Molecular systematics of Australian rhinolophid bats (Chiroptera : Rhinolophidae)

1998 ◽  
Vol 46 (3) ◽  
pp. 203 ◽  
Author(s):  
S. J. B. Cooper ◽  
T. B. Reardon ◽  
J. Skilins
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Distinct Species ◽  
Surprising Result ◽  
Separate Species ◽  
Phylogenetic Species Concept ◽  
South Wales ◽  
Mtdna Sequence ◽  
Geographic Populations

Genetic variation in two morphologically distinct species of Australian Rhinolophus, R. megaphyllus, and R. philippinensis, and a third putative species (‘the intermediate’) were examined using allozyme electrophoresis and sequencing of the mitochondrial DNA (mtDNA) control region with the aim of resolving their taxonomic status. The surprising result was that no fixed allozymic differences and low allozyme divergence existed among these three taxa over 45 loci examined. In contrast, levels of intra-generic divergence among eight species of Rhinolophus showed up to 50% fixed allozyme differences between species, indicating that low allozyme divergence was not a common feature of the genus and that the three Australian taxa are likely to be monophyletic and recently diverged. Phylogenetic analyses of mtDNA sequence data revealed that populations of R. megaphyllus and R. philippinensis from Sabah, New Guinea, and Australia were represented by distinct mtDNA clades and that the two species are polyphyletic. These data suggest a reclassification of the different geographic populations of R. megaphyllus and R. philippinensis as separate species on the basis of a phylogenetic species concept. Within Australia, three distinct mtDNA clades were found, one of which showed ‘the intermediate’ in paraphyly with R. philippinensis from Queensland, but does not resolve the taxonomic status of ‘the intermediate’. Two mtDNA clades were also found representing R. megaphyllus from Queensland and R. megaphyllus from Victoria and New South Wales respectively. The finding of genetic subdivision along the east coast of Australia in an apparently continuously distributed bat species raises questions of the origin and historical biogeography of these bats in Australia.

Phylogenetic relationships within Cicuta (Apiaceae tribe Oenantheae) inferred from nuclear rDNA ITS and cpDNA sequence data

2006 ◽  
Vol 84 (3) ◽  
pp. 453-468 ◽  
Author(s):  
Chang-Shook Lee ◽  
Stephen R. Downie
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Distinct Species ◽  
Sister Group ◽  
Nuclear Ribosomal Dna ◽  
Hybrid Origin ◽  
Rdna Its ◽  
The North

The genus Cicuta (Apiaceae tribe Oenantheae Dumort.) is the most virulently poisonous group of flowering plants native to the north temperate zone. A recent treatment recognized four species ( C. bulbifera L., C. douglasii (DC.) J.M. Coult. & Rose, C. maculata L., and C. virosa L.), with C. maculata divided into four varieties. We present results of phylogenetic analyses of the nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) locus and the region bounded by the chloroplast genes psbI and trnK 5′ exon to determine taxonomic limits and relationships among these taxa, and to assess the taxonomic status of C. douglasii, a polyploid thought to be derived from C. maculata and C. virosa. Cicuta bulbifera and C. virosa are each resolved as monophyletic, the latter is a sister group to all other species. Discordance between the ITS- and plastid-derived phylogenies and lack of resolution in the ITS trees preclude unequivocal hypotheses of relationship; all trees do suggest, however, that the allotetraploid C. douglasii is polyphyletic and possibly polytopic, with all examined accessions but one nested within C. maculata. This single outstanding accession is from California and, pending further study, might warrant recognition as a distinct species. The diploid C. bulbifera may also be of hybrid origin, as revealed by significant discordance between data sets. Within C. maculata, only the western North American var. angustifolia Hook. is resolved in the ITS trees. In the cpDNA trees, C. maculata var. angustifolia comprises a strongly supported clade with C. maculata var. bolanderi (S. Watson) G.A. Mulligan and C. douglasii, both of primarily western North American distribution. The eastern North American taxa, C. maculata vars. maculata and victorinii (Fernald) B. Boivin, also comprise a clade, sister group to C. bulbifera.

Mimaporia, a new genus of Epicopeiidae (Lepidoptera), with description of a new species from Vietnam

Zootaxa ◽  
2017 ◽  
Vol 4254 (5) ◽  
pp. 537 ◽  
Author(s):  
CHIA-HSUAN WEI ◽  
SHEN-HORN YEN
Keyword(s):  
New Species ◽  
New Genus ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Sister Group ◽  
Morphological Evidence ◽  
New Taxon ◽  
The Family ◽  
A New Species

The Epicopeiidae is a small geometroid family distributed in the East Palaearctic and Oriental regions. It exhibits high morphological diversity in body size and wing shape, while their wing patterns involve in various complex mimicry rings. In the present study, we attempted to describe a new genus, and a new species from Vietnam, with comments on two assumed congeneric novel species from China and India. To address its phylogenetic affinity, we reconstructed the phylogeny of the family by using sequence data of COI, EF-1α, and 28S gene regions obtained from seven genera of Epicopeiidae with Pseudobiston pinratanai as the outgroup. We also compared the morphology of the new taxon to other epicopeiid genera to affirm its taxonomic status. The results suggest that the undescribed taxon deserve a new genus, namely Mimaporia gen. n. The species from Vietnam, Mimaporia hmong sp. n., is described as new to science. Under different tree building strategies, the new genus is the sister group of either Chatamla Moore, 1881 or Parabraxas Leech, 1897. The morphological evidence, which was not included in phylogenetic analyses, however, suggests its potential affinity with Burmeia Minet, 2003. This study also provides the first, although preliminary, molecular phylogeny of the family on which the revised systematics and interpretation of character evolution can be based. 

scholarly journals Caractérisation génétique des virus Tilligerry et Mitchell River

2009 ◽  
Vol 62 (2-4) ◽  
pp. 151
Author(s):  
M. Belaganahalli ◽  
S. Maan ◽  
P. P.C. Mertens
Keyword(s):  
Reverse Genetics ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Cross Reactivity ◽  
Emerging Diseases ◽  
Full Length ◽  
Virus Species ◽  
Livestock Farming

Viruses that are normally safely contained within their host spe­cies can emerge due to intense livestock farming, trade, travel, climate change and encroachment of human activities into new environments. The unexpected emergence of bluetongue virus (BTV), the prototype species of the genus Orbivirus, in economi­cally important livestock species (sheep and cattle) across the whole of Europe (since 1998), indicates that other orbiviruses represent a potential further threat to animal and human popula­tions in Europe and elsewhere. The genus Orbivirus is the largest within the family Reoviridae, containing 22 virus species, as well as 14 unclassified orbiviruses, some of which may repre­sent additional or novel species. The orbiviruses are transmitted primarily by arthropod vectors (e.g. Culicoides, mosquitoes or ticks).  Viral genome sequence data provide a basis for virus taxonomy and diagnostic test development, and make it possible to address fundamental questions concerning virus biology, pathogenesis, virulence and evolution, that can be further explored in mutation and reverse genetics studies. Genome sequences also provide criteria for the classification of novel isolates within individual Orbivirus species, as well as the identification of different sero­types, topotypes, reassortants and even closely related but dis­tinct virus lineages.  Full-length genome characterization of Tilligerry virus (TILV), a member of the Eubenangee virus species, and Mitchell River virus (MRV), a member of the Warrego virus species, have revealed highly conserved 5’ and 3’ terminal hexanucleotide sequences. Phylogenetic analyses of orbivirus T2 ‘sub-core-shell’ protein sequences reinforce the hypothesis that this protein is an important evolutionary marker for these viruses. The T2 protein shows high levels of amino acid (AA) sequence identity (> 91%) within a single Orbivirus species / serogroup, which can be used for species identification. The T2-protein gene has therefore been given priority in sequencing studies. The T2 protein of TILV is closely related to that of Eubenangee virus (~91% identity), con­firming that they are both members of the same Eubenangee virus species. Although TILV is reported to be related to BTV in serological assays, the TILV T2 protein shows only 68-70% AA identity to BTV. This supports its current classification within a different serogroup (Eubenangee).  Warrego virus and MRV are currently classified as two distinct members (different serotypes) within the Warrego virus species. However, they show only about 79% AA identity in their T2 pro­tein (based on partial sequences). It is therefore considered likely that they could be reclassified as members of distinct Orbivirus species. The taxonomic classification of MRV will be reviewed after generating full length sequences for the entire genomes of both viruses. The taxonomic status of each of these viruses will also be tested further by co-infections and attempts to create reassortants between them (only viruses belonging to the same species can reassort their genome segments). TILV and MRV are the first viruses from their respective serogroups / virus species to be genetically fully characterized, and will provide a basis for the further characterization / identification of additional viruses within each group / species. These data will assist in the devel­opment of specific diagnostic assays and potentially in control of emerging diseases. The sequences generated will also help to evaluate current diagnostic [reverse transcriptase - polymerase chain reaction (RT-PCR)] tests for BTV, African horse sickness virus, epizootic haemorrhagic disease virus, etc., in silico, by identifying any possibility of cross reactivity.

Phaeosphaeria chinensis sp. nov. (Phaeosphaeriaceae) with an asexual/sexual morph connection from GuangDong Province, China

Phytotaxa ◽  
2019 ◽  
Vol 419 (1) ◽  
pp. 28-38 ◽  
Author(s):  
KE-KE ZHANG ◽  
SINANG HONGSANAN ◽  
DANUSHKA S. TENNAKOON ◽  
SHENG-LI TIAN ◽  
NING XIE
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Guangdong Province ◽  
Distinct Species ◽  
Bootstrap Support ◽  
Comprehensive Description ◽  
High Bootstrap ◽  
Asexual Morphs

Phaeosphaeria chinensis sp. nov. was found on dead leaves, collected from Guangdong Province, China. Morphology of the new species was compared with other Phaeosphaeria species and related genera of Phaeosphaeriaceae. Phylogenetic analyses of combined ITS, LSU, SSU and TEF-1 sequence data based on maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) revealed that P. chinensis as a distinct species within the Phaeosphaeria with high bootstrap support. The comparison of the new species with other Phaeosphaeria species and a comprehensive description and micrographs are provided. The linkage of sexual and asexual morphs of the new species is also showed.

The Dogma of Dingoes—Taxonomic status of the dingo: A reply to Smith et al.

Zootaxa ◽  
2019 ◽  
Vol 4564 (1) ◽  
pp. 198 ◽  
Author(s):  
STEPHEN M. JACKSON ◽  
PETER J.S. FLEMING ◽  
MARK D.B. ELDRIDGE ◽  
SANDY INGLEBY ◽  
TIM FLANNERY ◽  
...  
Keyword(s):  
Taxonomic Status ◽  
Distinct Species ◽  
Domestic Dogs ◽  
Current Evidence ◽  
Morphological Evidence ◽  
Evolutionary Divergence ◽  
Gray Wolf ◽  
Separate Species ◽  
Gray Wolves ◽  
Narrow Scope

Adopting the name Canis dingo for the Dingo to explicitly denote a species-level taxon separate from other canids was suggested by Crowther et al.  (2014) as a means to eliminate taxonomic instability and contention. However, Jackson et al.  (2017), using standard taxonomic and nomenclatural approaches and principles, called instead for continued use of the nomen C. familiaris for all domestic dogs and their derivatives, including the Dingo. (This name, C. familiaris, is applied to all dogs that derive from the domesticated version of the Gray Wolf, Canis lupus, based on nomenclatural convention.) The primary reasons for this call by Jackson et al.  (2017) were: (1) a lack of evidence to show that recognizing multiple species amongst the dog, including the Dingo and New Guinea Singing Dog, was necessary taxonomically, and (2) the principle of nomenclatural priority (the name familiaris Linnaeus, 1758, antedates dingo Meyer, 1793). Overwhelming current evidence from archaeology and genomics indicates that the Dingo is of recent origin in Australia and shares immediate ancestry with other domestic dogs as evidenced by patterns of genetic and morphological variation. Accordingly, for Smith et al.  (2019) to recognise Canis dingo as a distinct species, the onus was on them to overturn current interpretations of available archaeological, genomic, and morphological datasets and instead show that Dingoes have a deeply divergent evolutionary history that distinguishes them from other named forms of Canis (including C. lupus and its domesticated version, C. familiaris). A recent paper by Koepfli et al.  (2015) demonstrates exactly how this can be done in a compelling way within the genus Canis—by demonstrating deep evolutionary divergence between taxa, on the order of hundreds of thousands of years, using data from multiple genetic systems. Smith et al.  (2019) have not done this; instead they have misrepresented the content and conclusions of Jackson et al.  (2017), and contributed extraneous arguments that are not relevant to taxonomic decisions. Here we dissect Smith et al.  (2019), identifying misrepresentations, to show that ecological, behavioural and morphological evidence is insufficient to recognise Dingoes as a separate species from other domestic dogs. We reiterate: the correct binomial name for the taxon derived from Gray Wolves (C. lupus) by passive and active domestication, including Dingoes and other domestic dogs, is Canis familiaris. We are strongly sympathetic to arguments about the historical, ecological, cultural, or other significance of the Dingo, but these are issues that will have to be considered outside of the more narrow scope of taxonomy and nomenclature. 

Case of mistaken identity: resolving the taxonomy between Trioza eugeniae Froggatt and T. adventicia Tuthill (Psylloidea: Triozidae)

2019 ◽  
Vol 110 (3) ◽  
pp. 340-351 ◽  
Author(s):  
Gary S. Taylor ◽  
Francesco Martoni
Keyword(s):  
Biological Control ◽  
Control Program ◽  
Distinct Species ◽  
Type Specimens ◽  
Separate Species ◽  
Mistaken Identity ◽  
South Wales ◽  
The Usa ◽  
History Of ◽  
Native And Introduced Ranges

AbstractThe ‘Eugenia psyllid’ or ‘Lilly pilly psyllid’, widely recognized in Australia and in the USA as Trioza eugeniae Froggatt (Hemiptera: Triozidae), is not T. eugeniae, but rather T. adventicia Tuthill. In this study we assessed morphological comparisons of materials from throughout the native and introduced ranges and re-examined original descriptions of both taxa, together with Froggatt's type specimens of T. eugeniae. Furthermore, through DNA barcoding analyses, we confirmed the validity of both T. adventicia and T. eugeniae as separate species. We re-described both species to include additional characters not previously included and designated a lectotype for T. eugeniae. T. eugeniae has smaller fore wings that are slightly more elongate. These lack infuscation around veins R and R1, vein Rs is relatively longer, meeting the costa closer to the wing apex; with certain veins bearing long, fine divergent setae, a character not previously described. It has consistently three inner and one outer metatibial spurs. The male parameres appear narrowly pyriform with a weak dorsolateral lobe and weakly sclerotized apices. T. adventicia has larger fore wings that are slightly more ovate with dark infuscation around veins R and R1; vein Rs is relatively shorter, meeting the costa further from the wing apex, with veins lacking long, fine divergent setae. The usual configuration of two inner and one outer metatibial spurs, previously used to separate the two species, appears inconsistent. The male parameres appear a little more broadly pyriform with slightly more sclerotized apices. T. eugeniae refers to a distinct species which has a restricted distribution only in its native range in southern subcoastal New South Wales, Australia. T. adventicia refers to a separate species, with a natural distribution in eastern subcoastal Australia, but has been introduced widely in southern Australia, to New Zealand and the USA. This study elucidates a long history of misidentification of T. eugeniae in the nursery industry and in almost 30 years of literature on its biological control in the USA. Regardless, the biological control program, unknowingly, targeted the correct species of psyllid, T. adventicia, in its foreign exploration and importation of the appropriate parasitoid as a biocontrol agent in the USA. Despite being firmly entrenched in both the nursery trade and scientific literature, the name T. eugeniae is misapplied. While the acceptance of the valid name, T. adventicia, might be regarded as both problematic and protracted, this is the correct taxonomical attribution.

scholarly journals Veterinary Fusarioses within the United States

2016 ◽  
Vol 54 (11) ◽  
pp. 2813-2819 ◽  
Author(s):  
Kerry O'Donnell ◽  
Deanna A. Sutton ◽  
Nathan Wiederhold ◽  
Vincent A. R. G. Robert ◽  
Pedro W. Crous ◽  
...  
Keyword(s):  
United States ◽  
Dna Sequence ◽  
Species Complex ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
The United States ◽  
Content Type ◽  
Dna Sequence Data ◽  
Species Complexes

Multilocus DNA sequence data were used to assess the genetic diversity and evolutionary relationships of 67Fusariumstrains from veterinary sources, most of which were from the United States. Molecular phylogenetic analyses revealed that the strains comprised 23 phylogenetically distinct species, all but two of which were previously known to infect humans, distributed among eight species complexes. The majority of the veterinary isolates (47/67 = 70.1%) were nested within theFusarium solanispecies complex (FSSC), and these included 8 phylospecies and 33 unique 3-locus sequence types (STs). Three of the FSSC species (Fusarium falciforme,Fusarium keratoplasticum, andFusariumsp. FSSC 12) accounted for four-fifths of the veterinary strains (38/47) and STs (27/33) within this clade. Most of theF. falciformestrains (12/15) were recovered from equine keratitis infections; however, strains ofF. keratoplasticumandFusariumsp. FSSC 12 were mostly (25/27) isolated from marine vertebrates and invertebrates. Our sampling suggests that theFusarium incarnatum-equisetispecies complex (FIESC), with eight mycoses-associated species, may represent the second most important clade of veterinary relevance withinFusarium. Six of the multilocus STs within the FSSC (3+4-eee, 1-b, 12-a, 12-b, 12-f, and 12-h) and one each within the FIESC (1-a) and theFusarium oxysporumspecies complex (ST-33) were widespread geographically, including three STs with transoceanic disjunctions. In conclusion, fusaria associated with veterinary mycoses are phylogenetically diverse and typically can only be identified to the species level using DNA sequence data from portions of one or more informative genes.

scholarly journals Aspergillus lentulus sp. nov., a New Sibling Species of A. fumigatus

2005 ◽  
Vol 4 (3) ◽  
pp. 625-632 ◽  
Author(s):  
S. Arunmozhi Balajee ◽  
Jennifer L. Gribskov ◽  
Edward Hanley ◽  
David Nickle ◽  
Kieren A. Marr
Keyword(s):  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Bootstrap Support ◽  
Mitochondrial Cytochrome ◽  
Phylogenetic Species Concept ◽  
Protein Encoding ◽  
Strong Bootstrap Support ◽  
Dna Pcr ◽  
A New Species

ABSTRACT In a prior study, we identified seven clinical isolates of an Aspergillus sp. that were slow to sporulate in multiple media and demonstrated decreased in vitro susceptibilities to multiple antifungals, including amphotericin B, itraconazole, voriconazole, and caspofungin. These isolates were initially considered to be variants of Aspergillus fumigatus because of differences in mitochondrial cytochrome b sequences and unique randomly amplified polymorphic DNA PCR patterns (S. A. Balajee, M. Weaver, A. Imhof, J. Gribskov, and K. A. Marr, Antimicrob. Agents Chemother. 48: 1197-1203, 2004). The present study was performed to clarify the taxonomic status of these organisms by phylogenetic analyses based on multilocus sequence typing of five genes (the β-tubulin gene, the rodlet A gene, the salt-responsive gene, the mitochondrial cytochrome b gene, and the internal transcribed spacer regions). Results revealed that four of the seven variant isolates clustered together in a clade very distant from A. fumigatus and distinct from other members of the A. fumigatus group. This new clade, consisting of four members, was monophyletic with strong bootstrap support when the protein-encoding regions were analyzed, indicating a new species status under the phylogenetic species concept. Phenotype studies revealed that the variant isolate has smaller conidial heads with diminutive vesicles compared to A. fumigatus and is not able to survive at 48°C. Our findings suggest the presence of a previously unrecognized, potentially drug-resistant Aspergillus species that we designate A. lentulus.

Maluti Mystery: A systematic review of Amietia vertebralis (Hewitt, 1927) and Strongylopus hymenopus (Boulenger, 1920) (Anura: Pyxicephalidae)

Zootaxa ◽  
2008 ◽  
Vol 1962 (1) ◽  
pp. 33-48 ◽  
Author(s):  
JEANNE TARRANT ◽  
MICHAEL J. CUNNINGHAM ◽  
LOUIS H. DU PREEZ
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Original Description ◽  
Type Specimen ◽  
Systematic Position ◽  
Type Specimens ◽  
Morphological Examination ◽  
Species Type ◽  
Original Application

The taxonomic status of Amietia vertebralis and Strongylopus hymenopus, two frogs restricted to the Maluti-Drakensberg highlands in southern Africa, is unclear. Here, morphological examination and phylogenetic analyses elucidate the systematic position of these two species. Type specimens of both species were examined and compared with more recent collections to clarify their identity. These comparisons revealed discrepancies between the original application of these names and their current usage. The holotype and original description of A. vertebralis match specimens from an extant population at that species’ type locality that are currently assigned to S. hymenopus. Furthermore, the type specimen of S. hymenopus is of uncertain provenance and does not match well with either of the forms currently associated with these names. We assessed both intraspecific and interspecific variability using DNA sequence data. Broad sampling of the form currently assigned to A. vertebralis revealed very little genetic variation thereby dispelling the hypothesis that this is a compound taxon. The generic placement of both species within the family Pyxicephalidae was resolved using a combined dataset of mitochondrial 16S rDNA and nuclear RAG1 gene sequences. The form currently recognised as S. hymenopus was excluded from the otherwise monophyletic genus Strongylopus, and was placed instead within Amietia. Based on these data a revised application of both species names is recommended here. Populations currently assigned to Amietia vertebralis are referred to Amietia umbraculata and those attributed to Strongylopus hymenopus are referred instead to Amietia vertebralis.

scholarly journals Penicillium simile sp. nov. revealed by morphological and phylogenetic analysis

2012 ◽  
Vol 62 (2) ◽  
pp. 451-458 ◽  
Author(s):  
Domenico Davolos ◽  
Biancamaria Pietrangeli ◽  
Anna Maria Persiani ◽  
Oriana Maggi
Keyword(s):  
Sequence Data ◽  
Taxonomic Status ◽  
Distinct Species ◽  
Rrna Genes ◽  
Chain Gene ◽  
Sequencing Analysis ◽  
Internal Transcribed Spacer Region ◽  
Protein Coding ◽  
Nuclear Loci ◽  
Dna Sequencing Analysis

The morphology of three phenetically identical Penicillium isolates, collected from the bioaerosol in a restoration laboratory in Italy, displayed macro- and microscopic characteristics that were similar though not completely ascribable to Penicillium raistrickii. For this reason, a phylogenetic approach based on DNA sequencing analysis was performed to establish both the taxonomic status and the evolutionary relationships of these three peculiar isolates in relation to previously described species of the genus Penicillium. We used four nuclear loci (both rRNA and protein coding genes) that have previously proved useful for the molecular investigation of taxa belonging to the genus Penicillium at various evolutionary levels. The internal transcribed spacer region (ITS1–5.8S–ITS2), domains D1 and D2 of the 28S rDNA, a region of the tubulin beta chain gene (benA) and part of the calmodulin gene (cmd) were amplified by PCR and sequenced. Analysis of the rRNA genes and of the benA and cmd sequence data indicates the presence of three isogenic isolates belonging to a genetically distinct species of the genus Penicillium, here described and named Penicillium simile sp. nov. (ATCC MYA-4591T  = CBS 129191T). This novel species is phylogenetically different from P. raistrickii and other related species of the genus Penicillium (e.g. Penicillium scabrosum), from which it can be distinguished on the basis of morphological trait analysis.

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