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Haag J, Hübner L, Kozlov AM, Stamatakis A. The Free Lunch is not over yet-systematic exploration of numerical thresholds in maximum likelihood phylogenetic inference. BIOINFORMATICS ADVANCES 2023; 3:vbad124. [PMID: 37750068 PMCID: PMC10518076 DOI: 10.1093/bioadv/vbad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 09/27/2023]
Abstract
Summary Maximum likelihood (ML) is a widely used phylogenetic inference method. ML implementations heavily rely on numerical optimization routines that use internal numerical thresholds to determine convergence. We systematically analyze the impact of these threshold settings on the log-likelihood and runtimes for ML tree inferences with RAxML-NG, IQ-TREE, and FastTree on empirical datasets. We provide empirical evidence that we can substantially accelerate tree inferences with RAxML-NG and IQ-TREE by changing the default values of two such numerical thresholds. At the same time, altering these settings does not significantly impact the quality of the inferred trees. We further show that increasing both thresholds accelerates the RAxML-NG bootstrap without influencing the resulting support values. For RAxML-NG, increasing the likelihood thresholds ϵ LnL and ϵ brlen to 10 and 103, respectively, results in an average tree inference speedup of 1.9 ± 0.6 on Data collection 1, 1.8 ± 1.1 on Data collection 2, and 1.9 ± 0.8 on Data collection 2 for the RAxML-NG bootstrap compared to the runtime under the current default setting. Increasing the likelihood threshold ϵ LnL to 10 in IQ-TREE results in an average tree inference speedup of 1.3 ± 0.4 on Data collection 1 and 1.3 ± 0.9 on Data collection 2. Availability and implementation All MSAs we used for our analyses, as well as all results, are available for download at https://cme.h-its.org/exelixis/material/freeLunch_data.tar.gz. Our data generation scripts are available at https://github.com/tschuelia/ml-numerical-analysis.
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Affiliation(s)
- Julia Haag
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - Lukas Hübner
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Alexey M Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- Biodiversity Computing Group, Institute of Computer Science, Foundation for Research and Technology – Hellas, 70013 Heraklion, Greece
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2
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Kim HT, Kim JS. The complete chloroplast genome sequence of the Korean maple tree ( Acer pseudosieboldianum (Pax) Kom.). Mitochondrial DNA B Resour 2023; 8:691-694. [PMID: 37383607 PMCID: PMC10294752 DOI: 10.1080/23802359.2023.2224623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023] Open
Abstract
The complete chloroplast genome sequence of Acer pseudosieboldianum (Sapindaceae) was determined. The chloroplast genome of A. pseudosieboldianum is 157,053 bp in length with two inverted repeats (26,747 bp) between a large single-copy (85,391 bp) and a small single-copy (18,168 bp). The GC content was 37.8% and it was composed of 86 coding genes, eight rRNA genes, 37 tRNA genes, and two pseudogenes, rps2, and ycf1. Molecular phylogenetic analysis based on the plastid genome sequences strongly supported the hypothesis that A. pseudosieboldianum was embedded in the series Palmata of section Palmata. However, the phylogenetic positions of A. ukurunduense and A. buergerianum, which are a members of the series Penninervia of sections Palmata and Pentaphylla, respectively, were incongruent with the recent sectional classification system.
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Affiliation(s)
- Hyoung Tae Kim
- Department of Ecological and Environmental System, Kyungpook National University, Kyungpook, South Korea
| | - Jung Sung Kim
- Department of Forest Science, Chungbuk National University, Cheongju, South Korea
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3
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Haag J, Höhler D, Bettisworth B, Stamatakis A. From Easy to Hopeless-Predicting the Difficulty of Phylogenetic Analyses. Mol Biol Evol 2022; 39:6832260. [PMID: 36395091 PMCID: PMC9728795 DOI: 10.1093/molbev/msac254] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic analyzes under the Maximum-Likelihood (ML) model are time and resource intensive. To adequately capture the vastness of tree space, one needs to infer multiple independent trees. On some datasets, multiple tree inferences converge to similar tree topologies, on others to multiple, topologically highly distinct yet statistically indistinguishable topologies. At present, no method exists to quantify and predict this behavior. We introduce a method to quantify the degree of difficulty for analyzing a dataset and present Pythia, a Random Forest Regressor that accurately predicts this difficulty. Pythia predicts the degree of difficulty of analyzing a dataset prior to initiating ML-based tree inferences. Pythia can be used to increase user awareness with respect to the amount of signal and uncertainty to be expected in phylogenetic analyzes, and hence inform an appropriate (post-)analysis setup. Further, it can be used to select appropriate search algorithms for easy-, intermediate-, and hard-to-analyze datasets.
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Affiliation(s)
| | - Dimitri Höhler
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Ben Bettisworth
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Cardoni S, Piredda R, Denk T, Grimm GW, Papageorgiou AC, Schulze E, Scoppola A, Salehi Shanjani P, Suyama Y, Tomaru N, Worth JRP, Cosimo Simeone M. 5S-IGS rDNA in wind-pollinated trees (Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:909-926. [PMID: 34808015 PMCID: PMC9299691 DOI: 10.1111/tpj.15601] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 11/02/2021] [Accepted: 11/18/2021] [Indexed: 05/31/2023]
Abstract
Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind-pollinated trees with long evolutionary histories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi-copy, potentially multi-locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination. Therefore, it can provide unique insights into the dynamic speciation processes of lineages that diversified tens of millions of years ago. Here, we provide the first high-throughput sequencing (HTS) of the 5S intergenic spacers (5S-IGS) for a lineage of wind-pollinated subtropical to temperate trees, the Fagus crenata - F. sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4963 unique 5S-IGS variants reflect a complex history of hybrid origins, lineage sorting, mixing via secondary gene flow, and intra-genomic competition between two or more paralogous-homoeologous 5S rDNA lineages. We show that modern species are genetic mosaics and represent a striking case of ongoing reticulate evolution during the past 55 million years.
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Affiliation(s)
- Simone Cardoni
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
| | - Roberta Piredda
- Department of Veterinary MedicineUniversity of Bari ‘Aldo Moro’Valenzano70010Italy
| | - Thomas Denk
- Swedish Museum of Natural HistoryStockholm10405Sweden
| | | | | | | | - Anna Scoppola
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
| | - Parvin Salehi Shanjani
- Natural Resources Gene Bank, Research Institute of Forests and RangelandsAgricultural Research, Education and Extension OrganizationTehranIran
| | - Yoshihisa Suyama
- Graduate School of Agricultural ScienceTohoku UniversityOsakiMiyagi989‐6711Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaAichi464‐8601Japan
| | - James R. P. Worth
- Ecological Genetics LaboratoryForestry and Forest Products Research Institute (FFPRI)TsukubaIbaraki305‐8687Japan
| | - Marco Cosimo Simeone
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
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5
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Saeki I, Hirao AS, Kenta T. Genetic variation of the relict maple Acer miyabei: uncovering its history of disjunct occurrence and the role of mountain refugia in shaping genetic diversity. AMERICAN JOURNAL OF BOTANY 2022; 109:309-321. [PMID: 34761814 DOI: 10.1002/ajb2.1803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Relict species provide valuable insights into the origin and formation of extant vegetation. Here, we aimed to elucidate the genetic structure and diversity of a riparian relic, Acer miyabei, in Japan. Once widely distributed, it now occurs in three isolated regions. The most northern regional group is located at low elevation on Hokkaido Island, whereas the southernmost group in central Honshu Island is at high elevation in a mountainous landscape. This contrastive distribution enables us to examine the effects of climate oscillations on genetic diversity in relation to topographic variation. METHODS We collected 604 individuals of A. miyabei from 43 sites. Their genetic structure and diversity were analyzed using 12 microsatellite markers and cpDNA sequences. RESULTS According to structure analyses, ∆K was lowest at K = 2; the clustering essentially separated many of the individuals in the most northern regional group from the others. In contrast, the two southern groups were not clearly differentiated from each other, despite their geographic discontinuity. The proportion of private alleles was high in populations from the mountain terrain in the southern group although the number of extant populations is limited. CONCLUSIONS Genetic clustering of A. miyabei is not perfectly congruent with the current patterns of geographic distribution. We infer that disjunction of the two southern groups occurred more recently than that between these groups and the northern group. The mountainous landscape in the most southern region likely provided multiple refugia and contributed to the retention of distinctive genetic variation.
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Affiliation(s)
- Ikuyo Saeki
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
- Makino Herbarium, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Akira S Hirao
- Faculty of Symbiotic Systems Science, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima, 960-1296, Japan
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan
| | - Tanaka Kenta
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294 Sugadaira-kogen, Ueda, 386-2204, Japan
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Dong PB, Wang RN, Afzal N, Liu ML, Yue M, Liu JN, Tan JL, Li ZH. Phylogenetic relationships and molecular evolution of woody forest tree family Aceraceae based on plastid phylogenomics and nuclear gene variations. Genomics 2021; 113:2365-2376. [PMID: 34051325 DOI: 10.1016/j.ygeno.2021.03.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 02/18/2021] [Accepted: 03/25/2021] [Indexed: 11/29/2022]
Abstract
The forest tree family Aceraceae is widespread in the northern hemisphere and it has ecological and economic importance. However, the phylogenetic relationships and classifications within the family are still controversial due to transitional intraspecific morphological characteristics and introgression hybridization among species. In this study, we determined the evolutionary relationships and molecular evolution of Aceraceae based on plastid phylogenomics and two nuclear gene variations. Phylogenetic analysis based on the plastid genomes suggested that Aceraceae species can be divided into two larger sub-clades corresponding to the two genera Acer and Dipteronia. Conjoint analysis of the plastid and nuclear gene sequences supported the classification with two genera in the family. Molecular dating showed that the two genera diverged 60.2 million years ago, which is generally consistently with previously reported results. Divergence hotspots and positively selected genes identified in the plastid genomes could be useful genetic resources in Aceraceae.
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Affiliation(s)
- Peng-Bin Dong
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ruo-Nan Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Nawal Afzal
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Jian-Ni Liu
- Early Life Institute, State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an 710069, China
| | - Jiang-Li Tan
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
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Areces-Berazain F, Hinsinger DD, Strijk JS. Genome-wide supermatrix analyses of maples (Acer, Sapindaceae) reveal recurring inter-continental migration, mass extinction, and rapid lineage divergence. Genomics 2021; 113:681-692. [PMID: 33508445 DOI: 10.1016/j.ygeno.2021.01.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/05/2021] [Accepted: 01/22/2021] [Indexed: 11/18/2022]
Abstract
Acer (Sapindaceae) is an exceptional study system for understanding the evolutionary history, divergence, and assembly of broad-leaved deciduous forests at higher latitudes. Maples stand out due to their high diversity, disjunct distribution pattern across the northern continents, and rich fossil record dating back to the Paleocene. Using a genome-wide supermatrix combining plastomes and nuclear sequences (~585 kb) for 110 Acer taxa, we built a robust time-calibrated hypothesis investigating the evolution of maples, inferring ancestral ranges, reconstructing diversification rates over time, and exploring the impact of mass-extinction on lineage accumulation. Contrary to fossil evidence, our results indicate Acer first originated in the (north)eastern Palearctic region, which acted as a source for recurring outward migration. Warm conditions favored rapid Eocene-onward divergence, but ranges and diversity declined extensively as a result of the Plio-Pleistocene glacial cycles. These signals in genome-wide sequence data corroborate paleobotanical evidence for other major woody north-temperate groups, highlighting the significant (disparate) impact of climatic changes on the evolution, composition, and distribution of the vegetation in the northern hemisphere.
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Affiliation(s)
- Fabiola Areces-Berazain
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, DaXueDongLu 100, Nanning, Guangxi 530005, China; Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, Laos
| | - Damien D Hinsinger
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, Laos; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commisariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Joeri S Strijk
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, Laos; Institute for Biodiversity and Environmental Research, Universiti Brunei Darussalam, Jalan Tungku Link, BE1410, Brunei Darussalam.
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8
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Gao J, Liao PC, Huang BH, Yu T, Zhang YY, Li JQ. Historical biogeography of Acer L. (Sapindaceae): genetic evidence for Out-of-Asia hypothesis with multiple dispersals to North America and Europe. Sci Rep 2020; 10:21178. [PMID: 33273626 PMCID: PMC7712834 DOI: 10.1038/s41598-020-78145-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023] Open
Abstract
Biogeography is the study of where, when, and how modern species evolved and diversified. Acer L. (maple) is one of the most diverse and widespread genera in the Northern Hemisphere. It comprises 124–156 species in the world, approximately 80% species of Acer are native in Asia. The current diversity center of Acer is not congruent with the distribution of the oldest fossils of the genus. Therefore, we herein used 84 species and subspecies to reconstruct the phylogeny and investigate the biogeographic history of Acer using nuclear ITS and three cpDNA fragments (psbA-trnH spacer, rpl16 intron, and trnL-trnF spacer) with maximum likelihood, maximum parsimony, and Bayesian inference methods. The analyses showed that the current diversity center and the origin center of Acer is Asia. Additionally, the North American and Euro-Mediterranean species originated from multiple sources from Asia via the North Atlantic Land Bridge and the Bering Land Bridge, and intercontinental migration has mainly occurred since the Miocene. This study not only provides a novel insight of the origin and dispersal routes of Acer but also exemplifies how past climatic changes affect the diversification-rates of Northern Hemisphere forest trees.
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Affiliation(s)
- Jian Gao
- Faculty of Resources and Environment, Baotou Teachers' College, Inner Mongolia University of Science and Technology, Baotou, China
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan.
| | - Bing-Hong Huang
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Tao Yu
- Beijing Key Laboratory for Forest Resources and Ecosystem Processes, Beijing Forestry University, Beijing, China
| | - Yu-Yang Zhang
- Beijing Key Laboratory for Forest Resources and Ecosystem Processes, Beijing Forestry University, Beijing, China
| | - Jun-Qing Li
- Beijing Key Laboratory for Forest Resources and Ecosystem Processes, Beijing Forestry University, Beijing, China.
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Areces-Berazain F, Wang Y, Hinsinger DD, Strijk JS. Plastome comparative genomics in maples resolves the infrageneric backbone relationships. PeerJ 2020; 8:e9483. [PMID: 32742784 PMCID: PMC7365138 DOI: 10.7717/peerj.9483] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 06/15/2020] [Indexed: 12/28/2022] Open
Abstract
Maples (Acer) are among the most diverse and ecologically important tree genera of the north-temperate forests. They include species highly valued as ornamentals and as a source of timber and sugar products. Previous phylogenetic studies employing plastid markers have not provided sufficient resolution, particularly at deeper nodes, leaving the backbone of the maple plastid tree essentially unresolved. We provide the plastid genome sequences of 16 species of maples spanning the sectional diversity of the genus and explore the utility of these sequences as a source of information for genetic and phylogenetic studies in this group. We analyzed the distribution of different types of repeated sequences and the pattern of codon usage, and identified variable regions across the plastome. Maximum likelihood and Bayesian analyses using two partitioning strategies were performed with these and previously published sequences. The plastomes ranged in size from 155,212 to 157,023 bp and had structure and gene content except for Acer palmatum (sect. Palmata), which had longer inverted repeats and an additional copy of the rps19 gene. Two genes, rps2 and rpl22, were found to be truncated at different positions and might be non-functional in several species. Most dispersed repeats, SSRs, and overall variation were detected in the non-coding sequences of the LSC and SSC regions. Fifteen loci, most of which have not been used before in the genus, were identified as the most variable and potentially useful as molecular markers for barcoding and genetic studies. Both ML and Bayesian analyses produced similar results irrespective of the partitioning strategy used. The plastome-based tree largely supported the topology inferred in previous studies using cp markers while providing resolution to the backbone relationships but was highly incongruous with a recently published nuclear tree presenting an opportunity for further research to investigate the causes of discordance, and particularly the role of hybridization in the diversification of the genus. Plastome sequences are valuable tools to resolve deep-level relationships within Acer. The variable loci and SSRs identified in this study will facilitate the development of markers for ecological and evolutionary studies in the genus. This study underscores the potential of plastid genome sequences to improve our understanding of the evolution of maples.
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Affiliation(s)
- Fabiola Areces-Berazain
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
| | - Yixi Wang
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
| | - Damien D. Hinsinger
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commisariat à l’Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Joeri S. Strijk
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi, China
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10
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Liede-Schumann S, Grimm GW, Nürk NM, Potts AJ, Meve U, Hartmann HE. Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae). PeerJ 2020; 8:e8999. [PMID: 32426182 PMCID: PMC7213013 DOI: 10.7717/peerj.8999] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/26/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Drosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum, together with the highly succulent and species-rich tribe Ruschieae, constitute the 'core ruschioids' in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution. METHODS Using chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species of Drosanthemum with multiple accessions for widespread species. A well-curated, geo-referenced occurrence dataset comprising the 134 genetically analysed and 863 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole. RESULTS Phylogenetic inference supports nine clades within Drosanthemum, seven of which group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as cryptic species. In-depth analyses of sequence patterns in each gene region were used to reveal phylogenetic affinities inside the retrieved clades in more detail. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are genetically and morphologically diverse. In contrast, less species-rich, genetically less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest that the main lineages arose from an initial rapid radiation, with subsequent diversification in some clades.
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Affiliation(s)
| | | | - Nicolai M. Nürk
- Department of Plant Systematics, University of Bayreuth, Bayreuth, Germany
| | - Alastair J. Potts
- African Centre for Coastal Palaeoscience, Nelson Mandela University, Port Elizabeth, Eastern Cape, South Africa
| | - Ulrich Meve
- Department of Plant Systematics, University of Bayreuth, Bayreuth, Germany
| | - Heidrun E.K. Hartmann
- Department of Systematics and Evolution of Plants, University of Hamburg, Hamburg, Germany
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11
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Grímsson F, Bouchal JM, Xafis A, Zetter R. Combined LM and SEM study of the middle Miocene (Sarmatian) palynoflora from the Lavanttal Basin, Austria: Part V. Magnoliophyta 3 - Myrtales to Ericales. GRANA 2020; 59:127-193. [PMID: 32406427 DOI: 10.1080/00173134.2011.585804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/09/2019] [Indexed: 05/26/2023]
Abstract
The continued investigation of the middle Miocene palynoflora from the Lavanttal Basin reveals numerous additional angiosperm taxa. The Myrtales to Ericales pollen record documented here comprises 46 different taxa belonging to Onagraceae (Ludwigia), Ericaceae (Craigia, Reevesia, Tilia), Anacardiaceae (Pistacia), Rutaceae (Zanthoxylum), Sapindaceae (Acer), Santalaceae (Arceuthobium), Amaranthaceae, Caryophyllaceae, Polygonaceae (Persicaria, Rumex), Cornaceae (Alangium, Cornus, Nyssa), Ebenaceae (Diospyros), Ericaceae (Andromeda, Arbutus, Empetrum, Erica), Sapotaceae (Pouteria, Sideroxylon), Styracaceae (Rehderodendron) and Symplocaceae (Symplocos). Köppen signatures of potential modern analogues of the additional fossil woody elements confirm the hypothesis of a subtropical (Cfa, Cwa) climate at lower elevations and subsequent transition into a temperate climate with altitudinal succession (Cfa → Cfb/Dfa → Dfb; Cwa → Cwb → Dwb-climate). The fossil plants represent different vegetation units, from wetland lowlands to well-drained montane forests. Many of the fossil taxa have potential modern analogues that can be classified as nemoral and/or meridio-nemoral and/or semihumid-meridional vegetation elements. New is the recognition of oreotropical elements, which are direct indicators for a substantial altitudinal gradient.
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Affiliation(s)
- Friđgeir Grímsson
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Johannes M Bouchal
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Alexandros Xafis
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Reinhard Zetter
- Department of Palaeontology, University of Vienna, Vienna, Austria
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Grímsson F, Bouchal JM, Xafis A, Zetter R. Combined LM and SEM study of the middle Miocene (Sarmatian) palynoflora from the Lavanttal Basin, Austria: Part V. Magnoliophyta 3 - Myrtales to Ericales. GRANA 2020; 59:127-193. [PMID: 32406427 PMCID: PMC7195176 DOI: 10.1080/00173134.2019.1696400] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/09/2019] [Indexed: 06/11/2023]
Abstract
The continued investigation of the middle Miocene palynoflora from the Lavanttal Basin reveals numerous additional angiosperm taxa. The Myrtales to Ericales pollen record documented here comprises 46 different taxa belonging to Onagraceae (Ludwigia), Ericaceae (Craigia, Reevesia, Tilia), Anacardiaceae (Pistacia), Rutaceae (Zanthoxylum), Sapindaceae (Acer), Santalaceae (Arceuthobium), Amaranthaceae, Caryophyllaceae, Polygonaceae (Persicaria, Rumex), Cornaceae (Alangium, Cornus, Nyssa), Ebenaceae (Diospyros), Ericaceae (Andromeda, Arbutus, Empetrum, Erica), Sapotaceae (Pouteria, Sideroxylon), Styracaceae (Rehderodendron) and Symplocaceae (Symplocos). Köppen signatures of potential modern analogues of the additional fossil woody elements confirm the hypothesis of a subtropical (Cfa, Cwa) climate at lower elevations and subsequent transition into a temperate climate with altitudinal succession (Cfa → Cfb/Dfa → Dfb; Cwa → Cwb → Dwb-climate). The fossil plants represent different vegetation units, from wetland lowlands to well-drained montane forests. Many of the fossil taxa have potential modern analogues that can be classified as nemoral and/or meridio-nemoral and/or semihumid-meridional vegetation elements. New is the recognition of oreotropical elements, which are direct indicators for a substantial altitudinal gradient.
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Affiliation(s)
- Friđgeir Grímsson
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Johannes M. Bouchal
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Alexandros Xafis
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Reinhard Zetter
- Department of Palaeontology, University of Vienna, Vienna, Austria
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Grímsson F, Bouchal JM, Xafis A, Zetter R. Combined LM and SEM study of the middle Miocene (Sarmatian) palynoflora from the Lavanttal Basin, Austria: Part V. Magnoliophyta 3 - Myrtales to Ericales. GRANA 2020; 59:127-193. [PMID: 32406427 DOI: 10.1080/00173134.2011.641450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/09/2019] [Indexed: 05/26/2023]
Abstract
The continued investigation of the middle Miocene palynoflora from the Lavanttal Basin reveals numerous additional angiosperm taxa. The Myrtales to Ericales pollen record documented here comprises 46 different taxa belonging to Onagraceae (Ludwigia), Ericaceae (Craigia, Reevesia, Tilia), Anacardiaceae (Pistacia), Rutaceae (Zanthoxylum), Sapindaceae (Acer), Santalaceae (Arceuthobium), Amaranthaceae, Caryophyllaceae, Polygonaceae (Persicaria, Rumex), Cornaceae (Alangium, Cornus, Nyssa), Ebenaceae (Diospyros), Ericaceae (Andromeda, Arbutus, Empetrum, Erica), Sapotaceae (Pouteria, Sideroxylon), Styracaceae (Rehderodendron) and Symplocaceae (Symplocos). Köppen signatures of potential modern analogues of the additional fossil woody elements confirm the hypothesis of a subtropical (Cfa, Cwa) climate at lower elevations and subsequent transition into a temperate climate with altitudinal succession (Cfa → Cfb/Dfa → Dfb; Cwa → Cwb → Dwb-climate). The fossil plants represent different vegetation units, from wetland lowlands to well-drained montane forests. Many of the fossil taxa have potential modern analogues that can be classified as nemoral and/or meridio-nemoral and/or semihumid-meridional vegetation elements. New is the recognition of oreotropical elements, which are direct indicators for a substantial altitudinal gradient.
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Affiliation(s)
- Friđgeir Grímsson
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Johannes M Bouchal
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Alexandros Xafis
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Reinhard Zetter
- Department of Palaeontology, University of Vienna, Vienna, Austria
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Liu ZW, Zhou J, Peng H, Freudenstein JV, Milne RI. Relationships between Tertiary relict and circumboreal woodland floras: a case study in Chimaphila (Ericaceae). ANNALS OF BOTANY 2019; 123:1089-1098. [PMID: 30852591 PMCID: PMC6589512 DOI: 10.1093/aob/mcz018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/24/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND AND AIMS Tertiary relict and Arctic/circumboreal distributions are two major patterns of Northern Hemisphere intercontinental disjunctions with very different histories. Each has been well researched, but members of one biome have generally not been incorporated in the biogeographical analyses of the other, and links or transitions between these two biomes have rarely been addressed. METHODS Phylogenies of Chimaphila were generated based on cpDNA and nuclear ITS, using Bayesian and maximum likelihood methods. A time-calibrated phylogeny was generated using BEAST. Ancestral area reconstruction was inferred using both statistical dispersal-vicariance analysis and a dispersal-extinction-cladogenesis model. KEY RESULTS The Chimaphila crown group was estimated to have originated in the early Miocene. The lineages of C. umbellata diverged early, but its present circumboreal distribution was not achieved until around the middle Pliocene or later. Sister to this is a clade of four species with Tertiary relict distribution. Among these, two expansions occurred from North America to Asia, probably via the Bering Land Bridge, generating its current disjunctions. CONCLUSIONS Our data concur with a few other studies, indicating that the circumboreal woodland biome has an older origin than most true Arctic-alpine taxa, having gradually recruited taxa since the early Oligocene. For the origin of Asia-North America disjunctions in Chimaphila, an 'out-of-America' migration was supported. It is not clear in which direction Pyroloideae lineages moved between Tertiary relict disjunctions and Arctic/circumboreal distributions; each biome might have recruited species from the other.
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Affiliation(s)
- Zhen-Wen Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jing Zhou
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Hua Peng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - John V Freudenstein
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
| | - Richard I Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Kim HT, Pak JH, Kim JS. The complete chloroplast genome sequence of Acer takesimense (Sapindaceae), an endemic to Ullenung Island of Korea. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1601521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Hyoung Tae Kim
- Institute of Agriculture Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Jae-Hong Pak
- Research Institute for Dokdo and Ulleungdo Island, Kyungpook National University, Daegu, Republic of Korea
- Department of Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Jung Sung Kim
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
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Phylogenomics recovers monophyly and early Tertiary diversification of Dipteronia (Sapindaceae). Mol Phylogenet Evol 2019; 130:9-17. [DOI: 10.1016/j.ympev.2018.09.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/16/2018] [Accepted: 09/19/2018] [Indexed: 11/23/2022]
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Abstract
With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analysis tools. Software developers appear to rarely assess the quality of their code, and this can have potential negative consequences for end-users. To this end, we assessed the code quality of 16 highly cited and compute-intensive tools mainly written in C/C++ (e.g., MrBayes, MAFFT, SweepFinder, etc.) and JAVA (BEAST) from the broader area of evolutionary biology that are being routinely used in current data analysis pipelines. Because, the software engineering quality of the tools we analyzed is rather unsatisfying, we provide a list of best practices for improving the quality of existing tools and list techniques that can be deployed for developing reliable, high quality scientific software from scratch. Finally, we also discuss journal as well as science policy and, more importantly, funding issues that need to be addressed for improving software engineering quality as well as ensuring support for developing new and maintaining existing software. Our intention is to raise the awareness of the community regarding software engineering quality issues and to emphasize the substantial lack of funding for scientific software development.
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Affiliation(s)
- Diego Darriba
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Tomáš Flouri
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Harris AJ, Chen Y, Olsen RT, Lutz S, Wen J. On merging Acer sections Rubra and Hyptiocarpa: Molecular and morphological evidence. PHYTOKEYS 2017; 86:9-42. [PMID: 29033667 PMCID: PMC5624197 DOI: 10.3897/phytokeys.86.13532] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
In this study, we expanded Acer sect. Rubra Pax to include A. sect. Hyptiocarpa Fang. Traditionally, section Rubra comprises two iconic species, Acer rubrum Linnaeus (red maple) and A. saccharinum Linnaeus (silver maple), of eastern North American forests as well as the rare Japanese montane species, A. pycnanthum K. Koch. Section Hyptiocarpa consists of A. laurinum Hasskarl and A. pinnatinervium Merrill, which occur in subtropical and tropical regions of southwestern China to southeast Asia. Here, we confirm prior phylogenetic results showing the close relationship between sects. Rubra and Hyptiocarpa, and we use scanning electron microscopy to demonstrate that leaves of species within these sections have similar arrangements of cuticular waxes, which account for the silvery color of their abaxial surfaces. We describe that the sections also share labile sex expression; inflorescences that range from compound racemose thyrses, to racemes or umbels and that may have undergone evolutionary reduction; and several features of their fruits, such as seed locules without keels, basal portion of wings straight, acute attachment angle between mericarps, and production of some mericarps that are seedless and partially developed at maturity. Our expansion of sect. Rubra to include sect. Hyptiocarpa better elucidates the biogeographic and evolutionary history of these species. Additionally, we show that A. laurinum and A. pinnatinervium have intergrading morphology and are probably synonymous, but we note that further studies are required to conclude their taxonomic status.
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Affiliation(s)
- AJ Harris
- Smithsonian Institution, Department of Botany, MRC 166, Washington, D.C. 20013-7012 USA
| | - Yousheng Chen
- Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing 100093 China
| | - Richard T. Olsen
- United States National Arboretum, 3501 New York Avenue, NE, Washington, D.C. 20002- 1958 USA
| | - Sue Lutz
- Smithsonian Institution, Department of Botany, MRC 166, Washington, D.C. 20013-7012 USA
| | - Jun Wen
- Smithsonian Institution, Department of Botany, MRC 166, Washington, D.C. 20013-7012 USA
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Bomfleur B, Grimm GW, McLoughlin S. The fossil Osmundales (Royal Ferns)-a phylogenetic network analysis, revised taxonomy, and evolutionary classification of anatomically preserved trunks and rhizomes. PeerJ 2017; 5:e3433. [PMID: 28713650 PMCID: PMC5508817 DOI: 10.7717/peerj.3433] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 05/17/2017] [Indexed: 12/03/2022] Open
Abstract
The Osmundales (Royal Fern order) originated in the late Paleozoic and is the most ancient surviving lineage of leptosporangiate ferns. In contrast to its low diversity today (less than 20 species in six genera), it has the richest fossil record of any extant group of ferns. The structurally preserved trunks and rhizomes alone are referable to more than 100 fossil species that are classified in up to 20 genera, four subfamilies, and two families. This diverse fossil record constitutes an exceptional source of information on the evolutionary history of the group from the Permian to the present. However, inconsistent terminology, varying formats of description, and the general lack of a uniform taxonomic concept renders this wealth of information poorly accessible. To this end, we provide a comprehensive review of the diversity of structural features of osmundalean axes under a standardized, descriptive terminology. A novel morphological character matrix with 45 anatomical characters scored for 15 extant species and for 114 fossil operational units (species or specimens) is analysed using networks in order to establish systematic relationships among fossil and extant Osmundales rooted in axis anatomy. The results lead us to propose an evolutionary classification for fossil Osmundales and a revised, standardized taxonomy for all taxa down to the rank of (sub)genus. We introduce several nomenclatural novelties: (1) a new subfamily Itopsidemoideae (Guaireaceae) is established to contain Itopsidema, Donwelliacaulis, and Tiania; (2) the thamnopteroid genera Zalesskya, Iegosigopteris, and Petcheropteris are all considered synonymous with Thamnopteris; (3) 12 species of Millerocaulis and Ashicaulis are assigned to modern genera (tribe Osmundeae); (4) the hitherto enigmatic Aurealcaulis is identified as an extinct subgenus of Plenasium; and (5) the poorly known Osmundites tuhajkulensis is assigned to Millerocaulis. In addition, we consider Millerocaulis stipabonettiorum a possible member of Palaeosmunda and Millerocaulis estipularis as probably constituting the earliest representative of the (Todea-)Leptopteris lineage (subtribe Todeinae) of modern Osmundoideae.
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Affiliation(s)
- Benjamin Bomfleur
- Institut für Geologie und Paläontologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Guido W. Grimm
- Department für Paläontologie, Universität Wien, Wien, Austria
- Orléans, France
| | - Stephen McLoughlin
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
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Banag CI, Mouly A, Alejandro GJD, Bremer B, Meve U, Grimm GW, Liede-Schumann S. Ixora (Rubiaceae) on the Philippines - crossroad or cradle? BMC Evol Biol 2017; 17:131. [PMID: 28592249 PMCID: PMC5463362 DOI: 10.1186/s12862-017-0974-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 05/18/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Philippine archipelago is globally one of the most important model island systems for studying evolutionary processes. However, most plant species on this archipelago have not yet been studied in sufficient detail. The main aim of this study is to unravel the evolutionary history and biogeographic relationships of the Philippine members of the pantropical genus Ixora. RESULTS The complex plastid and nuclear divergence patterns in Philippine Ixora, documented using tree and network approaches, reveal a highly dynamic evolution in Ixora, involving several phases of radiation and recolonization. Philippine Ixora comprises at least five lineages, of which one is most closely related to species from Wallacea, and the remaining four to species from Asia. CONCLUSIONS Our study highlights the importance of Philippine species for understanding phytogeographic patterns in the Indomalayan-Australasian eco-region. The overall genetic differentiation, as well as the incongruence between genealogies based on the biparentally inherited nucleome and the maternally inherited plastome in Ixora, reflect the complex tectonic history of the Philippine archipelago. The Ixora lineage related to Wallacean species supports the delimitation of different ecozones along Huxley's line, because it is absent from Palawan. The remaining four lineages are all allied with Asian taxa, reflecting several waves of colonization. Close relationships between some widespread Philippine species and locally adapted narrow endemics suggest that the widespread, genetically diverse species act as pools for the formation of new species in a process of ongoing speciation. Our results suggest that the species concepts of some of the more widespread taxa need to be revised.
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Affiliation(s)
- Cecilia I. Banag
- Department of Biological Sciences, College of Science, University of Santo Tomas, España Boulevard, 1015 Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Boulevard, 1015 Manila, Philippines
| | - Arnaud Mouly
- UMR CNRS 6249 Chrono-environnement, Université Bourgogne - Franche-Comté, 16 Route de Gray, 25030 Besançon cedex, France
| | - Grecebio Jonathan D. Alejandro
- Department of Biological Sciences, College of Science, University of Santo Tomas, España Boulevard, 1015 Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Boulevard, 1015 Manila, Philippines
| | - Birgitta Bremer
- Bergius Botanic Garden, Stockholm University, 106 91 Stockholm, Sweden
| | - Ulrich Meve
- Department of Plant Systematics, University of Bayreuth, Universitätstraße 30, 95440 Bayreuth, Germany
| | | | - Sigrid Liede-Schumann
- Department of Plant Systematics, University of Bayreuth, Universitätstraße 30, 95440 Bayreuth, Germany
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Grímsson F, Kapli P, Hofmann CC, Zetter R, Grimm GW. Eocene Loranthaceae pollen pushes back divergence ages for major splits in the family. PeerJ 2017; 5:e3373. [PMID: 28607837 PMCID: PMC5466002 DOI: 10.7717/peerj.3373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/04/2017] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND We revisit the palaeopalynological record of Loranthaceae, using pollen ornamentation to discriminate lineages and to test molecular dating estimates for the diversification of major lineages. METHODS Fossil Loranthaceae pollen from the Eocene and Oligocene are analysed and documented using scanning-electron microscopy. These fossils were associated with molecular-defined clades and used as minimum age constraints for Bayesian node dating using different topological scenarios. RESULTS The fossil Loranthaceae pollen document the presence of at least one extant root-parasitic lineage (Nuytsieae) and two currently aerial parasitic lineages (Psittacanthinae and Loranthinae) by the end of the Eocene in the Northern Hemisphere. Phases of increased lineage diversification (late Eocene, middle Miocene) coincide with global warm phases. DISCUSSION With the generation of molecular data becoming easier and less expensive every day, neontological research should re-focus on conserved morphologies that can be traced through the fossil record. The pollen, representing the male gametophytic generation of plants and often a taxonomic indicator, can be such a tracer. Analogously, palaeontological research should put more effort into diagnosing Cenozoic fossils with the aim of including them into modern systematic frameworks.
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Affiliation(s)
| | - Paschalia Kapli
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | | | - Reinhard Zetter
- Department of Palaeontology, University of Vienna, Wien, Austria
| | - Guido W. Grimm
- Department of Palaeontology, University of Vienna, Wien, Austria
- Orléans, France
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22
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Schliep K, Potts AJ, Morrison DA, Grimm GW. Intertwining phylogenetic trees and networks. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12760] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Grímsson F, Grimm GW, Zetter R. Evolution of pollen morphology in Loranthaceae. GRANA 2017; 57:16-116. [PMID: 29386990 PMCID: PMC5771552 DOI: 10.1080/00173134.2016.1261939] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 10/04/2016] [Indexed: 05/30/2023]
Abstract
Earlier studies indicate a strong correlation of pollen morphology and ultrastructure with taxonomy in Loranthaceae. Using high-resolution light microscopy and scanning electron microscopy imaging of the same pollen grains, we document pollen types of 35 genera including 15 studied for the first time. Using a molecular phylogenetic framework based on currently available sequence data with good genus-coverage, we reconstruct trends in the evolution of Loranthaceae pollen and pinpoint traits of high diagnostic value, partly confirming earlier intuitive hypotheses based on morphological observations. We find that pollen morphology in Loranthaceae is strongly linked to phylogenetic relationships. Some pollen types are diagnostic for discrete genera or evolutionary lineages, opening the avenue to recruit dispersed fossil pollen as age constraints for dated phylogenies and as independent data for testing biogeographic scenarios; so far based exclusively on modern-day data. Correspondences and discrepancies between palynological and molecular data and current taxonomic/systematic concepts are identified and suggestions made for future palynological and molecular investigations of Loranthaceae.
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Affiliation(s)
| | - Guido W. Grimm
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Reinhard Zetter
- Department of Palaeontology, University of Vienna, Vienna, Austria
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Han YW, Duan D, Ma XF, Jia Y, Liu ZL, Zhao GF, Li ZH. Efficient Identification of the Forest Tree Species in Aceraceae Using DNA Barcodes. FRONTIERS IN PLANT SCIENCE 2016; 7:1707. [PMID: 27899929 PMCID: PMC5110567 DOI: 10.3389/fpls.2016.01707] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/31/2016] [Indexed: 05/20/2023]
Abstract
Aceraceae is a large forest tree family that comprises many economically and ecologically important species. However, because interspecific and/or intraspecific morphological variations result from frequent interspecific hybridization and introgression, it is challenging for non-taxonomists to accurately recognize and identify the tree species in Aceraceae based on a traditional approach. DNA barcoding is a powerful tool that has been proposed to accurately distinguish between species. In this study, we assessed the effectiveness of three core standard markers (matK, rbcL and ITS) plus the chloroplast locus trnS-trnG as Aceraceae barcodes. A total of 231 sequences representing 85 species in this forest family were collected. Of these four barcode markers, the discrimination power was highest for the ITS (I) region (50%) and was progressively reduced in the other three chloroplast barcodes matK (M), trnS-trnG (T) and rbcL (R); the discrimination efficiency of the ITS marker was also greater than any two-locus combination of chloroplast barcodes. However, the combinations of ITS plus single or combined chloroplast barcodes could improve species resolution significantly; T+I (90.5% resolution) and R+M+T+I (90.5% resolution) differentiated the highest portion of species in Aceraceae. Our current results show that the nuclear ITS fragment represents a more promising DNA barcode marker than the maternally inherited chloroplast barcodes. The most efficient and economical method to identify tree species in Aceraceae among single or combined DNA barcodes is the combination of T+I (90.5% resolution).
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Affiliation(s)
- Yu-Wei Han
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Dong Duan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Xiong-Feng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Yun Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Zhan-Lin Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
- *Correspondence: Zhong-Hu Li
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Bomfleur B, Grimm GW, McLoughlin S. Osmunda pulchella sp. nov. from the Jurassic of Sweden--reconciling molecular and fossil evidence in the phylogeny of modern royal ferns (Osmundaceae). BMC Evol Biol 2015; 15:126. [PMID: 26123220 PMCID: PMC4487210 DOI: 10.1186/s12862-015-0400-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 06/01/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The classification of royal ferns (Osmundaceae) has long remained controversial. Recent molecular phylogenies indicate that Osmunda is paraphyletic and needs to be separated into Osmundastrum and Osmunda s.str. Here, however, we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov.) that combines diagnostic features of both Osmundastrum and Osmunda, calling molecular evidence for paraphyly into question. We assembled a new morphological matrix based on rhizome anatomy, and used network analyses to establish phylogenetic relationships between fossil and extant members of modern Osmundaceae. We re-analysed the original molecular data to evaluate root-placement support. Finally, we integrated morphological and molecular data-sets using the evolutionary placement algorithm. RESULTS Osmunda pulchella and five additional Jurassic rhizome species show anatomical character suites intermediate between Osmundastrum and Osmunda. Molecular evidence for paraphyly is ambiguous: a previously unrecognized signal from spacer sequences favours an alternative root placement that would resolve Osmunda s.l. as monophyletic. Our evolutionary placement analysis identifies fossil species as probable ancestral members of modern genera and subgenera, which accords with recent evidence from Bayesian dating. CONCLUSIONS Osmunda pulchella is likely a precursor of the Osmundastrum lineage. The recently proposed root placement in Osmundaceae-based solely on molecular data-stems from possibly misinformative outgroup signals in rbcL and atpA genes. We conclude that the seemingly conflicting evidence from morphological, anatomical, molecular, and palaeontological data can instead be elegantly reconciled under the assumption that Osmunda is indeed monophyletic.
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Affiliation(s)
- Benjamin Bomfleur
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden.
| | - Guido W Grimm
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden. .,Department of Palaeontology, University of Vienna, Vienna, Austria.
| | - Stephen McLoughlin
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden.
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Hubert F, Grimm GW, Jousselin E, Berry V, Franc A, Kremer A. Multiple nuclear genes stabilize the phylogenetic backbone of the genusQuercus. SYST BIODIVERS 2014. [DOI: 10.1080/14772000.2014.941037] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Potts AJ, Hedderson TA, Grimm GW. Constructing Phylogenies in the Presence Of Intra-Individual Site Polymorphisms (2ISPs) with a Focus on the Nuclear Ribosomal Cistron. Syst Biol 2013; 63:1-16. [DOI: 10.1093/sysbio/syt052] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alastair J. Potts
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Cape Town, Western Cape, 7700, South Africa; and 2Department of Palaeobiology, Swedish Museum of Natural History, P.O. Box 50007, 104 05 Stockholm, Sweden
| | - Terry A. Hedderson
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Cape Town, Western Cape, 7700, South Africa; and 2Department of Palaeobiology, Swedish Museum of Natural History, P.O. Box 50007, 104 05 Stockholm, Sweden
| | - Guido W. Grimm
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Cape Town, Western Cape, 7700, South Africa; and 2Department of Palaeobiology, Swedish Museum of Natural History, P.O. Box 50007, 104 05 Stockholm, Sweden
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Chen S, Kim DK, Chase MW, Kim JH. Networks in a large-scale phylogenetic analysis: reconstructing evolutionary history of Asparagales (Lilianae) based on four plastid genes. PLoS One 2013; 8:e59472. [PMID: 23544071 PMCID: PMC3605904 DOI: 10.1371/journal.pone.0059472] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 02/18/2013] [Indexed: 12/19/2022] Open
Abstract
Phylogenetic analysis aims to produce a bifurcating tree, which disregards conflicting signals and displays only those that are present in a large proportion of the data. However, any character (or tree) conflict in a dataset allows the exploration of support for various evolutionary hypotheses. Although data-display network approaches exist, biologists cannot easily and routinely use them to compute rooted phylogenetic networks on real datasets containing hundreds of taxa. Here, we constructed an original neighbour-net for a large dataset of Asparagales to highlight the aspects of the resulting network that will be important for interpreting phylogeny. The analyses were largely conducted with new data collected for the same loci as in previous studies, but from different species accessions and greater sampling in many cases than in published analyses. The network tree summarised the majority data pattern in the characters of plastid sequences before tree building, which largely confirmed the currently recognised phylogenetic relationships. Most conflicting signals are at the base of each group along the Asparagales backbone, which helps us to establish the expectancy and advance our understanding of some difficult taxa relationships and their phylogeny. The network method should play a greater role in phylogenetic analyses than it has in the past. To advance the understanding of evolutionary history of the largest order of monocots Asparagales, absolute diversification times were estimated for family-level clades using relaxed molecular clock analyses.
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Affiliation(s)
- Shichao Chen
- College of Life Science and Technology, Tongji University, Shanghai, China
| | - Dong-Kap Kim
- Division of Forest Resource Conservation, Korea National Arboretum, Pocheon, Gyeonggi-do, Korea
| | - Mark W. Chase
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Korea
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Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? J Comput Biol 2010; 17:337-54. [PMID: 20377449 DOI: 10.1089/cmb.2009.0179] [Citation(s) in RCA: 571] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Phylogenetic bootstrapping (BS) is a standard technique for inferring confidence values on phylogenetic trees that is based on reconstructing many trees from minor variations of the input data, trees called replicates. BS is used with all phylogenetic reconstruction approaches, but we focus here on one of the most popular, maximum likelihood (ML). Because ML inference is so computationally demanding, it has proved too expensive to date to assess the impact of the number of replicates used in BS on the relative accuracy of the support values. For the same reason, a rather small number (typically 100) of BS replicates are computed in real-world studies. Stamatakis et al. recently introduced a BS algorithm that is 1 to 2 orders of magnitude faster than previous techniques, while yielding qualitatively comparable support values, making an experimental study possible. In this article, we propose stopping criteria--that is, thresholds computed at runtime to determine when enough replicates have been generated--and we report on the first large-scale experimental study to assess the effect of the number of replicates on the quality of support values, including the performance of our proposed criteria. We run our tests on 17 diverse real-world DNA--single-gene as well as multi-gene--datasets, which include 125-2,554 taxa. We find that our stopping criteria typically stop computations after 100-500 replicates (although the most conservative criterion may continue for several thousand replicates) while producing support values that correlate at better than 99.5% with the reference values on the best ML trees. Significantly, we also find that the stopping criteria can recommend very different numbers of replicates for different datasets of comparable sizes. Our results are thus twofold: (i) they give the first experimental assessment of the effect of the number of BS replicates on the quality of support values returned through BS, and (ii) they validate our proposals for stopping criteria. Practitioners will no longer have to enter a guess nor worry about the quality of support values; moreover, with most counts of replicates in the 100-500 range, robust BS under ML inference becomes computationally practical for most datasets. The complete test suite is available at http://lcbb.epfl.ch/BS.tar.bz2, and BS with our stopping criteria is included in the latest release of RAxML v7.2.5, available at http://wwwkramer.in.tum.de/exelixis/software.html.
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Affiliation(s)
- Nicholas D Pattengale
- Department of Computer Science, University of New Mexico, Albuquerque, New Mexico 87123, USA.
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Renner SS, Grimm GW, Schneeweiss GM, Stuessy TF, Ricklefs RE. Rooting and dating maples (Acer) with an uncorrelated-rates molecular clock: implications for north American/Asian disjunctions. Syst Biol 2008; 57:795-808. [PMID: 18853365 DOI: 10.1080/10635150802422282] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Simulations suggest that molecular clock analyses can correctly identify the root of a tree even when the clock assumption is severely violated. Clock-based rooting of phylogenies may be particularly useful when outgroup rooting is problematic. Here, we explore relaxed-clock rooting in the Acer/Dipteronia clade of Sapindaceae, which comprises genera of highly uneven species richness and problematic mutual monophyly. Using an approach that does not presuppose rate autocorrelation between ancestral and descendant branches and hence does not require a rooted a priori topology, we analyzed data from up to seven chloroplast loci for some 50 ingroup species. For comparison, we used midpoint and outgroup rooting and dating methods that rely on rooted input trees, namely penalized likelihood, a Bayesian autocorrelated-rates model, and a strict clock. The chloroplast sequences used here reject a single global substitution rate, and the assumption of autocorrelated rates was also rejected. The root was placed between Acer and Dipteronia by all three rooting methods, albeit with low statistical support. Analyses of Acer diversification with a lineage-through-time plot and different survival models, although sensitive to missing data, suggest a gradual decrease in the average diversification rate. The nine North American species of Acer diverged from their nearest relatives at widely different times: eastern American Acer diverged in the Oligocene and Late Miocene; western American species in the Late Eocene and Mid Miocene; and the Acer core clade, including A. saccharum, dates to the Miocene. Recent diversification in North America is strikingly rare compared to diversification in eastern Asia.
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Morrison DA. Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences. Syst Biol 2008; 56:988-1010. [PMID: 18066931 DOI: 10.1080/10635150701779808] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Even when the maximum likelihood (ML) tree is a better estimate of the true phylogenetic tree than those produced by other methods, the result of a poor ML search may be no better than that of a more thorough search under some faster criterion. The ability to find the globally optimal ML tree is therefore important. Here, I compare a range of heuristic search strategies (and their associated computer programs) in terms of their success at locating the ML tree for 20 empirical data sets with 14 to 158 sequences and 411 to 120,762 aligned nucleotides. Three distinct topics are discussed: the success of the search strategies in relation to certain features of the data, the generation of starting trees for the search, and the exploration of multiple islands of trees. As a starting tree, there was little difference among the neighbor-joining tree based on absolute differences (including the BioNJ tree), the stepwise-addition parsimony tree (with or without nearest-neighbor-interchange (NNI) branch swapping), and the stepwise-addition ML tree. The latter produced the best ML score on average but was orders of magnitude slower than the alternatives. The BioNJ tree was second best on average. As search strategies, star decomposition and quartet puzzling were the slowest and produced the worst ML scores. The DPRml, IQPNNI, MultiPhyl, PhyML, PhyNav, and TreeFinder programs with default options produced qualitatively similar results, each locating a single tree that tended to be in an NNI suboptimum (rather than the global optimum) when the data set had low phylogenetic information. For such data sets, there were multiple tree islands with very similar ML scores. The likelihood surface only became relatively simple for data sets that contained approximately 500 aligned nucleotides for 50 sequences and 3,000 nucleotides for 100 sequences. The RAxML and GARLI programs allowed multiple islands to be explored easily, but both programs also tended to find NNI suboptima. A newly developed version of the likelihood ratchet using PAUP* successfully found the peaks of multiple islands, but its speed needs to be improved.
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Affiliation(s)
- David A Morrison
- Department of Parasitology (SWEPAR), National Veterinary Institute and Swedish University of Agricultural Sciences, Uppsala, Sweden.
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Voglmayr H, Jaklitsch WM. Prosthecium species with Stegonsporium anamorphs on Acer. ACTA ACUST UNITED AC 2008; 112:885-905. [PMID: 18554889 DOI: 10.1016/j.mycres.2008.01.020] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 01/10/2008] [Accepted: 01/24/2008] [Indexed: 11/28/2022]
Abstract
Data from microscopic morphology, single-spore cultures, and DNA analyses of teleomorphs and anamorphs support the recognition of five species of Prosthecium with Stegonsporium anamorphs on Acer: P. acerinum sp. nov., the teleomorph of S. acerinum; P. acerophilum comb. nov., formerly known as Dictyoporthe acerophila; P. galeatum comb. nov., originally described as Massaria galeata; P. opalus sp. nov.; and P. pyriforme sp. nov., the teleomorph of S. pyriforme s. str. The morphology of both type specimens and freshly collected material was investigated. The teleomorphs have brown ellipsoidal ascospores with five distosepta and often a longitudinal distoseptum. The anamorphs of all species described here belong to Stegonsporium; their connection to the Prosthecium teleomorphs was demonstrated by morphology and DNA sequences of single spore cultures derived from both ascospores and conidia. The anamorphs and teleomorphs of all five Prosthecium species are described and illustrated by LM images, and a key to these species is provided. As perceived from this work, S. pyriforme is restricted to Europe and does not occur in North America, whereas S. acerinum is restricted to North America, not found in Europe. The host associations given in the literature are revised and evidence is provided that only A. opalus, A. pseudoplatanus, and A. saccharum are confirmed hosts of Prosthecium with Stegonsporium anamorphs. Molecular phylogenetic analyses of tef1, ITS rDNA, and partial nuLSU rDNA sequences confirm that the species with Stegonsporium anamorphs are closely related to P. ellipsosporum, the generic type species. Stilbospora macrosperma is confirmed as the anamorph of P. ellipsosporum by DNA data of single spore isolates obtained from both ascospores and conidia.
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Affiliation(s)
- Hermann Voglmayr
- Department of Systematic and Evolutionary Botany, Faculty Center Botany, University of Vienna, Rennweg 14, A-1030 Wien, Austria.
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Grimm GW, Denk T. Its evolution in Platanus (Platanaceae): homoeologues, pseudogenes and ancient hybridization. ANNALS OF BOTANY 2008; 101:403-19. [PMID: 18089582 PMCID: PMC2701810 DOI: 10.1093/aob/mcm305] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Platanaceae is an old family of angiosperms extending back to the Early Cretaceous but consisting of a single extant genus, Platanus. Species of Platanus have long been known to hybridize, and the London plane, Platanus x hispanica, is a well-known example of a hybrid species that formed in historical times. In addition, morphological studies have suggested past interspecific or interlineage hybridization and reticulation as possibly important factors in the evolution of the genus. This study aims at unravelling the complex evolutionary information contained in internal transcribed spacer (ITS) sequences. METHODS The ITS of the 35S nuclear ribosomal DNA are biparentally inherited, multi-copy markers with a high potential for resolving intrageneric relationships especially when ancient hybridization (reticulation) is involved. Phylogenetic trees, splits graphs and motif analysis are used to extract phylogenetic information from 223 cloned ITS sequences, representing ten species and varieties of Platanus. Non-pseudogenous and pseudogenous sequence motives are assessed to explain how different evolutionary modes contribute to possibly conflicting character state patterns in the ITS. KEY RESULTS It was found that putative non-functional ITS copies ('pseudogenes') form distinct groups in phylograms and splits graphs, and that pseudogenous lineages reflect ancient hybridization events conserved in the ITS. Specifically, pseudogenous clones of an 'Atlantic' North American clade share sequence motives with non-pseudogenous clones of the western ('Pacific') North American P. racemosa species aggregate. In addition, evidence was found for recent lateral gene flow as a possible factor in the evolution of the central Mexican P. rzedowskii. CONCLUSIONS Broad ITS data sets that cover intra- and interindividual variability reveal past and ongoing speciation processes in Platanus. Evolutionary pathways can be visualized with splits graphs, but not with bifurcating trees.
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Affiliation(s)
- Guido W. Grimm
- Institute of Geosciences, Eberhard-Karls-University, Sigwart Strasse 10, 72076 Tübingen, Germany
| | - Thomas Denk
- Department of Palaeobotany, Natural History Museum, Box 50007, 10405 Stockholm, Sweden
- For correspondence. E-mail
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Renner SS, Beenken L, Grimm GW, Kocyan A, Ricklefs RE. The evolution of dioecy, heterodichogamy, and labile sex expression in Acer. Evolution 2007; 61:2701-19. [PMID: 17894810 DOI: 10.1111/j.1558-5646.2007.00221.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The northern hemisphere tree genus Acer comprises 124 species, most of them monoecious, but 13 dioecious. The monoecious species flower dichogamously, duodichogamously (male, female, male), or in some species heterodichogamously (two morphs that each produce male and female flowers but at reciprocal times). Dioecious species cannot engage in these temporal strategies. Using a phylogeny for 66 species and subspecies obtained from 6600 nucleotides of chloroplast introns, spacers, and a protein-coding gene, we address the hypothesis (Pannell and Verdú, Evolution 60: 660-673. 2006) that dioecy evolved from heterodichogamy. This hypothesis was based on phylogenetic analyses (Gleiser and Verdú, New Phytol. 165: 633-640. 2005) that included 29-39 species of Acer coded for five sexual strategies (duodichogamous monoecy, heterodichogamous androdioecy, heterodichogamous trioecy, dichogamous subdioecy, and dioecy) treated as ordered states or as a single continuous variable. When reviewing the basis for these scorings, we found errors that together with the small taxon sample, cast doubt on the earlier inferences. Based on published studies, we coded 56 species of Acer for four sexual strategies, dioecy, monoecy with dichogamous or duodichogamous flowering, monoecy with heterodichogamous flowering, or labile sex expression, in which individuals reverse their sex allocation depending on environment-phenotype interactions. Using Bayesian character mapping, we infer an average of 15 transformations, a third of them involving changes from monoecy-cum-duodichogamy to dioecy; less frequent were changes from this strategy to heterodichogamy; dioecy rarely reverts to other sexual systems. Contra the earlier inferences, we found no switches between heterodichogamy and dioecy. Unexpectedly, most of the species with labile sex expression are grouped together, suggesting that phenotypic plasticity in Acer may be a heritable sexual strategy. Because of the complex flowering phenologies, however, a concern remains that monoecy in Acer might not always be distinguishable from labile sex expression, which needs to be addressed by long-term monitoring of monoecious trees. The 13 dioecious species occur in phylogenetically disparate clades that date back to the Late Eocene and Oligocene, judging from a fossil-calibrated relaxed molecular clock.
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Affiliation(s)
- S S Renner
- Department of Biology, University of Munich, Menzinger Str. 67, D-80638 Munich, Germany.
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