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Darienko T, Pröschold T. Solotvynia, a New Coccoid Lineage among the Ulvophyceae (Chlorophyta). Microorganisms 2024; 12:868. [PMID: 38792698 PMCID: PMC11123690 DOI: 10.3390/microorganisms12050868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 04/06/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Coccoid Ulvophyceae are often overlooked despite their wide distribution. They occur as epiphytes on marine seaweeds or grow on stones or on shells of mussels and corals. Most of the species are not easy to identify based solely on morphology. However, they form two groups based on the flagellated cells during asexual reproduction. The biflagellated coccoids are monophyletic and represent the genus Sykidion (Sykidiales). In contrast, the quadriflagellated taxa are polyphyletic and belong to different genera and orders. The newly investigated strains NIES-1838 and NIES-1839, originally identified as Halochlorococcum, belong to the genus Chlorocystis (C. john-westii) among the order Chlorocystidales. The unidentified strain CCMP 1293 had almost an identical SSU and ITS-2 sequence to Symbiochlorum hainanense (Ignatiales) but showed morphological differences (single chloroplast, quadriflagellated zoospores) compared with the original description of this species (multiple chloroplasts, aplanospores). Surprisingly, the strain SAG 2662 (= ULVO-129), together with the published sequence of MBIC 10461, formed a new monophyletic lineage among the Ulvophyceae, which is highly supported in all of the bootstrap and Bayesian analyses and approximately unbiased tests of user-defined trees. This strain is characterized by a spherical morphology and also form quadriflagellated zoospores, have a unique ITS-2 barcode, and can tolerate a high variation of salinities. Considering our results, we emend the diagnosis of Symbiochlorum and propose the new genus Solotvynia among the new order Solotvyniales.
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Affiliation(s)
- Tatyana Darienko
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, Georg-August-University of Göttingen, D-37077 Göttingen, Germany;
- Research Department for Limnology, Leopold-Franzens-University of Innsbruck, A-5310 Mondsee, Austria
| | - Thomas Pröschold
- Research Department for Limnology, Leopold-Franzens-University of Innsbruck, A-5310 Mondsee, Austria
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Widespread Occurrence of Two Planktonic Ciliate Species (Urotricha, Prostomatida) Originating from High Mountain Lakes. DIVERSITY 2022. [DOI: 10.3390/d14050362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ciliates of the genus Urotricha are widely distributed and occur in almost any freshwater body. Thus far, almost all species have been described from morphology only. Here, we applied an integrative approach on the morphology, molecular phylogeny and biogeography of two species isolated from high mountain lakes in the Central Alps, Austria. As these remote lakes are known to have water temperatures <15 °C, our hypothesis was that these urotrichs might prefer ‘cold’ environments. We studied the morphological details from living and silver-stained individuals, and their molecular sequences (ribosomal operon, ITS), and screened available datasets for their biogeography. The two Urotricha species resembled morphological features of several congeners. An accurate species assignment was difficult due to several overlapping characteristics. However, we tentatively attributed the investigated species to Urotricha nais and Urotricha globosa. The biogeographic analyses revealed their occurrence in Europe, Africa and Asia, and no correlations to (cold) temperatures were found. Our findings suggest that these two urotrichs, originating from two cold and remote habitats, are probably cryptic species well adapted to their harsh environment.
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Complete Mitochondrial Genomes of Five Racerunners (Lacertidae: Eremias) and Comparison with Other Lacertids: Insights into the Structure and Evolution of the Control Region. Genes (Basel) 2022; 13:genes13050726. [PMID: 35627111 PMCID: PMC9141765 DOI: 10.3390/genes13050726] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 12/04/2022] Open
Abstract
Comparative studies on mitochondrial genomes (mitogenomes) as well as the structure and evolution of the mitochondrial control region are few in the Lacertidae family. Here, the complete mitogenomes of five individuals of Eremias scripta (2 individuals), Eremias nikolskii, Eremias szczerbaki, and Eremias yarkandensis were determined using next-generation sequencing and were compared with other lacertids available in GenBank. The circular mitogenomes comprised the standard set of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and a long non-coding control region (CR). The extent of purifying selection was less pronounced for the COIII and ND2 genes in comparison with the rest of the PCGs. The codons encoding Leucine (CUN), Threonine, and Isolecucine were the three most frequently present. The secondary structure of rRNA of Lacertidae (herein, E. scripta KZL15 as an example) comprised four domains and 28 helices for 12S rRNA, with six domains and 50 helices for 16S rRNA. Five types and twenty-one subtypes of CR in Lacertidae were described by following the criteria of the presence and position of tandem repeats (TR), termination-associated sequence 1 (TAS1), termination-associated sequence 2 (TAS2), conserved sequence block 1 (CBS1), conserved sequence block 2 (CSB2), and conserved sequence block 3 (CSB3). The compositions of conserved structural elements in four genera, Acanthodactylus, Darevskia, Eremias, and Takydromus, were further explored in detail. The base composition of TAS2 – TATACATTAT in Lacertidae was updated. In addition, the motif “TAGCGGCTTTTTTG” of tandem repeats in Eremias and the motif ”GCGGCTT” in Takydromus were presented. Nucleotide lengths between CSB2 and CSB3 remained 35 bp in Eremias and Darevskia. The phylogenetic analyses of Lacertidae recovered the higher-level relationships among the three subfamilies and corroborated a hard polytomy in the Lacertinae phylogeny. The phylogenetic position of E. nikolskii challenged the monophyly of the subgenus Pareremias within Eremias. Some mismatches between the types of CR and their phylogeny demonstrated the complicated evolutionary signals of CR such as convergent evolution. These findings will promote research on the structure and evolution of the CR and highlight the need for more mitogenomes in Lacertidae.
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Sen P, Aziz R, Deka RC, Feil EJ, Ray SK, Satapathy SS. Stem Region of tRNA Genes Favors Transition Substitution Towards Keto Bases in Bacteria. J Mol Evol 2022; 90:114-123. [PMID: 35084523 DOI: 10.1007/s00239-021-10045-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/21/2021] [Indexed: 11/25/2022]
Abstract
Transversion and transition mutations have variable effects on the stability of RNA secondary structure considering that the former destabilizes the double helix geometry to a greater extent by introducing purine:purine (R:R) or pyrimidine:pyrimidine (Y:Y) base pairs. Therefore, transversion frequency is likely to be lower than that of transition in the secondary structure regions of RNA genes. Here, we performed an analysis of transition and transversion frequencies in tRNA genes defined well with secondary structure and compared with the intergenic regions in five bacterial species namely Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Staphylococcus aureus and Streptococcus pneumoniae using a large genome sequence data set. In general, the transversion frequency was observed to be lower than that of transition in both tRNA genes and intergenic regions. The transition to transversion ratio was observed to be greater in tRNA genes than that in the intergenic regions in all the five bacteria that we studied. Interestingly, the intraspecies base substitution analysis in tRNA genes revealed that non-compensatory substitutions were more frequent than compensatory substitutions in the stem region. Further, transition to transversion ratio in the loop region was observed to be significantly lesser than that among the non-compensatory substitutions in the stem region. This indicated that the transversion is more deleterious than transition in the stem regions. In addition, substitutions from amino bases (A/C) to keto bases (G/T) were also observed to be more than the reverse substitutions in the stem region. Substitution from amino bases to keto bases are likely to facilitate the stable G:U pairing unlike the reverse substitution that facilitates the unstable A:C pairing in the stem region of tRNA. This work provides additional support that the secondary structure of tRNA molecule is what drives the different substitutions in its gene sequence.
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Affiliation(s)
- Piyali Sen
- Department of Computer Science and Engineering, Tezpur University, Napaam, Tezpur, Assam, 784028, India
| | - Ruksana Aziz
- Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur, Assam, 784028, India
| | - Ramesh C Deka
- Chemical Sciences, Tezpur University, Napaam, Tezpur, Assam, 784028, India
- Center for Multidisciplinary Research, Tezpur University, Napaam, Tezpur, Assam, 784028, India
| | - Edward J Feil
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, BA2 7AY, UK.
| | - Suvendra Kumar Ray
- Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur, Assam, 784028, India.
- Center for Multidisciplinary Research, Tezpur University, Napaam, Tezpur, Assam, 784028, India.
| | - Siddhartha Sankar Satapathy
- Department of Computer Science and Engineering, Tezpur University, Napaam, Tezpur, Assam, 784028, India.
- Center for Multidisciplinary Research, Tezpur University, Napaam, Tezpur, Assam, 784028, India.
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Llorens-Revull M, Gregori J, Dopazo C, Rodriguez-Frías F, Garcia-Cehic D, Soria ME, Chen Q, Rando A, Perales C, Esteban JI, Quer J, Bilbao I. Study of Quasispecies Complexity and Liver Damage Progression after Liver Transplantation in Hepatitis C Virus Infected Patients. Genes (Basel) 2021; 12:genes12111731. [PMID: 34828337 PMCID: PMC8625210 DOI: 10.3390/genes12111731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023] Open
Abstract
Cirrhosis derived from chronic hepatitis C virus (HCV) infection is still a common indication for liver transplantation (LT). Reinfection of the engrafted liver is universal in patients with detectable viral RNA at the time of transplant and causes fast progression of cirrhosis (within 5 years) in around one-third of these patients. To prevent damage to the liver graft, effective direct-acting antiviral (DAA) therapy is required as soon as possible. However, because of post-LT clinical instability, it is difficult to determine the optimal time to start DAAs with a low risk of complications. Evaluate changes in quasispecies complexity following LT and seek a predictive index of fast liver damage progression to determine the timing of DAA initiation. HCV genomes isolated from pre-LT and 15-day post-LT serum samples of ten patients, who underwent orthotopic LT, were quantified and sequenced using a next-generation sequencing platform. Sequence alignments, phylogenetic trees, quasispecies complexity measures, biostatistics analyses, adjusted R2 values, and analysis of variance (ANOVA) were carried out. Three different patterns of reinfection were observed (viral bottlenecking, conserved pre-LT population, and mixed populations), suggesting that bottlenecking or homogenization of the viral population is not a generalized effect after liver graft reinfection. None of the quasispecies complexity measures predicted the future degree of liver damage. Higher and more uniform viral load (VL) values were observed in all pre-LT samples, but values were more dispersed in post-LT samples. However, VL increased significantly from the pre-LT to 15-day post-LT samples in patients with advanced fibrosis at 1-year post-LT, suggesting that a VL increase on day 15 may be a predictor of fast liver fibrosis progression. HCV kinetics after LT differ between patients and are not fibrosis-dependent. Higher VL at day 15 post-LT versus pre-LT samples may predict fast liver fibrosis progression.
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Affiliation(s)
- Meritxell Llorens-Revull
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Biochemistry, Molecular Biology, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Roche Diagnostics SL, Avinguda de la Generalitat, 171-173, 08174 Sant Cugat del Vallès, Spain
| | - Cristina Dopazo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Hepatobiliopancreatic Surgery and Transplant Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Francisco Rodriguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Biochemistry, Molecular Biology, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
- Biochemistry and Microbiology Departments, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| | - Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
| | - Maria Eugenia Soria
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
| | - Qian Chen
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
| | - Ariadna Rando
- Biochemistry and Microbiology Departments, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| | - Celia Perales
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
| | - Juan Ignacio Esteban
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Medicine, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Biochemistry, Molecular Biology, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
- Correspondence: or
| | - Itxarone Bilbao
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Hepatobiliopancreatic Surgery and Transplant Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Surgery, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
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Molecular Phylogeny of Unicellular Marine Coccoid Green Algae Revealed New Insights into the Systematics of the Ulvophyceae (Chlorophyta). Microorganisms 2021; 9:microorganisms9081586. [PMID: 34442668 PMCID: PMC8401757 DOI: 10.3390/microorganisms9081586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/17/2022] Open
Abstract
Most marine coccoid and sarcinoid green algal species have traditionally been placed within genera dominated by species from freshwater or soil habitats. For example, the genera Chlorocystis and Halochlorococcum contain exclusively marine species; however, their familial and ordinal affinities are unclear. They are characterized by a vegetative cell with lobated or reticulated chloroplast, formation of quadriflagellated zoospores and living epi- or endophytically within benthic macroalgae. They were integrated into the family Chlorochytriaceae which embraces all coccoid green algae with epi- or endophytic life phases. Later, they were excluded from the family of Chlorococcales based on studies of their life histories in culture, and transferred to their newly described order, Chlorocystidales of the Ulvophyceae. Both genera form a "Codiolum"-stage that serves as the unicellular sporophyte in their life cycles. Phylogenetic analyses of SSU and ITS rDNA sequences confirmed that these coccoid taxa belong to the Chlorocystidales, together with the sarcinoid genus Desmochloris. The biflagellated coccoid strains were members of the genus Sykidion, which represented its own order, Sykidiales, among the Ulvophyceae. Considering these results and the usage of the ITS-2/CBC approach revealed three species of Desmochloris, six of Chlorocystis, and three of Sykidion. Three new species and several new combinations were proposed.
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Pröschold T, Darienko T. Choricystis and Lewiniosphaera gen. nov. (Trebouxiophyceae Chlorophyta), two different green algal endosymbionts in freshwater sponges. Symbiosis 2020; 82:175-188. [PMID: 33328698 PMCID: PMC7725700 DOI: 10.1007/s13199-020-00711-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/27/2020] [Indexed: 11/11/2022]
Abstract
Associations of freshwater sponges with coccoid green algae have been known for a long time. Two types of coccoid green algae, which are commonly assigned as zoochlorellae, are recognized by morphology: small coccoids (< 3 μm) without pyrenoids and larger Chlorella-like algae (4–6 μm) with pyrenoids. Despite their wide distribution in some freshwater sponges, these green algae were never studied using a combined analysis of morphology and molecular phylogeny. We investigated several endosymbiotic strains isolated from different Spongilla species, which were available in culture collections. Phylogenetic analyses of SSU and ITS rDNA sequences revealed that the strain SAG 211-40a is a member of the Chlorellaceae and represents a new species of the newly erected genus Lewiniosphaera, L symbiontica. The phylogenetic position was confirmed by morphology and ITS-2 barcode. The endosymbionts without pyrenoid were identified as Choricystis parasitica by morphology and phylogenetic analyses. The comparison with free-living strains revealed the recognition of two new Choricystis species, C. krienitzii and C. limnetica, which were confirmed by molecular signatures in V9 region of SSU rDNA and ITS-2 barcode.
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Affiliation(s)
- Thomas Pröschold
- Research Department for Limnology, Leopold-Franzens-University of Innsbruck, Mondsee, Mondseestr. 9, A-5310 Mondsee, Austria
| | - Tatyana Darienko
- Albrecht-von-Haller-Institute of Plant Sciences, Experimental Phycology and Culture Collection of Algae, Georg-August-University of Göttingen, D-37073 Göttingen, Germany
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Complete mitochondrial genome of a blue-tailed skink Plestiodon capito (Reptilia, Squamata, Scincidae) and comparison with other Scincidae lizards. Genetica 2020; 148:229-241. [PMID: 33044712 DOI: 10.1007/s10709-020-00107-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 09/24/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
Abstract
Vertebrate mitochondrial genomes (mitogenomes) are valuable for studying phylogeny, evolutionary genetics and genomics. To date, however, compared to other vertebrate groups, our knowledge about the mitogenomes of skinks (the family Scincidae), even of reptile, has been relatively limited. In the present study, we determined the complete mitogenome of a blue-tailed skink Plestiodon capito for the first time, and compared it with other skinks available in GenBank. The circular genome is 17,344 bp long, showing a typical vertebrate pattern with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region (CR). The gene organization, nucleotide composition, and codon usage are similar to those from skinks previously published. Twelve out of 13 PCGs initiates with canonical start codon (ATG), while COX1 starts with GTG. The codon usage analysis revealed a preferential use of the LeuCUN (Leu1), Pro, and Thr codons with the A/U ending. All tRNAs in P. capito were predicted to fold into typical clover-leaf secondary structure, except tRNA-Ser AGY. The secondary structures of 12S rRNA and 16S rRNA comprises 34 helices and 56 helices, respectively. The alignment of the Plesitodon species CRs exhibited high genetic variability and rich A + T content. Besides, variable types and numbers of tandem repeat units were also identified in the CR of Plestiodon. Phylogenetic analyses recovered P. capito as the sister species to P. tunganus; monophyly of the Scincidae is well supported. Our results will help to better understand structure and evolution of the mitochondrial DNA control region in reptiles as well as the evolutionary status of P. capito, and to lay foundation for further phylogenetic study of skinks in a mitogenomic framework.
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Micractinium tetrahymenae (Trebouxiophyceae, Chlorophyta), a New Endosymbiont Isolated from Ciliates. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12050200] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Endosymbiosis between coccoid green algae and ciliates are widely distributed and occur in various phylogenetic lineages among the Ciliophora. Most mixotrophic ciliates live in symbiosis with different species and genera of the so-called Chlorella clade (Trebouxiophyceae). The mixotrophic ciliates can be differentiated into two groups: (i) obligate, which always live in symbiosis with such green algae and are rarely algae-free and (ii) facultative, which formed under certain circumstances such as in anoxic environments an association with algae. A case of the facultative endosymbiosis is found in the recently described species of Tetrahymena, T. utriculariae, which lives in the bladder traps of the carnivorous aquatic plant Utricularia reflexa. The green endosymbiont of this ciliate belonged to the genus Micractinium. We characterized the isolated algal strain using an integrative approach and compared it to all described species of this genus. The phylogenetic analyses using complex evolutionary secondary structure-based models revealed that this endosymbiont represents a new species of Micractinium, M. tetrahymenae sp. nov., which was further confirmed by the ITS2/CBC approach.
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Zhang X, Cao Y, Zhang W, Simmons MP. Adenine·cytosine substitutions are an alternative pathway of compensatory mutation in angiosperm ITS2. RNA (NEW YORK, N.Y.) 2020; 26:209-217. [PMID: 31748405 PMCID: PMC6961544 DOI: 10.1261/rna.072660.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/14/2019] [Indexed: 06/01/2023]
Abstract
Compensatory mutations are crucial for functional RNA because they maintain RNA configuration and thus function. Compensatory mutation has traditionally been considered to be a two-step substitution through the GU-base-pair intermediate. We tested for an alternative AC-mediated compensatory mutation (ACCM). We investigated ACCMs by using a comprehensive sampling of ribosomal internal transcribed spacer 2 (ITS2) from 3934 angiosperm species in 80 genera and 55 families. We predicted ITS2 consensus secondary structures by using LocARNA for structure-based alignment and partitioning paired and unpaired regions. We examined and compared the substitution rates and frequencies among base pairs by using RNA-specific models. Base-pair states of ACCMs were mapped onto the inferred phylogenetic trees to infer their evolution. All types of compensatory mutations involving the AC intermediate were observed, but the most frequent substitutions were with AU or GC pairs, which are part of the AU-AC-GC pathway. Compared with the GU intermediate, AC had a lower frequency and higher mutability. Within the AU-AC-GC pathway, the AU-AC substitution rate was much slower than the AC-GC substitution rate. No consistently higher overall rate was identified for either pathway among all 80 sampled lineages, though compensatory mutations through the AC intermediate averaged about half that through the GU intermediate. These results demonstrate an alternative compensatory mutation between AU and GC that helps address the controversial inference of inferred simultaneous double substitutions.
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Affiliation(s)
- Xinwan Zhang
- Marine College, Shandong University, Weihai 264209, China
| | - Yong Cao
- Marine College, Shandong University, Weihai 264209, China
| | - Wei Zhang
- Marine College, Shandong University, Weihai 264209, China
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
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11
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Zhang ML, Li ML, Ayoola AO, Murphy RW, Wu DD, Shao Y. Conserved sequences identify the closest living relatives of primates. Zool Res 2019; 40:532-540. [PMID: 31393097 PMCID: PMC6822925 DOI: 10.24272/j.issn.2095-8137.2019.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.
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Affiliation(s)
- Mei-Ling Zhang
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming Yunnan 650022, China
| | - Ming-Li Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.,Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Adeola Oluwakemi Ayoola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.,Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto M5S 2C6, Canada
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China, E-mail:
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China, E-mail:
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12
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Li M, Zhao H, Zhao F, Jiang L, Peng H, Zhang W, Simmons MP. Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae). ANNALS OF BOTANY 2019; 124:233-243. [PMID: 31152554 PMCID: PMC6758584 DOI: 10.1093/aob/mcz062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 04/03/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND AND AIMS Compensatory base changes (CBCs) that occur in stems of ribosomal internal transcribed spacer 2 (ITS2) can have important phylogenetic implications because they are not expected to occur within a single species and also affect selection of appropriate DNA substitution models. These effects have been demonstrated when studying ancient lineages. Here we examine these effects to quantify their importance within a more recent lineage by using both DNA- and RNA-specific models. METHODS We examined the phylogenetic implications of the CBC process by using a comprehensive sampling of ITS2 from ten closely related species of Corydalis. We predicted ITS2 secondary structures by using homology modelling, which was then used for a structure-based alignment. Paired and unpaired regions were analysed separately and in combination by using both RNA-specific substitution models and conventional DNA models. We mapped all base-pair states of CBCs on the phylogenetic tree to infer their evolution and relative timing. KEY RESULTS Our results indicate that selection acted to increase the thermodynamic stability of the secondary structure. Thus, the unpaired and paired regions did not evolve under a common substitution model. Only two CBCs occurred within the lineage sampled and no striking differences in topology or support for the shared clades were found between trees constructed using DNA- or RNA-specific substitution models. CONCLUSIONS Although application of RNA-specific substitution models remains preferred over more conventional DNA models, we infer that application of conventional DNA models is unlikely to be problematic when conducting phylogenetic analyses of ITS2 within closely related lineages wherein few CBCs are observed. Each of the two CBCs was found within the same lineages but was not observed within a given species, which supports application of the CBC species concept.
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Affiliation(s)
- Meihui Li
- Marine College, Shandong University, Weihai, China
| | - Hong Zhao
- Marine College, Shandong University, Weihai, China
| | - Fengxi Zhao
- Marine College, Shandong University, Weihai, China
| | - Lu Jiang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Huasheng Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Wei Zhang
- Marine College, Shandong University, Weihai, China
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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13
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Smith WH, Wooten JA, Camp CD, Stevenson DJ, Jensen JB, Turner M, Alexander NR. Genetic divergence correlates with the contemporary landscape in populations of Slimy Salamander (Plethodon glutinosus) species complex across the lower Piedmont and Coastal Plain of the southeastern United States. CAN J ZOOL 2018. [DOI: 10.1139/cjz-2018-0050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A primary goal of landscape genetics is to elucidate factors associated with genetic structure among populations. Among the important patterns identified have been isolation by distance (IBD), isolation by barrier (IBB), and isolation by environment (IBE). We tested hypotheses relating each of these possible patterns to genetic divergence in the Slimy Salamander (Plethodon glutinosus (Green, 1818)) species complex across the lower Piedmont and Coastal Plain of Georgia, USA, and adjacent areas of South Carolina, USA. We sequenced 2148 total bp, including three regions of the mitochondrial genome and a nuclear intron, and related genetic distance to GIS-derived surrogate variables representing possible IBD (geographic distance), IBE (principal components of 19 climate variables, watershed, and normalized difference vegetation index (NDVI)), and IBB (streams of fourth order and higher). Multiple matrix regression with randomization analysis indicated significant relationships between genetic distance and two principal components of climate, as well as NDVI. These results support roles for environment (IBE) in helping to drive genetic divergence in this group of salamanders. The absence of a significant influence of IBD and IBB was surprising. It is possible that the signal effects of geographic distance and barriers on genetic divergence may have been erased by more recent responses to the environment.
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Affiliation(s)
- Walter H. Smith
- Department of Natural Sciences, University of Virginia College at Wise, One College Avenue, Wise, VA 24293, USA
| | - Jessica A. Wooten
- Department of Biology, Piedmont College, 1021 Central Avenue, Demorest, GA 30535, USA
| | - Carlos D. Camp
- Department of Biology, Piedmont College, 1021 Central Avenue, Demorest, GA 30535, USA
| | - Dirk J. Stevenson
- Altamaha Environmental Consulting, 414 Club Drive, Hinesville, GA 31313, USA
| | - John B. Jensen
- Georgia Department of Natural Resources, Wildlife Resources Division, Non-game Conservation Section, 116 Rum Creek Drive, Forsyth, GA 31029, USA
| | - Megan Turner
- The University of Cincinnati, College of Medicine, CARE/Crawley Building, SuiteE-870, 3235 Eden Avenue, Cincinnati, OH 45267, USA
| | - N. Reed Alexander
- Department of Biology, Piedmont College, 1021 Central Avenue, Demorest, GA 30535, USA
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14
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Jayaswal V, Jermiin LS, Robinson J. Estimation of Phylogeny Using a General Markov Model. Evol Bioinform Online 2017. [DOI: 10.1177/117693430500100005] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The non-homogeneous model of nucleotide substitution proposed by Barry and Hartigan ( Stat Sci, 2: 191–210) is the most general model of DNA evolution assuming an independent and identical process at each site. We present a computational solution for this model, and use it to analyse two data sets, each violating one or more of the assumptions of stationarity, homogeneity, and reversibility. The log likelihood values returned by programs based on the F84 model ( J Mol Evol, 29: 170–179), the general time reversible model ( J Mol Evol, 20: 86–93), and Barry and Hartigan's model are compared to determine the validity of the assumptions made by the first two models. In addition, we present a method for assessing whether sequences have evolved under reversible conditions and discover that this is not so for the two data sets. Finally, we determine the most likely tree under the three models of DNA evolution and compare these with the one favoured by the tests for symmetry.
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Affiliation(s)
- Vivek Jayaswal
- School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia; Sydney University Biological Informatics and Technology Centre, University of Sydney, NSW 2006, Australia
| | - Lars S. Jermiin
- School of Biological Sciences, University of Sydney, NSW 2006, Australia; Sydney University Biological Informatics and Technology Centre, University of Sydney, NSW 2006, Australia. Unité de Biologie Moléculaire de Gène chez les Extrêmophiles, Institut Pasteur, 75724 Paris Cedex 15, France
| | - John Robinson
- School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia
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15
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Seo H, Cho DH. A new alignment free genome comparison algorithm based on statistically estimated feature frequency profile. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2017; 2017:4265-4268. [PMID: 29060839 DOI: 10.1109/embc.2017.8037798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The sequence comparison is an important part in bioinformatics to understand the biological property of genome. Although the alignment based sequence comparison is traditional and reliable algorithm, alignment free methods have been actively researched because of their advantage in terms of computational complexity. In this paper, we suggest a new alignment free genome comparison scheme based on statistical approach. From sequence components, word frequency information of the sequence is estimated. By investigating the relationship between estimated frequency information and actual word frequency, the characteristics of the sequence are numerically represented. The phylogenetic tree and the sequence classification of mammalian sequences are provided to reveal the remarkable performance of our statistical algorithm.
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16
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Abstract
Most phylogenetic methods are model-based and depend on models of evolution designed to approximate the evolutionary processes. Several methods have been developed to identify suitable models of evolution for phylogenetic analysis of alignments of nucleotide or amino acid sequences and some of these methods are now firmly embedded in the phylogenetic protocol. However, in a disturbingly large number of cases, it appears that these models were used without acknowledgement of their inherent shortcomings. In this chapter, we discuss the problem of model selection and show how some of the inherent shortcomings may be identified and overcome.
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Affiliation(s)
| | - Vivek Jayaswal
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Faisal M Ababneh
- Department of Mathematics & Statistics, Al-Hussein Bin Talal University, Ma'an, Jordan
| | - John Robinson
- School of Mathematics & Statistics, University of Sydney, Sydney, NSW, Australia
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17
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Bayegan AH, Garcia-Martin JA, Clote P. New tools to analyze overlapping coding regions. BMC Bioinformatics 2016; 17:530. [PMID: 27964762 PMCID: PMC5155393 DOI: 10.1186/s12859-016-1389-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 11/26/2016] [Indexed: 11/10/2022] Open
Abstract
Background Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop secondary structure, together called frameshift stimulating signal (FSS). It follows that the molecular evolution of this genomic region of HIV-1 is highly constrained, since the retroviral genome must contain a slippery sequence (sequence constraint), code appropriate peptides in reading frames 0 and 1 (coding requirements), and form a thermodynamically stable stem-loop secondary structure (structure requirement). Results We describe a unique computational tool, RNAsampleCDS, designed to compute the number of RNA sequences that code two (or more) peptides p,q in overlapping reading frames, that are identical (or have BLOSUM/PAM similarity that exceeds a user-specified value) to the input peptides p,q. RNAsampleCDS then samples a user-specified number of messenger RNAs that code such peptides; alternatively, RNAsampleCDS can exactly compute the position-specific scoring matrix and codon usage bias for all such RNA sequences. Our software allows the user to stipulate overlapping coding requirements for all 6 possible reading frames simultaneously, even allowing IUPAC constraints on RNA sequences and fixing GC-content. We generalize the notion of codon preference index (CPI) to overlapping reading frames, and use RNAsampleCDS to generate control sequences required in the computation of CPI. Moreover, by applying RNAsampleCDS, we are able to quantify the extent to which the overlapping coding requirement in HIV-1 [resp. HCV] contribute to the formation of the stem-loop [resp. double stem-loop] secondary structure known as the frameshift stimulating signal. Using our software, we confirm that certain experimentally determined deleterious HCV mutations occur in positions for which our software RNAsampleCDS and RNAiFold both indicate a single possible nucleotide. We generalize the notion of codon preference index (CPI) to overlapping coding regions, and use RNAsampleCDS to generate control sequences required in the computation of CPI for the Gag-Pol overlapping coding region of HIV-1. These applications show that RNAsampleCDS constitutes a unique tool in the software arsenal now available to evolutionary biologists. Conclusion Source code for the programs and additional data are available at http://bioinformatics.bc.edu/clotelab/RNAsampleCDS/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1389-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amir H Bayegan
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill MA, 02467, USA
| | | | - Peter Clote
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill MA, 02467, USA.
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18
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Darienko T, Gustavs L, Pröschold T. Species concept and nomenclatural changes within the genera Elliptochloris and Pseudochlorella (Trebouxiophyceae) based on an integrative approach. JOURNAL OF PHYCOLOGY 2016; 52:1125-1145. [PMID: 27734501 DOI: 10.1111/jpy.12481] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 08/03/2016] [Indexed: 06/06/2023]
Abstract
The genera Elliptochloris and Pseudochlorella were erected for Chlorella-like green algae producing two types of autospores and cell packages, respectively. Both genera are widely distributed in different soil habitats, either as free living or as photobionts of lichens. The species of these genera are often difficult to identify because of the high phenotypic plasticity and occasional lack of characteristic features. The taxonomic and nomenclatural status of these species, therefore, remains unclear. In this study, 34 strains were investigated using an integrative approach. Phylogenetic analyses demonstrated that the isolates belong to two independent lineages of the Trebouxiophyceae (Elliptochloris and Prasiola clades) and confirmed that the genera are not closely related. The comparison of morphology, molecular phylogeny, and analyses of secondary structures of SSU and ITS rDNA sequences revealed that all of the strains belong to three genera: Elliptochloris, Pseudochlorella, and Edaphochlorella. As a consequence of the taxonomic revisions, we propose two new combinations (Elliptochloris antarctica and Pseudochlorella signiensis) and validate Elliptochloris reniformis, which is invalidly described according to the International Code for Nomenclature (ICN), by designating a holotype. To reflect the high phenotypic plasticity of P. signiensis, two new varieties were described: P. signiensis var. magna and P. signiensis var. communis. Chlorella mirabilis was not closely related to any of these genera and was, therefore, transferred to the new genus Edaphochlorella. All of the taxonomic changes were highly supported by all phylogenetic analyses and were confirmed by the ITS-2 Barcodes using the ITS-2/CBC approach.
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Affiliation(s)
- Tatyana Darienko
- M.G. Kholodny Institute of Botany, National Academy Science of Ukraine, Kyiv, 01601, Ukraine
- Experimental Phycology and Culture Collection of Algae, University of Göttingen, D-37073, Göttingen, Germany
| | - Lydia Gustavs
- Department of Applied Ecology and Phycology, University of Rostock, D-18059, Rostock, Germany
| | - Thomas Pröschold
- Department of Limnology and Biooceanography, University of Vienna, A-1090, Vienna, Austria
- Department of Botany, Universidad de Concepción, Concepción, Chile
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19
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Foley NM, Springer MS, Teeling EC. Mammal madness: is the mammal tree of life not yet resolved? Philos Trans R Soc Lond B Biol Sci 2016; 371:20150140. [PMID: 27325836 PMCID: PMC4920340 DOI: 10.1098/rstb.2015.0140] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2016] [Indexed: 11/12/2022] Open
Abstract
Most molecular phylogenetic studies place all placental mammals into four superordinal groups, Laurasiatheria (e.g. dogs, bats, whales), Euarchontoglires (e.g. humans, rodents, colugos), Xenarthra (e.g. armadillos, anteaters) and Afrotheria (e.g. elephants, sea cows, tenrecs), and estimate that these clades last shared a common ancestor 90-110 million years ago. This phylogeny has provided a framework for numerous functional and comparative studies. Despite the high level of congruence among most molecular studies, questions still remain regarding the position and divergence time of the root of placental mammals, and certain 'hard nodes' such as the Laurasiatheria polytomy and Paenungulata that seem impossible to resolve. Here, we explore recent consensus and conflict among mammalian phylogenetic studies and explore the reasons for the remaining conflicts. The question of whether the mammal tree of life is or can be ever resolved is also addressed.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
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Affiliation(s)
- Nicole M Foley
- School of Biology and Environmental Science, Science Centre East, University College Dublin, Dublin 4, Ireland
| | - Mark S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Emma C Teeling
- School of Biology and Environmental Science, Science Centre East, University College Dublin, Dublin 4, Ireland
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20
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Mühlhausen S, Findeisen P, Plessmann U, Urlaub H, Kollmar M. A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes. Genome Res 2016; 26:945-55. [PMID: 27197221 PMCID: PMC4937558 DOI: 10.1101/gr.200931.115] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 04/28/2016] [Indexed: 01/12/2023]
Abstract
The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including “codon capture,” “genome streamlining,” and “ambiguous intermediate” theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons, we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNACAG is an anticodon-mutated tRNAAla containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects.
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Affiliation(s)
- Stefanie Mühlhausen
- Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Peggy Findeisen
- Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Uwe Plessmann
- Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany; Bioanalytics Group, Department of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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21
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Soligo C, Smaers JB. Contextualising primate origins--an ecomorphological framework. J Anat 2016; 228:608-29. [PMID: 26830706 PMCID: PMC4804135 DOI: 10.1111/joa.12441] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2015] [Indexed: 12/15/2022] Open
Abstract
Ecomorphology - the characterisation of the adaptive relationship between an organism's morphology and its ecological role - has long been central to theories of the origin and early evolution of the primate order. This is exemplified by two of the most influential theories of primate origins: Matt Cartmill's Visual Predation Hypothesis, and Bob Sussman's Angiosperm Co-Evolution Hypothesis. However, the study of primate origins is constrained by the absence of data directly documenting the events under investigation, and has to rely instead on a fragmentary fossil record and the methodological assumptions inherent in phylogenetic comparative analyses of extant species. These constraints introduce particular challenges for inferring the ecomorphology of primate origins, as morphology and environmental context must first be inferred before the relationship between the two can be considered. Fossils can be integrated in comparative analyses and observations of extant model species and laboratory experiments of form-function relationships are critical for the functional interpretation of the morphology of extinct species. Recent developments have led to important advancements, including phylogenetic comparative methods based on more realistic models of evolution, and improved methods for the inference of clade divergence times, as well as an improved fossil record. This contribution will review current perspectives on the origin and early evolution of primates, paying particular attention to their phylogenetic (including cladistic relationships and character evolution) and environmental (including chronology, geography, and physical environments) contextualisation, before attempting an up-to-date ecomorphological synthesis of primate origins.
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Affiliation(s)
| | - Jeroen B Smaers
- Department of Anthropology, Stony Brook University, Stony Brook, NY, USA
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22
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Pignatelli M, Vilella AJ, Muffato M, Gordon L, White S, Flicek P, Herrero J. ncRNA orthologies in the vertebrate lineage. Database (Oxford) 2016; 2016:bav127. [PMID: 26980512 PMCID: PMC4792531 DOI: 10.1093/database/bav127] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 12/23/2015] [Accepted: 12/23/2015] [Indexed: 01/07/2023]
Abstract
Annotation of orthologous and paralogous genes is necessary for many aspects of evolutionary analysis. Methods to infer these homology relationships have traditionally focused on protein-coding genes and evolutionary models used by these methods normally assume the positions in the protein evolve independently. However, as our appreciation for the roles of non-coding RNA genes has increased, consistently annotated sets of orthologous and paralogous ncRNA genes are increasingly needed. At the same time, methods such as PHASE or RAxML have implemented substitution models that consider pairs of sites to enable proper modelling of the loops and other features of RNA secondary structure. Here, we present a comprehensive analysis pipeline for the automatic detection of orthologues and paralogues for ncRNA genes. We focus on gene families represented in Rfam and for which a specific covariance model is provided. For each family ncRNA genes found in all Ensembl species are aligned using Infernal, and several trees are built using different substitution models. In parallel, a genomic alignment that includes the ncRNA genes and their flanking sequence regions is built with PRANK. This alignment is used to create two additional phylogenetic trees using the neighbour-joining (NJ) and maximum-likelihood (ML) methods. The trees arising from both the ncRNA and genomic alignments are merged using TreeBeST, which reconciles them with the species tree in order to identify speciation and duplication events. The final tree is used to infer the orthologues and paralogues following Fitch's definition. We also determine gene gain and loss events for each family using CAFE. All data are accessible through the Ensembl Comparative Genomics ('Compara') API, on our FTP site and are fully integrated in the Ensembl genome browser, where they can be accessed in a user-friendly manner. Database URL: http://www.ensembl.org.
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Affiliation(s)
- Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute
| | - Albert J Vilella
- European Molecular Biology Laboratory, European Bioinformatics Institute
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute
| | - Leo Gordon
- European Molecular Biology Laboratory, European Bioinformatics Institute
| | - Simon White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Javier Herrero
- European Molecular Biology Laboratory, European Bioinformatics Institute UCL Cancer Institute, University College London, London WC1E 6BT, UK
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23
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Zhou X, Sun F, Xu S, Yang G, Li M. The position of tree shrews in the mammalian tree: Comparing multi-gene analyses with phylogenomic results leaves monophyly of Euarchonta doubtful. Integr Zool 2015; 10:186-98. [PMID: 25311886 DOI: 10.1111/1749-4877.12116] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The well-accepted Euarchonta grandorder is a pruned version of Archonta nested within the Euarchontoglires (or Supraprimates) clade. At present, it includes tree shrews (Scandentia), flying lemurs (Dermoptera) and primates (Primates). Here, a phylogenomic dataset containing 1912 exons from 22 representative mammals was compiled to investigate the phylogenetic relationships within this group. Phylogenetic analyses and hypothesis testing suggested that tree shrews can be classified as a sister group to Primates or to Glires or even as a basal clade within Euarchontoglires. Further analyses of both modified and original previously published datasets found that the phylogenetic position of tree shrews is unstable. We also found that two of three exonic indels reported as synapomorphies of Euarchonta in a previous study do not unambiguously support the monophyly of such a clade. Therefore, the monophyly of both Euarchonta and Sundatheria (Dermoptera + Scandentia) are suspect. Molecular dating and divergence rate analyses suggested that the ancestor of Euarchontoglires experienced a rapid divergence, which may cause the unresolved position of tree shrews even using the whole genomic data.
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Affiliation(s)
- Xuming Zhou
- Key laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
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Mariné M, Brown NA, Riaño-Pachón DM, Goldman GH. On and Under the Skin: Emerging Basidiomycetous Yeast Infections Caused by Trichosporon Species. PLoS Pathog 2015; 11:e1004982. [PMID: 26226483 PMCID: PMC4520462 DOI: 10.1371/journal.ppat.1004982] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Marçal Mariné
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Neil Andrew Brown
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | | | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol—CTBE, Campinas, São Paulo, Brazil
- * E-mail:
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Darienko T, Gustavs L, Eggert A, Wolf W, Pröschold T. Evaluating the Species Boundaries of Green Microalgae (Coccomyxa, Trebouxiophyceae, Chlorophyta) Using Integrative Taxonomy and DNA Barcoding with Further Implications for the Species Identification in Environmental Samples. PLoS One 2015; 10:e0127838. [PMID: 26080086 PMCID: PMC4469705 DOI: 10.1371/journal.pone.0127838] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/16/2015] [Indexed: 11/19/2022] Open
Abstract
Integrative taxonomy is an approach for defining species and genera by taking phylogenetic, morphological, physiological, and ecological data into account. This approach is appropriate for microalgae, where morphological convergence and high levels of morphological plasticity complicate the application of the traditional classification. Although DNA barcode markers are well-established for animals, fungi, and higher plants, there is an ongoing discussion about suitable markers for microalgae and protists because these organisms are genetically more diverse compared to the former groups. To solve these problems, we assess the usage of a polyphasic approach combining phenotypic and genetic parameters for species and generic characterization. The application of barcode markers for database queries further allows conclusions about the ‘coverage’ of culture-based approaches in biodiversity studies and integrates additional aspects into modern taxonomic concepts. Although the culture-dependent approach revealed three new lineages, which are described as new species in this paper, the culture-independent analyses discovered additional putative new species. We evaluated three barcode markers (V4, V9 and ITS-2 regions, nuclear ribosomal operon) and studied the morphological and physiological plasticity of Coccomyxa, which became a model organism because its whole genome sequence has been published. In addition, several biotechnological patents have been registered for Coccomyxa. Coccomyxa representatives are distributed worldwide, are free-living or in symbioses, and colonize terrestrial and aquatic habitats. We investigated more than 40 strains and reviewed the biodiversity and biogeographical distribution of Coccomyxa species using DNA barcoding. The genus Coccomyxa formed a monophyletic group within the Trebouxiophyceae separated into seven independent phylogenetic lineages representing species. Summarizing, the combination of different characteristics in an integrative approach helps to evaluate environmental data and clearly identifies microalgae at generic and species levels.
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Affiliation(s)
- Tatyana Darienko
- M. G. Kholodny Institute of Botany, National Academy Science of Ukraine, Kyiv 01601, Ukraine
| | - Lydia Gustavs
- University of Rostock, Institute of Biological Sciences, Applied Ecology and Phycology, Albert-Einstein-Strasse 3, D-18059 Rostock, Germany
| | - Anja Eggert
- Leibniz Institute for Baltic Sea Research Warnemünde, Physical Oceanography, D-18119 Rostock, Germany
| | - Wiebke Wolf
- University of Rostock, Institute of Biological Sciences, Applied Ecology and Phycology, Albert-Einstein-Strasse 3, D-18059 Rostock, Germany
| | - Thomas Pröschold
- University of Rostock, Institute of Biological Sciences, Applied Ecology and Phycology, Albert-Einstein-Strasse 3, D-18059 Rostock, Germany
- University of Vienna, Department of Limnology and Biooceanography, A-1090 Vienna, Austria
- * E-mail:
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26
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A mitochondrial genome phylogeny of owlet moths (Lepidoptera: Noctuoidea), and examination of the utility of mitochondrial genomes for lepidopteran phylogenetics. Mol Phylogenet Evol 2015; 85:230-7. [DOI: 10.1016/j.ympev.2015.02.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 01/27/2015] [Accepted: 02/06/2015] [Indexed: 11/17/2022]
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Allen JE, Whelan S. Assessing the state of substitution models describing noncoding RNA evolution. Genome Biol Evol 2014; 6:65-75. [PMID: 24391153 PMCID: PMC3914692 DOI: 10.1093/gbe/evt206] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic inference is widely used to investigate the relationships between homologous sequences. RNA molecules have played a key role in these studies because they are present throughout life and tend to evolve slowly. Phylogenetic inference has been shown to be dependent on the substitution model used. A wide range of models have been developed to describe RNA evolution, either with 16 states describing all possible canonical base pairs or with 7 states where the 10 mismatched nucleotides are reduced to a single state. Formal model selection has become a standard practice for choosing an inferential model and works well for comparing models of a specific type, such as comparisons within nucleotide models or within amino acid models. Model selection cannot function across different sized state spaces because the likelihoods are conditioned on different data. Here, we introduce statistical state-space projection methods that allow the direct comparison of likelihoods between nucleotide models and 7-state and 16-state RNA models. To demonstrate the general applicability of our new methods, we extract 287 RNA families from genomic alignments and perform model selection. We find that in 281/287 families, RNA models are selected in preference to nucleotide models, with simple 7-state RNA models selected for more conserved families with shorter stems and more complex 16-state RNA models selected for more divergent families with longer stems. Other factors, such as the function of the RNA molecule or the GC-content, have limited impact on model selection. Our models and model selection methods are freely available in the open-source PHASE 3.0 software.
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Affiliation(s)
- James E Allen
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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Oliveira JVDC, Borges TA, Corrêa Dos Santos RA, Freitas LFD, Rosa CA, Goldman GH, Riaño-Pachón DM. Pseudozyma brasiliensis sp. nov., a xylanolytic, ustilaginomycetous yeast species isolated from an insect pest of sugarcane roots. Int J Syst Evol Microbiol 2014; 64:2159-2168. [PMID: 24682702 DOI: 10.1099/ijs.0.060103-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel ustilaginomycetous yeast isolated from the intestinal tract of an insect pest of sugarcane roots in Ribeirão Preto, São Paulo State, Brazil, represents a novel species of the genus Pseudozyma based on molecular analyses of the D1/D2 rDNA large subunit and the internal transcribed spacer (ITS1+ITS2) regions. The name Pseudozyma brasiliensis sp. nov. is proposed for this species, with GHG001(T) ( = CBS 13268(T) = UFMG-CM-Y307(T)) as the type strain. P. brasiliensis sp. nov. is a sister species of Pseudozyma vetiver, originally isolated from leaves of vetiver grass and sugarcane in Thailand. P. brasiliensis sp. nov. is able to grow well with xylan as the sole carbon source and produces high levels of an endo-1,4-xylanase that has a higher specific activity in comparison with other eukaryotic xylanases. This enzyme has a variety of industrial applications, indicating the great biotechnological potential of P. brasiliensis.
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Affiliation(s)
- Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6170, 13083-970 Campinas, São Paulo, Brazil
| | - Thuanny A Borges
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6170, 13083-970 Campinas, São Paulo, Brazil
| | - Renato Augusto Corrêa Dos Santos
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6170, 13083-970 Campinas, São Paulo, Brazil
| | - Larissa F D Freitas
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Minas Gerais, Brazil
| | - Carlos Augusto Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Minas Gerais, Brazil
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil.,Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6170, 13083-970 Campinas, São Paulo, Brazil
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6170, 13083-970 Campinas, São Paulo, Brazil
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Phylogeny and evolution of RNA structure. Methods Mol Biol 2014. [PMID: 24639167 DOI: 10.1007/978-1-62703-709-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Darwin's conviction that all living beings on Earth are related and the graph of relatedness is tree-shaped has been essentially confirmed by phylogenetic reconstruction first from morphology and later from data obtained by molecular sequencing. Limitations of the phylogenetic tree concept were recognized as more and more sequence information became available. The other path-breaking idea of Darwin, natural selection of fitter variants in populations, is cast into simple mathematical form and extended to mutation-selection dynamics. In this form the theory is directly applicable to RNA evolution in vitro and to virus evolution. Phylogeny and population dynamics of RNA provide complementary insights into evolution and the interplay between the two concepts will be pursued throughout this chapter. The two strategies for understanding evolution are ultimately related through the central paradigm of structural biology: sequence ⇒ structure ⇒ function. We elaborate on the state of the art in modeling both phylogeny and evolution of RNA driven by reproduction and mutation. Thereby the focus will be laid on models for phylogenetic sequence evolution as well as evolution and design of RNA structures with selected examples and notes on simulation methods. In the perspectives an attempt is made to combine molecular structure, population dynamics, and phylogeny in modeling evolution.
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Wu J, Hasegawa M, Zhong Y, Yonezawa T. Importance of synonymous substitutions under dense taxon sampling and appropriate modeling in reconstructing the mitogenomic tree of Eutheria. Genes Genet Syst 2014; 89:237-51. [DOI: 10.1266/ggs.89.237] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Jiaqi Wu
- School of Life Sciences, Fudan University
| | - Masami Hasegawa
- The Institute of Statistical Mathematics
- School of Life Sciences, Fudan University
| | - Yang Zhong
- Institute of Biodiversity Science and Geobiology, Tibet University
- School of Life Sciences, Fudan University
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Hu JY, Zhang YP, Yu L. Summary of Laurasiatheria (mammalia) phylogeny. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2013; 33:E65-74. [PMID: 23266984 DOI: 10.3724/sp.j.1141.2012.e05-06e65] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Laurasiatheria is one of the richest and most diverse superorders of placental mammals. Because this group had a rapid evolutionary radiation, the phylogenetic relationships among the six orders of Laurasiatheria remain a subject of heated debate and several issues related to its phylogeny remain open. Reconstructing the true phylogenetic relationships of Laurasiatheria is a significant case study in evolutionary biology due to the diversity of this suborder and such research will have significant implications for biodiversity conservation. We review the higher-level (inter-ordinal) phylogenies of Laurasiatheria based on previous cytogenetic, morphological and molecular data, and discuss the controversies of its phylogenetic relationship. This review aims to outline future researches on Laurasiatheria phylogeny and adaptive evolution.
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Morgan CC, Foster PG, Webb AE, Pisani D, McInerney JO, O'Connell MJ. Heterogeneous models place the root of the placental mammal phylogeny. Mol Biol Evol 2013; 30:2145-56. [PMID: 23813979 PMCID: PMC3748356 DOI: 10.1093/molbev/mst117] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Heterogeneity among life traits in mammals has resulted in considerable phylogenetic conflict, particularly concerning the position of the placental root. Layered upon this are gene- and lineage-specific variation in amino acid substitution rates and compositional biases. Life trait variations that may impact upon mutational rates are longevity, metabolic rate, body size, and germ line generation time. Over the past 12 years, three main conflicting hypotheses have emerged for the placement of the placental root. These hypotheses place the Atlantogenata (common ancestor of Xenarthra plus Afrotheria), the Afrotheria, or the Xenarthra as the sister group to all other placental mammals. Model adequacy is critical for accurate tree reconstruction and by failing to account for these compositional and character exchange heterogeneities across the tree and data set, previous studies have not provided a strongly supported hypothesis for the placental root. For the first time, models that accommodate both tree and data set heterogeneity have been applied to mammal data. Here, we show the impact of accurate model assignment and the importance of data sets in accommodating model parameters while maintaining the power to reject competing hypotheses. Through these sophisticated methods, we demonstrate the importance of model adequacy, data set power and provide strong support for the Atlantogenata over other competing hypotheses for the position of the placental root.
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Affiliation(s)
- Claire C Morgan
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland
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33
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Kober KM, Bernardi G. Phylogenomics of strongylocentrotid sea urchins. BMC Evol Biol 2013; 13:88. [PMID: 23617542 PMCID: PMC3637829 DOI: 10.1186/1471-2148-13-88] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/09/2013] [Indexed: 11/10/2022] Open
Abstract
Background Strongylocentrotid sea urchins have a long tradition as model organisms for studying many fundamental processes in biology including fertilization, embryology, development and genome regulation but the phylogenetic relationships of the group remain largely unresolved. Although the differing isolating mechanisms of vicariance and rapidly evolving gamete recognition proteins have been proposed, a stable and robust phylogeny is unavailable. Results We used a phylogenomic approach with mitochondrial and nuclear genes taking advantage of the whole-genome sequencing of nine species in the group to establish a stable (i.e. concordance in tree topology among multiple lies of evidence) and robust (i.e. high nodal support) phylogenetic hypothesis for the family Strongylocentrotidae. We generated eight draft mitochondrial genome assemblies and obtained 13 complete mitochondrial genes for each species. Consistent with previous studies, mitochondrial sequences failed to provide a reliable phylogeny. In contrast, we obtained a very well-supported phylogeny from 2301 nuclear genes without evidence of positive Darwinian selection both from the majority of most-likely gene trees and the concatenated fourfold degenerate sites: ((P. depressus, (M. nudus, M. franciscanus), (H. pulcherrimus, (S. purpuratus, (S. fragilis, (S. pallidus, (S. droebachiensis, S. intermedius)). This phylogeny was consistent with a single invasion of deep-water environments followed by a holarctic expansion by Strongylocentrotus. Divergence times for each species estimated with reference to the divergence times between the two major clades of the group suggest a correspondence in the timing with the opening of the Bering Strait and the invasion of the holarctic regions. Conclusions Nuclear genome data contains phylogenetic signal informative for understanding the evolutionary history of this group. However, mitochondrial genome data does not. Vicariance can explain major patterns observed in the phylogeny. Other isolating mechanisms are appropriate to explore in this system to help explain divergence patterns not well supported by vicariance, such as the effects of rapidly evolving gamete recognition proteins on isolating populations. Our findings of a stable and robust phylogeny, with the increase in mitochondrial and nuclear comparative genomic data, provide a system in which we can enhance our understanding of molecular evolution and adaptation in this group of sea urchins.
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Affiliation(s)
- Kord M Kober
- Department of Ecology & Evolutionary Biology, University Of California Santa Cruz, Santa Cruz, CA, USA.
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Zhuang WY, Liu CY. What an rRNA secondary structure tells about phylogeny of fungi in Ascomycota with emphasis on evolution of major types of ascus. PLoS One 2012; 7:e47546. [PMID: 23110078 PMCID: PMC3482189 DOI: 10.1371/journal.pone.0047546] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2011] [Accepted: 09/18/2012] [Indexed: 11/25/2022] Open
Abstract
Background RNA secondary structure is highly conserved throughout evolution. The higher order structure is fundamental in establishing important structure-function relationships. Nucleotide sequences from ribosomal RNA (rRNA) genes have made a great contribution to our understanding of Ascomycota phylogeny. However, filling the gaps between molecular phylogeny and morphological assumptions based on ascus dehiscence modes and type of fruitbodies at the higher level classification of the phylum remains an unfulfilled task faced by mycologists. Methodology/Principal Findings We selected some major groups of Ascomycota to view their phylogenetic relationships based on analyses of rRNA secondary structure. Using rRNA secondary structural information, here, we converted nucleotide sequences into the structure ones over a 20-symbol code. Our structural analyses together with ancestral character state reconstruction produced reasonable phylogenetic position for the class Geoglossomycetes as opposed to the classic nucleotide analyses. Judging from the secondary structure analyses with consideration of mode of ascus dehiscence and the ability of forming fruitbodies, we draw a clear picture of a possible evolutionary route for fungal asci and some major groups of fungi in Ascomycota. The secondary structure trees show a more reasonable phylogenetic position for the class Geoglossomycetes. Conclusions Our results illustrate that asci lacking of any dehiscence mechanism represent the most primitive type. Passing through the operculate and Orbilia-type asci, bitunicate asci occurred. The evolution came to the most advanced inoperculate type. The ascus-producing fungi might be derived from groups lacking of the capacity to form fruitbodies, and then evolved multiple times. The apothecial type of fruitbodies represents the ancestral state, and the ostiolar type is advanced. The class Geoglossomycetes is closely related to Leotiomycetes and Sordariomycetes having a similar ascus type other than it was originally placed based on nucleotide sequence analyses.
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Affiliation(s)
- Wen-Ying Zhuang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China.
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Bompfünewerer AF, Flamm C, Fried C, Fritzsch G, Hofacker IL, Lehmann J, Missal K, Mosig A, Müller B, Prohaska SJ, Stadler BMR, Stadler PF, Tanzer A, Washietl S, Witwer C. Evolutionary patterns of non-coding RNAs. Theory Biosci 2012; 123:301-69. [PMID: 18202870 DOI: 10.1016/j.thbio.2005.01.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Accepted: 01/24/2005] [Indexed: 01/04/2023]
Abstract
A plethora of new functions of non-coding RNAs (ncRNAs) have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple regulatory layers from transcription, RNA maturation, and RNA modification to translational regulation. Nevertheless, very little is known about the evolution of this "Modern RNA World" and its components. In this contribution, we attempt to provide at least a cursory overview of the diversity of ncRNAs and functional RNA motifs in non-translated regions of regular messenger RNAs (mRNAs) with an emphasis on evolutionary questions. This survey is complemented by an in-depth analysis of examples from different classes of RNAs focusing mostly on their evolution in the vertebrate lineage. We present a survey of Y RNA genes in vertebrates and study the molecular evolution of the U7 snRNA, the snoRNAs E1/U17, E2, and E3, the Y RNA family, the let-7 microRNA (miRNA) family, and the mRNA-like evf-1 gene. We furthermore discuss the statistical distribution of miRNAs in metazoans, which suggests an explosive increase in the miRNA repertoire in vertebrates. The analysis of the transcription of ncRNAs suggests that small RNAs in general are genetically mobile in the sense that their association with a hostgene (e.g. when transcribed from introns of a mRNA) can change on evolutionary time scales. The let-7 family demonstrates, that even the mode of transcription (as intron or as exon) can change among paralogous ncRNA.
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36
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Cheng N, Mao Y, Shi Y, Tao S. Coevolution in RNA molecules driven by selective constraints: evidence from 5S rRNA. PLoS One 2012; 7:e44376. [PMID: 22973441 PMCID: PMC3433437 DOI: 10.1371/journal.pone.0044376] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 08/06/2012] [Indexed: 11/20/2022] Open
Abstract
Understanding intra-molecular coevolution helps to elucidate various structural and functional constraints acting on molecules and might have practical applications in predicting molecular structure and interactions. In this study, we used 5S rRNA as a template to investigate how selective constraints have shaped the RNA evolution. We have observed the nonrandom occurrence of paired differences along the phylogenetic trees, the high rate of compensatory evolution, and the high TIR scores (the ratio of the numbers of terminal to intermediate states), all of which indicate that significant positive selection has driven the evolution of 5S rRNA. We found three mechanisms of compensatory evolution: Watson-Crick interaction (the primary one), complex interactions between multiple sites within a stem, and interplay of stems and loops. Coevolutionary interactions between sites were observed to be highly dependent on the structural and functional environment in which they occurred. Coevolution occurred mostly in those sites closest to loops or bulges within structurally or functionally important helices, which may be under weaker selective constraints than other stem positions. Breaking these pairs would directly increase the size of the adjoining loop or bulge, causing a partial or total structural rearrangement. In conclusion, our results indicate that sequence coevolution is a direct result of maintaining optimal structural and functional integrity.
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Affiliation(s)
- Nan Cheng
- StateKey Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, People’s Republic of China
- Bioinformatics Center, Northwest A&F University, Yangling, People’s Republic of China
| | - Yuanhui Mao
- StateKey Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, People’s Republic of China
| | - Youyi Shi
- College of Science, Northwest A&F University, Yangling, People’s Republic of China
| | - Shiheng Tao
- StateKey Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, People’s Republic of China
- Bioinformatics Center, Northwest A&F University, Yangling, People’s Republic of China
- * E-mail:
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Erpenbeck D, Sutcliffe P, Cook SDC, Dietzel A, Maldonado M, van Soest RW, Hooper JN, Wörheide G. Horny sponges and their affairs: On the phylogenetic relationships of keratose sponges. Mol Phylogenet Evol 2012; 63:809-16. [DOI: 10.1016/j.ympev.2012.02.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 11/28/2011] [Accepted: 02/22/2012] [Indexed: 10/28/2022]
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38
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Nie W. Molecular cytogenetic studies in strepsirrhine primates, Dermoptera and Scandentia. Cytogenet Genome Res 2012; 137:246-58. [PMID: 22614467 DOI: 10.1159/000338727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Since the first chromosome painting study between human and strepsirrhine primates was performed in 1996, nearly 30 species in Strepsirrhini, Dermoptera and Scandentia have been analyzed by cross-species chromosome painting. Here, the contribution of chromosome painting data to our understanding of primate genome organization, chromosome evolution and the karyotype phylogenetic relationships within strepsirrhine primates, Dermoptera and Scandentia is reviewed. Twenty-six to 43 homologous chromosome segments have been revealed in different species with human chromosome-specific paint probes. Various landmark rearrangements characteristic for each different lineage have been identified, as cytogenetic signatures that potentially unite certain lineages within strepsirrhine primates, Dermoptera and Scandentia.
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Affiliation(s)
- W Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China.
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Voigt O, Wülfing E, Wörheide G. Molecular phylogenetic evaluation of classification and scenarios of character evolution in calcareous sponges (Porifera, Class Calcarea). PLoS One 2012; 7:e33417. [PMID: 22479395 PMCID: PMC3314023 DOI: 10.1371/journal.pone.0033417] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 02/08/2012] [Indexed: 12/02/2022] Open
Abstract
Calcareous sponges (Phylum Porifera, Class Calcarea) are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU) rDNA and the almost complete large subunit (LSU) rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae) and Leucettidae and between Leucascandra (Jenkinidae) and Sycon carteri (Sycettidae). According to our results, the taxonomy of Calcarea is in desperate need of a thorough revision, which cannot be achieved by considering morphology alone or relying on a taxon sampling based on the current classification below the subclass level.
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Affiliation(s)
- Oliver Voigt
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, München, Germany
| | - Eilika Wülfing
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, München, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, München, Germany
- GeoBio-Center LMU, Ludwig-Maximilians-Universität München, München, Germany
- Bayerische Staatssammlung für Paläontologie und Geologie, München, Germany
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Arima S, Tardella L. Improved harmonic mean estimator for phylogenetic model evidence. J Comput Biol 2012; 19:418-38. [PMID: 22414153 DOI: 10.1089/cmb.2010.0139] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bayesian phylogenetic methods are generating noticeable enthusiasm in the field of molecular systematics. Many phylogenetic models are often at stake, and different approaches are used to compare them within a Bayesian framework. The Bayes factor, defined as the ratio of the marginal likelihoods of two competing models, plays a key role in Bayesian model selection. We focus on an alternative estimator of the marginal likelihood whose computation is still a challenging problem. Several computational solutions have been proposed, none of which can be considered outperforming the others simultaneously in terms of simplicity of implementation, computational burden and precision of the estimates. Practitioners and researchers, often led by available software, have privileged so far the simplicity of the harmonic mean (HM) estimator. However, it is known that the resulting estimates of the Bayesian evidence in favor of one model are biased and often inaccurate, up to having an infinite variance so that the reliability of the corresponding conclusions is doubtful. We consider possible improvements of the generalized harmonic mean (GHM) idea that recycle Markov Chain Monte Carlo (MCMC) simulations from the posterior, share the computational simplicity of the original HM estimator, but, unlike it, overcome the infinite variance issue. We show reliability and comparative performance of the improved harmonic mean estimators comparing them to approximation techniques relying on improved variants of the thermodynamic integration.
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Affiliation(s)
- Serena Arima
- Dipartimento di Metodi e Modelli per l'Economia, il Territorio e la Finanza, Sapienza Università di Roma, Rome, Italy.
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Letsch HO, Kjer KM. Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: evidence from case studies in the Metazoa. BMC Evol Biol 2011; 11:146. [PMID: 21619604 PMCID: PMC3123606 DOI: 10.1186/1471-2148-11-146] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 05/27/2011] [Indexed: 11/10/2022] Open
Abstract
Background Failure to account for covariation patterns in helical regions of ribosomal RNA (rRNA) genes has the potential to misdirect the estimation of the phylogenetic signal of the data. Furthermore, the extremes of length variation among taxa, combined with regional substitution rate variation can mislead the alignment of rRNA sequences and thus distort subsequent tree reconstructions. However, recent developments in phylogenetic methodology now allow a comprehensive integration of secondary structures in alignment and tree reconstruction analyses based on rRNA sequences, which has been shown to correct some of these problems. Here, we explore the potentials of RNA substitution models and the interactions of specific model setups with the inherent pattern of covariation in rRNA stems and substitution rate variation among loop regions. Results We found an explicit impact of RNA substitution models on tree reconstruction analyses. The application of specific RNA models in tree reconstructions is hampered by interaction between the appropriate modelling of covarying sites in stem regions, and excessive homoplasy in some loop regions. RNA models often failed to recover reasonable trees when single-stranded regions are excessively homoplastic, because these regions contribute a greater proportion of the data when covarying sites are essentially downweighted. In this context, the RNA6A model outperformed all other models, including the more parametrized RNA7 and RNA16 models. Conclusions Our results depict a trade-off between increased accuracy in estimation of interdependencies in helical regions with the risk of magnifying positions lacking phylogenetic signal. We can therefore conclude that caution is warranted when applying rRNA covariation models, and suggest that loop regions be independently screened for phylogenetic signal, and eliminated when they are indistinguishable from random noise. In addition to covariation and homoplasy, other factors, like non-stationarity of substitution rates and base compositional heterogeneity, can disrupt the signal of ribosomal RNA data. All these factors dictate sophisticated estimation of evolutionary pattern in rRNA data, just as other molecular data require similarly complicated (but different) corrections.
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Affiliation(s)
- Harald O Letsch
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für molekulare Biodiversitätsforschung, Adenauerallee, Bonn, Germany.
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Escobar JS, Glémin S, Galtier N. GC-Biased Gene Conversion Impacts Ribosomal DNA Evolution in Vertebrates, Angiosperms, and Other Eukaryotes. Mol Biol Evol 2011; 28:2561-75. [DOI: 10.1093/molbev/msr079] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Xie Q, Lin J, Qin Y, Zhou J, Bu W. Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction. Protein Cell 2011; 2:161-70. [PMID: 21400046 DOI: 10.1007/s13238-011-1017-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 01/30/2011] [Indexed: 10/18/2022] Open
Abstract
Ribosomal RNAs are important because they catalyze the synthesis of peptides and proteins. Comparative studies of the secondary structure of 18S rRNA have revealed the basic locations of its many length-conserved and length-variable regions. In recent years, many more sequences of 18S rDNA with unusual lengths have been documented in GenBank. These data make it possible to recognize the diversity of the secondary and tertiary structures of 18S rRNAs and to identify the length-conserved parts of 18S rDNAs. The longest 18S rDNA sequences of almost every known eukaryotic phylum were included in this study. We illustrated the bioinformatics-based structure to show that, the regions that are more length-variable, regions that are less length-variable, the splicing sites for introns, and the sites of A-minor interactions are mostly distributed in different parts of the 18S rRNA. Additionally, this study revealed that some length-variable regions or insertion positions could be quite close to the functional part of the 18S rRNA of Foraminifera organisms. The tertiary structure as well as the secondary structure of 18S rRNA can be more diverse than what was previously supposed. Besides revealing how this interesting gene evolves, it can help to remove ambiguity from the alignment of eukaryotic 18S rDNAs and to improve the performance of 18S rDNA in phylogenetic reconstruction. Six nucleotides shared by Archaea and Eukaryota but rarely by Bacteria are also reported here for the first time, which might further support the supposed origin of eukaryote from archaeans.
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Affiliation(s)
- Qiang Xie
- Department of Zoology and Developmental Biology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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Linder M, Britton T, Sennblad B. Evaluation of Bayesian models of substitution rate evolution--parental guidance versus mutual independence. Syst Biol 2011; 60:329-42. [PMID: 21386113 DOI: 10.1093/sysbio/syr009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have evaluated the performance of two classes of probabilistic models for substitution rate variation over phylogenetic trees. In the first class, branch rates are considered to be independent and identically distributed (i.i.d.) stochastic variables. Three versions with respect to the underlying distribution (Gamma, Inverse Gaussian, and LogNormal) are considered. The i.i.d. models are compared with the autocorrelated (AC) model, where rates of adjacent nodes in the tree are AC, so that a node rate is LogNormal distributed around the rate of the parent node. The performance of different models is evaluated using three empirical data sets. For all data sets, it was clear that all tested models extracted substantial knowledge from data when posterior divergence time distributions were compared with the prior distributions and, furthermore, that they clearly outperformed a molecular clock. Moreover, the descriptive power of the i.i.d. models, as evaluated by Bayes factors, was either equal to or clearly better than that of the AC model. The latter effect increased with extended taxon sampling. Likewise, under none of the models could we find compelling evidence, in any of the data sets, for rate correlation between adjacent branches/nodes. These findings challenge previous suggestions of universality of autocorrelation in sequence evolution. We also performed an additional comparison with a divergence time prior including calibration information from fossil evidence. Adding fossil information to the prior had negligible effect on Bayes factors and mainly affected the width of the posterior distribution of the divergence times, whereas the relative position of the mean divergence times were largely unaffected.
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Affiliation(s)
- Martin Linder
- Department of Mathematics, Uppsala University, Box 480, SE-751 06 Uppsala, Sweden
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Gazave E, Lapébie P, Renard E, Vacelet J, Rocher C, Ereskovsky AV, Lavrov DV, Borchiellini C. Molecular phylogeny restores the supra-generic subdivision of homoscleromorph sponges (Porifera, Homoscleromorpha). PLoS One 2010; 5:e14290. [PMID: 21179486 PMCID: PMC3001884 DOI: 10.1371/journal.pone.0014290] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 11/16/2010] [Indexed: 01/02/2023] Open
Abstract
Background Homoscleromorpha is the fourth major sponge lineage, recently recognized to be distinct from the Demospongiae. It contains <100 described species of exclusively marine sponges that have been traditionally subdivided into 7 genera based on morphological characters. Because some of the morphological features of the homoscleromorphs are shared with eumetazoans and are absent in other sponges, the phylogenetic position of the group has been investigated in several recent studies. However, the phylogenetic relationships within the group remain unexplored by modern methods. Methodology/Principal Findings Here we describe the first molecular phylogeny of Homoscleromorpha based on nuclear (18S and 28S rDNA) and complete mitochondrial DNA sequence data that focuses on inter-generic relationships. Our results revealed two robust clades within this group, one containing the spiculate species (genera Plakina, Plakortis, Plakinastrella and Corticium) and the other containing aspiculate species (genera Oscarella and Pseudocorticium), thus rejecting a close relationship between Pseudocorticium and Corticium. Among the spiculate species, we found affinities between the Plakortis and Plakinastrella genera, and between the Plakina and Corticium. The validity of these clades is furthermore supported by specific morphological characters, notably the type of spicules. Furthermore, the monophyly of the Corticium genus is supported while the monophyly of Plakina is not. Conclusions/Significance As the result of our study we propose to restore the pre-1995 subdivision of Homoscleromorpha into two families: Plakinidae Schulze, 1880 for spiculate species and Oscarellidae Lendenfeld, 1887 for aspiculate species that had been rejected after the description of the genus Pseudocorticium. We also note that the two families of homoscleromorphs exhibit evolutionary stable, but have drastically distinct mitochondrial genome organizations that differ in gene content and gene order.
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Affiliation(s)
- Eve Gazave
- Aix-Marseille Université, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, Marseilles, France
| | - Pascal Lapébie
- Aix-Marseille Université, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, Marseilles, France
| | - Emmanuelle Renard
- Aix-Marseille Université, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, Marseilles, France
| | - Jean Vacelet
- Aix-Marseille Université, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, Marseilles, France
| | - Caroline Rocher
- Aix-Marseille Université, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, Marseilles, France
| | - Alexander V. Ereskovsky
- Aix-Marseille Université, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, Marseilles, France
- Department of Embryology, Faculty of Biology and Soils, Saint-Petersburg State University, St Petersburg, Russia
| | - Dennis V. Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Iowa, Ames, United States of America
| | - Carole Borchiellini
- Aix-Marseille Université, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, Marseilles, France
- * E-mail:
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Gazave E, Carteron S, Chenuil A, Richelle-Maurer E, Boury-Esnault N, Borchiellini C. Polyphyly of the genus Axinella and of the family Axinellidae (Porifera: Demospongiaep). Mol Phylogenet Evol 2010; 57:35-47. [DOI: 10.1016/j.ympev.2010.05.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 05/20/2010] [Accepted: 05/31/2010] [Indexed: 10/19/2022]
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Letsch HO, Kück P, Stocsits RR, Misof B. The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods. Mol Biol Evol 2010; 27:2507-21. [PMID: 20530152 DOI: 10.1093/molbev/msq140] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The use of secondary structures has been advocated to improve both the alignment and the tree reconstruction processes of ribosomal RNA (rRNA) data sets. We used simulated and empirical rRNA data to test the impact of secondary structure consideration in both steps of molecular phylogenetic analyses. A simulation approach was used to generate realistic rRNA data sets based on real 16S, 18S, and 28S sequences and structures in combination with different branch length and topologies. Alignment and tree reconstruction performance of four recent structural alignment methods was compared with exclusively sequence-based approaches. As empirical data, we used a hexapod rRNA data set to study the influence of nucleotide interdependencies in sequence alignment and tree reconstruction. Structural alignment methods delivered significantly better sequence alignments compared with pure sequence-based methods. Also, structural alignment methods delivered better trees judged by topological congruence to simulation base trees. However, the advantage of structural alignments was less pronounced and even vanished in several instances. For simulated data, application of mixed RNA/DNA models to stems and loops, respectively, led to significantly shorter branches. The application of mixed RNA/DNA models in the hexapod analyses delivered partly implausible relationships. This can be interpreted as a stronger sensitivity of mixed model setups to nonphylogenetic signal. Secondary structure consideration clearly influenced sequence alignment and tree reconstruction of ribosomal genes. Although sequence alignment quality can considerably be improved by the use of secondary structure information, the application of mixed models in tree reconstructions needs further studies to understand the observed effects.
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Affiliation(s)
- Harald O Letsch
- Molecular Biodiversity Research Unit, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.
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Makowsky R, Cox CL, Roelke C, Chippindale PT. Analyzing the relationship between sequence divergence and nodal support using Bayesian phylogenetic analyses. Mol Phylogenet Evol 2010; 57:485-94. [PMID: 20472081 DOI: 10.1016/j.ympev.2010.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 05/06/2010] [Accepted: 05/11/2010] [Indexed: 11/26/2022]
Abstract
Determining the appropriate gene for phylogeny reconstruction can be a difficult process. Rapidly evolving genes tend to resolve recent relationships, but suffer from alignment issues and increased homoplasy among distantly related species. Conversely, slowly evolving genes generally perform best for deeper relationships, but lack sufficient variation to resolve recent relationships. We determine the relationship between sequence divergence and Bayesian phylogenetic reconstruction ability using both natural and simulated datasets. The natural data are based on 28 well-supported relationships within the subphylum Vertebrata. Sequences of 12 genes were acquired and Bayesian analyses were used to determine phylogenetic support for correct relationships. Simulated datasets were designed to determine whether an optimal range of sequence divergence exists across extreme phylogenetic conditions. Across all genes we found that an optimal range of divergence for resolving the correct relationships does exist, although this level of divergence expectedly depends on the distance metric. Simulated datasets show that an optimal range of sequence divergence exists across diverse topologies and models of evolution. We determine that a simple to measure property of genetic sequences (genetic distance) is related to phylogenic reconstruction ability in Bayesian analyses. This information should be useful for selecting the most informative gene to resolve any relationships, especially those that are difficult to resolve, as well as minimizing both cost and confounding information during project design.
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Affiliation(s)
- Robert Makowsky
- University of Texas at Arlington, Department of Biology, Box 19498, Arlington, TX 76019, USA.
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Mallatt J, Craig CW, Yoder MJ. Nearly complete rRNA genes assembled from across the metazoan animals: Effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction. Mol Phylogenet Evol 2010; 55:1-17. [DOI: 10.1016/j.ympev.2009.09.028] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 08/28/2009] [Accepted: 09/22/2009] [Indexed: 10/20/2022]
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50
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ZHAO YJ, WANG ZZ. RNA Sequence-structural Alignment Based on Quantum Evolutionary Algorithm. PROG BIOCHEM BIOPHYS 2010. [DOI: 10.3724/sp.j.1206.2009.00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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