concentrated at the apex and septa. Small intensely amyloid nodules in the hairs are furthermore characteristic for Resinoscypha and Eupezizella. To elucidate species limits and diversity in Arachnopeziza, mainly from Northern Europe, we applied genealogical concordance phylogenetic species recognition (GCPSR) using analyses of individual datasets (ITS, LSU, RPB1, RPB2, TEF-1α) and comparative morphology. Eight species were identified as highly supported and reciprocally monophyletic. Four of these are newly discovered species, with two formally described here, viz. A. estonica and A. ptilidiophila. In addition, Belonium sphagnisedum, which completely lacks prominent hairs, is here combined in Arachnopeziza, widening the concept of the genus. Numerous publicly available sequences named A. aurata represent A. delicatula and the confusion between these two species is clarified. An additional four singletons are considered to be distinct species, because they were genetically divergent from their sisters. A highly supported five-gene phylogeny of Arachnopezizaceae identified four major clades in Arachnopeziza, with Eriopezia as a sister group. Two of the clades include species with a strong connection to bryophytes; the third clade includes species growing on bulky woody substrates and with pigmented exudates on the hairs; and the fourth clade species with hyaline exudates growing on both bryophytes and hardwood. A morphological account is given of the composition of Hyaloscyphaceae and Arachnopezizaceae, including new observations on vital and histochemical characters. Citation: Kosonen T, Huhtinen S, Hansen K. 2021. Taxonomy and systematics of Hyaloscyphaceae and Arachnopezizaceae. Persoonia 46: 26-62. https://doi.org/10.3767/persoonia.2021.46.02.

Evolutionary history of Spalacidae inferred from fossil occurrences and molecular phylogeny

AbstractThe Spalacidae is a family of strictly subterranean rodents with a long evolutionary history. It is unclear how ecological changes have influenced the evolutionary history of these mammals, and the phylogenetic relationship of the subfamilies within Spalacidae is controversial.Through compiling fossil records, reconstructing molecular phylogeny from molecular data, determining the date of divergence, and analysing their geographical evolution based on molecular data and fossil taxa, we explore the origin and evolutionary process of Spalacidae in detail. Diversification within Spalacidae dates to the Late Oligocene, approximately 25 million years ago, based on molecular data.This family originated in South and East Asia in the Late Oligocene, and then split into four clades. The first clade includes Rhizomyinae, which was highly diversified in South Asia in the Early‐to‐Middle Miocene. Then Rhizomyinae from Asia migrated to northern Africa in multiple waves through the Afro‐Eurasian land bridge. Its range largely contracted in the Late Miocene, notably in Central Asia. The second clade includes the extinct Tachyoryctoidinae, which was confined to East and Central Asia, and survived from the Late Oligocene to the Late Miocene. The third clade includes Spalacinae, which have remained around the Mediterranean region since the Late Oligocene with slight trend of northward expansion. The fourth clade is Myospalacinae. Ancient genera of this subfamily in East Asia dispersed eastward during the Late Miocene and reached northern China and south‐east Russia.The general distribution pattern of Spalacidae has persisted since the Late Miocene. Extinction of Tachyoryctoidinae and clear range contraction of Rhizomyinae in Central and East Asia are likely to have resulted from increased aridification, while the slight northward expansion of Myospalacinae and Spalacinae since the Quaternary was probably a response to a similar northward expansion of suitable vegetation for these animals.

Tracing the Lineage of Two Traits Associated with the Coat Protein of the Tombusviridae: Silencing Suppression and HR Elicitation in Nicotiana Species.

In this paper we have characterized the lineage of two traits associated with the coat proteins (CPs) of the tombusvirids: Silencing suppression and HR elicitation in Nicotiana species. We considered that the tombusvirid CPs might collectively be considered an effector, with the CP of each CP-encoding species comprising a structural variant within the family. Thus, a phylogenetic analysis of the CP could provide insight into the evolution of a pathogen effector. The phylogeny of the CP of tombusvirids indicated that CP representatives of the family could be divided into four clades. In two separate clades the CP triggered a hypersensitive response (HR) in Nicotiana species of section Alatae but did not have silencing suppressor activity. In a third clade the CP had a silencing suppressor activity but did not have the capacity to trigger HR in Nicotiana species. In the fourth clade, the CP did not carry either function. Our analysis illustrates how structural changes that likely occurred in the CP effector of progenitors of the current genera led to either silencing suppressor activity, HR elicitation in select Nicotiana species, or neither trait.

Morphological and molecular data for species of Lecithaster Lühe, 1901 and Hysterolecithoides Yamaguti, 1934 (Digenea: Lecithasteridae) from fish of East Asia and phylogenetic relationships within the Hemiuroidea Looss, 1899.

Four representatives of the genus Lecithaster and one representative of the genus Hysterolecithoides were found during investigation of the trematode fauna of fish species in Vietnamese, Japanese and eastern coastal waters of the Russian Far East. Based on morphometric data, adult trematodes from Vietnamese Strongylura strongylura and Russian Acanthogobius flavimanus were identified as Lecithaster confusus, trematodes from Vietnamese Hemirhamphus marginatus as L. sayori and from osmerid fishes as L. salmonis. Further, a single specimen of Lecithaster sp. and representatives of Hysterolecithoides epinepheli were found in Vietnamese Siganus fuscescens. Morphological and molecular data, including 18S ribosomal DNA (rDNA) V4 fragment, 28S rDNA D1-D3 fragment, internal transcribed spacers (ITS) and a mitochondrial COI gene fragment were analysed for Lecithaster spp. The results revealed that L. sayori and L. salmonis are not synonyms of L. stellatus and L. gibbosus, respectively, but that Hysterolecithoides frontilatus and H. guangdongensis are junior synonyms of H. epinepheli. The 28S-rDNA-based phylogenetic tree of Hemiuroidea showed a distinct position for the genus Lecithaster with internal differentiation into three subclades, including L. confusus, L. sayori and Lecithaster sp. within the first subclade, L. mugilis and L. sudzuhensis within the second subclade and L. salmonis and L. gibbosus within the third subclade. Bayesian phylogenetic reconstructions of Hemiuroidea showed four clades for members of Hemiuridae and Lecithasteridae. The first clade consisted of Hemiuridae representatives and the second clade represented the genus Lecithaster. The third clade included genera Aponurus and Lecithophyllum (Lecithasteridae) and the fourth clade combined members of lecithasterid Quadrifoliovariinae and Hysterolecithinae and hemiurid Opisthadeninae and Bunocotylidae with high statistical support.

Molecular Evidences of a Hidden Complex Scenario in Leporinus cf. friderici.

The megadiversity of the neotropical ichthyofauna has been associated to recent diversification processes, reflecting in subtle or lacking morphological differentiation between species, challenging the classical taxonomic identification. Leporinus friderici occurs in several river basins of South America, and its nominal taxonomic validity has been questioned. Its wide distribution within the Brazilian Shield suggests that this species could be genetically structured among the hydrographic basins, despite a sharp morphological similarity. In this study, we performed phylogenetic analyses, based on three nuclear (recombination activating gene 1, RAG1, recombination activating gene 2, RAG2, and myosin heavy chain 6 cardiac muscle alpha gene, Myh6) and two mitochondrial (COI and Cytochrome b, Cytb) markers, in specimens morphologically similar to L. friderici and related species from different hydrographic basins in South America. Our phylogenetic tree identified four well-supported clades, which point out to the existence of taxonomic inconsistencies within this fish group. A clade named L. cf. friderici sensu stricto included eight Molecular Operational Taxonomic Units recently diversified in the Brazilian Shield basins. These results were also confirmed by a single-gene species delimitation analysis. It is suggested that this clade includes a species complex, characterizing taxonomic uncertainties. Another clade recovered only L. friderici from the Suriname rivers, validating this nominal species in its type locality. A third no-named clade, characterized by deeper species divergence, recovered five different nominal species interleaved with other undescribed forms previously also recognized as L. cf. friderici, indicating taxonomic errors. The fourth clade only included L. taeniatus. Our results showed a complex scenario involving the morphotype L. cf. friderici and allowed us to address aspects related to evolutionary diversification of this fish group and historical processes involved with, highlighting the importance of revealing hidden biodiversity for the taxonomy and conservationist action plans of these fish.