scholarly journals Molecular data supports the inclusion of Ildobates neboti Español in Zuphiini (Coleoptera: Carabidae: Harpalinae)

2006 ◽  
Vol 17 (3) ◽  
Author(s):  
Ignacio Ribera ◽  
Sergio Montagud ◽  
Santiago Teruel ◽  
Xavier Bellés
Keyword(s):  
Phylogenetic Relationships ◽  
18S Rrna ◽  
Molecular Data ◽  
Nuclear Genes ◽  
Posterior Probabilities ◽  
Data Set ◽  
Morphological Criteria ◽  
Relationship Of

The phylogenetic relationships of Ildobates neboti Español (Coleoptera: Carabidae: Harpalinae) were investigated based on three nuclear genes (full 18S rRNA, and a fragment of each 28S rRNAand wingless).We compiled a data set using published sequences of 32 members of Harpalinae including one example each of Dryptini (genus Desera), Galeritini (Galerita) and Zuphiini (Thalpius), plus three Brachininae as outgroups. These three tribes form the “Dryptitae”, within which various relationships of Ildobates had been proposed. The analyses of the datamatrix using parsimony (with equally weighted and reweighted characters) and Bayesian posterior probabilities all support the monophyly of the three tribes in “Dryptitae”, as well as a closest relationship of Ildobates with Thalpius to the exclusion of Desera plus Galerita. This confirms the previous inclusion of Ildobates among the Zuphiini, and corroborates current taxonomic classifications based on morphological criteria.

scholarly journals The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 995-1010 ◽  
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Large Data ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Living Fossil ◽  
Latimeria Chalumnae ◽  
Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

scholarly journals Phylogenetic relationships of the neon tetras Paracheirodon spp. (Characiformes: Characidae: Stethaprioninae), including comments on Petitella georgiae and Hemigrammus bleheri

2020 ◽  
Vol 18 (2) ◽  
Author(s):  
Pedro Senna Bittencourt ◽  
Valéria Nogueira Machado ◽  
Bruce Gavin Marshall ◽  
Tomas Hrbek ◽  
Izeni Pires Farias
Keyword(s):  
Phylogenetic Relationships ◽  
Species Complex ◽  
Molecular Data ◽  
Morphological Data ◽  
Sister Taxon ◽  
Taxonomic History ◽  
Relationship Of

ABSTRACT Neon tetras (Paracheirodon spp.) are three colorful characid species with a complicated taxonomic history, and relationships among the species are poorly known. Molecular data resolved the relationships among the three neon tetras, and strongly supported monophyly of the genus and its sister taxon relationship to Brittanichthys. Additionally, the sister-taxon relationship of the rummy-nose tetras Hemigrammus bleheri and Petitella georgiae was strongly supported by molecular and morphological data. Therefore, we propose to transfer the rummy-nose tetras H. bleheri and H. rhodostomus to the genus Petitella. Furthermore, Petitella georgiae is likely to be a species complex comprised of at least two species.

“Endangered or an artifact of unsound taxonomy? Case of the critically endangered bush frog Philautus sanctisilvaticus Das and Chanda, 1997”

Zootaxa ◽  
2019 ◽  
Vol 4683 (4) ◽  
pp. 563-576 ◽  
Author(s):  
ZEESHAN A. MIRZA ◽  
PRIYA WAREKAR ◽  
PRATYUSH P. MOHAPATRA ◽  
DAVID RAJU ◽  
PRANAD PATIL ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Relationships ◽  
Molecular Data ◽  
Eastern Ghats ◽  
Rrna Gene ◽  
16S Gene ◽  
Mitochondrial 16S Rrna Gene ◽  
Fragmented Forests ◽  
Relationship Of

We investigated the phylogenetic relationship of the Critically Endangered bush frog Philautus sanctisilvaticus Das and Chanda, 1997 and other species distributed across the fragmented forests of Deccan Peninsula and the northern Eastern Ghats. A short fragment of the mitochondrial 16S rRNA gene was employed to assess phylogenetic relationships across Philautus sanctisilvaticus Das and Chanda, 1997, Raorchestes terebrans (Das and Chanda, 1998) and Philautus similipalensis Dutta, 2003. All sequenced specimens, including material from near the type localities of P. sanctisilvaticus (Amarkantak) and P. similipalensis (Simlipal) were genetically extremely similar, with pairwise uncorrected distances <1% in the 16S gene, and were phylogenetically placed within the genus Raorchestes. The results based on morphology are ambiguous and do not go hand in hand with molecular data, which however do not provide support for a three species hypothesis either. our findings advocate the need for making nomenclatural amendments. Philautus sanctisilvaticus Das and Chanda, 1997, is the first available nomen for this taxon, and we propose to include this species in Raorchestes as Raorchestes sanctisilvaticus (Das and Chanda, 1997), and to consider the nomina Philautus terebrans Das and Chanda, 1998 syn. nov. and Philautus similipalensis Dutta, 2003 syn. nov. as junior subjective synonyms for this nomen following the Principle of Priority in article 23.1 of the ICZN. The findings are notable from the point of conservation of the species and present a novel case with remarkable genetic homogeneity across the fragmented forests of Deccan Peninsula and Eastern Ghats. 

scholarly journals RETRACTED ARTICLE: Molecular Phylogeny and Revision of Copepod Orders (Crustacea: Copepoda)

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Sahar Khodami ◽  
J. Vaun McArthur ◽  
Leocadio Blanco-Bercial ◽  
Pedro Martinez Arbizu
Keyword(s):  
Molecular Phylogeny ◽  
New Taxa ◽  
Phylogenetic Relationships ◽  
18S Rrna ◽  
Histone H3 ◽  
Molecular Data ◽  
Coi Mtdna ◽  
The Family ◽  
Retracted Article ◽  
First Time

Abstract For the first time, the phylogenetic relationships between representatives of all 10 copepod orders have been investigated using 28S and 18S rRNA, Histone H3 protein and COI mtDNA. The monophyly of Copepoda (including Platycopioida Fosshagen, 1985) is demonstrated for the first time using molecular data. Maxillopoda is rejected, as it is a polyphyletic group. The monophyly of the major subgroups of Copepoda, including Progymnoplea Lang, 1948 (=Platycopioida); Neocopepoda Huys and Boxshall, 1991; Gymnoplea Giesbrecht, 1892 (=Calanoida Sars, 1903); and Podoplea Giesbrecht, 1892, are supported in this study. Seven copepod orders are monophyletic, including Platycopioida, Calanoida, Misophrioida Gurney, 1933; Monstrilloida Sars, 1901; Siphonostomatoida Burmeister, 1834; Gelyelloida Huys, 1988; and Mormonilloida Boxshall, 1979. Misophrioida (=Propodoplea Lang, 1948) is the most basal Podoplean order. The order Cyclopoida Burmeister, 1835, is paraphyletic and now encompasses Poecilostomatoida Thorell, 1859, as a sister to the family Schminkepinellidae Martinez Arbizu, 2006. Within Harpacticoida Sars, 1903, both sections, Polyarthra Lang, 1948, and Oligoarthra Lang, 1948, are monophyletic, but not sister groups. The order Canuelloida is proposed while maintaining the order Harpacticoida s. str. (Oligoarthra). Cyclopoida, Harpacticoida and Cyclopinidae are redefined, while Canuelloida ordo. nov., Smirnovipinidae fam. nov. and Cyclopicinidae fam. nov are proposed as new taxa.

RELATIONSHIP OF THE ORDER APIALES TO SUBCLASS ASTERIDAE: A RE-EVALUATION OF MORPHOLOGICAL CHARACTERS BASED ON INSIGHTS FROM MOLECULAR DATA

2001 ◽  
Vol 58 (2) ◽  
pp. 183-200 ◽  
Author(s):  
G. M. PLUNKETT
Keyword(s):  
Phylogenetic Relationships ◽  
Morphological Character ◽  
Morphological Characters ◽  
Molecular Data ◽  
Monophyletic Group ◽  
Character State ◽  
Molecular Analyses ◽  
Taxonomic Level ◽  
State Evolution ◽  
Relationship Of

Phylogenetic relationships involving the angiosperm order Apiales (Apiaceae and Araliaceae) are troublesome at nearly every taxonomic level and have eluded several generations of botanists. Because of difficulties in interpreting and polarizing morphological character states at deeper phylogenetic levels, most studies in Apiales have focused on relationships between the two families and among/within the apialean genera. In the present study, however, recent contributions from molecular analyses are reviewed and combined using a ‘supertree’ approach to test traditional hypotheses of relationships involving Apiales, and to re-evaluate assumptions of character-state evolution in the order. Results from this study confirm that Apiales form a monophyletic group with Pittosporaceae (along with Griselinia G. Forst., Melanophylla Baker, Torricellia DC. and Aralidium Miq.), and should be transferred out of subclass Rosidae (away from both Cornales and Sapindales) to the Asteridae (in a position close to Asterales and Dipsacales). These findings are also supported by several lines of morphological, anatomical, and phytochemical evidence, and provide a more satisfactory framework for interpreting relationships and character-state evolution within the major clades of Apiales.

DNA and ascomycete systematics

1995 ◽  
Vol 73 (S1) ◽  
pp. 784-789 ◽  
Author(s):  
Ove E. Eriksson
Keyword(s):  
Key Words ◽  
Phylogenetic Relationships ◽  
18S Rrna ◽  
Present Knowledge ◽  
Parsimony Analysis ◽  
Phylogenetic Information ◽  
Key Words Dna ◽  
Morphological Criteria ◽  
Different Types ◽  
Signature Sequences

Present knowledge of different types of RNAs as phylogenetic markers among the fungi is discussed, and examples of phylogenetically informative 18S rRNA signature sequences are given. Such signatures give phylogenetic information that is not provided by parsimony or distance analyses of longer gene sequences. A single signature cannot be used as a decisive criterion for defining taxa, but signature sequences give invaluable hints on phylogenetic relationships and can be included in data matrices as morphological criteria when using parsimony analysis. Key words: DNA, ascomycete phylogeny, signature sequences.

scholarly journals Molecular taxonomy of some sponges (Demospongiae) using ribosomal (18s rrna) and partial mitochondrial (coi) genes

2018 ◽  
Vol 40 (4) ◽  
Author(s):  
Ton That Huu Dat ◽  
Nguyen Thi Kim Cuc ◽  
Pham Viet Cuong
Keyword(s):  
18S Rrna ◽  
Molecular Taxonomy ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Rrna Genes ◽  
Mitochondrial Coi ◽  
Rrna Tree ◽  
The Individual ◽  
18S Rrna Genes ◽  
Relationship Of

Sponges, the most ancient multicellular metazoan, were widely distributed across habitats. Vietnam is known to possess a high biodiversity of sponges, however, they are mostly identified based on morphological characteristics and lack the molecular data. In the current study, the phylogenetic relationship of some sponges (Demospongiae) in Vietnam was constructed using two independent markers (COI and 18S rRNA). In this paper the individual markers (COI and 18S rRNA) were successfully used to identify some sponge taxa at the species level. The obtained results showed the congruence of molecular taxonomy using two independent markers. However, our study showed that a combination of the two markers provided more information and supported better for sponge identification. At order level, the COI tree and 18S rRNA tree also recovered the same clades, indicating the congruence of COI and 18S rRNA genes in sponge classification. However, branching order of the clades in COI tree was weakly supported and slightly different from those in 18S rRNA tree. 

scholarly journals Combination of nuclear and mitochondrial markers as a useful tool to identify Ctenophthalmus species and subspecies (Siphonaptera: Ctenophthalmidae)

2021 ◽  
Author(s):  
Antonio Zurita ◽  
Cristina Cutillas
Keyword(s):  
Taxonomic Status ◽  
Molecular Study ◽  
Molecular Data ◽  
Point Of View ◽  
Morphological Data ◽  
Molecular Approach ◽  
Nuclear Marker ◽  
Mitochondrial Markers ◽  
Morphological Criteria ◽  
Mtdna Markers

AbstractCtenophthalmus is considered the largest genus within the Order Siphonaptera. From a morphological point of view, only males of this genus can be identified at species and subspecies levels using morphological keys, whereas there are no morphological criteria in order to classify females at these taxonomical levels. Furthermore, the amount of available molecular and phylogenetic data for this genus is quite scarce so far. The main objective of this work was to assess the utility of the combination of nuclear and mitochondrial markers with respect to their ability to differentiate among different subspecies within the Ctenophthalmus genus. With this purpose, we carried out a comparative morphological and molecular study of three different subspecies (Ctenophthalmus baeticus arvernus, Ctenophthalmus nobilis dobyi, and Ctenophthalmus andorrensis catalaniensis) in order to clarify and discuss its taxonomic status. In addition, our study complemented the molecular data previously provided for Ctenophthalmus baeticus boisseauorum and Ctenophthalmus apertus allani subspecies. We sequenced five different molecular markers: EF1-α, ITS1, ITS2, cox1, and cytb. Our results confirmed that morphological data by themselves are not able to discriminate among Ctenophthalmus female taxa; however, the combination of the nuclear marker EF1-α together with mtDNA markers cytb and cox1 constituted a useful taxonomical and phylogenetic tool to solve this issue. Based on these results, we consider that the use of this molecular approach should be gradually used within Ctenophthalmus genus in order to complement its classical taxonomy and clarifying the complex taxonomy of other congeneric species of fleas.

Whale falls, multiple colonisations of the deep, and the phylogeny of Hesionidae (Annelida)

2015 ◽  
Vol 29 (2) ◽  
pp. 105 ◽  
Author(s):  
Mindi Summers ◽  
Fredrik Pleijel ◽  
Greg W. Rouse
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
16S Rrna ◽  
Deep Sea ◽  
Phylogenetic Relationships ◽  
18S Rrna ◽  
Shallow Waters ◽  
28S Rrna ◽  
Mitochondrial Cytochrome ◽  
New Members

Phylogenetic relationships within Hesionidae Grube, 1850 are assessed via maximum parsimony and maximum likelihood analyses of mitochondrial (cytochrome c oxidase subunit I and 16S rRNA) and nuclear (18S rRNA, and 28S rRNA) data. The analyses are based on 42 hesionid species; six of these being new species that are described here. The new species, all from deep (>200 m depth) benthic environments (including whale falls) in the eastern Pacific, are Gyptis shannonae, sp. nov., Neogyptis julii, sp. nov., Sirsoe sirikos, sp. nov., Vrijenhoekia ketea, sp. nov., Vrijenhoekia falenothiras, sp. nov., and Vrijenhoekia ahabi, sp. nov. The molecular divergence among the new members of Vrijenhoekia is pronounced enough to consider them cryptic species, even though we cannot distinguish among them morphologically. Our results also showed that the subfamily Hesioninae Grube, 1850, as traditionally delineated, was paraphyletic. We thus restrict Hesioninae to include only Hesionini Grube, 1850 and refer the remaining members to Psamathinae Pleijel, 1998. The present study increases the number of hesionid species associated with whale falls from one to six and markedly increases the number of described deep-sea hesionid taxa. There appear to have been multiple colonisations of the deep sea from shallow waters by hesionids, though further sampling is warranted.

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