The characterization of complete mitochondrial genome and phylogenetic relationship within Rattus genus (Rodentia: Muridae)

The genus Rattus is one of the main pest genus of rodent. Most species of the genus carry all kinds of pathogenic bacteria to human being. They are traditionally considered to be a least understood group. The complete mitochondrial genome of the White-Footed Indochinese Rat, Rattus nitidus was determined in this study. The characterization of mitochondrial genomes of Rattus genus was also analyzed based on comprehensive comparison. The result of evolutionary patterns of protein-coding genes (PCGs) suggested purifying selection was the predominant evolutionary forces in the mitochondrial genomes of Rattus genus. The NADH dehydrogenase 4 gene (ND4) showed a highly elevated Ka/Ks ratio compared to the other protein-coding genes, which indicated ND4 was most likely under relaxed selection pressure. Phylogenetic analysis provided a well-supported outline of Rattus genus, and revealed two groups in the genus. R. nitidus had a sister relationship with R. norvegicus.     

The phylogenetic structure of the genus Acinetobacter

Abstract A N-acetyl-D-galactosamine (GalNAc) specific bacterial lectin-like substance from Eikenella corrodens 1073 (EcLS) was found to have potent mitogenic activity when cultured with splenocytes from BALB/c mice. The results indicated that B lymphocytes are the major cell type responding to EcLS. The mitogenic activity of EcLS was dose-dependent, and the optimal concentration was around 5 μg/ml. The mitogenic activity did not appear to be due to a bacterial endotoxin, as GalNAc inhibited the mitogenic activity of EcLS, but did not inhibit the activity of lipopolysaccharide isolated from E. corrodens . EcLS stimulated murine B lymphocytes not only to proliferate, but also to differentiate into antibody-secreting cells, as demonstrated by the production of immunoglobulin by B lymphocytes stimulated with EcLS. These findings suggest that EcLS is a novel lectin that not only induces B lymphocyte proliferation, but also differentiation.     

Morphology of the macula neglecta in sharks of the genus Carcharhinus

Ears from several species of carcharhinid sharks were studied by gross dissection, light microscopy, transmission electron microscopy, and scanning electron microscopy. Structures along a possible sound transmission path to the ear are described, but main consideration is given to the structure of the macula neglecta. The macula neglecta is composed of two patches of sensory epithelium which line part of the posterior canal duct. In an adult shark the larger of these contains 224,000 sensory hair cells oriented so as to detect forces directed posteroventrolaterally in the duct. The smaller patch contains 43,000 hair cells oriented so as to detect oppositely directed forces. These receptor cells project through numerous small terminals to a total for both patches of 4,700 myelinated nerve fibers. Cytostructural variations throughout the hair cell population are also reported. Estimated acoustic properties of the tissues in this complex and the processing potential of the neural elements are interpreted as suggestive of auditory function. A mechanism based on the geometry of the receptor arrays is proposed to explain behaviorally observed instantaneous sound localization from the farfield. Evolution of the macula neglecta is reviewed, and evidence for homology of the macula neglecta and amphibian papilla is presented.     

Evolutionary trends of microsatellites during the speciation process and phylogenetic relationships within the genus Secale

Eleven weedy or wild species or subspecies of the genus Secale L. were compared with a set of cultivated rye accessions, based on inter-simple sequence repeat (ISSR) markers to analyze their phylogenetic relationships. A total of 846 bands were amplified from reactions using 12 screening primers, including 79 loci with a mean of 10.1 alleles per locus. The number of amplified bands for each primer ranged from 12 to 134, with a mean of 70.5 amplified bands per primer. The presence and distribution of amplified bands in different accessions demonstrate that a rapid evolutionary trend of microsatellite repeats occurred during the speciation process from the perennial wild form to annual cultivated rye. In addition, variation, amplification, and deletion of microsatellites in genomes revealed phylogenetic relationships in the genus Secale. Analysis of the presence, number, and distribution of amplified bands in genomes, as well as the comparison with genetic similarity (GS) indices based on ISSR, indicate that Secale strictum subsp. africanum (Stapf) Hammer, Secale strictum anatolicum (Boiss.) Hammer, Secale sylvestre Host, and Secale strictum subsp. strictum (C. Presl) Hammer emerged in succession from a common ancestor of Secale following geographic separation and genetic differentiation. The annual weedy rye evolved from S. strictum subsp. strictum, which was domesticated as present-day cultivated rye. Data from ISSR analyses separated all investigated accessions of the genus Secale into three distinct groups. These results support the division of the genus Secale into three species: the annual wild species S. sylvestre; the perennial wild species S. strictum, including several differential subspecies forms such as strictum, africanum, and anatolicum; and S. cereale, including cultivated and weedy rye as subspecies forms.     

Evaluation of Lespedeza germplasm genetic diversity and its phylogenetic relationship with the genus Kummerowia

The genetic diversity of the genus Lespedeza is not well known and the phylogenetic relationship of Lespedeza with the genus Kummerowia is unclear. We report the first study in which polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers derived from Medicago, cowpea and soybean were used to assess the genetic diversity of the USDA Lespedeza germplasm collection and clarify its phylogenetic relationship with the genus Kummerowia. Phylogenetic analysis partitioned 44 Lespedeza accessions into three main groups some of which were species-specific and eight subgroups. This data set revealed some misidentified accessions, and indicated that the two species in the genus Kummerowia are closely related to the genus Lespedeza. Morphological reexamination was used to correct the misidentified accessions within the genus Lespedeza. Our results demonstrated that phylogenetic analysis with morphological reexamination provides a more complete approach to classify accessions in plant germplasm collection and conservation.     

The relationship of the genus Schizopera Sars within the family Diosaccidae (Copepoda: Harpacticoida)

A review of Schizopera Sars indicates that four species are so much more primitive in the antenna and leg setation that they should be removed to a new genus, Eoschizopera, which can be considered as a direct and immediate ancestor of Schizopera. A further, new, species is described in this new genus. The relationships within this branch of the family Diosaccidae are discussed and the scheme of family evolution proposed by Lang is modified to include Eoschizopera and other genera not considered by him (Goffinella, Protopsammotopa, Psammotopa, Actopsyllus, Balucopsylla, Schizoperoides). Actopsyllus hartmannorum Kunz is removed to a further new genus- Helmutkunzia.     

The phylogenetic position of the Pterosauria within the Archosauromorpha

In recent years the hypothesis that pterosaurs were the major sister-group of dinosaurs and a closely-linked hypothesis that pterosaurs evolved flight from the ground up have gained general acceptance. A cladistic analysis of the Archosauromorpha using characters presented by previous workers results in a single most parsimonious tree with the Pterosauria as the major sister-group of the Dinosauria. However, that sister-group relationship is supported only by a suite of hindlimb characters that are correlated with bipedal digitigrade locomotion in dinosaurs. In pterosaurs the characters have been interpreted as correlates of bipedal cursorial locomotion, arboreal leaping, or involvement of the hindlimb in the wing. The homology of those characters in dinosaurs and pterosaurs cannot be supported. Reanalysis of the data after exclusion of those hindlimb characters results in most parsimonious trees with the Pterosauria as the sister-group of the Erythrosuchidae + Proterochampsidae + Euparkeria + Archosauria, in that order. This sister-group relationship is supported by a diverse assemblage of functionally independent skeletal characters from all regions of the skeleton. The results of the analysis cast doubt on the hypothesis that pterosaurs evolved flight from the ground up.     

Molecular phylogenetic evidence for multiple gains or losses of ant mutualism within the aphid genus Chaitophorus

Mutualism with ants is suspected to be a highly labile trait within homopteran evolution. We used molecular phylogenetic evidence to test whether the mutualism has multiple origins within a single aphid genus. We constructed a molecular phylogeny of 15 Chaitophorus Koch (Hemiptera: Aphidoidea) species, using mitochondrial cytochrome oxidase I and II sequences. Ant tending evolved, or was lost, at least five times during Chaitophorus evolution. Parametric bootstrapping rejected the hypothesis of a single origin of ant tending in this genus. Further, the Chaitophorus made at least two host genus switches from poplars (Populus) to willow (Salix), and four switches in feeding position, from leaf feeding to stem feeding or vice versa. This is the first phylogenetic confirmation that ant tending is an evolutionarily labile trait in aphids.     

Multilocus phylogenetic analysis of the genus Aeromonas

A broad multilocus phylogenetic analysis (MLPA) of the representative diversity of a genus offers the opportunity to incorporate concatenated inter-species phylogenies into bacterial systematics. Recent analyses based on single housekeeping genes have provided coherent phylogenies of Aeromonas. However, to date, a multi-gene phylogenetic analysis has never been tackled. In the present study, the intra- and inter-species phylogenetic relationships of 115 strains representing all Aeromonas species described to date were investigated by MLPA. The study included the independent analysis of seven single gene fragments (gyrB, rpoD, recA, dnaJ, gyrA, dnaX, and atpD), and the tree resulting from the concatenated 4705 bp sequence. The phylogenies obtained were consistent with each other, and clustering agreed with the Aeromonas taxonomy recognized to date. The highest clustering robustness was found for the concatenated tree (i.e. all Aeromonas species split into 100% bootstrap clusters). Both possible chronometric distortions and poor resolution encountered when using single-gene analysis were buffered in the concatenated MLPA tree. However, reliable phylogenetic species delineation required an MLPA including several “bona fide” strains representing all described species.     

Molecular phylogenetic analysis of all members of the genus Elminia confirms their presence within the Stenostiridae clade

The genus Elminia has had a jumbled taxonomic history, being placed among ‘old world flycatchers’ or ‘monarch flycatchers’, where it was for a long time lumped with Trochocercus. It was recently suggested that it might represent a deep clade in the large sylvioid radiation. Using one mitochondrial protein‐coding gene (ND2, 1041 bp) and one nuclear intron (myoglobin intron 2, 700 bp) DNA sequences, we obtained robust evidence for the phylogenetic placement of Elminia in the new family Stenostiridae, which is strongly supported by a synapomorphic insertion of one base in the nuclear myoglobin intron 2 sequence. Our analyses confirm the monophyly of Elminia and resolve relationships within this genus, but cannot confidently identify its sister‐taxon within the stenostirid clade. Two clades were strongly supported within the genus Elminia: one with the two fairy blue flycatchers and another with the three white‐tailed crested‐flycatchers. Within the first clade, Elminia longicauda appears non‐monophyletic but remains strongly related to E. albicauda. In the second clade, E. albiventris is sister to E. albonotata while the Dusky Crested Flycatcher (E. nigromitrata) appears in a basal position within this clade. According to our molecular dating, several geological events in western Africa and the Albertine Rift area seem to be related to the historical distribution of Elminia. Thus, the differentiation between E. albonotata and E. albiventris could be directly related to the tectonic history of these two regions. According to our molecular dating, at least one intercontinental dispersal event involving Culicicapa took place within the Stenostiridae clade at a time when the Middle East was forested.     

A phylogenetic study of the genus Cookeina

Cookeina, with seven recognized species, is one of the commonly encountered genera of the Sarcoscyphaceae (Pezizales) in tropical and subtropical areas around the world. Morphologically the species are distinguished by combinations of several features including ascospore shape and surface relief, presence and origin of apothecial hairs and presence or absence of gelatinous material within the cortical layer of the excipular tissue. Color of the hymenium, attributed to carotenoid pigments, is particularly variable in some collections especially those referred to as C. speciosa. In this study phylogenetic analyses were carried out using rDNA ITS and rDNA LSU sequences. Forty-four collections were studied which included a broad sampling of color variants of C. speciosa from a field site in Venezuela. The genus was shown to be monophyletic with several well-supported lineages. These analyses generally support the established, morphologically distinguished taxa within a monophyletic genus Cookeina. Collections referred to as C. speciosa segregate within a clade in which hymenial color differences are associated with groups within the clade. Cookeina sinensis is sister to C. tricholoma but is distinct from it; C. indica fails to resolve with any of the major clades. The placement of C. insititia is ambiguous but it falls within Cookeina and thus is considered in the genus Cookeina rather than in a separate genus, Boedijnopeziza.     

Bioactive compounds of marine dinoflagellate isolates from western Greenland and their phylogenetic association within the genus Alexandrium

The diversity and biogeography of populations of the toxigenic marine dinoflagellate genus Alexandrium, a major global cause of paralytic shellfish poisoning (PSP), are represented by only a few studies based upon a low number of cultured isolates and remain poorly described in Arctic and sub-Arctic waters. Multiple clonal isolates (n = 22) of the Alexandrium tamarense species complex, and a single isolate of A. tamutum, were collected from the water column while on board an oceanographic expedition to the west coast of Greenland. After culturing of these isolates under controlled conditions, their phylogenetic affinities within the genus Alexandrium were characterized by sequence analysis of nuclear large sub-unit (LSU) rDNA. Based upon morphological and molecular genetic criteria, all isolates of the A. tamarense species complex were consistent with membership in the Group I ribotype (previously known as the North American ribotype). Phenotypic signatures were also analyzed based upon their respective profiles of paralytic shellfish toxins (PST) and allelochemical interactions against a target cryptophyte Rhodomonas, as determined by lytic potency. All isolates conforming to the A. tamarense Group I produced PST, but no toxins were detected in A. tamutum P2E2. Unusually, only carbamoyl toxins were produced among the A. tamarense Group I isolates from Greenland; sulfocarbamoyl derivatives, generally present in A. tamarense population from other locations, including the Arctic, North Pacific and North Atlantic, were absent from all isolates. Allelochemical activity, causing cell lysis of Rhodomonas, but generally being unrelated to cellular PST, was expressed by all A. tamarense isolates and also by A. tamutum, but varied widely in potency. Comparison of the genotypic (rDNA) and phenotypic (PST profile, allelochemical activity) characteristics of Greenland isolates with those of other Arctic populations reveals a complex pattern of intra-specific diversity. Estimation of diversity relationships is problematic because of the distinct patterns of divergence and lack of evidence of linkage among the alternative biomarkers and morphology. Nevertheless, such studies are necessary as the basis for constructing hindcasting scenarios and predicting changes in Alexandrium species distribution in the Arctic from the regional to the global scale.     

A new species of Anisopappus (Asteraceae, Inuleae) and its phylogenetic relationships within the genus

A new species of the genus Anisopappus (Asteraceae, Inuleae) from Angola, A. fruticosus , is described. The principal differences with respect to A. chinensis are discussed, and phylogenetic relationships with the other species of the genus are investigated by means of a cladistic analysis using morphological characters.     

The Baikalian genus Rhyacodriloides in Europe: phylogenetic assessment of Rhyacodriloidinae subfam. n. within the Naididae (Annelida)

Martin, P., Martínez‐Ansemil, E. & Sambugar, B. (2010). The Baikalian genus Rhyacodriloides in Europe: phylogenetic assessment of Rhyacodriloidinae subfam. n. within the Naididae (Annelida). —Zoologica Scripta, 39, 462–482. Two new species of the oligochaete genus Rhyacodriloides Chekanovskaya, Rhyacodriloides aeternorum sp. n. and Rhyacodriloides latinus sp. n., are described from subterranean water bodies of Italy and Slovenia. A comparison with the known species of this genus, Rhyacodriloides abyssalis Chekanovskaya, 1975 and Rhyacodriloides gladiiseta Martin & Brinkhurst, 1998, both from Lake Baikal, shows that the enigmatic ‘cellular masses’ of the latter two species must be interpreted as different, not homologous structures. As a result, R. gladiiseta is to be ascribed to the Phallodrilinae, a primarily marine naidid subfamily, mentioned for the first time in Lake Baikal, and placed in its own genus, Phallobaikalus gen. n. The two new species are morphologically very similar, but their penial setae differ slightly. The phylogenetic relationships of R. latinus sp. n. and R. abyssalis within the Naididae (formerly the Tubificidae) were investigated using a combination of three genes, one nuclear (18S rDNA) and two mitochondrial (12S rDNA and 16S rDNA). A fragment of the mitochondrial COI gene, used as a barcode, also genetically characterized all Rhyacodriloides species. Sequences of 34 Naididae were obtained from EMBL, representative of five naidid subfamilies, and including five oligochaete outgroups. The data were analysed by parsimony, maximum likelihood and Bayesian inference. Taken in combination, the three genes investigated confirm that the two Rhyacodriloides species analysed are closer to each other than to any other naidid species. However, they are separated by 16S and COI distances that amount to 18.5% and 27.2%, respectively, suggesting an ancient separation between species, in good accordance with their present biogeographic distribution. Rhyacodriloides cannot be considered as a rhyacodriline, as assumed so far, as they never appeared related to this subfamily in any analysis considered. In contrast, they appear at the base of a naidid group, including the Tubificinae, the Phallodrilinae, the Limnodrilinae, as well as Branchiura sowerbyi, a species whose phylogenetic association with the rhyacodrilines has been questioned for a long time. Despite a lack of phylogenetic support, this position is congruent with a morphological reassessment of the Rhyacodrilinae, and strongly supports the erection of a new naidid subfamily to accommodate Rhyacodriloides.     

Conservation of the S10-spc-alpha locus within otherwise highly plastic genomes provides phylogenetic insight into the genus Leptospira

S10-spc-alpha is a 17.5 kb cluster of 32 genes encoding ribosomal proteins. This locus has an unusual composition and organization in Leptospira interrogans. We demonstrate the highly conserved nature of this region among diverse Leptospira and show its utility as a phylogenetically informative region. Comparative analyses were performed by PCR using primer sets covering the whole locus. Correctly sized fragments were obtained by PCR from all L. interrogans strains tested for each primer set indicating that this locus is well conserved in this species. Few differences were detected in amplification profiles between different pathogenic species, indicating that the S10-spc-alpha locus is conserved among pathogenic Leptospira. In contrast, PCR analysis of this locus using DNA from saprophytic Leptospira species and species with an intermediate pathogenic capacity generated varied results. Sequence alignment of the S10-spc-alpha locus from two pathogenic species, L. interrogans and L. borgpetersenii, with the corresponding locus from the saprophyte L. biflexa serovar Patoc showed that genetic organization of this locus is well conserved within Leptospira. Multilocus sequence typing (MLST) of four conserved regions resulted in the construction of well-defined phylogenetic trees that help resolve questions about the interrelationships of pathogenic Leptospira. Based on the results of secY sequence analysis, we found that reliable species identification of pathogenic Leptospira is possible by comparative analysis of a 245 bp region commonly used as a target for diagnostic PCR for leptospirosis. Comparative analysis of Leptospira strains revealed that strain H6 previously classified as L. inadai actually belongs to the pathogenic species L. interrogans and that L. meyeri strain ICF phylogenetically co-localized with the pathogenic clusters. These findings demonstrate that the S10-spc-alpha locus is highly conserved throughout the genus and may be more useful in comparing evolution of the genus than loci studied previously.     

Gobius xoriguer,a new offshore Mediterranean goby (Gobiidae), and phylogenetic relationships within the genus Gobius

Ichthyological Research - Gobius xoriguer sp. nov., a new ofshore species of goby (Teleostei: Gobiidae: Gobiinae) is described based on three specimens collected in 2010, 2012 and 2018 in the...