20 results on '"*MOLECULAR phylogeny"'
Search Results
2. Capsid protein evolution and comparative phylogeny of novel porcine parvoviruses
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Cadar, Dániel, Cságola, Attila, Kiss, Timea, and Tuboly, Tamás
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CAPSIDS , *COMPARATIVE studies , *MOLECULAR phylogeny , *VIRUS diseases in swine , *PARVOVIRUSES , *BIOLOGICAL evolution , *NUCLEOTIDE sequence - Abstract
Abstract: In addition to the well known “classical” porcine parvovirus (PPV1; responsible for reproductive failure of susceptible sows) several new porcine parvoviruses have been recognized (PPV2, PPV3 and PPV4) in recent years. The genetic variation, characteristics and evolutionary factors shaping these novel PPVs were studied by comparing the complete capsid (cap) genes of PPVs from domestic pigs and wild boars. Using Bayesian coalescent methods we estimated the rate of nucleotide substitution for PPV2, PPV3 and PPV4 to be of the order of 3.86×10−4–8.23×10−4 subs site−1 year−1, similar to those commonly measured for RNA viruses, although this rate in case of PPV2 is probably influenced by frequent recombination events. Given such rapid evolutionary dynamics, it is likely that novel PPVs will continue to improve their capacity to spread among Suidae hosts worldwide. The mean time to the most recent common ancestor for the sampled genetic diversity of the newly discovered porcine parvoviruses was estimated. The results indicated that novel PPVs originated within approximately the last 70years. Incongruent phylogenetic relationships of several strains suggested recombination events supported by several recombination-detecting methods and by split-decomposition phylogenetic networks. Analyses of the selective constraints acting on each codon suggest that some regions of PPV cap genes were under positive selection. This study showed that inter- and intraspecies recombination and diversifying selection pressures are prevalent across the cap genes of novel PPVs, and beside host switching and gene flow are important driving forces of their evolution and may be significant factors in the emergence of new viral variants. [Copyright &y& Elsevier]
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- 2013
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3. The phylogenetic relationships of the extant pelicans inferred from DNA sequence data
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Kennedy, Martyn, Taylor, Scott A., Nádvorník, Petr, and Spencer, Hamish G.
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MOLECULAR phylogeny , *PELICANS , *DNA analysis , *NUCLEOTIDE sequence , *WATER birds , *BIOLOGICAL evolution , *MITOCHONDRIAL DNA - Abstract
Abstract: The pelicans are a charismatic group of large water birds, whose evolutionary relationships have been long debated. Here we use DNA sequence data from both mitochondrial and nuclear genes to derive a robust phylogeny of all the extant species. Our data rejects the widespread notion that pelicans can be divided into white- and brown-plumaged groups. Instead, we find that, in contrast to all previous evolutionary hypotheses, the species fall into three well-supported clades: an Old World clade of the Dalmatian, Spot-billed, Pink-backed and Australian Pelicans, a New World clade of the American White, Brown and Peruvian Pelicans, and monospecific clade consisting solely of the Great White Pelican, weakly grouped with the Old World clade. We discuss possible evolutionary scenarios giving rise to this diversity. [Copyright &y& Elsevier]
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- 2013
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4. The analysis of rRNA sequence-structure in phylogenetics: An application to the family Pectinidae (Mollusca: Bivalvia)
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Salvi, Daniele, Bellavia, Gabriella, Cervelli, Manuela, and Mariottini, Paolo
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SCALLOPS , *MOLECULAR phylogeny , *RIBOSOMAL DNA , *BIOLOGICAL evolution , *MOLECULAR genetics , *NUCLEOTIDE sequence , *GENETIC markers , *MITOCHONDRIAL DNA - Abstract
Abstract: Several studies pointed out the relevance of integrating secondary structure information in sequence analysis and phylogenetics, both in terms of phylogenetic resolution and of marker suitability for phylogenetic reconstruction at higher taxonomic-rank. In this study we explore in a phylogenetic framework the primary and secondary structure information from nuclear (ITS2) and mitochondrial (16S) ribosomal DNA sequences from the Pectinidae, commonly known as scallops. Primary sequences were analysed under neighbour-joining, maximum parsimony, maximum likelihood, and Bayesian approaches. The individual RNA secondary structures were analysed alone and with primary sequences employing a combined model of sequence-structure evolution. The information from primary sequences and secondary structure of the ITS2 are concordant and provide good phylogenetic resolution, while the mitochondrial marker 16S fails to resolve the relationships between the major clades and shows a lack of structural signals. Our phylogenetic reconstruction provided evidence for the monophyly of the subfamily Pectininae and the tribes Aequipectinini and Pectinini while the subfamily Chlamydinae, although recovered in some analyses, did not receive good support. The secondary structure analysis of the derived pectinid ITS2 rRNA sequence revealed three striking differences between Pectininae and Chlamydinae subfamilies: (a) Chlamydinae ITS2 rRNA folding shows the typical four domains architecture, while the one of Pectininae only three; (b) the Pectinidae basal DI pairing shows a different sequence-structure consensus between Pectininae and Chlamydinae; (c) the Pectininae DIII domain holds a specific short secondary stem (Pec STEM). Furthermore, the scallop ITS2 rRNA folding analysis has shown the presence of a conserved sequence motif (invariably located on apical portion of the DIII domain) which emerges as a common feature across Bivalvia. The combined sequence-structure approach employed in this study, corroborates the deep significance of including the secondary structure information in phylogenetic analysis both as combined sequence-structure alignment as well as pointing out conserved elements of the RNA folding. [Copyright &y& Elsevier]
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- 2010
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5. Two aspects along the continuum of pigeon evolution: A South-Pacific radiation and the relationship of pigeons within Neoaves
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Gibb, Gillian C. and Penny, David
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BIOLOGICAL evolution , *PIGEONS , *MOLECULAR phylogeny , *BIOLOGICAL divergence , *NUCLEOTIDE sequence , *MITOCHONDRIAL DNA , *COLUMBIFORMES - Abstract
Abstract: Phylogenetics explores the continuum of shallower to deeper genetic divergences between taxa. Along this continuum increasing lengths of DNA sequence can be used to answer deeper and deeper questions about biological relationships. We use shorter, and then longer mitochondrial DNA sequences to address two aspects of pigeon evolution. Firstly, we examine the phylogenetic relationships of the eight genera within the South Pacific Ducula–Ptilinopus radiation, and examine how this radiation fits into pigeons generally. Within Ducula, taxa are closely related, whereas Ptilinopus is very diverse, and paraphyletic. One third of all pigeon species are within the Ducula–Ptilinopus radiation, however all are very similar ecologically. Secondly, we study the deeper phylogenetic question regarding the relationship of pigeons to other birds. To this end, we report the complete mitochondrial genome of Hemiphaga novaeseelandiae, a member of the Ducula–Ptilinopus radiation. We use this mitochondrial genome, along with additional sandgrouse (Pterocles namaqua) mitochondrial genes to assess various candidates for the closest relative of pigeons. Of parrots, shorebirds, and sandgrouse, we find highest support for the sandgrouse–pigeon grouping. Furthermore in these analyses the pigeon and sandgrouse group closer to the falcons than any other included taxon. The finding that pigeons and sandgrouse may be more closely related to falcons than to previous candidates such as shorebirds or parrots invites further investigation. [Copyright &y& Elsevier]
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- 2010
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6. Evolution and biogeographic diversification of the witch-hazel genus (Hamamelis L., Hamamelidaceae) in the Northern Hemisphere
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Xie, Lei, Yi, Ting-Shuang, Li, Rong, Li, De-Zhu, and Wen, Jun
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BIOLOGICAL evolution , *BIOGEOGRAPHY , *SPECIES diversity , *BIOLOGICAL divergence , *HAMAMELIDACEAE , *NUCLEOTIDE sequence , *MOLECULAR phylogeny , *WITCH hazels - Abstract
Abstract: The evolution of the eastern Asian and eastern North American disjunction of the witch-hazel genus Hamamelis L. (Hamamelidaceae) was examined through phylogenetic and biogeographic analyses. Phylogenetic relationships of all Hamamelis species were reconstructed using parsimony and Bayesian analyses of sequence data from six plastid (trnL-F, psaA-ycf3, rps16, matK, atpB-rbcL, and psbA-trnH) and two nuclear (ITS and ETS) DNA regions. The phylogeny was then used to infer the biogeographic origin and subsequent diversification using both event-based (DIVA) and maximum likelihood (LAGRANGE) methods incorporating fossil data. The times of divergence within Hamamelis were estimated with the Bayesian approach using the program BEAST. A very low level of molecular variation was detected in both the plastid and the nuclear DNA regions within Hamamelis. The combined analyses resulted in a phylogeny of the genus with higher resolution and support values. Hamamelis was supported to be monophyletic with H. mollis from eastern China diverged first in the genus. All North American species formed a clade and was sister to the eastern Asian H. japonica. Within the North American clade, H. mexicana was sister to H. vernalis, and the recently described species H. ovalis was found to be closely related to the widespread species H. virginiana. The stem age of Hamamelis was estimated to be at the Eocene (51.2mya, with 95% HDP: 49.0–54.6mya), and the crown age of the genus was dated to be at the late Miocene (9.7mya, with 95% HDP: 3.6–18.1mya, or 10.6mya, with 95% HDP: 4.2–19.6mya). The disjunction between the eastern Asian and the eastern North American species was dated to be 7.1mya (95% HDP: 3.1–13.6mya) or 7.7mya (95% HDP: 3.4–13.6mya). Biogeographic analyses incorporating fossils resulted in more equally possible solutions at the stem lineage of Hamamelis than those including extant species only. Eastern Asia is inferred to be the most-likely area for the origin of Hamamelis. The current disjunction was due to the extinction in western North America and Europe from Eocene to late Miocene, and later migration from eastern Asia into North America. The Bering land bridge was hypothesized to have played an important role in the evolution of this disjunction. The current species diversity of the genus was the result of relatively recent diversification events during the late Miocene rather than long accumulation of lineages from the early Tertiary. [Copyright &y& Elsevier]
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- 2010
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7. Evolutionary dynamics of the N1 neuraminidases of the main lineages of influenza A viruses
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Fourment, Mathieu, Wood, Jeffrey T., Gibbs, Adrian J., and Gibbs, Mark J.
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BIOLOGICAL evolution , *MOLECULAR dynamics , *NEURAMINIDASE , *INFLUENZA A virus , *IMMUNE system , *NUCLEOTIDE sequence , *VIRAL genomes , *MOLECULAR phylogeny - Abstract
Abstract: Influenza A virus infects a wide range of hosts including birds, humans, pigs, horses, and other mammals. Because hosts differ in immune system structure and demography, it is therefore expected that host populations leave different imprints on the viral genome. In this study, we investigated the evolutionary trajectory of the main lineages of N1 type neuraminidase (NA) gene sequences of influenza A viruses by estimating their evolutionary rates and the selection pressures exerted upon them. We also estimated the time of emergence of these lineages. The Eurasian (avian-like) and North American (classical) swine lineages, the human (seasonal) and avian H5N1 lineages, and a long persisting avian lineage were studied and compared. Nucleotide substitution rates ranged from 1.9×10−3 to 4.3×10−3 substitutions per site per year, with the H5N1 lineage estimated to have the greatest rate. The evolutionary rates of the H1N1 human lineage appeared to be slightly greater after it re-emerged in 1977 than before it disappeared in the 1950s. Comparing across the lineages, substitution rates appeared to correlate with the number of positively selected sites and with the degree of asymmetry of the phylogenetic trees. Some lineages had strongly asymmetric trees, implying repeated genotype replacement and narrow genetic diversity. Positively selected sites were identified in all lineages, with the H5N1 lineage having the largest number. A great number of isolates of the H5N1 lineage were sequenced in a short time period and the phylogeny of the lineage was more symmetric. We speculate that the rate and selection estimations made for this lineage could have been influenced by sampling and may not represent the long-term trends. [Copyright &y& Elsevier]
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- 2010
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8. Mitochondrial phylogenomics of anchovies (family Engraulidae) and recurrent origins of pronounced miniaturization in the order Clupeiformes
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Lavoué, Sébastien, Miya, Masaki, and Nishida, Mutsumi
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MOLECULAR phylogeny , *ANCHOVIES , *CLUPEIFORMES , *BIOLOGICAL evolution , *NUCLEOTIDE sequence , *MITOCHONDRIA - Abstract
Abstract: We investigated the phylogenetic relationships among the major lineages of anchovies (Engraulidae) based on the comparison of mitogenome sequences. Analyses support the Engraulidae’s monophyly but its placement remains uncertain. Within the Engraulidae, our results are congruent with the current morphology-based hypothesis in dividing the Engraulidae into two subfamilies: the Coiliinae comprises exclusively Indo-Pacific genera, while the Engraulinae includes the widespread genus Engraulis, the so-called “New World anchovies” group and the two Indo-Pacific genera Encrasicholina and Stolephorus. Amazonsprattus belongs to the subfamily Engraulinae. Our results support at least three independent origins of miniaturization within the Clupeiformes. [Copyright &y& Elsevier]
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- 2010
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9. Evolutionary characterization of the West Nile Virus complete genome
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Gray, R.R., Veras, N.M.C., Santos, L.A., and Salemi, M.
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BIOLOGICAL evolution , *WEST Nile virus , *VIRAL genomes , *BIOGEOGRAPHY , *NUCLEOTIDE sequence , *MOLECULAR phylogeny , *EPIDEMICS - Abstract
Abstract: The spatial dynamics of the West Nile Virus epidemic in North America are largely unknown. Previous studies that investigated the evolutionary history of the virus used sequence data from the structural genes (prM and E); however, these regions may lack phylogenetic information and obscure true evolutionary relationships. This study systematically evaluated the evolutionary patterns in the eleven genes of the WNV genome in order to determine which region(s) were most phylogenetically informative. We found that while the E region lacks resolution and can potentially result in misleading conclusions, the full NS3 or NS5 regions have strong phylogenetic signal. Furthermore, we show that geographic structure of WNV infection within the US is more pronounced than previously reported in studies that used the structural genes. We conclude that future evolutionary studies should focus on NS3 and NS5 in order to maximize the available sequences while retaining maximal interpretative power to infer temporal and geographic trends among WNV strains. [Copyright &y& Elsevier]
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- 2010
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10. Studying sources of incongruence in arthropod molecular phylogenies: Sea spiders (Pycnogonida) as a case study
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Arabi, Juliette, Cruaud, Corinne, Couloux, Arnaud, and Hassanin, Alexandre
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PYCNOGONIDA , *ARTHROPODA , *MOLECULAR phylogeny , *BIOMARKERS , *MITOCHONDRIAL DNA , *NUCLEOTIDE sequence , *BIOLOGICAL evolution , *CASE studies - Abstract
Abstract: In this report, we analyze the phylogeny of Pycnogonida using the three nuclear and three mitochondrial markers currently sequenced for studying inter- and intrafamilial relationships within Arthropoda: 18S and 28S rRNA genes, Histone H3, cytochrome c oxidase subunit 1 (CO1), 12S and 16S rRNA genes. We identify several problems in previous studies, due to the use of inappropriate sequences (taxonomic misidentification, DNA contamination, sequencing errors, missing data) or taxa (outgroup choice). Our analyses show that most markers are not powerful to study the phylogeny of sea spiders. The results suggest however a recent diversification of the group (Mesozoic rather than Paleozoic) and the early divergence of Austrodecidae, followed by Colossendeidae, Pycnogonidae and Rhynchothoracidae. Except Ammotheidae and Callipallenidae, all other families were recovered as monophyletic. Analyses of synonymous sites in CO1 sequences reveal an extreme heterogeneity of nucleotide composition within sea spiders, as six unrelated species show a reverse strand-specific bias. We therefore suggest that several independent reversals of asymmetric mutational constraints occurred during the evolution of Pycnogonida, as a consequence of genomic inversions involving either the control region or a fragment containing the CO1 gene. These hypotheses are supported by the comparison of two complete mitochondrial genomes of sea spiders (Achelia bituberculata and Nymphon gracile) with that of Limulus. [Copyright &y& Elsevier]
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- 2010
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11. Molecular phylogenetics of North American phoxinins (Actinopterygii: Cypriniformes: Leuciscidae) based on RAG1 and S7 nuclear DNA sequence data
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Bufalino, Angelo P. and Mayden, Richard L.
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CYPRINIFORMES , *MOLECULAR phylogeny , *NUCLEOTIDE sequence , *MITOCHONDRIAL DNA , *BIOLOGICAL evolution - Abstract
Abstract: Most molecular phylogenetic hypotheses for North American (NA) phoxinins are based on mitochondrial DNA sequences (mtDNA) and the resulting hypotheses are rather variable, though there is general support for three major lineages of NA phoxinins: western, creek chub-plagopterin (CC-P), and open posterior myodome (OPM) clades. Support for a monophyletic NA phoxinin group has varied among studies. This study utilizes nuclear DNA (nDNA) sequences from the RAG1 (exon 3) and S7 (intron 1) gene regions to evaluate the phylogenetic relationships and monophyly of NA phoxinins. Results from the nDNA analyses provide overall support for the western, CC-P, and OPM clades. The CC-P clade had the best overall resolution and support in the individual and combined analyses of the nDNA data. Resolution of the western clade was fairly good, with most analyses recovering a monophyletic Gila clade. The OPM clade demonstrated the highest degree of topological variability among the analyses. The RAG1 analyses failed to recover a monophyletic NA phoxinin group by resolving the European leuciscins, inclusive Notemigonus crysoleucas, within the NA phoxinin topology. Most analyses recovered a strongly supported shiner clade though, similar to several mtDNA studies; there was a high degree of topological variability among the results. [Copyright &y& Elsevier]
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- 2010
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12. Molecular systematics of the bubblegum coral genera (Paragorgiidae, Octocorallia) and description of a new deep-sea species
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Herrera, Santiago, Baco, Amy, and Sánchez, Juan A.
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OCTOCORALLIA , *MOLECULAR phylogeny , *DEEP-sea corals , *ANIMAL diversity conservation , *BIOLOGICAL evolution , *NUCLEOTIDE sequence - Abstract
Abstract: Bubblegum octocorals (Paragorgia and Sibogagorgia) play an important ecological role in many deep-sea ecosystems. However, these organisms are currently threatened by destructive fishing methods such as bottom trawling. Taxonomic knowledge of conservation targets is necessary for the creation and implementation of efficient conservation strategies. However, for most deep-sea coral groups this knowledge remains incomplete. For instance, despite its similarities with Paragorgia, Sibogagorgia is particular in lacking polyp sclerites, which are present in groups like Paragorgia and the Coralliidae. Although two kinds of sclerites are very similar between Paragorgia and Sibogagorgia, other characters challenge the monophyly of these genera. Here we help to clarify the taxonomy and evolutionary relationships of the bubblegum octocorals and related taxa by examining molecular data. We employed nucleotide sequences of mitochondrial (ND6, ND6-ND3 intergenic spacer, ND3, ND2, COI, msh1 and 16S) and nuclear (28S and ITS2) genomic regions from several taxa to infer molecular phylogenetics and to examine the correspondence of morphological features with the underlying genetic information. Our data strongly supported the monophyly of the genus Paragorgia, the family Coralliidae (precious corals), and a group of undescribed specimens resembling Sibogagorgia. Further morphological observations were congruent regarding the uniqueness of the undescribed specimens, here defined as a new species, Sibogagorgia cauliflora sp. nov., which occurs in both sides of the North American landmass at depths below 1700m. This new species resembles S. dennisgordoni with branching in one plane but has fairly different radiate sclerites and significantly divergent DNA sequences. The existence of several diagnostic characters of Sibogagorgia in S. cauliflora indicates that they indeed belong to this genus. It is however remarkable that a small number of medullar canals are also found in this species; medullar canals have been considered as the main diagnostic character of Paragorgia. Thus, the evidence generated here indicates that the presence or absence of these canals per se is not a conclusively diagnostic character for either genus. The lack of internal-node resolution in the inferred phylogenetic hypotheses of these genera does not allow us to propose a clear scenario regarding the evolution of these traits. [Copyright &y& Elsevier]
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- 2010
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13. The long way to diversity – Phylogeny and evolution of the Heterobranchia (Mollusca: Gastropoda)
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Dinapoli, Angela and Klussmann-Kolb, Annette
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GASTROPODA , *ANIMAL diversity , *MOLECULAR phylogeny , *BIOLOGICAL evolution , *NUCLEOTIDE sequence , *GENETIC markers , *DATA quality - Abstract
Abstract: Heterobranchia are one of the most species rich groups within Gastropoda, with poorly resolved phylogenetic relationships especially in basal taxa. In order to resolve phylogenetic relationships within the Heterobranchia, we pursued a molecular systematic approach by sequencing and analysing a variety of genetic markers (including nuclear 28S rDNA+18S rDNA and mitochondrial 16S rDNA+COI sequences). Maximum likelihood as well as Bayesian inference methods were used for phylogenetic reconstruction. Moreover, data quality was estimated for the purpose of proving the plausibility of the novel phylogenetic hypothesis using a variety of statistical tests as well as network analyses. Finally, a case study was conducted in order to estimate divergence ages using a “relaxed” molecular clock approach with fossils as minimum age constraints. All phylogenetic analyses revealed the Heterobranchia as monophyletic. Within the Heterobranchia, several well supported clades could be resolved. However, the traditional classification based on morphological data could not be confirmed due to paraphyletic Euthyneura as well as paraphyletic Pulmonata and polyphyletic Opisthobranchia. The estimation of data quality yielded a high degree of substitution saturation in many of the nucleotide positions while the Relative-Rate-Test revealed the highest evolution rates within the “Lower Heterobranchia”. Although the dataset shows much conflict, many of the proposed hypotheses are supported by splits of the network analysis. The molecular clock approach was able to confirm some evolutionary hypotheses based on fossils such as the late occurrence of Pulmonata and Stylommatophora, respectively, during the Mesozoic. However, large 95% highest posterior density (HPD) intervals at some of the nodes made a precise dating of these nodes difficult. This molecular phylogenetic investigation provides the most comprehensive molecular study of relationships within the Heterobranchia to date. Due to the outstanding taxon sampling of the “Lower Heterobranchia”, which have been poorly represented in earlier morphological and molecular studies, substantial insights into the evolution and phylogeny of this enigmatic taxon have been gained. [Copyright &y& Elsevier]
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- 2010
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14. New insights to the molecular phylogenetics and generic assessment in the Rhacophoridae (Amphibia: Anura) based on five nuclear and three mitochondrial genes, with comments on the evolution of reproduction
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Li, Jia-tang, Che, Jing, Murphy, Robert W., Zhao, Hui, Zhao, Er-mi, Rao, Ding-qi, and Zhang, Ya-ping
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RHACOPHORIDAE , *PHYLOGENY , *MOLECULAR genetics , *BIOLOGICAL evolution , *ANURA , *NUCLEOTIDE sequence , *MITOCHONDRIA , *REPRODUCTION - Abstract
Abstract: The phylogenetic relationships among 12 genera of treefrogs (Family, Rhacophoridae), were investigated based on a large sequence data set, including five nuclear (brain-derived neurotrophic factor, proopiomelanocortin, recombination activating gene 1, tyrosinase, rhodopsin) and three mitochondrial (partial 12S and 16S ribosomal RNA and the complete valine t-RNA) genes. Phylogenetic analysis of the nuclear gene sequences resolved three major clades. The first group included Philautus, Pseudophilautus, Kurixalus, Gracixalus, and Theloderma moloch; Pseudophilautus and Kurixalus were sister taxa. The second group consisted of Nyctixalus and Theloderma. The third group contained Feihyla, Polypedates, Rhacophorus, and Chiromantis vittatus; Polypedates and Feihyla were sister taxa. Analyses of the nuclear and mitochondrial genes supported the following results: (1) Genus Liuixalus formed the sister group of all other rhacophorines. (2) Philautus, Theloderma, and Chiromantis were not resolved as monophyletic genera. Four groups, including Philautus ocellatus and P. hainanus, P. longchuanensis and P. gryllus, P. banaensis, and P. quyeti nested well within the genera Liuixalus, Pseudophilautus, Kurixalus, and Gracixalus, respectively. (3) Theloderma moloch and Chiromantis vittatus did not cluster with other species of Theloderma and Chiromantis, respectively. Foam nesting evolved only once, as did laying eggs in a jelly-like matrix containing some bubbles. Terrestrial direct development evolved twice in the Rhacophoridae. [Copyright &y& Elsevier]
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- 2009
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15. Concatenated SSU and LSU rDNA data confirm the main evolutionary trends within myxosporeans (Myxozoa: Myxosporea) and provide an effective tool for their molecular phylogenetics
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Bartošová, Pavla, Fiala, Ivan, and Hypša, Václav
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MOLECULAR phylogeny , *MYXOSPOREA , *RIBOSOMAL DNA , *BIOLOGICAL evolution , *NUCLEOTIDE sequence , *GENE amplification - Abstract
Abstract: Views on myxosporean phylogeny and systematics have recently undergone substantial changes resulting from analyses of SSU rDNA. Here, we further investigate the evolutionary trends within myxosporean lineages by using 35 new sequences of the LSU rDNA. We show a good agreement between the two rRNA genes and confirm the main phylogenetic split between the freshwater and marine lineages. The informative superiority of the LSU data is shown by an increase of the resolution, nodal supports and tree indexes in the LSU rDNA and combined analyses. We determine the most suitable part of LSU for the myxosporean phylogeny by comparing informative content in various regions of the LSU sequences. Based on this comparison, we propose the D5–3′-end part of the LSU rRNA gene as the most informative region which provides in concatenation with the complete SSU a well resolved and robust tree. To allow for simple amplification of the marker, we design specific primer set for this part of LSU rDNA. [Copyright &y& Elsevier]
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- 2009
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16. ITS2 sequence–structure analysis in phylogenetics: A how-to manual for molecular systematics
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Schultz, Jörg and Wolf, Matthias
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MOLECULAR phylogeny , *NUCLEOTIDE sequence , *GENE mapping , *NON-coding RNA , *BIOLOGICAL evolution , *BIOMARKERS - Abstract
Abstract: The information that can be obtained from the secondary structure of the nuclear ribosomal internal transcribed spacer 2 (ITS2) is substantial, and yet many studies exploit this information inconsistently or inappropriately. This review introduces a remedy in the form of a flowchart where we detail the steps involved in estimating structure-based phylogenetic trees from ITS2 data. The pipeline described consists of the ITS2 Database, 4SALE, the CBCAnalyzer, and ProfDistS. Based on these tools, we describe how to utilize ITS2 sequence and secondary structure information together with an ITS2 specific scoring matrix and an ITS2 specific substitution model. The phylogenetic results thus obtained have been shown to be more reliable than approaches based on primary sequence data alone. Moreover, compensatory base changes (CBCs) in ITS2 sequence–structure pairs are identified as a possible marker for distinguishing species. [Copyright &y& Elsevier]
- Published
- 2009
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17. Molecular phylogeny of the tribe Sphodrini (Coleoptera: Carabidae) based on mitochondrial and nuclear markers
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Ruiz, Carlos, Jordal, Bjarte, and Serrano, José
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MOLECULAR phylogeny , *BEETLES , *GENETIC markers , *NUCLEOTIDE sequence , *HABITAT partitioning (Ecology) , *CLADISTIC analysis , *BIOLOGICAL evolution - Abstract
Abstract: A phylogenetic analysis of 6.4kb of nucleotide sequence data from seven genes (mitochondrial cox1-cox2 and tRNAleu, and nuclear Ef-1α C0, Ef-1α C1, 28S, and 18S) was done to reconstruct the phylogenetic relationships of the ground-beetle tribe Sphodrini. Gene regions of variable nucleotide length were aligned using both a secondary structure model, Clustal W, and a combination of the two. Sensitivity analysis was performed in order to explore the effect of alignment methods. The ribosomal and protein-coding genes were largely congruent based on the ILD test and partitioned Bremer support measures. MtDNA analysis provided high resolution and high support for most clades. The tribe Sphodrini and the related tribes Platynini, Pterostichini and Zabrini made up monophyletic clades, but the relationship between them was weakly resolved and sensitive to alignment strategy. Previously suggested relationships between subtribes of Sphodrini were not corroborated, and only the subtribe Atranopsina revealed high support as the sister clade to the other subtribes. The analyses clearly demonstrated the importance of exploring effects of alignment methods that may become particularly important in resolving polytomies and nodes with low support. [Copyright &y& Elsevier]
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- 2009
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18. Convergent evolution and paraphyly of the hawk-eagles of the genus Spizaetus (Aves, Accipitridae) – phylogenetic analyses based on mitochondrial markers.
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Haring, E., Kvaløy, K., Gjershaug, J.-O., Røv, N., and Gamauf, A.
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CONVERGENT evolution , *BIOLOGICAL evolution , *SPIZAETUS , *PHYLOGENY , *MITOCHONDRIAL DNA , *NUCLEOTIDE sequence , *CYTOCHROME b - Abstract
The phylogenetic relationships within the New and Old World hawk-eagle assemblage (genus Spizaetus; Aves: Accipitridae) were studied using mitochondrial DNA sequences ( cytochrome b, control region). Eighty-four specimens representing all Spizaetus species and almost all currently distinguished subspecies as well as 11 other booted and non-booted ‘eagle’ genera from the Neotropics, Africa, Eurasia, South Asia and Australasia ( Oroaetus, Harpia, Morphnus, Lophaetus, Stephanoaetus, Hieraaetus, Aquila, Ictinaetus, Spilornis, Pithecophaga, Harpyopsis) were investigated. Although the basal branching could not be resolved, our investigations clearly indicate that hawk-eagles represent a paraphyletic assemblage and thus their external similarities have to be ascribed to convergent evolution. The New World taxa of Spizaetus cluster together, but the South American species Oroaetus isidori appears embedded within this clade. The taxa from Southeast to East Asia form a clearly separated monophyletic group. It is further divided into two subgroups, which are also characterized by distinct juvenile plumage patterns. Spizaetus africanus, the only African representative of the genus, is found in a mixed cluster consisting of members of the genera Aquila and Hieraaetus. These findings are in accordance with previous studies of other authors based on various molecular markers and different sets of taxa, but disagree with current taxonomy. Therefore, we suggest assigning the species of the genus Spizaetus to three different genera: (1) Spizaetus (including Oroaetus isidori) in Central and South America and (2) Nisaetus for the Southeast to East Asian group. (3) The African taxon ( Spizaetus africanus) is discussed to be included into the genus Aquila. Furthermore, we propose to use the former genus name Lophotriorchis Sharpe, 1874, for the monotypic species Hieraaetus kienerii, which has an isolated phylogenetic position. [ABSTRACT FROM AUTHOR]
- Published
- 2007
- Full Text
- View/download PDF
19. MOLECULAR PHYLOGENY OF MACARANGA, MALLOTUS, AND RELATED GENERA (EUPHORBIACEAE S.S.): INSIGHTS FROM PLASTID AND NUCLEAR DNA SEQUENCE DATA.
- Author
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Kulju, Kristo K. M., Sierra, Soraya E. C., Draisma, Stefano G. A., Samuel, Rosabelle, and Van Welzen, Peter C.
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EUPHORBIACEAE , *MOLECULAR phylogeny , *MOLECULAR biology , *PHYLOGENY , *PLASTIDS , *NUCLEOTIDE sequence , *MALLOTUS , *BIOGEOGRAPHY , *BIOLOGICAL evolution - Abstract
Macaranga and Mallotus (Euphorbiaceae s.s.) are two closely related, large paleo(sub)tropical genera. To investigate the phylogenetic relationships between and within them and to determine the position of related genera belonging to the subtribe Rottlerinae, we sequenced one plastid (trnL-F) and three nuclear (ITS, ncpGS, phyC) markers for species representative of these genera. The analyses demonstrated the monophyly of Macaranga and the paraphyly of Mallotus and revealed three highly supported main clades. The genera Cordemoya and Deuteromallotus and the Mallotus sections Hancea and Oliganthae form a basal Cordemoya s.l. clade. The two other clades, the Macaranga clade and the Mallotus s.s. clade (the latter with Coccoceras, Neotrewia, Octospermum, and Trewia), are sister groups. In the Macaranga clade, two basal lineages (comprising mostly sect. Pseudorottlera) and a crown group with three geographically homogenous main clades were identified. The phylogeny of the Mallotus s.s. clade is less clear because of internal conflict in all four data sets. Many of the sections and informal infrageneric groups of Macaranga and Mallotus do not appear to be monophyletic. In both the Macaranga and Mallotus s.s. clades, the African and/or Madagascan taxa are nested in Asian clades, suggesting migrations or dispersals from Asia to Africa and Madagascar. [ABSTRACT FROM AUTHOR]
- Published
- 2007
- Full Text
- View/download PDF
20. CLADOGENESIS AS THE RESULT OF LONG-DISTANCE RAFTING EVENTS IN SOUTH PACIFIC TOPSHELLS (GASTROPODA, TROCHIDAE).
- Author
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Donald, Kirsten M., Kennedy, Martyn, Spencer, Hamish G., and Ó Foighil, Diarmaid
- Subjects
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PHYLOGENY , *NUCLEOTIDE sequence , *MITOCHONDRIAL DNA , *BIOLOGICAL evolution , *BIOLOGY - Abstract
We used DNA sequences of lecithotrophic monodontine topshells, belonging to the genera Diloma, Melagraphia, and Austrocochlea, to ascertain how this group became established over a large area of the South Pacific Ocean. The phylogeny of the topshells was estimated using portions of two mitochondrial genes (16S and cytochrome oxidase 1) and one nuclear gene (actin). A range of divergence rates was used to estimate the approximate timing of cladogenetic events within their phylogenetic tree. These estimates allow us to unambiguously reject vicariant explanations for several major divergence events and to infer several dispersal events across wide stretches of ocean. The first were two initial dispersal events from Australia (1) to an area between Samoa and Japan and (2) to New Zealand. Subsequently, at least one, and possibly two, recent eastward dispersals took place from New Zealand to Chile and the Juan Fernandez Islands, and one further dispersal occurred from somewhere in the tropical Pacific to Samoa. Moreover, owing to the short-lived nature of the topshell larvae, transoceanic larval dispersal is unlikely. The apparent paradox of a short larval phase and broad geographic range suggests that dispersal most probably occurred by rafting of adults on a suitable platform such as macroalgae; indeed, naturally buoyant bull kelp is the natural habitat of the most geographically widespread species in this group. Our molecular phylogenies imply that, despite of being an unlikely event, adult rafting in ocean currents has occurred on several occasions throughout the evolutionary history of topshells, resulting in their wide present-day distribution. [ABSTRACT FROM AUTHOR]
- Published
- 2005
- Full Text
- View/download PDF
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