scholarly journals Multigene phylogeny of the scyphozoan jellyfish family Pelagiidae reveals that the common U.S. Atlantic sea nettle comprises two distinct species (Chrysaora quinquecirrhaandC. chesapeakei)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3863 ◽  
Author(s):  
Keith M. Bayha ◽  
Allen G. Collins ◽  
Patrick M. Gaffney
Keyword(s):  
Gulf Of Mexico ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Source Region ◽  
Historical Review ◽  
Distinct Species ◽  
Chrysaora Quinquecirrha ◽  
Western Africa ◽  
Sea Nettle ◽  
The U.S

BackgroundSpecies of the scyphozoan family Pelagiidae (e.g.,Pelagia noctiluca,Chrysaora quinquecirrha) are well-known for impacting fisheries, aquaculture, and tourism, especially for the painful sting they can inflict on swimmers. However, historical taxonomic uncertainty at the genus (e.g., new genusMawia) and species levels hinders progress in studying their biology and evolutionary adaptations that make them nuisance species, as well as ability to understand and/or mitigate their ecological and economic impacts.MethodsWe collected nuclear (28SrDNA) and mitochondrial (cytochromecoxidase I and16SrDNA) sequence data from individuals of all four pelagiid genera, including 11 of 13 currently recognized species ofChrysaora. To examine species boundaries in the U.S. Atlantic sea nettleChrysaora quinquecirrha, specimens were included from its entire range along the U.S. Atlantic and Gulf of Mexico coasts, with representatives also examined morphologically (macromorphology and cnidome).ResultsPhylogenetic analyses show that the genusChrysaorais paraphyletic with respect to other pelagiid genera. In combined analyses,Mawia, sampled from the coast of Senegal, is most closely related toSanderia malayensis, andPelagiaforms a close relationship to a clade of PacificChrysaoraspecies (Chrysaora achlyos, Chrysaora colorata,Chrysaora fuscescens, andChrysaora melanaster).Chrysaora quinquecirrhais polyphyletic, with one clade from the U.S. coastal Atlantic and another in U.S. Atlantic estuaries and Gulf of Mexico. These genetic differences are reflected in morphology, e.g., tentacle and lappet number, oral arm length, and nematocyst dimensions. Caribbean sea nettles (Jamaica and Panama) are genetically similar to the U.S. Atlantic estuaries and Gulf of Mexico clade ofChrysaora quinquecirrha.DiscussionOur phylogenetic hypothesis for Pelagiidae contradicts current generic definitions, revealing major disagreements between DNA-based and morphology-based phylogenies. A paraphyleticChrysaoraraises systematic questions at the genus level for Pelagiidae; accepting the validity of the recently erected genusMawia, as well as past genera, will require the creation of additional pelagiid genera. Historical review of the species-delineating genetic and morphological differences indicates thatChrysaora quinquecirrhaDesor 1848 applies to the U.S. Coastal AtlanticChrysaoraspecies (U.S. Atlantic sea nettle), while the nameC. chesapeakeiPapenfuss 1936 applies to the U.S. Atlantic estuarine and Gulf of Mexico Chrysaora species (Atlantic bay nettle). We provide a detailed redescription, with designation of a neotype forChrysaora chesapeakei, and clarify the description ofChrysaora quinquecirrha. Since CaribbeanChrysaoraare genetically similar toChrysaora chesapeakei, we provisionally term themChrysaorac.f.chesapeakei. The presence ofMawia benovicioff the coast of Western Africa provides a potential source region for jellyfish introduced into the Adriatic Sea in 2013.

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.

Two new species of the Phimochirus holthuisi complex from the Gulf of Mexico, supported by morphology, color, and genetics (Crustacea: Anomura: Paguridae)

Zootaxa ◽  
2019 ◽  
Vol 4683 (4) ◽  
pp. 531-551
Author(s):  
DARRYL L. FELDER ◽  
RAFAEL LEMAITRE ◽  
CATHERINE CRAIG
Keyword(s):  
New Species ◽  
Gulf Of Mexico ◽  
Continental Shelf ◽  
Gene Sequence ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Two New Species ◽  
Molecular Phylogenetic ◽  
Gene Sequence Data

Coloration, gene-sequence data (H3, 12s, 16s), and subtle features in morphology support the description of two new species, both formerly regarded to represent accepted variants of Phimochirus holthuisi s.l. While color in life consistently separates these species from P. holthuisi s.s. and from each other, morphological distinctions are subtle and less than absolute in small specimens, being based on ventral spine counts of walking leg dactyls and relative development of the superior crest on the major chela. Molecular phylogenetic analyses clearly support the separation of sister clades, representing two new species, from P. holthuisi s.s. as well as other congeners available for analysis. Both of the new species are presently known to occur widely throughout the northern Gulf of Mexico, though one occurs more commonly in the northeastern and southeastern Gulf, and may range as far south as Suriname. The other has been taken primarily in the northwestern Gulf, and is not known from outside Gulf waters. While both of the new species appear restricted to relatively deep subtidal waters of the continental shelf, Phimochirus holthuisi s.s. is instead more commonly found in shallow nearshore tropical waters on or near coral reefs. Previous literature reports of P. holthuisi usually represent, at least in part, one or both of these two new species. 

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.

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.

scholarly journals Sarcocystis cristata sp. nov. (Apicomplexa, Sarcocystidae) in the imported great blue turaco Corythaeola cristata (Aves, Musophagidae)

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ondřej Máca ◽  
David González-Solís
Keyword(s):  
Czech Republic ◽  
New Species ◽  
Phylogenetic Analyses ◽  
Central Africa ◽  
Distinct Species ◽  
Valid Species ◽  
Intermediate Hosts ◽  
Leg Muscles ◽  
Western Africa ◽  
Private Breeder

Abstract Background Species of Sarcocystis are parasitic protozoa in poikilothermic and homeothermic animals. Out of the 26 valid species in birds as intermediate hosts, none has been reported in those of the order Musophagiformes, such as the great blue turaco Corythaeola cristata (Vieillot, 1816), which is a bird endemic to Central and Western Africa. The examination of great blue turacos imported from the Central Africa Republic to Czech Republic allowed the morphological and molecular characterization of a new species of Sarcocystis. Methods Four turacos imported from the Central Africa Republic to a private breeder (Czech Republic) underwent parasitological examination for the presence of sarcocysts through wet mounts of breast, heart and leg muscles. Found parasites were molecularly and histologically studied by four loci (18S rRNA, 28S rRNA, ITS1 and cox1) and haematoxylin and eosin staining, respectively. Results Three out of four examined birds harboured numerous sarcocysts in the breast and leg muscles. No macroscopic lesions where observed. Sarcocysts were microscopic, elongate and ribbon-shaped with a wall characterised by the presence of finger-shaped villar protrusions and filled with numerous elongate, banana-shaped bradyzoites, 11.87–14.84 × 2.05–2.92 µm in size. The new species was most closely related to Sarcocystisalbifronsi, Sarcocystisanasi, Sarcocystisatraii, Sarcocystischloropusae, Sarcocystisrileyi, Sarcocystiswenzeli and Sarcocystis sp. isolate from chicken in the four loci. Conclusions To our knowledge, this is the first species of Sarcocystis found in a musophagiform bird worldwide. Genetically, S. cristata sp. nov. represents a distinct species. Phylogenetic analyses are useful for predicting potential definitive hosts of the new Sarcocystis species.

scholarly journals Sarcocystis Cristata sp. nov. (Apicomplexa, Sarcocystidae) in The Imported Great Blue Turaco Corythaeola Cristata (Aves, Musophagidae) from Czech Republic

2020 ◽  
Author(s):  
Ondřej Máca ◽  
David González
Keyword(s):  
Czech Republic ◽  
New Species ◽  
Phylogenetic Analyses ◽  
Central Africa ◽  
Distinct Species ◽  
Leg Muscles ◽  
Western Africa ◽  
Private Breeder ◽  
Haematoxylin And Eosin Stain

Abstract Background: Species of Sarcocystis are parasitic protozoan in poikilothermic and homeothermic animals. Out of the 25 valid avian species, none has been reported in birds of the order Musophagiformes, as the great blue turaco Corythaeola cristata (Vieillot, 1816), which is an endemic bird inhabiting Central and Western Africa. The examination of great blue turacos imported from the Central Africa Republic to Czech Republic allowed the morphological and molecular characterization of a new species of Sarcocystis.Methods: Four turacos imported from the Central Africa Republic to private breeder (Czech Republic) were parasitologically examined through wet mounts of breast, heart and legs muscles for the presence of sarcocysts. Found parasites were molecular and histologically studied by 4 loci (18S rRNA, 28S rRNA, ITS1 and cox1) and haematoxylin and eosin stain, respectively. Results: Three out of 4 examined birds (prevalence: 75%) harboured numerous sarcocysts in breast and leg muscles. No macroscopic lesions where observed. Sarcocysts were microscopic, elongate and ribbon-shaped with a wall characterised by the presence of finger-shaped villar protrusions. The new species is molecularly similar to S. albifronsi, S. anasi, S. atraii, S. chloropusae, S. lari and S. rileyi) in the four loci. Conclusions: This is the first species of Sarcocystis in a musophagiform bird around the world. Genetically, S. cristata sp. nov. represents a distinct species. Phylogenetic analyses are useful for predicting potential definitive hosts of the new Sarcocystis species.

scholarly journals Molecular systematics of New Zealand Cyanoramphus parakeets: conservation of Orange-fronted and Forbes' Parakeets

2000 ◽  
Vol 10 (3) ◽  
pp. 211-239 ◽  
Author(s):  
W. M. Boon ◽  
J. C. Kearvell ◽  
C. H. Daugherty ◽  
G. K. Chambers
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
Biological Species ◽  
Biological Species Concept ◽  
Allozyme Data ◽  
Dna Sequence Data ◽  
Data Support ◽  
High Conservation

The controversy that presently surrounds the taxonomy of the Orange-fronted Cyanoramphus malherbi and Forbes' C. forbesi Parakeets has important implications for the conservation of both birds. Both taxa are critically endangered, but consensus regarding their specific status has not yet been achieved. We present mitochondrial DNA sequences for the cytochrome b gene and the control region from 17 Cyanoramphus parakeets representing nine populations and six taxa together with field observations of courtship and breeding behaviour in a sympatric population of Orange-fronted and Yellow-crowned Parakeets C. auriceps. Field data support species status of the Orange-fronted Parakeet under the Biological Species Concept. Phylogenetic analyses of our DNA sequence data support earlier hypotheses based on allozyme data that both Orange-fronted and Forbes' Parakeets represent distinct species under four species concepts and indicate that high conservation priority is warranted for both taxa.

scholarly journals Using Core Genome Alignments To Assign Bacterial Species

mSystems ◽  
2018 ◽  
Vol 3 (6) ◽  
Author(s):  
Matthew Chung ◽  
James B. Munro ◽  
Hervé Tettelin ◽  
Julie C. Dunning Hotopp
Keyword(s):  
High Resolution ◽  
Core Genome ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Distinct Species ◽  
Obligate Intracellular ◽  
Wide Range ◽  
Obligate Intracellular Bacteria ◽  
Neighbor Network

ABSTRACTWith the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method to assign species designations is needed that is consistent with classically obtained taxonomic analyses. This is particularly acute for unculturable, obligate intracellular bacteria with which classically defined methods, like DNA-DNA hybridization, cannot be used, such as those in theRickettsiales. In this study, we generated nucleotide-based core genome alignments for a wide range of genera with classically defined species, as well as those within theRickettsiales. We created a workflow that uses the length, sequence identity, and phylogenetic relationships inferred from core genome alignments to assign genus and species designations that recapitulate classically obtained results. Using this method, most classically defined bacterial genera have a core genome alignment that is ≥10% of the average input genome length. BothAnaplasmaandNeorickettsiafail to meet this criterion, indicating that the taxonomy of these genera should be reexamined. Consistently, genomes from organisms with the same species epithet have ≥96.8% identity of their core genome alignments. Additionally, these core genome alignments can be used to generate phylogenomic trees to identify monophyletic clades that define species and neighbor-network trees to assess recombination across different taxa. By these criteria,Wolbachiaorganisms are delineated into species different from the currently used supergroup designations, whileRickettsiaorganisms are delineated into 9 distinct species, compared to the current 27 species. By using core genome alignments to assign taxonomic designations, we aim to provide a high-resolution, robust method to guide bacterial nomenclature that is aligned with classically obtained results.IMPORTANCEWith the increasing availability of genome sequences, we sought to develop and apply a robust, portable, and high-resolution method for the assignment of genera and species designations that can recapitulate classically defined taxonomic designations. Using cutoffs derived from the lengths and sequence identities of core genome alignments along with phylogenetic analyses, we sought to evaluate or reevaluate genus- and species-level designations for diverse taxa, with an emphasis on the orderRickettsiales, where species designations have been applied inconsistently. Our results indicate that theRickettsiagenus has an overabundance of species designations, that the currentAnaplasmaandNeorickettsiagenus designations are both too broad and need to be divided, and that there are clear demarcations ofWolbachiaspecies that do not align precisely with the existing supergroup designations.

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