Resurrecting a subgenus to genus: molecular phylogeny ofEuphylliaandFimbriaphyllia(order Scleractinia; family Euphyllidae; clade V)

BackgroundThe corallum is crucial in building coral reefs and in diagnosing systematic relationships in the order Scleractinia. However, molecular phylogenetic analyses revealed a paraphyly in a majority of traditional families and genera among Scleractinia showing that other biological attributes of the coral, such as polyp morphology and reproductive traits, are underutilized. Among scleractinian genera, theEuphyllia, with nine nominal species in the Indo-Pacific region, is one of the groups that await phylogenetic resolution. Multiple genetic markers were used to construct the phylogeny of sixEuphylliaspecies, namelyE. ancora, E. divisa, E. glabrescens, E. paraancora, E. paradivisa,andE. yaeyamaensis.The phylogeny guided the inferences on the contributions of the colony structure, polyp morphology, and life history traits to the systematics of the largest genus in Euphyllidae (clade V) and, by extension, to the rest of clade V.ResultsAnalyses of cytochrome oxidase 1 (cox1), cytochrome b (cytb), and β-tubulin genes of 36 colonies representingEuphylliaand a confamilial species,Galaxea fascicularis,reveal two distinct groups in theEuphylliathat originated from different ancestors.Euphyllia glabrescensformed a separate group.Euphyllia ancora, E. divisa, E. paraancora, E. paradivisa,andE. yaeyamaensisclustered together and diverged from the same ancestor asG. fascicularis.The 3′-end of thecox1gene ofEuphylliawas able to distinguish morphospecies.DiscussionSpecies ofEuphylliawere traditionally classified into two subgenera,EuphylliaandFimbriaphyllia,which represented a dichotomy on colony structure. The paraphyletic groups retained the original members of the subgenera providing a strong basis for recognizingFimbriaphylliaas a genus. However, colony structure was found to be a convergent trait betweenEuphylliaandFimbriaphyllia,while polyp shape and length, sexuality, and reproductive mode defined the dichotomy better. Species in a genus are distinguished by combining polyp morphology and colony form. The cluster ofE. glabrescensof theEuphylliagroup is a hermaphroditic brooder with long, tubular tentacles with knob-like tips, and a phaceloid colony structure. TheFimbriaphylliagroup, withF. paraancora, F. paradivisa, F. ancora, F. divisa,andF. yaeyamaensis,are gonochoric broadcast spawners with short polyps, mixed types of tentacle shapes, and a phaceloid or flabello-meandroid skeleton. Soft-tissue morphology ofG. fascicularisandCtenella chagiuswere found to be consistent with the dichotomy.ConclusionsThe paraphyly of the original members of the previous subgenera justify recognizingFimbriaphylliaas a genus. The integrated approach demonstrates that combining polyp features, reproductive traits, and skeletal morphology is of high systematic value not just toEuphylliaandFimbriaphylliabut also to clade V; thus, laying the groundwork for resolving the phylogeny of clade V.

Download Full-text

A glimpse in the dark? A first phylogenetic approach in a widespread freshwater snail from tropical Asia and northern Australia (Cerithioidea, Thiaridae)

Zoosystematics and Evolution ◽

10.3897/zse.95.34486 ◽

2019 ◽

Vol 95 (2) ◽

pp. 373-390 ◽

Cited By ~ 1

Author(s):

Dusit Boonmekam ◽

Duangduen Krailas ◽

France Gimnich ◽

Marco T. Neiber ◽

Matthias Glaubrecht

Keyword(s):

Phylogenetic Analyses ◽

Molecular Genetic ◽

Reproductive Mode ◽

Freshwater Snail ◽

Shell Morphology ◽

Integrative Approach ◽

Nominal Species ◽

Oriental Region ◽

Tropical Asia ◽

Tropical Areas

Thiaridae are a speciose group of freshwater snails in tropical areas including a high number of described nominal taxa for which modern revisions are mostly lacking. Using an integrative approach, the systematic status of a group of thiarids from the Oriental region, including the nominal speciesMelaniaasperaandM.rudis, is reassessed on the basis of shell morphology and biometry, radula dentition patterns, and reproductive biology along with molecular genetic methods. Our results suggest that populations from the Oriental region cannot be distinguished on the basis of shell morphology, radula characters and their reproductive mode and are monophyletic based on mitochondrial sequences. Hence,M.rudiswithM.asperaare regarded as belonging to the same species along with several other nominal taxa that were previously included inM.rudis. Moreover, populations from Thailand and Australia, from where the species was not previously recorded, could be shown to form a monophyletic group together with samples from Indonesia. However, a generic affiliation withThiara, in which the investigated taxa were often included in the past, was not supported in our phylogenetic analyses, highlighting the need for a comprehensive revision of the genus-group systematics of Thiaridae as a whole.

Download Full-text

Actin type I introns offer potential for increasing phylogenetic resolution in Asterochloris (Chlorophyta: Trebouxiophyceae)

The Lichenologist ◽

10.1017/s0024282906005779 ◽

2006 ◽

Vol 38 (5) ◽

pp. 435-440 ◽

Cited By ~ 21

Author(s):

Matthew P. NELSEN ◽

Andrea GARGAS

Keyword(s):

Population Genetics ◽

Phylogenetic Analyses ◽

Species Concepts ◽

Its Rdna ◽

Type I ◽

Phylogenetic Resolution

Primers are presented to amplify an intron-containing portion of the actin type I locus from Asterochloris algae. The amount of variation and phylogenetic resolution provided by the ITS rDNA are compared with that from the actin locus. The number of variable and parsimony-informative sites within the actin locus was drastically higher than that of the ITS. Phylogenetic analyses of the ITS resulted in poorly resolved trees with low support values. In contrast, phylogenetic analyses of the actin locus yielded trees with better support and resolution. It is concluded that the actin type I introns will be useful for studies investigating species concepts and population genetics.

Download Full-text

Systematic status of Campydora Cobb, 1920 (Nematoda: Campydorina)

Nematology ◽

10.1163/156854103322746878 ◽

2003 ◽

Vol 5 (5) ◽

pp. 699-711 ◽

Cited By ~ 6

Author(s):

Peter Mullin ◽

Timothy Harris ◽

Thomas Powers

Keyword(s):

Maximum Likelihood ◽

Ribosomal Dna ◽

Dna Sequences ◽

Maximum Parsimony ◽

Phylogenetic Analyses ◽

Small Subunit ◽

Systematic Position ◽

Nominal Species ◽

Competing Hypotheses ◽

Small Subunit Ribosomal Dna

AbstractThe systematic position of Campydora Cobb, 1920, which possesses many unique morphological features, especially in pharyngeal structure and stomatal armature, has long been a matter of uncertainty with the 'position of the Campydorinae' (containing only Campydora) being questionable. A review of the morphology of C. demonstrans, the only nominal species of Campydora concluded that the species warranted placement as the sole member of a monotypic suborder, Campydorina, in the order Dorylaimida. Others placed Campydorina in the order Enoplida. We conducted phylogenetic analyses, using 18s small subunit ribosomal DNA sequences generated from a number of taxa in the subclasses Enoplia and Dorylaimia, to evaluate these competing hypotheses. Although precise taxonomic placement of the genus Campydora and the identity of its closest living relatives is in need of further investigation, our analyses, under maximum parsimony, distance, and maximum likelihood criteria, unambiguously indicate that Campydora shares a common, more recent, ancestry with genera such as Alaimus, Pontonema, Tripyla and Ironus (Enoplida), rather than with any members of Dorylaimida, Mononchida or Triplonchida.

Download Full-text

Molecular forms of Anopheles subpictus and Anopheles sundaicus in the Indian subcontinent

Malaria Journal ◽

10.1186/s12936-020-03492-2 ◽

2020 ◽

Vol 19 (1) ◽

Author(s):

Ankita Sindhania ◽

Manoj K. Das ◽

Gunjan Sharma ◽

Sinnathamby N. Surendran ◽

B. R. Kaushal ◽

...

Keyword(s):

Sibling Species ◽

Molecular Form ◽

Indian Subcontinent ◽

Phylogenetic Analyses ◽

Coastal Areas ◽

Molecular Forms ◽

Nominal Species ◽

Anopheles Subpictus ◽

Species Complexes ◽

Molecular Phylogenetic

Abstract Background Anopheles subpictus and Anopheles sundaicus are closely related species, each comprising several sibling species. Ambiguities exist in the classification of these two nominal species and the specific status of members of these species complexes. Identifying fixed molecular forms and mapping their spatial distribution will help in resolving the taxonomic ambiguities and understanding their relative epidemiological significance. Methods DNA sequencing of Internal Transcribed Spacer-2 (ITS2), 28S-rDNA (D1-to-D3 domains) and cytochrome oxidase-II (COII) of morphologically identified specimens of two nominal species, An. subpictus sensu lato (s.l.) and An. sundaicus s.l., collected from the Indian subcontinent, was performed and subjected to genetic distance and molecular phylogenetic analyses. Results Molecular characterization of mosquitoes for rDNA revealed the presence of two molecular forms of An. sundaicus s.l. and three molecular forms of An. subpictus s.l. (provisionally designated as Form A, B and C) in the Indian subcontinent. Phylogenetic analyses revealed two distinct clades: (i) subpictus clade, with a single molecular form of An. subpictus (Form A) prevalent in mainland India and Sri Lanka, and (ii) sundaicus clade, comprising of members of Sundaicus Complex, two molecular forms of An. subpictus s.l. (Form B and C), prevalent in coastal areas or islands in Indian subcontinent, and molecular forms of An. subpictus s.l. reported from Thailand and Indonesia. Based on the number of float-ridges on eggs, all An. subpictus molecular Form B were classified as Species B whereas majority (80%) of the molecular Form A were classified as sibling species C. Fixed intragenomic sequence variation in ITS2 with the presence of two haplotypes was found in molecular Form A throughout its distribution. Conclusion A total of three molecular forms of An. subpictus s.l. and two molecular forms of An. sundaicus s.l. were recorded in the Indian subcontinent. Phylogenetically, two forms of An. subpictus s.l. (Form B and C) prevalent in coastal areas or islands in the Indian subcontinent and molecular forms reported from Southeast Asia are members of Sundaicus Complex. Molecular Form A of An. subpictus is distantly related to all other forms and deserve a distinct specific status.

Download Full-text

Species Delineation Within the Euwallacea fornicatus (Coleoptera: Curculionidae) Complex Revealed by Morphometric and Phylogenetic Analyses

Insect Systematics and Diversity ◽

10.1093/isd/ixy018 ◽

2018 ◽

Vol 2 (6) ◽

Cited By ~ 17

Author(s):

Demian F Gomez ◽

James Skelton ◽

M Sedonia Steininger ◽

Richard Stouthamer ◽

Paul Rugman-Jones ◽

...

Keyword(s):

Species Complex ◽

Phylogenetic Analyses ◽

Integrated Approach ◽

Type Specimen ◽

Morphological Characters ◽

Morphological Evidence ◽

Pest Species ◽

Species Delineation ◽

Genetic Lineages ◽

C Subunit

Abstract The ambrosia beetle Euwallacea fornicatus Eichhoff sensu lato is a complex of genetically divergent emerging pests responsible for damages to tree industries and ecosystems around the world. All lineages within the species complex are currently considered morphologically identical, presenting problems for their delineation and highlighting the shortcomings of species concepts based solely on type-specimen morphology. The objectives of this work were to 1) broaden the geographic sampling of the E. fornicatus complex in Asia, 2) reconstruct relationships between clades and populations, 3) find morphological characters or combinations of characters which are useful in delimiting the genetic lineages of the E. fornicatus species complex, and 4) propose taxonomic delimitation of species where morphology and phylogenetic identity correlate. Our integrated approach using molecular and morphological evidence suggests four clades that differ morphologically, but with overlap, therefore, cytochrome oxidase c subunit I (COI) barcoding remains necessary for assigning specimens to a clade. The following taxonomic changes are proposed: E. fornicatus (Eichhoff 1868) (= ‘Tea Shot Hole Borer Clade a’); E. fornicatior (Eggers 1923), stat. rev. (= ‘Tea Shot Hole Borer Clade b’); E. whitfordiodendrus (Schedl 1942), stat. rev. (= ‘Polyphagous Shot Hole Borer’); and E. kuroshio Gomez and Hulcr, sp. nov. (= ‘Kuroshio Shot Hole Borer’). This approach delivers a practical, evidence-based guidance for species delineation that can address overlapping variation in morphological characters of an emerging pest species complex.

Download Full-text

Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae)

Plants ◽

10.3390/plants9091143 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1143 ◽

Cited By ~ 1

Author(s):

Hang Ran ◽

Yanyan Liu ◽

Cui Wu ◽

Yanan Cao

Keyword(s):

Genomic Structure ◽

Phylogenetic Analyses ◽

Sister Relationship ◽

Plastome Evolution ◽

Chloroplast Genomes ◽

Flora Of China ◽

Phylogenetic Resolution ◽

Sister Relationships ◽

Phylogenomic Analyses ◽

Cp Genome

Phylogenetic analyses of complete chloroplast genome sequences have yielded significant improvements in our understanding of relationships in the woody flowering genus Viburnum (Adoxaceae, Dipsacales); however, these relationships were evaluated focusing only on Viburnum species within Central and South America and Southeast Asia. By contrast, despite being a hotspot of Viburnum diversity, phylogenetic relationships of Viburnum species in China are less well known. Here, we characterized the complete chloroplast (cp) genomes of 21 Viburnum species endemic to China, as well as three Sambucus species. These 24 plastomes were highly conserved in genomic structure, gene order and content, also when compared with other Adoxaceae. The identified repeat sequences, simple sequence repeats (SSRs) and highly variable plastid regions will provide potentially valuable genetic resources for further population genetics and phylogeographic studies on Viburnum and Sambucus. Consistent with previous combined phylogenetic analyses of 113 Viburnum species, our phylogenomic analyses based on the complete cp genome sequence dataset confirmed the sister relationship between Viburnum and the Sambucus-Adoxa-Tetradoxa-Sinadoxa group, the monophyly of four recognized sections in Flora of China (i.e., Viburnum sect. Tinus, Viburnum sect. Solenotinus, Viburnum sect. Viburnum and Viburnum sect. Pseudotinus) and the nonmonophyly of Viburnum sect. Odontotinus and Viburnum sect. Megalotinus. Additionally, our study confirmed the sister relationships between the clade Valvatotinus and Viburnum sect. Pseudotinus, as well as between Viburnum sect. Opulus and the Odontotinus-Megalotinus group. Overall, our results clearly document the power of the complete cp genomes in improving phylogenetic resolution, and will contribute to a better understanding of plastome evolution in Chinese Adoxaceae.

Download Full-text

Molecular divergence between two sympatric species of Dondice (Mollusca: Nudibranchia) with distinct feeding specializations

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315413000465 ◽

2013 ◽

Vol 93 (7) ◽

pp. 1887-1893 ◽

Cited By ~ 2

Author(s):

Luis Gonzalez ◽

Dieta Hanson ◽

Ángel Valdés

Keyword(s):

Feeding Habits ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Sympatric Species ◽

Developmental Differences ◽

Nominal Species ◽

Western Atlantic ◽

16S Gene ◽

Putative Species ◽

Gene Data

Analysis of mitochondrial (16S) and nuclear (H3) gene data using phylogenetic and population genetic approaches has revealed some genetic differences between two putative species of western Atlantic Dondice opisthobranchs that feed differentially on hydroids or on up-side-down jellies of the genus Cassiopeia. These results partially support the validity of the species Dondice parguerensis, which was described for the jelly-eating Dondice. However, phylogenetic analyses revealed that the hydroid-feeding species Dondice occidentalis and D. parguerensis are not reciprocally monophyletic and they are identical for the nuclear H3 gene. Although there are morphological and developmental differences between these two nominal species, the molecular data are inconclusive. A possible explanation is that the two putative species are in the process of speciation due to different feeding habits, resulting in the presence of genetic synapomorphies in D. parguerensis, but only in the more variable 16S gene. Because the ranges D. occidentalis and D. parguerensis overlap and there are no obvious barriers to gene flow between the two putative species, this may constitute a possible example of incipient sympatric speciation in benthic marine organisms.

Download Full-text

Variation of Reproductive Traits and Female Body Size in the Most Widely-Ranging Terrestrial Reptile: Testing the Effects of Reproductive Mode, Lineage, and Climate

Evolutionary Biology ◽

10.1007/s11692-013-9247-2 ◽

2013 ◽

Vol 40 (3) ◽

pp. 420-438 ◽

Cited By ~ 20

Author(s):

Evgeny S. Roitberg ◽

Valentina N. Kuranova ◽

Nina A. Bulakhova ◽

Valentina F. Orlova ◽

Galina V. Eplanova ◽

...

Keyword(s):

Body Size ◽

Female Body ◽

Reproductive Traits ◽

Reproductive Mode ◽

Female Body Size

Download Full-text

Molecular characterization and phylogenetic analyses of Lophodermella needle pathogens (Rhytismataceae) on Pinus species in the USA and Europe

PeerJ ◽

10.7717/peerj.11435 ◽

2021 ◽

Vol 9 ◽

pp. e11435

Author(s):

Jessa P. Ata ◽

Kelly S. Burns ◽

Suzanne Marchetti ◽

Isabel A. Munck ◽

Ludwig Beenken ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Ribosomal Subunit ◽

Elongation Factor ◽

Translation Elongation ◽

Phenotypic Characters ◽

Elongation Factor 1 Alpha ◽

The Usa ◽

Phylogenetic Resolution ◽

Elongation Factor 1

Increasing prevalence of conifer needle pathogens globally have prompted further studies on pathogen identification and a better understanding of phylogenetic relationships among needle pathogens. Several Lophodermella species can be aggressive pathogens causing needle cast in natural pine forests in the USA and Europe. However, their relationships with other Rhytismataceae species have historically been based on similarities of only limited phenotypic characters. Currently, no molecular studies have been completed to elucidate their relationships with other Lophodermella needle pathogens. This study collected and sequenced three gene loci, namely: internal transcribed spacer, large ribosomal subunit, and translation elongation factor 1-alpha, from five Lophodermella needle pathogens from North America (L. arcuata, L. concolor, L. montivaga) and Europe (L. conjuncta and L. sulcigena) to distinguish phylogeny within Rhytismatacaeae, including Lophophacidium dooksii. Phylogenetic analyses of the three loci revealed that all but L. conjuncta that were sampled in this study consistently clustered in a well-supported clade within Rhytismataceae. The multi-gene phylogeny also confirmed consistent nesting of L. dooksii, a needle pathogen of Pinus strobus, within the clade. Potential synapomorphic characters such as ascomata position and ascospore shape for the distinct clade were also explored. Further, a rhytismataceous species on P. flexilis that was morphologically identified as L. arcuata was found to be unique based on the sequences at the three loci. This study suggests a potential wider range of host species within the genus and the need for genetic characterization of other Lophodermella and Lophophacidium species to provide a higher phylogenetic resolution.

Download Full-text

A review of Euryoryzomys legatus (Rodentia, Sigmodontinae): morphological redescription, cytogenetics, and molecular phylogeny

PeerJ ◽

10.7717/peerj.9884 ◽

2020 ◽

Vol 8 ◽

pp. e9884

Author(s):

Mariana D. Guilardi ◽

Pablo Jayat ◽

Marcelo Weksler ◽

James L. Patton ◽

Pablo Edmundo Ortiz ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Phylogenetic Reconstruction ◽

Chromosome Complement ◽

Integrated Approach ◽

Morphological Characters ◽

Valid Species ◽

Data Types ◽

Comparative Cytogenetics ◽

Morphometric Characters ◽

The Status

The taxonomic history of Euryoryzomys legatus has been complex and controversial, being either included in the synonymy of other oryzomyine species or considered as a valid species, as in the most recent review of the genus. Previous phylogenetic analyses segregated E. legatus from E. russatus, its putative senior synonym, but recovered it nested within E. nitidus. A general lack of authoritative evaluation of morphological attributes, details of the chromosome complement, or other data types has hampered the ability to choose among alternative taxonomic hypotheses, and thus reach a general consensus for the status of the taxon. Herein we revisit the status of E. legatus using an integrated approach that includes: (1) a morphological review, especially centered on specimens from northwestern Argentina not examined previously, (2) comparative cytogenetics, and (3) phylogenetic reconstruction, using mitochondrial genes. Euryoryzomys legatus is morphologically and phylogenetically distinct from all other species-level taxa in the genus, but its 2n=80, FN=86 karyotype is shared with E. emmonsae, E. nitidus, and E. russatus. Several morphological and morphometric characters distinguish E. legatus from other species of Euryoryzomys, and we provide an amended diagnosis for the species. Morphological characters useful in distinguishing E. legatus from E. nitidus, its sister taxon following molecular analyses, include: larger overall size, dorsal fur with a strong yellowish brown to orange brown tinge, flanks and cheeks with an orange lateral line, ventral color grayish-white with pure white hairs present only on the chin, presence of a thin blackish eye-ring, tail bicolored, presence of an alisphenoid strut and a well-developed temporal and lambdoid crests in the skull, and a labial cingulum on M3. Molecular phylogenetic analyses recovered E. legatus as a monophyletic group with high support nested within a paraphyletic E. nitidus; genetic distances segregated members of both species, except for an exemplar of E. nitidus. Our integrated analyses reinforce E. legatus as a full species, but highlight that E. macconnelli, E. emmonsae, and E. nitidus each may be a species complex and worthy of systematic attention. Finally, we also evaluated the chromosome evolution of the genus within a phylogenetic context.

Download Full-text