Molecular phylogeny of Diploschistes inferred from ITS sequence data

2003 ◽  
Vol 35 (1) ◽  
pp. 27-32 ◽  
Author(s):  
María P. Martín ◽  
Scott LaGreca ◽  
H. Thorsten Lumbsch
Keyword(s):  
Sequence Data ◽  
Cladistic Analysis ◽  
Sister Group ◽  
Morphological Data ◽  
Bootstrap Support ◽  
Evolutionary Trend ◽  
5.8S Rdna ◽  
Rdna Sequences ◽  
Strong Bootstrap Support ◽  
Nuclear Its

AbstractThe phylogeny of the genus Diploschistes was investigated using nucleotide sequences of the nuclear ITS rDNA region (ITS1, ITS2 and 5.8S rDNA). Sequences of 22 Diploschistes species were aligned to those of six other species of Thelotremataceae, Graphis scripta and Aspicilia cinerea, with the last used as an outgroup. The alignment was analysed cladistically using maximum parsimony. In the most parsimonious trees, Diploschistes is monophyletic, with D. ocellatus being a sister group to the remaining Diploschistes spp. (= Diploschistes s. str.). A previous cladistic analysis of morphological data suggested an evolutionary trend within the genus from perithecioid to urceolate ascomata. The present ITS data suggest the opposite: perithecioid ascomata are apparently an apomorphic character within the genus, with the actinostomus group forming a derived monophyletic clade. However, the topology within Diploschistes s. str. Lacks strong bootstrap support.

Phylogenetic assessment of the monotypic genera Sundacarpus and Manoao (Coniferales: Podocarpaceae) utilising evidence from 18S rDNA sequences

2002 ◽  
Vol 15 (1) ◽  
pp. 29 ◽  
Author(s):  
Dean G. Kelch
Keyword(s):  
Sequence Data ◽  
Morphological Data ◽  
Bootstrap Support ◽  
Conservative Approach ◽  
Parsimony Analysis ◽  
Rdna Sequences ◽  
The Family ◽  
18S Rdna Sequences ◽  
High Bootstrap ◽  
Lagarostrobos Franklinii

The Podocarpaceae are the most morphologically diverse of conifer families. A taxonomic trend has resulted in recognising this diversity via smaller generic groupings, including several monotypes. A phylogenetic assessment of the monotypic genera Sundacarpus and Manoao was conducted employing maximum parsimony the analysis of sequence data from 18S-ribosomal DNA from 34 gymnosperm taxa, including 29 Podocarpaceae. In resulting trees, there is high bootstrap support for Podocarpaceae, including Phyllocladus, but the order of deep branches within the family is equivocal. Prumnopitys (Sundacarpus) amara (Blume) de Laub. and four other Prumnopitys spp. comprise a clade with a bootstrap value of 100%, supporting the retention of Sundacarpus as a section of Prumnopitys. Lagarostrobos franklinii (Hook.f.) Quinn and L. (Manoao) colensoi (Hook.) Quinn comprise a clade with equivocal bootstrap support, echoing previous results from parsimony analysis of morphological data. A conservative approach (i.e. one avoiding unnecessary monotypes) favours the retention of L. colensoi in Lagarostrobos, pending further evidence of relationships within the group.

scholarly journals Corrigendum to: Phylogeny and biogeography of the ant subfamily Myrmeciinae (Hymenoptera : Formicidae)

2003 ◽  
Vol 17 (4) ◽  
pp. 605 ◽  
Author(s):  
Philip S. Ward ◽  
Seán G. Brady
Keyword(s):  
Sequence Data ◽  
Strong Support ◽  
Sister Group ◽  
Molecular Data ◽  
Morphological Data ◽  
Recent Common Ancestor ◽  
Bootstrap Support ◽  
Data Set ◽  
Molecular Sequence Data ◽  
Most Recent Common Ancestor

We investigated phylogenetic relationships among the 'primitive' Australian ant genera Myrmecia and Nothomyrmecia (stat. rev.) and the Baltic amber fossil genus Prionomyrmex, using a combination of morphological and molecular data. Outgroups for the analysis included representatives from a variety of potential sister-groups, including five extant subfamilies of ants and one extinct group (Sphecomyrminae). Parsimony analysis of the morphological data provides strong support (~95% bootstrap proportions) for the monophyly of (1) genus Myrmecia, (2) genus Prionomyrmex, and (3) a clade containing those two genera plus Nothomyrmecia. A group comprising Nothomyrmecia and Prionomyrmex is also upheld (85% bootstrap support). Molecular sequence data (~2200 base pairs from the 18S and 28S ribosomal RNA genes) corroborate these findings for extant taxa, with Myrmecia and Nothomyrmecia appearing as sister-groups with ~100% bootstrap support under parsimony, neighbour-joining and maximum-likelihood analyses. Neither the molecular nor the morphological data set allows us to identify unambiguously the sister-group of (Myrmecia + (Nothomyrmecia + Prionomyrmex)). Rather, Myrmecia and relatives are part of an unresolved polytomy that encompasses most of the ant subfamilies. Taken as a whole, our results support the contention that many of the major lineages of ants – including a clade that later came to contain Myrmecia, Nothomyrmecia and Prionomyrmex – arose at around the same time during a bout of diversification in the middle or late Cretaceous. On the basis of Bayesian dating analysis, the estimated age of the most recent common ancestor of Myrmecia and Nothomyrmecia is 74 million years (95% confidence limits, 53–101�million years), a result consistent with the origin of the myrmeciine stem lineage in the Cretaceous. The ant subfamily Myrmeciinae is redefined to contain two tribes, Myrmeciini (genus Myrmecia) and Prionomyrmecini (Nothomyrmecia and Prionomyrmex). Phylogenetic analysis of the enigmatic Argentine fossils Ameghinoia and Polanskiella demonstrates that they are also members of the Myrmeciinae, probably more closely related to Prionomyrmecini than to Myrmeciini. Thus, the myrmeciine ants appear to be a formerly widespread group that retained many ancestral formicid characteristics and that became extinct everywhere except in the Australian region.

Further phylogenetic studies of the Polychaeta using 18S rDNA sequence data

2004 ◽  
Vol 84 (5) ◽  
pp. 949-960 ◽  
Author(s):  
Kathryn A. Hall ◽  
Pat A. Hutchings ◽  
Donald J. Colgan
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Cladistic Analysis ◽  
Sister Group ◽  
Morphological Data ◽  
Phylogenetic Studies ◽  
Rdna Sequence Data ◽  
Substantial Progress ◽  
18S Rdna Sequence

The integration of molecular and morphological approaches has produced substantial progress in understanding the higher classification of most major invertebrate groups. The striking exception to this is the Polychaeta. Neither the membership nor the higher classification of this group has been robustly established. Major inconsistencies exist between the only comprehensive cladistic analysis of Polychaeta using morphological data and the DNA sequence studies covering all or part of the taxon.We have compiled a dataset of available nearly complete 18S ribosomal DNA sequences and collected an additional 22 sequences (20 Polychaeta in 19 taxa, one Myzostomida and one Phoronida) to obtain more comprehensive coverage of polychaete diversity for this gene. Analyses of the data do not resolve all inconsistencies among current hypotheses of polychaete phylogeny. They do support the recognition (in whole or part) of some clades such as the Eunicida, Phyllodocida and Terebellida that have been proposed on morphological grounds. Our analyses contradict the Canalipalpata and the Scolecida. Although the polychaete sister-group to the Clitellata is not clearly resolved in our analyses, the clitellates are always recovered as a derived clade within the Polychaeta. Increased taxon sampling is required to elucidate further the phylogeny of the Polychaeta.

Molecular and morphological phylogenetic analysis and taxonomic revision of the genus Orleanesia (Laeliinae, Epidendroideae, Orchidaceae)

Phytotaxa ◽  
2019 ◽  
Vol 392 (1) ◽  
pp. 1
Author(s):  
GABRIEL F. GONÇALVES ◽  
ANNA VICTORIA S. R. MAUAD ◽  
GIULIANA TAQUES ◽  
ERIC C. SMIDT ◽  
FÁBIO DE BARROS
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Sister Group ◽  
Morphological Data ◽  
Data Sets ◽  
New Synonyms ◽  
Nuclear Its

In order to evaluate the monophyly of the genus Orleanesia (Orchidaceae) and to assess its position within Laeliinae, a phylogenetic analysis was performed using molecular (nuclear ITS and plastid matK DNA sequences) and morphological data. A taxonomic revision of Orleanesia was also performed, with a description of the genus and its species using fresh living plants and 115 exsiccates from 31 herbaria. All phylogenetic analyses were highly congruent, and thus the sequence data from all three data sets were combined. The resulting phylogeny corroborated the monophyly of Orleanesia, with two strongly supported clades, and confirmed Caularthron as its sister group. Character analysis was not very informative due to a high degree of homoplasy. Two lectotypifications and three new synonyms were proposed for the genus, thereby reducing the number of accepted species to six. Although none of the species of Orleanesia are considered endangered, it is clear that some populations are threatened with deforestation and habitat reduction.

Phylogeny and biogeography of the ant subfamily Myrmeciinae (Hymenoptera : Formicidae)

2003 ◽  
Vol 17 (3) ◽  
pp. 361 ◽  
Author(s):  
Philip S. Ward ◽  
Seán G. Brady
Keyword(s):  
Sequence Data ◽  
Strong Support ◽  
Sister Group ◽  
Molecular Data ◽  
Morphological Data ◽  
Recent Common Ancestor ◽  
Bootstrap Support ◽  
Data Set ◽  
Molecular Sequence Data ◽  
Most Recent Common Ancestor

We investigated phylogenetic relationships among the 'primitive' Australian ant genera Myrmecia and Nothomyrmecia (stat. rev.) and the Baltic amber fossil genus Prionomyrmex, using a combination of morphological and molecular data. Outgroups for the analysis included representatives from a variety of potential sister-groups, including five extant subfamilies of ants and one extinct group (Sphecomyrminae). Parsimony analysis of the morphological data provides strong support (~95% bootstrap proportions) for the monophyly of (1) genus Myrmecia, (2) genus Prionomyrmex, and (3) a clade containing those two genera plus Nothomyrmecia. A group comprising Nothomyrmecia and Prionomyrmex is also upheld (85% bootstrap support). Molecular sequence data (~2200 base pairs from the 18S and 28S ribosomal RNA genes) corroborate these findings for extant taxa, with Myrmecia and Nothomyrmecia appearing as sister-groups with ~100% bootstrap support under parsimony, neighbour-joining and maximum-likelihood analyses. Neither the molecular nor the morphological data set allows us to identify unambiguously the sister-group of (Myrmecia + (Nothomyrmecia + Prionomyrmex)). Rather, Myrmecia and relatives are part of an unresolved polytomy that encompasses most of the ant subfamilies. Taken as a whole, our results support the contention that many of the major lineages of ants – including a clade that later came to contain Myrmecia, Nothomyrmecia and Prionomyrmex – arose at around the same time during a bout of diversification in the middle or late Cretaceous. On the basis of Bayesian dating analysis, the estimated age of the most recent common ancestor of Myrmecia and Nothomyrmecia is 74 million years (95% confidence limits, 53–101million years), a result consistent with the origin of the myrmeciine stem lineage in the Cretaceous. The ant subfamily Myrmeciinae is redefined to contain two tribes, Myrmeciini (genus Myrmecia) and Prionomyrmecini (Nothomyrmecia and Prionomyrmex). Phylogenetic analysis of the enigmatic Argentine fossils Ameghinoia and Polanskiella demonstrates that they are also members of the Myrmeciinae, probably more closely related to Prionomyrmecini than to Myrmeciini. Thus, the myrmeciine ants appear to be a formerly widespread group that retained many ancestral formicid characteristics and that became extinct everywhere except in the Australian region.

Nucleotide sequences of rbcL confirm the capparalean affinity of the Australian endemis Gyrostemonaceae

1994 ◽  
Vol 7 (1) ◽  
pp. 57 ◽  
Author(s):  
JE Rodman ◽  
KG Karol ◽  
RA PRice ◽  
E Conti ◽  
KJ Systma
Keyword(s):  
Sequence Data ◽  
Stop Codon ◽  
Large Subunit ◽  
Cladistic Analysis ◽  
Sister Group ◽  
Nucleotide Sequences ◽  
Mustard Oil ◽  
Rbcl Gene ◽  
Bisphosphate Carboxylase ◽  
Weak Support

Nucleotide sequences (1452 base pairs) from the chloroplast gene for the large subunit of ribulose-1, 5-bisphosphate carboxylase/oxygenase (rbcL) were obtained for three species of Gyrostemon and Tersonia of the Australian endemic family Gyrostemonaceae. Phylogenetic reconstruction based on parsimony robustly allies the family with other mustard oil-producing plants in Dahlgren's expanded order Capparales. Within this clade, Gyrostemonaceae are the sister group to Resedaceae, but the sequence data provide only weak support for this particular linkage. The new molecular data corroborate recent embryological and ultrastructural findings for Gyrosternonaceae and confirm results from Rodman's cladistic analysis of traditional morphological features of these plants. The rbcL sequences for the three species of Gyrostemonaceae were consistent in possessing a stop codon ending at position 1452, well beyond the usual 1428 site for many dicots. An extended terminus for the rbcL gene appears to be a marker within the expanded order Capparales for a derived clade that comprises the traditional core Capparales (Brassicaceae, Capparaceae, Resedaceae and Tovariaceae) plus Gyrostemonaceae, the sister taxa Batis + Koeberlinia, and Limnanthaceae.

Sequence variability in two mitochondrial DNA regions and internal transcribed spacer among three cestodes infecting animals and humans from China

2011 ◽  
Vol 86 (2) ◽  
pp. 245-251 ◽  
Author(s):  
R.S. Dai ◽  
G.H. Liu ◽  
H.Q. Song ◽  
R.Q. Lin ◽  
Z.G. Yuan ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Sequence Variability ◽  
Taenia Hydatigena ◽  
Specific Sequence ◽  
5.8S Rdna ◽  
Rdna Sequences

AbstractSequence variability in two mitochondrial DNA (mtDNA) regions, namely cytochromecoxidase subunit 1 (cox1) and NADH dehydrogenase subunit 4 (nad4), and internal transcribed spacer (ITS) of rDNA among and within three cestodes,Spirometra erinaceieuropaei,Taenia multicepsandTaenia hydatigena, from different geographical origins in China was examined. A portion of thecox1 (pcox1),nad4 genes (pnad4) and the ITS (ITS1+5.8S rDNA+ITS2) were amplified separately from individual cestodes by polymerase chain reaction (PCR). Representative amplicons were subjected to sequencing in order to estimate sequence variability. While the intra-specific sequence variations within each of the tapeworm species were 0–0.7% for pcox1, 0–1.7% for pnad4 and 0.1–3.6% for ITS, the inter-specific sequence differences were significantly higher, being 12.1–17.6%, 18.7–26.2% and 31–75.5% for pcox1, pnad4 and ITS, respectively. Phylogenetic analyses based on the pcox1 sequence data revealed thatT. multicepsandT. hydatigenawere more closely related to the other members of theTaeniagenus, andS. erinaceieuropaeiwas more closely related to the other members of theSpirometragenus. These findings demonstrated clearly the usefulness of mtDNA and rDNA sequences for population genetic studies of these cestodes of socio-economic importance.

Phylogenetic relationships in Lasiocampidae (Lepidoptera): Initial evidence from elongation factor-1α sequences

2000 ◽  
Vol 31 (2) ◽  
pp. 179-186 ◽  
Author(s):  
Charles Mitter ◽  
Timothy P. Friedlander ◽  
Jerome C. Regier ◽  
Richard S. Peigler
Keyword(s):  
Phylogenetic Signal ◽  
Cladistic Analysis ◽  
Elongation Factor ◽  
Nuclear Gene ◽  
Sister Group ◽  
Bootstrap Support ◽  
Elongation Factor 1Α ◽  
Factor I ◽  
Protein Encoding ◽  
Synonymous Change

AbstractNo explicit higher-level cladistic analysis exists for Lasiocampidae, the largest family of Bombycoidea (s. lat.). As a start toward such a phylogeny, we sequenced the protein-encoding, nuclear gene elongation factor-I α (EF-1α) from 13 lasiocampids representing all the subfamilies and tribes present in North America, plus three outgroups. Phylogenetic signal, mainly from synonymous change, was strong, with seven of 11 potential groups in Lasiocampidae showing > 90% bootstrap support under parsimony and likelihood analyses. Separation between the two American subfamilies, Lasiocampinae and Macromphaliinae, was strongly supported. Within the largest tribe, Lasiocampini, EF-1α strongly resolves a clade of unusually large lasiocampids, containing a New World element ((Eutachyptera, Gloveria), (Prorifrons, Quadrina)) with a Eurasian sister group of Macrothylacia + Dendrolimus. Resolution of deeper relationships within Lasiocampinae, however, including those among tribes, is presently weak and will probably require expanded taxon sampling. The 'large Lasiocampini' group shares a possibly synapomorphic life cycle (not expressed in its tropical members) that includes overwintering by larvae. Larval sociality is found in three of the 'large Lasiocampini' genera, each of which may represent an origin separate from the others and from Malacosoma.

scholarly journals Phylogeny of infraorder Sejina (Acari: Mesostigmata)

Zootaxa ◽  
2004 ◽  
Vol 629 (1) ◽  
pp. 1 ◽  
Author(s):  
MARIAM LEKVEISHVILI ◽  
HANS KLOMPEN
Keyword(s):  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Sister Group ◽  
Morphological Characters ◽  
Morphological Data ◽  
Data Sets ◽  
Dna Sequence Data

Phylogenetic relationships among the families in the infraorder Sejina and the position of Sejina relative to other infraorders of Mesostigmata are re-examined based on molecular and morphological data. Data sets included DNA sequence data for complete 18S, EF-1 , partial CO1genes, and 69 morphological characters. The two families of Heterozerconina consistently group within Sejina, and we propose to synonymize Heterozerconina with Sejina (Sejina s.l). Microgyniina is not the closest relative of Sejina. Rather, Sejina s.l. most often groups with Gamasina. Uropodellidae and Ichthyostomatogasteridae are sister groups and this lineage forms the sister group to Discozerconidae plus Heterozerconidae. Overall, we recognize 5 families within Sejina: Uropodellidae, Ichthyostomatogasteridae, Sejidae, Discozerconidae, and Heterozerconidae.

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