Update on the Phylodynamics of SADS-CoV

Coronaviruses are known to be harmful and heterogeneous viruses, able to infect a large number of hosts. Among them, SADS-CoV (Swine Acute Diarrhea Syndrome Coronavirus), also known as PEAV (Porcine Enteric Alphacoronavirus), or SeA-CoV (Swine Enteric Alphacoronavirus), is the most recent Alphacoronavirus discovered, and caused several outbreaks reported in Chinese swine herds between late 2016 and 2019. We performed an upgraded phylodinamic reconstruction of SADS-CoV based on all whole genomes available on 21 June 2021. Results showed a very close relationship between SADS-CoV and HKU2-like CoV, which may represent the evolutionary intermediate step towards the present SADS-CoV. The direct progenitor of SADS-CoV is so far unknown and, although it is well known that horseshoe bats are reservoirs for Rhinolophus bat coronavirus HKU2-like (HKU2-like CoVs), the transmission path from bats to pigs is still unclear. The discrepancies in the phylogenetic position of rodent CoV, when different molecular markers were considered, corroborate the recombination hypothesis, suggesting that wild rats, which are frequent in farms, may have played a key role. The failure of the attempt at molecular dating, due to the lack of a clock signal, also corroborates the occurrence of a recombination event hypothesis. Zoonotic infections originating in wildlife can easily become a significant threat for human health. In such a context, due to the high recombination and cross-species capabilities of Coronavirus, SADS-CoV represents a possible high-risk pathogen for humans which needs a constant molecular monitoring.

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Resolving the Lourinia armata (Claus, 1866) complex with remarks on the monophyletic status of Louriniidae, Monard 1927 (Copepoda: Harpacticoida)

Zootaxa ◽

10.11646/zootaxa.5051.1.15 ◽

2021 ◽

Vol 5051 (1) ◽

pp. 346-386

Author(s):

SÜPHAN KARAYTUĞ ◽

SERDAR SAK ◽

ALP ALPER ◽

SERDAR SÖNMEZ

Keyword(s):

Comparative Evaluation ◽

Species Complex ◽

Detailed Examination ◽

The Other ◽

Phylogenetic Position ◽

Nicobar Island ◽

Other Hand ◽

The Family ◽

Close Relationship ◽

Almost All

An attempt was made to test if Lourinia armata (Claus, 1866)—as it is currently diagnosed—represents a species complex. Detailed examination and comparisons of several specimens collected from different localities suggest that L. armata indeed represents a complex of four closely related morphospecies that can be differentiated from one another by only detailed observations. One of the four species is identified as Lourinia aff. armata and the other three species are described as new to science and named as Lourinia wellsi sp. nov., L. gocmeni sp. nov., and L. aldabraensis sp. nov. Detailed review of previous species records indicates that the genus Lourinia Wilson, 1924 is distributed worldwide. Ceyloniella nicobarica Sewell, 1940, originally described from Nicobar Island and previously considered a junior subjective synonym of L. armata is reinstated as Lourinia nicobarica (Sewell, 1940) comb. nov. on the basis of the unique paddle-shaped caudal ramus seta V. It is postulated that almost all of these records are unreliable in terms of representing true Lourinia aff. armata described herein. On the other hand, the comparative evaluation of the illustrations and descriptions in the published literature indicates the presence of several new species waiting to be discovered in the genus Lourinia. It has been determined that, according to updated modern keys, the recent inclusion of the monotypic genus Archeolourinia Corgosinho & Schizas, 2013 in the Louriniidae is not justified since Archeolourinia shermani Corgosinho & Schizas, 2013 does not belong to this family but should be assigned to the Canthocamptidae. On the other hand, it has been argued that the exact phylogenetic position of the Louriniidae still remains problematic since none of the diagnostic characters supports the monophyly of the family within the Oligoarthra. It has also been argued that the close relationship between Louriniidae and Canthocamptidae is supported since both families share the homologous sexual dimorphism (apophysis) on P3 endopod. The most important characteristic that can possibly be used to define Louriniidae is the reduction of maxilliped.

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Morphology of a unique ophidiid, Hypopleuron caninum Radcliffe 1913 (Ophidiiformes, Ophidiidae, Neobythitinae), suggesting a close relationship with the family Carapidae

Zootaxa ◽

10.11646/zootaxa.4521.4.2 ◽

2018 ◽

Vol 4521 (4) ◽

pp. 499

Author(s):

SHINPEI OHASHI

Keyword(s):

Phylogenetic Position ◽

Dorsal Fin ◽

The Family ◽

Close Relationship ◽

Pelvic Fin

Osteological and myological characters of the ophidiid Hypopleuron caninum are described here in detail. In addition to well-known characters of Ophidiidae (e.g., anal-fin origin well posterior to dorsal-fin origin; barbel-like pelvic fin; many scales), many unique or rare conditions were also recognized, including predorsal bone and maxilla condition, and canine teeth on the premaxilla, which were suggestive of a relationship with Carapidae. Furthermore, the predorsal bone appear to be homologous with the vexillar support, a carapid synapomorphy. Although several characters differ from carapid counterparts (e.g., more anterior anal-fin origin and scales absent in Carapidae), some intermediate conditions between Ophidiidae and Carapidae are apparent in Hypopleuron caninum, which may therefore occupy an intermediate phylogenetic position between the two families. A unique morphology of small second infraorbital bone is recognized in all ophidiiform species observed in this study, and it may be a synapomorphic character of the order Ophidiiformes.

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Two new species of Roccellaceae (Ascomycota: Arthoniales) from Brazil, with the description of the new genus Sergipea

The Lichenologist ◽

10.1017/s0024282913000303 ◽

2013 ◽

Vol 45 (5) ◽

pp. 627-634 ◽

Cited By ~ 12

Author(s):

André APTROOT ◽

Damien ERTZ ◽

Edvaneide Leandro de LIMA ◽

Katia Almeida de JESUS ◽

Leonor Costa MAIA ◽

...

Keyword(s):

New Species ◽

New Genus ◽

Phylogenetic Position ◽

Generic Type ◽

Bright Orange ◽

Two New Species ◽

Basal Branch ◽

Close Relationship ◽

Relationship Of ◽

A New Species

AbstractThe new lichen genus Sergipea M. Cáceres, Ertz & Aptroot is described in the Roccellaceae, based on the new species Sergipea aurata M. Cáceres, Ertz & Aptroot from NE Brazil. The species was found in a remnant of Atlantic transition forest in Sergipe. It is similar in many respects to species of the genus Enterographa, but it is characterized by bright orange stromata, due to the presence of an anthraquinone, and a thallus with a somewhat byssoid hypothallus. Phylogenetically it is close to the genera Dichosporidium and Erythrodecton. The phylogenetic position of the generic type of Dichosporidium confirms the close relationship of the genus to Erythrodecton in the basal branch of the Roccellaceae. A new species of Enterographa is also described from NE Brazil. Enterographa rotundata E. L. Lima, M. Cáceres & Aptroot has solitary, round apothecia, which is unusual in this genus with mainly elongated apothecia or punctiform apothecia arranged in lines. It was found in Caatinga forest in Pernambuco.

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Phylogeny and morphology of genus Nephrocytium (Sphaeropleales, Chlorophyceae, Chlorophyta) from China

Phytotaxa ◽

10.11646/phytotaxa.319.1.4 ◽

2017 ◽

Vol 319 (1) ◽

pp. 84 ◽

Cited By ~ 2

Author(s):

XUDONG LIU ◽

HUAN ZHU ◽

BENWEN LIU ◽

GUOXIANG LIU ◽

ZHENGYU HU

Keyword(s):

Phylogenetic Analyses ◽

Light And Electron Microscopy ◽

Taxonomic Position ◽

Phylogenetic Position ◽

Phytoplankton Communities ◽

Close Phylogenetic Relationship ◽

The Family ◽

Close Relationship ◽

Molecular Phylogenetic

The genus Nephrocytium Nägeli is a common member of phytoplankton communities that has a distinctive morphology. Its taxonomic position is traditionally considered to be within the family Oocystaceae (Trebouxiophyceae). However, research on its ultrastructure is rare, and the phylogenetic position has not yet been determined. In this study, two strains of Nephrocytium, N. agardhianum Nägeli and N. limneticum (G.M.Smith) G.M.Smith, were identified and successfully cultured in the laboratory. Morphological inspection by light and electron microscopy and molecular phylogenetic analyses were performed to explore the taxonomic position. Ultrastructure implied a likely irregular network of dense and fine ribs on the surface of the daughter cell wall that resembled that of the genus Chromochloris Kol & Chodat (Chromochloridaceae). Phylogenetic analyses revealed that Nephrocytium formed an independent lineage in the order Sphaeropleales (Chlorophyceae) with high support values and a close phylogenetic relationship with Chromochloris. Based on combined morphological, ultrastructural and phylogenetic data, we propose a re-classification of Nephrocytium into Sphaeropleales, sharing a close relationship with Chromochloris.

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The genetic analysis of new Polish strains of European brown hare syndrome virus

Polish Journal of Veterinary Sciences ◽

10.2478/pjvs-2014-0048 ◽

2014 ◽

Vol 17 (2) ◽

pp. 353-355

Author(s):

E. Kwit ◽

M. Chrobocińska ◽

Z. Grądzki ◽

Ł. Jarosz ◽

B. Majer-Dziedzic ◽

...

Keyword(s):

Genetic Analysis ◽

Phylogenetic Position ◽

Brown Hare ◽

Gene Encoding ◽

European Brown Hare ◽

Close Relationship ◽

Provinces Of Poland ◽

Pcr Method ◽

European Brown Hare Syndrome ◽

Hare Population

Abstract In this paper we describe recently occurring outbreaks of European brown hare syndrome (EBHS) in a captive hare population. The aim of our study was to evaluate the phylogenetic position of detected Polish strains compared to other European strains of EBHSV. Investigations were undertaken in hares from different provinces of Poland. Liver or spleen samples were tested for viral RNA using the RT-nested PCR method and the products were subsequently sequenced. The genetic analysis was based on the fragment of gene encoding viral capsid protein; it revealed a high homology and close relationship between Polish and European EBHSV strains isolated between 2001 and 2011

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Whole Genome Shotgun Phylogenomics Resolves the Pattern and Timing of Swallowtail Butterfly Evolution

Systematic Biology ◽

10.1093/sysbio/syz030 ◽

2019 ◽

Vol 69 (1) ◽

pp. 38-60 ◽

Cited By ~ 15

Author(s):

Rémi Allio ◽

Céline Scornavacca ◽

Benoit Nabholz ◽

Anne-Laure Clamens ◽

Felix AH Sperling ◽

...

Keyword(s):

Missing Data ◽

Shotgun Sequencing ◽

Whole Genome Shotgun ◽

Amino Acid Sequences ◽

Molecular Dating ◽

Whole Genome ◽

Gene Trees ◽

Data Set ◽

Whole Genomes ◽

Bayesian Mixture Models

Abstract Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recently, it has become possible to sequence the entire genomes of numerous nonbiological models in parallel at reasonable cost, particularly with shotgun sequencing. Here, we identify orthologous coding sequences from whole-genome shotgun sequences, which we then use to investigate the relevance and power of phylogenomic relationship inference and time-calibrated tree estimation. We study an iconic group of butterflies—swallowtails of the family Papilionidae—that has remained phylogenetically unresolved, with continued debate about the timing of their diversification. Low-coverage whole genomes were obtained using Illumina shotgun sequencing for all genera. Genome assembly coupled to BLAST-based orthology searches allowed extraction of 6621 orthologous protein-coding genes for 45 Papilionidae species and 16 outgroup species (with 32% missing data after cleaning phases). Supermatrix phylogenomic analyses were performed with both maximum-likelihood (IQ-TREE) and Bayesian mixture models (PhyloBayes) for amino acid sequences, which produced a fully resolved phylogeny providing new insights into controversial relationships. Species tree reconstruction from gene trees was performed with ASTRAL and SuperTriplets and recovered the same phylogeny. We estimated gene site concordant factors to complement traditional node-support measures, which strengthens the robustness of inferred phylogenies. Bayesian estimates of divergence times based on a reduced data set (760 orthologs and 12% missing data) indicate a mid-Cretaceous origin of Papilionoidea around 99.2 Ma (95% credibility interval: 68.6–142.7 Ma) and Papilionidae around 71.4 Ma (49.8–103.6 Ma), with subsequent diversification of modern lineages well after the Cretaceous-Paleogene event. These results show that shotgun sequencing of whole genomes, even when highly fragmented, represents a powerful approach to phylogenomics and molecular dating in a group that has previously been refractory to resolution.

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Indopolystoma n. gen. (Monogenea, Polystomatidae) with the description of three new species and reassignment of eight known Polystoma species from Asian frogs (Anura, Rhacophoridae)

Parasite ◽

10.1051/parasite/2019067 ◽

2019 ◽

Vol 26 ◽

pp. 67

Author(s):

Amira Chaabane ◽

Olivier Verneau ◽

Louis Du Preez

Keyword(s):

New Species ◽

New Genus ◽

Phylogenetic Analyses ◽

The Body ◽

Molecular Dating ◽

Phylogenetic Position ◽

Morphological Evidence ◽

Freshwater Turtles ◽

Three New Species ◽

Japan And China

The polystomes (Monogenea, Polystomatidae) radiated across semi-aquatic tetrapods including all three amphibian orders, freshwater turtles and the hippopotamus. Prior to this study, phylogenetic analyses revealed that the most diverse and widespread genus, Polystoma, was not monophyletic; a lineage comprising four undescribed species from the bladder of Zhangixalus spp. (Rhacophoridae) in Asia occupied a deep phylogenetic position. Regarding vicariance biogeography and molecular dating, the origin of this lineage is correlated with the breakup of Gondwanaland in the Mesozoic period. Based on a Bayesian analysis of four concatenated genes (18S, 28S, COI and 12S) and morphological evidence, one new genus, Indopolystoma n. gen., and three new species, sampled in Japan and China, are described here: Indopolystoma viridi n. sp. from Z. viridis of Japan, Indopolystoma elongatum n. sp. from Z. arboreus of Japan, and Indopolystoma parvum n. sp. from Z. omeimontis of China. Indopolystoma is unique amongst polystome genera infecting anurans by possessing a small haptor relative to the body size, posteriormost marginal hooklet C1 much bigger than hooklets C2–C8 with conspicuous broad blade and guard and a pair of hamuli lacking a deep notch. Eight species of Asian Polystoma, all from rhacophorids, are transferred as Indopolystoma carvirostris (Fan, Li & He, 2008) n. comb., I. hakgalense (Crusz & Ching, 1975) n. comb., I. indicum (Diengdoh & Tandon, 1991) n. comb., I. leucomystax (Zhang & Long, 1987) n. comb., I. mutus (Meng, Song & Ding, 2010) n. comb., I. pingbianensis (Fan, Wang & Li, 2004) n. comb., I. rhacophori (Yamaguti, 1936) n. comb., and I. zuoi (Shen, Wang & Fan, 2013) n. comb.

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Molecular systematics and phylogeography of the genus Echinops (Compositae, Cardueae–Echinopsinae): focus on the Iranian centre of diversification

Phytotaxa ◽

10.11646/phytotaxa.297.2.1 ◽

2017 ◽

Vol 297 (2) ◽

pp. 101 ◽

Cited By ~ 1

Author(s):

SOMAYEH MONTAZEROLGHAEM ◽

ALFONSO SUSANNA ◽

JUAN ANTONIO CALLEJA ◽

VALIOLLAH MOZAFFARIAN ◽

MOHAMMAD REZA RAHIMINEJAD

Keyword(s):

Eastern Mediterranean ◽

Eastern Mediterranean Region ◽

Taxonomic Status ◽

Morphological Characters ◽

Molecular Dating ◽

Ancestral Area ◽

Close Relationship ◽

Taxonomic Changes ◽

High Level ◽

Relationship Of

A molecular phylogeny of the genus Echinops (Asteraceae, Cardueae) based on plastid and nuclear markers is presented. The study focuses on the Iranian representatives of the genus, which constitute a larger part of Echinops. The Bayesian cpDNA tree resulted in a large polytomy. However, the Bayesian ITS tree displayed a well-resolved topology more compatible with the taxonomic treatment generally accepted in Echinops. An ITS network illustrates a close relationship of haplotypes. Mapping diagnostic morphological characters onto the ITS tree revealed a high level of homoplasy among the studied taxa. Except for the life cycle, all other morphological characters evolved many times among the clades and most of them appeared to be of low taxonomical value. Based on the nucleotide polymorphism and haplotypes, the taxonomic status of some taxa was evaluated. The independent status of E. sect. Phaeochaete was confirmed by molecular analyses and morphological characters. The paraphyletic nature of E. sect. Echinops was confirmed. As for the molecular dating, our results suggest that the genus evolved in the early Miocene but the main speciation events took place in the Pliocene-Pleistocene. The biogeographic results do not support any specific ancestral area for Echinops, yet the model states that its current diversity originated in the Irano-Turanian Region and the Eastern Mediterranean region. Some taxonomic changes are suggested, in the synonymy and placement of some taxa.

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The double odyssey of Madagascan polystome flatworms leads to new insights on the origins of their amphibian hosts

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2008.1530 ◽

2009 ◽

Vol 276 (1662) ◽

pp. 1575-1583 ◽

Cited By ~ 13

Author(s):

Olivier Verneau ◽

Louis H Du Preez ◽

Véronique Laurent ◽

Liliane Raharivololoniaina ◽

Frank Glaw ◽

...

Keyword(s):

Molecular Dating ◽

Phylogenetic Position ◽

Late Mesozoic ◽

Biogeographic History ◽

On This Island ◽

The Family ◽

Molecular Phylogenetic ◽

History Of ◽

Recent Origin ◽

High Species Richness

Polystomatid flatworms are parasites of high host specificity, which mainly infect amphibian hosts. Only one polystome species has so far been recorded from Madagascar despite the high species richness and endemicity of amphibians on this island. Out of the 86 screened Malagasy frog species, we recovered polystomes from 25 in the families Ptychadenidae and Mantellidae. Molecular phylogenetic analysis uncovered an unexpected diversity of polystome species belonging to two separate clades: one forming a lineage within the genus Metapolystoma , with one species in Ptychadena and several species in the mantellid host genera Aglyptodactylus and Boophis ; and the second corresponding to an undescribed genus that was found in the species of the subfamily Mantellinae in the family Mantellidae. The phylogenetic position of the undescribed genus along with molecular dating suggests that it may have colonized Madagascar in the Late Mesozoic or Early Cainozoic. By contrast, the more recent origin of Metapolystoma in Madagascar at ca 14–2 Myr ago strongly suggests that the ancestors of Ptychadena mascareniensis colonized Madagascar naturally by overseas dispersal, carrying their Metapolystoma parasites. Our findings provide a striking example of how parasite data can supply novel insights into the biogeographic history of their hosts.

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Usnea nipparensis and U. sinensis form a ‘species pair ’ presuming morphological, chemical and molecular phylogenetic data

Plant and Fungal Systematics ◽

10.35535/pfsyst-2020-0023 ◽

2020 ◽

pp. 265-271

Author(s):

Yoshihito Ohmura

Keyword(s):

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Its Rdna ◽

Phylogenetic Position ◽

Species Pair ◽

Rdna Sequences ◽

Phylogenetic Data ◽

Close Relationship ◽

Molecular Phylogenetic ◽

Molecular Phylogenetic Data

Phylogenetic relationships between Usnea nipparensis and U. sinensis, caperatic acid containing Usnea species, were examined based on ITS rDNA, and the phylogenetic position of U. nipparensis was inferred based on multi-locus gene analysis using ITS rDNA, nuLSU, and MCM7. Although U. nipparensis and U. sinensis have a sorediate and an esorediate shrubby thallus, respectively, and in general look quite different, other detailed morphological and chemical features are similar. Analysis of the ITS rDNA sequences suggests their close relationship, but also confirms the independence of both species, and that they most likely form a ‘species pair’ based on morphological, chemical and molecular phylogenetic data. Phylogenetic trees based on both multi-locus gene and ITS rDNA alone strongly support that U. nipparensis and U. angulata belong to the same clade.

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