scholarly journals Mitochondrial cob and cox1 Genes and Editing of the Corresponding mRNAs in Dinophysis acuminata from Narragansett Bay, with Special Reference to the Phylogenetic Position of the Genus Dinophysis

2007 ◽  
Vol 74 (5) ◽  
pp. 1546-1554 ◽  
Author(s):  
Huan Zhang ◽  
Debashish Bhattacharya ◽  
Lucie Maranda ◽  
Senjie Lin
Keyword(s):  
Flow Cytometry ◽  
Phylogenetic Trees ◽  
Gene Tree ◽  
Narragansett Bay ◽  
Bootstrap Support ◽  
Phylogenetic Position ◽  
Data Set ◽  
Specific Pcr ◽  
Dinophysis Acuminata ◽  
Unbiased Test

ABSTRACT Dinophysis acuminata cells were isolated from Narragansett Bay water samples in June 2005 using flow cytometry. Dinoflagellate-specific PCR primers were used to isolate small-subunit rRNA (18S rRNA), mitochondrial cytochrome b (cob), and cytochrome c oxidase I (cox1) genes and the encoded cDNAs. Maximum-likelihood analysis of a concatenated data set of ribosomal DNA and cDNA sequences of cob and cox1 showed that D. acuminata was sister to Gonyaulacoids, but without strong bootstrap support. The approximately unbiased test could not reject alternative positions of D. acuminata. To gain better resolution, mRNA editing of cob and cox1 was inferred for D. acuminata and 13 other dinoflagellate species. The location and type of editing as well as the distribution pattern in D. acuminata were generally similar to those in other dinoflagellates except for two edited sites that are unique to this species. Bayesian analyses of a matrix that recorded the location and type of editing, and of a matrix that included the protein sequences of COB and COX1 with the editing data yielded tree topologies similar to the three-gene tree but again failed to resolve the phylogenetic position of D. acuminata. However, the density of edited sites in the D. acuminata mitochondrial genes, consistent with phylogenetic trees, indicated that Dinophysis is a derived dinoflagellate lineage, diverging after other lineages such as Oxyrrhis, Amphidinium, and Symbiodinium. We demonstrate that dinoflagellate-specific PCR coupled with flow cytometry can be a useful tool to analyze genes and their transcripts from a natural dinoflagellate population.

Can the Cambrian explosion be inferred through molecular phylogeny?

Development ◽  
1994 ◽  
Vol 1994 (Supplement) ◽  
pp. 15-25
Author(s):  
Hervé Philippe ◽  
Anne Chenuil ◽  
André Adoutte
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Phylogenetic Reconstruction ◽  
Cambrian Explosion ◽  
Bootstrap Support ◽  
Time Interval ◽  
Short Time Interval ◽  
Data Set ◽  
Molecular Phylogenetic ◽  
Animal Phyla

Most of the major invertebrate phyla appear in the fossil record during a relatively short time interval, not exceeding 20 million years (Myr), 540-520 Myr ago. This rapid diversification is known as the `Cambrian explosion'. In the present paper, we ask whether molecular phylogenetic reconstruction provides confirmation for such an evolutionary burst. The expectation is that the molecular phylogenetic trees should take the form of a large unresolved multifurcation of the various animal lineages. Complete 18S rRNA sequences of 69 extant representatives of 15 animal phyla were obtained from data banks. After eliminating a major source of artefact leading to lack of resolution in phylogenetic trees (mutational saturation of sequences), we indeed observe that the major lines of triploblast coelomates (arthropods, molluscs, echinoderms, chordates...) are very poorly resolved i.e. the nodes defining the various clades are not supported by high bootstrap values. Using a previously developed procedure consisting of calculating bootstrap proportions of each node of the tree as a function of increasing amount of nucleotides (Lecointre, G., Philippe, H. Le, H. L. V. and Le Guyader, H. (1994) Mol. Phyl. Evol., in press) we obtain a more informative indication of the robustness of each node. In addition, this procedure allows us to estimate the number of additional nucleotides that would be required to resolve confidently the currently uncertain nodes; this number turns out to be extremely high and experimentally unfeasible. We then take this approach one step further: using parameters derived from the above analysis, assuming a molecular clock and using palaeontological dates for calibration, we establish a relationship between the number of sites contained in a given data set and the time interval that this data set can confidently resolve (with 95% bootstrap support). Under these assumptions, the presently available 18S rRNA database cannot confidently resolve cladogenetic events separated by less than about 40 Myr. Thus, at the present time, the potential resolution by the palaeontological approach is higher than that by the molecular one.

scholarly journals Relict groups of spiny frogs indicate Late Paleogene-Early Neogene trans-Tibet dispersal of thermophile faunal elements

2021 ◽  
Author(s):  
Sylvia Hofmann ◽  
Daniel Jablonski ◽  
Spartak Litvinchuk ◽  
Rafaqat Masroor ◽  
Joachim Schmidt
Keyword(s):  
Sequence Data ◽  
Gene Tree ◽  
Early Miocene ◽  
Phylogenetic Position ◽  
Published Data ◽  
Data Set ◽  
Sister Clade ◽  
Early Neogene ◽  
Warm Temperate ◽  
Temperate Climates

AbstractBackgroundThe Himalaya-Tibet orogen (HTO) presents an outstanding geologically active formation that contributed to, and fostered, modern Asian biodiversity. However, our concepts of the historical biogeography of its biota are far from conclusive, as are uplift scenarios for the different parts of the HTO. Here, we revisited our previously published data set of the tribe Paini extending it with sequence data from the most western Himalayan spiny frogs Allopaa and Chrysopaa and using them as an indirect indicator for the paleoecological development of Tibet.MethodsWe obtained sequence data of two mitochondrial loci (16S rRNA, COI) and one nuclear marker (Rag1) from Allopaa samples from Kashmir Himalaya as well as Chrysopaa sequence data from the Hindu Kush available from GenBank to complement our previous data set. A Maximum likelihood and dated Bayesian gene tree were generated based on the concatenated data set. To resolve the inconsistent placement of Allopaa, we performed different topology tests.ResultsConsistent with previous results, the Southeast Asian genus Quasipaa is sister to all other spiny frogs. The results further reveal a basal placement of Chrysopaa relative to Allopaa and Nanorana with an estimated age of ca. 26 Mya. Based on the topology tests, the phylogenetic position of Allopaa as a sister clade to Chaparana seems to be most likely, resulting in a paraphyletic genus Nanorana and a separation from the latter clade around 20 Mya. Both, the placements of Chrysopaa and Allopaa support the presence of basal Paini lineages in the far north western part of the HTO, which is diametrically opposite end of the HTO with respect to the ancestral area of spiny frogs in Southeast Asia. These striking distributional patterns can be most parsimoniously explained by trans-Tibet dispersal during the late Oligocene (subtropical Chrysopaa) respectively early Miocene (warm temperate Allopaa). Within spiny frogs, only members of the monophyletic Nanorana+Paa clade are adapted to the colder temperate climates, indicating that high-altitude environments did not dominate in the HTO before ca. 15 Mya. Our results are consistent with fossil records suggesting that large parts of Tibet were characterized by subtropical to warm temperate climates at least until the early Miocene.

scholarly journals Mitochondrial DNA Sequence Phylogeny of Daucus

2020 ◽  
Vol 45 (2) ◽  
pp. 403-408 ◽  
Author(s):  
David M. Spooner ◽  
Holly Ruess ◽  
Philipp Simon ◽  
Douglas Senalik
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Plastid Dna ◽  
Nuclear Data ◽  
Bootstrap Support ◽  
Illumina Hiseq ◽  
Data Set ◽  
Closely Related Species ◽  
Mitochondrial Sequences

Abstract—We explored the phylogenetic utility of mitochondrial DNA sequences in Daucus and compared the results with prior phylogenetic results using the same 36 accessions of Daucus (and two additional outgroups) with plastid DNA sequences and with other nuclear results. As in the plastid study we used Illumina HiSeq sequencer to obtain resequencing data of the same accessions of Daucus and outgroups, and analyzed the data with maximum parsimony and maximum likelihood. We obtained data from 47 of 71 total mitochondrial genes but only 17 of these 47 genes recovered major clades that were common in prior plastid and nuclear studies. Our phylogenetic trees of the concatenated data set of 47 genes were moderately resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. There are areas of hard incongruence with phylogenies using plastid and nuclear data. In agreement with other studies, we conclude that mitochondrial sequences are generally poor phylogenetic markers, at least at the genus level, despite their utility in some other studies.

Molecular phylogenetic reconstruction of the endemic Asian salamander family Hynobiidae (Amphibia, Caudata)

Zootaxa ◽  
2013 ◽  
Vol 3626 (1) ◽  
pp. 77-93 ◽  
Author(s):  
DAVID W. WEISROCK ◽  
J. ROBERT MACEY ◽  
MASAFUMI MATSUI ◽  
DANIEL G. MULCAHY
Keyword(s):  
Mitochondrial Dna ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Bootstrap Support ◽  
Phylogenetic Study ◽  
Taxon Sampling ◽  
12S Rrna ◽  
Sister Relationship ◽  
Data Set ◽  
History Of

The salamander family Hynobiidae contains over 50 species and has been the subject of a number of molecular phylo-genetic investigations aimed at reconstructing branches across the entire family. In general, studies using the greatest amount of sequence data have used reduced taxon sampling, while the study with the greatest taxon sampling has used a limited sequence data set. Here, we provide insights into the phylogenetic history of the Hynobiidae using both dense taxon sampling and a large mitochondrial DNA sequence data set. We report exclusive new mitochondrial DNA data of 2566 aligned bases (with 151 excluded sites, of included sites 1157 are variable with 957 parsimony informative). This is sampled from two genic regions encoding a 12S–16S region (the 3’ end of 12S rRNA, tRNAVAl, and the 5’ end of 16S rRNA), and a ND2–COI region (ND2, tRNATrp, tRNAAla, tRNAAsn, the origin for light strand replication—OL, tRNACys, tRNATyr, and the 5’ end of COI). Analyses using parsimony, Bayesian, and maximum likelihood optimality criteria produce similar phylogenetic trees, with discordant branches generally receiving low levels of branch support. Monophyly of the Hynobiidae is strongly supported across all analyses, as is the sister relationship and deep divergence between the genus Onychodactylus with all remaining hynobiids. Within this latter grouping our phylogenetic results identify six clades that are relatively divergent from one another, but for which there is minimal support for their phy-logenetic placement. This includes the genus Batrachuperus, the genus Hynobius, the genus Pachyhynobius, the genus Salamandrella, a clade containing the genera Ranodon and Paradactylodon, and a clade containing the genera Liua and Pseudohynobius. This latter clade receives low bootstrap support in the parsimony analysis, but is consistent across all three analytical methods. Our results also clarify a number of well-supported relationships within the larger Batrachu-perus and Hynobius clades. While the relationships identified in this study do much to clarify the phylogenetic history of the Hynobiidae, the poor resolution among major hynobiid clades, and the contrast of mtDNA-derived relationships with recent phylogenetic results from a small number of nuclear genes, highlights the need for continued phylogenetic study with larger numbers of nuclear loci.

scholarly journals Mitochondrial Evidence on the Phylogenetic Position of Caecilians (Amphibia: Gymnophiona)

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 765-775
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Tandem Repeats ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Maximum Parsimony Analysis ◽  
Bootstrap Support ◽  
Phylogenetic Position ◽  
Trna Genes ◽  
Data Sets ◽  
Data Set ◽  
Protein Coding

Abstract The complete nucleotide sequence (17,005 bp) of the mitochondrial genome of the caecilian Typhlonectes natans (Gymnophiona, Amphibia) was determined. This molecule is characterized by two distinctive genomic features: there are seven large 109-bp tandem repeats in the control region, and the sequence for the putative origin of replication of the L strand can potentially fold into two alternative secondary structures (one including part of the tRNACys). The new sequence data were used to assess the phylogenetic position of caecilians and to gain insights into the origin of living amphibians (frogs, salamanders, and caecilians). Phylogenetic analyses of two data sets—one combining protein-coding genes and the other combining tRNA genes—strongly supported a caecilian + frog clade and, hence, monophyly of modern amphibians. These two data sets could not further resolve relationships among the coelacanth, lungfishes, and tetrapods, but strongly supported diapsid affinities of turtles. Phylogenetic relationships among a larger set of species of frogs, salamanders, and caecilians were estimated with a mitochondrial rRNA data set. Maximum parsimony analysis of this latter data set also recovered monophyly of living amphibians and favored a frog + salamander (Batrachia) relationship. However, bootstrap support was only moderate at these nodes. This is likely due to an extensive among-site rate heterogeneity in the rRNA data set and the narrow window of time in which the three main groups of living amphibians were originated.

scholarly journals Relict groups of spiny frogs indicate Late Paleogene-Early Neogene trans-Tibet dispersal of thermophile faunal elements

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11793
Author(s):  
Sylvia Hofmann ◽  
Daniel Jablonski ◽  
Spartak N. Litvinchuk ◽  
Rafaqat Masroor ◽  
Joachim Schmidt
Keyword(s):  
Sequence Data ◽  
Gene Tree ◽  
Early Miocene ◽  
Phylogenetic Position ◽  
Published Data ◽  
Northwestern Part ◽  
Data Set ◽  
Early Neogene ◽  
Warm Temperate ◽  
Temperate Climates

Background The Himalaya-Tibet orogen (HTO) presents an outstanding geologically active formation that contributed to, and fostered, modern Asian biodiversity. However, our concepts of the historical biogeography of its biota are far from conclusive, as are uplift scenarios for the different parts of the HTO. Here, we revisited our previously published data set of the tribe Paini extending it with sequence data from the most western Himalayan spiny frogs Allopaa and Chrysopaa and using them as an indirect indicator for the potential paleoecological development of Tibet. Methods We obtained sequence data of two mitochondrial loci (16S rRNA, COI) and one nuclear marker (Rag1) from Allopaa samples from Kashmir Himalaya as well as Chrysopaa sequence data from the Hindu Kush available from GenBank to complement our previous data set. A Maximum likelihood and dated Bayesian gene tree were generated based on the concatenated data set. To resolve the inconsistent placement of Allopaa, we performed different topology tests. Results Consistent with previous results, the Southeast Asian genus Quasipaa is sister to all other spiny frogs. The results further reveal a basal placement of Chrysopaa relative to Allopaa and Nanorana with an estimated age of ca. 26 Mya. Based on the topology tests, the phylogenetic position of Allopaa as a sister clade to Chaparana seems to be most likely, resulting in a paraphyletic genus Nanorana and a separation from the latter clade around 20 Mya, although a basal position of Allopaa to the genus Nanorana cannot be entirely excluded. Both, the placements of Chrysopaa and Allopaa support the presence of basal Paini lineages in the far northwestern part of the HTO, which is diametrically opposite end of the HTO with respect to the ancestral area of spiny frogs in Southeast Asia. These striking distributional patterns can be most parsimoniously explained by trans-Tibet dispersal during the late Oligocene (subtropical Chrysopaa) respectively early Miocene (warm temperate Allopaa). Within spiny frogs, only members of the monophyletic Nanorana+Paa clade are adapted to the colder temperate climates, indicating that high-altitude environments did not dominate in the HTO before ca. 15 Mya. Our results are consistent with fossil records suggesting that large parts of Tibet were characterized by subtropical to warm temperate climates at least until the early Miocene. They contradict prevalent geological models of a highly uplifted late Paleogene proto-Plateau.

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.

Typing for all known HLA-DR alleles by group-specific PCR and flow cytometry-based multiplexed single nucleotide extension

2003 ◽  
Vol 64 (10) ◽  
pp. S38
Author(s):  
Yanzheng Zhang ◽  
Charlie Costin ◽  
Christopher Giang ◽  
Robert Vorhaben ◽  
Peter Stastny
Keyword(s):  
Flow Cytometry ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Hla Dr

scholarly journals Intergeneric Relationships within the Early-Diverging Angiosperm Family Nymphaeaceae Based on Chloroplast Phylogenomics

2018 ◽  
Vol 19 (12) ◽  
pp. 3780 ◽  
Author(s):  
Dingxuan He ◽  
Andrew Gichira ◽  
Zhizhong Li ◽  
John Nzei ◽  
Youhao Guo ◽  
...  
Keyword(s):  
Genome Structure ◽  
Morphological Data ◽  
Basal Angiosperm ◽  
Phylogenetic Position ◽  
Data Set ◽  
Protein Coding ◽  
Plastid Genomes ◽  
Chloroplast Genomes ◽  
Gene Data ◽  
High Degree

The order Nymphaeales, consisting of three families with a record of eight genera, has gained significant interest from botanists, probably due to its position as a basal angiosperm. The phylogenetic relationships within the order have been well studied; however, a few controversial nodes still remain in the Nymphaeaceae. The position of the Nuphar genus and the monophyly of the Nymphaeaceae family remain uncertain. This study adds to the increasing number of the completely sequenced plastid genomes of the Nymphaeales and applies a large chloroplast gene data set in reconstructing the intergeneric relationships within the Nymphaeaceae. Five complete chloroplast genomes were newly generated, including a first for the monotypic Euryale genus. Using a set of 66 protein-coding genes from the chloroplast genomes of 17 taxa, the phylogenetic position of Nuphar was determined and a monophyletic Nymphaeaceae family was obtained with convincing statistical support from both partitioned and unpartitioned data schemes. Although genomic comparative analyses revealed a high degree of synteny among the chloroplast genomes of the ancient angiosperms, key minor variations were evident, particularly in the contraction/expansion of the inverted-repeat regions and in RNA-editing events. Genome structure, and gene content and arrangement were highly conserved among the chloroplast genomes. The intergeneric relationships defined in this study are congruent with those inferred using morphological data.

The systematics of Raspailiidae (Demospongiae: Poecilosclerida: Microcionina) re-analysed with a ribosomal marker

2007 ◽  
Vol 87 (6) ◽  
pp. 1571-1576 ◽  
Author(s):  
Dirk Erpenbeck ◽  
Sue List-Armitage ◽  
Belinda Alvarez ◽  
Bernard M. Degnan ◽  
Gert Wörheide ◽  
...  
Keyword(s):  
Gene Tree ◽  
Morphological Characters ◽  
Character Evolution ◽  
28S Rdna ◽  
The Other ◽  
Data Set ◽  
Rdna Gene ◽  
Insight Into

We present a 28S rDNA gene tree of selected Raspailiidae, Axinellidae and other demosponges to obtain insight into raspailiid phylogeny and character evolution. The Raspailiidae in our data set cluster in a well-supported clade, distinguished from Axinellidae, Agelasida and Hadromerida. Raspailia (s.s.), Eurypon, Sollasella, Aulospongus and Ectyoplasia form a Raspailiidae clade. Some Raspailia subgenera, in particular R. (Parasyringella), are not retrieved monophyletically. Trikentrion falls into the Thrinacophorinae, and not the Cyamoninae as earlier hypothesized. The axinellid genera Ptilocaulis and Reniochalina also cluster with Raspailiidae, distant from the other Axinellidae. The suitability of particular morphological characters for raspailiid phylogeny is discussed.

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