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Iglhaut C, Pečerska J, Gil M, Anisimova M. Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels. Mol Biol Evol 2024; 41:msae109. [PMID: 38842253 PMCID: PMC11221656 DOI: 10.1093/molbev/msae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/07/2024] Open
Abstract
Despite having important biological implications, insertion, and deletion (indel) events are often disregarded or mishandled during phylogenetic inference. In multiple sequence alignment, indels are represented as gaps and are estimated without considering the distinct evolutionary history of insertions and deletions. Consequently, indels are usually excluded from subsequent inference steps, such as ancestral sequence reconstruction and phylogenetic tree search. Here, we introduce indel-aware parsimony (indelMaP), a novel way to treat gaps under the parsimony criterion by considering insertions and deletions as separate evolutionary events and accounting for long indels. By identifying the precise location of an evolutionary event on the tree, we can separate overlapping indel events and use affine gap penalties for long indel modeling. Our indel-aware approach harnesses the phylogenetic signal from indels, including them into all inference stages. Validation and comparison to state-of-the-art inference tools on simulated data show that indelMaP is most suitable for densely sampled datasets with closely to moderately related sequences, where it can reach alignment quality comparable to probabilistic methods and accurately infer ancestral sequences, including indel patterns. Due to its remarkable speed, our method is well suited for epidemiological datasets, eliminating the need for downsampling and enabling the exploitation of the additional information provided by dense taxonomic sampling. Moreover, indelMaP offers new insights into the indel patterns of biologically significant sequences and advances our understanding of genetic variability by considering gaps as crucial evolutionary signals rather than mere artefacts.
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Affiliation(s)
- Clara Iglhaut
- Institute of Computational Life Science, Zurich University of Applied Science, Wädenswil, Switzerland
- Faculty of Mathematics and Science, University of Zurich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jūlija Pečerska
- Institute of Computational Life Science, Zurich University of Applied Science, Wädenswil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Manuel Gil
- Institute of Computational Life Science, Zurich University of Applied Science, Wädenswil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maria Anisimova
- Institute of Computational Life Science, Zurich University of Applied Science, Wädenswil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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2
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Fouquet A, Kok PJR, Recoder RS, Prates I, Camacho A, Marques-Souza S, Ghellere JM, McDiarmid RW, Rodrigues MT. Relicts in the mist: Two new frog families, genera and species highlight the role of Pantepui as a biodiversity museum throughout the Cenozoic. Mol Phylogenet Evol 2024; 191:107971. [PMID: 38000706 DOI: 10.1016/j.ympev.2023.107971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 11/26/2023]
Abstract
The iconic mountains of the Pantepui biogeographical region host many early-diverging endemic animal and plant lineages, concurring with Conan Doyle's novel about an ancient "Lost World". While this is the case of several frog lineages, others appear to have more recent origins, adding to the controversy around the diversification processes in this region. Due to its remoteness, Pantepui is challenging for biological surveys, and only a glimpse of its biodiversity has been described, which hampers comprehensive evolutionary studies in many groups. During a recent expedition to the Neblina massif on the Brazil-Venezuela border, we sampled two new frog species that could not be assigned to any known genus. Here, we perform phylogenetic analyses of mitogenomic and nuclear loci to infer the evolutionary relationships of the new taxa and support their description. We find that both species represent single lineages deeply nested within Brachycephaloidea, a major Neotropical clade of direct-developing frogs. Both species diverged >45 Ma from their closest relatives: the first is sister to all other Brachycephaloidea except for Ceuthomantis, another Pantepui endemic, and the second is sister to Brachycephalidae, endemic to the Brazilian Atlantic Forest. In addition to these considerable phylogenetic and biogeographic divergences, external morphology and osteological features support the proposition of two new family and genus-level taxa to accommodate these new branches of the amphibian tree of life. These findings add to other recently described ancient vertebrate lineages from the Neblina massif, providing a bewildering reminder that our perception of the Pantepui's biodiversity remains vastly incomplete. It also provides insights into how these mountains acted as "museums" during the diversification of Brachycephaloidea and of Neotropical biotas more broadly, in line with the influential "Plateau theory". Finally, these discoveries point at the yet unknown branches of the tree of life that may go extinct, due to global climate change and zoonotic diseases, before we even learn about their existence, amphibians living at higher elevations being particularly at risk.
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Affiliation(s)
- Antoine Fouquet
- Laboratoire Évolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1 31062 cedex 9, 118 Route de Narbonne, 31077 Toulouse, France.
| | - Philippe J R Kok
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, 12/16 Banacha Str., Łódź 90-237, Poland; Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom.
| | - Renato Sousa Recoder
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil.
| | - Ivan Prates
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Agustin Camacho
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil
| | - Sergio Marques-Souza
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil
| | - José Mario Ghellere
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil
| | - Roy W McDiarmid
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013, USA
| | - Miguel Trefaut Rodrigues
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil
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Li J, Fan R, Xu J, Hu L, Su F, Hao C. Comparative analysis of the chloroplast genomes of eight Piper species and insights into the utilization of structural variation in phylogenetic analysis. Front Genet 2022; 13:925252. [PMID: 36246585 PMCID: PMC9556897 DOI: 10.3389/fgene.2022.925252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
With more than 2000 species, Piper is regarded as having high medicinal, cosmetic, and edible value. There also remain some taxonomic and evolutionary uncertainties about the genus. This study performed chloroplast genome sequencing of eight poorly studied Piper species and a comparative analysis with black pepper (Piper nigrum). All examined species were highly similar in gene content, with 79 protein-coding genes, 24 tRNAs, and four rRNAs. They also harbored significant structural differences: The number of SSRs ranged from 63 to 87, over 10,000 SNPs were detected, and over 1,000 indels were found. The spatial distribution of structural differences was uneven, with the IR and LSC being relatively more conserved and the SSC region highly variable. Such structural variations of the chloroplast genome can help in evaluating the phylogenetic relationships between species, deciding some hard-to-distinguish evolutionary relationships, or eliminating improper markers. The SSC region may be evolving at high speed, and some species showed a high degree of sequence variation in the SSC region, which seriously affected marker sequence detection. Conversely, CDS sequences tended to lack variation, and some CDSs can serve as ideal markers for phylogenetic reconstruction. All told, this study provides an effective strategy for selecting chloroplast markers, analyzing difficult-to-distinguish phylogenetic relationships and avoiding the taxonomic errors caused by high degree of sequence variations.
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Affiliation(s)
- Jing Li
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, Hainan, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan, China
- Academician Soonliang Sim of Hainan Province Research Station, Wanning, Hainan, China
| | - Rui Fan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, Hainan, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan, China
- Academician Soonliang Sim of Hainan Province Research Station, Wanning, Hainan, China
| | - Jintao Xu
- Yangtze Normal University, Chongqing, China
| | - Lisong Hu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, Hainan, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan, China
- Academician Soonliang Sim of Hainan Province Research Station, Wanning, Hainan, China
| | - Fan Su
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, Hainan, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan, China
- Academician Soonliang Sim of Hainan Province Research Station, Wanning, Hainan, China
| | - Chaoyun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, Hainan, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan, China
- Academician Soonliang Sim of Hainan Province Research Station, Wanning, Hainan, China
- *Correspondence: Chaoyun Hao,
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Molecular tools for resolving Merodon ruficornis group (Diptera, Syrphidae) taxonomy. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00571-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Birth N, Dencker T, Morgenstern B. Insertions and deletions as phylogenetic signal in an alignment-free context. PLoS Comput Biol 2022; 18:e1010303. [PMID: 35939516 PMCID: PMC9387925 DOI: 10.1371/journal.pcbi.1010303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 08/18/2022] [Accepted: 06/14/2022] [Indexed: 11/18/2022] Open
Abstract
Most methods for phylogenetic tree reconstruction are based on sequence alignments; they infer phylogenies from substitutions that may have occurred at the aligned sequence positions. Gaps in alignments are usually not employed as phylogenetic signal. In this paper, we explore an alignment-free approach that uses insertions and deletions (indels) as an additional source of information for phylogeny inference. For a set of four or more input sequences, we generate so-called quartet blocks of four putative homologous segments each. For pairs of such quartet blocks involving the same four sequences, we compare the distances between the two blocks in these sequences, to obtain hints about indels that may have happened between the blocks since the respective four sequences have evolved from their last common ancestor. A prototype implementation that we call Gap-SpaM is presented to infer phylogenetic trees from these data, using a quartet-tree approach or, alternatively, under the maximum-parsimony paradigm. This approach should not be regarded as an alternative to established methods, but rather as a complementary source of phylogenetic information. Interestingly, however, our software is able to produce phylogenetic trees from putative indels alone that are comparable to trees obtained with existing alignment-free methods. Phylogenetic tree inference based on DNA or protein sequence comparison is a fundamental task in computational biology. Given a multiple alignment of a set of input sequences, most approaches compare aligned sequence positions to each other, to find a suitable tree, based on a model of molecular evolution. Insertions and deletions that may have happened since the input sequences evolved from their last common ancestor are ignored by most phylogeny methods. Herein, we show that insertions and deletions can provide an additional source of information for phylogeny inference, and that such information can be obtained with a simple alignment-free approach. We provide an implementation of this idea that we call Gap-SpaM. The proposed approach is complementary to existing phylogeny methods since it is based on a completely different source of information. It is, thus, not meant to be an alternative to those existing methods but rather as a possible additional source of information for tree inference.
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Affiliation(s)
- Niklas Birth
- Department of Bioinformatics, Institute of Microbiology and Genetics, Universisät Göttingen, Göttingen, Germany
| | - Thomas Dencker
- Department of Bioinformatics, Institute of Microbiology and Genetics, Universisät Göttingen, Göttingen, Germany
| | - Burkhard Morgenstern
- Department of Bioinformatics, Institute of Microbiology and Genetics, Universisät Göttingen, Göttingen, Germany
- Göttingen Center of Molecular Biosciences (GZMB), Göttingen, Germany
- Campus-Institute Data Science (CIDAS), Göttingen, Germany
- * E-mail:
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Interactomes: Experimental and In Silico Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:107-117. [DOI: 10.1007/978-3-030-80352-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Hou H, Ye H, Wang Z, Wu J, Gao Y, Han W, Na D, Sun G, Wang Y. Demographic history and genetic differentiation of an endemic and endangered Ulmus lamellosa (Ulmus). BMC PLANT BIOLOGY 2020; 20:526. [PMID: 33203402 PMCID: PMC7672979 DOI: 10.1186/s12870-020-02723-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 10/26/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Ulmus lamellosa (one of the ancient species of Ulmus) is an endemic and endangered plant that has undergone climatic oscillations and geographical changes. The elucidation of its demographic history and genetic differentiation is critical for understanding the evolutionary process and ecological adaption to forests in Northern China. RESULTS Polymorphic haplotypes were detected in most populations of U. lamellosa via DNA sequencing. All haplotypes were divided into three phylogeographic clades fundamentally corresponding to their geographical distribution, namely THM (Taihang Mountains), YM (Yinshan Mountains), and YSM (Yanshan Mountains) groups. The YSM group, which is regarded as ancestral, possessed higher genetic diversity and significant genetic variability in contrast to the YSM and YM groups. Meanwhile, the divergence time of intraspecies haplotypes occurred during the Miocene-Pliocene, which was associated with major Tertiary geological and/or climatic events. Different degrees of gene exchanges were identified between the three groups. During glaciation, the YSM and THM regions might have served as refugia for U. lamellosa. Based on ITS data, range expansion was not expected through evolutionary processes, except for the THM group. A series of mountain uplifts (e.g., Yanshan Mountains and Taihang Mountains) following the Miocene-Pliocene, and subsequently quaternary climatic oscillations in Northern China, further promoted divergence between U. lamellosa populations. CONCLUSIONS Geographical topology and climate change in Northern China played a critical role in establishing the current phylogeographic structural patterns of U. lamellosa. These results provide important data and clues that facilitate the demographic study of tree species in Northern China.
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Affiliation(s)
- Huimin Hou
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Hang Ye
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Zhi Wang
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Jiahui Wu
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Yue Gao
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Wei Han
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Dongchen Na
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Genlou Sun
- Saint Mary’s University, Halifax, Canada
| | - Yiling Wang
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
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8
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Suvorov A, Hochuli J, Schrider DR. Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning. Syst Biol 2020; 69:221-233. [PMID: 31504938 PMCID: PMC8204903 DOI: 10.1093/sysbio/syz060] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/28/2019] [Indexed: 11/13/2022] Open
Abstract
Reconstructing the phylogenetic relationships between species is one of the most formidable tasks in evolutionary biology. Multiple methods exist to reconstruct phylogenetic trees, each with their own strengths and weaknesses. Both simulation and empirical studies have identified several "zones" of parameter space where accuracy of some methods can plummet, even for four-taxon trees. Further, some methods can have undesirable statistical properties such as statistical inconsistency and/or the tendency to be positively misleading (i.e. assert strong support for the incorrect tree topology). Recently, deep learning techniques have made inroads on a number of both new and longstanding problems in biological research. In this study, we designed a deep convolutional neural network (CNN) to infer quartet topologies from multiple sequence alignments. This CNN can readily be trained to make inferences using both gapped and ungapped data. We show that our approach is highly accurate on simulated data, often outperforming traditional methods, and is remarkably robust to bias-inducing regions of parameter space such as the Felsenstein zone and the Farris zone. We also demonstrate that the confidence scores produced by our CNN can more accurately assess support for the chosen topology than bootstrap and posterior probability scores from traditional methods. Although numerous practical challenges remain, these findings suggest that the deep learning approaches such as ours have the potential to produce more accurate phylogenetic inferences.
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Affiliation(s)
- Anton Suvorov
- Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, UNC-Chapel Hill, Chapel Hill, NC 27599-7264, USA
| | - Joshua Hochuli
- Biological and Biomedical Sciences Program, University of North Carolina at Chapel Hill, 130 Mason Farm Road, UNC-Chapel Hill Chapel Hill, NC 27599-7264, USA
| | - Daniel R Schrider
- Biological and Biomedical Sciences Program, University of North Carolina at Chapel Hill, 130 Mason Farm Road, UNC-Chapel Hill Chapel Hill, NC 27599-7264, USA
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Ben-Menni Schuler S, López-Pujol J, Blanca G, Vilatersana R, Garcia-Jacas N, Suárez-Santiago VN. Influence of the Quaternary Glacial Cycles and the Mountains on the Reticulations in the Subsection Willkommia of the Genus Centaurea. FRONTIERS IN PLANT SCIENCE 2019; 10:303. [PMID: 30949188 PMCID: PMC6437100 DOI: 10.3389/fpls.2019.00303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Late Neogene and Quaternary climatic oscillations have greatly shaped the genetic structure of the Mediterranean Basin flora, with mountain plant species tracking warm interglacials/cold glacials by means of altitudinal shifts instead of broad latitudinal ones. Such dynamics may have enhanced population divergence but also secondary contacts. In this paper, we use a case example of subsection Willkommia of Centaurea (comprising three narrowly distributed endemic species, Centaurea gadorensis, C. pulvinata, and C. sagredoi) to test for reticulate evolution and recurrent hybridizations between nearby populations. For this, we combine analyses of genetic diversity and structuring, gene flow and spatial correlation, and ecological niche modeling. Our results support the contention that the current genetic structure of the three species is the result of historical gene flow at sites of secondary contact during the glacial periods, followed by isolation after the retraction of populations to the middle-upper areas of the mountains during the interglacial periods. The extent and direction of the gene flow was determined largely by the location of the populations on mountainsides oriented toward the same valley or toward different valleys, suggesting the intermountain valleys as the areas where secondary contacts occurred.
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Affiliation(s)
| | | | - Gabriel Blanca
- Departamento de Botánica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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Genotypic Characterization of Rickettsia bellii Reveals Distinct Lineages in the United States and South America. BIOMED RESEARCH INTERNATIONAL 2018; 2018:8505483. [PMID: 29850579 PMCID: PMC5911327 DOI: 10.1155/2018/8505483] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/11/2018] [Accepted: 02/28/2018] [Indexed: 12/02/2022]
Abstract
The bacterium Rickettsia bellii belongs to a basal group of rickettsiae that diverged prior to the pathogenic spotted fever group and typhus group Rickettsia species. Despite a diverse representation of R. bellii across more than 25 species of hard and soft ticks in the American continent, phylogeographical relationships among strains of this basal group-Rickettsia species are unknown; the work described here explores these relationships. DNA was extracted from 30 R. bellii tick isolates: 15 from the United States, 14 from Brazil, and 1 from Argentina. A total of 2,269 aligned nucleotide sites of 3 protein coding genes (gltA, atpA, and coxA) and 2 intergenic regions (rpmE-tRNAfmet and RC1027-xthA2) were concatenated and subjected to phylogenetic analysis by Bayesian methods. Results showed a separation of almost all isolates between North and South Americas, suggesting that they have radiated within their respective continents. Phylogenetic positions of the 30 isolates could be a result of not only their geographical origin but also the tick hosts they have coevolved with. Whether R. bellii originated with ticks in North or South America remains obscure, as our analyses did not show evidence for greater genetic divergence of R. bellii in either continent.
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11
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Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet 2018; 50:285-296. [DOI: 10.1038/s41588-018-0040-0] [Citation(s) in RCA: 289] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 12/18/2017] [Indexed: 11/08/2022]
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Wu YZ, Rédei D, Eger J, Wang YH, Wu HY, Carapezza A, Kment P, Cai B, Sun XY, Guo PL, Luo JY, Xie Q. Phylogeny and the colourful history of jewel bugs (Insecta: Hemiptera: Scutelleridae). Cladistics 2017; 34:502-516. [DOI: 10.1111/cla.12224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 11/30/2022] Open
Affiliation(s)
- Yan-Zhuo Wu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Dávid Rédei
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Joseph Eger
- Dow AgroSciences; LLC; 2606 S. Dundee Street Tampa FL 32629 USA
| | - Yan-Hui Wang
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road, Nankai District Tianjin 300071 China
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; No. 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
| | - Hao-Yang Wu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road, Nankai District Tianjin 300071 China
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; No. 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
| | - Attilio Carapezza
- University of Palermo; Via Sandro Botticelli, 15 I-90144 Palermo Italy
| | - Petr Kment
- Department of Entomology; National Museum; Cirkusová 1740 CZ-193 00 Praha 9 Czech Republic
| | - Bo Cai
- Hainan Entry-Exit Inspection and Quarantine Bureau; 9 West Haixiu Road Haikou Hainan 570311 China
| | - Xiao-Ya Sun
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Peng-Lei Guo
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Jiu-Yang Luo
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Qiang Xie
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; No. 135 Xingangxi Road Guangzhou 510275 Guangdong China
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Li J, Wingfield MJ, Liu Q, Barnes I, Roux J, Lombard L, Crous PW, Chen S. Calonectria species isolated from Eucalyptus plantations and nurseries in South China. IMA Fungus 2017; 8:259-286. [PMID: 29242775 PMCID: PMC5729712 DOI: 10.5598/imafungus.2017.08.02.04] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/01/2017] [Indexed: 11/19/2022] Open
Abstract
Diseases caused by species of Calonectria (Ca.) represent a serious threat to the growth and sustainability of Eucalyptus plantations in China. Symptoms caused by these fungi mainly include leaf blight on trees in plantations and rotting of stems and leaves in nurseries. Extensive surveys have recently been conducted where Calonectria species were collected in Eucalyptus plantations and nurseries in the FuJian, GuangDong, GuangXi, and YunNan Provinces of South China. Additional isolates were baited from soil samples in the Hong Kong Region. The aim of this study was to identify the 115 Calonectria isolates obtained using comparisons of DNA sequence data for the β-tubulin (tub2), calmodulin (cmdA), histone H3 (his3) and partial translation elongation factor-1α (tef1) gene regions as well as their morphological features. Seven known species were identified, including Calonectria arbusta, Ca. asiatica, Ca. chinensis, Ca. eucalypti, Ca. hongkongensis, Ca. mossambicensis and Ca. pentaseptata. In addition, six novel taxa were collected and are described here as Ca. aciculata, Ca. honghensis, Ca. lantauensis, Ca. pseudoturangicola, Ca. pseudoyunnanensis, and Ca. yunnanensis spp. nov. Overall, the results reflect a high diversity of Calonectria species in China.
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Affiliation(s)
- JieQiong Li
- China Eucalypt Research Centre (CERC), Chinese Academy of Forestry (CAF), ZhanJiang 524022, GuangDong Province, China
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Michael J. Wingfield
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - QianLi Liu
- China Eucalypt Research Centre (CERC), Chinese Academy of Forestry (CAF), ZhanJiang 524022, GuangDong Province, China
| | - Irene Barnes
- Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa
| | - Jolanda Roux
- Department of Plant and Soil Sciences, FABI, University of Pretoria, Pretoria, 0028, South Africa
| | - Lorenzo Lombard
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Pedro W. Crous
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - ShuaiFei Chen
- China Eucalypt Research Centre (CERC), Chinese Academy of Forestry (CAF), ZhanJiang 524022, GuangDong Province, China
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
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Pritt BS, Allerdice MEJ, Sloan LM, Paddock CD, Munderloh UG, Rikihisa Y, Tajima T, Paskewitz SM, Neitzel DF, Hoang Johnson DK, Schiffman E, Davis JP, Goldsmith CS, Nelson CM, Karpathy SE. Proposal to reclassify Ehrlichia muris as Ehrlichia muris subsp. muris subsp. nov. and description of Ehrlichia muris subsp. eauclairensis subsp. nov., a newly recognized tick-borne pathogen of humans. Int J Syst Evol Microbiol 2017; 67:2121-2126. [PMID: 28699575 DOI: 10.1099/ijsem.0.001896] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have previously described a novel taxon of the genus Ehrlichia (type strain WisconsinT), closely related to Ehrlichia muris, that causes human ehrlichiosis among patients with exposures to ticks in the upper midwestern USA. DNA from this bacterium was also detected in Ixodes scapularis and Peromyscus leucopus collected in Minnesota and Wisconsin. To determine the relationship between the E. muris-like agent (EMLA) and other species of the genus Ehrlichia phenotypic, genotypic and epidemiologic comparisons were undertaken, including sequence analysis of eight gene loci (3906 nucleotides) for 39 EMLA DNA samples and the type strain of E. muris AS145T. Three loci were also sequenced from DNA of nine strains of E. muris from mouse spleens from Japan. All sequences from E. muris were distinct from homologous EMLA sequences, but differences between them were less than those observed among other species of the genus Ehrlichia. Phenotypic comparison of EMLA and E. muris revealed similar culture and electron microscopic characteristics, but important differences were noted in their geographic distribution, ecological associations and behavior in mouse models of infection. Based on these comparisons, we propose that type strain WisconsinT represents a novel subspecies, Ehrlichia murissubsp. eauclairensis,subsp. nov. This strain is available through the Centers for Disease Control and Prevention Rickettsial Isolate Reference Collection (CRIRC EMU002T) and through the Collection de Souches de l'Unité des Rickettsies (CSURP2883 T). The subspecies Ehrlichia murissubsp. muris subsp. nov. is automatically created and the type strain AS145T is also available through the same collections (CRIRC EMU001T, CSUR E2T). Included is an emended description of E. muris.
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Affiliation(s)
- Bobbi S Pritt
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Rochester, MN, USA
| | - Michelle E J Allerdice
- Division of Vector-Borne Infectious Diseases, Centers for Disease Control and Prevention, Rickettsial Zoonoses Branch, Atlanta, GA, USA
| | - Lynne M Sloan
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Rochester, MN, USA
| | - Christopher D Paddock
- Division of Vector-Borne Infectious Diseases, Centers for Disease Control and Prevention, Rickettsial Zoonoses Branch, Atlanta, GA, USA
| | | | | | | | - Susan M Paskewitz
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | | | - Cynthia S Goldsmith
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Infectious Diseases Pathology Branch, Atlanta, GA, USA
| | - Curtis M Nelson
- Department of Entomology, University of Minnesota, St. Paul, MN, USA
| | - Sandor E Karpathy
- Division of Vector-Borne Infectious Diseases, Centers for Disease Control and Prevention, Rickettsial Zoonoses Branch, Atlanta, GA, USA
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15
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Karpathy SE, Slater KS, Goldsmith CS, Nicholson WL, Paddock CD. Rickettsia amblyommatis sp. nov., a spotted fever group Rickettsia associated with multiple species of Amblyomma ticks in North, Central and South America. Int J Syst Evol Microbiol 2016; 66:5236-5243. [PMID: 27638476 DOI: 10.1099/ijsem.0.001502] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In 1973, investigators isolated a rickettsial organism, designated strain WB-8-2T, from an adult Amblyomma americanum tick collected at Land Between the Lakes National Recreation Area, TN, USA. This organism is now recognized as highly prevalent in A. americanum, as well as several other Amblyomma species found throughout the Western hemisphere. It has been suggested that cross-reactivity to WB-8-2T and similar strains contributes to the increasing number of spotted fever cases reported in the USA. In 1995, investigators provided preliminary evidence that this strain, as well as another strain from Missouri, represented a distinct taxonomic unit within the genus Rickettsia by evaluating sequences of the 16S rRNA and 17 kDa protein genes. However, the bacterium was never formally named, despite the use of the designation 'Rickettsia amblyommii' and later 'Candidatus Rickettsia amblyommii', for more than 20 years in the scientific literature. Herein, we provide additional molecular evidence to identify strain WB-8-2T as a representative strain of a unique rickettsial species and present a formal description for the species, with the proposed name modified to Rickettsia amblyommatis sp. nov. to conform to the International Code of Nomenclature of Prokaryotes. We also establish a pure culture of strain WB-8-2T and designate it as the type strain for the species. The type strain is WB-8-2T (=CRIRC RAM004T=CSURP2882T).
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Affiliation(s)
- Sandor E Karpathy
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA
| | - Kimetha S Slater
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA
| | - Cynthia S Goldsmith
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA
| | - William L Nicholson
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA
| | - Christopher D Paddock
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA
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16
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Stierandová S, Vukić J, Vasil’eva ED, Zogaris S, Shumka S, Halačka K, Vetešník L, Švátora M, Nowak M, Stefanov T, Koščo J, Mendel J. A multilocus assessment of nuclear and mitochondrial sequence data elucidates phylogenetic relationships among European spirlins (Alburnoides, Cyprinidae). Mol Phylogenet Evol 2016; 94:479-491. [DOI: 10.1016/j.ympev.2015.10.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 10/21/2015] [Accepted: 10/23/2015] [Indexed: 01/12/2023]
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17
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Wang Y, Cui Y, Rédei D, Baňař P, Xie Q, Štys P, Damgaard J, Chen P, Yi W, Wang Y, Dang K, Li C, Bu W. Phylogenetic divergences of the true bugs (Insecta: Hemiptera: Heteroptera), with emphasis on the aquatic lineages: the last piece of the aquatic insect jigsaw originated in the Late Permian/Early Triassic. Cladistics 2015; 32:390-405. [DOI: 10.1111/cla.12137] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2015] [Indexed: 11/26/2022] Open
Affiliation(s)
- Yan‐hui Wang
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Ying Cui
- Tianjin State Key Laboratory of Modern Chinese Medicine Tianjin University of Traditional Chinese Medicine Tianjin 300193 China
| | - Dávid Rédei
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Petr Baňař
- Department of Entomology Moravian Museum Hviezdoslavova 29 CZ‐627 00 Czech Republic
| | - Qiang Xie
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Pavel Štys
- Faculty of Science Department of Zoology Charles University in Prague Viničná 7 CZ‐128 44 Praha 2 Czech Republic
| | - Jakob Damgaard
- Natural History Museum of Denmark Universitetsparken 15 2100 Copenhagen Ø Denmark
| | - Ping‐ping Chen
- Netherlands Centre of Biodiversity Naturalis 2300 RA Leiden Netherlands
| | - Wen‐bo Yi
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Ying Wang
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Kai Dang
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Chuan‐ren Li
- College of Agriculture Yangtze University Jingzhou Hubei 434025 China
| | - Wen‐jun Bu
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
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Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences. Sci Rep 2015; 5:13957. [PMID: 26355750 PMCID: PMC4564799 DOI: 10.1038/srep13957] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 08/13/2015] [Indexed: 01/21/2023] Open
Abstract
Rice is the most important crop in the world, acting as the staple food for over half of the world’s population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genome Oryza species, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species. The pan tropical distribution of these rice relatives was found to be explained by long distance dispersal within the last million years. The analysis resulted in a clustering pattern that showed strong geographical differentiation. The species were defined in two primary clades with a South American/African clade with two species, O glumaepatula and O longistaminata, distinguished from all other species. The largest clade was comprised of an Australian clade including newly identified taxa and the African and Asian clades. This refined knowledge of the relationships between cultivated rice and the related wild species provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation.
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Schlick-Steiner BC, Arthofer W, Moder K, Steiner FM. Recent insertion/deletion (reINDEL) mutations: increasing awareness to boost molecular-based research in ecology and evolution. Ecol Evol 2014; 5:24-35. [PMID: 25628861 PMCID: PMC4298431 DOI: 10.1002/ece3.1330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/27/2014] [Accepted: 10/30/2014] [Indexed: 01/18/2023] Open
Abstract
Today, the comparative analysis of DNA molecules mainly uses information inferred from nucleotide substitutions. Insertion/deletion (INDEL) mutations, in contrast, are largely considered uninformative and discarded, due to our lacking knowledge on their evolution. However, including rather than discarding INDELs would be relevant to any research area in ecology and evolution that uses molecular data. As a practical approach to better understanding INDEL evolution in general, we propose the study of recent INDEL (reINDEL) mutations – mutations where both ancestral and derived state are seen in the sample. The precondition for reINDEL identification is knowledge about the pedigree of the individuals sampled. Sound reINDEL knowledge will allow the improved modeling needed for including INDELs in the downstream analysis of molecular data. Both microsatellites, currently still the predominant marker system in the analysis of populations, and sequences generated by next-generation sequencing, a promising and rapidly developing range of technologies, offer the opportunity for reINDEL identification. However, a 2013 sample of animal microsatellite studies contained unexpectedly few reINDELs identified. As most likely explanation, we hypothesize that reINDELs are underreported rather than absent and that this underreporting stems from common reINDEL unawareness. If our hypothesis applies, increased reINDEL awareness should allow gathering data rapidly. We recommend the routine reporting of either the absence or presence of reINDELs together with standardized key information on the nature of mutations when they are detected and the use of the keyword “reINDEL” to increase visibility in both instances of successful and unsuccessful search.
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Affiliation(s)
- Birgit C Schlick-Steiner
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck Technikerstr. 25, 6020, Innsbruck, Austria
| | - Wolfgang Arthofer
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck Technikerstr. 25, 6020, Innsbruck, Austria
| | - Karl Moder
- Institute of Applied Statistics and Computing, University of Natural Resources and Life Sciences Peter Jordan-Str. 82, 1180, Vienna, Austria
| | - Florian M Steiner
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck Technikerstr. 25, 6020, Innsbruck, Austria
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20
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Identification of nucleotide-level changes impacting gene content and genome evolution in orthopoxviruses. J Virol 2014; 88:13651-68. [PMID: 25231308 DOI: 10.1128/jvi.02015-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
UNLABELLED Poxviruses are composed of large double-stranded DNA (dsDNA) genomes coding for several hundred genes whose variation has supported virus adaptation to a wide variety of hosts over their long evolutionary history. Comparative genomics has suggested that the Orthopoxvirus genus in particular has undergone reductive evolution, with the most recent common ancestor likely possessing a gene complement consisting of all genes present in any existing modern-day orthopoxvirus species, similar to the current Cowpox virus species. As orthopoxviruses adapt to new environments, the selection pressure on individual genes may be altered, driving sequence divergence and possible loss of function. This is evidenced by accumulation of mutations and loss of protein-coding open reading frames (ORFs) that progress from individual missense mutations to gene truncation through the introduction of early stop mutations (ESMs), gene fragmentation, and in some cases, a total loss of the ORF. In this study, we have constructed a whole-genome alignment for representative isolates from each Orthopoxvirus species and used it to identify the nucleotide-level changes that have led to gene content variation. By identifying the changes that have led to ESMs, we were able to determine that short indels were the major cause of gene truncations and that the genome length is inversely proportional to the number of ESMs present. We also identified the number and types of protein functional motifs still present in truncated genes to assess their functional significance. IMPORTANCE This work contributes to our understanding of reductive evolution in poxviruses by identifying genomic remnants such as single nucleotide polymorphisms (SNPs) and indels left behind by evolutionary processes. Our comprehensive analysis of the genomic changes leading to gene truncation and fragmentation was able to detect some of the remnants of these evolutionary processes still present in orthopoxvirus genomes and suggests that these viruses are under continual adaptation due to changes in their environment. These results further our understanding of the evolutionary mechanisms that drive virus variation, allowing orthopoxviruses to adapt to particular environmental niches. Understanding the evolutionary history of these virus pathogens may help predict their future evolutionary potential.
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21
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Pola M, Padula V, Gosliner TM, Cervera JL. Going further on an intricate and challenging group of nudibranchs: description of five novel species and a more complete molecular phylogeny of the subfamily Nembrothinae (Polyceridae). Cladistics 2014; 30:607-634. [DOI: 10.1111/cla.12097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Marta Pola
- Departamento de Biología; Edificio de Biología; Campus de Excelencia Internacional UAM+CSIC; Universidad Autónoma de Madrid; C/ Darwin 2 28049 Madrid Spain
| | - Vinicius Padula
- Zoologische Staatssammlung München; Mollusca Sektion; Münchhausenstrasse 21 81247 München Germany
| | - Terrence M. Gosliner
- Department of Invertebrate Zoology; California Academy of Sciences; 55 Music Concourse Drive, Golden Gate Park San Francisco CA 94118 USA
| | - Juan Lucas Cervera
- Departamento de Biología; Facultad de Ciencias del Mar y Ambientales; Campus de Excelencia Internacional del Mar (CEI MAR); Universidad de Cádiz; Polígono Río San Pedro s/n, Ap.40, 11510, Puerto Real; Cádiz Spain
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22
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A phylogenetic analysis of the genus Fragaria (strawberry) using intron-containing sequence from the ADH-1 gene. PLoS One 2014; 9:e102237. [PMID: 25078607 PMCID: PMC4117466 DOI: 10.1371/journal.pone.0102237] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 06/17/2014] [Indexed: 11/19/2022] Open
Abstract
The genus Fragaria encompasses species at ploidy levels ranging from diploid to decaploid. The cultivated strawberry, Fragaria×ananassa, and its two immediate progenitors, F. chiloensis and F. virginiana, are octoploids. To elucidate the ancestries of these octoploid species, we performed a phylogenetic analysis using intron-containing sequences of the nuclear ADH-1 gene from 39 germplasm accessions representing nineteen Fragaria species and one outgroup species, Dasiphora fruticosa. All trees from Maximum Parsimony and Maximum Likelihood analyses showed two major clades, Clade A and Clade B. Each of the sampled octoploids contributed alleles to both major clades. All octoploid-derived alleles in Clade A clustered with alleles of diploid F. vesca, with the exception of one octoploid allele that clustered with the alleles of diploid F. mandshurica. All octoploid-derived alleles in clade B clustered with the alleles of only one diploid species, F. iinumae. When gaps encoded as binary characters were included in the Maximum Parsimony analysis, tree resolution was improved with the addition of six nodes, and the bootstrap support was generally higher, rising above the 50% threshold for an additional nine branches. These results, coupled with the congruence of the sequence data and the coded gap data, validate and encourage the employment of sequence sets containing gaps for phylogenetic analysis. Our phylogenetic conclusions, based upon sequence data from the ADH-1 gene located on F. vesca linkage group II, complement and generally agree with those obtained from analyses of protein-encoding genes GBSSI-2 and DHAR located on F. vesca linkage groups V and VII, respectively, but differ from a previous study that utilized rDNA sequences and did not detect the ancestral role of F. iinumae.
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23
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Muñoz-Pajares AJ. SIDIER: substitution and indel distances to infer evolutionary relationships. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12118] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Antonio Jesús Muñoz-Pajares
- Centro de Investigação em Biodiversidade e Recursos Genéticos; CIBIO; Campus Agrário de Vairão Rua Padre Armando Quintas 4485-661 Vairão Portugal
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24
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Baum BR, Edwards T, Johnson DA. What does the 5S rRNA multigene family tell us about the origin of the annual Triticeae (Poaceae)? Genome 2013; 56:245-66. [PMID: 23789993 DOI: 10.1139/gen-2012-0195] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have investigated the complex relationships among the annual genera within the tribe Triticeae through phylogenetic analyses of the 5S rRNA multigene family. Cloned sequences were assigned to groups of orthologous sequences, called unit classes, that were subjected to several analyses including BLAST (Basic Local Alignment Search Tool) searches to assess possible ancestral relationships with perennial genera; phylogenetic analyses using parsimony (Pars), maximum likelihood (ML), and Bayesian methods; and minimum reticulation networks from the Pars, ML, and Bayesian trees. In this study, we included genera with both annual and perennial species, such as Dasypyrum, Hordeum, and Secale. BLAST pointed to Pseudoroegneria (carrier of the St genome) and possibly Thinopyrum (carrier of the J genome) as the potential next of kin. However, Thinopyrum and Pseudoroegneria have never fallen together on the individual trees with the former generally associated with Crithopsis, Aegilops, Triticum, and Dasypyrum, while the latter is usually associated with the rest of the genera within Triticeae. The "long" unit classes placed Dasypyrum breviaristatum together with Dasypyrum villosum, whereas the "short" unit classes put them far apart on the trees. None of the gene trees alone was able to summarize the complex relationships among the genera, in line with previous results in the Triticeae. However, the application of tools designed to display phylogenetic networks was able to depict the complex links among the genera based on the short and the long gene trees, including the close link between Thinopyrum and Pseudoroegneria suggested by the phylogenetic analyses. In addition, our analyses provide support for the hypothesis that at least some annual Triticeae taxa are derived from their perennial relatives.
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Affiliation(s)
- B R Baum
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, Neatby Building, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada.
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Genetic Analysis and Captive Breeding Program Design for the Eastern Massasauga Sistrurus catenatus catenatus. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2013. [DOI: 10.3996/032012-jfwm-026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
The eastern massasauga Sistrurus catenatus catenatus is a declining species for which a captive breeding program was established in 2006. To effectively manage wild and captive populations, an understanding of genetic diversity within the species is necessary. We analyzed mitochondrial DNA sequences of 186 individuals: 109 wild snakes from 34 U.S. and Canadian counties and districts, all 52 breeding program members (23 of known and 29 of unknown origin), 18 other captives of unknown origin, and 7 outgroup representatives of desert massasauga S. c. edwardsii, and western massasauga, S. c. tergeminus. Statistical parsimony, maximum likelihood, and maximum parsimony analyses all identified eastern massasaugas as divergent from western and desert massasaugas. We found 18 different haplotypes among eastern massasaugas, comprising three geographically and genetically differentiated NADH dehydrogenase II (ND2) subunits that potentially reflect post-Pleistocene range expansion from unglaciated into formerly glaciated regions. Snakes of unknown origin could all be assigned unambiguously to these ND2 subunits. To maintain natural genetic variation, preserve diversity in captive lineages, and allow future augmentation or reintroduction, the Association of Zoos and Aquariums is managing these three geographic ND2 subunits separately within the Eastern Massasauga Species Survival Plan breeding program.
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Vázquez-Sánchez M, Terrazas T, Arias S, Ochoterena H. Molecular phylogeny, origin and taxonomic implications of the tribe Cacteae (Cactaceae). SYST BIODIVERS 2013. [DOI: 10.1080/14772000.2013.775191] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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27
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Suwannasai N, Martín MP, Phosri C, Sihanonth P, Whalley AJS, Spouge JL. Fungi in Thailand: a case study of the efficacy of an ITS barcode for automatically identifying species within the Annulohypoxylon and Hypoxylon genera. PLoS One 2013; 8:e54529. [PMID: 23390499 PMCID: PMC3563529 DOI: 10.1371/journal.pone.0054529] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 12/13/2012] [Indexed: 11/20/2022] Open
Abstract
Thailand, a part of the Indo-Burma biodiversity hotspot, has many endemic animals and plants. Some of its fungal species are difficult to recognize and separate, complicating assessments of biodiversity. We assessed species diversity within the fungal genera Annulohypoxylon and Hypoxylon, which produce biologically active and potentially therapeutic compounds, by applying classical taxonomic methods to 552 teleomorphs collected from across Thailand. Using probability of correct identification (PCI), we also assessed the efficacy of automated species identification with a fungal barcode marker, ITS, in the model system of Annulohypoxylon and Hypoxylon. The 552 teleomorphs yielded 137 ITS sequences; in addition, we examined 128 GenBank ITS sequences, to assess biases in evaluating a DNA barcode with GenBank data. The use of multiple sequence alignment in a barcode database like BOLD raises some concerns about non-protein barcode markers like ITS, so we also compared species identification using different alignment methods. Our results suggest the following. (1) Multiple sequence alignment of ITS sequences is competitive with pairwise alignment when identifying species, so BOLD should be able to preserve its present bioinformatics workflow for species identification for ITS, and possibly therefore with at least some other non-protein barcode markers. (2) Automated species identification is insensitive to a specific choice of evolutionary distance, contributing to resolution of a current debate in DNA barcoding. (3) Statistical methods are available to address, at least partially, the possibility of expert misidentification of species. Phylogenetic trees discovered a cryptic species and strongly supported monophyletic clades for many Annulohypoxylon and Hypoxylon species, suggesting that ITS can contribute usefully to a barcode for these fungi. The PCIs here, derived solely from ITS, suggest that a fungal barcode will require secondary markers in Annulohypoxylon and Hypoxylon, however. The URL http://tinyurl.com/spouge-barcode contains computer programs and other supplementary material relevant to this article.
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Affiliation(s)
- Nuttika Suwannasai
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
| | - María P. Martín
- Department of Mycology, Real Jardín Botánico-CSIC, Plaza de Murillo 2, Madrid, Spain
| | - Cherdchai Phosri
- Microbiology Programme, Faculty of Science and Technology, Pibulsongkram Rajabhat University, Phitsanulok, Thailand
| | - Prakitsin Sihanonth
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Anthony J. S. Whalley
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - John L. Spouge
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, United States of America
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Warnow T. Large-Scale Multiple Sequence Alignment and Phylogeny Estimation. MODELS AND ALGORITHMS FOR GENOME EVOLUTION 2013. [DOI: 10.1007/978-1-4471-5298-9_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Luan PT, Ryder OA, Davis H, Zhang YP, Yu L. Incorporating indels as phylogenetic characters: impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora). Mol Phylogenet Evol 2012; 66:748-56. [PMID: 23147269 DOI: 10.1016/j.ympev.2012.10.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 10/27/2012] [Accepted: 10/29/2012] [Indexed: 10/27/2022]
Abstract
Insertion and deletion events (indels) provide a suite of markers with enormous potential for molecular phylogenetics. Using many more indel characters than those in previous studies, we here for the first time address the impact of indel inclusion on the phylogenetic inferences of Arctoidea (Mammalia: Carnivora). Based on 6843 indel characters from 22 nuclear intron loci of 16 species of Arctoidea, our analyses demonstrate that when the indels were not taken into consideration, the monophyly of Ursidae and Pinnipedia tree and the monophyly of Pinnipedia and Musteloidea tree were both recovered, whereas inclusion of indels by using three different indel coding schemes give identical phylogenetic tree topologies supporting the monophyly of Ursidae and Pinnipedia. Our work brings new perspectives on the previously controversial placements among Arctoidea families, and provides another example demonstrating the importance of identifying and incorporating indels in the phylogenetic analyses of introns. In addition, comparison of indel incorporation methods revealed that the three indel coding methods are all advantageous over treating indels as missing data, given that incorporating indels produces consistent results across methods. This is the first report of the impact of different indel coding schemes on phylogenetic reconstruction at the family level in Carnivora, which indicates that indels should be taken into account in the future phylogenetic analyses.
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Affiliation(s)
- Peng-Tao Luan
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
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Linnakoski R, de Beer ZW, Duong TA, Niemelä P, Pappinen A, Wingfield MJ. Grosmannia and Leptographium spp. associated with conifer-infesting bark beetles in Finland and Russia, including Leptographium taigense sp. nov. Antonie van Leeuwenhoek 2012; 102:375-99. [PMID: 22580615 DOI: 10.1007/s10482-012-9747-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 04/24/2012] [Indexed: 11/26/2022]
Abstract
Species of Grosmannia with Leptographium anamorphs include important forest pathogens and agents of blue stain in timber. They are commonly found in association with forest pests, such as bark beetles. During a survey of ophiostomatoid fungi in eastern parts of Finland and neighboring Russia, species belonging to the genus Grosmannia were isolated from 12 different bark beetle species infesting Picea abies and Pinus sylvestris, the most economically important conifers in the region. Identification of these fungi was based on morphology, DNA sequence comparisons for three gene regions and phylogenetic analyses. A total of ten taxa were identified. These belonged to six different species complexes in Grosmannia. The phylogenetic analyses provided an opportunity to redefine the G. galeiformis-, L. procerum-, L. lundbergii-, G. piceiperda-, G. olivacea- and G. penicillata-complexes, and to consider the species emerging from the survey within the context of these complexes. The species included G. galeiformis, G. olivacea, L. chlamydatum, L. lundbergii, L. truncatum and a novel taxon, described here as L. taigense sp. nov. In addition, species closely related to G. cucullata, G. olivaceapini comb. nov., G. piceiperda and L. procerum were isolated but their identity could not be resolved. The overall results indicate that the diversity of Grosmannia species in the boreal forests remains poorly understood and that further studies are needed to clarify the status of several species or species complexes.
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Affiliation(s)
- Riikka Linnakoski
- Section of Biodiversity and Environmental Science, Department of Biology, University of Turku, Finland.
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Riggins CW, Seigler DS. The genus Artemisia (Asteraceae: Anthemideae) at a continental crossroads: molecular insights into migrations, disjunctions, and reticulations among Old and New World species from a Beringian perspective. Mol Phylogenet Evol 2012; 64:471-90. [PMID: 22580463 DOI: 10.1016/j.ympev.2012.05.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 04/30/2012] [Accepted: 05/02/2012] [Indexed: 11/17/2022]
Abstract
Artemisia is the largest genus (ca. 350-500+ spp.) in the tribe Anthemideae and is composed of ecologically, morphologically, and chemically diverse species that are found primarily throughout the Northern Hemisphere. Two major centers of diversity for the genus are located in Eurasia and western North America, but phytogeographic links connecting these two regions are observed all across the North Pacific Rim and adjacent areas in the Arctic, including many islands and archipelagos. Previous phylogenetic studies have helped to clarify major lineages and identify likely sister relationships, but many questions remain unanswered regarding the relationships and migration history of New and Old World species. Here we investigate the phylogenetics of Artemisia within a biogeographic context centered in the Beringian Region and offer new hypotheses concerning species relationships, migration history, and the likely role of reticulate evolution in the genus. Our sampling included many new taxa and emphasized multiple accessions of widespread species, species from proposed refugia, and species with disjunct/vicariant distributions. The ITS phylogeny contained 173 accessions (94 new and 79 from GenBank) and indicated that Artemisia is paraphyletic by the exclusion of several small Asian genera and the North American genus Sphaeromeria. Following a survey of thirteen chloroplast loci, phylogenies based on two plastid markers (psbA-trnH and rpl32-trnL spacers) were constructed with a reduced data set, and though largely consistent with the ITS topology, revealed several cases of possible introgression among New World and Beringian species. Our analysis reveals that North American Artemisia species have multiple origins, and that western North America has served as a source for some colonizing elements in eastern Asia and South America.
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Affiliation(s)
- Chance W Riggins
- Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA.
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32
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FREELAND JOANNA, VACHON NICOLE. Repetitive sequences in phylogeographic inference: a reply to Saltonstall and Lambertini (2012). Mol Ecol Resour 2012. [DOI: 10.1111/j.1755-0998.2012.03145.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- JOANNA FREELAND
- Department of Biology, Trent University, Peterborough, Ontario, Canada K9J 7B8
| | - NICOLE VACHON
- Department of Biology, Trent University, Peterborough, Ontario, Canada K9J 7B8
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Warnow T. Standard maximum likelihood analyses of alignments with gaps can be statistically inconsistent. PLOS CURRENTS 2012; 4:RRN1308. [PMID: 22453901 PMCID: PMC3299439 DOI: 10.1371/currents.rrn1308] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/12/2012] [Indexed: 12/04/2022]
Abstract
BackgroundMost statistical methods for phylogenetic estimation in use today treat a gap (generally representing an insertion or deletion, i.e., indel) within the input sequence alignment as missing data. However, the statistical properties of this treatment of indels have not been fully investigated.ResultsWe prove that maximum likelihood phylogeny estimation, treating indels as missing data, can be statistically inconsistent for a general (and rather simple) model of sequence evolution, even when given the true alignment. Therefore, accurate phylogeny estimation cannot be guaranteed for maximum likelihood analyses, even given arbitrarily long sequences, when indels are present and treated as missing data.ConclusionsOur result shows that the standard statistical techniques used to estimate phylogenies from sequence alignments may have unfavorable statistical properties, even when the sequence alignment is accurate and the assumed substitution model matches the generation model. This suggests that the recent research focus on developing statistical methods that treat indel events properly is an important direction for phylogeny estimation.
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Affiliation(s)
- Tandy Warnow
- Professor of Computer Science, Department of Computer Science, University of Texas at Austin
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34
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Carrasco PA, Mattoni CI, Leynaud GC, Scrocchi GJ. Morphology, phylogeny and taxonomy of South American bothropoid pitvipers (Serpentes, Viperidae). ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2011.00511.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Bryant LM, Donnellan SC, Hurwood DA, Fuller SJ. Phylogenetic relationships and divergence date estimates among Australo-Papuan mosaic-tailed rats from the Uromys division (Rodentia: Muridae). ZOOL SCR 2011. [DOI: 10.1111/j.1463-6409.2011.00482.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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36
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Jacquemin J, Chaparro C, Laudié M, Berger A, Gavory F, Goicoechea JL, Wing RA, Cooke R. Long-range and targeted ectopic recombination between the two homeologous chromosomes 11 and 12 in Oryza species. Mol Biol Evol 2011; 28:3139-50. [PMID: 21616911 DOI: 10.1093/molbev/msr144] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Whole genome duplication (WGD) and subsequent evolution of gene pairs have been shown to have shaped the present day genomes of most, if not all, plants and to have played an essential role in the evolution of many eukaryotic genomes. Analysis of the rice (Oryza sativa ssp. japonica) genome sequence suggested an ancestral WGD ∼50-70 Ma common to all cereals and a segmental duplication between chromosomes 11 and 12 as recently as 5 Ma. More recent studies based on coding sequences have demonstrated that gene conversion is responsible for the high sequence conservation which suggested such a recent duplication. We previously showed that gene conversion has been a recurrent process throughout the Oryza genus and in closely related species and that orthologous duplicated regions are also highly conserved in other cereal genomes. We have extended these studies to compare megabase regions of genomic (coding and noncoding) sequences between two cultivated (O. sativa, Oryza glaberrima) and one wild (Oryza brachyantha) rice species using a novel approach of topological incongruency. The high levels of intraspecies conservation of both gene and nongene sequences, particularly in O. brachyantha, indicate long-range conversion events less than 4 Ma in all three species. These observations demonstrate megabase-scale conversion initiated within a highly rearranged region located at ∼2.1 Mb from the chromosome termini and emphasize the importance of gene conversion in cereal genome evolution.
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Affiliation(s)
- J Jacquemin
- Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche Centre National de la Recherche Scientifique/Institut de Recherche pour le Développement/Université de Perpignan Via Domitia, Université de Perpignan, Perpignan-Cedex, France.
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The utility of indels in population genetics: The Tpi intron for host race genealogy of Acrocercops transecta (Insecta: Lepidoptera). Mol Phylogenet Evol 2011; 59:469-76. [DOI: 10.1016/j.ympev.2011.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 02/09/2011] [Accepted: 03/04/2011] [Indexed: 11/21/2022]
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38
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Becker RE, Valverde RA, Crother BI. Proopiomelanocortin (POMC) and testing the phylogenetic position of turtles (Testudines). J ZOOL SYST EVOL RES 2010. [DOI: 10.1111/j.1439-0469.2010.00589.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Ophiostoma spp. associated with pine- and spruce-infesting bark beetles in Finland and Russia. Persoonia - Molecular Phylogeny and Evolution of Fungi 2010; 25:72-93. [PMID: 21339968 PMCID: PMC3028507 DOI: 10.3767/003158510x550845] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 09/27/2010] [Indexed: 11/25/2022]
Abstract
The timber and pulp industries of Finland rely heavily on importations from Russia as source of raw timber. These imports raise the risk of accidentally importing forest pests and pathogens, especially bark beetles and their associated fungi, into Finland. Although ophiostomatoid fungi have previously been reported from Finland and Russia, the risks of accidentally moving these fungi has prompted a first survey to compare the diversity of conifer-infesting bark beetles and associated fungi from boreal forests on both sides of the Finnish-Russian border. The aim of the present study was to identify and characterise Ophiostoma species isolated in association with 11 bark beetle species infesting Pinus sylvestris and Picea abies during this survey in the eastern parts of Finland and neighbouring Russia. Fungal isolates were grouped based on morphology and representatives of each morphological group were subjected to DNA sequence comparisons of the internal transcribed spaced region (ITS1, 5.8S, ITS2) and β-tubulin gene region. A total of 15 species of Ophiostoma were identified, including seven known species, five new species, and three species for which the identity remains uncertain. In the O. piceae-complex we identified O. canum, O. floccosum, O. karelicum and O. rachisporum sp. nov., and related to these, some isolates belonging to the European clade of O. minus in the O. minus-complex. Ophiostoma bicolor and O. fuscum sp. nov. were identified in the O. ips-complex, while O. ainoae, O. brunneo-ciliatum, O. tapionis sp. nov. and O. pallidulum sp. nov. were shown to group close to, but not in a strict monophyletic lineage with species of the O. ips-complex. Together with a single O. abietinum-like isolate, the only species that grouped close to the Sporothrix schenckii- O. stenoceras complex, was O. saponiodorum sp. nov.
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40
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Lehtonen S. Phylogeny estimation and alignment via POY versus Clustal + PAUP*: a response to Ogden and Rosenberg (2007). Syst Biol 2010; 57:653-7. [PMID: 18709601 DOI: 10.1080/10635150802302476] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Samuli Lehtonen
- Department of Biology, Section of Biodiversity and Environmental Science, University of Turku, Turku, Finland.
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41
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Blair C, Murphy RW. Recent trends in molecular phylogenetic analysis: where to next? J Hered 2010; 102:130-8. [PMID: 20696667 DOI: 10.1093/jhered/esq092] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The acquisition of large multilocus sequence data is providing researchers with an unprecedented amount of information to resolve difficult phylogenetic problems. With these large quantities of data comes the increasing challenge regarding the best methods of analysis. We review the current trends in molecular phylogenetic analysis, focusing specifically on the topics of multiple sequence alignment and methods of tree reconstruction. We suggest that traditional methods are inadequate for these highly heterogeneous data sets and that researchers employ newer more sophisticated search algorithms in their analyses. If we are to best extract the information present in these data sets, a sound understanding of basic phylogenetic principles combined with modern methodological techniques are necessary.
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Affiliation(s)
- Christopher Blair
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
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Liu L, Mondal MMH, Idris MA, Lokman HS, Rajapakse PRVJ, Satrija F, Diaz JL, Upatham ES, Attwood SW. The phylogeography of Indoplanorbis exustus (Gastropoda: Planorbidae) in Asia. Parasit Vectors 2010; 3:57. [PMID: 20602771 PMCID: PMC2914737 DOI: 10.1186/1756-3305-3-57] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 07/05/2010] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The freshwater snail Indoplanorbis exustus is found across India, Southeast Asia, central Asia (Afghanistan), Arabia and Africa. Indoplanorbis is of economic importance in that it is responsible for the transmission of several species of the genus Schistosoma which infect cattle and cause reduced livestock productivity. The snail is also of medical importance as a source of cercarial dermatitis among rural workers, particularly in India. In spite of its long history and wide geographical range, it is thought that Indoplanorbis includes only a single species. The aims of the present study were to date the radiation of Indoplanorbis across Asia so that the factors involved in its dispersal in the region could be tested, to reveal potential historical biogeographical events shaping the phylogeny of the snail, and to look for signs that I. exustus might be polyphyletic. RESULTS The results indicated a radiation beginning in the late Miocene with a divergence of an ancestral bulinine lineage into Assam and peninsular India clades. A Southeast Asian clade diverged from the peninsular India clade late-Pliocene; this clade then radiated at a much more rapid pace to colonize all of the sampled range of Indoplanorbis in the mid-Pleistocene. CONCLUSIONS The phylogenetic depth of divergences between the Indian clades and Southeast Asian clades, together with habitat and parasitological differences suggest that I. exustus may comprise more than one species. The timescale estimated for the radiation suggests that the dispersal to Arabia and to Southeast Asia was facilitated by palaeogeographical events and climate change, and did not require human involvement. Further samples from Afghanistan, Africa and western India are required to refine the phylogeographical hypothesis and to include the African Recent dispersal.
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Affiliation(s)
- Liang Liu
- State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Mohammed MH Mondal
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Mohamed A Idris
- Department of Microbiology and Immunology, College of Medicine, Sultan Qaboos University, Oman
| | - Hakim S Lokman
- Infectious Diseases Research Centre, IMR, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - PRV Jayanthe Rajapakse
- Department of Veterinary Pathobiology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Fadjar Satrija
- Department of Animal Diseases and Veterinary Public Health, Faculty of Veterinary Medicine, Bogor Agricultural University (IPB), Jl. Agathis-Kampus IPB Darmaga, Bogor 16680, Indonesia
| | - Jose L Diaz
- Veterinary Inspection Board, Vitas, Tondo, Metro Manila, Philippines
| | - E Suchart Upatham
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Department of Medical Science, Faculty of Science, Burapha University, Bangsaen, Chonburi, Thailand
| | - Stephen W Attwood
- State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
- Department of Zoology, The Natural History Museum, London, UK
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Wolsan M, Sato JJ. Effects of data incompleteness on the relative performance of parsimony and Bayesian approaches in a supermatrix phylogenetic reconstruction of Mustelidae and Procyonidae (Carnivora). Cladistics 2010; 26:168-194. [DOI: 10.1111/j.1096-0031.2009.00281.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Prevosti FJ, Chemisquy MA. The impact of missing data on real morphological phylogenies: influence of the number and distribution of missing entries. Cladistics 2009; 26:326-339. [DOI: 10.1111/j.1096-0031.2009.00289.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Abstract
Natural products researchers are increasingly employing evolutionary analyses of genes and gene products that rely on phylogenetic trees. The field of phylogenetic inference and of evolutionary analyses based on phylogenies is growing at an amazing rate, making it difficult to keep up with the latest methodologies. Here, we summarize phylogenetic applications in natural products research, and review methods and software useful for carrying out analyses inferring or using phylogenetic trees. We include an updated overview of available alignment methods and programs, as well as a selection of some useful phylogenetic analysis tools. This review covers primarily the period 2000-2009 for applications of phylogenetic methods in natural product research, and 1990-2009 for phylogenetic methods, with some references going back to the 1960s.
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Affiliation(s)
- Imke Schmitt
- Department of Plant Biology and Bell Museum of Natural History, University of Minnesota, 250 Biological Sciences Center, 1445 Gortner Ave., St. Paul, MN 55108, USA.
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46
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Exploring the utility of an indel-rich, mitochondrial intergenic region as a molecular barcode for bamboo corals (Octocorallia: Isididae). Mar Genomics 2009; 2:183-92. [DOI: 10.1016/j.margen.2009.10.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 08/19/2009] [Accepted: 10/08/2009] [Indexed: 11/24/2022]
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47
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Dwivedi B, Gadagkar SR. Phylogenetic inference under varying proportions of indel-induced alignment gaps. BMC Evol Biol 2009; 9:211. [PMID: 19698168 PMCID: PMC2746219 DOI: 10.1186/1471-2148-9-211] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 08/23/2009] [Indexed: 01/19/2023] Open
Abstract
Background The effect of alignment gaps on phylogenetic accuracy has been the subject of numerous studies. In this study, we investigated the relationship between the total number of gapped sites and phylogenetic accuracy, when the gaps were introduced (by means of computer simulation) to reflect indel (insertion/deletion) events during the evolution of DNA sequences. The resulting (true) alignments were subjected to commonly used gap treatment and phylogenetic inference methods. Results (1) In general, there was a strong – almost deterministic – relationship between the amount of gap in the data and the level of phylogenetic accuracy when the alignments were very "gappy", (2) gaps resulting from deletions (as opposed to insertions) contributed more to the inaccuracy of phylogenetic inference, (3) the probabilistic methods (Bayesian, PhyML & "MLε, " a method implemented in DNAML in PHYLIP) performed better at most levels of gap percentage when compared to parsimony (MP) and distance (NJ) methods, with Bayesian analysis being clearly the best, (4) methods that treat gapped sites as missing data yielded less accurate trees when compared to those that attribute phylogenetic signal to the gapped sites (by coding them as binary character data – presence/absence, or as in the MLε method), and (5) in general, the accuracy of phylogenetic inference depended upon the amount of available data when the gaps resulted from mainly deletion events, and the amount of missing data when insertion events were equally likely to have caused the alignment gaps. Conclusion When gaps in an alignment are a consequence of indel events in the evolution of the sequences, the accuracy of phylogenetic analysis is likely to improve if: (1) alignment gaps are categorized as arising from insertion events or deletion events and then treated separately in the analysis, (2) the evolutionary signal provided by indels is harnessed in the phylogenetic analysis, and (3) methods that utilize the phylogenetic signal in indels are developed for distance methods too. When the true homology is known and the amount of gaps is 20 percent of the alignment length or less, the methods used in this study are likely to yield trees with 90–100 percent accuracy.
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Affiliation(s)
- Bhakti Dwivedi
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 46469-2320, USA.
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WILSON NERIDAG, SCHRÖDL M, HALANYCH KENNETHM. Ocean barriers and glaciation: evidence for explosive radiation of mitochondrial lineages in the Antarctic sea slugDoris kerguelenensis(Mollusca, Nudibranchia). Mol Ecol 2009; 18:965-984. [DOI: 10.1111/j.1365-294x.2008.04071.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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49
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Pérez-Portela R, Bishop J, Davis A, Turon X. Phylogeny of the families Pyuridae and Styelidae (Stolidobranchiata, Ascidiacea) inferred from mitochondrial and nuclear DNA sequences. Mol Phylogenet Evol 2009; 50:560-70. [DOI: 10.1016/j.ympev.2008.11.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 11/10/2008] [Accepted: 11/15/2008] [Indexed: 11/29/2022]
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50
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Goebel AM, Ranker TA, Corn PS, Olmstead RG. Mitochondrial DNA evolution in the Anaxyrus boreas species group. Mol Phylogenet Evol 2009; 50:209-25. [DOI: 10.1016/j.ympev.2008.06.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 06/10/2008] [Accepted: 06/24/2008] [Indexed: 11/27/2022]
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