Porcelain crabs of the genera Pachycheles Stimpson and Neopisosoma Haig (Decapoda : Anomura : Porcellanidae): new premises based on molecular data and comments on phylogenetic relationships in the family

2016 ◽  
Vol 30 (5) ◽  
pp. 509
Author(s):  
Ivana Miranda ◽  
Fernando L. Mantelatto
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Phylogenetic Reconstruction ◽  
Morphological Characteristics ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Significant Advance ◽  
Body Region ◽  
Isthmus Of Panama ◽  
Porcelain Crabs

Porcellanidae Haworth, 1825 is a family of marine anomuran crabs distributed throughout tropical and temperate regions of all the oceans, typically littoral and sublittoral waters, with a considerable diversity of lifestyles, habitats and colouration. Pachycheles Stimpson, 1858 and Neopisosoma Haig, 1960 share, among other morphological characteristics, the fragmentation of the lateral carapace walls. The morphology of this body region was key to supporting the establishment of Neopisosoma, which increased uncertainty about the taxonomic status of these genera due to the high intraspecific variation of this character. Our study reconstructs the phylogenetic relationship between Pachycheles and Neopisosoma based on mitochondrial and nuclear DNA sequences to evaluate whether these are valid taxa. While Pachycheles seems to be monophyletic, the position of Neopisosoma mexicanum (Streets, 1871) indicates that the group is polyphyletic, and deserves further investigation. Pachycheles is revealed to be older than Neopisosoma, and likely originated in the Indo-Pacific, later spreading to the American continent during the early Tertiary. Neopisosoma may have arisen much later in the Caribbean Province before the closure of the Isthmus of Panama, explaining its distribution, which is restricted mainly to Central America. The inclusion of a considerable number of species from both genera represents a significant advance in the study of this controversial group. The phylogenetic reconstruction of Pachycheles unveiled clades corroborated by morphology, but also revealed unclear relationships, which may indicate the potential existence of cryptic species.

A molecular phylogeny of the “Madascincus polleni species complex”, with description of a new species of scincid lizard from the coastal dune area of northern Madagascar

Zootaxa ◽  
2011 ◽  
Vol 2876 (1) ◽  
pp. 1 ◽  
Author(s):  
AURÉLIEN MIRALLES ◽  
JÖRN KÖHLER ◽  
FRANK GLAW ◽  
MIGUEL VENCES
Keyword(s):  
Dna Sequences ◽  
Species Complex ◽  
Nuclear Dna ◽  
Taxonomic Status ◽  
Nominal Species ◽  
Morphological Examination ◽  
Closely Related Species ◽  
A New Species ◽  
Evolutionary Lineages ◽  
Dune Area

The present paper constitutes a study on a taxonomically confusing group of closely related species belonging to the Malagasy skink genus Madascincus, currently encompassing the nominal species M. polleni, M. intermedius and M. stumpffi. Based on combined analyses of mitochondrial and nuclear DNA sequences (ND1 and RAG2 genes, respectively), and morphological examination, we provide evidence for the existence of at least four distinct evolutionary lineages within this complex: Madascincus stumpffi; Madascincus arenicola sp. nov. from northern Madagascar; and two cryptic species morphologically similar to the name-bearing types of M. polleni and M. intermedius. The two latter species, although genetically distinct, appear to be morphologically indistinguishable and their taxonomic status cannot be resolved until a better sampling will be available.

Molecular phylogeny of the Fusarium solani species complex (FSSC) isolated from soils in Iran

Botany ◽  
2014 ◽  
Vol 92 (11) ◽  
pp. 815-820 ◽  
Author(s):  
Khosrow Chehri
Keyword(s):  
Dna Sequences ◽  
Fusarium Solani ◽  
Species Complex ◽  
Agricultural Soils ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Taxonomic Status ◽  
Its Region ◽  
Phylogenetic Study ◽  
Fusarium Solani Species Complex

Members of Fusarium solani species complex (FSSC) are frequently isolated from soils, food, feeds, trees, and to some extent from humans and other animals. The taxonomic status of these fungi is being revised but no attempt has been made to identify those isolated in Iran, a mountainous country with a high biodiversity. The objective of the present research was to study the phylogenetic diversity of FSSC strains recovered from soils in Iran by analyzing morphological characteristics and DNA sequences. A total of 65 strains belonging to the FSSC were recovered from agricultural soils in western Iran. Based on differences in their morphological characters, 25 strains were selected for phylogenetic analysis employing translation elongation factor-1α (tef1) and internal transcribed spacer (ITS) region sequences. Comparisons of DNA sequence data revealed that all isolates belonged to Fusarium falciforme, Fusarium keratoplasticum, Fusarium petroliphilum, the unnamed species FSSC 5, and unknown species of Fusarium, which represents a new lineage within members of Clade 3. Based on morphological features and phylogenetic study, F. keratoplasticum and F. petroliphilum were reported for the first time in Iran.

Syntopy of cryptic Phyllomys (Rodentia: Echimyidae) species: description of the karyotype of Phyllomys nigrispinus and an expansion of the geographic distribution of Phyllomys sulinus

Mammalia ◽  
2018 ◽  
Vol 82 (3) ◽  
pp. 266-275 ◽  
Author(s):  
Ana Cláudia Delciellos ◽  
Ana Carolina Loss ◽  
Marcia Aguieiras ◽  
Lena Geise ◽  
Oscar Rocha-Barbosa
Keyword(s):  
Atlantic Forest ◽  
Molecular Analysis ◽  
Dna Sequences ◽  
National Park ◽  
Phylogenetic Reconstruction ◽  
First Record ◽  
Molecular Data ◽  
Geographic Range ◽  
Undescribed Species ◽  
First Time

Abstract The echimyid rodents of the genus Phyllomys are medium-sized arboreal spiny rats endemic to the Atlantic Forest of Brazil. The genus is currently composed of 13 species, although there are at least four other undescribed species. The ecology, zoogeography and diversity of the genus are still poorly understood. Here, we provide the first record of Phyllomys sulinus from the Brazilian state of Rio de Janeiro, based on a specimen collected in the Serra da Bocaina National Park, which extends the known geographic range of the species approximately 130 km to the northeast. At this site, P. sulinus occurred in syntopy with the cryptic Phyllomys nigrispinus. We describe the karyotype of P. nigrispinus for the first time and identify two different diploid numbers (2n=84 and 85). We also conducted a molecular analysis of the cytochrome b gene of five specimens, which we identified by phylogenetic reconstruction. Our findings reinforce the importance of molecular data, such as DNA sequences, and karyotypes for the differentiation of cryptic, syntopic species.

Description of a new genus and two new species of killifish (Cyprinodontiformes: Nothobranchiidae) from West Africa, with a discussion of the taxonomic status of Aphyosemion maeseni Poll, 1941

Zootaxa ◽  
2009 ◽  
Vol 2294 (1) ◽  
pp. 1-22 ◽  
Author(s):  
RAINER SONNENBERG ◽  
ECKHARD BUSCH
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
New Genus ◽  
Nuclear Dna ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Color Pattern ◽  
Monophyletic Group ◽  
Morphological Data ◽  
Adult Males

The phylogeny of the West African genus Archiaphyosemion was studied with mitochondrial and nuclear DNA sequences. The results of the combined dataset presented here did not support a monophyletic group. After the exclusion of the type species of the genus, A. guineense, the remaining species form a well-supported monophyletic group. Based on these molecular results and supported by morphological data, we suggest a new name for this group, Nimbapanchax, new genus. Additionally, based on a recent collection in Guinea, two new Nimbapanchax species were described. The taxon Nimbapanchax leucopterygius, new species, is described for a nothobranchiid fish formerly misidentified as Archiaphyosemion maeseni (Poll, 1941). Nimbapanchax melanopterygius, new species, is described from the Mount Nimba region in southeastern Guinea. Both new Nimbapanchax species are clearly distinguished from their congeners by the coloration pattern of adult males. The results of the DNA data support the assumption based on color pattern and morphological characters that the new described species are sister taxa. The type of Aphyosemion maeseni Poll, 1941 was reexamined and transferred to the genus Epiplatys, a decision based on diagnostic morphological characters.

scholarly journals Evolution of Australasian Plantago (Plantaginaceae)

2021 ◽  
Author(s):  
◽  
Mei Lin Tay
Keyword(s):  
New Zealand ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Molecular Dating ◽  
Evolutionary Patterns ◽  
Its Phylogeny ◽  
Suitable Habitats

<p>Phylogenetic analyses using molecular data were used to investigate biogeographic and evolutionary patterns of Australasian Plantago. The Internal Transcribed Spacers (ITS) from nuclear DNA, ndhF-rpl32 from chloroplast DNA and cox1 from mitochondrial DNA were selected from a primer assay of 24 primer pairs for further phylogenetic analyses. Phylogenetic reconstruction and molecular dating of a dataset concatenated from these regions comprising 20 Australasian Plantago species rejected a hypothesis of Gondwanan vicariance for the Australasian group. The phylogeny revealed three independent dispersal events from Australia to New Zealand that match expected direction because of West Wind Drift and ocean currents. Following this study, a dataset with 150 new ITS sequences from Australasian Plantago, combined with 89 Plantago sequences from previous studies, revealed that the New Zealand species appear to have a recent origin from Australia, not long after the formation of suitable habitats formed by the uplift of the Southern Alps (about 5 mya), followed by radiation. The ITS phylogeny also suggests that a single migration event of alpine species to lowland habitats has occurred and that recurrent polyploidy appears to be an important speciation mechanism in the genus. Species boundaries between New Zealand Plantago were unclear using both morphological and molecular data, which was a result of low genetic divergences and plastic morphology. The taxonomy of several New Zealand Plantago species need revision based on the ITS phylogeny.</p>

scholarly journals Toward a Natural Classification of Botryosphaeriaceae: A Study of the Type Specimens of Botryosphaeria sensu lato

2021 ◽  
Vol 12 ◽  
Author(s):  
Ying Zhang ◽  
Yupei Zhou ◽  
Wei Sun ◽  
Lili Zhao ◽  
D. Pavlic-Zupanc ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Phylogenetic Position ◽  
Type Specimens ◽  
Natural Classification ◽  
Dna Sequence Data

The genus Botryosphaeria includes more than 200 epithets, but only the type species, Botryosphaeria dothidea and a dozen or more other species have been identified based on DNA sequence data. The taxonomic status of the other species remains unconfirmed because they lack either morphological information or DNA sequence data. In this study, types or authentic specimens of 16 “Botryosphaeria” species are reassessed to clarify their identity and phylogenetic position. nuDNA sequences of four regions, ITS, LSU, tef1-α and tub2, are analyzed and considered in combination with morphological characteristics. Based on the multigene phylogeny and morphological characters, Botryosphaeria cruenta and Botryosphaeria hamamelidis are transferred to Neofusicoccum. The generic status of Botryosphaeria aterrima and Botryosphaeria mirabile is confirmed in Botryosphaeria. Botryosphaeria berengeriana var. weigeliae and B. berengeriana var. acerina are treated synonyms of B. dothidea. Botryosphaeria mucosa is transferred to Neodeightonia as Neodeightonia mucosa, and Botryosphaeria ferruginea to Nothophoma as Nothophoma ferruginea. Botryosphaeria foliicola is reduced to synonymy with Phyllachorella micheliae. Botryosphaeria abuensis, Botryosphaeria aesculi, Botryosphaeria dasylirii, and Botryosphaeria wisteriae are tentatively kept in Botryosphaeria sensu stricto until further phylogenetic analysis is carried out on verified specimens. The ordinal status of Botryosphaeria apocyni, Botryosphaeria gaubae, and Botryosphaeria smilacinina cannot be determined, and tentatively accommodate these species in Dothideomycetes incertae sedis. The study demonstrates the significance of a polyphasic approach in characterizing type specimens, including the importance of using of DNA sequence data.

scholarly journals Defining phylogenetic relationship of Nepeta x tmolea and its parents via DNA barcoding

PhytoKeys ◽  
2019 ◽  
Vol 134 ◽  
pp. 83-96
Author(s):  
Taner Özcan
Keyword(s):  
Molecular Structure ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Molecular Data ◽  
Hybrid Nature ◽  
Molecular Approaches ◽  
Primer Sets ◽  
Morphological And Molecular Data ◽  
Chloroplast Dna Regions ◽  
Relationship Of

Nepeta viscida and N. nuda subsp. nuda and N. × tmolea were examined in this study. Mainly fresh leaf pieces, dried with silica grains, were used for DNA extraction procedures via DNA isolation kits. Standard PCR techniques were executed using three different primer sets (one nuclear DNA region (nrITS) and two chloroplast DNA regions (rpl32-trnL and trnA(Leu)-trnA(Phe)-trnL-F). DNA sequences were analysed and evaluated using different molecular approaches and software. Consequently, the inconstant molecular structure and hybrid nature of N. × tmolea specimens were shown and interpreted in this study. According to our result, N. × tmolea have some intermediate characters compared to its parents. nrITS data give more information phylogenetically, and also the most polymorphic loci are seen in nrITS data. Morphological and molecular data contribute to define separation of N. × tmolea. Consequently, the inconstant molecular structure and hybrid nature of N. × tmolea specimens were shown and interpreted in this study.

scholarly journals Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae)

2019 ◽  
Vol 42 (1) ◽  
pp. 75-100 ◽  
Author(s):  
C.G. Boluda ◽  
V.J. Rico ◽  
P.K. Divakar ◽  
O. Nadyeina ◽  
L. Myllys ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Species Delimitation ◽  
Sequence Data ◽  
Species Recognition ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Haplotype Network ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Molecular Sequence Data

In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach – including morphological, chemical, molecular, and distributional characters – to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined.

The taxonomic status of Cryptobatrachus frogs (Anura: Hemiphractidae) from the Serranía del Perijá

Zootaxa ◽  
2021 ◽  
Vol 5068 (2) ◽  
pp. 247-262
Author(s):  
FABIO LEONARDO MEZA-JOYA ◽  
ELIANA RAMOS ◽  
FERNANDO J. M. ROJAS-RUNJAIC ◽  
ANDRÉS OVALLE-PACHECO
Keyword(s):  
Dna Sequences ◽  
Genetic Divergence ◽  
Morphological Traits ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Molecular Data ◽  
The Other ◽  
Taxon Sampling ◽  
Morphological Similarity ◽  
Morphological And Molecular Data

The Neotropical frog genus Cryptobatrachus includes six currently recognized species distributed throughout the northern Andes in Colombia and Venezuela. Cryptobatrachus conditus, C. pedroruizi, and C. remotus were described from the Colombian and Venezuelan slopes of the Serranía del Perijá. Due to the great morphological similarity among these species, we re-assess their taxonomic status based on morphological and molecular data from types, topotypes, and specimens from localities referred to in the original descriptions of these species. Morphometric comparisons showed that all these species are virtually indistinguishable, although some subtle qualitative differences in morphological traits distinguish C. conditus from the other species. Phylogenetic analyses of DNA sequences found that C. remotus and C. pedroruizi are not reciprocally monophyletic and exhibit low genetic divergence (< 1 %). Therefore, C. remotus should be considered a junior synonym of C. pedroruizi. This work stresses the importance of comprehensive taxon sampling in poorly explored areas, especially between neighbouring countries.  

Phylogenetic reconstruction of the genus Helianthemum (Cistaceae) using plastid and nuclear DNA-sequences: Systematic and evolutionary inferences

Taxon ◽  
2017 ◽  
Vol 66 (4) ◽  
pp. 868-885 ◽  
Author(s):  
Abelardo Aparicio ◽  
Sara Martín-Hernanz ◽  
Clara Parejo-Farnés ◽  
Juan Arroyo ◽  
Sébastien Lavergne ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Phylogenetic Reconstruction
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