scholarly journals Latrocimicinae completes the phylogeny of Cimicidae: meeting old morphologic data rather than modern host phylogeny

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Sándor Hornok ◽  
Tamara Szentiványi ◽  
Nóra Takács ◽  
Áron Botond Kovács ◽  
Olivier Glaizot ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Evolutionary Relationships ◽  
Bed Bugs ◽  
Relevant Study ◽  
Phylogenetic Methods ◽  
Close Phylogenetic Relationship ◽  
The Family ◽  
Host Phylogeny ◽  
Medical Importance ◽  
Morphologic Data

AbstractThe family Cimicidae includes obligate hematophagous ectoparasites (bed bugs and their relatives) with high veterinary/medical importance. The evolutionary relationships of Cimicidae and their hosts have recently been reported in a phylogenetic context, but in the relevant study, one of the six subfamilies, the bat-specific Latrocimicinae, was not represented. In this study the only known species of Latrocimicinae, i.e., Latrocimex spectans, was analyzed with molecular and phylogenetic methods based on four (two nuclear and two mitochondrial) genetic markers. The completed subfamily-level phylogeny of Cimicidae showed that Latrocimicinae is most closely related to Haematosiphoninae (ectoparasites of birds and humans), with which it shares systematically important morphologic characters, but not hosts. Moreover, in the phylogenetic analyses, cimicid bugs that are known to infest phylogenetically distant bat hosts clustered together (e.g., Leptocimex and Stricticimex within Cacodminae), while cimicid subfamilies (Latrocimicinae, Primicimicinae) that are known to infest bat hosts from closely related superfamilies clustered distantly. In conclusion, adding Latrocimicinae significantly contributed to the resolution of the phylogeny of Cimicidae. The close phylogenetic relationship between Latrocimicinae and Haematosiphoninae is consistent with long-known morphologic data. At the same time, phylogenetic relationships of genera within subfamilies are inconsistent with the phylogeny of relevant hosts. Graphical abstract

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

Phytotaxa ◽  
2017 ◽  
Vol 319 (1) ◽  
pp. 84 ◽  
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.

scholarly journals Enhanced genome annotation strategy provides novel insights on the phylogeny of Flaviviridae

2019 ◽  
Author(s):  
Adriano de Bernardi Schneider ◽  
Denis Jacob Machado ◽  
Daniel Janies
Keyword(s):  
Phylogenetic Relationship ◽  
Soybean Cyst Nematode ◽  
Phylogenetic Analyses ◽  
Optimality Criteria ◽  
Entire Family ◽  
Close Phylogenetic Relationship ◽  
The Family ◽  
Relationship Of ◽  
Reference Genomes ◽  
Annotation Strategy

The ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and zika, demand a greater understanding of how these viruses evolve, emerge and spread in order to respond. Central to this understanding is an updated phylogeny of the entire family. Unfortunately, most cladograms of Flaviviridae focus on specific lineages, ignore outgroups, and rely on midpoint rooting, hampering their ability to test ingroup monophyly and estimate ingroup relationships. This problem is partly due to the lack of fully annotated genomes of Flaviviridae, which has genera with slightly different gene content, hindering genome analysis without partitioning. To tackle these problems, we developed an annotation pipeline for Flaviviridae that uses a combination of ab initio and homology-based strategies. The pipeline recovered 100% of the genes in reference genomes and annotated over 97% of the expected genes in the remaining non curated sequences. We further demonstrate that the combined analysis of genomes of all genera of Flaviviridae (Flavivirus, Hepacivirus, Pegivirus, and Pestivirus), as made possible by our annotation strategy, enhances the phylogenetic analyses of these viruses for all optimality criteria that we tested (parsimony, maximum likelihood, and posterior probability). The final tree sheds light on the phylogenetic relationship of viruses that are divergent from most Flaviviridae and should be reclassified, especially the soybean cyst nematode virus 5 (SbCNV-5) and the Tamana bat virus. We also corroborate the close phylogenetic relationship of dengue and zika viruses with an unprecedented degree of support.

Anchialine adjustments: an updated phylogeny and classification for the family Barbouriidae Christoffersen, 1987 (Decapoda: Caridea)

2020 ◽  
Vol 40 (4) ◽  
pp. 401-411 ◽  
Author(s):  
Robert E Ditter ◽  
Luis M Mejía-Ortíz ◽  
Heather D Bracken-Grissom
Keyword(s):  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Morphological Characters ◽  
Molecular Data ◽  
Genetic Distances ◽  
Evolutionary Relationships ◽  
The Bahamas ◽  
16S Gene ◽  
Dichotomous Key ◽  
The Family

Abstract Barbouriidae Christoffersen, 1987 is a family comprised of 4 genera and 11 species of enigmatic shrimps restricted to anchialine or marine caves whose evolutionary history and relationships remain elusive. We investigated the evolutionary relationships among members of Barbouriidae with the inclusion of four genera and nine species, and newly collected material from Belize, the Bahamas, and the Yucatán Peninsula, Mexico. Phylogenetic analyses based on seven mitochondrial and nuclear gene regions and genetic distances calculated using partial 16S gene regions have identified a need to revisit the relationships and classification within Barbouriidae. More specifically, we find evidence to suggest Janicea Manning & Hart, 1984 as a junior synonym of Parhippolyte Borradaile, 1900, B. yanezi Mejía, Zarza & López, 2008 as a synonym of Barbouria cubensis (von Martens, 1872), and define two new subfamilies, Calliasmatinae Holthuis, 1973 and Barbouriinae Christoffersen, 1987. Included is a dichotomous key for the species of Barbouriidae that summarizes previous literature and includes new morphological characters. Our findings shed light on existing inaccuracies and gaps in molecular data from barbouriids. We also provide further clarity into evolutionary relationships among genera of Barbouriidae and their allies, suggesting phylogeographic divisions within the family. Our findings suggest an early Atlantic-Pacific divide among genera originating from a shallow-water reef ancestor.

Evaluating internal versus external characters: Phylogenetic analyses of the Echinoconchidae, Buxtoniinae, and Juresaniinae (phylum Brachiopoda)

2002 ◽  
Vol 76 (4) ◽  
pp. 659-671 ◽  
Author(s):  
Lindsey R. Leighton ◽  
Christopher G. Maples
Keyword(s):  
Nearest Neighbor ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Shell Shape ◽  
Evolutionary Relationships ◽  
Cardinal Process ◽  
Invertebrate Paleontology ◽  
The Family ◽  
The Subject ◽  
Strong Agreement

Evolutionary relationships between the Echinoconchidae, Productidae, Buxtoniinae, and Juresaniinae (Phylum Brachiopoda, Order Productida) have been the subject of debate for the better part of a century. The original (Muir-Wood and Williams, 1965) and revised (Brunton et al., 2000) Brachiopoda volumes of the Treatise on Invertebrate Paleontology use markedly different classifications and emphasize different characters. The 1965 Treatise classification for these taxa primarily was based on internal features, especially the cardinal process; the revised Treatise (2000) relied on external ornament and shell shape. Multiple phylogenetic analyses (global parsimony, stratocladistics, nearest-neighbor) of 14 genera, representing all of the relevant subfamilies and outgroups, are in strong agreement that 1) the subfamily Buxtoniinae belongs in the family Echinoconchidae, not to the Productidae; 2) the subfamily Juresaniinae is more closely related to the Echinoconchinae than to the Buxtoniinae; and 3) that internal characters, such as a shafted cardinal process and anterio-medial position of the brachial valve adductor field, provide the best phylogenetic signal, and are synapomorphic for the Echinoconchidae. Jackknifing and Bremer Support corroborate these results.

scholarly journals Genetic variation and phylogenetic analysis of rabbit haemorrhagic disease virus (RHDV) strains.

2012 ◽  
Vol 59 (4) ◽  
Author(s):  
Beata Hukowska-Szematowicz ◽  
Beata Tokarz-Deptuła ◽  
Wiesław Deptuła
Keyword(s):  
Genetic Variation ◽  
Disease Virus ◽  
Current Knowledge ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationships ◽  
Rabbit Haemorrhagic Disease Virus ◽  
Structural Protein ◽  
Rabbit Haemorrhagic Disease ◽  
The Family ◽  
Haemorrhagic Disease

Rabbit haemorrhagic disease virus (RHDV) belongs to the family Caliciviridae and is the etiological agent of the haemorrhagic disease, also known as rabbit plague. Its genome is a linear single-stranded (ss) RNA of 7437 nucleotides and the capsid is built from a single structural protein VP60. In connection with the discovery of new RHDV strains, there is a constant need to investigate the genetic variation of this virus and perform phylogenetic analyses which may show the evolutionary relationships among the RHDV strains. Studies on the divergence of RHDV have shown that it is genetically quite stable, although recent observations indicate that some new RHDV strains, significantly different from the original RHDV subtype and the new RHDVa subtype, are appearing. These latest findings suggest that a new group of RHDV strains has evolved. The present review summarizes the current knowledge on the genetic variation and the latest achievements in phylogenetic analyses of RHDV strains isolated in various countries.

Evolutionary relationships among life-history traits in Caninae (Mammalia: Carnivora)

2019 ◽  
Author(s):  
Lucas Marafina Vieira Porto ◽  
Renan Maestri ◽  
Leandro Da Silva Duarte
Keyword(s):  
Life History ◽  
Life History Traits ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationships ◽  
Phenotypic Traits ◽  
Complete Understanding ◽  
Ecological Features ◽  
The Family ◽  
Highly Correlated ◽  
Solitary Species

Abstract Over the last few years, a debate about the relative roles of distinct factors on the evolution of lineages has gained prominence. The family Canidae is an excellent group for exploring this idea, owing to its rich fossil history. One of the most intriguing traits in canids is social organization, which varies from highly social to solitary species. However, we do not have a complete understanding of how sociality evolved in this clade. Here, we use a combination of phylogenetic analyses, ancestral character reconstructions and comparative methods on the only extant subfamily, Caninae, to understand how traits expressing ecological features evolved over the last 12.6 Myr. Our findings suggest that the evolution of low, medium and high sociality forms was abrupt and highly correlated with the evolution of hypo-, meso- and hypercarnivorous forms, respectively. In addition, our results suggest that the evolution of phenotypic traits in Caninae occurred through a sequential cause–effect relationship, where changes in habitat use and body size probably triggered changes in social behaviour, which in turn drove the evolution of diet.

scholarly journals Molecular evolutionary relationships of Vietnamese and global pulmonary Paragonimus species in the family paragonimidae and suborder xiphidiata (Platyhelminthes: Trematoda)

2021 ◽  
Vol 18 (4) ◽  
pp. 653-662
Author(s):  
Nguyen Thi Khue ◽  
Pham Thi Khanh Linh ◽  
Do Thi Roan ◽  
Doan Thi Thanh Huong ◽  
Pham Ngoc Doanh ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
The Philippines ◽  
28S Rdna ◽  
Evolutionary Relationships ◽  
Evolutionary Analysis ◽  
North West ◽  
Rdna Sequences ◽  
The Family ◽  
28S Rdna Sequences

Paragonimiasis, caused by Paragonimus species belonging to the family Paragonimidae of the suborder Xiphidiata (Platyhelminthes: Trematoda), often occurs in poor, upland, ethnic minorities, in Vietnam and the world. Asian Paragonimus species are distributed from Japan, South Korea, along with North and Southeast China, North-West and Central Vietnam, the Philippines, Thailand, Bangladesh, India, and Sri Lanka. There are various genetic variants, strains, and genotypes forming different complexes and evolutionary lineages. The 18S, 28S rDNA sequences and the intergenic transcribed spacer regions (ITS-1, ITS-2) of nuclear ribosomal transcription units are commonly used as molecular markers in genetic studies and phylogenetic analyses. We obtained a portion of 28S rDNA (domains D1–D3) of Paragonimus spp. including P. heterotremus (from Vietnam), P. ohirai (Japan), P. iloktsuenensis (Japan), and P. westermani (India and Vietnam) and conducted phylogenetic analysis for molecular evolutionary studies. The results showed that the family Paragonimidae formed the biggest cluster in a phylogenetic tree, which comprises of 46 sequences of 11 species belonging to 11 subgroups, among which the P. westermani complex of strains originating from China, Korea, Japan, India, Philippines, Malaysia, and Vietnam is present. P. westermani complex is arranged in a position of "sister" (sister group) with the subgroup P. siamensis. The P. heterotremus and P. ohirai complexes, and the P. miyazakii, P. harinasutai, P. mexicanus, P. kellicotti, and P. macrorchis complexes are clustered in a common population. P. westermani of Vietnam is in close proximity to the East Asian strains, as of which has been previously reported. P. ohirai and P. iloktsuenensis are considered “sibling” species, sharing the same clade. Phylogenetic analysis using the 28S rDNA sequences directly presented species position and their molecular evolutionary relationships in the families Paragonimidae, Troglotrematidae, Nanophyetidae, and Collyriclidae. Evolutionary analysis has also clarified a number of complex delineation problems and made a clear nomenclature for Paragonimus sp. of Vietnam, in particular, which has scientific grounds merited to recognize as that it is really the P. westermani species.

A new enigmatic genus of subterranean amphipod (Amphipoda : Bogidielloidea) from Terrell County, Texas, with the establishment of Parabogidiellidae, fam. nov., and notes on the family Bogidiellidae

2020 ◽  
Author(s):  
A. G. Cannizzaro ◽  
J. R. Gibson ◽  
T. R. Sawicki
Keyword(s):  
New Genus ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Morphological Characters ◽  
Sensu Stricto ◽  
Evolutionary Relationships ◽  
New Genus And Species ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Large Distribution

The superfamily Bogidielloidea is one of the most wide-ranging hypogean amphipod taxa currently known, comprising over 130 species in 43 genera occurring on every continent except Antarctica. This large distribution among such cryptic organisms is curious, especially when combined with weak morphological characters uniting the superfamily. A unique new genus and species of bogidielloid amphipod, Simplexia longicrus, gen. et sp. nov., described from Terrell County, Texas, sheds light on the evolutionary relationships within this grouping. Molecular phylogenetic analyses of the order Amphipoda using two nuclear genes and one mitochondrial gene reveal that this species and the sympatric Parabogidiella americana form a clade removed from other sequenced members of Bogidiellidae sensu stricto, and, as such, the two species are placed in the newly erected Parabogidiellidae, fam. nov. Additional phylogenetic analyses of the cosmopolitan Bogidiellidae are recommended to further resolve its systematics.

scholarly journals Towards a Natural Classification of Hyphodontia Sensu Lato and the Trait Evolution of Basidiocarps within Hymenochaetales (Basidiomycota)

2021 ◽  
Vol 7 (6) ◽  
pp. 478
Author(s):  
Xue-Wei Wang ◽  
Tom W. May ◽  
Shi-Liang Liu ◽  
Li-Wei Zhou
Keyword(s):  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Ancestral State ◽  
Trait Evolution ◽  
Natural Classification ◽  
Multiple Loci ◽  
The Family ◽  
Phylogenetic Perspective ◽  
Taxonomic Framework ◽  
First Time

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.

scholarly journals Multiple Types of Novel Enteric Bopiviruses (Picornaviridae) with the Possibility of Interspecies Transmission Identified from Cloven-Hoofed Domestic Livestock (Ovine, Caprine and Bovine) in Hungary

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 66
Author(s):  
Zoltán László ◽  
Péter Pankovics ◽  
Gábor Reuter ◽  
Attila Cságola ◽  
Ádám Bálint ◽  
...  
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Interspecies Transmission ◽  
Background Information ◽  
Type Ii ◽  
Rt Pcr ◽  
Faecal Samples ◽  
The Family ◽  
Domestic Livestock

Most picornaviruses of the family Picornaviridae are relatively well known, but there are certain “neglected” genera like Bopivirus, containing a single uncharacterised sequence (bopivirus A1, KM589358) with very limited background information. In this study, three novel picornaviruses provisionally called ovipi-, gopi- and bopivirus/Hun (MW298057-MW298059) from enteric samples of asymptomatic ovine, caprine and bovine respectively, were determined using RT-PCR and dye-terminator sequencing techniques. These monophyletic viruses share the same type II-like IRES, NPGP-type 2A, similar genome layout (4-3-4) and cre-localisations. Culture attempts of the study viruses, using six different cell lines, yielded no evidence of viral growth in vitro. Genomic and phylogenetic analyses show that bopivirus/Hun of bovine belongs to the species Bopivirus A, while the closely related ovine-origin ovipi- and caprine-origin gopivirus could belong to a novel species “Bopivirus B” in the genus Bopivirus. Epidemiological investigation of N = 269 faecal samples of livestock (ovine, caprine, bovine, swine and rabbit) from different farms in Hungary showed that bopiviruses were most prevalent among <12-month-old ovine, caprine and bovine, but undetectable in swine and rabbit. VP1 capsid-based phylogenetic analyses revealed the presence of multiple lineages/genotypes, including closely related ovine/caprine strains, suggesting the possibility of ovine–caprine interspecies transmission of certain bopiviruses.

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